A translational framework for ileal Crohn's disease separates direct tissue-state ordering from upstream restoration priority

This record contains the reproducible research release associated with the manuscript “Divergent tissue-state prominence and upstream restoration priorities define ileal Crohn’s disease.”

This updated preprint presents a structured translational analysis of ileal Crohn’s disease that resolves a central interpretive problem: the most visible biological state in chronically diseased tissue does not necessarily identify the optimal point for restoring upstream function. Ileal Crohn’s disease is best understood as a layered mucosal disorder in which microbial sensing, autophagy-linked bacterial handling, epithelial stress, inflammatory amplification, and barrier dysfunction coexist within the same tissue environment, but do not necessarily occupy the same position in disease initiation, persistence, or repair.

In this manuscript, Crohn’s biology is organised into a reduced five-node scaffold linking NOD2, ATG16L1/IRGM, XBP1, IL23R, and MUC2. Rather than assuming that a single ordering captures both observed tissue structure and therapeutic relevance, the analysis explicitly separates three quantities: best-fitting direct tissue-state topology, dominant direct tissue-state prominence, and upstream restoration priority. This separation is treated as the central biological question rather than a secondary complication.

Across the direct ileal tissue layer, comprising over 500,000 cells from 190 donors, epithelial stress and barrier-output biology dominate the observed chronic state, with XBP1 and MUC2 consistently occupying the highest ranks. At the same time, comparative topology analysis shows that an immune-first ordering best fits the observed tissue-state structure. However, when broader genetic, mechanistic, and disease-association evidence are integrated, the strongest restoration-focused rationale remains centred on NOD2 and the autophagy-linked branch. These results demonstrate that tissue-state prominence, topology fit, and restoration priority are distinct biological quantities that do not collapse into a single hierarchy.

The resulting structure is biologically coherent. In a mucosa exposed to sustained microbial challenge and repeated injury, downstream epithelial stress, inflammatory throughput, and barrier dysfunction are expected to accumulate and dominate the observable tissue state, while upstream defects in microbial sensing and bacterial handling retain deeper etiologic leverage. Tissue-state prominence and restoration priority therefore represent different biological dimensions rather than competing interpretations of the same signal.

The key contribution of this work is the identification of a structured divergence between what is most visible in chronically diseased tissue and what is most informative for upstream biological restoration. This divergence is not a contradiction but a biologically expected feature of chronic disease, and it provides a clearer basis for experimental prioritisation.

The framework presented here is translational in its intent. It does not attempt to reduce ileal Crohn’s disease to a single causal layer, but instead provides a falsifiable and auditable map linking observed tissue state to upstream restoration targets. By distinguishing amplifier suppression from restoration of epithelial-innate function, it creates a clearer experimental roadmap for testing whether upstream recovery of NOD2 and autophagy-linked processes can reshape the downstream mucosal landscape.

This version supersedes earlier releases by introducing a two-layer analysis framework, explicit separation of tissue-state and restoration logic, expanded robustness testing, and substantially improved biological interpretation. This Zenodo record contains the full manuscript, supplementary materials, analysis code, and processed outputs required to reproduce the results presented in the paper, and represents the exact release corresponding to the current version of the manuscript.