Chamaillard, Mathias

Objective How tumour-adherent microbiome can influence outcomes in patients with colorectal cancer (CRC). Methods and analysis CRC tissues (n=97) were analysed using RNAseq, whole exome sequencing (WES) and 16 r sRNA sequencing. Inflammatory/immune cells were quantified by immunohistochemistry in mice and human tissues. Patient outcomes were analysed according to virulent bacteria and gene RNA levels in tumour tissues. We performed faecal microbiota transfer (FMT) in germ-free mice using presurgery stool samples from nine patients with sporadic CRC. Changes in gene mutations and DNA methylation in the colonic mucosa were measured and compared with those in mice receiving FMT from nine healthy individuals. Immune cells in the tumour tissues of donor and mouse recipients were compared. Results FMT from CRC donors led to preferential DNA demethylation, but specific host genes, including pleckstrin homology domain and leucine-rich repeat protein phosphatase 1 (PHLPP1), were hypermethylated compared with FMT from healthy donors. CRC faecal samples showed elevated levels of virulent bacteria, reduced levels of commensals and triggered colon inflammation in mice. Notably, PHLPP1 was downregulated in CRC tumours, and its expression varied in accordance with other CRC cardinal genes (n=137, as identified in the scientific literature to be involved in colon carcinogenesis), and was most pronounced in inflammatory bowel disease associated CRC. Tumours with reduced PHLPP1 expression are more inflammatory and correspond to patients with a higher relative abundance of adherent virulent bacteria and poorer outcomes. Conclusion The composition of CRC tumour-adherent bacteria predicts epigenetic modifications and altered expression of cardinal CRC genes such as PHLPP1. PHLPP1 downregulation characterises patients with CRC with inflammatory tumours and poor survival outcomes.

Summary Background Colorectal 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. Methods The 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). Results IBD-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, IFNγ 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. Conclusion The 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 Know BACKGROUND AND CONTEXT Colorectal cancer (CRC) is associated with gut microbiota dysbiosis. Inflammatory bowel disease-related CRC (IBD-CRC) is classified as an environment-related condition. NEW FINDINGS In 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. LIMITATIONS Lack of animal experiments using FMT of fresh stool from IBD-CRC patients. CLINICAL AND TRANSLATIONAL RESEARCH RELEVANCE Among the different types of CRC, IBD-CRC patients showed a greater imbalance between harmful and beneficial bacteria, along with immune response failure. Lay summary This 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.