Barcoded viral tracing of single-cell interactions in central nervous system inflammation

Abstract

Cell-cell interactions control the physiology and pathology of the central nervous system (CNS). To study astrocyte cell interactions in vivo, we developed rabies barcode interaction detection followed by sequencing (RABID-seq), which combines barcoded viral tracing and single-cell RNA sequencing (scRNA-seq). Using RABID-seq, we identified axon guidance molecules as candidate mediators of microglia-astrocyte interactions that promote CNS pathology in experimental autoimmune encephalomyelitis (EAE) and, potentially, multiple sclerosis (MS). In vivo cell-specific genetic perturbation EAE studies, in vitro systems, and the analysis of MS scRNA-seq datasets and CNS tissue established that Sema4D and Ephrin-B3 expressed in microglia control astrocyte responses via PlexinB2 and EphB3, respectively. Furthermore, a CNS-penetrant EphB3 inhibitor suppressed astrocyte and microglia proinflammatory responses and ameliorated EAE. In summary, RABID-seq identified microglia-astrocyte interactions and candidate therapeutic targets.

Diversity of Reactive Astrogliosis in CNS Pathology: Heterogeneity or Plasticity?

“…When used alone these tools provide a powerful means of assessing astrocyte diversity but do not clearly distinguish between heterogeneity and plasticity unless they are combined with other complementary experiments, such as those looking at lineage-tracing. With that being said, recent papers highlight the potential of these single-cell technologies to yield information about lineage ( Weinreb et al, 2020 ) as well as connectivity analysis ( Clark et al, 2021 ) to be performed in high-throughput, with cell-type resolution. Furthermore, new techniques, such as sc-ATAC-seq will provide information about chromatin accessibility, which is likely to be an important determinant of astrocyte plasticity ( Buenrostro et al, 2015 ).…”

“…Furthermore, use of RNA-seq has the potential to identify cluster-specific, context-specific, or lineage-specific astrocyte markers across CNS states that will enable a more detailed interrogation of functionality and origin (e.g., with fate-mapping studies). New methods are also surfacing with the ability to predict ligand-targets links between interacting cells ( Browaeys et al, 2020 ) and using RABID-seq facilitates the simultaneous investigation of the transcriptome of specific cells interacting with your cell type of interest ( Clark et al, 2021 ) in disease modeling which could further be a powerful tool. In addition, recent tools, such as transposase-accessible chromatin profiling (sc-ATAC-seq; Jia et al, 2018 ) have the potential to yield information about how chromatin accessibility dictates astrocyte diversity.…”

Histamine, Neuroinflammation and Neurodevelopment: A Review

“…The mechanisms underlying the induction of a specific neuroinflammatory process remains poorly understood. Recent cutting-edge approaches have started to describe key target molecules important for the interactions between astrocytes and microglia in these neuroinflammatory processes (Clark et al, 2021). It is hoped that improved understanding of astrocytemicroglia cross-talk may then reveal new potential therapeutic targets for modulation that could be relevant in an array of neurodevelopmental disorders.…”

Reassessment of Pioglitazone for Alzheimer’s Disease

“…To the best of our knowledge, these observations have not been followed-up. Given the potential for cross-talk between astrocytes and microglia ( Clark et al, 2021 ), such an indirect pathway might also contribute to PPARγ agonist-mediated in vivo regulation of microglial function.…”