Pyramidal neuron subtype diversity governs microglia states in the neocortex [MERFISH]
Dataset ID: STDS0000148
20,200 Spots
115 Genes


Dataset information
Microglia are the resident immune cells of the brain, and have critical roles in circuit development and plasticity. During embryonic and postnatal development, microglia exist in multiple transcriptional states. However, it is still poorly understood how these states are established, and whether they are influenced by their cellular environment. Here we show that in the juvenile neocortex, microglia exist in multiple states whose identity and laminar distribution is instructed by the neuronal class identity of local pyramidal neurons. Using single-cell RNA sequencing, we unveil molecular signatures of distinct microglia sub-states, and show that they can be divided into layer-restricted or broadly-distributed states. Strikingly, conversion of deep-layer pyramidal neurons to an alternate class identity reconfigures both the density and molecular state of local layer-restricted microglia to correspond to the new neuronal niche, thus identifying specific populations of microglia that are sensitive to pyramidal neuron subtypes. Ligand-receptor interactomes for individual neuronal subtype-microglia pairings uncovers two categories of neuron-to-microglia communication: one associated with neuronal class identity and one associated with microglial state. Our findings highlight the fundamental role that neuronal identity and neuronal niches play in locally controlling the transcriptional status of postnatal microglia.
Overall design:
Examination of Mg states from different neuronal niches of the cerebral cortex.
10x Visium, MERFISH
Microglia MERFISH
Mus musculus(mm10)
Organ parts:
Development stage:
8-10 weeks
Stogsdill, Jeffrey A et al. “Pyramidal neuron subtype diversity governs microglia states in the neocortex.” Nature vol. 608,7924 (2022): 750-756. doi:10.1038/s41586-022-05056-7
Submission date: 2022-01-15Update date: 2022-08-17
Sample number: 1Section number: 1

Stogsdill; Jeffrey A; Kim; Kwanho; Binan; Loic; Farhi; Samouil L; Levin; Joshua Z; Arlotta; Paola

GEO Series Accessions: GSE193760