Integrated transcriptomic, epigenetic, and TCR clonality analysis of CD4? Tm subsets in liver and lung during chronic GVHD in mice [ATAC-seq]

Pathogenic CD4+ T cells perpetuate chronic tissue inflammation, but mechanisms remain largely undefined. Here, with transcriptome, epigenome, and clonal analysis, we compared CD4+Tm subsets among the liver and lung in the No GVHD and cGVHD recipients. Four CD4+Tm subsets identified with Ly108 versus CD69 expression were compared. Overall design: cGVHD mice were established with BALB/c recipients in receiving graft from B6 donors. CD4+T cells from lungs of cGVHD mice were enriched at day 60 after HCT and four Tm subsets were sorted with Ly108 vs CD69 expression among H2Kb+TCRb+CD4+ cells. Cell quality were checked and processed for ATAC-seq.