Bioinformatics mining and experimental validation of prognostic biomarkers in colorectal cancer

Abstract

Colorectal cancer (CRC) is a prevalent malignancy with rising incidence and mortality rates. It is essential to identify potential prognostic gene biomarkers for CRC. We analyzed public datasets, revealing 5408 differentially expressed genes (DEGs) between CRC and adjacent normal tissues. Utilizing the Gene Expression Omnibus (GEO) and the Cancer Genome Atlas (TCGA) databases, we identified 2779 up-regulated and 2629 down-regulated genes. Weighted gene co-expression network analysis (WGCNA) yielded the MEbrown module, containing 1639 genes highly correlated with CRC. A total of 926 differentially expressed CRC-related genes were screened for subsequent analysis. Then, a prognostic risk model with five characteristic genes (TIMP1, PCOLCE2, MEIS2, HDC and CXCL13) was constructed. This model demonstrated strong predictive ability in the GSE32323 dataset and an internal test set. All five characteristic genes harbored predominantly missense mutations, with TIMP1 exhibiting the highest variant allele frequency. Functional enrichment analysis, including gene set enrichment analysis (GSEA) and histological expression analysis in the HPA database, highlighted the biological significance of TIMP1 in CRC. TIMP1 is upregulated in the tumor tissue and enriched in CRC-related pathways such as type I interferon receptor binding, oxidative phosphorylation, and Notch signaling pathways. Additionally, using siRNA technology, the impact of TIMP1 on cellular proliferation and apoptosis in CRC cell lines (HCT116 and HT29) was investigated, showing that TIMP1 knockdown significantly inhibited proliferation and promoted apoptosis. This study presents a novel prognostic risk model comprising five characteristic genes (TIMP1, PCOLCE2, MEIS2, HDC and CXCL13) for CRC, which are strongly associated with overall survival in CRC patients with TIMP1 identified as having cancer-promoting properties in CRC. Our study suggests that TIMP1 holds promise as both a biomarker and a therapeutic target for CRC.