Poor prognosis in IBD-complicated colon cancer through gut dysbiosis-related immune response failure

Sobhani, I.; De Oliveira Alves, N.; Sadeghi, M.; Charpy, C.; Bergsten Emma, E.; Amiot, A.; Barau, C.; Brunetti, F.; Vaysse, A.; Tournigand, C.; Chamaillard, M.; Khashayarsha, K.; Mestivier, D.

doi:10.1101/2025.03.25.645177

bioRxiv · 10.1101/2025.03.25.645177

Poor prognosis in IBD-complicated colon cancer through gut dysbiosis-related immune response failure

Sobhani, I.·De Oliveira Alves, N.·Sadeghi, M.·Charpy, C.·Bergsten Emma, E.·Amiot, A.·Barau, C.·Brunetti, F.·Vaysse, A.·Tournigand, C.·Chamaillard, M.·Khashayarsha, K.·Mestivier, D.

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Abstract

BackgroundColorectal cancer (CRC) results from the accumulation of mutations and epigenetic changes in gut epithelial cells likely due to gut microbiota dysbiosis. However, limited research has been done to explore the link between host tumour dysbiosis and disease outcome. MethodsThe mechanisms influencing outcomes of 97 colorectal cancer (CRC) patients, including 13 with Lynch syndrome, 20 with inflammatory bowel disease (IBD), and 64 sporadic cases, were analyzed using a multiomics approach. These patients were categorized into two groups: "disease-free/stable disease" and "progression disease" survival outcomes. The analysis included tumor adherent microbiota composition (16S rRNA), somatic gene mutations (WES), gene expression (RNAseq), immune markers (RNAscope), and immune infiltrate cells (immunohistochemistry). ResultsIBD-CRC patients had worse outcomes than those with Lynch or sporadic CRC, regardless of TNM staging or treatment. Symbiotic bacteria like Lactococcus lactis were significantly reduced in IBD-CRC tissues. Patient outcomes were influenced by the abundance of virulent (Escherichia coli) relative to beneficial bacteria (Lactococcus lactis). Although no significant increase in deleterious somatic mutations was found in IBD-CRC. 16sRNA revealed increased virulent- and decreased anti-inflammatory symbiotic-bacteria correlating with the upregulation of oncogenes and downregulation of anti-oncogenes like PHLPP1. The multiplex in situ hybridization of CD8, IFN{gamma} and PHLPP1 an anti-oncogene revealed significant decrease of immune cells with detectable PHLPP1 expression in IBD-CRC tumour tissues as compared to sporadic CRCs. ConclusionThe poor outcomes in IBD-CRC patients are likely due to gut dysbiosis and immune cell alterations, possibly triggered by microbiota-related epigenetic pathways. What You Need to KnowO_ST_ABSBACKGROUND AND CONTEXTC_ST_ABSColorectal cancer (CRC) is associated with gut microbiota dysbiosis. Inflammatory bowel disease-related CRC (IBD-CRC) is classified as an environment-related condition. NEW FINDINGSIn relation with patient outcomes, tumour tissues from three types of CRC (Sporadic-, IBD-, and Lynch syndrome-CRC) were analyzed using a multiomic approach. This included examining tissue adherent virulent bacteria, gene analyses, and quantifying immune cell infiltration in the mucosa. IBD-CRC patients had the worst outcomes, associated with the down regulation of PHLPP1 gene, virulent/symbiotic imbalance, and immune response failure. LIMITATIONSLack of animal experiments using FMT of fresh stool from IBD-CRC patients. CLINICAL AND TRANSLATIONAL RESEARCH RELEVANCEAmong the different types of CRC, IBD-CRC patients showed a greater imbalance between harmful and beneficial bacteria, along with immune response failure. Lay summaryThis study compares the pathological and clinical characteristics of patients with colorectal cancer (CRC) across three distinct etiologies: sporadic CRC, inflammatory bowel disease (IBD)-associated CRC, and Lynch syndrome-associated CRC (LS-CRC). Distinct differences in tumor-adherent microbiota, gene expression and immune response profiles were observed. Notably, IBD-CRC patients demonstrated the poorest prognosis depending on microbe-host gene interaction highlighting potential biomarkers for disease prognosis and treatment strategies.

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Sobhani, I., De Oliveira Alves, N., Sadeghi, M., Charpy, C., Bergsten Emma, E., Amiot, A., Barau, C., Brunetti, F., Vaysse, A., Tournigand, C., Chamaillard, M., Khashayarsha, K., Mestivier, D.. 2025-03-28. Poor prognosis in IBD-complicated colon cancer through gut dysbiosis-related immune response failure. https://doi.org/10.1101/2025.03.25.645177

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