Professor University Hospital Schleswig-Holstein, Campus Kiel Kiel, Germany
Introduction/Rationale: Advanced drug therapies (ADTs), including antibodies targeting pro-inflammatory cytokines such as TNF and IL12/23, have transformed treatment outcomes in human inflammatory bowel disease (IBD). Despite these advances, up to 40% of patients exhibit primary non-response. The lack of robust predictive or dynamic biomarkers hampers individualized treatment strategies and timely switching between therapies. Single-cell RNA sequencing (scRNA-seq) enables high-resolution mapping of immune heterogeneity and treatment effects.
Methods: We performed longitudinal scRNA-seq of peripheral blood mononuclear cells (PBMCs) from 23 IBD patients initiating therapy with infliximab or ustekinumab, alongside age-matched healthy controls. Samples were collected at baseline, 2 weeks, and 6 weeks post-treatment initiation, yielding >800,000 single-cell transcriptomes. Cellular signatures were validated using flow cytometry and OLINK-based protein profiling in independent prospective cohorts of IBD patients .
Results: Active disease showed increased CD14⁺ monocytes and plasma cells, loss of TGFb signals and strong TNF/IFN-γ signatures. A unique CD3E⁺CD14⁺ T–monocyte complex correlated with inflammation and non-response. Early anti-TNF responders showed suppression of inflammation-regulatory genes (e.g., TNFAIP3, STAT3). Anti-TNF induced lipid metabolismactivation in UC , whereas anti-IL-12/23 enhanced glycolysis. Responder circulating T cells to anti-TNF showed increased effector memory and CD69 activation at baseline, while B cells exhibited distinct Fc receptor patterns (e.g., FCRL1 vs. FCRLA) and metabolic shifts to each drug over time.
Conclusion: This study provides a comprehensive longitudinal single-cell atlas of early ADT in IBD. Comparative profiling of anti-TNF and anti-IL-12/23 therapies revealed shared and unique immunomodulatory shifts in different cellular compartments. These early transcriptional programs reflect candidate dynamic molecular biomarkers and clearly connote potential or early stratification.
