Introduction
Intestinal CD4+ T cells closely interact with the microbiota. In inflammatory bowel disease (IBD), microbial dysbiosis promotes the pathological activation of CD4+ T cells and thereby intestinal inflammation. Notably, a fraction of CD4+ T cells retains a degree of phenotypic plasticity, but whether this occurs locally in the intestine in established human disease is unclear. Moreover, strategies to manipulate T cell plasticity in vivo toward a regulatory phenotype remain unexplored. Here, we show that intestinal CD4+ T cells in mice and humans are plastic, and their fate is shaped by the microbial composition.
Aims & Methods
We aimed to investigate whether by targeting the intestinal microbiota we can orchestrate the in vivo conversion of pathogenic CD4+ T cells into regulatory T cells. To study human intestinal T cell plasticity, paired biopsies were longitudinally collected from healthy individuals (n=5) and patients (n=4) with >10 years of intestinal disease. Microbiota composition was altered using antibiotics. At each time point, single-cell RNA and TCR sequencing were performed on intestinal CD4+ T cells. The TCR was used as a barcode to track clones over time and compare transcriptional changes. IL-17A fate-mapping mice, an antibiotic-dependent relapsing IBD mouse model, gnotobiotic mice and conditional knockouts were used to dissect how the microbiota controls T cell plasticity and its relevance to restore tissue homeostasis.
Results
A principal coordinate analysis revealed higher transcriptional heterogeneity in CD4+ T cells from inflamed compared with healthy human intestine. In line with this, human CD4+ T cell clones from the inflamed tissue showed increased longitudinal transcriptional variability compared to clones isolated from the healthy gut. Antibiotic-induced microbial shifts strongly reduced IL-17A expression on intestinal CD4+ T cells, as shown by unsupervised analysis of differentially expressed genes. Interestingly, after antibiotic treatment we found a higher conversion of former IL-17A+ T cell clones into FOXP3+ clones. In contrast, CD4+ T cell clones in the healthy intestine were more stable over time. In mice, antibiotic treatment enhanced the conversion of IL-17A+ (Th17) cells into regulatory Foxp3+ T cells, which correlated with the expansion of beneficial bacteria. Antibiotic withdrawal reversed both the clinical phenotype and T cell plasticity, accompanied by the re-expansion of pro-inflammatory bacteria. Mechanistically, colonization of germ-free mice with the antibiotic-treated microbiota mirrored the protective effects, indicating microbiota-driven regulation of T cell plasticity. Finally, a conditional deletion of Foxp3 in Th17 cells curtailed antibiotic-induced mucosal healing, indicating a key functional role of T cell plasticity in restoring gut homeostasis.
Conclusion
Intestinal CD4+ T cell plasticity is dynamically shaped by the local environment in mice and humans, even during chronic inflammation. The microbiota is a key determinant of intestinal Th17 cell fate. Microbiota manipulation enables the in vivo modulation of T cell plasticity toward a regulatory Foxp3+ phenotype, restoring immune homeostasis. Overall, these findings identify CD4+ T cell plasticity as a potential therapeutic target in IBD.