Introduction
Ileocecal resection (ICR) is frequently required in Crohn’s disease (CD); however, this intervention is not curative, and postoperative endoscopic recurrence occurs in up to 60% of patients. Consequently, many patients require additional medical therapy, including biologic agents, to control disease recurrence and prevent further complications. Among these, targeting interleukin (IL)-23 has emerged as a highly effective therapeutic strategy. Interleukin (IL)-23 is a central driver of intestinal inflammation. IL-23 protein consists of two subunits, p19 and p40, of which the latter is shared with Il-12. Both subunits are therapeutic targets to inhibit IL-23 signaling. However, the cellular and molecular mechanisms underlying the efficacy of this class of biologicals, and differential clinical and endoscopic outcomes observed between these therapeutic strategies remain poorly defined. In particular, tissue-resident innate lymphoid cells (ILCs) and mucosal-associated invariant T (MAIT) cells are though to play an important role in IL-23 driven intestinal inflammation. Here, we aimed to delineate IL-23-driven pathways and downstream cellular responses within the human intestinal microenvironment.
Aims & Methods
To characterize the IL-23-driven molecular and cellular pathways within the intestinal microenvironment of patients with CD, we performed single cell sequencing on cells derived from intestinal biopsies that were obtained prior to treatment initiation (baseline), and following therapy with either anti-p19 antibodies (RISA, N=6) or treated with anti-p40 antibodies (USTE, N=6). Prior sequencing we performed a FACS-based enrichment strategy for IL-23R-expressing populations. This strategy resulted in specifically enrichment ILCs and MAIT cells, which are typically underrepresented in single-cell datasets due to their low abundance.
Results
We identified four major IL-23R–expressing cell types: Th17 cells, MAIT cells, Tregs, and ILC3s. MAIT cells and Tregs did not exhibit significant transcriptional changes between baseline and post-treatment. Sub-clustering strategies identified inflamed ILC3 subsets that displayed elevated expression of GNLY, TNFSF4, and ITGAX compared to post-treatment samples, demonstrating that both RISA and USTE drive transcriptional and phenotypic remodeling at the cellular level in ILC3s. Furthermore, an expanded set of previously underappreciated IL-23-associated genes was identified in ILCs prior to treatment, including, but not limited to, VDR, BATF, FURIN, and ZNRF1.
To identify predictors of therapeutic response, baseline transcriptional profiles were compared between responders and non-responders. At baseline (V1), ILC3s displayed distinct transcriptional signatures, with reduced CCR7 expression and increased LTB and ZFP36L1 expression in responders, while , no significant differences were observed in other IL-23R⁺ populations.
Conclusion
Together, these findings identify ILC3s as a IL-23-responsive cell populations in intestinal inflammation, that may serve as potential biomarkers of therapeutic response to IL-23 directed biologicals.