Studies from multiple laboratories implicate two main potential cellular sources for newly proliferated astrocytes around CNS injuries: local astrocytes18,19,20,26,34 and local oligodendrocyte progenitor cells (OPCs)34,35,36,37. Here, we used lineage tracing based on tamoxifen-regulated Cre-reporter expression31 to determine the proportional contributions of these cell types to newly proliferated border-forming astrocytes around hemorrhagic lesions after crush SCI or around ischemic lesions after forebrain stroke caused by infusion of N5-(1-iminoethyl)-l-ornithine (L-NIO, Fig. 1 and Extended Data Fig. 1). We targeted the reporter, tdTomato (tdT), to mature astrocytes by using Aldh1l1-CreERT38, and to OPCs by using either Pdgfra-CreERT-tdT39 or NG2-CreERT-tdT40,41, and induced temporary Cre expression with a 5-day regimen of tamoxifen dosing in healthy young adult (>8 week old) mice (Fig. 1a).

a, Lineage tracing procedures. b, Spinal cord, uninjured and after SCI, stained by immunohistochemistry for astrocytes (Gfap) or stromal cells (Cd13). c,d, Images (c) and cell counts (d) of Sox9-positive lesion border astrocytes (LBAs) plus Gfap-IHC or of lineage tracing with Aldh1l1-tdT or Pdgfra-tdT after SCI. e, Proliferating astrocytes labeled with Ki67. f, Staining for Sox9 plus Ng2-tdT. g,h, Newly proliferated BrdU-labeled astrocytes positive for Aldh1l1-tdT or Pdgfra-tdT after SCI (individual fluorescence channels are shown in Extended Data Fig. 1h). i,j, Striatum uninjured and after L-NIO stroke, with images (i) and cell counts (j) of Sox9-positive LBAs plus Gfap-IHC or of lineage tracing with Aldh1l1-tdT or Pdgfra-tdT after stroke. k,l, Newly proliferated BrdU-labeled astrocytes positive for Aldh1l1-tdT or Pdgfra-tdT after stroke. n = 4 mice per group. All graphs were evaluated with one-way ANOVA with Tukey’s post-hoc comparison. Bar graphs are mean values; error bars, s.e.m. P values are indicated on graphs. NS, nonsignificant; LC, lesion core; AB, astrocyte border.

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Newly proliferated astrocytes around CNS lesions organize into permanent, high cell density borders with overlapping cell processes that surround non-neural lesion cores of stromal and fibrotic tissue after SCI or stroke (Fig. 1b,c,i and Extended Data Fig. 1a)13. We quantified tdT-labeled, lineage-traced, border-forming astrocytes within representative 250 µm zones immediately adjacent to lesion core stromal tissue at 14 days after SCI or forebrain stroke (Fig. 1a–d,i,j), a timepoint by which border formation is largely complete13. As benchmarks against which to compare tdT labeling, we used Gfap and Sox9, which together label essentially all newly proliferated border-forming astrocytes around lesions13,26,32 (Fig. 1c,d,i,j).

In healthy adult spinal cord or striatum, essentially all astrocytes expressed Sox9 and Aldh1l1-CreERT-tdT, confirming previous reports38, and no astrocytes were detectably derived from OPCs as indicated by Pdgfra lineage tracing (Extended Data Fig. 1b). In uninjured spinal cord, all Sox9-positive and Aldh1l1-tdT-positive astrocytes expressed detectable Gfap, whereas in uninjured striatum, only about 13% did so (Extended Data Fig. 1b).

Lineage tracing showed that after both SCI and stroke, over 90% of Gfap plus Sox9-positive lesion border astrocytes also expressed Aldh1l1-CreERT-tdT, indicating that these cells derived from local mature astrocytes (Fig. 1c,d,i,j). Approximately 10% of Gfap plus Sox9-positive lesion border astrocytes expressed Pdgfra-CreERT-tdT and transcription factors Sox10 and Id3, indicating that these cells derived from local OPCs and exhibited molecular features of reactive astrocytes17,42 (Fig. 1c,d,f,i,j and Extended Data Fig. 1c–e). The proportion of OPC-derived border-forming astrocytes was essentially equivalent using NG2-CreERT-tdT lineage tracing (Fig. 1f and Extended Data Fig. 1c,d). In both SCI and stroke, about 75% of the Pdgfra-CreERT-tdT-positive cells in the lesion border zone were Olig2-positive but Gfap-negative and Sox9-negative OPCs (Extended Data Fig. 1f).

To identify newly proliferated cells, bromodeoxyuridine (BrdU) was administered during a 6-day period from 2 to 7 days after injury (Fig. 1a). In healthy adult spinal cord or striatum, no astrocytes were detectably BrdU-labeled, whereas about 8–10% of OPCs were (Extended Data Fig. 1g). At 5 days after injuries, lineage-traced astrocytes expressed the active proliferation marker Ki67 (Fig. 1e). Quantification of BrdU showed that at 14 days after either SCI or stroke, at least 75–85% of lesion border astrocytes that were derived from either astrocytes or OPCs were newly proliferated (Fig. 1g,h,k,l and Extended Data Fig. 1h), and this is probably a conservative estimate because BrdU was administered only once daily.

As mature Aldh1l1-expressing astrocytes are the predominant source of border-forming cells, we characterized their temporally dependent transcriptional changes after SCI. We used young adult (3–4 months old) male and female Aldh1l1-CreERT-RiboTag mice for hemagglutinin-positive ribosome immunoprecipitation and cell-specific transcriptome profiling of astrocytes33,38 in healthy, uninjured spinal cord and at 2, 5, 14, 28, 42 and 70 days after SCI (Fig. 2a, Extended Data Fig. 2a and Supplementary Data 1), spanning periods of proliferation, border formation and chronic border persistence13,17,25. Specificity of Aldh1l1-CreERT-RiboTag for astrocyte transcriptome analyses has been demonstrated in brain38 and was confirmed here for spinal cord (Extended Data Fig. 2a–k). Sequencing of mRNA from the flow-through solution after RiboTag immunoprecipitation was used to characterize gene expression by other local cells and enabled assessment of astrocyte enrichment (Extended Data Fig. 2a,d–k). Aldh1l1-CreERT-RiboTag gave equivalent astrocyte-enriched transcriptional profiles as mGfap-Cre-RiboTag17,27 but showed depleted genetic signatures originating from ependyma or OPC-derived cells that acquire Gfap expression after SCI; and astrocytes derived from OPCs after SCI had immunohistochemically detectable hemagglutinin expression in mGfap-Cre-RiboTag but not in Aldh1l1-CreERT-RiboTag spinal cords (Extended Data Fig. 2a,d–l). Consistent with previous reports after stroke43, we detected negligible sex-dependent transcriptomic differences in astrocytes after SCI, with four Y-chromosome and two X-chromosome genes detected as the only differentially expressed genes (DEGs) (false discovery rate of <0.01) across two independent post-SCI timepoints comparing eight female and eight male mice (Extended Data Fig. 2m–o).

a, Experimental design. b, Numbers of astrocyte DEGs significantly different (up or down; false discovery rate, FDR < 0.01) from uninjured healthy mice at different times. c, Number of astrocyte DEGs significantly (FDR < 0.01) changed between different timepoints. d, Number of healthy astrocyte expressed genes (EGs) compared with DEGs after SCI that are up, down or not regulated from healthy, or not expressed in healthy. e, PCA of all DEGs. f, Number of DEGs defining PC1 or PC2. g,h, Heatmaps and mean DEG log2 (fold change) (log2 FC) of DEGs defining PC1 (g) and PC2 (h). Heatmaps are arranged with the most upregulated DEGs at the top to most downregulated at the bottom on day 2 after SCI (g) and on day 70 (h). White spaces indicate no significant change. i, GO-BPs significantly upregulated (red) or downregulated (blue) as identified by unbiased evaluations of DEGs defined by PC1 or PC2. FL, PC factor loading. P values in i were calculated by two-sided Fisher’s exact test. n = 4 mice for uninjured and all post-SCI timepoints except day 2 (n = 5).

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Using Aldh1l1-CreERT-RiboTag (Astro-RiboTag) across all six post-SCI timepoints, a total of 13,527 unique DEGs were identified compared to healthy baseline levels, with more genes upregulated than downregulated at all timepoints (Fig. 2b and Supplementary Data 2). The most DEGs, 9,924, were detected at 2 days, with over 6,000 DEGs persisting at 28, 42 and 70 days (Fig. 2b). The greatest changes occurred between 0–2 and 2–5 days, with far fewer changes after 14 days (Fig. 2c).

Over 15,722 genes were identified as expressed by healthy spinal cord astrocytes. Of these genes, 37% (5,755) were primarily downregulated after SCI, 36% (5,598) were primarily upregulated, 7% (1,153) were dynamically regulated down or up at different timepoints and 20% (3,216) were not significantly different at any timepoint examined (Fig. 2d). Notably, 92% (12,506 out of 13,527) of the total DEGs identified across all times after SCI were expressed by astrocytes in healthy tissue (Fig. 2d). Induction of newly expressed genes that were not detectable in healthy astrocytes accounted for only 12% (889 out of 7640) of DEGs upregulated by astrocytes after SCI (Fig. 2d and Supplementary Data 2).

Principal component analysis (PCA) of the 13,527 DEGs identified across all timepoints revealed a clear temporal progression of astrocyte transcriptional responses, with two principal components that accounted for over two-thirds of the total system variation (Fig. 2e and Extended Data Fig. 2p). PC1, defining the most dominant effect, revealed acute and transient changes. DEGs with a PC1 factor loading of >|0.8| in the positive or negative direction peaked at 2–5 days after SCI before returning essentially to baseline healthy astrocyte levels by 28 days, with roughly equal numbers transiently upregulated or downregulated (Fig. 2f,g). DEGs defining PC2 increased quickly and largely persisted with mean values of >2 or less than −1 across the entire time course, with more upregulated (854) than downregulated (547) (Fig. 2f,h).

Unsupervised analysis of Gene Ontology Biological Processes (GO-BPs) showed that transiently upregulated DEGs defining PC1 were associated with the regulation of gene expression and translational, cell proliferation, innate immune signaling and antigen presentation, whereas transiently downregulated DEGs defining PC1 were associated with mature CNS structure and glia cell differentiation (Fig. 2i). Persistently upregulated DEGs defining PC2 were associated with cytokine production, innate and adaptive immune regulation and extracellular matrix (ECM) organization, whereas persistently downregulated DEGs defining PC2 were associated with cholesterol and lipid metabolism, neurotransmitter transport and synapse organization (Fig. 2i).

These findings demonstrate that local healthy mature Aldh1l1-expressing astrocytes undergo pronounced, temporally dependent transcriptional changes during border formation after SCI, including both transient and persisting changes. Remarkably, 88% of DEGs upregulated by astrocytes after SCI were already expressed at detectable levels by healthy astrocytes. Astrocyte border formation involves permanent transcriptional reprogramming, given that almost 50% of total DEGs persist at 70 days post SCI, including many genes not detectably expressed by healthy astrocytes. GO analyses parsed astrocyte transcriptional changes into profiles related to astrocyte dedifferentiation and proliferation, astrocyte reactivity, regulation of inflammation and immune signaling, wound healing and persisting border formation, examined in more detail below.

We next defined more precisely how local mature astrocytes change in response to SCI. Of the 15,722 total genes expressed by healthy astrocytes (Fig. 2d), about 60% were upregulated or downregulated at 2 and 5 days, and about 35–40% from 28 through 70 days, with the rest remaining unchanged (Fig. 3a). To characterize astrocyte-enriched genes, we first examined a panel of 429 consensus healthy astrocyte-enriched genes (cAEGs) identified in at least five of eight published archival datasets42, which we confirmed as enriched in our healthy astrocytes by at least twofold and up to over 50-fold (Extended Data Fig. 3a,b and Supplementary Data 2). Nearly all cAEGs (97%; 417 out of 429) were DEGs after SCI and only 3% (12 out of 429) were not significantly different at any timepoint. Remarkably, 74% (317 out of 429) of cAEGs were primarily downregulated and only 11% (49 out of 429) were primarily upregulated, with 15% changing in either direction at different times (Fig. 3b). These changes were reflected in a pronounced decrease in mean expression of all 429 cAEGs, which had a negative peak at 2 days followed by a return towards baseline by 14 and 28 days, but with an overall downregulation persisting through 70 days (Fig. 3c). Notably, cAEGs with the highest enrichment in healthy astrocytes relative to other local cells were the most downregulated (Extended Data Fig. 3b).

a, Numbers of up, down or nonsignificant changes (FDR < 0.01) in 15,722 genes expressed by uninjured astrocytes at different times after SCI. b, Numbers of up, down or nonsignificant changes (FDR < 0.01) in 429 cAEGs at different times after SCI. c, Mean log2 FC of downregulated cAEGs at different times after SCI relative to uninjured, and changes between individual timepoints. d, Heatmap of mean log2 FC of selected downregulated cAEGs at different times after SCI. e, Four different fluorescence channels illuminating different molecular markers within the same region to reveal the spatial distribution and colocalization of Gpc5 staining at LBA and GM astrocytes. Markedly Gpc5 immunoreactivities are reduced in LBAs compared with more distal gray matter (GM) astrocytes after SCI. f, Kcnj10 immunoreactivities in LBAs compared with more distal GM astrocytes after SCI. For individual fluorescence channels, see Extended Data Fig. 3c. g, Time course of mean expression changes after SCI of ipAEGs (see main text) associated with representative examples of the most significantly changed GO-BPs associated with ipAEGs. h, Highly downregulated GO-BPs associated with all downregulated astrocyte DEGs (whether enriched versus other cells or not). i, Time course after SCI of mean changes of DEGs associated with cell proliferation-related GO-BPs identified by PC1 in Fig. 2i. j, Time course after SCI of mean changes in all unsupervised 91 proliferation-related astrocyte DEGs examined in i, plus two additional canonical proliferation DEGs, Mki67 and Top2a. k, Time courses after SCI of mean changes in consensus genes associated with astrocyte maturity or immaturity. l, Time courses after SCI comparing downregulation of all maturation-associated genes versus consensus genes expressed by mature astrocytes (cAEGs). m, Time courses after SCI of mean changes in two specific examples of DEGs, Padi2 and Nes, associated with astrocyte maturity or immaturity, respectively. n = 4 mice for uninjured and all post-SCI timepoints except at day 2 (n = 5). Bar and line plots are mean values; error bars, s.e.m. P values in g–i calculated by two-sided Fisher’s exact test.

Prominent cAEGs that were acutely downregulated and returned to baseline included the water channel (Aqp4), the calcium binding protein (S100b) and Hepacam4, which regulates astrocyte branching complexity44 (Fig. 3d). Prominent cAEGs that were persistently downregulated included transporters for glutamate (Slc1a2 and Slc1a3), GABA (Slc6a1 and Slc6a11), glutamine (Slc38ac) and d-serine (Slc7a10), potassium channels (Kcnj10 and Kcnj16), glutamate receptor subunits (Grin2c and Grm) and synapse modulating molecules (Gpc5 and Sparcl1)10,45 (Fig. 3d). Immunohistochemistry (IHC) confirmed certain changes at the protein level and showed, for example, that many, but not all, lesion border astrocytes had low or undetectable levels of Gpc5 and Kcnj10 (Fig. 3e,f and Extended Data Fig. 3c).

To explore more broadly how local healthy astrocytes acutely changed functional states after SCI, we examined additional specific DEG cohorts. We first examined 2,806 genes identified by our RiboTag immunoprecipitation as significantly enriched in healthy astrocytes by at least twofold and up to 50-fold versus other local cells (Extended Data Fig. 3a,b and Supplementary Data 2). Similar to cAEGs, these immunoprecipitation astrocyte-enriched genes (ipAEGs) exhibited a preponderance of downregulation after SCI, particularly among those ipAEGs most highly enriched in healthy astrocytes (Extended Data Fig. 3b). We conducted unsupervised analysis of GO-BPs associated with significant changes among these 2,806 ipAEGs after SCI and tracked over time after SCI the mean expression of ipAEGs associated with representative examples of the most significantly changed GO-BPs. The majority of significantly altered GO-BPs were associated with downregulated ipAEGs related to cell differentiation, fatty acid metabolism, general metabolic processes, vascular morphogenesis, transport across the blood–brain barrier, synapse assembly, glutathione production and cholesterol production (Fig. 3g). The few GO-BPs associated with upregulated ipAEGs were related to epithelial-to-mesenchymal transition (EMT), immune functions and ECM reorganization.

We next examined GO-BPs associated with all 5,755 DEGs downregulated by astrocytes at any time after SCI, and again tracked over time the mean expression of DEGs associated with representative examples of the most significantly changed. This analysis further confirmed a pronounced acute and persistent attenuation in the expression by astrocytes of genes associated with astrocyte–neuron interactions, neurotransmitter transport, synapse organization, synaptic transmission and potassium regulation (Fig. 3h).

Cell dedifferentiation can be associated with proliferation46. Past13 and present Ki67 and BrdU evaluations (Fig. 1e,g,h,k,l) and GO-BP analysis (Fig. 2i) indicate pronounced astrocyte proliferation starting around 2 days after SCI. We tracked over time after SCI changes among genes associated with three of the most significantly upregulated cell proliferation-related GO-BPs identified by PCA (Figs. 2i and 3i,j). Astrocyte DEGs associated with each of these GO-BPs, and the mean expression of the unsupervised 91 proliferation-related genes associated with all three GO-BPs, were highly upregulated by local astrocytes at 2 and 5 days and returned to near baseline levels by 14 days (Fig. 3i,j and Supplementary Data 2).

Dedifferentiation and proliferation of local healthy Aldh1l1-expressing astrocytes after SCI suggested a potential return to an immature or progenitor-like state47. We compared astrocyte DEGs after SCI with DEG panels positively or negatively associated with astrocyte maturation during postnatal development derived by PCA of transcriptomes from healthy astrocytes at postnatal days (P) from P0 to P63 (Extended Data Fig. 3d–h). By 2 and 5 days after SCI, astrocytes had markedly downregulated mean expression of 2,417 genes associated with maturity and upregulated mean expression of 2,120 genes associated with immaturity, and these changes returned to essentially baseline levels by 28 days, with a modest upregulation of some immaturity genes persisting to 70 days (Fig. 3k and Extended Data Fig. 3d–h). Of the 429 cAEGs, 192 were positively associated with the progression toward maturity, and their mean expression declined and remained persistently low after SCI (Fig. 3l,m). Notably, healthy P0 astrocytes expressed high levels of Mki67 and Top2a associated with active proliferation (Fig. 3j), whereas mature astrocytes in healthy CNS are proliferation-dormant and exist in a potentially reversible G0 state (Extended Data Fig. 1g). They required two or more days after injury to express these genes and never reach fragments per kilobase of transcript per million mapped reads (FPKM) levels of healthy proliferating P0 astrocytes (Fig. 3j).

These findings demonstrate that local healthy mature Aldh1l1-expressing astrocytes respond acutely to SCI with downregulation of most astrocyte-enriched genes and a transient phase of proliferation and immaturity. This is followed by a return of many transcriptional features of mature astrocytes but with persisting differences, including a persistent downregulation of molecules associated with astrocyte–neuron interactions such as maintenance of extracellular neurotransmitter and ion homeostasis, and synapse organization and function. These findings point towards persistent transcriptional reprogramming of newly proliferated lesion border astrocytes to new and different functional states.

To look for potential new functions adopted by newly proliferated and reprogrammed astrocytes after SCI, we first examined changes in 170 consensus astrocyte reactivity genes (cARGs) derived from a meta-analysis of six archival datasets from multiple laboratories42 (Supplementary Data 2). All 170 cARGs were upregulated on at least one timepoint after SCI, 93% (158 out of 170) were upregulated at all timepoints and 92% (157 out of 170) were detectably expressed by healthy astrocytes (Fig. 4a). Mean cARG expression increased 16-fold by 2 days after SCI, increased to over 50-fold by 5 days and then declined moderately but remained persistently elevated by over eightfold at 70 days (Fig. 4b), consistent with reprogramming to an essentially permanent reactive state after SCI. Notably, 41 of the top 50 GO-BPs most significantly associated with cARGs upregulated at all timepoints involved regulation of inflammation, while other upregulated GO-BPs included phagocytosis, ECM organization, synapse pruning and homotypic cell–cell adhesion (Extended Data Fig. 4a). cARGs that were upregulated by 14 days after SCI and remained persistently and highly upregulated at 70 days included well-studied cARGs such as Gfap, Vim and Lgals3, as well as molecules that appear in multiple reactive astrocyte RNA evaluation studies such as S100a6, Serpina3n, Lyz2, Lcn2, Hsbp1, C1qa, Tyrobp, Trem2, Tgm1, Ccl3 and Ccl4 (Fig. 4c). IHC confirmed protein expression by border-forming astrocytes for many of these molecules after SCI and stroke, and revealed that whereas certain proteins such as Gfap and S100a6 were readily detectable in essentially all Sox9-positive lesion border astrocytes, many proteins, such as Lgals3 and others discussed below, were highly expressed in some lesion border astrocytes that were intermingled with other astrocytes with low or no detectable expression (Fig. 4d and Extended Data Fig. 4b).

a, Numbers of up, down or nonsignificant (FDR < 0.01) changes in 170 cARGs at different times after SCI. b, Mean log2 FC of upregulated cARGs at different times after SCI and changes between individual timepoints. c, Scatterplot showing log2 FC and FPKM of cARGs at 70 days after SCI. Selected examples of highly expressed and highly upregulated DEGs are labeled. d, Examples of cARGs with high levels of protein immunoreactivity in LBAs. e, Heatmap of 1,129 astrocyte DEGs upregulated at least twofold at all times after SCI. f, Scatterplot showing log2 FC and FPKM of 1,129 astrocyte DEGs upregulated at least twofold at all times after SCI. g, Top GO-BTs associated with 1,129 astrocyte DEGs upregulated at least twofold at all times after SCI. h, Heatmaps of log2 (fold enrichment) (log2 FE) and log2 FC of 40 DEGs enriched in astrocytes by a mean of at least twofold compared with other cells and upregulated by at least twofold at all timepoints after SCI. i, Top GO-BPs associated either with 40 DEGs expressed more highly by astrocytes than other cells, or with 765 DEGs expressed at similar levels by astrocytes and other cells, or with 209 DEGs expressed more highly by other cells. n = 4 mice for uninjured and all post-SCI timepoints except at day 2 (n = 5). Bar and line plots are mean values; error bars, s.e.m. P values in g and i were calculated by two-sided Fisher’s exact test.

Given that the injury response involves many cell types3, we compared the expression of the same genes by astrocytes and other cells (Extended Data Fig. 3a). Many highly upregulated cARGs (Fig. 4c) were also highly enriched in other cells, such as Tgm1, Steap4, Serpina3n and others (Extended Data Fig. 4c). Nevertheless, many highly upregulated cARGs were de-enriched in astrocytes relative to other cells, such as Tyrobp, Trem2, C1qc, Ccl4 and others, indicating that although these genes were used by reactive astrocytes, they were also more prominently used by other cells (Extended Data Fig. 4d). Notably, astrocytes and other cells often exhibited different temporal patterns of upregulation or downregulation of these DEGs after SCI, including changes in opposite directions at different times, suggesting potentially different roles exerted by different cell types at different times and supporting the specificity of the expression of these transcripts by astrocytes (Extended Data Fig. 4e).

We next examined 1,129 DEGs upregulated by at least twofold at all timepoints after SCI (Fig. 4e,f and Supplementary Data 2). Most of these DEGs had peak expressions at 5 days and remained markedly elevated for at least 70 days (Fig. 4e). We then tracked over time the mean expression changes of astrocyte DEGs associated with representative examples of the top GO-BPs associated with these 1,129 DEGs (Fig. 4g). Remarkably, all top 15 and 40 of the top 50 GO-BPs involved regulation of inflammation, including both innate and adaptive immune responses such as cytokine production, granulocyte chemotaxis, macrophage activation and lymphocyte regulation (Fig. 4g). Other persistently upregulated GO-BPs included regulation of angiogenesis, phagocytosis and cell adhesion (Fig. 4g).

To identify functions that might be preferentially associated with transcriptional changes in reactive astrocytes, we compared GO-BPs associated with upregulated DEGs enriched either in astrocytes or in other cells. As noted above, ipAEGs exhibited a mean downregulation of DEGs but included some upregulated DEGs (Extended Data Fig. 3b), of which only 40 were also enriched in astrocytes by over twofold (Fig. 4h). The top GO-BPs associated with these 40 upregulated and astrocyte-enriched ipAEGs included response to interferon-gamma and cytokines, cytosolic calcium regulation and negative regulation of programmed cell death (Fig. 4i). The top GO-BPs associated with DEGs enriched and upregulated in other cells (non-astrocytes) were reorganization of ECM and angiogenesis, and the top GO-BPs associated with DEGs similarly upregulated by both astrocytes and non-astrocytes were cytokine signaling and regulation of innate immunity and inflammation (Fig. 4i). These findings indicated that gene expression changes in astrocytes and non-astrocytes contribute to overlapping as well as to differing biological functions after SCI. Notably, ECM reorganization was more prominently associated with DEGs deriving from non-astrocytes (Fig. 4i). Chondroitin sulfate proteoglycans (CSPGs) are ECM components that have received prominent attention in SCI and have previously been attributed primarily to astrocytes. Nevertheless,