Heterogeneity analysis of astrocytes following spinal cord injury at single‐cell resolution

Abstract

Astrocytes play many important functions in response to spinal cord injury (SCI) in an activated manner, including clearance of necrotic tissue, formation of protective barrier, maintenance of microenvironment balance, interaction with immune cells, and formation of the glial scar. More and more studies have shown that the astrocytes are heterogeneous, such as inflammatory astrocyte 1 (A1) and neuroprotective astrocyte 2 (A2) types. However, the subtypes of astrocyte resulting from SCI have not been clearly defined. In this study, using single‐cell RNA sequencing, we constructed the transcriptomic profile of astrocytes from uninjured spinal cord tissue and injured tissue nearby the lesion epicenter at 0.5, 1, 3, 7, 14, 60, and 90 days after mouse hemisection spinal cord surgery. Our analysis uncovered six transcriptionally distinct astrocyte states, including Atp1b2+, S100a4+, Gpr84+, C3+/G0s2+, GFAP+/Tm4sf1+, and Gss+/Cryab+ astrocytes. We used these new signatures combined with canonical astrocyte markers to determine the distribution of morphologically and physiologically distinct astrocyte population at injured sites by immunofluorescence staining. Then we identified the dynamic evolution process of each astrocyte subtype following SCI. Finally, we also revealed the evolution of highly expressed genes in these astrocyte subtypes at different phases of SCI. Together, we provided six astrocyte subtypes at single‐cell resolution following SCI. These data not only contribute to understand the heterogeneity of astrocytes during SCI but also help to find new astrocyte subtypes as a target for SCI repair.

Single-cell transcriptomic profile of satellite glial cells in trigeminal ganglion

“…Our results and other studies ( Li et al, 2016 ; Hockley et al, 2019 ; Renthal et al, 2020 ; Parpaite et al, 2021 ; Wang et al, 2021 ) have shown that neurons in the peripheral ganglion have distinct subpopulations that are consistent with neurons of different functions, but there are fewer relevant studies on SGCs subtypes in the peripheral ganglion. Astrocytes, as glial cells similar to SGCs in the CNS, a series of correlative studies based on scRNA-seq have demonstrated the diversity of astrocytes in different regions of the brain and the variation of astrocyte subtypes in different disease ( Batiuk et al, 2020 ; Hasel et al, 2021 ; Hou et al, 2022 ; Ma et al, 2022 ; Sadick et al, 2022 ). Compared to astrocytes, there are currently fewer studies on single-cell transcription of SGCs subtypes.…”

Construction of a searchable database for gene expression changes in spinal cord injury experiments

“…Single cell transcriptomics. More recent transcriptome work in the SCI field has included studies utilizing single cell RNA-Seq (scRNA-Seq) [98,[110][111][112][113][114][115][116], including a recent atlas of spinal cord injury in mice [114]. Due to the complexities of scRNA-Seq data, including cell typing and the disparity between limited sample numbers and large numbers of cells per sample, as well as a different modality for viewing scRNA-Seq data, we chose not to include that data at this time to focus on the more broadly available bulk RNA-Seq datasets.…”

Combination of single-cell and bulk RNA seq reveals the immune infiltration landscape and targeted therapeutic drugs in spinal cord injury

“…The bulk RNA-seq datasets (GSE5296 and GSE47681), all based on the GPL1261 platform and contained 10 samples (four control and six SCI) and 12 samples (four control and eight SCI) were sequenced at 3 days post-injury (dpi) and 7 dpi, respectively ( 10 , 11 ). The GSE189070 dataset based on the GPL24247 platform containing single-cell RNA data from six mice in the uninjured group and 12 mice in the injured group were sequenced at 3 dpi and 7 dpi, which corresponds to the sequencing time of bulk RNA seq datasets ( 12 ). The study flow chart is shown in Figure 1 .…”