Bioinformatics analysis of SOXF family genes reveals potential regulatory mechanism and diagnostic value in cancers.

ABSTRACT

Background: SOXF family genes (SOX7, SOX17, SOX18) have been reported to involved in tumorigenesis and development in previous articles, separately. But data sources, analysis contents and criteria are not same. Here, we focused on SOXF genes to analyze the regulatory mechanisms and diagnostic value at the same standards. Methods: This study analyzed functions, expressions, methylations, and mutations of SOXF genes through public databases including Metascape, Gene Expression Profiling Interactive Analysis (GEPIA), cBioPortal, Tumor IMmune Estimation Resource (TIMER), and Kaplan-Meier Plotter. TIMER applies a deconvolution method to infer the abundance of tumor-infiltrating immune cells (TIICs) from gene expression profiles. Metascape combines several biological functions and over 40 independent knowledge bases within one integrated portal. GEPIA analyses RNA sequencing expression data from the The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) projects. The cBioPortal visualizes and analyses genetic data from cancer studies. Results: This study found that SOXF genes had low expressions in multiple types of cancer, such as lung cancer and breast cancer (ANOVA differential methods, |log2FC| cutoff 1, q value cutoff 0.01). The lung adenocarcinoma (LUAD) patients with high expression of SOX7 [HR =0.72 (0.61-0.85), logrank P=8.1e-05) and SOX17 [HR =0.54 (0.45-0.64), logrank P=1.7e-12] had a higher overall survival (OS) rate. Expression of SOX7 was significantly related to the copy number variation (CNV) (P=3.02e-8) and promoter methylation level (P=5.33e-14), while SOX17 was only related to the promoter methylation level (P=3.32e-12). The expression of SOXF genes was positively correlated with CD4+ T cell infiltration (SOX7 P=8.32e-07, SOX17 P=4.93e-06, SOX18 P=1.61e-11). The AUC for cg07660671 site of SOX7, cg15377283 site of SOX17, and cg24199599 site of SOX18 in distinguishing between normal and tumor in LUAD, intestinal cancer, and breast cancer reached 0.9. SOXF genes were mainly involved in transcriptional regulation, and the Wnt signaling pathway and low expression of SOXF genes in tumor tissue had a strong negative correlation with tumor hypoxia (correlation -0.35, P≤0.001). Conclusions: This study implied that the expression of SOX7 and SOX17 are potential prognosis markers for patients with Lung cancer and the SOXF genes methylation is potential biomarkers for pan-cancer screening. The SOX7 and SOX17 might modulate the Wnt signaling pathway and the expression of SOXF family genes was significantly negatively correlated with tumor hypoxia.