Using single cell RNAseq to study stem cell activity after spinal cord injury

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 DESCRIPTION (provided by applicant): Prior efforts towards spinal cord injury (SCI) repair had been focused on promoting long-distance growth of severed nerves by relieving the inhibition from myelin components or to enhance the innate regeneration ability of CNS neurons. Recently, accumulating evidences have pointed out an alternative approach, i.e., through introducing/activation of exogenous/endogenous neural stem cells (NSCs), allowing for generation of new neurons, which form nascent neural circuits, serving as relay stations connecting signals from ascending and descending nerves to achieve functional restoration. One major obstacle is that the CNS injury environment, such as the one after spinal cord injury (SCI), is rather inhibitory and inflammatory, limiting the ability for activated NSCs to differentite into neurons. Meanwhile, the scarcity of NSC and the complexity of their surrounding environment have made molecular characterization of these cells particularly challenging, because RNAseq analysis of tissues with heterogeneous cellular composition provide the sum or averaging of all of the different cells in such tissue, which often provide unintentional misleading readouts unrelated to NSC activities. With single cell transcriptome profiling technique established in the lab, we uncovered quiescent NSC features of CD133 (encoded by prominin1 gene) positive ependymal cells in the adult mouse forebrain neurogenic zone. Using ROSA26-Td-tomato reporter mice with electroporation of prominin1 promoter driven Cre, we further demonstrated that upon VEGF and bFGF stimulation, likely as in the case of injury, CD133+ ependymal cells can be mitotically activated and differentiate into downstream neural lineage cells (MAP2+ neurons and GFAP+ glia), even at the ependymal/ventricular surface of the 4th ventricle, which has not been reported to be neurogenic in vivo in postnatal mice. In this application, we propose to trace CD133 progenies by crossing the B6N;129S-Prom1tm1(cre/ERT2)Gilb/J (the Jackson Lab) mice with the Cre-LoxP reporter mice, Rosa26-Td-tomato to study proliferation, migration and differentiation of CD133+ ependymal cells lining the spinal cord central canal after crush injury at T9-11. Based on temporal and spatial activities of CD133 progenies after SCI, we will perform single cell transcriptome profiling on CD133 + ependymal cell at several regions and time points before and after SCI, followed by weighted gene co-expression network analysis (WGCNA) to characterize the molecular features and activaties of CD133+ ependymal cells after SCI. We believe such study will be instrumental for future development of the new therapeutic strategies to enhance endogenous NSC mediated regeneration after SCI.