Table_3_Whole Transcriptome Analysis Revealed a Stress Response to Deep Underground Environment Conditions in Chinese Hamster V79 Lung Fibroblast Cells.XLSX

Background: Prior studies have shown that the proliferation of V79 lung fibroblast cells could be inhibited by low background radiation (LBR) in deep underground laboratory (DUGL). In the current study, we revealed further molecular changes by performing whole transcriptome analysis on the expression profiles of long non-coding RNA (lncRNA), messenger RNA (mRNA), circular RNA (circRNA) and microRNA (miRNA) in V79 cells cultured for two days in a DUGL.
Methods: Whole transcriptome analysis including lncRNA, mRNAs, circ RNA and miRNA was performed in V79 cells cultured for two days in DUGL and above ground laboratory (AGL), respectively. The differentially expressed (DE) lncRNA, mRNA, circRNA, and miRNA in V79 cells were identified by the comparison between DUGL and AGL groups. Quantitative real-time polymerase chain reaction(qRT-PCR)was conducted to verify the selected RNA sequencings. Then, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway was analyzed for the DE mRNAs which enabled to predict target genes of lncRNA and host genes of circRNA.
Results: With |log2(Fold-change)| ≥ 1.0 and p < 0.05, a total of 1257 mRNAs (353 mRNAs up-regulated, 904 mRNAs down-regulated), 866 lncRNAs (145 lncRNAs up-regulated, 721 lncRNAs down-regulated), and 474 circRNAs (247 circRNAs up-regulated, 227 circRNAs down-regulated) were significantly altered between the two groups. There was no significant difference in miRNA between the two groups. The altered RNA profiles were mainly discovered in lncRNAs, mRNAs and circRNAs. DE RNAs were involved in many pathways including ECM-RI, PI3K-Akt signaling, RNA transport and the cell cycle under the LBR stress of the deep underground environment.
Conclusion: Taken together, these results suggest that the LBR in the DUGL could induce transcriptional repression, thus reducing metabolic process and reprogramming the overall gene expression profile in V79 cells.

背景：已有研究表明，深部地下实验室（deep underground laboratory, DUGL）中的低本底辐射（low background radiation, LBR）可抑制V79肺成纤维细胞的增殖。本研究通过对在深部地下实验室培养2天的V79细胞进行全转录组分析，解析其长链非编码RNA（long non-coding RNA, lncRNA）、信使RNA（messenger RNA, mRNA）、环状RNA（circular RNA, circRNA）及微小RNA（microRNA, miRNA）的表达谱，进一步揭示了相关分子变化。
方法：分别将V79细胞在深部地下实验室与地面实验室（above ground laboratory, AGL）中培养2天后，对其开展包含lncRNA、mRNA、circRNA及miRNA的全转录组分析。通过对比深部地下实验室组与地面实验室组的细胞样本，筛选得到V79细胞中差异表达（differentially expressed, DE）的lncRNA、mRNA、circRNA及miRNA。采用实时定量聚合酶链反应（quantitative real-time polymerase chain reaction, qRT-PCR）对筛选得到的RNA测序结果进行验证。随后，针对差异表达mRNA，开展基因本体论（Gene Ontology, GO）与京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes, KEGG）通路富集分析，并以此预测lncRNA的靶基因以及circRNA的宿主基因。
结果：以|log₂(倍数变化)|≥1.0且P<0.05作为筛选标准，两组间共筛选得到1257个差异表达mRNA（其中353个上调、904个下调）、866个差异表达lncRNA（其中145个上调、721个下调）以及474个差异表达circRNA（其中247个上调、227个下调）。两组间miRNA表达无显著差异。表达谱发生显著变化的RNA主要为lncRNA、mRNA及circRNA。在深部地下环境的低本底辐射胁迫下，差异表达RNA参与了包括ECM-RI、PI3K-Akt信号通路、RNA转运及细胞周期在内的多条通路。
结论：综上，本研究结果表明，深部地下实验室中的低本底辐射可诱导V79细胞产生转录抑制，进而降低细胞代谢过程并重塑整体基因表达谱。