BIOACTIVE INTERLEUKIN-1 DETECTED IN IBD PATIENT INTESTINAL BIOPSIES IS A HALLMARK OF ULCERS AND CORRELATES WITH TRANSCRIPTOMIC ASSESSMENTS, INCLUDING AN ULCER-SPECIFIC GENE MODULE ASSOCIATED WITH STROMAL CELL DIFFERENTIATION

Background: Multiple studies have identified interleukin (IL)-1 proteins (IL-1α, IL-1β) as playing a key role in intestinal inflammation, including the expansion of IL-1 expressing cells as a hallmark of severe and anti-TNFα non-responsive inflammatory bowel disease (IBD). However, little is known about the presence of bioactive IL-1 proteins within the cell-free gastrointestinal (GI) mucosal environment or whether IL-1-driven programs affect epithelial regeneration in severe IBD with ulcers.
Methods: We established a highly sensitive functional assay (~500-fold greater than ELISA) to assess bioactive extracellular IL-1 protein from previously cryopreserved GI biopsies. We assessed differential cell-free IL-1 bioactivity in a cohort of Crohn’s disease (CD, n=23), ulcerative colitis (UC, n=18) and non-IBD (n=17) patients, with biopsies from paired inflamed and uninflamed intestinal regions per patient (primarily colon but also ileal). We performed RNA-seq, including weighted gene co-expression network analysis (WGCNA), of the biospecimens’ matched cellular compartments. An ulcer-associated gene signature was interrogated in a single-cell (sc)RNA-seq cohort (n=42) of very early onset (VEO)IBD including monogenic disorders, as well as publicly available IBD bulk and scRNA-seq datasets.
Results: Bioactive intestinal mucosal IL-1α and IL-1β corresponded with disease and ulcer severity in CD and UC. The most extreme signals were seen in select CD patients with deep ulceration. Bioactive IL-1α was the predominant contributor to total IL-1 signal in most patients although several with ulcers displayed an IL-1β-predominant signal. Matched RNA-seq analysis demonstrated enhanced IL-1 transcripts, correlating with IL-1 bioactivity. WGCNA revealed a compelling ulcer-specific module with genes enriched in IL-1 signaling, wound repair processes, as well as transcription factors related to stromal cell differentiation. We validated our findings in several published (e.g., RISK cohort of ileal CD) datasets as well as in unpublished independent adult and pediatric RNA-seq datasets from our group. Deconvolution of the ulcer-specific gene module and projection onto a scRNA-seq cohort of VEOIBD patients (including IBD-causative mutations such as IL-10R deficiency characterized by deep ulceration) implicated specific stromal/myeloid populations and IL-1 driven stromal cell responses in ulcer biology.
Conclusion: Mucosal ulceration in IBD is associated with bioactive IL-1 proteins, and transcriptomic evaluation of the same correlates with bioactive signal. An ulcer-specific gene module, validated in other datasets, sheds light on IL-1 biology in intestinal epithelial repair and stromal cell differentiation. Results strongly suggest the IL-1 signaling pathway as being an attractive and precision-based therapeutic target in subsets of IBD patients.