Introduction
Genome-wide association studies identified hundreds of risk loci for Crohn’s disease (CD), with NOD2 variants showing the largest effects. These risk variants predispose to bacterial invasion of the epithelial barrier and dysregulated immune responses by impairing bacterial clearance of the mucosal layer. A 2007 study showed that NOD2 risk variant carriers with CD had higher antibody responses against bacterial flagellins, but this work was limited to a narrow set of antigens1. Phage-display immunoprecipitation sequencing (PhIP-Seq) enables massively parallel serology against 100,000s of antigens at epitope-level resolution2. This approach recently revealed hundreds of novel CD-specific reactivities3. Strikingly, these antibodies preferentially target stimulator flagellins4, which activate the pro-inflammatory TLR5 receptor, unlike the silent- or evader-type found in many commensals to bypass immune detection5.
Aims & Methods
We aimed to determine whether these distinct immunological patterns are driven by NOD2 risk variants. Using PhIP-Seq, we profiled serum antibody epitope repertoires of 1,263 individuals (Table 1) against 344,000 microbial, immune, and food-related antigens. NOD2 variant status was derived from genome-wide genotyping and carriers were defined as individuals with ≥1 risk allele. We performed peptide-level logistic regression combined with enrichment analyses to investigate antigens associated with carriers among patients with CD and controls, while adjusting for differences in age, sex, BMI and smoking status. We used DIAMOND to evaluate sequence similarity between antibody-bound flagellins and reference stimulator-, silent-, and evader-type flagellins.
Table 1
| Controls (N = 1008) | CD (N = 255) | p-value |
| Age, Median (Q1, Q3) | 45 (34, 53) | 35 (26, 46) | <0.001 |
Sex, Female (%)
| 583 (58%) | 181 (71%) | <0.001
|
Smoking, n (%)
| 198 (20%) | 80 (31%) | <0.001
|
NOD2 variant carriers, n (%)
| 149 (15%) | 96 (38%) | <0.001
|
Results
Among CD patients, the ten antigens most positively associated with NOD2 risk variants were exclusively flagellins, derived from Agathobacter rectalis, Roseburia, Borreliaceae, Eubacterium spp. and Clostridiales. Grouping by biological origin confirmed a dominant flagellar response alongside increased anti-Clostridialesand Staphylococcus signatures, and a significantly lower response to cytomegalovirus (CMV) (FDR<0.05). In contrast, among controls, NOD2 risk variant carriers displayed a significant reduction in anti-flagellin responses (FDR<0.05). While this elevated anti-flagellin immunity was comparable across ileal and colonic disease locations, it varied by disease behaviour: responses were elevated in both stricturing and penetrating CD, but direct comparison revealed a significantly more pronounced signature in stricturing disease (FDR<0.05). Finally, when comparing overrepresented flagellins to reference stimulator, silent, and evader sequences, we observed elevated C-terminal antibody binding in NOD2 risk variant carriers with CD. These antibody-bound flagellins strongly resembled stimulator flagellins (FDR<0.05).
Conclusion
This study represents the most comprehensive analysis of antibody epitope repertoires in NOD2 risk variant carriers with CD. We expand upon previously established links to anti-flagellin immunity by detailing responses against specific flagellin types, while also identifying novel associations, such as altered reactivity to CMV. These findings provide a fundamental basis for future research and contribute to our understanding of CD pathogenesis and its link to stricturing behaviour 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. Bourgonje AR, Hörstke NV, Fehringer M, Innocenti G, Vogl T. Systemic antibody responses against gut microbiota flagellins implicate shared and divergent immune reactivity in Crohn’s disease and chronic fatigue syndrome. Microbiome. 2024/07/29 2024;12(1):141. doi:10.1186/s40168-024-01858-1.
4. 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.
5. Clasen SJ, Bell MEW, Borbón A, et al. Silent recognition of flagellins from human gut commensal bacteria by Toll-like receptor 5. Science Immunology. 2023;8(79):eabq7001. doi:doi:10.1126/sciimmunol.abq7001.
Disclosure
A.R.B. received speaker's fees from AbbVie and Ferring, outside the submitted work. R.K.W. acted as a consultant for Takeda; received unrestricted research grants from Takeda, Johnson & Johnson, Tramedico and Ferring; and received speaker fees from MSD, Falk, AbbVie and Janssen Pharmaceuticals. All other authors have no conflicts of interest to declare.