Comprehensive Analysis of the Differential Expression and Prognostic Value of Histone Deacetylases in Glioma

Li, Jinwei; Yan, Xianlei; Liang, Cong; Chen, Hongmou; Liu, Meimei; Wu, Zhikang; Zheng, Jiemin; Dang, Junsun; La, Xiaojin; Liu, Quan

doi:10.3389/fcell.2022.840759

Cited by 10 publications

(9 citation statements)

References 80 publications

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“…TIMER Database Analysis. For the inclusive analysis of the TIICs, such as B cells, neutrophils, dendritic cells, CD4 + T cells, CD8 + T cells, and macrophages, the TIMER database (https://cistrome.shinyapps.io/timer/) was utilized by using the RNA-seq expression profile data [21,22]. We used the "Gene" module plots to evaluate the link of TTC7B expression and immune infiltrate level with tumor purity.…”

Section: Cibersort Analysismentioning

confidence: 99%

TTC7B Is a Novel Prognostic-Related Biomarker in Glioma Correlating with Immune Infiltrates and Response to Oxidative Stress by Temozolomide

Chen

Cui²,

Dai

et al. 2022

Oxidative Medicine and Cellular Longevity

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Background. Gliomas are one of the most prevalent malignant brain tumors. Hence, identifying biological markers for glioma is imperative. TTC7B (Tetratricopeptide Repeat Domain 7B) is a gene whose role in cancer in currently identified. To this end, we examined the TTC7B expression as well as its prognostic significance, biological roles, and immune system impacts in patients with glioma. Methods. We evaluated the function of TTC7B in GBM and LGG through the published CGGA (Chinese Glioma Genome Atlas) and TCGA (The Cancer Genome Atlas) databases. CIBERSORT and TIMER were used to analyze the link between TTC7B and immune cells, while R was used for statistical analysis. In addition, Transwell analysis, including migration and invasion assays, was performed to identify the relationship between TTC7B and temozolomide. Results. Low expression of TTC7B was observed in GBM and LGG. 1p/19q codeletion, IDH mutation, chemotherapy, and grade were found to have a significant correlation with TTC7B. Besides, low TTC7B expression was linked with low overall survival (OS) in both GBM and LGG. In the Cox analysis, TTC7B was found to independently function as a risk element for OS of patients with glioma. Furthermore, CIBERSORT analysis demonstrated a positive link between TTC7B and multiple immune cells, especially activated NK cells. Transwell analysis, including migration and invasion assays, revealed that temozolomide reduced the migration and invasion capacity of glioma cells and increased the expression of TTC7B. Conclusion. In all, TTC7B could serve as a promising prognostic indicator of LGG and GBM, and is closely associated with immune infiltration and response to oxidative stress by temozolomide.

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Section: Cibersort Analysismentioning

confidence: 99%

TTC7B Is a Novel Prognostic-Related Biomarker in Glioma Correlating with Immune Infiltrates and Response to Oxidative Stress by Temozolomide

Chen

Cui²,

Dai

et al. 2022

Oxidative Medicine and Cellular Longevity

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“…Previous research demonstrated an elevated HDAC3 protein level in patients with glioma, indicating its potential role in glioma diagnosis and treatment ( 20 ). HDAC1, 4, 5, 8, 9, and 10 proteins have also been shown to be elevated in glioma ( 21 - 23 ). Furthermore, the combination of RGFP109, an inhibitor of HDAC3, and temozolomide (TMZ) was reported to be a promising therapeutic option for patients with TMZ-resistant GBM ( 24 ).…”

Section: Resultsmentioning

confidence: 99%

A pancancer analysis of histone deacetylase 3 in human tumors

Chen,

Xu,

Qin

et al. 2024

Transl Cancer Res

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Background Histone deacetylase 3 ( HDAC3 ) is known to be an important role in various kinds of cancer, but its effect has not been examined on the pancancer level. Thus, a systematic pancancer analysis was conducted to explore its potential role in pancancer diagnosis, prognosis, and immune correlation research. Methods We used a series of databases including The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx) Project, The University of Alabama at Birmingham Cancer data analysis portal (UALCAN), Tumor Immune Estimation Resource (TIMER), and Search Tool for the Retrieval of Interacting Genes/Proteins (STRING), among others, to analyze the relationship between the expression of HDAC3 and the diagnosis and prognosis of cancer, the tumor microenvironment (TME), immune infiltration, tumor mutational burden (TMB), microsatellite instability (MSI), mismatch repair (MMR) system using various bioinformatics methods. Downstream pathways of HDAC3 were identified by gene set enrichment analysis (GSEA). Furthermore, the protein expression of HDAC3 in tumor tissues and normal tissues of 17 patients with gliomas was analyzed via western blotting. Results The expression of HDAC3 changed in most types of tumors, which was closely related to most tumor diagnoses and negatively related to some patients’ overall survival (OS) and recurrence-free survival (RFS). The pan-cancer analysis demonstrated that it was tightly correlated to DNA methylation and RNA methylation modifications and associated with TMB and MSI. The expression level of HDAC3 was positively correlated with many immune checkpoint molecules and regulators and positively associated with the infiltration levels of immune cells in the TME in most tumor types. Furthermore, enrichment analysis revealed that transcriptional misregulation in cancer and RNA splicing functions were involved in the functional mechanism of HDAC3 -related genes. Experimental research showed that the protein expression of HDAC3 was elevated in tumor tissues of patients with glioma. Conclusions Through our comprehensive bioinformatics analysis, we evaluated the role of HDAC3 in pancancer, and our findings suggest that it may be an indicator for some cancer diagnoses and influence immune balance.

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“…In our study, the NCAPG2 and BAZ1B genes were positively related to NUP205 and have been reported as oncogenes for glioma. In addition, HDAC11 , which was negatively correlated with the expression of NUP205 , was found to have low expression in glioma tissue and was associated with a better prognosis in glioma patients ( 37 ). Interestingly, AVPI1 , FKBP8 , and ALDH2 , which were most negatively correlated with NUP205 in LGG, were all reported to be tumor suppressor genes in cancer ( 36 , 38 , 39 ).…”

Section: Discussionmentioning

confidence: 99%

Exploring the relationship between abnormally high expression of NUP205 and the clinicopathological characteristics, immune microenvironment, and prognostic value of lower-grade glioma

Liang

Zhu

et al. 2023

Front. Oncol.

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Nuclear pore complex (NPC) is a major transport pivot for nucleocytoplasmic molecule exchange. Nucleoporin 205 (NUP205)—a main component of NPC—plays a key regulatory role in tumor cell proliferation; however, few reports document its effect on the pathological progression of lower-grade glioma (LGG). Therefore, we conducted an integrated analysis using 906 samples from multiple public databases to explore the effects of NUP205 on the prognosis, clinicopathological characteristics, regulatory mechanism, and tumor immune microenvironment (TIME) formation in LGG. First, multiple methods consistently showed that the mRNA and protein expression levels of NUP205 were higher in LGG tumor tissue than in normal brain tissue. This increased expression was mainly noted in the higher WHO Grade, IDH-wild type, and 1p19q non-codeleted type. Second, various survival analysis methods showed that the highly expressed NUP205 was an independent risk indicator that led to reduced survival time of patients with LGG. Third, GSEA analysis showed that NUP205 regulated the pathological progress of LGG via the cell cycle, notch signaling pathway, and aminoacyl-tRNA biosynthesis. Ultimately, immune correlation analysis suggested that high NUP205 expression was positively correlated with the infiltration of multiple immune cells, particularly M2 macrophages, and was positively correlated with eight immune checkpoints, particularly PD-L1. Collectively, this study documented the pathogenicity of NUP205 in LGG for the first time, expanding our understanding of its molecular function. Furthermore, this study highlighted the potential value of NUP205 as a target of anti-LGG immunotherapy.

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Comprehensive Analysis of the Differential Expression and Prognostic Value of Histone Deacetylases in Glioma

Cited by 10 publications

References 80 publications

TTC7B Is a Novel Prognostic-Related Biomarker in Glioma Correlating with Immune Infiltrates and Response to Oxidative Stress by Temozolomide

TTC7B Is a Novel Prognostic-Related Biomarker in Glioma Correlating with Immune Infiltrates and Response to Oxidative Stress by Temozolomide

A pancancer analysis of histone deacetylase 3 in human tumors

Exploring the relationship between abnormally high expression of NUP205 and the clinicopathological characteristics, immune microenvironment, and prognostic value of lower-grade glioma

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