SARS-CoV-2 and Influenza A Virus Induce Longitudinal Transcriptomic Changes in Hamster Spinal Cord Tissue.
SARS-CoV-2 and Influenza A Virus Induce Longitudinal Transcriptomic Changes in Hamster Spinal Cord Tissue.
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SARS-CoV-2 和甲型流感病毒诱导仓鼠脊髓组织的纵向转录组变化。
DOI：
10.1097/brs.0000000000004765
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发表时间：
2024
期刊：
影响因子：
3
通讯作者：
Zachariou,Venetia
中科院分区：
文献类型：
--
作者：
Serafini,RandalA;Frere,JustinJ;tenOever,Benjamin;Zachariou,Venetia
材料和方法如前所述进行动物和RNA测序实验。2，3简言之，仓鼠接受100 μL磷酸盐缓冲盐水鼻内接种，其中含有1000空斑形成单位的SARS-CoV-2（USAWA 1/2020）、100，000空斑形成单位的IAV（大流行性H1N1分离株A/加州/04/2009）或单独的磷酸盐缓冲盐水。将仓鼠安乐死，并在3和31 dpi收获tSC组织（每组n= 3）。从组织中提取RNA并在Illumina NextSeq 500平台上测序。使用BaseSpace（Illumina）、DESeq 2、Qiagen Influence Pathway Analysis和Gene Set Enrichment Analysis（MSigDB）处理测序数据。使用ggplot 2、秩-秩超几何重叠（RRHO）、RRHO 2和gplots软件包在R中可视化数据。根据IACUC方案，在CDC/USDA批准的生物安全三级实验室中进行测序工作。为了评估SARS-CoV-2与IAV攻击后tSC中的宿主应答，我们在3dpi进行RNA测序，结果显示469个差异表达的基因在SARS-CoV-2感染的动物中有963个DEG（DEG; P< 0.05; 84个P-adj< 0.1的基因）（图1A），在IAV感染的动物中有963个DEG（P< 0.05; 136个P-adj< 0.1的基因）（图1B）。当使用RRHO分析比较这些组织之间广泛的无阈值变化时，我们观察到条件之间直接一致的转录组学变化（图1C），表明tSC中对两种病毒的细胞应答相似。
MATERIALS AND METHODSAnimal and RNA-sequencing experiments were conducted as described previously. 2, 3 Briefly, hamsters received an intranasal inoculation of 100 μL of phosphate-buffered saline containing 1000 plaque-forming units of SARS-CoV-2 (USAWA1/2020), 100,000 plaque-forming units of IAV (pandemic H1N1 isolate A/California/04/2009), or phosphate-buffered saline alone. Hamsters were euthanized, and tSC tissues were harvested at 3 and 31 dpi (n= 3 per group). RNA was extracted from tissues and sequenced on an Illumina NextSeq 500 platform. Sequencing data were processed using BaseSpace (Illumina), DESeq 2, Qiagen Ingenuity Pathway Analysis, and Gene Set Enrichment Analysis (MSigDB). Data were visualized in R using ggplot2, Rank-Rank Hypergeometric Overlap (RRHO), RRHO2, and gplots packages. Hamster work was performed in a CDC/USDA-approved biosafety level three laboratory in accordance with IACUC protocols.RESULTSTo assess the host response in the tSC following challenge with SARS-CoV-2 versus IAV, we performed RNA-sequencing at 3 dpi, which revealed 469 differentially-expressed genes (DEGs; P< 0.05; 84 genes with P-adj< 0.1) in SARS-CoV-2-infected animals (Fig. 1A) and 963 DEGs (P< 0.05; 136 genes with P-adj< 0.1) in IAV-infected animals (Fig. 1B). When comparing broad, threshold-free changes between these tissues using RRHO analysis, we observed directly concordant transcriptomic changes between the conditions (Fig. 1C), suggesting a similar cellular response in the tSC to both viruses.