Functional immune profiling reveals CD4+ T cell dysregulation associated with celiac disease

Farchione, A. J.; Cheon, H.; Vremec, D.; Neumann, J.; Verstappen, G. M.; Hardy, M. Y.; Margetts, M. B.; Howson, L. J.; Henneken, L. M.; Ford, M.; Tye-Din, J. A.; Heinzel, S.; Hodgkin, P. D.; Bryant, V. L.

doi:10.1101/2025.06.06.658209

bioRxiv · 10.1101/2025.06.06.658209

Functional immune profiling reveals CD4+ T cell dysregulation associated with celiac disease

Farchione, A. J.·Cheon, H.·Vremec, D.·Neumann, J.·Verstappen, G. M.·Hardy, M. Y.·Margetts, M. B.·Howson, L. J.·Henneken, L. M.·Ford, M.·Tye-Din, J. A.·Heinzel, S.·Hodgkin, P. D.·Bryant, V. L.

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Abstract

T cells integrate signals from antigen and co-stimulatory receptors to calibrate the strength and quality of their responses. This signal integration is influenced by genetic background, which can modulate thresholds for immune tolerance and strength of responses to threat. Celiac disease (CeD) is an autoimmune disorder driven by well-defined genetic risk and characterised by immune dysregulation in response to dietary gluten. However, whether sensitivity or response differences in naive T cell programming contributes to disease susceptibility is not known. To investigate such variation, we developed a sensitive quantitative platform, the momentum assay, which combines standardised, T cell activation with subsequent stimulus withdrawal, enabling measurement of T cell proliferation and survival over time. This assay is integrated with the Cyton2 mathematical model to infer underlying cellular timer programs from population-level dynamics. We applied this method to assess whether naive T cells from individuals with celiac disease (CeD) exhibited altered responses compared to healthy donors (HDs). We found that CD4+ but not CD8+ T cells from CeD patients showed a hypo-proliferative response following stimulation, associated with impaired secretion of the proliferative and pro-survival cytokine IL-2. Moreover, surface expression of early activation marker, CD69 remained elevated for longer on CD4+ T cells from CeD donors after stimulus withdrawal, suggesting prolonged activation and subtle alterations in regulatory feedback mechanisms. These findings reveal previously unrecognised quantitative alterations in naive T cell programming in CeD and underscore the utility of model-based analytical frameworks for detecting subtle functional perturbations in complex immune-mediated diseases.

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Farchione, A. J., Cheon, H., Vremec, D., Neumann, J., Verstappen, G. M., Hardy, M. Y., Margetts, M. B., Howson, L. J., Henneken, L. M., Ford, M., Tye-Din, J. A., Heinzel, S., Hodgkin, P. D., Bryant, V. L.. 2025-06-07. Functional immune profiling reveals CD4+ T cell dysregulation associated with celiac disease. https://doi.org/10.1101/2025.06.06.658209

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