bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.64898/2026.10.21.760764

TCF21 loss identifies a conserved inflammation-associated fibroblast state across Crohn's disease and ulcerative colitis

Hindi Malowany, M.·Franklin, N.·Russo, M. V.·Arpinati, L.·Stein, Y.·Grundman, A.·Scherz-Shouval, R.·Gieseck, R. L.
View original source ↗Export metadata ↓

Abstract

Background and Aims: Inflammatory bowel diseases (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), are associated with stromal remodeling; however, the fibroblast states that contribute to chronic inflammation remain incompletely defined. We aimed to identify conserved pathogenic fibroblast programs across CD and UC and determine whether these states are linked to loss of homeostatic stromal regulators. Methods: We integrated publicly available single-cell RNA sequencing datasets from healthy and inflamed intestinal tissues to define stromal populations across CD, UC, and control samples. Fibroblast subsets were annotated using cluster-specific markers and patient-level abundance analyses. Multiplex immunofluorescence of human gastrointestinal tissue microarrays assessed protein expression. Human colonic fibroblasts were stimulated with IL1B and TNF to model inflammation-associated fibroblast polarization, and restoration of homeostatic factors was evaluated using mRNA-loaded lipid nanoparticles (LNPs). Results: A conserved inflammation-associated fibroblast (IAF) population was expanded in both CD and UC and expressed inflammatory chemokines, matrix-remodeling genes, and activation markers including CXCL1, MMP3, FAP, and PDPN. In contrast, a homeostatic ADAMDEC1/TCF21-enriched fibroblast population was reduced in inflamed tissue. TCF21 expression positively correlated with ADAMDEC1 and negatively correlated with activation markers. Multiplex immunofluorescence confirmed depletion of TCF21-positive non-immune, stromal cells in IBD tissue. In vitro, IL1B and TNF induced an IAF-like phenotype and reduced TCF21. TCF21 mRNA-LNP restoration attenuated inflammatory mediators including IL1B and IL6. Conclusions: TCF21 loss identifies a conserved inflammation-associated fibroblast state across CD and UC. Restoring TCF21 partially suppresses inflammatory fibroblast programs, supporting stromal reprogramming as a therapeutic concept in IBD.

Explore related subjects

immunologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Hindi Malowany, M., Franklin, N., Russo, M. V., Arpinati, L., Stein, Y., Grundman, A., Scherz-Shouval, R., Gieseck, R. L.. 2026-10-26. TCF21 loss identifies a conserved inflammation-associated fibroblast state across Crohn's disease and ulcerative colitis. https://doi.org/10.64898/2026.10.21.760764

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Proteome-wide discovery of novel diagnostic antigens for coccidioidomycosis

Coccidioidomycosis, commonly called Valley Fever (VF), caused by Coccidioides spp., is an understudied fungal disease that accounts for a substantial fraction of pneumonias in endemic areas. Diagnosis remains challenging because the mainstay of diagnosis is serology, and current assays have modest sensitivity in early infection. Discovery of new antigens could improve serologic detection early in disease. Here, we use PepSeq, a DNA-programmable serology platform, to represent the complete proteome of Coccidioides within a library of 244,000 DNA-barcoded peptides. By profiling antibody reactivity at the protein and epitope levels in VF patients, naturally infected pigtail macaques, and healthy controls, we identify numerous previously-unrecognized antigens and epitopes, including some shared between humans and macaque responses. When translated into a pooled peptide ELISA, we show that a subset of identified antigens can discriminate VF cases from controls in an independent cohort with high accuracy (AUC = 0.91). These findings establish high-dimensional peptide serology as a scalable approach for fungal antigen discovery and identify new targets for improved VF diagnosis.

immunology↗
bioRxiv2026

Establishing an ex vivo platform for molecular profiling of skin structural cells using frozen human skin biopsies

Skin structural cells, including keratinocytes, melanocytes, endothelial cells, and fibroblasts, play critical roles in the development of chronic inflammatory skin disease. Inflammatory stimuli induce transcriptional reprogramming and epigenetic changes in skin structural cells, which contribute to disease pathogenesis. Although two-dimensional (2D) and three-dimensional (3D) skin culture models have been widely used to investigate inflammatory responses in skin structural cells, ex vivo systems that maintain skin structure and cellular composition remain limited. To address this gap, we explored using frozen skin biopsies as an experimental platform to study the responses of skin structural cells to inflammatory stimuli. Using a simple air-liquid interface culture method on permeable Transwell inserts, we showed that viable skin structural cells that retain cell-type-specific transcriptional profiles can be recovered from frozen skin biopsies after prolonged in vitro culture. Stimulation with IFN-{gamma} induced robust transcriptional and chromatin accessibility changes that were largely resolved after stimulus removal, with transcriptional responses to secondary stimulation comparable to the primary stimulation. Treatment of cultured skin biopsies with histone-modifying enzyme inhibitors effectively altered global histone modification levels, but did not substantially affect the transcriptional resolution of IFN-{gamma}-induced responses. Collectively, these findings establish cryopreserved human skin biopsies as a scalable ex vivo platform that enables mechanistic studies of inflammatory responses of multiple populations of skin structural cells.

immunology↗
bioRxiv2026

γδ T cell-derived IL-17A aggravates experimental epidermolysis bullosa acquisita in response to IL-1β

Epidermolysis bullosa acquisita (EBA) is a mucocutaneous autoimmune blistering disorder mediated by autoantibodies against type VII collagen and subsequent splitting of the dermal-epidermal junction. Interleukin (IL)-17A promotes the production of chemokines and cytokines involved in neutrophil recruitment and activation, suggesting that IL-17A may contribute to EBA pathogenesis. We aimed to clarify the role of IL-17A in experimental EBA. Using an antibody transfer-induced EBA mouse model, we demonstrate that IL-17A promotes disease development, as pharmacological blockade of IL-17A with a neutralizing antibody ameliorated skin lesions. Gamma-delta ({gamma}{delta}) T cells were identified as the predominant cellular source of IL-17A, supported by the attenuated disease phenotype observed in {gamma}{delta}TCR-deficient mice. In addition, CD4+ T cells and neutrophils contributed to IL-17A production in experimental EBA. Mechanistically, IL-1-beta, rather than IL-23, was identified as a critical mediator of IL-17A production by {gamma}{delta} T cells in vitro, consistent with our in vivo findings. Whereas EBA severity was not reduced in IL-23p19-deficient mice, disease was markedly attenuated in IL-1R-deficient animals. Together, our study provides the first evidence that {gamma}{delta} T cell-derived IL-17A plays a pivotal role in experimental EBA and identifies a previously unrecognized IL-1{beta}/{gamma}{delta} T cell/IL-17A axis that expands current understanding of EBA immunopathogenesis.

immunology↗