FOXD subfamily genes serve as biomarkers and therapy targets in colorectal cancer

Abstract

Abstract Background: The forkhead box (FOX) family of proteins regulates gene transcription and expression. It regulates various biological processes, such as tumorigenesis and cell proliferation. FOXD, a subfamily of FOX, is associated with poor prognosis. However, the potential clinical value of FOXD subfamily members has not yet been elucidated. Methods: We used The Cancer Genome Atlas Project (TCGA), which was used to analyze the HTSeq-count data, clinical data, and single-nucleotide polymorphisms (SNPS). Furthermore, we used the DESEQ2 software to detect differentially expressed genes (DEGs). Batch survival analysis was performed using the survival and survminer packages in R to obtain genes with different expression levels. The intersection of the two results was used to identify the FOXD subfamily as the principal variable. Each gene was analyzed using RT-qPCR, western blotting, and immunohistochemistry. Functional enrichment analysis of FOXD subfamily-related DEGs was performed using the ClusterProfiler package. A protein network of FOXD subfamily-related DEGs was constructed using the STRING online database. We used CIBERSORT to determine the relationship between FOXD subfamily expression and immune cell infiltration. We established a survival analysis model to explore the clinical correlation between FOXD subfamily members and CRC. Results: In contrast to the normal tissue/cell line, FOXD1, FOXD2, FOXD3, and FOXD4 expression was higher. No FOXD1 mutations were detected. Moreover, FOXD2 was detected in both COAD and READ groups. FOXD3 and FOXD4 were onlymutated in COAD. Among the FOXD subfamily members, the AUC of FOXD3 was 0.949, indicating that FOXD3 has a high overall diagnostic accuracy for CRC. The results of the GSEA showed that the genes related to the FOXD subfamily were mainly related to the KEGG pathway, such as cytokine, cytokine, and ECM receptor interactions. Kaplan-Meier curves and nomograms showed that FOXD1, FOXD3, and FOXD4 were prognostically significant. Conclusions: We explored the correlation between the expression of the FOXD subfamily genes and the clinical and immunological characteristics of patients with CRC. The FOXD subfamily may serve as a diagnostic and prognostic biomarker for CRC and be used as an immunotherapy target in patients with CRC.