Advertisement

Hyperactivated Interferon-gamma Pathways in Perianal Fistulizing Crohn’s Disease by Single-Cell and Spatial Multi-omics

Siyan Cao,¹ Khai M. Nguyen,² Kaiming Ma,¹ Tingyi Tan,¹ Xin Yao,¹ Ta-Chiang Liu,² Malek Ayoub,¹ Jalpa Devi,¹ Sami Samaan,¹ Yizhou Liu,² Radhika Smith,³ Matthew L. Silviera,³ Steven R. Hunt,³ Paul E. Wise,³ Matthew G. Mutch,³ Sean C. Glasgow,³ William C. Chapman Jr,³ Michelle L. Cowan,³ Mathew A. Ciorba,¹ Marco Colonna,² and Parakkal Deepak¹

Published July 3, 2025 - More info

Perianal fistulizing Crohn’s disease (PCD) is a common and debilitating complication with elusive pathophysiology. To define actionable immunologic targets in PCD, we recruited patients with PCD (n = 24), CD without perianal disease (NPCD, n = 10), and idiopathic/cryptoglandular perianal fistulas (IPF, n = 29). Biopsies from fistula tracts, fistula opening, and rectal mucosa were analyzed using single-cell RNA-sequencing (scRNA-seq), mass cytometry (CyTOF), and spatial transcriptomics (ST). Global hyperactivation of IFN-g pathways distinguished PCD from idiopathic perianal fistulas and CD without perianal disease in the fistula tracts and/or intestinal mucosa. IFN-g and TNF-a signaling directly induced genes involved in epithelial-to-mesenchymal transition in PCD rectal epithelial cells. Enhanced IFN-g signaling in PCD was driven by pathogenic Th17 (pTh17) cells, which were recruited and activated by myeloid cells overexpressing LPS signature (LPS_myeloid). pTh17 and LPS_myeloid cells co-localized adjacent to PCD fistula tracts on ST and drove local IFN-g signaling. Anti-TNFs facilitated fistula healing by downregulating T and myeloid cell signatures, while promoting mucosal barrier repair and immunoregulatory processes. Key single-cell findings were validated by bulk RNA-seq data of an independent CD cohort. To summarize, we identified IFN-g-driven mechanisms contributing to pathogenesis and highlighted its blockade as a therapeutic strategy for PCD.

Advertisement

Advertisement