PRJNA520853: Single cell analysis of HSV-1 infection reveals anti-viral and developmental programs are activated in distinct sub-populations with opposite outcomes
概要: Viral infection is usually studied at the population level by averaging over millions of cells. However, infection at the single-cell level is highly heterogeneous, where most infected cells give rise to none or few viral progeny while some cells produce thousands. Analysis of HSV-1 infection by population averaged measurements has taught us a lot about the course of viral infection, but has also produced contradictory results, such as the concurrent activation and inhibition of type I interferon signaling during infection. Here, we combine live-cell imaging and single-cell RNA sequencing to characterize viral and host transcriptional heterogeneity during HSV-1 infection of primary human cells. We find extreme variability in the level of viral gene expression among individually infected cells and show that they cluster into transcriptionally distinct sub-populations. We find that anti-viral signaling is initiated in a rare group of abortively infected cells, while highly infected cells undergo cellular reprogramming to an embryonic-like transcriptional state. This reprogramming includes the re-localization of b-catenin into the host nucleus and viral replication compartments and is required for late viral gene expression and progeny production. These findings uncover the transcriptional differences in cells with variable infection outcomes and shed new light on the manipulation of host pathways by HSV-1.
项目整体设计: HDFn cells mock-infeted, infected with wt HSV-1 or dICP0 HSV-1 for 5 hours. drop-seq data for single-cell RNA-sequncing as well as bulk RNA-seq of sorted cell population (ICP4 positive or negative in each experimet, in duplicates)
Cells were infected with HSV-1 for 1 hr at room temperature in miminal volume, washed and incubated for 5 hours. For sorting, cells were detached and sorted on a FACSAria Fusion
提取方案:
For bulk RNA Qiagen miniprep RNA extractio colum were used. For drop-seq we followed the drop-seq protocol in Macosko et al 2015.Standard Illuimina protocol for bulk RNA-seq, according to Macosko et al. 2015 for drop-seq
建库方案:
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测序信息
分子类型:
poly(A)+ RNA
库的片段类型:
PAIRED
库的链类型:
Forward
测序平台:
ILLUMINA
测序仪型号:
Illumina NextSeq 550
链特异性:
Specific
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文章
HSV-1 single-cell analysis reveals the activation of anti-viral and developmental programs in distinct sub-populations.
