Insights from proteomic analysis in Crohn's disease

Crohn's Disease (CD) presents a challenging inflammatory bowel disease with rising incidences. Although biologic agents have improved treatment outcomes, response rates remain variable, and predictive biomarkers are lacking. This study investigates the proteomic profile of CD patients undergoing treatment, aiming to uncover molecular mechanisms during treatment and predict therapeutic outcomes.

We analysed two patient cohorts: one comprising 34 samples classified as either inflammation or remission, and another with 47 samples taken pre- or post-therapy, with treatment response assessed via clinical and endoscopic criteria. Formalin-fixed, paraffin-embedded (FFPE) ileum biopsies were subjected to robotic sample preparation and submitted to liquid chromatography-tandem mass spectrometry (LC-MS/MS) using data-independent acquisition – parallel accumulation serial fragmentation (dia-PASEF).

The proteomic analysis revealed a rich proteomic landscape, identifying an average of 6,700 proteins per sample. Cluster analyses differentiated inflammation from clinical remission, revealing a notable upregulation of 2,100 proteins during acute inflammation, including markers like myeloperoxidase and calprotectin. Treatment interventions showed significant attenuation of inflammatory pathways in responders, contrasting with minimal changes in non-responders, highlighting heterogeneous treatment responses. Gene Ontology Enrichment Analysis indicated an upregulation of metabolic and cellular respiration processes after successful treatment, suggesting a restoration of cellular homeostasis.

Integrating proteomic data with clinical parameters provides a comprehensive understanding of CD pathophysiology and treatment response. Our next steps will focus on deeper analysis of the proteomic dataset, comparing different treatment strategies, and examining proteolytic activity as well as the metaproteome.