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  • Meta-Analysis on Gene Expression: the Therapeutic Efficacy of Inulin in Caco-2 Cancer Cells

  • Fatemeh Abolmashadi,1 Mahdi Moridi Farimani,2 Gholamreza Farnoosh,3,*
    1. Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Tehran, Iran
    2. Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Tehran, Iran
    3. Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran


  • Introduction: Colorectal cancer (CRC) is one of the most prevalent cancers globally. Strong epidemiological evidence indicates that dietary fiber intake, particularly prebiotic types such as inulin, is associated with a reduced risk of developing CRC. However, the precise molecular mechanisms underlying this protective effect, especially the direct impact of inulin on the intestinal epithelium, remain not fully understood. The present study focuses on inulin as a key prebiotic fiber, utilizing an in vitro model of human intestinal epithelial cells (Caco-2) and transcriptomic analysis to conduct a meta-analysis of the gene responses induced by inulin and its potential role in modulating pathways related to gut health and cancer prevention.
  • Methods: This study utilized microarray bioinformatics to identify potential indicator genes associated with Caco-2 cancer cells. The analysis concentrated on the microarray dataset GSE99610, contrasting cells that were treated with inulin against untreated cells. Additionally, pathway analysis, gene ontology (GO) enrichment, and protein-protein interaction (PPI) network analyses were conducted to reveal critical biological pathways. The datasets were subjected to meta-analysis employing bioinformatics tools to pinpoint significant differentially expressed genes (DEGs) and their corresponding hub genes.
  • Results: The study identified HLA-DQA2, HLA-DPB1, and COL11A2 as key hub genes. The analysis of differentially expressed genes (DEGs) through gene ontology (GO) indicated that these genes were notably enriched in pathways related to Intestinal immune network for IgA production, as well as the Inflammatory bowel disease.
  • Conclusion: Our findings provide compelling evidence that inulin exerts significant anticancer effects on Caco-2 colorectal cancer cells by inducing meaningful changes in the expression patterns of differentially expressed genes (DEGs) associated with inflammation regulation and immune modulation. The genetic factors identified in this study are essential for understanding the therapeutic effects of inulin on Caco-2 cancer cells. Although these findings are primarily based on in vitro models, they clearly demonstrate the potential of inulin as an adjunct or preventive agent in colorectal cancer treatment strategies, underscoring the necessity for further in vivo and clinical research.
  • Keywords: Colorectal cancer, Inulin, Bioinformatics, Meta-analysis

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