Single-nucleus RNA sequencing identified cells with ependymal cell-like features enriched in neonatal mice after spinal cord injury

Utilization of ethanolamine phosphate phospholyase as a unique astrocytic marker

“…In the stroke model dataset produced by Shi et al (2021) , some of the clusters did not solely and selectively express their markers [ CD3 antigen, epsilon polypeptide ( Cd3e ), T cell marker ( Shi et al, 2021 ); membrane-spanning 4-domains, subfamily A, member 7 ( Ms4a7 ), macrophage marker ( Milich et al, 2021 ); natural killer cell group 7 sequence ( Nkg7 ), natural killer (NK) cell marker ( Wu et al, 2021 ), Fc receptor, IgE, high affinity I, alpha polypeptide ( Fcer1a ), dendritic cell marker ( Wu et al, 2021 ); solute carrier family 4, sodium bicarbonate cotransporter, member 5 ( Slc4a5 ), choroid plexus epithelial cell marker ( Shi et al, 2021 ); collagen, type I, alpha 1 ( Col1a1 ), fibroblast marker ( Milich et al, 2021 ); Cx3cr1 , microglial marker; ( Supplementary Figure 3B )]. However, the other cells, including astrocytes that are the focus of this study, selectively expressed their markers [ Lactotransferrin ( Ltf ), neutrophil (granulocyte) marker ( Milich et al, 2021 ); RNA binding protein, fox-1 homolog 3 ( Rbfox3 ), neuronal marker ( Ikeda-Yorifuji et al, 2022 ); platelet/endothelial cell adhesion molecule 1 ( Pecam1 ), endothelial cell marker ( Ikeda-Yorifuji et al, 2022 ); Slc7a1 ( Ikeda-Yorifuji et al, 2022 ) and Aldh1l1 , astrocyte markers; myelin oligodendrocyte glycoprotein ( Mog ), oligodendrocyte marker; Ikeda-Yorifuji et al, 2022 ; Supplementary Figure 3B ]. In a systemic inflammation model produced by intraperitoneal injection of lipopolysaccharide (LPS) by Hasel et al (2021) , all clusters (oligodendrocytes, microglia, neurons, endothelial cells, and astrocytes) selectively expressed these markers ( Supplementary Figure 3C ).…”

“…Data processing for scRNA-seq was performed as previously described ( Ikeda-Yorifuji et al, 2022 ), with modifications. Raw read data for the stroke model ( Shi et al, 2021 ) were downloaded from the SRA (SRP308347).…”

“…Genes were annotated using org.Mm.eg.db (Carlson, 2018), and normalized read counts were plotted using ggplot2 (Wickham, 2009) and ggbeeswarm (Clarke and Sherrill-Mix, 2017). Data processing for scRNA-seq was performed as previously described (Ikeda-Yorifuji et al, 2022), with modifications. Raw read data for the stroke model (Shi et al, 2021) were downloaded from the SRA (SRP308347).…”

SnRNA-seq reveals the heterogeneity of spinal ventral horn and mechanism of motor neuron axon regeneration

“…Neurons in SNC underwent significant gene expression changes, with the largest number of differentially up-regulated genes, and the total number was nearly three times that of other cell types, followed by microglia ( Figure S1 D). Marker genes specific to each cell type, such as Mobp in oligodendrocyte, 30 Syt1 in neuron, 31 Gfap in astrocyte, 25 Pcdh15 in OPCs, C1qa in microglia, 32 Dcn in fibroblasts, 33 Adgr14 in endo-SMC, 26 Rgs5 in pericytes 27 and Dynlrb2 in ependymal cells 26 were demonstrated in a composite violin diagram. Some rarely reported genes with significantly differentially expressed effects in our study are also shown in our diagram ( Figure 1 D).…”

“… 22 , 23 , 24 Researchers also have revealed dynamic changes of neural cells in human spinal cord under single cell resolution 25 and cellular heterogeneity of spinal cord after spinal cord injury. 26 , 27 Significant progress has also been made in single cell spatiotemporal transcriptome analysis. The team of scientists analyzed and compared the process of salamander brain development and regeneration, and constructed the first spatiotemporal map of axolotl brain regeneration.…”