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CC BY 4.0 · Indian Journal of Neurotrauma
DOI: 10.1055/s-0045-1809063
Methods Article

Single-Cell RNA Sequencing of Brain Tissue Samples from Severe Traumatic Brain Injury Patients: A Protocol for Cellular Heterogeneity and Transcriptional Alteration Study

Venencia Albert 
1   Department of Laboratory Medicine, All India Institute of Medical Sciences, New Delhi, India
,
Mohammed Faruq
2   CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
,
Satish Verma 
3   Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India
,
Viren Sardana
2   CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
,
Kumardeep Choudhary
2   CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
,
Deepak Agrawal 
3   Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India
› Author Affiliations Funding This work was supported by the AIIMS-CSIR Collaborative Projects Grant.
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Abstract

Background

Severe traumatic brain injury (sTBI) leads to significant morbidity and mortality, often complicated by cerebral edema and raised intracranial pressure (ICP). Understanding the molecular impact of these pathophysiological changes on the injured and adjacent noninjured brain is crucial for improving patient outcomes. Single-cell ribonucleic acid sequencing (scRNA-seq) offers a high-resolution approach to studying cellular heterogeneity and transcriptional alterations in TBI.

Objective

This study aims to utilize scRNA-seq to analyze injured and noninjured brain tissue in patients with sTBI, identify differentially expressed genes, and characterize the cellular response to injury and its relation to ICP.

Materials and Methods

A cross-sectional study will be conducted, and brain tissue samples will be collected from sTBI patients. Tissue samples will be obtained during decompressive craniectomy, processed, and analyzed using the 10× Chromium system. Libraries will be sequenced on Illumina NovaSeq 6000, and transcriptomic data will be analyzed using Seurat and other bioinformatics tools. Bulk RNA sequencing will be performed for validation.

Results

This study is expected to identify unique gene expression patterns associated with cerebral edema, characterize cellular responses in injured versus noninjured brain regions, and provide insights into molecular pathways contributing to secondary brain injury.

Conclusion

By leveraging scRNA-seq, this study will provide a deeper understanding of the transcriptomic changes in sTBI. The findings may aid in discovering novel biomarkers and therapeutic targets, ultimately improving clinical management strategies for TBI patients.

Keywords

severe traumatic brain injury - single-cell RNA sequencing - cerebral edema - intracranial pressure - transcriptomics - biomarker discovery

Ethical Approval

This study will be conducted under ethical guidelines and regulations. Ethical approval was obtained from the All India Institute of Medical Sciences (AIIMS) Institutional Ethics Committee before the commencement of the study [AIIMS AI1320 dates 04–05–2024]. Informed consent will be obtained from all patients or their legal representatives before any study-related procedures are performed. The rights and privacy of the patients will be protected throughout the study.




Publication History

Article published online:
10 May 2025

© 2025. The Author(s). This is an open access article published by Thieme under the terms of the Creative Commons Attribution License, permitting unrestricted use, distribution, and reproduction so long as the original work is properly cited. (https://creativecommons.org/licenses/by/4.0/)

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  • References

  • 1 Guan B, Anderson DB, Chen L, Feng S, Zhou H. Global, regional and national burden of traumatic brain injury and spinal cord injury, 1990-2019: a systematic analysis for the Global Burden of Disease Study 2019. BMJ Open 2023; 13 (10) e075049
    CrossrefPubMedSearch in Google Scholar
  • 2 Government of India, Ministry of Road Transport and Highways. Road Accidents in India 2019. Published 2019. Accessed March 16, 2025 at: https://morth.nic.in/sites/default/files/RA_Uploading.pdf
    PubMed
  • 3 Kamal VK, Agrawal D, Pandey RM. Epidemiology, clinical characteristics and outcomes of traumatic brain injury: evidences from integrated level 1 trauma center in India. J Neurosci Rural Pract 2016; 7 (04) 515-525
    Thieme ConnectPubMedSearch in Google Scholar
  • 4 Jha RM, Kochanek PM, Simard JM. Pathophysiology and treatment of cerebral edema in traumatic brain injury. Neuropharmacology 2019; 145 (Pt B): 230-246
    PubMedSearch in Google Scholar
  • 5 Zusman BE, Kochanek PM, Jha RM. Cerebral edema in traumatic brain injury: a historical framework for current therapy. Curr Treat Options Neurol 2020; 22 (03) 9
    PubMedSearch in Google Scholar
  • 6 Caffes N, Stokum JA, Zhao R, Jha RM, Simard JM. Post-traumatic cerebral edema: pathophysiology, key contributors, and contemporary management. Med Res Arch 2022; 10 (10)
    CrossrefPubMedSearch in Google Scholar
  • 7 Jovic D, Liang X, Zeng H, Lin L, Xu F, Luo Y. Single-cell RNA sequencing technologies and applications: a brief overview. Clin Transl Med 2022; 12 (03) e694
    PubMedSearch in Google Scholar
  • 8 Qiu X, Guo Y, Liu MF. et al. Single-cell RNA-sequencing analysis reveals enhanced non-canonical neurotrophic factor signaling in the subacute phase of traumatic brain injury. CNS Neurosci Ther 2023; 29 (11) 3446-3459
    PubMedSearch in Google Scholar
  • 9 Zhang L, Yang Q, Yuan R. et al. Single-nucleus transcriptomic mapping of blast-induced traumatic brain injury in mice hippocampus. Sci Data 2023; 10 (01) 638
    PubMedSearch in Google Scholar
  • 10 Xing J, Ren L, Xu H. et al. Single-cell RNA sequencing reveals cellular and transcriptional changes associated with traumatic brain injury. Front Genet 2022; 13: 861428
    PubMedSearch in Google Scholar
  • 11 Davis JE, Eberwine JH, Hinkle DA, Marciano PG, Meaney DF, McIntosh TK. Methodological considerations regarding single-cell gene expression profiling for brain injury. Neurochem Res 2004; 29 (06) 1113-1121
    PubMedSearch in Google Scholar
  • 12 Shi R, Chen H, Zhang W. et al. Single-cell RNA sequencing in stroke and traumatic brain injury: Current achievements, challenges, and future perspectives on transcriptomic profiling. J Cereb Blood Flow Metab 2024; X241305914
    PubMedSearch in Google Scholar
  • 13 Garza R, Sharma Y, Atacho DAM. et al. Single-cell transcriptomics of human traumatic brain injury reveals activation of endogenous retroviruses in oligodendroglia. Cell Rep 2023; 42 (11) 113395
    PubMedSearch in Google Scholar
  • 14 Pullin JM, McCarthy DJ. A comparison of marker gene selection methods for single-cell RNA sequencing data. Genome Biol 2024; 25 (01) 56
    PubMedSearch in Google Scholar
  • 15 Zheng RZ, Xing J, Huang Q, Yang XT, Zhao CY, Li XY. Integration of single-cell and bulk RNA sequencing data reveals key cell types and regulators in traumatic brain injury. Math Biosci Eng 2021; 18 (02) 1201-1214
    PubMedSearch in Google Scholar
  • 16 Arneson D, Zhang G, Ahn IS. et al. Systems spatiotemporal dynamics of traumatic brain injury at single-cell resolution reveals humanin as a therapeutic target. Cell Mol Life Sci 2022; 79 (09) 480
    PubMedSearch in Google Scholar
  • 17 Addison A, Obafemi-Ajayi T. Comparative single-cell RNA-sequencing cluster analysis for traumatic brain injury marker genes detection. In: Al-Mubaid H, Aldwairi T, Eulenstein O. eds. Proceedings of 14th International Conference on Bioinformatics and Computational Biology. EasyChair; 2022: 155-164
    CrossrefSearch in Google Scholar