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a single-cell atlas of mouse brain macrophages reveals unique transcriptional identities shaped by ontogeny and tissue environment

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There is mounting evidence that macrophages play a key role in regulating brain health and illness. Parenchymal microglia have a crucial role, but other brain-resident myeloid cells are still difficult to find.

Uncovered the astounding diversity of non-parenchymal brain macrophages by dividing border regions and integrating single-cell RNA sequencing with high-dimensional cytometry, bulk RNA sequencing, fate-mapping, and imaging.

In the dura mater, subdural meninges, and choroid plexus, there were different subsets of border-associated macrophages, or BAMs, that displayed tissue-specific transcriptional fingerprints and underwent significant compositional changes during postnatal development. It was discovered that BAMs' gene regulation networks were fundamentally different from microglia's.

Importantly, discovered a distinct population that was not homeostatic and resided on the apical surface of the choroid plexus epithelium. Niche accessibility controlled BAM ontogeny and decided whether or not bone marrow progenitors gradually replaced embryonic macrophages.

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