基于单细胞测序数据的拉克罗斯病毒感染神经系统细胞基因表达差异分析

Differential Analysis of Gene Expression in Nervous System Cells Infected with La Cross Virus Based on Single Cell Sequencing Data

目的分析受拉克罗斯病毒(LACV)感染的人脑类器官细胞不同亚群相关基因表达差异,揭示不同亚群之间的转录组特性。方法选择GEO数据库中编号为GSE131434的单细胞转录组数据,包含2个样本,1个为模拟感染COs的作为阴性对照组,1个为受LACV感染的COs。采用R语言“seurat”包对数据进行过滤、归一化、主成分分析、UMAP聚类分析,寻找COs亚群。通过“SingleR”包进行基因注释,“iTALK”包分析细胞通讯。通过“clusterProfile”包对差异基因进行富集分析,后构建PPI网络筛选关键基因。结果单细胞测序数据分析表明,受感染的COs能够分成7个细胞亚群,3种细胞类型,分别为浆细胞样树突状细胞、祖细胞、髓样树突状细胞,其中细胞通讯主要发生在祖细胞和浆细胞样树突状细胞之间,尤其是APOE-LDLR这对配体和受体中。样本的差异基因主要富集于翻译起始、mRNA和RNA分解过程、核糖体等过程中,与冠状病毒感染、帕金森等疾病的信号通路相关。进一步获得的4个关键基因为RPS27A、UBA52、RPLP0、RPL13A。结论拉克罗斯病毒感染对人脑类器官细胞的关键基因表达差异以及涉及APOE-LDLR的细胞通讯可能在感染过程中发挥关键作用,为未来的研究提供了重要线索。

Objective To analyze the expression differences of related genes in different subsets of human brain organoid cells infected by La Cross virus(LACV),and to reveal the transcriptome characteristics between different subsets.Methods The single-cell transcriptome data numbered GSE131434 in the GEO database was selected,including two samples,one for simulated COs infection as a negative control group,and one for COs infected by LACV.The R language"seurat"package was used to filter,normalize,principal component analysis,and UMAP cluster analysis of the data to find COs subsets.Gene annotation was performed by the"SingleR"package,and cell communication was analyzed by the"iTALK"package.Enrichment analysis of differential genes was performed by"clusterProfile"package,and then PPI network was constructed to screen key genes.Results Single-cell sequencing data analysis showed that infected COs could be divided into 7 cell subsets and 3 cell types,including plasmacytoid dendritic cells,progenitor cells,and myeloid dendritic cells.Cell communication mainly occurs between progenitor cells and plasmacytoid dendritic cells,especially in APOE-LDLR ligands and receptors.The differential genes of the samples were mainly enriched in the processes of translation initiation,mRNA and RNA decomposition,ribosome,etc.,which were related to the signaling pathways of coronavirus infection,Parkinson's disease and other diseases.The four key genes were RPS27A,UBA52,RPLP0 and RPL13A.Conclusion The differential expression of key genes in human brain organoid cells infected with La Cross virus and the cell communication involving APOE-LDLR may play a key role in the infection process,which provides important clues for future research.