Molecular characterization of response to etrolizumab and anti-TNF reveals treatment resistance in ulcerative colitis is associated with the abundance of residual neutrophil subsets and inflammatory fibroblast populations

Ulcerative colitis (UC) is a chronic inflammatory large bowel disease characterized by immune cell infiltration and continuous erosion of intestinal crypts, causing severe ulceration and abdominal pain. In the etrolizumab Phase 3 studies, transcriptional analyses of colonic biopsies revealed reductions in genes associated with aEb7+ intraepithelial lymphocytes with etrolizumab but not adalimumab. Both treatments significantly reduced stromal and myeloid cell-associated genes, with changes associated with MCS remission status. Generation of a single-cell atlas from inflamed and uninflamed colonic biopsies from UC patients led to the identification of thirty-six discrete cell populations, including cells of the myeloid compartment. The UC atlas was used to generate cell-specific signatures, allowing for cellular deconvolution of the Phase 3 datasets. It revealed significant reductions in neutrophil subsets, monocyte-derived macrophages, and inflammatory fibroblasts, as well as increases in colonic epithelial cells common to both etrolizumab and adalimumab. Pseudo-time trajectory analyses identified four unique neutrophil subsets with unique cell phenotypes reflecting changes in cell state or differentiation from PADI4hi, OSMhi, MX1hi, and ultimately to CXCR4hi populations. PADI4hi and OSMhi neutrophils exhibited high levels of proteases (MMP9, LYZ), inflammatory cytokines (CXCL1, IL1B, OSM), and abundant cytokine or chemokine receptors (CXCR1, CXCR2). MX1 populations expressed markers indicating prior IFN exposure (MX1, IFIT1). In contrast, more differentiated or mature neutrophils exhibited high levels of CXCL2, TNF-a, and CXCR4, as well as angiogenic factors like VEGFA. PADI4hi and OSMhi neutrophils, we predict, have abundant cytokine and chemokine interactions with inflammatory fibroblasts within the inflamed colon, such as OSM: OSMR and IL1B: IL1R1 interactions. Changes in PADI4hi and OSMhi neutrophils were closely associated with MCS remission in both etrolizumab and adalimumab-treated patients. In contrast, only minor changes in CXCR4hi neutrophils were observed and not associated with clinical outcomes. Our results suggest that neutrophils are not only heterogeneous in phenotype but have abundant cell-cell interactions in inflamed colonic tissue that are likely implicated in maintaining chronic disease activity. We hypothesize that limiting the interactions between neutrophils and other myeloid cells with resident cells such as inflammatory fibroblasts may reduce the production of inflammatory mediators and limit activation and infiltration of neutrophils, which may be necessary for achieving greater rates of clinical remission in response to interventional agents.