| Summary: | Gut microbiota appears to be involved in the pathogenesis of primary sclerosing cholangitis (PSC). The protein tyrosine phosphatase nonreceptor 2 (PTPN2) gene risk variant rs1893217 is associated with gut dysbiosis in inflammatory bowel disease (IBD), and PTPN2 was mentioned as a possible risk gene for PSC. This study assessed the microbial profile of ulcerative colitis (UC) patients with PSC and without PSC (non-PSC). Additionally, effects of the PTPN2 risk variant were assessed. In total, 216 mucosal samples from ileum, colon, and rectum were collected from 7 PSC and 42 non-PSC patients, as well as 28 control subjects (non-IBD). The microbial composition was derived from 16S rRNA sequencing data. Overall, bacterial richness was highest in PSC patients, who also had a higher relative abundance of the genus <i>Roseburia</i> compared to non-PSC, as well as <i>Haemophilus</i>, <i>Fusobacterium</i>, <i>Bifidobacterium,</i> and <i>Actinobacillus</i> compared to non-IBD, as well as a lower relative abundance of <i>Bacteroides</i> compared to non-PSC and non-IBD, respectively. After exclusion of patients with the PTPN2 risk variant, <i>Brachyspira</i> was higher in PSC compared to non-PSC, while, solely in colon samples, <i>Eubacterium</i> and <i>Tepidimonas</i> were higher in PSC vs. non-IBD. In conclusion, this study underlines the presence of gut mucosa-associated microbiome changes in PSC patients and rather weakens the role of PTPN2 as a PSC risk gene.
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