The presence of genetic risk variants within PTPN2 and PTPN22 is associated with intestinal microbiota alterations in Swiss IBD cohort patients

Abstract

Background: Genetic risk factors, intestinal microbiota and a dysregulated immune system contribute to the pathogenesis of inflammatory bowel disease (IBD). We have previously demonstrated that dysfunction of protein tyrosine phosphatase non-receptor type 2 (PTPN2) and PTPN22 contributes to alterations of intestinal microbiota and the onset of chronic intestinal inflammation in vivo. Here, we investigated the influence of PTPN2 and PTPN22 gene variants on intestinal microbiota composition in IBD patients.

Methods: Bacterial DNA from mucosa-associated samples of 75 CD and 57 UC patients were sequenced using 16S rRNA sequencing approach. Microbial analysis, including alpha diversity, beta diversity and taxonomical analysis by comparing to PTPN2 (rs1893217) and PTPN22 (rs2476601) genotypes was performed in QIIME, the phyloseq R package and MaAsLin pipeline.

Results: In PTPN2 variant UC patients, we detected an increase in relative abundance of unassigned genera from Clostridiales and Lachnospiraceae families and reduction of Roseburia when compared to PTPN2 wild-type (WT) patients. Ruminoccocus was increased in PTPN22 variant UC patients. In CD patients with severe disease course, Faecalibacterium, Bilophila, Coprococcus, unclassified Erysipelotrichaeceae, unassigned genera from Clostridiales and Ruminococcaceae families were reduced and Bacteroides were increased in PTPN2 WT carriers, while Faecalibacterium, Bilophila, Coprococcus, and Erysipelotrichaeceae were reduced in PTPN22 WT patients when compared to patients with mild disease. In UC patients with severe disease, relative abundance of Lachnobacterium was reduced in PTPN2 and PTPN22 WT patients, Dorea was increased in samples from PTPN22 WT carriers and an unassigned genus from Ruminococcaceae gen. was increased in patients with PTPN2 variant genotype.

Conclusions: We identified that IBD-associated genetic risk variants, disease severity and the interaction of these factors are related to significant alterations in intestinal microbiota composition of IBD patients.

Fig 1. The microbial features associated with disease phenotype and IBD-associated risk variant rs1893217 and rs2476601.

Species richness is calculated using Shannon index in CD (A) and UC (B) samples. Beta diversity is calculated for CD (C) and UC (D) samples in the context of PTPN2 variant and for CD (E) and UC (F) samples in the context of PTPN22 variant using Bray-Curtis dissimilarity matrix. Heterozygous variants are red color while homozygous wild-type ones are turquoise. Colon samples are labeled as closed circle and ileum samples are labeled as closed triangles. Ellipses represent dispersion of samples and ellipses for colon samples are labeled with straight line while ellipses for ileum samples are labeled are label dashed line. A p-value <0.05 is considered significant. Significant differences are marked through the panels.

Fig 2. The microbial differences associated with disease and risk variants.

The relative abundance of significantly different taxa (q<0.05) were plotted for PTPN2 variant in (A) when analyzed for CD and in (B) when analyzed for UC. The relative abundance of significantly different taxa (q<0.05) was plotted for PTPN22 variants when analyzed for UC (C) samples. The “gen.,” was used for the classification of a distinct but unnamed genus in the Greengenes reference database and “unclassified” used for identification of unclassified taxa in Greengenes reference database, as previously used in another study [53].

Fig 3. The microbial differences associated with disease severity within same PTPN disease variants.

The relative abundance of significantly different microbial taxa (q<0.05) were plotted according to disease severity status for PTPN2 wild-type variant in (A) and PTPN22 wild type variant in (B) when analyzed for CD. The relative abundance of significantly different microbial taxa (q<0.05) were plotted according to disease severity status PTPN2 wild-type variant in (C) and heterozygous variant (D) and PTPN22 wild-type variant in (E) when analyzed for UC.

Fig 4. Effects of PTPN2 dysfunction on intestinal microbiota composition.

PTPN2-mediated dysfunction of several immune mechanisms that are important for the body’s immune response to luminal bacteria and for maintaining intestinal homeostasis. In particular, dysfunction of autophagy, aberrant inflammasome activation and altered T-cell activation and differentiation seems to play a crucial role for the observed correlation between PTPN2 dysfunction and alterations in intestinal microbiota composition.