中国神经再生研究(英文版) ›› 2023, Vol. 18 ›› Issue (3): 626-633.doi: 10.4103/1673-5374.350209

• 原著:脊髓损伤修复保护与再生 • 上一篇    下一篇

脊髓损伤中铁死亡的生物信息学分析

  

  • 出版日期:2023-03-15 发布日期:2022-08-28
  • 基金资助:

    国家干细胞与转化研究重点研发项目(2019YFA0112100);天津市重点研发计划科技支撑重点项目(19YFZCSY00660

Bioinformatics analysis of ferroptosis in spinal cord injury

Jin-Ze Li1, #, Bao-You Fan1, #, Tao Sun1, #, Xiao-Xiong Wang2, 3, Jun-Jin Li1, Jian-Ping Zhang1, Guang-Jin Gu1, Wen-Yuan Shen1, De-Rong Liu1, Zhi-Jian Wei1, 2, 3, *, Shi-Qing Feng1, 2, 3, *   

  1. 1International Cooperation Base of Spinal Cord Injury, Tianjin Key Laboratory of Spine and Spinal Cord Injury, Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, China; 2Department of Orthopedics, Qilu Hospital of Shandong University, Jinan, Shandong Province, China; 3Shandong University Centre for Orthopedics, Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, China
  • Online:2023-03-15 Published:2022-08-28
  • Contact: Zhi-Jian Wei, PhD, MD, weizhijian2002@126.com; Shi-Qing Feng, PhD, MD, sqfeng@tmu.edu.cn.
  • Supported by:
    The study was supported by National Key Research and Development Project of Stem Cell and Transformation Research, No. 2019YFA0112100 and Tianjin Key Research and Development Plan, Key Projects for Science and Technology Support, No. 19YFZCSY00660 (both to SQF).

摘要:

铁死亡可能参与加重脊髓损伤的进展,但具体作用未知。实验首先以改良Allen法构建了T10脊髓损伤大鼠模型,发现损伤后1,3,7d时分别有48,44和27种基因发生显著的差异表达。由于与假手术组及其他时间点相比,损伤后1d时,脊髓组织中铁死亡标志物长链脂酰辅酶 A 合成酶 4表达和氧化应激标志物丙二醛含量较高,且谷胱甘肽含量较低,同时综合生物信息学的结果,确定出脊髓损伤铁死亡的关键进展期为损伤后1d。基于蛋白互作网络分析得出损伤后1d时脊髓组织中10种枢纽基因为STAT3、JUN、TLR4、ATF3、HMOX1、MAPK1、MAPK9、PTGS2、VEGFA和RELA,然后应用实时聚合酶链反应验证得出STAT3、JUN、TLR4、ATF3、HMOX1、PTGS2和RELA 的mRNA表达水平上调,VEGFA、MAPK1和MAPK9的mRNA表达水平下调。随后基于DSigDB数据库筛选出10种潜在化合物可能作为靶向铁死亡进而修复脊髓损伤的潜在药物分子。最后实验还构建了包含66种长链非编码RNA、10种微小RNA和12种基因的有助于脊髓损伤进展的重要铁死亡相关mRNA-微小RNA-长链非编码RNA网络。这项研究结果有助于认识脊髓损伤中铁死亡的机制。

https://orcid.org/0000-0002-2226-1514 (Zhi-Jian Wei); https://orcid.org/0000-0001-9437-7674 (Shi-Qing Feng)

关键词: 脊髓损伤, 铁死亡, 生物信息学, GO富集分析, KEGG分析, 关键期, 基因-微小RNA网络, mRNA-微小RNA-长链非编码RNA网络, 药物

Abstract: Ferroptosis plays a key role in aggravating the progression of spinal cord injury (SCI), but the specific mechanism remains unknown. In this study, we constructed a rat model of T10 SCI using a modified Allen method. We identified 48, 44, and 27 ferroptosis genes that were differentially expressed at 1, 3, and 7 days after SCI induction. Compared with the sham group and other SCI subgroups, the subgroup at 1 day after SCI showed increased expression of the ferroptosis marker acyl-CoA synthetase long-chain family member 4 and the oxidative stress marker malondialdehyde in the injured spinal cord while glutathione in the injured spinal cord was lower. These findings with our bioinformatics results suggested that 1 day after SCI was the important period of ferroptosis progression. Bioinformatics analysis identified the following top ten hub ferroptosis genes in the subgroup at 1 day after SCI: STAT3, JUN, TLR4, ATF3, HMOX1, MAPK1, MAPK9, PTGS2, VEGFA, and RELA. Real-time polymerase chain reaction on rat spinal cord tissue confirmed that STAT3, JUN, TLR4, ATF3, HMOX1, PTGS2, and RELA mRNA levels were up-regulated and VEGFA, MAPK1 and MAPK9 mRNA levels were down-regulated. Ten potential compounds were predicted using the DSigDB database as potential drugs or molecules targeting ferroptosis to repair SCI. We also constructed a ferroptosis-related mRNA-miRNA-lncRNA network in SCI that included 66 lncRNAs, 10 miRNAs, and 12 genes. Our results help further the understanding of the mechanism underlying ferroptosis in SCI.

Key words: bioinformatics, drug, ferroptosis, Gene Ontology enrichment analysis, gene-miRNA network, Kyoto Encyclopedia of Genes and Genomes pathway, mRNA-miRNA-lncRNA network, progression, spinal cord injury