Original Article
Open Access
Tao Yang, Yongxiang Yang, Jingmin Cheng, Kexia Fan, Yuan Ma, Dongbo Zou, Sixun Yu
Published online September 18, 2026
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Neurosurgical Subspecialties.
doi:10.14218/NSSS.2026.00014
Abstract
Traumatic brain injury (TBI) induces neuroimmune activation and metabolic reprogramming in microglia, but the transcriptional regulators underlying these responses remain unclear.
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Traumatic brain injury (TBI) induces neuroimmune activation and metabolic reprogramming in microglia, but the transcriptional regulators underlying these responses remain unclear. This study aimed to integrate single-cell and bulk transcriptomic datasets to identify microglia-associated regulatory genes and characterize their potential roles in post-TBI neuroinflammatory and immunometabolic dysregulation.
We integrated single-cell RNA sequencing data (GSE101901) with a bulk training dataset (GSE58485) and an independent bulk validation dataset (GSE242025) from murine TBI models. hdWGCNA, differential expression, pseudotime, CIBERSORT, and in silico transcription factor binding-site analyses were performed to identify and characterize candidate genes. Key-gene expression was additionally validated by RT-qPCR in male C57BL/6 mice assigned to Sham and TBI groups (n = 5 per group). The Drug Gene Interaction Database was used for exploratory drug-gene prediction.
Single-cell profiling suggested descriptive shifts in the proportions of microglia, astrocytes, and neurons after TBI. hdWGCNA identified 90 microglia-associated genes, 43 of which overlapped with nominally differentially expressed genes; 89 genes met the Benjamini–Hochberg-adjusted P < 0.05 threshold in the bulk analysis. Cross-dataset validation identified increased Ccl4 and Lgals3 expression and decreased Egr1 expression. Motif scanning identified four predicted EGR1 motif occurrences in the Ccl4 promoter and six occurrences at three unique locations in the Lgals3 promoter. RT-qPCR in TBI and Sham mice (n = 5 per group) supported the same directional expression changes in Ccl4, Lgals3, and Egr1.
A candidate Ccl4/Lgals3/Egr1 expression pattern characterized by Ccl4 and Lgals3 upregulation and Egr1 downregulation was associated with post-TBI neuroinflammatory and immunometabolic changes. Further mechanistic validation is required.
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