The Tabulae Paralytica: Multimodal single-cell and spatial atlases of spinal cord injury

Abstract

Here, we introduce the Tabulae Paralytica—a compilation of four atlases of spinal cord injury (SCI) comprising a single-nucleus transcriptome atlas of half a million cells; a multiome atlas pairing transcriptomic and epigenomic measurements within the same nuclei; and two spatial transcriptomic atlases of the injured spinal cord spanning four spatial and temporal dimensions. We integrated these atlases into a common framework to dissect the molecular logic that governs the responses to injury within the spinal cord. The Tabulae Paralytica exposed new biological principles that dictate the consequences of SCI, including conserved and divergent neuronal responses to injury; the priming of specific neuronal subpopulations to become circuit-reorganizing neurons after injury; an inherent trade-off between neuronal stress responses and the activation of circuit reorganization programs; the necessity of reestablishing a tripartite neuroprotective barrier between immune-privileged and extra-neural environments after SCI; and a catastrophic failure to form this barrier in old mice. We leveraged the Tabulae Paralytica to develop a rejuvenative gene therapy that reestablished this tripartite barrier, and restored the natural recovery of walking after paralysis in old mice. The Tabulae Paralytica provides an unprecedented window into the pathobiology of SCI, while establishing a framework for integrating multimodal, genome-scale measurements in four dimensions to study biology and medicine.