Atlas of temporal molecular pathological alterations after traumatic brain injury based on RNA-Seq

Abstract

Traumatic brain injury (TBI) involves diverse molecular pathological alterations and biological processes in a temporally dynamic manner. However, current knowledge on the various processes during the acute phase of TBI is still rather limited. RNA-seq analysis was performed on brain tissues from C57/BL6 mice at 10 time points(0 h, 1 h, 2 h, 3 h, 4 h, 6 h, 12 h, 1d, 3d, and 7d) following TBI modeling. Subsequently, a bioinformatics approach, Weighted Gene Co-expression Network Analysis (WGCNA), was employed to identify characteristic modules, which were then validated using the Mfuzz method. Pathway enrichment analysis was conducted on WGCNA module genes, and hub genes were screened using the STRING database. After exploring the various potential pathways and expression patterns (neuroinflammation, cognition, gliosis and myelin regeneration etc.), we focus on pyroptosis, a inflammatory cell death influencing immune response, for in-depth analysis. RT-qPCR, Western blot(WB) and Immunofluorescence(IF) were used to validate the hub genes and key pyroptosis-related genes(Casp1, Casp11, GSDMD). Additionally, single-cell RNA sequencing data at 7 day post injury(dpi) was also used to validate the expression of the identified hub genes. Our approach to intensive transcriptomic analysis comprehensively reveals the temporal molecular pathological alterations during TBI progression. Pyroptosis may be a key mechanism in the neuroinflammatory process. Intervention strategies targeting specific molecular pathways may offer novel approach for the treatment of TBI.