Multiomic spatial landscape of innate immune cells at human central nervous system borders

The innate immune system of the human central nervous system (CNS) is highly diverse already during homeostasis. Several immune cell populations such as macrophages that are frequent in the brain parenchyma (microglia) and less numerous at the brain interfaces as CNS-associated macrophages (CAMs) constitute the local immune compartment. Due to their scantiness and particular location, little is known about the presence of temporally and spatially restricted CAM subclasses during development, health and perturbation. Here, we combined several high-dimensional technologies, such as single-cell RNA-sequencing, time-of-flight mass cytometry and single-cell spatial transcriptomics with fate mapping and advanced immunohistochemistry to comprehensively characterize the immune system at human CNS interfaces. We also provide a comprehensive analysis of resident and engrafted myeloid cells in the brains of individuals with peripheral blood stem cell transplantation, revealing remarkable dynamics. These approaches enabled us to identify a previously unappreciated spectrum of transcriptional classes of human CAMs and to decipher their turnover with circulating cells. CAM signatures profoundly changed during ontogeny and pathology. Our results highlight myeloid diversity at the interfaces of the human CNS with the periphery and provide new insights into the human brain’s immune system. Single-cell RNA sequencing using 10x and Cel-Seq2 was conducted on cell suspensions and after nuclei extraction from fresh frozen sections or formalin-fixed formalin embedded tissues. A part of the single cell analyses was multilexed and analyzed using CITE-Seq. The raw fastq files can be found in the access controlled European genome phenome Archive under the accession number EGAS50000000030 https://ega-archive.org/studies/EGAS50000000030. NOTE FROM SUBMITTER: The raw fastq filese can be found in the access controlled European genome phenome Archive account associated with the study.