Single-Cell Profiling Links T-Cell Accumulation and TH2/TH17 Dynamics to Eosinophilic Esophagitis (EoE) Activity in Children.

BACKGROUND

According to current guidelines, disease activity in eosinophilic esophagitis (EoE) is measured based on eosinophil infiltration in the esophageal tissue. To investigate the functional role of non-eosinophilic immune cells, we examined immune cell infiltrate over the disease course in pediatric patients with EoE and performed single-cell molecular analysis of the T-cell infiltrate.

METHODS

We collected clinical data and biopsies from pediatric patients with EoE (N = 50, baseline, up to six follow-up endoscopies), gastroesophageal reflux disease (GERD, N = 33), or functional disorders (FD, N = 67). Multiparametric immunofluorescence staining (mIF; n = 114 biopsies) and single-cell RNA sequencing of CD45+CD3+ T-cells (n = 82 biopsies; 35,112 cells) with T cell receptor repertoire analysis were performed.

RESULTS

Immune cell infiltration was significantly higher in active EoE than in inactive EoE, GERD, and FD (inactive: EPX p = 0.0156, MCT p = 0.0312, CD3 p = 0.0078). During remission, CD8+ T-cell infiltration was significantly greater with PPI treatment compared to TS (p = 0.0092). GNLY-positive activated CD8+ T-cells (R = 0.33, p = 0.038), and TH2 cells (R = 0.36, p = 0.036) positively correlated with esophageal eosinophilia in the single-cell analysis, whereas IL17-positive CD4+ T-cells showed a negative correlation (R = -0.43, p = 0.016). During active EoE, TH2 cells were enriched (p = 0.002). Absolute clone size was higher in active EoE than in inactive EoE and controls, while mean clone size only differed for CD4 clones between active EoE and controls. Diversity and the ratio of expanded clonotypes did not differ.

CONCLUSION

Distinct immunophenotypic profiles are associated with treatment response and disease activity in pediatric EoE. TS were associated with lower residual T cell infiltration than PPI. The evaluation of therapy-induced phenotypic changes by single-cell analysis was limited by low T cell yields in biopsies after TS treatment.