Evidence map›Paper›PMID 37848024›Full record

ArticleNeuron2023

Deep scRNA sequencing reveals a broadly applicable Regeneration Classifier and implicates antioxidant response in corticospinal axon regeneration.

Hugo J Kim, Junmi M Saikia, Katlyn Marie A Monte, Eunmi Ha, Daniel Romaus-Sanjurjo, Joshua J Sanchez, Andrea X Moore, Marc Hernaiz-Llorens, Carmine L Chavez-Martinez, Chimuanya K Agba and 5 more

Open access · hybridAbstract read
In one paragraph

Article in Neuron, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.

0numbers the graph read from it
0cells of the map it votes in
20citing papers in PubMed
3.3field-weighted citation impact, top 7% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

20 citing papers in PubMed, 22 citations in OpenAlex.

  1. Article
  2. Article
  3. Transcriptomics Insights into Spinal Cord Injury for Therapy Development.International journal of molecular sciences · 2026
    Review
  4. Article
  5. Article
  6. Review
  7. Article
  8. Cutting-edge technologies in neural regeneration.Cell regeneration (London, England) · 2025
    Review
  9. Review
  10. Article
  11. Article
  12. Review
  13. Article
  14. Review
  15. Lipin1 depletion coordinates neuronal signaling pathways to promote motor and sensory axon regeneration after spinal cord injury.Proceedings of the National Academy of Sciences of the United States of America · 2024
    Article
  16. Article
  17. Article
  18. Article
  19. Review
  20. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

15 authors at 1 institution in 1 country.

Hugo J KimDepartment of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA.
Junmi M SaikiaDepartment of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA; Neurosciences Graduate Program, University of California San Diego, La Jolla, CA, USA USA.
Katlyn Marie A MonteDepartment of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA.
Eunmi HaDepartment of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA.
Daniel Romaus-SanjurjoDepartment of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA.
Joshua J SanchezDepartment of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA.
Andrea X MooreDepartment of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA.
Marc Hernaiz-LlorensDepartment of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA.
Carmine L Chavez-MartinezDepartment of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA; Graduate program in Biological Sciences, University of California San Diego, La Jolla, CA, USA.
Chimuanya K AgbaDepartment of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA; Neurosciences Graduate Program, University of California San Diego, La Jolla, CA, USA USA.
Haoyue LiDepartment of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA.
Joseph ZhangDepartment of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA.
Daniel T LuskDepartment of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA.
Kayla M CervantesDepartment of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA.
Binhai ZhengDepartment of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA, USA; VA San Diego Research Service, San Diego, CA, USA. Electronic address: bizheng@health.ucsd.edu.
University of California San Diego · US

Funding

Viral ModuleP30EY012196 · NEI · HARVARD UNIVERSITY (MEDICAL SCHOOL) · PI ZHIGANG HE · 1998 to 2026
$21.3M
U of Calif, San Diego Neuroscience Microscopy ImagingP30NS047101 · NINDS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI GLEESON, JOSEPH G, ZHENG, BINHAI · 2003 to 2022
$9.0M
Training Program in Basic Clinical GeneticsT32GM008666 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI HAMILTON, BRUCE A · 1998 to 2021
$8.6M
Neurosciences Graduate Training ProgramT32NS061847 · NINDS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Brenda L Bloodgood · 2008 to 2026
$7.7M
The Role of a Pair of MAP3Ks in the Multicellular Response to Spinal Cord InjuryR01NS093055 · NINDS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI ZHENG, BINHAI · 2015 to 2024
$4.0M
Genetic analysis of myelin inhibitors and PTEN in injury-inducedCNS axon growthR01NS054734 · NINDS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI ZHENG, BINHAI · 2007 to 2015
$3.2M
UC San Diego Genetics Training ProgramT32GM145427 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI BRUCE A HAMILTON · 2022 to 2026
$2.6M
Illumina NovaSeq 6000 Sequencing SystemS10OD026929 · OD · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI JEPSEN, KRISTEN LYNN · 2019 to 2019
$600k
Harnessing Corticospinal Axon Sprouting for Functional Recovery in Chronic InjuryI01RX002483 · VA · VA SAN DIEGO HEALTHCARE SYSTEM · PI ZHENG, BINHAI · 2019 to 2023
–
NEI NIH HHS P30 EY012196NIGMS NIH HHS T32 GM008666NIGMS NIH HHS T32 GM145427NIH HHS S10 OD026929NINDS NIH HHS P30 NS047101NINDS NIH HHS R01 NS054734NINDS NIH HHS R01 NS093055NINDS NIH HHS T32 NS061847RRD VA I01 RX002483
6 · The paper itself

Abstract

Despite substantial progress in understanding the biology of axon regeneration in the CNS, our ability to promote regeneration of the clinically important corticospinal tract (CST) after spinal cord injury remains limited. To understand regenerative heterogeneity, we conducted patch-based single-cell RNA sequencing on rare regenerating CST neurons at high depth following PTEN and SOCS3 deletion. Supervised classification with Garnett gave rise to a Regeneration Classifier, which can be broadly applied to predict the regenerative potential of diverse neuronal types across developmental stages or after injury. Network analyses highlighted the importance of antioxidant response and mitochondrial biogenesis. Conditional gene deletion validated a role for NFE2L2 (or NRF2), a master regulator of antioxidant response, in CST regeneration. Our data demonstrate a universal transcriptomic signature underlying the regenerative potential of vastly different neuronal populations and illustrate that deep sequencing of only hundreds of phenotypically identified neurons has the power to advance regenerative biology.

Indexed as

AxonsSpinal Cord InjuriesAntioxidantsHumansNerve RegenerationNeuronsPyramidal TractsSingle-Cell AnalysisAntioxidantsantioxidant responseaxon regenerationCNS repaircorticospinal tractmouse geneticsNFE2L2Patch-seqRegeneration Classifiersingle-cell RNA sequencingspinal cord injury

Identifiers

PMID37848024
PMCPMC10843387
OpenAlexW4387675475

What Socratic holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.