Functional single-cell genomics of human cytomegalovirus infection

Hein, Marco Y.; Weissman, Jonathan S.

doi:10.1101/775080

Cited by 21 publications

(38 citation statements)

References 72 publications

(73 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We confidently identified infected cells with as low as 0.01% EBOV RNA out of total RNA (intracellular viral load), while some cells had up to 57.5% EBOV RNA ( Figures 6B and 6C) . Similar heterogeneity has been observed for the segmented -ssRNA virus influenza (Russell et al, 2018) , the +ssRNA virus dengue (Zanini et al, 2018a(Zanini et al, , 2018b , and the dsDNA virus HCMV (Hein and Weissman, 2019) , but this is the first demonstration for a non-segmented negative-sense (NNS) virus.…”

Section: Discussionsupporting

confidence: 68%

Single-cell profiling of Ebola virus infectionin vivoreveals viral and host transcriptional dynamics

Kotliar

Lin

Logue

et al. 2020

Preprint

View full text Add to dashboard Cite

Ebola virus (EBOV) causes epidemics with high case fatality rates, yet remains understudied due to the challenge of experimentation in high-containment and outbreak settings. To better understand EBOV infection in vivo , we used single-cell transcriptomics and CyTOF-based single-cell protein quantification to characterize peripheral immune cell activity during EBOV infection in rhesus monkeys. We obtained 100,000 transcriptomes and 15,000,000 protein profiles, providing insight into pathogenesis. We find that immature, proliferative monocyte-lineage cells with reduced antigen presentation capacity replace conventional circulating monocyte subsets within days of infection, while lymphocytes upregulate apoptosis genes and decline in abundance. By quantifying viral RNA abundance in individual cells, we identify molecular determinants of tropism and examine temporal dynamics in viral and host gene expression. Within infected cells, we observe that EBOV down-regulates STAT1 mRNA and interferon signaling, and up-regulates putative pro-viral genes (e.g., DYNLL1 and HSPA5 ), nominating cellular pathways the virus manipulates for its replication. Overall, this study sheds light on EBOV tropism, replication dynamics, and elicited immune response, and provides a framework for characterizing interactions between hosts and emerging viruses in a maximum containment setting. over-activation of innate and adaptive immunity underlies much of EVD pathology, rather than solely virus-mediated cytotoxicity (Geisbert et al., 2003a(Geisbert et al., , 2003b .

show abstract

Section: Discussionsupporting

confidence: 68%

Single-cell profiling of Ebola virus infectionin vivoreveals viral and host transcriptional dynamics

Kotliar

Lin

Logue

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…This makes it difficult to distinguish between changes in this region that interfere with RNA4.9 transcription and its downstream effects, and changes that interfere directly with OriLyt activity. Accordingly, we cannot rule out the possibility that DNA cleavage caused by the Cas9 system affected ssDBP expression and viral DNA replication, but previous work [50,51] and our data show that cleavage of HCMV DNA has only a modest impact on the expression of genes proximal to the cleavage site and minimal impact on HCMV replication. Moreover, the observation that much of the growth defect caused by RNA4.9-Cas9 KD could be rescued by overexpression of ssDBP further indicates that there is no major damage to OriLyt.…”

Section: Discussionsupporting

(Expert classified)

Human cytomegalovirus long noncoding RNA4.9 regulates viral DNA replication

et al. 2020

View full text Add to dashboard Cite

Viruses are known for their extremely compact genomes composed almost entirely of protein-coding genes. Nonetheless, four long noncoding RNAs (lncRNAs) are encoded by human cytomegalovirus (HCMV). Although these RNAs accumulate to high levels during lytic infection, their functions remain largely unknown. Here, we show that HCMV-encoded lncRNA4.9 localizes to the viral nuclear replication compartment, and that its depletion restricts viral DNA replication and viral growth. RNA4.9 is transcribed from the HCMV origin of replication (oriLyt) and forms an RNA-DNA hybrid (R-loop) through its G+C-rich 5' end, which may be important for the initiation of viral DNA replication. Furthermore, targeting the RNA4.9 promoter with CRISPR-Cas9 or genetic relocalization of oriLyt leads to reduced levels of the viral single-stranded DNA-binding protein (ssDBP), suggesting that the levels of ssDBP are coupled to the oriLyt activity. We further identified a similar, oriLyt-embedded, G +C-rich lncRNA in murine cytomegalovirus (MCMV). These results indicate that HCMV RNA4.9 plays an important role in regulating viral DNA replication, that the levels of ssDBP are coupled to the oriLyt activity, and that these regulatory features may be conserved among betaherpesviruses.

show abstract

“…1). These changes in protein abundance and network connectivity may reflect the establishment of an antiviral state in uninfected "bystander" cells exposed to circulating IFN, similar to that observed during viral infections [73][74][75].…”

Section: Discussionmentioning

confidence: 67%

Dynamic rewiring of the human interactome by interferon signaling

et al. 2020

View full text Add to dashboard Cite

Background: The type I interferon (IFN) response is an ancient pathway that protects cells against viral pathogens by inducing the transcription of hundreds of IFNstimulated genes. Comprehensive catalogs of IFN-stimulated genes have been established across species and cell types by transcriptomic and biochemical approaches, but their antiviral mechanisms remain incompletely characterized. Here, we apply a combination of quantitative proteomic approaches to describe the effects of IFN signaling on the human proteome, and apply protein correlation profiling to map IFN-induced rearrangements in the human protein-protein interaction network. Results: We identify > 26,000 protein interactions in IFN-stimulated and unstimulated cells, many of which involve proteins associated with human disease and are observed exclusively within the IFN-stimulated network. Differential network analysis reveals interaction rewiring across a surprisingly broad spectrum of cellular pathways in the antiviral response. We identify IFN-dependent protein-protein interactions mediating novel regulatory mechanisms at the transcriptional and translational levels, with one such interaction modulating the transcriptional activity of STAT1. Moreover, we reveal IFN-dependent changes in ribosomal composition that act to buffer IFN-stimulated gene protein synthesis. Conclusions: Our map of the IFN interactome provides a global view of the complex cellular networks activated during the antiviral response, placing IFN-stimulated genes in a functional context, and serves as a framework to understand how these networks are dysregulated in autoimmune or inflammatory disease.

show abstract

Functional single-cell genomics of human cytomegalovirus infection

Cited by 21 publications

References 72 publications

Single-cell profiling of Ebola virus infectionin vivoreveals viral and host transcriptional dynamics

Single-cell profiling of Ebola virus infectionin vivoreveals viral and host transcriptional dynamics

Human cytomegalovirus long noncoding RNA4.9 regulates viral DNA replication

Dynamic rewiring of the human interactome by interferon signaling

Contact Info

Product

Resources

About