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Single-nucleus analysis reveals human-specific oligodendrocyte polarization and conserved neuronal responses after severe traumatic brain injury.

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  1. Project Title
  2. Single-cell analysis reveals human-specific oligodendrocyte polarization and conserved neuronal responses after severe traumatic brain injury
  4. Overview:
  5. This repository contains processed data and analysis scripts for the single-cell transcriptomic study of human and mouse traumatic brain injury (TBI). It includes CCA-based data integration, differential expression analysis, pseudotime trajectory inference, co-expression network construction, edema correlation analysis, and GWAS enrichment. All analyses were performed using R version 4.0.5 or 4.2.3, except RNA velocity analysis, which was conducted using Python 3.8 (scVelo)
  7. Folder Description:
  9. TBI atlas human/ and TBI atlas mouse.txt:
  10. Contain human and mouse datasets respectively, including CCA integration, cell type annotation, differential gene analysis across TBI stages, and correlation with brain edema.
  12. microglia.txt:
  13. Includes human- and mouse-specific microglia subclustering, pseudotime trajectory analyses in human and mouse microglia, CALM2-centered co-expression networks, and NicheNet-based ligand–receptor predictions.
  15. oligodendrocyte.txt:
  16. Covers human- and mouse-specific oligodendrocyte subclustering, trajectory analysis, OLIG-ABCA1 co-expression network, and edema-related gene correlations, velocity analysis in PYTHON.
  18. excitatory neuron.txt:
  19. Contains TBI module detection via WGCNA, module conservation analysis, edema correlation, and GWAS enrichment linking TBI modules to neuropsychiatric risk.
  21. R version 4.0.5: Seurat, hdWGCNA, fgsea, monocle, NicheNet, etc.
  23. R version 4.2.3: clusterprofiler, fgsea, etc
  25. Python 3.8: scvelo, scanpy, cellrank, anndata, pandas, etc.

README.txt, under CC-BY-4.0 · at the source

Overview

Authors: Jiatong Ji1, Honglu Chao2, Chengzhi Chen2, Xinyue Wang2, Wenqian Shi2, Jun Liao3, Hai Qian4, Hao Shi2, Jingming Hu2, Yangfan Ye2, Yiming Tu2, Xiao Xu2, Zheng Li2, Zhen Yue2, Wei Yan2, Xunning Hong5, Huibo Wang2,6, Huimei Chen7,8,9, Enrico Petretto1,7,8,9, Jing Ji2,6,10
ORCID iDs: Jun Liao, Huimei Chen, Jing Ji
  1. Institute for Big Data and Artificial Intelligence in Medicine, School of Science, China Pharmaceutical University (CPU),Nanjing, Jiangsu China
  2. Department of Neurosurgery, the First Affiliated Hospital of Nanjing Medical University,Nanjing, Jiangsu China
  3. Big Data Center, School of Science, China Pharmaceutical University (CPU),Nanjing, Jiangsu China
  4. Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University (CPU),Nanjing, Jiangsu China
  5. Department of Radiology, The First Affiliated Hospital of Nanjing Medical University,Nanjing, Jiangsu China
  6. Institute for Brain Tumors, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University,Nanjing, China
  7. Centre for Biomedical Data Science (CBDS), Duke-NUS Medical School,Singapore, Republic of Singapore
  8. Duke-NUS AI + Medical Sciences Initiative (DAISI), Duke-NUS Medical School,Singapore, Republic of Singapore
  9. Cardiovascular and Metabolic Disorders (CVMD) Programme, Duke-NUS Medical School,Singapore, Republic of Singapore
  10. Department of Neurosurgery, The Affiliated Kizilsu Kirghiz Autonomous Prefecture People’s Hospital of Nanjing Medical University,Artux, Xinjiang China
Institutions: China Pharmaceutical University (China); Jiangsu Province Hospital (China); Nanjing Medical University (China); Duke-NUS Medical School (Singapore)
Journal: Nature communications, volume 17, issue 1, article 6910
Dates: received 11 August 2025; accepted 28 April 2026; published online 27 May 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1038/s41467-026-73036-w · PMID 42203771 · PMCID PMC13388710 · OpenAlex W7162524630
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: genetics / omics (modality), human (organism), mouse (organism), traumatic brain injury (population), cellular / molecular (subfield)
Methods: Statistics, Smoothing, state filtering, decompositions, Connectivity, Machine learning, fMRI & imaging
Keywords: Trauma, Computational biology and bioinformatics, Brain injuries, Oligodendrocyte
MeSH: Brain Injuries, Traumatic*, Cell Nucleus*, Neurons*, Oligodendroglia*, Animals, ATP Binding Cassette Transporter 1, Cell Polarity, Disease Models, Animal, HMGB1 Protein, Humans, Male, Mice, Mice, Inbred C57BL, Microglia, Transcriptome (* major topic)
Topic: Neurogenesis and neuroplasticity mechanisms (Developmental Neuroscience, Neuroscience), according to OpenAlex
Funding: National Natural Science Foundation of China (National Science Foundation of China) (81972153, 81901955, 82120108018, 82303835)
Citations: not cited yet (Europe PMC); 82 references in the paper

Abstract

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Repository

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Zenodo 19314276

License: CC-BY-4.0
State: the link answers, verified on 28 September 2026
Evidence: files inventoried
Size: 6 files, 0 scripts
Software Heritage: not checked
Found in: “Code availability”
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 28 September 2026: the link answers (HTTP 200)
  • 28 September 2026: the link answers (HTTP 200)
1 file
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Code availability statement

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Data

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Code and data availability statement

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Read it in the paper: doi.org/10.1038/s41467-026-73036-w.

Versions

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Version 1, 28 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 20 authors, 4 keywords, 15 MeSH terms, 1 funder, 82 references.

Cite

This paper

Ji, J., Chao, H., Chen, C., Wang, X., Shi, W., Liao, J., Qian, H., Shi, H., Hu, J., Ye, Y., Tu, Y., Xu, X., Li, Z., Yue, Z., Yan, W., Hong, X., Wang, H., Chen, H., Petretto, E., & Ji, J. (2026). Single-nucleus analysis reveals human-specific oligodendrocyte polarization and conserved neuronal responses after severe traumatic brain injury. Nature communications, 17(1), 6910. https://doi.org/10.1038/s41467-026-73036-w

BibTeX

@article{ji2026single,
author = {Ji, Jiatong and Chao, Honglu and Chen, Chengzhi and Wang, Xinyue and Shi, Wenqian and Liao, Jun and Qian, Hai and Shi, Hao and Hu, Jingming and Ye, Yangfan and Tu, Yiming and Xu, Xiao and Li, Zheng and Yue, Zhen and Yan, Wei and Hong, Xunning and Wang, Huibo and Chen, Huimei and Petretto, Enrico and Ji, Jing},
title = {{Single-nucleus analysis reveals human-specific oligodendrocyte polarization and conserved neuronal responses after severe traumatic brain injury}},
journal = {Nature communications},
year = {2026},
month = may,
volume = {17},
number = {1},
pages = {6910},
publisher = {Nature Publishing Group},
issn = {2041-1723},
doi = {10.1038/s41467-026-73036-w},
url = {https://doi.org/10.1038/s41467-026-73036-w},
pmid = {42203771},
pmcid = {PMC13388710}
}

RIS

TY - JOUR
AU - Ji, Jiatong
AU - Chao, Honglu
AU - Chen, Chengzhi
AU - Wang, Xinyue
AU - Shi, Wenqian
AU - Liao, Jun
AU - Qian, Hai
AU - Shi, Hao
AU - Hu, Jingming
AU - Ye, Yangfan
AU - Tu, Yiming
AU - Xu, Xiao
AU - Li, Zheng
AU - Yue, Zhen
AU - Yan, Wei
AU - Hong, Xunning
AU - Wang, Huibo
AU - Chen, Huimei
AU - Petretto, Enrico
AU - Ji, Jing
TI - Single-nucleus analysis reveals human-specific oligodendrocyte polarization and conserved neuronal responses after severe traumatic brain injury
T2 - Nature communications
J2 - Nat Commun
PY - 2026
DA - 2026/05/27
VL - 17
IS - 1
SP - 6910
SN - 2041-1723
PB - Nature Publishing Group
DO - 10.1038/s41467-026-73036-w
UR - https://doi.org/10.1038/s41467-026-73036-w
LA - en
ER -

CSL-JSON

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