Introduction
Defining immune dysregulation during the asymptomatic prodrome of immune-mediated diseases offers opportunities for early disease detection and interception. In inflammatory bowel disease (IBD), prodromal immune changes remain poorly characterized. This study aimed to define the antigen specificities, breadth, longitudinal stability, and predictive ability of pre-clinical serum antibody repertoires using a novel, high-throughput phage-display immunoprecipitation sequencing assay (PhIP-Seq).
Aims & Methods
Longitudinal serum samples from active component US military personnel collected at diagnosis and at ~10, ~4, and ~2 years pre-Crohn’s disease (CD, n=200), pre-ulcerative colitis (UC, n=200) and in age- and sex-matched healthy controls (HC, n=100) were analysed. Serum antibody repertoires were defined against 357,000 microbial-, viral-, food-, and immune-associated peptide antigens. Logistic regression analyses were performed to identify differentially abundant antibodies per timepoint. Temporal stability of antibodies was assessed using point-biserial correlations. Longitudinal sample analyses were performed using generalized linear mixed-effects models. Finally, machine learning models, including tree-based ensemble methods, were used for prediction of disease.
Results
Across 2,000 samples, 123,980 unique antibodies were identified. Antibody repertoire diversity was significantly lower in pre-CD (P<0.05) and pre-UC (P<0.001) sera compared to HC sera. Up to ~4 years pre-diagnosis, pre-CD samples exhibited more fluctuations in antibody repertoires compared to pre-UC and HC samples (both P<0.001). Distinct antibody responses were evident up to 10 years pre-CD and pre-UC versus HCs. Differential analyses revealed elevated herpesvirus-directed responses (notably Epstein-Barr virus and cytomegalovirus) and anti-flagellin antibodies, particularly in individuals who later developed complicated or ileal disease. In contrast, responses to encapsulated bacteria (e.g., Streptococcus pneumoniae, Haemophilus, Neisseria) progressively declined towards diagnosis. Pre-UC individuals exhibited rising antibody responses against herpesviruses and autoantigens including MAP-kinase-activating death domain (MADD) protein and reduced reactivity against encapsulated pathogens (e.g., Streptococcus pneumoniae- and Haemophilus influenzae). Machine learning models integrating antibody repertoires discriminated future CD (AUC=0.90) and UC (AUC=0.84) from controls up to 10 years pre-diagnosis. Additionally, antibody repertoires differentiated complicated from non-complicated CD up to ~10 years pre-diagnosis with high accuracy (AUC=0.85).
Conclusion
Antibody profiling delineates a previously unappreciated landscape of serological responses against microbial and non-microbial antigens up to 10 years before disease onset in patients with CD and UC. Large-scale serological profiling of archived pre-diagnostic samples enables systematic detection of disease-specific immune trajectories years before IBD onset, providing a scalable framework for early risk stratification and biomarker discovery.
Disclosure
The corresponding author confirms on behalf of all authors that there have been no involvements that might raise the question of bias in the work reported or in the conclusions, implications, or opinions stated. SM reports receiving research grants from Genentech and Takeda; receiving payment for lectures from Takeda, Genentech, Morphic; and receiving consulting fees from Takeda, Morphic, Ferring, and Arena Pharmaceuticals. ARB reports receiving research grants from Janssen Pharmaceuticals and received speaker’s fees from Ferring and AbbVie. SG reports other research funding from Genentech, Boehringer-Ingelheim, EMD Serono, Takeda, and Regeneron. JFC reports receiving research grants from AbbVie, Janssen Pharmaceuticals, Takeda and Bristol Myers Squibb; receiving payment for lectures from AbbVie, and Takeda; receiving consulting fees from AbbVie, Amgen, AnaptysBio, Allergan, Arena Pharmaceuticals, Boehringer Ingelheim, Bristol Myers Squibb, Celgene Corporation, Celltrion, Eli Lilly, Ferring Pharmaceuticals, Galmed Research, Glaxo Smith Kline, Genentech (Roche), Janssen Pharmaceuticals, Kaleido Biosciences, Immunic, Invea, Iterative Scopes, Merck, Landos, Microba Life Science, Novartis, Nautilus, Otsuka Pharmaceutical, Pfizer, Protagonist Therapeutics, Prometheus, Sanofi, Seres, Takeda, Teva, TiGenix, Vifor; and hold stock options in Intestinal Biotech Development. All other authors have no conflicts of interest to declare.
