Fig. 1: Spatiotemporal molecular decoding of SCI LRAs.
From: Lesion-remote astrocytes govern microglia-mediated white matter repair
a, Comparison of BFAs and hypertrophic reactive LRAs after iSCI. b, RNA-seq of LRAs. HA, haemagglutinin. c, DEGS in bulk RNA-seq of LRAs (false discovery rate (FDR) P ≤ 0.05) at 3 (n = 5), 7 (n = 4), 14 (n = 6), and 28 (n = 6) dpi versus healthy LRAs (n = 5). Rostral and caudal data are combined. d, BFA expression of LRA DEGs across acute (3 dpi), subacute (7 and 14 dpi), and chronic (28 dpi) post-injury phases. On average, 46% of LRA DEGs are either not regulated in BFAs or are regulated in the opposite direction across these phases. e, Principal component analysis of astrocyte DEGs from SCI LRAs and BFAs, EAE, amyotrophic lateral sclerosis (ALS) and lipopolysaccharide (LPS)-reactive spinal cord astrocytes relative to healthy spinal cord astrocytes. LRAs acquire a separable reactivity state with a distinct trajectory relative to SCI and non-traumatic CNS insults. f, Schematic of combined snRNA-seq and spatial transcriptomics approach for investigating SCI-reactive LRAs and neighbouring cell types. g, Uniform manifold approximation and projection (UMAP) of cell types identified by snRNA-seq in healthy and all post-injury (all time points) spinal cord (230,570 cells). Tissue collected from uninjured thoracic (n = 5), uninjured lumbar (n = 4), 3 dpi thoracic (n = 4), 3 dpi lumbar (n = 4), 7 dpi thoracic (n = 4), 7 dpi lumbar (n = 4), 28 dpi thoracic (n = 6) and 28 dpi lumbar (n = 3) spinal cords. h, Diagram of intraspinal regions used in deconvolution of spatial transcriptomic data (n = 4 mice per time point per region). GM, grey matter; WM, white matter. i, UMAP of healthy and iSCI astrocytes, illustrating neuroanatomically restricted LRA subtypes and their distinct molecular states. Ast, astrocytes; cGM, central grey matter; dGM, dorsal grey matter; vGM, ventral grey matter. j, Spatial transcriptomic characterization of vGM3 astrocytes illustrates restricted positioning in ventral horn grey matter. k, High-magnification image of vGM3 markers Arex and Thrsp in Gfap+/Aldoc+ ventral horn grey matter astrocytes. Scale bars, 10 µm. l, Spatial transcriptomic characterization of WM4 astrocytes illustrates unilaterally restricted white matter expression. m, High-magnification image of WM4 markers shows expression of Glipr2 and Ccn1 in Gfap+/Aldoc+ white matter astrocytes. Scale bars, 10 µm. n, Heat map showing relative expression of functionally related genes across regionally restricted LRA molecular states. ECM, extracellular matrix; MHC, major histocompatibility complex. Exact P values are provided in the Source Data.
