Abstract Background There has been a significant increase in the incidence of paediatric inflammatory bowel disease (IBD) over the last 25 years. However, aetiology and mechanistic understanding of the changes occurring in mucosa of these patients is insufficient. In this study we perform in-depth global proteomics profiling of a unique biobank of paediatric biopsies collected in collaboration with Uppsala University hospital from children and adults naïve to IBD treatment, providing insights into mucosal pathophysiology of paediatric IBD. Methods Since 2021, biopsies from six anatomical sites along the gastrointestinal tract (stomach, duodenum, ileum, ascending and descending colon and rectum) have been collected within the framework of ERC Consolidator Grant MAGNETO from children and adults undergoing IBD diagnostics at the Uppsala University hospital. These biopsies were analysed in-house using high resolution mass-spectrometry based global proteomics in bespoke data-independent acquisition (DIA) method on Orbitrap Q Exactive HF. Protein identification was performed using DIANN software, whilst subsequent data analysis was executed in R. Results We have analysed biopsies from 35 children and detected over 10100 proteins across these samples. In principal component analysis, mucosal samples clustered depending on the biopsy’s location across all biological donors. Further analysis highlighted regional expression difference in multitudes of proteins, creating a unique dataset of protein expression profiles along GIT. Above all, we preformed differential expression analysis comparing IBD and control individuals, and confirmed significant upregulation of known and proposed IBD biomarkers in children with confirmed IBD-diagnosis, e.g. S100A8/9/12 (calprotectin), IGHV1-24, lactoferrin, myeloperoxidase (MPO) and defensin, etc. An ongoing data analysis focuses on exploring the correlation between patient metadata parameters such as age, gender, endoscopic score and known IBD diagnosis in the immediate family, and significantly altered proteins and pathways. Lastly, pediatic mucosal proteomes and declared are benchmarked against adult mucosal samples collected within the same study. Conclusion To our knowledge, no studies have performed comprehensive global proteomics profiling of longitudinal mucosal samples of newly diagnosed paediatric patients. Here we aim to provide an extensive resource of knowledge that has the potential of improving the mechanistic understanding of paediatric IBD, as well as to aid in the development of novel IBD diagnostics. In addition, we issue a unique atlas of paediatric GIT proteomes, that could be further applied in physiologically based pharmacokinetic (PBPK) modelling of paediatric population. Conflict of interest: Dr. Mickols, Evgeniya: No conflict of interest Ideström, Maja: No conflict of interest Nyström, Niklas: Personal Fees: served as speaker for Abigo, Baxter, Ferring, Fresenius-Kabi, Mylan/Meda, Nutricia, Shire, Takeda, Thermo Fisher Scientific, Tillotts Pharma, and as consultant and advisory board member for Takeda Teleki, Alexandra: I declare no conflicts of interest.
Mickols et al. (Thu,) studied this question.