Application of transcriptome sequencing to identify and explore biomarkers in a rat model of optic nerve crush

Abstract

Traumatic optic neuropathy (TON) has a profound impact on affected individuals, yet the treatment of TON continues to present significant challenges. In this context, we aimed to explore diagnostic biomarkers and potential mechanisms underlying TON in a rat optic nerve crush (ONC) model via a transcriptomics approach. We extracted total RNA from 32 rat retina samples. First, candidate genes and hub genes were identified. The biomarkers were subsequently identified by random forest (RF) and receiver operating characteristic (ROC) analyses. A nomogram was constructed to assess the diagnostic value of the biomarkers. Finally, functional analysis, subcellular localization analysis, drug prediction, and gene expression verification were performed. IFIT3, IFI44, USP18, ZBP1, IRGM, and OAS1B were identified as biomarkers in the ONC model and exhibited strong diagnostic utility, with all areas under the curve (AUCs) exceeding 0.8. Furthermore, these biomarkers were found to be collectively involved in "cytokine-cytokine receptor interactions". Subcellular localization analysis revealed the predominant presence of these biomarkers in the cell nucleus and cytoplasm. Moreover, 8 drugs targeting OAS1B and 25 drugs targeting IRGM were predicted. Notably, the shared targeting of lipopolysaccharides, carbon nanotubes, pentachlorophenol, and silver by both OAS1B and IRGM has significant therapeutic potential. Additionally, IFIT3, IFI44, USP18, ZBP1, IRGM, and OAS1B expression levels were markedly elevated in ONC samples compared with control samples, underscoring their relevance as promising biomarkers for ONC. Therefore, we conclude that IFIT3, IFI44, USP18, ZBP1, IRGM, and OAS1B were identified as biomarkers of ONC, providing a potential theoretical basis for ONC related studies.

Keywords: Biomarkers; Diagnosis; Optic nerve crush; Transcriptomics.