Unraveling the Influence of Escherichia coli Strains on Gene Expression in Colorectal Cancer Cells through in Silico Analysis

Introduction: Various studies have demonstrated a clear link between mucosa-adherent Escherichia coli and colorectal cancer (CRC). This in silico study aims to identify commonly differentially expressed genes in CRC cells treated with distinct E. coli strains, regardless of their pathogenicity.
Methods: The raw data from the GEO database were normalized with the Affy package in the R software. We used computational methods (limma analysis, linear regression analysis, hierarchical clustering, and gene set enrichment analysis) to identify the transcriptome alterations induced by E. coli O:157.H7 and E. coli K-12 strains.
Results: Out of the 80 genes that were significantly differentially expressed in both E. coli-treated groups, only three genes (HIST1H4E, JUN, and TMEM267) demonstrated a high correlation (r>0.9) with the incubation time. TMEM267 is downregulated as the incubation time increases whereas HIST1H4E and JUN become upregulated. In addition, we determined nine common genesets that were significantly enriched in the Caco2 cell line after treatment either with E.coli O:157.H7 or K-12 strains. Discussion and Conclusion: In this study, the changes in gene expressions resulting from the treatment of colon cancer cells with different E. coli strains were investigated. These findings highlight the potential impact of E. coli on cancer development and suggest that certain genes may play a role in mediating the effects of E. coli in the context of CRC. Further research is warranted to elucidate the underlying mechanisms and specific pathways involved in the interactions between E. coli and cancer cells.

Keywords: Cancer molecular biology; Clinical microbiology; Colorectal cancer; Escherichia coli; Molecular biology; Transcriptome analysis