TL1A-activated T cells remodel the rectal mucosa in patients with Crohn’s disease with perianal fistulising disease

Background Perianal fistulising disease (PFD) is a complication that affects about 20% of patients with Crohn’s disease (CD) whose aetiology remains unknown. Objectives To identify predisposing events driving fistula formation. Design Rectal biopsies from patients with CD with or without PFD (CD+PFD and CD, respectively; n=31) were collected and subjected to single-cell RNA sequencing. Functional analyses were conducted using peripheral CD3 + T cells, intestinal tissue explants, primary fibroblasts and two-dimensional epithelial monolayer cell cultures. Results The rectal mucosa of patients with CD+PFD is imprinted with cellular and transcriptomic alterations specific to PFD and independent of luminal inflammation, potentially driven by tumour necrosis factor-like ligand 1A (TL1A) activation in CD4 + T cells. We identified lymphotoxin beta ( LTB or its functional heterotrimer LTα 1 β 2 ) as a novel mediator downstream of TL1A that, along with interleukin (IL)-22, induces a PFD-associated signature in rectal fibroblast and epithelial cells, respectively. This signature includes an increased abundance of fibroblasts, an induction of matrix-degrading enzymes, transcriptomic rewiring of the lamina propria S1 fibroblasts and an anti-bacterial and immune responses in epithelial cells. Notably, the induction of LTα 1 β 2 and IL-22 occurs independently of tumour necrosis factor (TNF) signalling, revealing a new TL1A-LTα 1 β 2 /IL-22 axis that remains active under anti-TNF therapy. Conclusion Our findings revealed unique cellular alterations in the rectum of patients with CD+PFD, highlighting the previously unrecognised involvement of TL1A in mediating this signature and supporting the need for exploring the role of TL1A inhibition as a therapeutic approach for PFD.