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The identification of biomarkers overexpressed during inflammation is critical for targeting diagnostic or therapeutic agents to the inflamed intestine in inflammatory bowel disease (IBD). The first part of this thesis employs global proteomic analysis to identify preclinical IBD biomarkers using in vitro and in vivo models. The study focuses on apical plasma membrane biomarkers and secreted biomarkers, identifying promising targets for diagnostic imaging probes. Proteomic analysis quantified 7340 proteins across ileum, proximal, and distal colon samples in vivo, revealing significant protein concentration changes primarily in the colon after DSS treatment. Functional annotation linked these changes to inflammatory responses. In vitro analysis using Caco-2 cells treated with TNF-α identified 465 proteins involved in defense and cytokine responses, showing greater relevance for modeling inflammation than DSS-treated cells.

Key inflammatory biomarkers were identified, including TGM2, ICAM1, CEACAM1, and ANXA1, with varied upregulation across models. These biomarkers were validated via immunohistochemistry, showing consistent expression in inflamed and healthy tissues. Additionally, luminal and immune cell-associated proteins such as myeloperoxidase and calprotectin were identified, suggesting their potential for in situ quantitative assessment of IBD activity.

The second part of this thesis details the development of MRI-active biosensors using superparamagnetic iron oxide nanoparticles (SPIONs) functionalized via click chemistry with ligands targeting the identified biomarkers. The synthesis and characterization of SiO2-coated γ-Fe₂O₃ SPIONs and their subsequent functionalization with antibodies targeting ICAM1 were optimized for enhanced biocompatibility and targeting efficacy. In vitro studies demonstrated specific binding and internalization of bioconjugated SPIONs in inflamed Caco-2 cells.

The third part explores in vivo targeting efficacy of bioconjugated SPIONs in colitis-induced mice. Ceacam1-conjugated SPIONs showed significant binding to inflamed tissues, highlighting their potential for targeted imaging and therapeutic delivery in IBD. This thesis underscores the importance of systematic nanoparticle modification and characterization, advancing precision medicine and diagnostic technologies for IBD.