When cell identities were classified (Supplementary Fig. 7c), peri-junctional niches consistently revealed higher innate immune cell concentrations in periodontitis (MPO+-neutrophils, CD14/CD68+-macrophages, CD56+-natural killer cells, CD11c+-dendritic cells), whereas the sulcular region revealed distinct adaptive immune foci (CD8+-cytotoxic T cells, CD4+-helper T cells, FOXP3+-regulatory T cells, and CD20+-B cells) (Fig. 7c, d). The gene discussed is FOXP3; the disease is periodontitis.