Tissue-specific immune transcriptional signatures in the bordering tissues of the mouse brain and retina
Bordering the central nervous system (CNS) parenchyma are the pia mater enveloping the brain and the choroid underlying the retina. Although in close proximity to the neural parenchyma, the pia mater and choroid are external to the immune privileged environment of the brain and retina and are distinct immune compartments. This study generated a single cell transcriptomic atlas of immune cells within the healthy adult mouse pia and choroid. Comparative analysis of immune populations within these tissues revealed heterogeneous subtypes of T cells, B cells, monocytes/macrophages and dendritic cells, which displayed tissue-specific transcriptomic signatures and potential functional specialisations. Single cell RNA-sequencing of choroidal immune cells from human eye tissue identified populations with similar transcriptional profiles to mouse choroidal immune cells.  This study provides a detailed understanding of the molecular signatures of immune cells within the bordering tissues of the brain and retina, and their potential roles in CNS immune surveillance. Overall design: Immune cells (CD45+ cells) were isolated from (i) pooled mouse choroid (n=20 C57Bl/6J healthy female mice, 7 weeks of age); (ii) pooled mouse pia mater (n=20 C57Bl/6J healthy female mice, 7 weeks of age); and (iii) human choroid (n=1 tissue donor), by FACS.  Sorted cells were partitioned into single cell droplets using the Chromium 10X Controller. Subsequently, scRNA-seq libraries were prepared using a Chromium single cell reaction 3' v3.1 kit. Single cell libraries were sequenced on an Illumina NovaSeq S1 instrument, producing paired-end reads.