Highlights of 2025: advances in the immunopathogenesis of celiac disease

In this research highlight, we explore 5 articles published in 2024 that provide new insight into the underlying immune mechanisms of celiac disease pathogenesis. Celiac disease is an autoimmune disease that affects approximately 1% of the population. Triggered by dietary gluten proteins found in wheat, barley, and rye, it displays classical autoimmune features, including a strong association with class II human leukocyte antigen (HLA) molecules HLA-DQ2 or HLA-DQ8 and autoantibody production against the enzyme tissue transglutaminase 2 (TG2). The key events of celiac pathogenesis are reviewed in depth elsewhere.1 Briefly, incompletely digested gluten peptides that cross the small intestinal epithelium are modified by TG2, which deamidates specific glutamine residues. Deamidation increases binding of gluten peptides to HLA-DQ2/8 on antigen-presenting cells, activating gluten-specific CD4+ T cells to drive a strong Th1-type immune response characterized by inflammatory cytokines such as interferon-γ (IFN-γ) and interleukin-21. This adaptive immune response induces autoantibody secretion against TG2 and deamidated gliadin, and activation of cytotoxic intraepithelial lymphocytes (IELs) that kill stressed epithelial cells. While the central mechanisms are established, many important questions remain: What drives progression from seropositive individuals without tissue damage to active celiac disease? How is the initial gluten-specific CD4+ T cell response primed, and where does this occur within the small intestine? What cellular mechanisms underlie nonresponsiveness to a gluten-free diet (refractory celiac disease)? Here, we highlight five studies published in 2025 that provide new insights into some of these unresolved areas (Figure 1). The anatomical location where TG2 encounters gluten and B cells receive T cell help remains incompletely understood. Using adoptively transferred TG2-specific B cells and gluten-specific CD4+ T cells in an HLA-DQ2.5 mouse model, Fleur du Pré et al. detected class-switched CD38− CD95+ TG2-specific B cells in Peyer's patches and in gut-draining mesenteric lymph nodes of mice immunized with a gliadin peptide Troybody construct. Luminal, fluorescently labeled TG2 was captured by TG2-specific B cells in the subepithelial dome of the Peyer's patches in a BCR-dependent manner.2 Gliadin peptides can be deamidated by catalytically active luminal TG2 derived from shed enterocytes, raising the possibility that TG2-specific B cells directly acquire TG2-deamidated gluten complexes from the lumen.3 Active sampling of luminal TG2-gluten complexes by TG2-specific B cells could facilitate efficient delivery of gluten peptides to activate gluten-responsive CD4+ T cells. However, the primary site at which B cells receive T cell help remains to be fully elucidated. The movement of partially digested gluten peptides and TG2-deamidated gluten complexes across the epithelium has largely been attributed to transcellular transport by epithelial enterocytes in celiac disease.4, 5 M cells are specialized epithelial cells located in the follicle-associated epithelium of Peyer's patches that transcytose antigens from the intestinal lumen to underlying immune cells. Using intestinal organoid models, Wang et al. demonstrated a previously unknown capacity for M cells to load gliadin peptides onto HLA-DQ2.5 and activate peripheral CD4+ T cells from celiac disease patients. Furthermore, M cells were also shown to express high levels of TGM2, raising the possibility that they can deamidate gliadin peptides.6 Evidence from in vitro and in vivo mouse studies demonstrates that gluten presentation is not limited to dendritic cells, B cells, macrophages, and short-lived CD19+ plasma cells, and gluten peptide deamidation may occur at multiple sites.6, 7 In response to inflammatory cytokines such as IFN-γ, enterocytes and M cells upregulate MHC II and costimulatory molecules to potentially function as nonhematopoietic APCs.6, 8 Collectively, these studies support a model where multiple epithelial and immune cell populations contribute to gluten transport, processing, and presentation. A defining histopathological feature of celiac disease is villous atrophy with crypt hyperplasia. Cytotoxic CD8+ T-IELs are thought to play a central role in epithelial cell killing through activating NK receptor interactions such as NKG2C and NKG2D binding to stress ligands MICA, MICB, and HLA-E upregulated on stressed epithelial cells.4 Villous atrophy is classically viewed as a consequence of epithelial damage, while crypt hyperplasia is considered a compensatory regenerative response to restore epithelial integrity. Emerging data suggest cytokine and stromal signaling also contribute to epithelial remodeling. Richards et al. used single-cell RNA sequencing to profile over 200 000 epithelial, immune and stromal cells from duodenal biopsies of individuals with active celiac disease and healthy controls. They revealed substantial stromal compartment alterations in celiac disease tissue, including enrichment of proinflammatory fibroblasts expressing PDGFRA, SMOC2, and RSPO3. Computational ligand-receptor interaction analyses suggested that inflammatory cytokines, particularly IFN-γ and IL-1β secreted by T and myeloid cells, respectively, may act upstream of stromal-epithelial interactions. In turn, SMOC2 expressing fibroblasts were predicted to signal to epithelial and stromal compartments through BMP, WNT and growth factor-associated pathways. These predicted interactions are consistent with shifts in epithelial cell composition observed in celiac disease, including an expansion of intestinal stem cells and secretory enterocytes alongside a reduction in mature absorptive enterocytes, suggesting a stem cell niche that favors crypt expansion and stem-to-secretory cell differentiation.9 This raises the possibility that activated fibroblast populations actively shape epithelial remodeling in celiac disease, although the functional effects of stromal signaling were not tested. Separately, Stamnaes et al. demonstrated that IFN-γ directly mediates epithelial changes in murine crypts.10 Administration of recombinant IFN-γ to C57BL/6 mice induced crypt elongation, villous blunting, and increased epithelial proliferation and migration, recapitulating key histological features of celiac disease. Importantly, these effects were abrogated in mice with epithelial-specific deletion of the IFN-γ receptor (Ifngr1IEC−/−), indicating that IFN-γ signaling within epithelial cells is required for crypt hyperplasia. Proteomic and histological examination of intestinal crypt cells from Ifngr1IEC−/− mice revealed preservation of crypt architecture and reversal of IFN-γ-associated metabolic changes. These observations in mice are consistent with the strong IFN-γ-driven inflammatory program in human disease identified by mass-spectrometry-based spatial proteomic profiling of the crypt region in longitudinal duodenal biopsies collected during active celiac disease and after remission on a gluten-free diet. Gene ontology pathway analysis showed enrichment of IFN-γ response pathways, accompanied by reduced expression of proteins involved in fatty-acid β-oxidation, indicating substantial metabolic reprogramming of crypt epithelial cells. In the small intestine, epithelial cell renewal occurs over 4–6 days whereas this process is accelerated (~24 h) in active celiac disease.11 Together, these studies suggest that in celiac disease, IFN-γ drives a high-turnover epithelial remodeling program resulting in crypt hyperplasia. Consequently, rapid proliferation and migration of metabolically altered epithelial cells along the crypt-villus axis may impair restoration of villous architecture.11 Beyond disrupting epithelial cell homeostasis, IFN-γ upregulates epithelial cell MHC class I and II antigen processing and presentation modules in untreated celiac disease, consistent with its canonical effects on antigen presentation.6, 8, 10 In line with this, IFN-γ treatment of C57BL/6 mice elevated MHC I and II pathway proteins, with this effect markedly attenuated but not abolished in Ifngr1IEC−/− mice.10 Together, these results suggest a proinflammatory cytokine profile induces antigen-presentation function across epithelial compartments. These observations raise the possibility that epithelial-T cell interactions in celiac disease are not driven solely by stress ligand recognition. Instead, NKG2C and NKG2D may act as costimulatory signals for TCR-dependent T cell activation. This prompts the question: can epithelial cells under inflammatory conditions present antigen to activate CD8+ T-IELs? The antigen specificity of expanded CD8+ T-IELs in celiac disease remains poorly defined. Refractory celiac disease (RCD) is defined by persistent symptoms and villous atrophy despite adherence to a strict gluten-free diet for over 12 months.12 RCD is classified into two subtypes: type 1 RCD (RCD1) is more common and characterized by phenotypically normal IELs. In contrast, type 2 RCD (RCD2) is defined by expansion of aberrant IEL clones that express intracellular CD3 but lack surface CD3, CD4, and CD8.13 These clonal populations frequently harbour somatic driver mutations commonly observed in lymphoma and exhibit highly cytotoxic and proinflammatory profiles, implicating them as key mediators of tissue damage.14, 15 Unlike RCD2, the mechanisms sustaining intestinal inflammation in RCD1 despite gluten withdrawal remain poorly understood. To address this, Singh et al. applied single-cell DNA, protein, RNA, and TCR sequencing to profile somatic mutations across ~48 000 immune cells from duodenal biopsies of patients with RCD1, RCD2, active celiac disease, and nonceliac controls.16 Somatic mutations in lymphoma-associated driver genes, including STAT3, STAT5B, and DDX3X, were identified in 7/10 RCD1 patients, predominantly within CD3+ CD8+ T cells. Many of these mutations, such as gain-of-function mutations in STAT3, are recurrently observed in RCD2 and T cell lymphoma.14, 17 However, the functional importance of these clones is unknown. These mutated T cells were clonally expanded with distinct proinflammatory and cytotoxic gene signatures, raising the possibility of ongoing antigenic stimulation. Notably, the mutated T cells expressed high protein levels of activating NK receptor molecules such as 2B4 or NKG2D, which may serve to lower the threshold for T cell activation.18 The accumulation of RCD1 CD3+ T cells with activating JAK–STAT pathway mutations supports a model in which these clones are hypersensitive to inflammatory cytokines such as IL-15, enabling their survival and expansion despite adherence to a gluten-free diet. To date, investigations into villous atrophy and crypt hyperplasia in celiac disease have largely focused on epithelial injury by cytotoxic T-IELs. Studies in 2025 expand the model to highlight crosstalk between immune, stromal, and epithelial cell subsets that may modulate tissue regeneration, even in the context of a gluten-free diet. In parallel, emerging evidence that M cells can present gluten peptides, that B cells directly capture TG2, and that lymphocytes carrying somatic driver mutations expand in RCD1 reveals previously unappreciated cellular mechanisms underlying celiac disease pathogenesis. Jennifer Chen: Conceptualization; visualization; writing – original draft; writing – review and editing; investigation. Mandeep Singh: Conceptualization; investigation; supervision; visualization; writing – original draft; funding acquisition; writing – review and editing; project administration; resources. The authors declare no conflicts of interest.