Longitudinal single cell RNA-seq of the inflamed colon

We demonstrate single-cell RNA sequencing with time course study on DSS-induced colitis mouse model to reveal the overall cellular status during colon inflammation. Based on single cell transcriptome analysis in inflamed colon, we showed that the stromal cell population of colon functions as a hub to coordinate dynamic change with other cell type. We also found the Serpina3n, a serine protease inhibitor is specific up-regulation in the stromal cells during the resolution phase of colon inflammation. Furthermore, we found that systemic administration of Serpina3n promoted the recovery of resolution phase and ameliorated colitis-related symptoms. This study provides a comprehensive understanding of cell-cell interactions during colorectal inflammation at the single-cell level and reveals a potential therapeutic target by hijacking the endogenous inflammation resolution mechanism. Mice were treated with 1.5%DSS for 6 days then switched to drinking water. Colon from each time points (Day 0, 3, 6, 9, 12 and 15) or treatment (PBS or Serpina3n) were collected. To limit mouse-to-mouse biased, three biological replicates from each group were pooled and analyzed using FACS-based, smart-seq2 method. The sequencing libraries were sequenced on the Illumina NextSeq500 platform.