Single cell ATAC-seq of mouse retinal CX3CR1+ myeloid cells for Naive, PBS and 4xLPS treatment

We report epigenetic changes in the chromatin accessibility landscape of retinal myeloid cells from mice preconditioned with 4xLPS injections persist after the initial inflammation has subsided. We compared the data of scATAC-seq performed on nuclei extracted from sorted CX3CR1+ retinal cells from mice 3 days after CNV induction, preconditioned with either PBS or 4xLPS 1 month before, or Naïve retinas without CNV induction, preconditioned with PBS. After quality control, filtering and dimension reduction, a two-dimensional UMAP was performed on the remaining 835, 821, and 588 cells in the PBS, 4xLPS, and Naive groups respectively. Unbiased clustering was applied using Leiden algorithm, which partitioned CX3CR1+ myeloid cells into 8 distinct clusters (C1–C8). Based on previously described cell-specific gene signatures, we identified microglia (clusters C1, C2 and C3), monocytes (clusters C4 and C5), and macrophages (cluster C6). Gene expression scores identified C4 as circulating monocytes and C5 as a mixture of classical and inflammatory monocytes. The three microglial populations (C1, C2, and C3), harbor the greatest epigenetic diversity following induction of CNV or preconditioning. GSEA analysis revealed that the C2 subpopulation was characterized by considerable enrichment in opened chromatin regions corresponding to genes coding for inflammation-related pathways. In contrast, the C1 subpopulation showed higher numbers of closed chromatin in genes coding for inflammatory processes. Moreover, when compared to the C1 and C2 subpopulations, C3 had open chromatin regions only in two gene sets coding for inflammation-related pathways, and three gene sets with closed chromatin regions. Together, these data demonstrate that the chromatin landscape of retina-resident microglia is impacted differently by both the prior systemic exposure to LPS and by CNV. Overall design: scATAC-seq of FACS-sorted CX3CR1+ retinal cells from mice 3 days after CNV induction, preconditioned with either PBS or 4xLPS 1 month before, or Naïve retinas without CNV induction, preconditioned with PBS.