Next generation sequencing of thymic dendritic cells after damage

The thymus, which is the primary site of T cell development, is particularly sensitive to insult but also has a remarkable capacity for repair. However, the mechanisms orchestrating regeneration are poorly understood and delayed repair is common after cytoreductive therapies. Here, we demonstrate a trigger of thymic repair, centered on detecting the loss of dying thymocytes which are abundant during steady-state T cell development. Specifically, apoptotic thymocytes suppressed production of the regenerative factors IL-23 and BMP4 TAM receptor signalling and downstream activation of the Rho-GTPase Rac1, the intracellular pattern recognition receptor NOD2, and micro-RNA-29c. We found that the intracellular pattern recognition receptor NOD2, via induction of microRNA-29c, suppressed levels of the regenerative factors IL-23 and BMP4, in DCs and ECs, respectively. Transcriptome analysis in highly purified DCs after damage revealed highly similar inflammatory gene signatures and enrichment for NOD2 expression Overall design: Thymi from 6-8wo mice were pooled and enzymatically digested. Freshly isolated and FACS purified thymic DCs (CD45+ MHC11+ CD11c+) were submitted for bulk RNA-seq. Library was generated using SMART-Seq v4 Ultra Low Input RNA Kit (Takara) and sequencing was run on Illumina HiSeq 2500. The sequence reads that passed Illumina's base call quality threshold were aligned to mm10 using STAR v2.5.2a, and then analyzed using Subread featureCounts v1.6.0, edgeR, and limma.