Gvhd-Induced Inflammatory Memory in Intestinal Stem Cells Enhances IFN-γ-Induced Antigen Presentation and Apoptosis of Intestinal Epithelial Cells

[Introduction] We have previously demonstrated that intestinal stem cells (ISCs) are targeted in gastrointestinal graft-versus-host disease (GI-GVHD), thereby compromising tissue regeneration and homeostasis after allogeneic hematopoietic cell transplantation (allo-HCT) (Takashima S: J Exp Med 2011). Recently, tissue stem cells have been found to acquire epigenetic changes after inflammation, a phenomenon termed inflammatory memory, which leads to a more robust response to subsequent stimuli (Naik S: Nature 2017). However, it remains unclear whether ISCs can acquire inflammatory memory in acute GVHD. In the current study, we evaluated the role of inflammatory memory of ISCs in GVHD, utilizing mouse models of allo-HCT and an intestinal organoid culture system. [Methods] Lethally irradiated BDF1 (H-2^b/d) recipient mice were transplanted from allogeneic B6 (H-2^b/b) or syngeneic BDF1 donors. Intestinal organoids were generated from the small intestines on day 21 post-transplant, cultured for 6 days, and subjected to RNA sequencing (RNA-seq) and ATAC sequencing (ATAC-seq). Antigen presentation by intestinal epithelial cells (IECs) was assessed using in vitro co-culture of recipient-derived organoids with intraepithelial T lymphocytes from donor mice, as previously shown (Nozaki K: J Gastroenterol 2016). [Results] RNA-seq demonstrated 199 genes significantly upregulated in intestinal organoids from allogeneic recipients compared to those from syngeneic controls, with enrichment in genes annotated as “antigen processing and presentation” and “IFN-γ response.” ATAC-seq identified 457 genes with significantly increased accessibility in organoids from allogeneic recipients. Hyper-accessible promotor peaks were enriched with genes related to “antigen processing and presentation” and “IFN-γ response.” Notably, genes involved in MHC class II (MHC-II) expression such as Cd74, H2-Aa, and H2-Eb1, were commonly enriched in both differentially expressed genes (DEGs) and differentially accessible genes (DAGs) in the organoids from allogeneic recipients. Given the well-established role of IFN-γ in inducing MHC-II expression on IECs, we hypothesized that GVHD-induced inflammatory memory in IECs enhances their antigen-presenting capacity in response to IFN-γ (Koyama M: Immunity 2019). Flow cytometric analysis demonstrated that MHC-II expression was slightly but significantly higher in organoids from allogeneic recipients compared to those from syngeneic controls. This difference was markedly enhanced upon stimulation with low-level IFN-γ (0.1 ng/mL) for 24 hours, indicating that inflammatory memory enhances IFN-γ responsiveness and antigen-presenting capacity. These findings were validated using organoids generated from a single Lgr5⁺ ISC purified from BDF1-Lgr5-GFP recipients transplanted from B6 or BDF1 mice, confirming that ISCs acquire inflammatory memory. Importantly, the differential MHC-II expression was maintained after serial organoid passages, further confirming GVHD-induced stable epigenetic changes in IECs. We verified that the enhanced responsiveness of intestinal organoids to IFN-γ in acute GVHD was observed in another mouse model of acute GVHD, in which B6 recipients were transplanted from BALB/c donors. This enhanced responsiveness was also observed after allo-HCT with chemotherapy-based conditioning using busulfan and cyclophosphamide, thus excluding the possibility that inflammatory memory was due to strain- or conditioning-specific effects. Next, we found that T cells incubated with organoids from allogeneic recipients produced significantly more IFN-γ compared to those incubated with organoids from syngeneic controls. Besides the induction of MHC-II molecules, a major response of IECs to IFN-γ is the induction of apoptosis. We also found that organoids from allogeneic recipients were more susceptible to IFN-γ-induced apoptosis, as assessed by morphological organoid damage scores (Eriguchi Y: JCI Insight 2018) or by measuring the fluorescent signal ratio of propidium iodide to Hoechst33342 using a plate reader. [Conclusions] We discovered that ISCs acquire inflammatory memory in GVHD, which enhances antigen presentation and apoptosis of IECs in response to IFN-γ. These changes could lead to the exaggeration and treatment refractoriness of GI-GVHD.