CoChat
Sign Up
Cited by 304Spinal Cord Injury ResearchNerve injury and regenerationStroke Rehabilitation and Recovery

The neurons that restore walking after paralysis

Open access
Kathe, Claudia, Skinnider, Michael A., Hutson, Thomas H., Regazzi, Nicola, Gautier, Matthieu, Demesmaeker, Robin, Komi, Salif, Ceto, Steven +18 more·2022·Nature
DOI 10.1038/s41586-022-05385-7PMC PMC9668750
Open this paper in CoChat — free accountOpen PDF

Abstract

A spinal cord injury interrupts pathways from the brain and brainstem that project to the lumbar spinal cord, leading to paralysis. Here we show that spatiotemporal epidural electrical stimulation (EES) of the lumbar spinal cord 1–3 applied during neurorehabilitation 4,5 (EES REHAB ) restored walking in nine individuals with chronic spinal cord injury. This recovery involved a reduction in neuronal activity in the lumbar spinal cord of humans during walking. We hypothesized that this unexpected reduction reflects activity-dependent selection of specific neuronal subpopulations that become essential for a patient to walk after spinal cord injury. To identify these putative neurons, we modelled the technological and therapeutic features underlying EES REHAB in mice. We applied single-nucleus RNA sequencing 6–9 and spatial transcriptomics 10,11 to the spinal cords of these mice to chart a spatially resolved molecular atlas of recovery from paralysis. We then employed cell type 12,13 and spatial prioritization to identify the neurons involved in the recovery of walking. A single population of excitatory interneurons nested within intermediate laminae emerged. Although these neurons are not required for walking before spinal cord injury, we demonstrate that they are essential for the recovery of walking with EES following spinal cord injury. Augmenting the activity of these neurons phenocopied the recovery of walking enabled by EES REHAB , whereas ablating them prevented the recovery of walking that occurs spontaneously after moderate spinal cord injury. We thus identified a recovery-organizing neuronal subpopulation that is necessary and sufficient to regain walking after paralysis. Moreover, our methodology establishes a framework for using molecular cartography to identify the neurons that produce complex behaviours.

AI snapshot

Written from the paper’s full text.

TL;DR

EESREHAB restored walking in nine people with chronic spinal cord injury and unexpectedly reduced lumbar spinal cord neuronal activity during walking. Using a mouse model, single-nucleus and spatial transcriptomics, the authors identified SCVsx2::Hoxa10 excitatory interneurons as necessary and sufficient for recovery of walking after paralysis.

Key findings

  • In nine individuals with chronic SCI, EESREHAB restored walking; walking-related lumbar FDG-PET metabolic activity decreased (mixed-effects model: t = −3.2, P = 0.002), lower-limb motor scores increased (paired t-test: t = 3.7, P = 0.0063), and 6-min walk distance improved (paired t-test: t = 3.5, P = 0.0076).
  • Mice with severe mid-thoracic contusion and EESREHAB recovered walking that persisted with EES off; cFosON neurons during walking were reduced after EESREHAB versus SCI (independent t-test: t = −5.7, P = 0.001).
  • snRNA-seq profiled 82,093 nuclei and 20,990 neurons, identifying 36 neuron subpopulations; spatial transcriptomics yielded 61 sections and 22,127 barcodes. Augur and Magellan prioritized SCVsx2::Hoxa10 excitatory interneurons in intermediate laminae across EESREHAB features.
  • SCVsx2::Hoxa10 neurons were necessary and sufficient for recovery: optogenetic inactivation suppressed EES-enabled walking (P = 0.0023), chemogenetic silencing suppressed walking (t = −21.3, P = 0.0002), activation phenocopied recovery (t = 5.3, P = 0.0013), chronic silencing prevented EESREHAB recovery (t = −3.5, P = 0.008), and ablation prevented spontaneous recovery after lateral hemisection (t = 5.9, P = 0.0004).

Methods

  • Human study: first-in-human STIMO trial (NCT02936453); nine participants with chronic SCI received implanted paddle-lead EES plus 5 months of EESREHAB 4–5 times per week; outcomes included ISNCSCI, FDG-PET/CT, 6-min walk test, 10-m walk test, and EMG.
  • Mouse model: mid-thoracic contusion (95 kDyn) or lateral hemisection; EESREHAB for 4 weeks with robotic body-weight support, EES, and optogenetic motor cortex stimulation; readouts included kinematics, cFos, trans-synaptic tracing, RNAscope, electrophysiology, optogenetics, chemogenetics, and diphtheria toxin ablation.
  • Molecular and computational analysis: 10x Genomics snRNA-seq and Visium spatial transcriptomics; clustering/integration, RNA velocity, RCTD deconvolution, GLMM differential expression, Augur cell-type prioritization, Magellan spatial prioritization, and PCA-based gait analysis.

Limitations

  • Stated in the paper: low immediate early gene expression in snRNA-seq impeded single-gene marker analysis; acute perturbation comparisons used RNA velocity because transcriptional output may not fully reflect perturbation impact; spatial deconvolution showed minor discrepancies attributed to large spatial barcodes, snRNA-seq depth, and transcriptional similarity among ventral neuronal subpopulations.
  • Evident from the text: human evidence comes from a single-arm feasibility trial of nine participants, with no randomized control group described; mouse findings rely on contusion and hemisection models plus transgenic manipulations, so generalizability to other SCI severities or types is not established here.
  • The paper does not include a formal limitations section; the above are either stated in Methods/Discussion or evident from the study design.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1038/s41586-022-05385-7

Cites

86 of 86 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

0 of 51 cited sources checked · 0 supported · 0 flagged

  • Findingown data

    The low expression of immediate early genes such as cFos in snRNA-seq data impeded analysis.

    “However, the low expression of immediate early genes such as cFos in snRNA-seq data impeded this analysis (Extended Data Fig. 8a).”
    Quote in the paperSubstantial claim
  • Findingown data

    EESREHAB induced a pronounced reduction in the number of cFosON neurons in mice compared with mice that did not undergo EESREHAB.

    “We found a pronounced reduction in the number of cFosON neurons in mice that had undergone EESREHAB compared with mice that did not undergo EESREHAB (Fig 1g,i and Extended Data Fig. 2f,g).”
    Quote in the paperSubstantial claim
  • Findingown data

    EESREHAB protocol restored walking in all the tested mice.

    “We incorporated all these developments into an EESREHAB protocol that restored walking in all the tested mice (Fig. 1h, Extended Data Fig. 2e and Supplementary Video 2).”
    Quote in the paperSubstantial claim
  • Findingown data

    This recovery persisted when EES was turned off.

    “This recovery persisted when EES was turned off (Extended Data Fig. 2e).”
    Quote in the paperSubstantial claim
  • Findingown data

    These protocols increased the range of stimulation amplitudes over which stepping could be improved.

    “These protocols increased the range of stimulation amplitudes over which stepping could be improved (Extended Data Fig. 2c).”
    Quote in the paperSubstantial claim
  • May combine two claims. 15
  • Classified as probably not a substantial claim. 37
  • The quote only partly states this claim. 1

  • May combine two claims.

    Findingcitation

    Virus-mediated neuronal tract-tracing combined with CLARITY-optimized light-sheet microscopy revealed complete interruption of corticospinal tract fibres and pronounced depletion of glutamatergic reticulospinal fibres below the injury.

    “Virus-mediated neuronal tract-tracing combined with CLARITY-optimized light-sheet microscopy23 revealed the complete interruption of corticospinal tract fibres and pronounced depletion of glutamatergic reticulospinal fibres below the injury (Fig. 1e and Extended Data Fig. 2a).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [23] Tomer, R., Ye, L., Hsueh, B. & Deisseroth, K. Advanced CLARITY for rapid and high-resolution imaging of intact tissues. Nat. Protoc. 9, 1682–1697 (2014). source

      Not checked in the free run.

  • May combine two claims.

    Findingown data

    Magellan circumscribed the walking-associated perturbation response to intermediate laminas, which coincided with the location of SCVsx2::Hoxa10 neurons, and to ventral laminas in which neurons producing motor patterns reside.

    “Within the spinal cord, Magellan circumscribed the walking-associated perturbation response to intermediate laminas, which coincided with the location of SCVsx2::Hoxa10 neurons, and to ventral laminas in which neurons producing motor patterns reside (Fig. 3c and Extended Data Fig. 10h).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Weight-bearing capacities improved considerably over time, enabling participants to walk outdoors with EES and an assistive device.

    “Weight-bearing capacities improved considerably over time (Extended Data Fig. 1e), which enabled the participants to walk outdoors with EESON and an assistive device for stability (Supplementary Video 1).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    High-quality transcriptomes were obtained from 82,093 nuclei that were evenly represented across 24 mice from all eight conditions.

    “We obtained high-quality transcriptomes from 82,093 nuclei that were evenly represented across 24 mice from all eight conditions (Extended Data Fig. 3a–g).”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    61 high-quality sections were sequenced to a median depth of 16,384 UMIs per barcode.

    “We sequenced 61 high-quality sections to a median depth of 16,384 UMIs per barcode (Extended Data Fig. 5a–n).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    SCVsx2::Hoxa10 neurons receive direct synaptic projections from large-diameter afferents of parvalbumin-expressing neurons located in dorsal root ganglia (PVON) and from neurons located in the vGi.

    “Monosynaptically restricted trans-synaptic tracing revealed that SCVsx2::Hoxa10 neurons receive direct synaptic projections from large-diameter afferents of parvalbumin-expressing neurons located in dorsal root ganglia (PVON) and from neurons located in the vGi (Fig. 3d and Extended Data Fig. 12a).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Activating motor cortex neurons during EES induced an immediate increase in step height that scaled up with laser intensity.

    “Here, we found that activating motor cortex neurons during EES induced an immediate increase in step height that scaled up with laser intensity (Extended Data Fig. 2d).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    This prevention of recovery coincided with an expected retraction of projections from SCVsx2::Hoxa10 neurons, combined with the suppression of the increase in the density of reticulospinal and large-diameter afferent projections onto SCVsx2::Hoxa10 neurons.

    “This prevention of recovery coincided with an expected retraction of projections from SCVsx2::Hoxa10 neurons, combined with the suppression of the increase in the density of reticulospinal and large-diameter afferent projections onto SCVsx2::Hoxa10 neurons (Extended Data Fig. 15f).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingcitation

    SCI led to the development of aberrant long-latency responses that have been linked to poor walking performance in rodents and humans.

    “We found that SCI led to the development of aberrant long-latency responses that have been linked to poor walking performance in rodents and humans39.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [39] Beauparlant, J. et al. Undirected compensatory plasticity contributes to neuronal dysfunction after severe spinal cord injury. Brain 136, 3347–3361 (2013). source

      Not checked in the free run.

  • May combine two claims.

    Findingown data

    SCVsx2::Hoxa10 neurons exclusively project to the ventral spinal cord, where they establish dense synaptic appositions onto 52% of glutamatergic (GluTON), 77% of GABAergic (GABAON) and 56% of cholinergic (ChATON) neurons located in the ventral spinal cord.

    “We found that SCVsx2::Hoxa10 neurons exclusively project to the ventral spinal cord, where they establish dense synaptic appositions onto 52% of glutamatergic (GluTON), 77% of GABAergic (GABAON) and 56% of cholinergic (ChATON) neurons located in the ventral spinal cord (Fig. 3d and Extended Data Fig. 12c).”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim.

    Premisecitation

    Reticulospinal neurons from the vGi mediate the volitional modulation of walking during EES.

    “We also know that reticulospinal neurons from the vGi mediate the volitional modulation of walking during EES28.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [28] Asboth, L. et al. Cortico–reticulo–spinal circuit reorganization enables functional recovery after severe spinal cord contusion. Nat. Neurosci. 21, 576–588 (2018). source

      Not checked in the free run.

  • May combine two claims.

    Interpretationown data

    SCVsx2::Hoxa10 neurons are necessary and sufficient to regain walking after paralysis.

    “We thus identified a recovery-organizing neuronal subpopulation that is necessary and sufficient to regain walking after paralysis.”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim.

    Premisecitation

    The brain broadcasts commands through descending pathways that cascade from the brainstem to activate lumbar spinal cord neurons.

    “To walk, the brain broadcasts commands through descending pathways that cascade from the brainstem to activate these neurons15,16.”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [15] Courtine, G. & Sofroniew, M. V. Spinal cord repair: advances in biology and technology. Nat. Med. 25, 898–908 (2019). source

      Not checked in the free run.

    • cites [16] Arber, S. & Costa, R. M. Connecting neuronal circuits for movement. Science 360, 1403–1404 (2018). source

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Lumbar spinal cord neurons are not directly damaged by SCI but become nonfunctional due to depletion of essential supraspinal commands.

    “Whereas the neurons located in the lumbar spinal cord are not directly damaged by the injury, the depletion of essential supraspinal commands renders them nonfunctional4.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [4] Courtine, G. et al. Transformation of nonfunctional spinal circuits into functional states after the loss of brain input. Nat. Neurosci. 12, 1333–1342 (2009). source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductown data

    The study was approved by the Swiss ethical authorities and conducted in accordance with the Declaration of Helsinki.

    “This study was approved by the Swiss ethical authorities (Swissethics protocol number 04/2014 ProjectID: PB_2016-00886, Swissmedic protocol 2016-MD-0002) and was conducted in accordance with the Declaration of Helsinki.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Study design and conductreasoning

    Neurons with a post-stimulus onset firing rate increase of P value less than 0.001 and response jitter (standard deviation of latency) less than 2 ms were considered to be directly activated and therefore SCVsx2::Hoxa10 neurons.

    “Those neurons with a post-stimulus onset firing rate increase of P value less than 0.001 and response jitter (standard deviation of latency) less than 2 ms were considered to be directly activated and therefore SCVsx2::Hoxa10 neurons”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    Low-quality cells were filtered by removing cells expressing less than 200 genes or with more than 5% mitochondrial reads.

    “Low-quality cells were filtered by removing cells expressing less than 200 genes or with more than 5% mitochondrial reads.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationreasoning

    This reorganization may contribute to the overall decrease in the number of transcriptionally active neurons during walking in response to EESREHAB.

    “This reorganization may contribute to the overall decrease in the number of transcriptionally active neurons during walking in response to EESREHAB.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductown data

    Optimal placing of intramuscular electrodes was confirmed by electrical stimulation.

    “To confirm optimal placing, the wires were electrically stimulated resulting in a muscle.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    The fabrication of the micro-LED array was based on a previously validated technological design40 that we adapted to incorporate electrodes to deliver EES.

    “The fabrication of the micro-LED array was based on a previously validated technological design40 that we adapted to incorporate electrodes to deliver EES, as illustrated in Extended Data Fig. 15a.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [40] Kathe, C. et al. Wireless closed-loop optogenetics across the entire dorsoventral spinal cord in mice. Nat. Biotechnol. 40, 198–209 (2022). source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    A new paddle lead (ONWARD Medical) was specifically developed to target the dorsal roots involved in the control of trunk and leg movements.

    “The last three participants were implanted with a new paddle lead that was specifically developed to target the dorsal roots involved in the control of trunk and leg movements18 (ONWARD Medical).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [18] Rowald, A. et al. Activity-dependent spinal cord neuromodulation rapidly restores trunk and leg motor functions after complete paralysis. Nat. Med. 28, 260–271 (2022). source

      Not checked in the free run.

  • Classified as probably not a substantial claim.

    Study design and conductreasoning

    SCVsx2::Hoxa10 neurons that displayed early responses to electrical stimulation (EES or reticular formation), indicative of putative monosynaptic inputs, were identified using the same firing rate test in addition to a jitter of less than 1.2 ms and minimum spike probability in the first 6 ms after stimulation greater than 20%.

    “SCVsx2::Hoxa10 neurons that displayed early responses to electrical stimulation (EES or reticular formation), indicative of putative monosynaptic inputs, were identified using the same firing rate test in addition to a jitter of less than 1.2 ms and minimum spike probability in the first 6 ms after stimulation greater than 20%.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductown data

    Due to the size and variability of the artefacts, periods containing residual stimulation artefacts were not sorted.

    “Due to the size and variability of the artefacts, periods containing residual stimulation artefacts were not sorted (–1.0 to +1.5 ms and +2.5 ms around stimulus onset for EES and reticular formation stimulation onset, respectively).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductown data

    For gene-expression samples, tissue was permeabilized for 12 min, selected as the optimal time based on tissue-optimization time-course experiments.

    “For gene-expression samples, tissue was permeabilized for 12 min, which was selected as the optimal time based on tissue-optimization time-course experiments.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    FDG-PET/CT imaging after walking was previously used to study the effect of spinal cord stimulation at the cervical level.

    “This technique was previously used to study the effect of spinal cord stimulation at the cervical level52.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [52] Clavo, B. et al. Modification of glucose metabolism in radiation-induced brain injury areas using cervical spinal cord stimulation. Acta Neurochir. 151, 1419–1425 (2009). source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    Behavioural assays were replicated 3 to 10 times depending on the experiments and averaged per animal.

    “Behavioural assays were replicated 3 to 10 times depending on the experiments and averaged per animal.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductown data

    Augur was applied at various clustering resolutions to evaluate the robustness of cell type prioritizations to the resolution at which neuronal subpopulations were defined.

    “To evaluate the robustness of cell type prioritizations to the resolution at which neuronal subpopulations were defined in the snRNA-seq data, we applied Augur at various clustering resolutions, and visualized the resulting cell type prioritizations both on a hierarchical clustering tree81 of neuron subpopulations and as a progression of UMAPs.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [81] Zappia, L. & Oshlack, A. Clustering trees: a visualization for evaluating clusterings at multiple resolutions. GigaScience 7, giy083 (2018). source

      Not checked in the free run.

    • The authors state this as an assumption: The key assumption underlying Augur is that cell types undergoing a profound response to a perturbation should become more separable, within the highly multidimensional space of gene expression, than less affected cell types.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductown data

    Only two participants (ST006, MB007) were evaluated with 5% body weight support for safety during the ten-metre walk test.

    “Only two participants were evaluated with 5% body weight support for safety (ST006, MB007).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductcitation

    Tangram was used to embed single-nucleus transcriptomes within the common coordinate system of the mouse spinal cord to corroborate the spatial prioritizations assigned by Magellan.

    “To corroborate the spatial prioritizations assigned by Magellan, we leveraged Tangram36 to embed single-nucleus transcriptomes within the common coordinate system of the mouse spinal cord.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [36] Biancalani, T. et al. Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram. Nat. Methods 18, 1352–1362 (2021). source

      Not checked in the free run.

    • The authors state this as an assumption: An ideal spatial prioritization method would be capable of detecting both sharp borders and smooth gradients, and would be capable of resolving quantitative differences between different aspects of a multifaceted perturbation response.

  • May combine two claims. The quote only partly states this claim.

    Interpretationown data

    This recovery demonstrates the therapeutic efficacy of EESREHAB in a large number of people who exhibited neurological deficits spanning the entire range of severities after SCI, thus opening a path for the clinical deployment of this therapy.

    “This recovery demonstrates the therapeutic efficacy of EESREHAB in a large number of people who exhibited neurological deficits spanning the entire range of severities after SCI, thus opening a path for the clinical deployment of this therapy.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    Representative experiments such as histological micrographs were repeated in a minimum of four mice.

    “Representative experiments such as histological micrographs were repeated in a minimum of four mice.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductreasoning

    To mitigate artefacts introduced by the registration procedure, the x-axis coordinate of each barcode was replaced with its absolute value.

    “In view of the left-right symmetry of the spinal cord, we replaced the coordinate of each barcode on the x-axis with its absolute value in order to mitigate artefacts introduced by the registration procedure.”
    Quote in the paperNot a substantial claim
    • The authors state this as an assumption: An ideal spatial prioritization method would be capable of detecting both sharp borders and smooth gradients, and would be capable of resolving quantitative differences between different aspects of a multifaceted perturbation response.

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Interpretationnone given

    The short-latency muscle responses to single-pulse dorsal spinal cord stimulation are likely monosynaptic.

    “short-latency responses (likely to be monosynaptic responses)”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationnone given

    The long-latency muscle responses to single-pulse dorsal spinal cord stimulation are likely polysynaptic.

    “long-latency responses (likely to be polysynaptic responses)”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Study design and conductnone given

    All participants provided written informed consent prior to their participation.

    “All participants provided written informed consent prior to their participation.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductown data

    Magellan cross-validation was repeated 100 times for each barcode in simulated data to estimate the number of repeated cross-validation folds required to obtain a robust estimate.

    “First, cross-validation was repeated 100 times for each barcode in order to estimate the number of repeated cross-validation folds required to obtain a robust estimate, which was achieved by comparing the AUC assigned to each barcode in the first 50 samples to the second 50 samples.”
    Quote in the paperNot a substantial claim
    • The authors state this as an assumption: An ideal spatial prioritization method would be capable of detecting both sharp borders and smooth gradients, and would be capable of resolving quantitative differences between different aspects of a multifaceted perturbation response.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductown data

    In the authors' dataset, Magellan was applied to four key comparisons between four experimental conditions, excluding white matter barcodes and two low-quality sections.

    “To enable spatial prioritization in our own dataset, we applied Magellan to four key comparisons between four experimental conditions. Barcodes from the white matter were excluded, and two low-quality sections excluded (Slide1_4_B1_M3_6wNT, Slide1_2_B3_M10_6wNT).”
    Quote in the paperNot a substantial claim
    • The authors state this as an assumption: An ideal spatial prioritization method would be capable of detecting both sharp borders and smooth gradients, and would be capable of resolving quantitative differences between different aspects of a multifaceted perturbation response.

  • Classified as probably not a substantial claim.

    Study design and conductnone given

    Image analysis parameters were kept constant among all samples.

    “Image analysis parameters were kept constant among all samples.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    Experiments involving chronic chemogenetic activation or silencing of SCVsx2::Hoxa10 neurons were performed two days after CNO was removed from the drinking water.

    “Experiments that involved chronic chemogenetic activation or silencing of SCVsx2::Hoxa10 neurons were performed two days after the CNO was removed from the drinking water.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    Low-quality barcodes were filtered by removing cells expressing less than 5,000 UMIs.

    “Low-quality barcodes were filtered by removing cells expressing less than 5,000 UMIs.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductcitation

    Prior to clustering analysis, batch effect correction and data integration were performed across the two different experimental conditions.

    “Prior to clustering analysis, we first performed batch effect correction and data integration across the two different experimental conditions as previously described30.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [30] Stuart, T. et al. Comprehensive integration of single-cell data. Cell 177, 1888–1902.e21 (2019). source

      Not checked in the free run.

  • Classified as probably not a substantial claim.

    Study design and conductnone given

    Final behavioural assessments of mice with contusion SCI were performed with EESOFF and repeated with EESON in the absence of 5-HT agonists.

    “All the final behavioural assessments of mice with contusion SCI were performed with EESOFF and repeated with EESON, but in the absence of 5-HT agonists.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    Sorting results were manually curated using Phy.

    “Sorting results were manually curated using Phy (https://github.com/cortex-lab/phy).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    The ISNCSCI is a comprehensive clinician-administered neurological examination of residual sensory and motor function that quantifies SCI severity.

    “Neurological status was assessed based on the ISNCSCI54, a comprehensive clinician-administered neurological examination of residual sensory and motor function quantifying SCI severity.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [54] Kirshblum, S. C. et al. International standards for neurological classification of spinal cord injury (revised 2011). J. Spinal Cord Med. 34, 535–546 (2011). source

      Not checked in the free run.

  • Classified as probably not a substantial claim. May combine two claims.

    Study design and conductnone given

    Single unit clusters were selected for analysis based on their biphasic waveforms and template amplitudes above 50 μV, as well as strong refractory period dips in their spike autocorrelograms.

    “Single unit clusters were selected for analysis based on their biphasic waveforms and template amplitudes above 50 µV, as well as strong refractory period dips in their spike autocorrelograms.”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim.

    Study design and conductreasoning

    For five acute comparisons, Augur was applied to a matrix of RNA velocity because the total transcriptional output of each cell may not yet fully reflect the impact of the perturbation at the time of snRNA-seq.

    “Five of these six comparisons involved acute perturbations on the timescale of transcription (minutes to hours), raising a risk that the total transcriptional output of each cell may not yet fully reflect the impact of the perturbation at the time of snRNA-seq12. Consequently, for these five comparisons, we applied Augur to a matrix of RNA velocity75, as previously described12,13,75.”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [12] Skinnider, M. A. et al. Cell type prioritization in single-cell data. Nat. Biotechnol. 39, 30–34 (2021). source

      Not checked in the free run.

    • cites [75] La Manno, G. et al. RNA velocity of single cells. Nature 560, 494–498 (2018). source

      Not checked in the free run.

    • The authors state this as an assumption: The key assumption underlying Augur is that cell types undergoing a profound response to a perturbation should become more separable, within the highly multidimensional space of gene expression, than less affected cell types.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Specific subpopulations of V2a neurons in the brainstem, cervical spinal cord and lumbar spinal cord have been implicated in different aspects of motor control.

    “Specific subpopulations of V2a neurons in the brainstem, cervical spinal cord and lumbar spinal cord have been implicated in different aspects of motor control35,41–45.”
    Quote in the paperNot a substantial claim0 of 6 sources checked
    • cites [35] Hayashi, M. et al. Graded arrays of spinal and supraspinal V2a interneuron subtypes underlie forelimb and hindlimb motor control. Neuron 97, 869–884 (2018). source

      Not checked in the free run.

    • cites [41] Zhong, G. et al. Electrophysiological characterization of V2a interneurons and their locomotor-related activity in the neonatal mouse spinal cord. J. Neurosci. 30, 170–182 (2010). source

      Not checked in the free run.

    • cites [42] Dougherty, K. J. & Kiehn, O. Functional organization of V2a-related locomotor circuits in the rodent spinal cord. Ann. NY Acad. Sci. 1198, 85–93 (2010). source

      Not checked in the free run.

    • cites [43] Dougherty, K. J. & Kiehn, O. Firing and cellular properties of V2a interneurons in the rodent spinal cord. J. Neurosci. 30, 24–37 (2010). source

      Not checked in the free run.

    • cites [44] Zholudeva, L. V. et al. Spinal interneurons as gatekeepers to neuroplasticity after injury or disease. J. Neurosci. 41, 845–854 (2021). source

      Not checked in the free run.

    • cites [45] Azim, E., Jiang, J., Alstermark, B. & Jessell, T. M. Skilled reaching relies on a V2a propriospinal internal copy circuit. Nature 508, 357–363 (2014). source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S4 (based).

    Study design and conductnone given

    All floxed AAV vectors used in the present study showed transgene expression only upon Cre-mediated recombination.

    “All floxed AAV vectors used in the present study showed transgene expression only upon Cre-mediated recombination.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationown data

    These neurons are not critical for walking in the absence of SCI, but they become recovery-organizing cells after SCI.

    “Whereas these neurons are not critical for walking in the absence of SCI, they become recovery-organizing cells after SCI.”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim.

    Premisecitation

    Computer simulations were performed on a previously validated spiking neural network model reproducing proprioceptive feedback circuits associated with a pair of antagonist muscles in the lumbar spinal cord of rodents.

    “We performed computer simulations on a previously validated spiking neural network model37,38, reproducing the proprioceptive feedback circuits associated with a pair of antagonist muscles in the lumbar spinal cord of rodents.”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [37] Capogrosso, M. et al. A computational model for epidural electrical stimulation of spinal sensorimotor circuits. J. Neurosci. 33, 19326–19340 (2013). source

      Not checked in the free run.

    • cites [38] Formento, E. et al. Electrical spinal cord stimulation must preserve proprioception to enable locomotion in humans with spinal cord injury. Nat. Neurosci. 21, 1728–1741 (2018). source

      Not checked in the free run.

50 of 50

  • The paper relies on this without support.

    The biological principles through which EESREHAB engages and remodels the lumbar spinal cord to restore walking remain unknown.

    “The biological principles through which EESREHAB engages and remodels the lumbar spinal cord to restore walking remain unknown.”

  • The paper relies on this without support.

    The severe mid-thoracic contusion replicates the most common pathophysiology of human SCIs.

    “Mice received a severe mid-thoracic contusion that replicates the most common pathophysiology of human SCIs (Fig. 1e and Extended Data Fig. 2a).”

  • The paper relies on this without support.

    The implanted medical devices used in the participants were not approved for MRI.

    “Since the participants were equipped with implanted medical devices that were not approved for MRI, we measured the spinal cord glucose consumption as a surrogate of neuronal activity during walking using non-invasive FDG-PET–computed tomography (PET/CT) imaging after walking.”

  • The paper relies on this without support.

    The Specify 5-6-5 paddle lead was originally designed to target the dorsal column in order to alleviate pain.

    “The first 6 participants were implanted with the Specify 5-6-5 paddle lead, which was originally designed to target the dorsal column in order to alleviate pain (Specify 5-6-5, Medtronic).”

  • The paper relies on this without support.

    Spinal cord glucose consumption measured by FDG-PET/CT is a surrogate of neuronal activity during walking.

    “Since the participants were equipped with implanted medical devices that were not approved for MRI, we measured the spinal cord glucose consumption as a surrogate of neuronal activity during walking using non-invasive FDG-PET–computed tomography (PET/CT) imaging after walking.”

  • The authors state this as an assumption.

    The key assumption underlying Augur is that cell types undergoing a profound response to a perturbation should become more separable, within the highly multidimensional space of gene expression, than less affected cell types.

    “The key assumption underlying Augur is that cell types undergoing a profound response to a perturbation should become more separable, within the highly multidimensional space of gene expression, than less affected cell types.”

  • The authors state this as an assumption.

    An ideal spatial prioritization method would be capable of detecting both sharp borders and smooth gradients, and would be capable of resolving quantitative differences between different aspects of a multifaceted perturbation response.

    “Our premise was that an ideal method would be capable of detecting both sharp borders and smooth gradients, and would be capable of resolving quantitative differences between different aspects of a multifaceted perturbation response.”
7 of 7

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • The physiological principles underlying targeted epidural electrical stimulation of the spinal cord have now been validated in nine out of nine treated individuals with incomplete and complete injuries.

    “First, the physiological principles underlying targeted epidural electrical stimulation of the spinal cord have now been validated in nine out nine treated individuals with incomplete4 and complete5 injuries6.”

    From Walking naturally after spinal cord injury using a brain–spine interface (2023) · cites this paper as [6]

  • The delivery of epidural electrical stimulation over the lumbar spinal cord has enabled many individuals with spinal cord injury to regain adaptive control over the activity of otherwise paralysed muscles.

    “The delivery of epidural electrical stimulation over the lumbar spinal cord has enabled many individuals with spinal cord injury to regain adaptive control over the activity of otherwise paralysed muscles.”

    From Walking naturally after spinal cord injury using a brain–spine interface (2023) · cites this paper as [6]

  • This recovery has been documented in various independent studies, including in participants with complete sensorimotor paralysis.

    “This recovery has been documented in various independent studies, including in participants with complete sensorimotor paralysis5,6,30–34.”

    From Walking naturally after spinal cord injury using a brain–spine interface (2023) · cites this paper as [6]

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

Each contradiction between two passages listed here was confirmed by an independent check.

  • ChrimsonR photostimulation is described as both silencing and activating neurons

    Major

    The Fig. 4 caption says light silenced neurons expressing ChrimsonR, while the recording methods classify an increase in firing after light stimulation of ChrimsonR-expressing neurons as direct activation. The stated direction of the manipulation therefore conflicts across the paper.

  • Spatial barcode count conflicts with Methods

    Minor

    The main text says 22,127 barcodes were registered across 61 sections, whereas Methods reports 9,755 barcodes across those sections. Methods identifies 22,127 as the number of genes, not barcodes.

2 of 2

Cites

Flagged first, then by citations

Research works printed but not linked: 1

  1. Sherrington, C. S. The Integrative Action of the Nervous System (Yale Univ. Press, 1906).

Cited by

Sorted by citations

Related

Authors
Kathe, C., Skinnider, M. A., Hutson, T. H., Regazzi, N., Gautier, M., Demesmaeker, R., Komi, S., Ceto, S., James, N. D., Cho, N., Baud, L., Galan, K., Matson, K. J. E., Rowald, A., Kim, K., Wang, R., Minassian, K., Prior, J. O., Asboth, L., Barraud, Q., Lacour, S. P., Levine, A. J., Wagner, F., Bloch, J., Squair, J. W., & Courtine, G.
Affiliations
  • Centre Hospitalier Universitaire Vaudois (CH)
  • University of British Columbia (CA)
  • National Institute of Neurological Disorders and Stroke (US)
  • École Polytechnique Fédérale de Lausanne (CH)
  • Medical University of Vienna (AT)
Corresponding author
  • Bloch, Jocelyne
  • Squair, Jordan W.
  • Courtine, Grégoire
ORCID
Venue
Nature
Publisher
Springer Science and Business Media LLC
Published
2022-11-09
Volume
611
Issue
7936
Pages
540-547
ISSN
  • 0028-0836 (ISSN-L)
  • 1476-4687
DOI
10.1038/s41586-022-05385-7
PMC
PMC9668750
OpenAlex
W4308620605
Semantic Scholar
358dd113fd790ef4882c254581453ae3be8bc450
Cited by
304
References
86
Citations by year
2026: 66 · 2025: 99 · 2024: 70 · 2023: 64 · 2022: 5
FWCI
40.30
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion, cc-by-nc-nd)
  • IRIS (submittedVersion, cc-by)
  • SERVAL (Université de Lausanne) (submittedVersion, cc-by)
Funders
  • National Science Foundation (51NF40_185543)
  • Fondation Bertarelli
  • Rolex
  • International Foundation for Research in Paraplegia
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (192558, 185543, 205563)
  • Innosuisse - Schweizerische Agentur für Innovationsförderung
  • Fondation Defitech
  • H2020 European Research Council (682999)
  • Eurostars
Topics
  • Health Sciences › Medicine › Pathology and Forensic Medicine › Spinal Cord Injury Research
  • Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Nerve injury and regeneration
  • Health Sciences › Medicine › Rehabilitation › Stroke Rehabilitation and Recovery
Keywords
spinal cord injury, epidural stimulation, walking recovery, lumbar spinal cord, excitatory interneurons, neurorehabilitation, single-nucleus RNA sequencing, spatial transcriptomics
MeSH terms
Neurological Rehabilitation, Animals, Electric Stimulation, Humans, Lumbosacral Region, Neurons, Paralysis, Spinal Cord, Spinal Cord Injuries, Walking, Sequence Analysis, RNA, Gene Expression Profiling, Mice

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-08.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-08.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review