Single-cell RNA-seq analysis of the immune response triggered by gut microbiota during inflammatory bowel disease

Whether gut microbiota is pro-inflammation or anti-inflammation during the development of inflammatory bowel disease (IBD) remains controversial. To clarify this issue, using a dextran sodium sulfate (DSS) induced IBD mouse model, we showed that compared to specific pathogen free (SPF) mice, pseudo germ-free (pGF) mice exhibit milder IBD symptoms, suggesting a pro-inflammatory role of gut microbiota. We then employed single-cell RNA-sequencing to profile the immune cells in the colon of SPF and pGF mice at day 0, 2, and 7 of DSS treatment. DSS induces the increment of innate immune cells, including macrophages and dendritic cells, as well as proliferative CD8+ T cells, in SPF mice, while the numbers of innate immune cells and proliferative CD8+ T cells decline in DSS-treated pGF mice. Conversely, more prominent activation of T cells, especially CD4+ regulatory T cells (Tregs), was observed in DSS-treated pGF mice. Further analyses revealed that the major histocompatibility complex-class I (MHC-I) -CD8 and MHC-class II (MHC-II) -CD4 interactions promote the expansion of proliferative CD8+ T cells and CD4+ Tregs respectively. Moreover, we demonstrated that guanine deaminase (GDA) promotes inflammation through facilitating microtubule polymerization in macrophages. 7-methylguanine, a GDA inhibitor, mitigates DSS-induced IBD. In summary, our results demonstrate the pro-inflammatory function of gut microbiota during IBD pathogenesis, shed light on the regulatory mechanism of immune responses, and identify potential therapeutic targets for IBD.