A Living Organoid Biobank of Crohn’s Disease Patients Reveals Distinct Clinical Correlates of Molecular Subtypes of Disease

In this work, Penrose et al. demonstrate the potential of PDOs as predictive tools in Crohn’s disease, that that capture the past, present, and future of disease behavior, thereby advancing PDO-informed precision medicine beyond oncology into complex inflammatory diseases. PDOs were isolated from colonic tissue specimens collected from CD subjects using established crypt isolation protocols as previously summarized [PMID: 39332415]. These intestinal crypts, which contain crypt-base columnar (CBC) cells, were enzymatically dissociated and processed for 3D organoid culture. Organoids and monolayers were lysed using 200 μl of RNA lysis buffer followed by RNA extraction per Zymo Research Quick-RNA MicroPrep Kit instructions (see key resources table). Tissue samples were lysed in TRI-Reagent and RNA was extracted using Zymo Research Direct-zol RNA Miniprep.