Prognostic Model of Eleven Genes Based on the Immune Microenvironment in Patients With Thymoma

Abstract

Purpose: The pathogenesis of thymoma (THYM) remains unclear, and there is no uniform measurement standard for the complexity of THYM derived from different thymic epithelial cells. Consequently, it is necessary to develop novel biomarkers of prognosis estimation for patients with THYM.Methods: Consensus clustering and single-sample gene-set enrichment analysis were used to divide THYM samples into different immunotypes. Differentially expressed genes (DEGs) between those immunotypes were used to do the Kyoto Encyclopedia of Genes and Genomes analysis, Gene Ontology annotations, and protein-protein interaction network. Furthermore, the survival-related DEGs were used to construct prognostic model with lasso regression. The model was verified by survival analysis, receiver operating characteristic curve, and principal component analysis. Furthermore, the correlation coefficients of stemness index and riskscore, tumor mutation burden (TMB) and riskscore, drug sensitivity and gene expression were calculated with Spearman method.Results: THYM samples were divided into immunotype A and immunotype B. A total of 707 DEGs were enriched in various cancer-related or immune-related pathways. An 11-genes signature prognostic model (CELF5, ODZ1, CD1C, DRP2, PTCRA, TSHR, HKDC1, KCTD19, RFX8, UGT3A2, and PRKCG) was constructed from 177 survival-related DEGs. The prognostic model was significantly related to overall survival, clinical features, immune cells, TMB, and stemness index. The expression of some genes were significantly related to drug sensitivity.Conclusion: For the first time, a prognostic model of 11 genes was identified based on the immune microenvironment in patients with THYM, which may be helpful for diagnosis and prediction. The associated factors (immune microenvironment, mutation status, and stemness) may be useful for exploring the mechanisms of THYM.

Tumor Microenvironment in Thymic Epithelial Tumors: A Narrative Review

“…The immunotype B group consisted of more immune factors, such as macrophages, NK cells, Treg, Type II IFN response, and aDCs, compared to the immunotype A group. Furthermore, the survival analysis revealed that the immunotype A group resulted in significantly better survival [ 33 ].…”

Identification of Ultrasound-Sensitive Prognostic Markers of LAML and Construction of Prognostic Risk Model Based on WGCNA

“…Te expression level of UGT3A2 is related to DNA methylation and afects the occurrence and development of LAML [43]. An 11-gene signature, including UGT3A2, established based on the immune microenvironment can be employed for the prediction of the prognosis of thymoma patients [44]. BLOCK1S1, also known as GCN5L1, is a new molecule homologous to the sequence of nuclear acetyltransferase GCN5, which is involved in the regulation of mitochondrial autophagy, fatty acid oxidation, and other mitochondrial biological processes [45][46][47].…”

Identification of Novel Biomarkers in Peripheral Blood Mononuclear Cells of Hepatocellular Carcinoma Patients

“…Dysregulation or mutation of genes encoding proteins essential for highfidelity DNA replication is often associated with disease, particularly cancer [17]. The histone genes are involved in chromatin organisation which is essential for the regulation of gene expression and DNA replication [18].…”

“…During cell division, chromatin condenses into chromosomes which can be separated into two daughter cells. Dysregulation of histone genes can lead to abnormal chromosome segregation during cell division [18]. In addition to their role in DNA replication and cell division, histones also play a role in regulating gene expression.…”

“…In addition to their role in DNA replication and cell division, histones also play a role in regulating gene expression. Histone modifications such as acetylation and methylation can activate or repress gene expression by altering the accessibility of DNA to transcription factors [18]. Dysregulation of histone genes can therefore lead to abnormal gene expression patterns.…”