mSphere of Influence: Virology in the noise-how cell-to-cell variability impacts viral infection outcomes.

Nir Drayman works at the intersection of virology and single-cell biology, studying how cellular heterogeneity shapes the outcome of viral infections (and specifically that of HSV-1). In this mSphere of Influence article, he reflects on how two papers, Remote activation of host cell DNA synthesis in uninfected cells signaled by infected cells in advance of virus transmission (N. Schmidt, T. Hennig, R. A. Serwa, M. Marchetti, and P. OHare, J Virol 89:11107-11115, 2015, https://doi.org/10.1128/jvi.01950-15) and Extreme heterogeneity of influenza virus infection in single cells (A. B. Russell, C. Trapnell, and J. D. Bloom, Elife 7:e32303, 2018, https://doi.org/10.7554/eLife.32303), impacted his research by trail blazing the analysis of viral infections in single cells, as well as by illuminating what is yet left to discover

HSV-1 single-cell analysis reveals the activation of anti-viral and developmental programs in distinct sub-populations

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, with most infected cells giving rise to no or few viral progeny while some cells produce thousands. Analysis of Herpes Simplex virus 1 (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 these cells 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 involves the recruitment of β-catenin to 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

Computer vision reveals hidden variables underlying NF-ΚB activation in single cells

Individual cells are heterogeneous when responding to environmental cues. Under an external signal, certain cells activate gene regulatory pathways, while others completely ignore that signal. Mechanisms underlying cellular heterogeneity are often inaccessible because experiments needed to study molecular states destroy the very states that we need to examine. Here, we developed an image-based support vector machine learning model to uncover variables controlling activation of the immune pathway nuclear factor ΚB (NF-ΚB). Computer vision analysis predicts the identity of cells that will respond to cytokine stimulation and shows that activation is predetermined by minute amounts of “leaky” NF-ΚB (p65:p50) localization to the nucleus. Mechanistic modeling revealed that the ratio of NF-ΚB to inhibitor of NF-ΚB predetermines leakiness and activation probability of cells. While cells transition between molecular states, they maintain their overall probabilities for NF-ΚB activation. Our results demonstrate how computer vision can find mechanisms behind heterogeneous single-cell activation under proinflammatory stimuli

Ultra-sensitive digital quantification of proteins and mRNA in single cells

Simultaneous measurement of proteins and mRNA in single cells enables quantitative understanding and modeling of cellular functions. Here, we present an automated microfluidic system for multi-parameter and ultra-sensitive protein/mRNA measurements in single cells. Our technology improves the sensitivity of digital proximity ligation assay by up to 55-fold, with a detection limit of 2277 proteins per cell and with detection efficiency of as few as 29 protein molecules. Our measurements using this system reveal higher mRNA/protein correlation in single mammalian cells than previous estimates. Furthermore, time-lapse imaging of herpes simplex virus 1 infected epithelial cells enabled by our device shows that expression of ICP4 -a major transcription factor regulating hundreds of viral genes- is only partially correlated with viral protein counts, suggesting that many cells go through abortive infection. These results highlight the importance of high-sensitivity protein/mRNA quantification for understanding fundamental molecular mechanisms in individual cells.ISSN:2041-172

Proposed model of the signaling events upon SV40 infectious entry.

<p>(A) The various players participating in the integrin-mediated signaling through host SV40 engagement. The respective time intervals during which these signaling events occur are also depicted.</p

p53 elevation in human cells halt SV40 infection by inhibiting T-ag expression

SV40 large T-antigen (T-ag) has been known for decades to inactivate the tumor suppressor p53 by sequestration and additional mechanisms. Our present study revealed that the struggle between p53 and T-ag begins very early in the infection cycle. We found that p53 is activated early after SV40 infection and defends the host against the infection. Using live cell imaging and single cell analyses we found that p53 dynamics are variable among individual cells, with only a subset of cells activating p53 immediately after SV40 infection. This cell-to-cell variabilty had clear consequences on the outcome of the infection. None of the cells with elevated p53 at the beginning of the infection proceeded to express T-ag, suggesting a p53-dependent decision between abortive and productive infection. In addition, we show that artificial elevation of p53 levels prior to the infection reduces infection efficiency, supporting a role for p53 in defending against SV40. We further found that the p53-mediated host defense mechanism against SV40 is not facilitated by apoptosis nor via interferon-stimulated genes. Instead p53 binds to the viral DNA at the T-ag promoter region, prevents its transcriptional activation by Sp1, and halts the progress of the infection. These findings shed new light on the long studied struggle between SV40 T-ag and p53, as developed during virus-host coevolution. Our studies indicate that the fate of SV40 infection is determined as soon as the viral DNA enters the nucleus, before the onset of viral gene expression

Dynamic Proteomics of Herpes Simplex Virus Infection

The cellular response to viral infection is usually studied at the level of cell populations. Currently, it remains an open question whether and to what extent cell-to-cell variability impacts the course of infection. Here we address this by dynamic proteomics—imaging and tracking 400 yellow fluorescent protein (YFP)-tagged host proteins in individual cells infected by herpes simplex virus 1. By quantifying time-lapse fluorescence imaging, we analyze how cell-to-cell variability impacts gene expression from the viral genome. We identify two proteins, RFX7 and geminin, whose levels at the time of infection correlate with successful initiation of gene expression. These proteins are cell cycle markers, and we find that the position in the cell cycle at the time of infection (along with the cell motility and local cell density) can reasonably predict in which individual cells gene expression from the viral genome will commence. We find that the onset of cell division dramatically impacts the progress of infection, with 70% of dividing cells showing no additional gene expression after mitosis. Last, we identify four host proteins that are specifically modulated in infected cells, of which only one has been previously recognized. SUMO2 and RPAP3 levels are rapidly reduced, while SLTM and YTHDC1 are redistributed to form nuclear foci. These modulations are dependent on the expression of ICP0, as shown by infection with two mutant viruses that lack ICP0. Taken together, our results provide experimental validation for the long-held notion that the success of infection is dependent on the state of the host cell at the time of infection

Inhibition of RhoA via GRAF1 promotes Ezrin inactivation and SV40 infection.

<p>(A) Constitutively active RhoA leads to increased levels of phosphorylated Ezrin that persist upon SV40 treatment. Inactive RhoA abrogates basal levels of p-ERM. A431 cells were transfected with RhoA-G14V-GFP or RhoA-T19N-GFP before SV40 was applied for 15 min and fixed cells were stained with a p-ERM antibody. (B) Expression of an inactive RhoA mutant form positively correlates with SV40 infection. Large populations of A431 cells were transfected with RhoA-G14V, RhoA-T19N and wild-type RhoA GFP constructs and subjected to SV40. Cells that were both transfected (GFP signal) and infected (T-antigen signal) were scored and compared with the expected number emerging from a random occurrence of the two signals. Positive log2 ratio values represent a positive correlation, demonstrating a stimulation of infection, whereas negative values denote anti-correlation, demonstrating an inhibition of infection (p-value 4.2×10⁻⁴). (C) Inhibition of GRAF1 function leads to increased levels of p-ERM. siRNA was applied onto A431 cells followed by addition of SV40 for 15 min. Levels of p-ERM were assessed using immunofluorescence in fixed cells. (D) RhoA is inactivated 10 min after SV40 treatment. Inhibition of PI3K and PDK1 with wortmannin or the PDK1 inhibitor, respectively, abolished the SV40-induced reduction in RhoA activity. Cells that had undergone the indicated treatment were subjected to RhoA-GTP immunoprecipitation, which was subsequently detected with a RhoA antibody using immunoblotting. The graph shows the quantification of the RhoA-GTP signal in SV40 exposed cells, as expressed in % reduction compared to the non-treated cells, and normalized against total RhoA and tubulin (quantification based on two different experiments). (E) PDK1 and GRAF1 act both upstream of RhoA to signal to ERM proteins. A431 cells were subjected to the following conditions before being scored for the presence or absence of p-ERM signal using immunofluorescence: transfection with RhoA-WT-GFP, RhoA-G14V-GFP or RhoA-T19N-GFP constucts, incubation with the PDK1 inhibitor for 1.5 h, siRNA treatment against GRAF1, or a combination of RhoA-T19N-GFP expression and the PDK1 inhibitor or GRAF1 siRNA. Acquired confocal images were processed with ImageJ to quantify the number of p-ERM-expressing cells. Inhibition of PDK1 function or silencing of GRAF1 led to partial or no restoration of the fraction of p-ERM-positive RhoA-T19N-expressing cells (asterisks), respectively. Values shown are the average of 2–4 independent experiments ± standard deviation. (F) Representative image used to extract the values shown in (E). The white line outlines manually segmented cells, whereas green and red depict RhoA-T19N-GFP transfected cells and p-ERM-positive cells, respectively. Dapi-stained nuclei are shown in blue.</p