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CancerGenetics

• Investigating hsa-miR-193-3p and hsa-let-7e-3p and Their Target Genes IGFBP5 and AGPAT5 Associated with Fusobacterium nucleatum in Patients with Colorectal Polyps and CRC: In Silico Predictions and Experimental Validation

• Fatemeh Sosanabadi Farahani,^1,* Haniyeh Rahimi-Kolour,² Zahra Sadeghloo,³ Nayeralsadat Fatemi,⁴
  1. 1.Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran,2.Islamic Azad University, Science and Research Branch, Tehran, Iran
  2. Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
  3. Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
  4. Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
  
  
  
• Introduction: Colorectal cancer (CRC) is among the most prevalent malignancies worldwide, often originating from adenomatous or serrated polyps through a series of genetic and epigenetic alterations. Growing evidence underscores the role of gut microbiota in CRC pathogenesis, with Fusobacterium nucleatum (Fn) identified as a key microbial contributor. This bacterium facilitates tumor progression and chemoresistance by modulating host microRNA (miRNA) expression. Despite these advances, the molecular interplay between Fn, regulatory miRNAs, and their downstream targets remains poorly characterized across distinct types of colorectal polyps.
• Methods: We analyzed the GSE122182 dataset using the limma package to identify differentially expressed miRNAs. Candidate target genes were predicted via the multiMiR package, followed by KEGG and GO enrichment analyses. To compare differentially expressed genes (DEGs) from GSE122183 with predicted miRNA targets, Venn diagrams were constructed. Primers were designed for selected candidate genes identified during the in silico phase. Two miRNA–gene pairs—hsa-miR-193-3p/IGFBP5 and hsa-let-7e-3p/AGPAT5—were selected for experimental validation. Tissue samples (n = 100; low-risk polyps, high-risk polyps, and Fn-associated cancer) underwent DNA and RNA extraction, cDNA synthesis, and qRT-PCR to quantify the expression levels of the selected miRNAs and their corresponding target genes. Statistical analysis was performed using ANOVA, with significance set at p ≤ 0.05.
• Results: A total of 100 colorectal tissue samples, including CRC, villous polyps, and tubular polyps, were analyzed. The expression of Fn 16S rRNA was higher in Fn⁺ tissues compared to Fn⁻ across all groups, with the highest levels observed in CRC–Fn⁺ samples. miR-193-3p and let-7e-3p were consistently downregulated in Fn⁺ tissues, while their target genes IGFBP5 and AGPAT5 were upregulated. Comparative analysis among Fn⁺ groups revealed progressive molecular alterations from tubular polyps to villous polyps and CRC, supporting the role of Fn-associated miRNA–gene dysregulation in colorectal tumorigenesis.
• Conclusion: In conclusion, our study highlights the potential pathogenic role of Fn in CRC and emphasizes the importance of miRNA–gene interactions in colorectal carcinogenesis. These findings offer new insights into the molecular mechanisms driving CRC development and suggest that targeting both bacterial abundance and miRNA-mediated pathways could present novel strategies for CRC prevention and treatment.
• Keywords: Colorectal cancer; Fusobacterium nucleatum; microRNA; biomarkers; polyps