Fecal metaproteomics enables functional characterization of remission in patients with inflammatory bowel disease

Inflammatory Bowel Disease (IBD) describes a condition characterized by chronic inflammation of the gastrointestinal tract. Its pathogenesis is linked to genetic susceptibility, environmental factors, host immune response, and gut microbiome. There are various therapy approaches, including treatment with biological antibodies. Alleviation of symptoms, which is termed remission, is often assessed by colonoscopy, which means an invasive measure for the patient. Therefore current research is focused on characterizing remission and finding microbial or human biomarkers for therapy success by non-invasive methods, like analysis of fecal samples by metaproteomics. The goal of this work was the functional characterization of differences in the fecal metaproteome of patients who did or did not achieve remission.

Therefore, fecal samples of a cohort of IBD patients were collected before and after 14 weeks of treatment with three different biologics. Clinical disease activity scores were used to determine clinical response and remission. The fecal metaproteomes of the remitting patients (n=12) and of non-remitting patients (n=12) were compared at baseline and changes within both groups were assessed over the course of the therapy to identify functional changes and potential human and microbial biomarkers. The proteins of these samples were extracted via bead beating with phenol and tryptically digested. The peptides were separated using reversed-phase liquid chromatography and measured with a timsTOF mass spectrometer. The MetaProteomeAnalyzer was used for protein identification and taxonomical and functional annotation.

The results show, that the therapy"s success is clearly depicted in the fecal metaproteome of IBD patients. The abundance of proteins associated with the intestinal barrier, neutrophilic granulocytes, and immunoglobulins significantly decreased in remitting patients, and showed, in contrast, an increase in non-remitting patients. Furthermore, the remission was characterized by an increased abundance of microbial proteins involved in the pentose phosphate pathway, tricarboxylic acid cycle, or butyrate fermentation. These results imply diminished immune system activity and a restored microbial metabolism in remitting patients. Finally, we proposed new potential biomarkers for monitoring of therapy success, e.g. human lysosome-associated membrane glycoprotein 1, a cytotoxicity marker, or microbial anthranilate synthase component 2, a part of the tryptophan metabolism, both increasing in non-remitting patients. Our study suggests, that there are distinct changes in gut inflammation and gut microbiome metabolism dependent on whether therapy with biologics induced remission or not, proving that metaproteomics could be a useful tool for monitoring remission in IBD therapies.