P0950CD19-CAR-T-cell therapy in multidrug-resistant ulcerative colitis: Clinical results and effects on microbiome composition and B-cell subsets

Abstract Background Activated gut B cells and plasma cells are enriched in the mucosa of refractory inflammatory bowel disease (IBD). We treated a 21-year-old female patient with resistant ulcerative colitis (UC) with the CD19-directed T-cell engager blinatumomab followed by adoptive transfer of autologous CD19-CAR-T-cells (1). Herein, we characterize the change of gut microbes and of immune cell composition upon both treatments, respectively. Methods 16S-based metabarcoding analysis with genomic DNA isolated from gut biopsies and whole genome shotgun sequencing with DNA from stool samples were performed. Isolated cells were subjected to high-dimensional flow cytometry and single-cell RNA deep sequencing (scRNA). Results Blinatumomab only led to a transient clinical response, while CD19-CAR-T-cells achieved a rapid induction of clinical, biochemical, endoscopic and histologic remission, which was sustained for the drug-free follow-up period of over 8 months. Overall, the treatment was well tolerated with only grade 1 cytokine release syndrome. CD19-CAR-T-cell treatment led to profound changes in beta-diversity and taxonomic composition, which were not observed during blinatumomab treatment. These alterations in taxonomic levels were particularly strong in mucosa-associated bacteria. Despite transiently reduced circulating B cell levels upon blinatumomab treatment, a high frequency of gut CD19+ B cells remained. scRNA revealed a transient increase in cytotoxic gut T cells and monocytes after blinatumomab therapy, but the dysregulated immune cell compartment with expanded B cells and plasmablasts was restored six weeks after the last application, in line with a clinical relapse. Following lympho-depletion, the infused CD19-CAR-T-cells peaked at 350 cells/µl on day +10, followed by a contraction phase and low-level persistence over the next 30 weeks. Circulating B cells were abrogated within days, but recovered 8 months after treatment with a naïve phenotype. Interestingly, mucosal B cells and plasmablasts were still detectable on day +3 after CD19-CAR-T-cell therapy, but were depleted shortly after expansion of CAR-T-cells from day +10 onwards. We verified mucosal CD19-CAR-T-cells on days +10 and +27. scRNA confirmed the loss of gut B cells and plasmablasts and the expansion of T cells. Moreover, selection and unsupervised re-clustering of T cells revealed significant changes in the T cell compartment following CD19-CAR-T-cell therapy. Conclusion These data demonstrate that successful CD19-CAR-T-cell therapy -but not blinatumomab- induces deep mucosal B cell depletion, reshapes the T cell compartment, and drives gut microbial shifts in UC. A second patient has since been treated to further evaluate this approach. Reference: 1. Müller F, Atreya R, Völkl S, Aigner M, Kretschmann S, Kharboutli S, Leppkes M, Sitte S, Strobel D, Hartmann A, Mehandru S, Colombel JF, Schett G, Mackensen A, Neurath MF. CD19 CAR T-Cell Therapy in Multidrug-Resistant Ulcerative Colitis. N Engl J Med. 2025 Sep 25;393(12):1239-1241. doi: 10.1056/NEJMc2508023. Conflict of interest: Prof. Dr. Atreya, Raja: No conflict of interest Müller, Fabian: RA has served as a speaker, or consultant, or received research grants from AbbVie, Abivax, AlfaSigma, Arena Pharmaceuticals, Astra-Zeneca, Biogen, Boehringer Ingelheim, Bristol-Myers Squibb, Celgene, Celltrion Healthcare, Dr Falk Pharma, Galapagos, Gilead, GlaxoSmithKline, InDex Pharmaceuticals, Johnson & Johnson, Lilly, Materia Prima, Merck Sharpe & Dohme, Pfizer, Roche Pharma, Takeda Pharma, Viatris. Wirtz, Stefan: No conflict of interest Schwingen, Nora Rebecca: No conflict of interest Aigner, Michael: No conflict of interest Hartebrodt, Anne: No conflict of interest Hitschfel, Julia: No conflict of interest Kretschmann, Sascha: No conflict of interest Kharboutli, Soraya: No conflict of interest Bruns, Heiko: No conflict of interest Ekici, Arif: No conflict of interest Leppkes, Moritz: No conflict of interest Sitte, Selina: No conflict of interest Fischer, Sarah: No conflict of interest Klett, Daniel: No conflict of interest Siebler, Jürgen: No conflict of interest Strobel, Deike: No conflict of interest Graw, Frederik: No conflict of interest Hartmann, Arndt: No conflict of interest Mehandru, Saurabh: Grant: Genentech, Brystol Myers Squib (BMS) Personal Fees: AbbVie, Adacyte, Alimentiv, Atticus, Brystol Myers Squib (BMS), Cabaletta, Georgia Immune, Merck, Novartis Colombel, Jean-Frédéric: Grant: AbbVie, Janssen Pharmaceuticals, Takeda, Prometheus and Bristol Myers Squibb Lectures from: AbbVie, Roche and Takeda Other: AbbVie, Amgen, AnaptysBio, Allergan, Apini, Arena Pharmaceuticals, Astellas, Boehringer Ingelheim, Bristol Myers Squibb, candidrx Celgene, Celltrion, Clearview Curogen, Eli Lilly, Envision Pharma Ferring Pharmaceuticals, Galmed Research, Glaxo Smith Kline, Roche, Janssen Pharmaceuticals, Kaleido Biosciences, Immunic, Iterative Scopes, Landos, Microba Life Science, Merck, Mirador, Novartis, Otsuka Pharmaceutical, Owkin, Pfizer, Protagonist Therapeutics, Sanofi, Sun Pharma, Takeda, Teva, TiGenix, and is holding stock options in Intestinal Biotech Development Grieshaber-Bouyer, Ricardo: No conflict of interest Blumenthal, David B.: No conflict of interest Schett, Georg: No conflict of interest Mackensen, Andreas: No conflict of interest Völkl, Simon: No conflict of interest Neurath, Markus Friedrich: Personal Fees: Janssen-Cilag GmbhConsulting BMA houseConsulting Pentax GmbHConsulting S. KargerConsulting Galapagos NVConsulting Boehringer Ingelheim International GmbHConsulting Aclaris TherapeuticsConsulting TRex Bio, Inc.Consulting SciRhom GmbHConsulting Pfizer Biopharmaceuticals GroupConsulting Aditum Bio Management Company, LLCConsulting Carpamel Ransford LLPConsulting Pfizer Pharma GmbHConsulting Janssen-Cilag GmbHSpeaker activities Falk Foundation e.v.Speaker activities Affiliate Faculty, Skaggs School of Pharmacy & Pharmaceutical Sciences Speaker activity Medi K S.r.lSpeaker activity AOCCSpeaker activity Lilly Deutschland GmbH Speaker activity Northwell FoundationSpeaker activity Takeda pharma GmbHSpeaker activity, Consulting AbbVie NV/SASpeaker activity, Consulting Fondazione Internazionale MenariniSpeaker activity ARIX Bioscience Holding Limited Speaker activity Takeda Pharma Vertrieb gmbH & Co. KGSpeaker activity, Consulting