An exploratory single-cell analysis of peripheral blood mononuclear cells from vedolizumab-treated Crohn's disease patients identifies response-associated differences among the plasmacytoid dendritic cells and classical monocytes

Andrew Yung Fong Li Yim^1*Ishtu Hageman¹Vincent W. Joustra²Ahmed M.I.M. Elfiky^1,3Mohammed Ghiboub¹Evgeni Levin⁴Jan Verhoeff¹Caroline Verseijden¹Iris Admiraal¹Manon de Krijger⁵Manon E. Wildenberg⁵Marcel Mannens⁶Marja Jakobs⁶Susan B Kenter⁶Alex T. Adams⁷Jack Satsangi⁷Geert R. D'Haens²Wouter De Jonge^1,8Peter Henneman⁶

• ¹Tytgat Institute for Liver and Intestinal Research, AmsterdamUMC, Amsterdam, Netherlands
• ²Department of Gastroenterology and Hepatology, AmsterdamUMC, Amsterdam, Netherlands
• ³Center of Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands, Netherlands
• ⁴Horaizon, Delft, Netherlands
• ⁵Amsterdam UMC Location AMC Tytgat Institute for Liver and Intestinal Research, Amsterdam, Netherlands
• ⁶Department of Human Genetics, AmsterdamUMC, Amsterdam, Netherlands
• ⁷Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, Oxfordshire, United Kingdom
• ⁸Department of Surgery, University of Bonn, Bonn, North Rhine-Westphalia, Germany

Background: Vedolizumab (VDZ) is a monoclonal antibody approved for the treatment of Crohn’s disease (CD). Despite its efficacy, non-response to VDZ is common in clinical practice with no clear understanding of how it manifests. Here, we performed an exploratory study characterizing the cellular repertoire of responders and non-responders to VDZ during treatment. Methods: Peripheral blood mononuclear cells (PBMCs) were isolated from CD patients on VDZ treatment that were either steroid-free responder (N = 4) or non-responder (N = 4). Response was defined as ≥3 drop in Simple Endoscopic Score for Crohn’s Disease (SES-CD) in combination with a ≥50% reduction in C-reactive protein (CRP) and fecal calprotectin and/or a ≥3 point drop in Harvey-Bradshaw Index (HBI). Single-cell repertoires were characterized using single-cell RNA-sequencing (scRNAseq) and mass cytometry by time of flight (CyTOF). Results: Non-responders to VDZ presented more T cells, but fewer myeloid cells, with plasmacytoid dendritic cells (pDCs) being the most notably lower among non-responders. At a transcriptional level we observed that T-cell expression of genes involved in for Toll-like receptor (TLR), NOD-like receptor (NLR), and mitogen-activated protein kinases (MAPK) signaling pathways were decreased among non-responders. Similarly, non-responder-derived classical monocytes presented lower expression of genes involved in cytokine-cytokine receptor signaling. Conclusions: Non-response to VDZ during treatment is associated with differences in abundance and expression among T and myeloid cells.