The Injured Sciatic Nerve Atlas (iSNAT), insights into the cellular and molecular basis of neural tissue degeneration and regeneration

  1. Xiao-Feng Zhao
  2. Lucas D. Huffman
  3. Hannah Hafner
  4. Mitre Athaiya
  5. Matthew Finneran
  6. Ashley L Kalinski
  7. Rafi Kohen
  8. Corey Flynn
  9. Ryan Passino
  10. Craig N Johnson
  11. David Kohrman
  12. Riki Kawaguchi
  13. Lynda Yang
  14. Jeffery L Twiss
  15. Daniel H Geschwind
  16. Gabriel Corfas
  17. Roman J Giger  Is a corresponding author
  1. University of Michigan-Ann Arbor, United States
  2. University of Michigan Medical School, United States
  3. University of California, Los Angeles, United States
  4. University of South Carolina, United States
  5. University of Michigan, United States

Abstract

Upon trauma, the adult murine PNS displays a remarkable degree of spontaneous anatomical and functional regeneration. To explore extrinsic mechanisms of neural repair, we carried out single cell analysis of naïve mouse sciatic nerve, peripheral blood mononuclear cells, and crushed sciatic nerves at 1-day, 3-days, and 7- days following injury. During the first week, monocytes and macrophages (Mo/Mac) rapidly accumulate in the injured nerve and undergo extensive metabolic reprogramming. Proinflammatory Mo/Mac in the injured nerve show high glycolytic flux compared to Mo/Mac in blood and dominate the early injury response. They subsequently give way to inflammation resolving Mac, programmed toward oxidative phosphorylation. Nerve crush injury causes partial leakiness of the blood-nerve-barrier, proliferation of endoneurial and perineurial stromal cells, and accumulation of select serum proteins. Micro-dissection of the nerve injury site and distal nerve, followed by single-cell RNA-sequencing, identified distinct immune compartments, triggered by mechanical nerve wounding and Wallerian degeneration, respectively. This finding was independently confirmed with Sarm1-/- mice, where Wallerian degeneration is greatly delayed. Experiments with chimeric mice showed that wildtype immune cells readily enter the injury site in Sarm1-/- mice, but are sparse in the distal nerve, except for Mo. We used CellChat to explore intercellular communications in the naïve and injured PNS and report on hundreds of ligand-receptor interactions. Our longitudinal analysis represents a new resource for nerve regeneration, reveals location specific immune microenvironments, and reports on large intercellular communication networks. To facilitate mining of scRNAseq datasets, we generated the injured sciatic nerve atlas (iSNAT): https://cdb-rshiny.med.umich.edu/Giger_iSNAT/

Data availability

All scRNA-seq datasets (fastq files and Seurat objects) are available online through the Gene Expression Omnibus (GEO) database https://www.ncbi.nlm.nih.gov/geo , accession number GSE198582.All code for iSNAT is available at https://github.com/GigerLab/iSNAT

The following data sets were generated

Article and author information

Author details

  1. Xiao-Feng Zhao

    Department of Cell and Developmental Biology, University of Michigan-Ann Arbor, Ann Arbor, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7574-7163
  2. Lucas D. Huffman

    University of Michigan Medical School, Ann Arbor, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7779-086X
  3. Hannah Hafner

    University of Michigan Medical School, Ann Arbor, United States
    Competing interests
    No competing interests declared.
  4. Mitre Athaiya

    University of Michigan Medical School, Ann Arbor, United States
    Competing interests
    No competing interests declared.
  5. Matthew Finneran

    University of Michigan Medical School, Ann Arbor, United States
    Competing interests
    No competing interests declared.
  6. Ashley L Kalinski

    University of Michigan Medical School, Ann Arbor, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7611-0810
  7. Rafi Kohen

    University of Michigan Medical School, Ann Arbor, United States
    Competing interests
    No competing interests declared.
  8. Corey Flynn

    University of Michigan Medical School, Ann Arbor, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5811-7269
  9. Ryan Passino

    University of Michigan Medical School, Ann Arbor, United States
    Competing interests
    No competing interests declared.
  10. Craig N Johnson

    Department of Cell and Developmental Biology, University of Michigan-Ann Arbor, Ann Arbor, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3955-7394
  11. David Kohrman

    University of Michigan Medical School, Ann Arbor, United States
    Competing interests
    No competing interests declared.
  12. Riki Kawaguchi

    University of California, Los Angeles, Los Angeles, United States
    Competing interests
    No competing interests declared.
  13. Lynda Yang

    University of Michigan Medical School, Ann Arbor, United States
    Competing interests
    No competing interests declared.
  14. Jeffery L Twiss

    Department of Biological Sciences, University of South Carolina, Columbia, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7875-6682
  15. Daniel H Geschwind

    University of California, Los Angeles, Los Angeles, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2896-3450
  16. Gabriel Corfas

    Kresge Hearing Research Institute, Department of Otolaryngology - Head and Neck Surgery, University of Michigan, Ann Arbor, United States
    Competing interests
    Gabriel Corfas, Except for Gabriel Corfas, the authors declare no competing financial or non-financial interests. Gabriel Corfas is a scientific founder of Decibel Therapeutics; he has an equity interest in and has received compensation for consulting. The company was not involved in this study..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5412-9473
  17. Roman J Giger

    Department of Cell and Developmental Biology, University of Michigan-Ann Arbor, Ann Arbor, United States
    For correspondence
    rgiger@umich.edu
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2926-3336

Funding

Adelson Family Foundation (APNRR)

  • Jeffery L Twiss
  • Daniel H Geschwind
  • Roman J Giger

NIH Blueprint for Neuroscience Research (MH119346)

  • Roman J Giger

NIH Blueprint for Neuroscience Research (R01DC018500)

  • Gabriel Corfas

NIH Blueprint for Neuroscience Research (T32 NS07222)

  • Ashley L Kalinski

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Animal experimentation: All procedures involving mice were approved by the Institutional Animal Care and Use Committees (IACUC) of the university of Michigan (PRO 00009851) and performed in accordance with guidelines developed by the National Institutes of Health

Reviewing Editor

  1. Beth Stevens, Boston Children's Hospital, United States

Publication history

  1. Received: June 8, 2022
  2. Preprint posted: June 29, 2022 (view preprint)
  3. Accepted: November 30, 2022
  4. Accepted Manuscript published: December 14, 2022 (version 1)
  5. Version of Record published: January 9, 2023 (version 2)
  6. Version of Record updated: February 3, 2023 (version 3)

Copyright

© 2022, Zhao et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Xiao-Feng Zhao
  2. Lucas D. Huffman
  3. Hannah Hafner
  4. Mitre Athaiya
  5. Matthew Finneran
  6. Ashley L Kalinski
  7. Rafi Kohen
  8. Corey Flynn
  9. Ryan Passino
  10. Craig N Johnson
  11. David Kohrman
  12. Riki Kawaguchi
  13. Lynda Yang
  14. Jeffery L Twiss
  15. Daniel H Geschwind
  16. Gabriel Corfas
  17. Roman J Giger
(2022)
The Injured Sciatic Nerve Atlas (iSNAT), insights into the cellular and molecular basis of neural tissue degeneration and regeneration
eLife 11:e80881.
https://doi.org/10.7554/eLife.80881

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