Identification and comprehensive analysis of gene characteristics related to chromatin remodeling in thyroid cancer...

Thyroid cancer (THCA) is the 9th most common endocrine tumor worldwide. However, its etiology and pathogenesis are not fully understood. Therefore, this study aimed to identify the biomarkers associated with chromatin remodeling in patients with THCA. THCA-related datasets and chromatin remodeling related genes were included in this study. Differential expression analysis and 2 machine learning algorithms were employed to identify candidate genes. Biomarkers were identified by receiver operating characteristic curve analysis. The prognostic potential of the biomarkers was explored using Kaplan-Meier (KM) survival analysis. Key genes linked to biomarkers were identified using weighted gene co-expression network analysis. Immune infiltration analysis was performed to explore differences in immune infiltration between THCA and control groups. Finally, the expression for biomarker was validated in clinical samples using reverse transcription quantitative polymerase chain reaction. Five biomarkers (CHD4, SMARCA2, CHD3, ATAD2, and SMARCA4) were screened. KM survival analysis revealed that patients with higher expression of SMARCA4, CHD4, and ATAD2 had a higher survival rate, whereas in the lower expression groups of CHD3 and SMARCA2, the survival rate of THCA patients was lower. A total of 98 genes related to biomarkers were identified using weighted gene co-expression network analysis. In addition, a total of 20 immune cells infiltrated differentially in THCA and controls, with the largest positive correlation between immature dendritic cells and ATAD2, with a correlation coefficient of 0.54, and a large positive correlation between CD56dim natural killer cells and SMARCA4, which was 0.5. Reverse transcription quantitative polymerase chain reaction revealed that the expression of biomarkers was consistent with the results of the bioinformatics analysis. In summary, SMARCA4, CHD4, and ATAD2 were overexpressed, whereas CHD3 and SMARCA2 were downregulated in THCA samples. This study identified 5 biomarkers (CHD4, SMARCA2, CHD3, ATAD2, and SMARCA4) associated with chromatin remodeling in THCA. Current reference points for the prevention and treatment.