Introduction
Crohn’s disease (CD) is a complex immune-mediated disease of the gastrointestinal (GI) tract where the gut microbiota plays an important role. Current biological treatment options in CD include the anti-TNFα agents adalimumab and infliximab (anti-TNF), vedolizumab (VEDO), and ustekinumab (USTE). Finding biomarkers to predict therapy response is still a clinically unmet need, for the majority of CD patients fail to reach endoscopic remission within one year of treatment. While most studies focus on fecal samples, mucosa-adherent microbial biopsies could bring forth more stable biomarkers.
Aims & Methods
In this study, we sought to identify microbial signatures in mucosal colon and ileum biopsies aimed at differentiating responders (R) from non-responders (NR), prior to the start of biological treatment. Ileal and colonic biopsies from CD patients were prospectively collected at the start of treatment with biological agents. Three distinct cohorts of patients were recruited: anti-TNF, VEDO and USTE. Patients were classified as either R or NR based on endoscopic response (≥50% reduction in SES-CD score) in combination with steroid-free clinical response (≥3 point drop in HBI or HBI ≤4, no systemic steroids) and/or biochemical response (≥50% reduction in CRP and fecal calprotectin or a basal CRP ≤5 g/mL and calprotectin ≤250 µg/g). Mucosal-associated microbiome composition was determined using 16S rRNA gene sequencing. Multivariate statistical analysis was performed in R statistical environment using the packages phyloseq, vegan and DESeq2.
Results
At baseline, colonic biopsies were collected from 117 CD patients. In anti-TNF cohort, alpha diversity, described by Shannon index, and species richness were significantly higher in R than NR. Accordingly, the relative abundance of 13 genera was higher in R, while only four genera had lower abundance in R than NR. In VEDO and USTE, differences in alpha and beta diversity were not significant, however, discriminatory analysis at genus level revealed 10 and 15 genera with significantly different relative abundance in R and NR of the VEDO and USTE, respectively. Overall analysis of the colon-derived signal (n=117) was performed combining the above discriminatory genera’s relative abundance, leading to
1) establishment of “treatment-specific” genera, discriminatory for only one biological;
2) “treatment-aspecific” response supporters, discriminatory in at least two biologicals sharing direction, and
3) “treatment-drivers”, discriminatory in at least two cohorts with contradicting direction.
Respective analysis was followed for the ileal biopsies (n=107). Intra-cohort approach showed that, at baseline, alpha and beta diversity did not differ between R and NR. However, analysis at genus level revealed 14, 25 and 13 discriminatory genera in the anti-TNF, VEDO and USTE cohorts, respectively, falling in the “treatment-specific”, “treatment-aspecific” and “treatment-drivers” categories, as well.
Conclusion
We established three group of microbial signatures that discriminate response to biological therapy:
(a) biological agent “treatment-specific” genera,
(b) “treatment-aspecific”, and
(c) “treatment-drivers”, distinct per GI location, namely ileum and colon.
We suggest microbial evaluation of these taxa at the treatment decision process, to support most suitable agent. Acknowledging that analysis at genus level may allow for species-level differences within a genus, sophisticated modelling at amplicon sequence variant level is currently undertaken.
Disclosure
ECCO Pioneer Grant