Single-cell analysis of the cellular heterogeneity and interactions in the injured mouse spinal cord

Abstract

The wound healing process that occurs after spinal cord injury is critical for maintaining tissue homeostasis and limiting tissue damage, but eventually results in a scar-like environment that is not conducive to regeneration and repair. A better understanding of this dichotomy is critical to developing effective therapeutics that target the appropriate pathobiology, but a major challenge has been the large cellular heterogeneity that results in immensely complex cellular interactions. In this study, we used single-cell RNA sequencing to assess virtually all cell types that comprise the mouse spinal cord injury site. In addition to discovering novel subpopulations, we used expression values of receptor–ligand pairs to identify signaling pathways that are predicted to regulate specific cellular interactions during angiogenesis, gliosis, and fibrosis. Our dataset is a valuable resource that provides novel mechanistic insight into the pathobiology of not only spinal cord injury but also other traumatic disorders of the CNS.

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

“…Importantly, there are limited peer-reviewed transcriptomics data available to date. scRNA-seq was used to generate transcriptomics data based on temporal changes post-injury after mouse contusion SCI at 1, 3, and 7 dpi ( Milich et al, 2021 ). Gene Ontology (GO) Enrichment Analysis for differentially expressed genes performed on astrocytes at 1 dpi were “translation” and “biosynthetic processes,” while by 3 dpi astrocytes were defined by “mitochondrial function” and “oxidative phosphorylation,” and at 7 dpi astrocytes were related to “lipid processing” ( Milich et al, 2021 ).…”

“…scRNA-seq was used to generate transcriptomics data based on temporal changes post-injury after mouse contusion SCI at 1, 3, and 7 dpi ( Milich et al, 2021 ). Gene Ontology (GO) Enrichment Analysis for differentially expressed genes performed on astrocytes at 1 dpi were “translation” and “biosynthetic processes,” while by 3 dpi astrocytes were defined by “mitochondrial function” and “oxidative phosphorylation,” and at 7 dpi astrocytes were related to “lipid processing” ( Milich et al, 2021 ). Despite numerous remaining questions regarding the extent and functional relevance of temporal astrocyte diversity following CNS traumatic injury, it appears probable that dynamic changes are evident following injury with shifting roles in the evolving injury and recovery processes, hence representing plasticity in response to environmental fluctuations.…”

Plasticity of the Injured Spinal Cord

“…Nevertheless, these results have been reproduced by other teams after contusive SCI [23,24]. Recently, a study, based on single cell experiments, has described the appearance of an astroependymal cell population present only after SCI in mice, confirming the reactivity and the differentiation potential of the ependymal cells in the lesioned spinal cord [25].…”

“…These results perfectly illustrate the underestimated cellular heterogeneity of the lesioned spinal cord. We can hypothesize that pericytes, astrocytes and ependymal cells are constituted of different subpopulations which will be characterized in the near future due to the increasing development of omics technologies, such as spatial proteomics or single cell RNA sequencing [25,27]. Indeed, recently, single nucleus sequencing technology identified the presence of newborn neurons in an adult uninjured spinal cord.…”

A Time-Course Study of the Expression Level of Synaptic Plasticity-Associated Genes in Un-Lesioned Spinal Cord and Brain Areas in a Rat Model of Spinal Cord Injury: A Bioinformatic Approach

“…More information can be obtained by scRNA-seq, but most of these studies have been performed on mouse models, which show huge differences with rats, especially in cavitation and scar formation, and is less similar to human SCI progression [60]. ScRNA-seq in mouse SCI acute (1, 3 DPL) and sub-acute (7 DPL) indicated that the main response is mediated by resident and infiltrating immune system and OPC activation [61]. This result is in line with our observations of the activation of ECM reorganization genes in the context of the synaptic plasticity pathway.…”