Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis

Abstract

Ulcerative colitis (UC) is driven by immune and stromal subsets, culminating in epithelial injury. Vedolizumab (VDZ) is an anti-integrin antibody that is effective for treating UC. VDZ is known to inhibit lymphocyte trafficking to the intestine, but its broader effects on other cell subsets are less defined. To identify the inflammatory cells that contribute to colitis and are affected by VDZ, we perform single-cell transcriptomic and proteomic analyses of peripheral blood and colonic biopsies in healthy controls and patients with UC on VDZ or other therapies. Here we show that VDZ treatment is associated with alterations in circulating and tissue mononuclear phagocyte (MNP) subsets, along with modest shifts in lymphocytes. Spatial multi-omics of formalin-fixed biopsies demonstrates trends towards increased abundance and proximity of MNP and fibroblast subsets in active colitis. Spatial transcriptomics of archived specimens pre-treatment identifies epithelial-, MNP-, and fibroblast-enriched genes related to VDZ responsiveness, highlighting important roles for these subsets in UC.

Dysregulation of CD4+and CD8+resident memory T, myeloid, and stromal cells in steroid-experienced, checkpoint inhibitor colitis

“…An important limitation in the CPI versus UC comparison is the limited sample size (n=2 UC biopsies with single cells from the multiplexed experiment), also these two UC patients had less active disease at the time of collection (endoscopic severity score 0), which may lead to overestimation of the difference between CPI and UC immunopathology. Despite that caveat, we separately embarked on a larger comparison of UC versus HC, multiplexed using the same methodology, and did not find significant enrichment of T cells in UC, 5 in contrast to our findings of enriched RM and cytotoxic effector T cells in CPI colitis, supporting the idea that these are distinct colitis states and that CPI colitis is more mechanistically driven by pathogenic T cells, as we describe in this work.…”

“…The immune checkpoints TIGIT and TNFRSF9 are uniquely upregulated in the direct CPI colitis versus UC comparison (and not vs HC), pointing to unique overexpression of these regulatory mechanisms in the CPI colitis disease state. Although the UC sample size was small (n=2 with multiplexed biopsy data), and heterogenous with regard to endoscopic activity (Discussion), a separate dedicated analysis of UC patients compared with HC 5 confirmed the unique immunopathology of CPI colitis highlighted here.…”

“…Viably cryopreserved intestinal biopsies were thawed in a single batch and digested into single-cell suspensions, which minimally impacts gene expression and cell representation in biopsies compared with fresh processing. 5 In a separate experiment, cryopreserved PBMCs from the same patients were also thawed in a single batch. For both workflows, biopsies or PBMCs were pooled in a single tube prior to processing for single-cell sequencing.…”