- 2021;24;E573-E581Using RNA-Seq to Explore the Hub Genes in the Trigeminal Root Entry Zone of Rats by Compression Injury
Ran Tao, BDS, Feng Huang, PhD, Kun Lin, MD, Shao-Wei Lin, PhD, De Wei, MD, and Dao-Shu Luo, PhD.
BACKGROUND: Mechanical compression on the trigeminal root entry zone (TREZ) by microvascular is the main etiology of primary trigeminal neuralgia (TN).
OBJECTIVES: To study the pathogenesis of TN, hub genes screening in the TREZ of TN in an animal model was performed.
STUDY DESIGN: A double blind, randomized study was designed in a controlled animal trial.
SETTING: The research took place in the Laboratory of Clinical Applied Anatomy at the School of Basic Medical Science of Fujian Medical University.
METHODS: Twelve male rats were randomly divided into a sham operation group and a TN animal model group. TN animal model was induced by chronic compression of trigeminal nerve root (CCT) operation. Gene expression in the TREZ were analyzed by RNA sequencing (RNA-Seq) technique. KEGG analysis, GO analysis, and PPI analysis were performed in the DEGs. Key signaling pathways analyzing by GSEA and the hub genes in the DEGs were also studied. Reverse transcription real-time polymerase chain reaction (RT-qPCR) was used to verify the RNA-Seq results.
RESULTS: Transcriptome data showed that 352 genes up-regulated and 59 genes down-regulated in DEGs on post-operation day 21, after CCT operation in the TN group. KEGG analysis revealed that, “neuroactive ligand receptor interaction” and “cytokine cytokine receptor interaction” may be related to the pathogenesis of TN. GO analysis showed “regulation of signing receptor activity”, “chemokine activity”, and “carbohydrate binging” may be related to TN. The RT-qPCR results were consistent with the test results, indicating that the transcriptome sequencing results were reliable.
LIMITATIONS: Although the incidence of TN in female rats was higher than in male rats, we only used male SD rats to establish the TN animal model, to avoid the effect of estrogen on experimental results. This study only presents some respects of RNA-Seq technique and, therefore, did not identify the DEGs at the protein level. The relationship between the DEGs at different levels shoud be done in the future.
CONCLUSIONS: Based on the results of RNA-seq, this study discovered 6 hub genes in the TREZ that are closely related to the TN animal model, which provide a potential breakthrough point to explore the pathogenesis of TN.
KEY WORDS: Animal model, compression injury, hub gene, rat, RNA-seq, transcriptome, trigeminal neuralgia, trigeminal root entry zone