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<p>Excessive or inappropriate radiation can seriously harm organisms. Radiation-induced thymus injury (RITI) is a severe complication driven by dysregulated RNA networks. However, current studies have mostly focused on single non-coding RNAs or late pathological stages, and a complete competing endogenous RNA (ceRNA) regulatory network had not been constructed.&#xa0;The thymus tissues of C57BL/6 mice exposed to 6&#xa0;Gy X-ray radiation for 24&#xa0;h were analyzed by RNA-sequencing (RNA-seq) with library construction. We functionally annotated target messenger RNAs (mRNAs) and predicted long non-coding RNA (lncRNA) -targeted microRNAs (miRNAs) and miRNA-targeted mRNAs post-irradiation, to construct the lncRNA-miRNA-mRNA ceRNA regulatory axis. Furthermore, multiple experimental approaches including quantitative real-time PCR (qRT-PCR), western blotting, flow cytometry and CCK-8 cell viability assays were utilized to validate the involvement of the phosphatidylinositol 3-kinase (PI3K)-Protein Kinase B (PKB or AKT) pathway.&#xa0;The results revealed that after irradiation, 6214 mRNAs, 160 miRNAs, and 1999 lncRNAs were significantly upregulated while 2676 mRNAs, 165 miRNAs, and 941 lncRNAs were considerably downregulated. The most significantly altered Gene Ontology (GO) terms were angiogenesis and ameboid cell migration (Biological Process, BP), actin cytoskeleton and cell-cell junctions (Cellular Component, CC), as well as actin binding and phospholipid binding (Molecular Function, MF). A total of 333 cellular functions mediated by phosphatase and tensin homologue deleted on chromosome ten (PTEN) exhibited significant alterations, whereas 175 cellular functions regulated by 3-phosphoinositide-dependent protein kinase 1 (PDPK1) showed substantial changes. Key biological pathways, including cancer-associated pathways, the PI3K-AKT signaling pathway, the human papillomavirus infection pathway, the focal adhesion pathway, the Rap1 signaling pathway, and the cardiomyocyte calcium signaling pathway, were uncovered through Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Based on the results of both GO enrichment analysis and KEGG pathway analysis, a consistent conclusion was drawn that RITI was closely associated with the PI3K-AKT signaling pathway. So the PI3K-AKT pathway was selected for experimental validation, which confirmed that it was a key regulatory pathway for thymic degeneration in RITI.&#xa0;A lncRNA-miRNA-mRNA ceRNA axis of RITI was successfully developed in a mouse model after irradiation. The PI3K-AKT pathway contributes to preventing radiation-induced cell death in RITI, and the differentially expressed RNAs in the initial stage of this injury may result in serious consequences.</p>

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Transcriptomic analysis of lncRNA-miRNA-mRNA competing endogenous RNA regulatory networks in radiation-induced mouse thymic degeneration

  • 期刊论文

  • 发表日期：

    2026年7月16日

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  • Fei Wang,
  • Qing-hua Yu,
  • Xin-ming Fan,
  • Cun-yang Guo,
  • Si-guang Xu,
  • Wen-bo Zhang,
  • Ping Xu

摘要

Excessive or inappropriate radiation can seriously harm organisms. Radiation-induced thymus injury (RITI) is a severe complication driven by dysregulated RNA networks. However, current studies have mostly focused on single non-coding RNAs or late pathological stages, and a complete competing endogenous RNA (ceRNA) regulatory network had not been constructed. The thymus tissues of C57BL/6 mice exposed to 6 Gy X-ray radiation for 24 h were analyzed by RNA-sequencing (RNA-seq) with library construction. We functionally annotated target messenger RNAs (mRNAs) and predicted long non-coding RNA (lncRNA) -targeted microRNAs (miRNAs) and miRNA-targeted mRNAs post-irradiation, to construct the lncRNA-miRNA-mRNA ceRNA regulatory axis. Furthermore, multiple experimental approaches including quantitative real-time PCR (qRT-PCR), western blotting, flow cytometry and CCK-8 cell viability assays were utilized to validate the involvement of the phosphatidylinositol 3-kinase (PI3K)-Protein Kinase B (PKB or AKT) pathway. The results revealed that after irradiation, 6214 mRNAs, 160 miRNAs, and 1999 lncRNAs were significantly upregulated while 2676 mRNAs, 165 miRNAs, and 941 lncRNAs were considerably downregulated. The most significantly altered Gene Ontology (GO) terms were angiogenesis and ameboid cell migration (Biological Process, BP), actin cytoskeleton and cell-cell junctions (Cellular Component, CC), as well as actin binding and phospholipid binding (Molecular Function, MF). A total of 333 cellular functions mediated by phosphatase and tensin homologue deleted on chromosome ten (PTEN) exhibited significant alterations, whereas 175 cellular functions regulated by 3-phosphoinositide-dependent protein kinase 1 (PDPK1) showed substantial changes. Key biological pathways, including cancer-associated pathways, the PI3K-AKT signaling pathway, the human papillomavirus infection pathway, the focal adhesion pathway, the Rap1 signaling pathway, and the cardiomyocyte calcium signaling pathway, were uncovered through Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Based on the results of both GO enrichment analysis and KEGG pathway analysis, a consistent conclusion was drawn that RITI was closely associated with the PI3K-AKT signaling pathway. So the PI3K-AKT pathway was selected for experimental validation, which confirmed that it was a key regulatory pathway for thymic degeneration in RITI. A lncRNA-miRNA-mRNA ceRNA axis of RITI was successfully developed in a mouse model after irradiation. The PI3K-AKT pathway contributes to preventing radiation-induced cell death in RITI, and the differentially expressed RNAs in the initial stage of this injury may result in serious consequences.