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This research aims to investigate how NOD2 risk variants affect antibody responses in Crohn's disease patients.

January 23, 2026

DOP027High-throughput antibody epitope repertoire profiling links NOD2 risk-variants to specific antibody responses in Crohn’s disease

Key Points

This research aims to investigate how NOD2 risk variants affect antibody responses in Crohn's disease patients.
High-throughput profiling of serum antibody epitope repertoires was performed using PhIP-Seq.
The analysis included 1,263 individuals, comprising 255 Crohn's disease patients and 1,008 controls.
NOD2 variant status was determined through genome-wide genotyping, focusing on individuals with risk alleles.
Peptide-level association testing and enrichment analyses were conducted to identify linked antigens.
2,680 antigens were detected in the study population, showing varied binding among individuals.
In Crohn's disease patients, NOD2 risk-variant carriers had heightened antibody responses to specific bacterial flagellins.
Contrarily, NOD2 risk-variant carriers in controls exhibited reduced anti-flagellin responses.
Further analysis indicated increased responses to Clostridiales and Staphylococcus antigens, while responses to CMV were less prevalent.

Abstract

Abstract Background Genome-wide association studies have identified hundreds of risk loci for Crohn’s Disease (CD), with variants in NOD2 showing the largest effects. NOD2 is a cytosolic receptor that detects the bacterial cell-wall motif muramyl dipeptide (MDP) and helps maintain host-microbiota homeostasis. NOD2 risk variants alter the MDP-sensing domain, reducing receptor responsiveness. This impairs bacterial clearance at the mucosal surface, leading to bacterial invasion and dysregulated immune responses. A 2007 study showed NOD2 risk-variant carriers with CD had higher antibody responses against bacterial flagellins, but this work was limited to a narrow set of antigens1. Recently, phage-display immunoprecipitation sequencing (PhIP-Seq) has emerged as a high-throughput platform enabling massively parallel serology against 100,000s of antigens at epitope-level resolution and revealing hundreds of novel CD-specific reactivities2,3. Using PhIP-Seq, we here aimed to investigate whether NOD2 risk-variant carriers also exhibit altered immune responses. Methods We profiled serum antibody epitope repertoires of 1,263 individuals (255 patients with CD and 1,008 population-based controls), targeting 344,000 microbial, immune and food antigens. NOD2 variant status was derived from genome-wide genotyping and carriers were defined as individuals with ≥1 risk allele. We performed peptide-level association testing combined with enrichment analyses to investigate the antigens linked with carriers among CD patients and controls. Results We detected 2,680 bound antigens in 5-95% of 1,263 individuals (Tab.1). Among patients with CD, the ten most positively associated antigens in NOD2 risk-variant carriers were all flagellins derived from Agathobacter, Roseburia, Borreliaceae, Eubacterium spp. and Clostridiales. This increased flagellin reactivity was further supported by enrichment analysis, whereas among controls NOD2 risk-variant carriers displayed significant reduction of anti-flagellin responses (Fig.1A). Next, when grouped by taxonomic origin, we observed a strong increase in antibody responses against Clostridiales and Staphylococcus antigens, alongside a markedly less prevalent response against CMV (Fig.1B). Notably, Cins1007fs showed binding patterns opposite to the other main variants. NOD2 risk-variants were not associated with CD location and behavior. Conclusion This study represents the most comprehensive analysis to date of antibody epitope repertoires in NOD2 risk-variant carriers with CD. We extend previously established links to anti-flagellin immunity and identify new associations, including altered immune responses against human herpesviruses, which may contribute to our understanding of CD pathogenesis in genetically susceptible individuals. References: 1.Devlin SM, Yang H, Ippoliti A, et al. NOD2 Variants and Antibody Response to Microbial Antigens in Crohn`s Disease Patients and Their Unaffected Relatives. Gastroenterology. 2007;132(2):576-586. doi:10.1053/j.gastro.2006.11.013 2.Bourgonje AR, Andreu-Sanchez S, Vogl T, et al. Phage-display immunoprecipitation sequencing of the antibody epitope repertoire in inflammatory bowel disease reveals distinct antibody signatures. Immunity. Jun 13 2023;56(6):1393-1409 e6. doi:10.1016/j.immuni.2023.04.017 3.Vogl T, Klompus S, Leviatan S, et al. Population-wide diversity and stability of serum antibody epitope repertoires against human microbiota. Nature Medicine. 2021/08/01 2021;27(8):1442-1450. doi:10.1038/s41591-021-01409-3 Conflict of interest: Erlmeier, Ludwig: No conflict of interest Bourgonje, Arno R.: A.R.B. received speaker’s fees from AbbVie and Ferring, outside the submitted work. Hidding, Iwan J.: No conflict of interest Weinberger, Adina: No conflict of interest Segal, Eran: No conflict of interest Vogl, Thomas: No conflict of interest Zhernakova, Alexandra: No conflict of interest Weersma, Rinse K: No conflict of interest

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