Current clinical decision-making lacks reliable preclinical models to predict patient outcomes. Here, we establish patient-derived organoids (PDOs) as predictive tools in Crohn's disease (CD), a complex, heterogeneous disorder. Using a living biobank of adult stem cell-derived colonic-PDOs, we identified two molecular CD subtypes-Immune-Deficient Infectious CD (IDICD) and Stress and Senescence-Induced Fibrostenotic CD (S2FCD)-each with distinct genomic, transcriptomic and functional profiles, along with paired therapeutics. By prospectively linking colonic PDO-derived phenotypes to real-world patient outcomes, we uncovered that while S2FCD associates with severe colonic disease, IDICD associates with severe ileal disease, prior ileocecal surgery, and future disease progression. This approach transforms PDOs from static descriptive models into dynamic tools that capture the past, present, and future of disease behavior and reveals their utility as patient-specific predictive platforms, extending their use beyond oncology to complex inflammatory diseases. Findings also suggest that colonic immune dysfunction may drive ileal-CD, independent of colonic involvement.

BSB has received research grants from Merck, Mirador, Gilead. BSB has served as a consultant for Abbvie, Merck, and Celltrion.

Funding for this work was supported by the Leona M. and Harry B. Helmsley Charitable Trust (to P.G.). Other sources of support include National Institutes of Health (NIH) grants AI141630, UG3TR003355 and AI55696 to P.G.; NIH grants P30DK120515 to B.S.B. H.M.P. was supported by The California Institute of Regenerative Medicine Training Grant for Clinical Fellows through Sanford-Burnham Prebys-UC San Diego. S.S. was supported by the American Association of Immunologists Intersect Fellowship Program for Computational Scientists and Immunologists.

I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.

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The details of the IRB/oversight body that provided approval or exemption for the research described are given below:

Human Subjects Utilized in Current Study Previously generated CD PDOs, which underwent comprehensive multi-omics analyses for molecular phenotyping, were utilized for univariate and multivariate analyses. In brief, patients were recruited during routine colonoscopy procedures at the University of California, San Diego (UCSD) IBD Center. This study was conducted under an Institutional Review Board (IRB)-approved protocol in compliance with the Human Research Protection Program (HRPP) (Project ID# 1132632; PIs: Boland and Sandborn). Each participant provided written informed consent for the collection of colonic biopsies, the derivation of 3D organoids, and the use of associated clinical metadata for research purposes. The isolation and biobanking of organoids from colonic biopsies were conducted under a separate IRB-approved protocol (Project ID# 190105; PIs: Ghosh and Das) at the UCSD HUMANOID Center of Research Excellence (CoRE). All human subject data-including age, gender, and disease history-were de-identified and handled in accordance with HIPAA regulations. The study was designed and conducted following the ethical principles outlined in the Declaration of Helsinki.

I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals.

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RESOURCE AVAILABILITY Lead Contacts Further information and requests for resources and reagents should be directed to and will be fulfilled by the lead contacts, Pradipta Ghosh, prghosh@ucsd.edu and Brigid S. Boland, bboland@health.ucsd.edu. Materials availability This study utilizes data generated from an organoid biobank. These materials are available from the lead contact with a completed Materials Transfer Agreement and patented technology agreement (Ghosh) following the guidelines of the Regents of the University of California, San Diego. Data and code availability Newly generated transcriptomic datasets reported in this paper involve re-analysis of GSE192819 which has been deposited in NCBI's Gene Expression Omnibus. The new GSE ID assignment is currently pending. This paper did not generate or use custom computer codes. Any additional information required to reanalyze the data reported in this work paper is available from Lead. Contact upon request.