Defining the transcriptional landscape during cytomegalovirus latency with single-cell RNA sequencing

Miri Shnayder, Aharon Nachshon, Benjamin Krishna, Emma Poole, Alina Boshkov, Amit Binyamin, Itay Maza, John Sinclair, Michal Schwartz, Noam Stern-Ginossar

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123 Scopus citations

Abstract

Primary infection with human cytomegalovirus (HCMV) results in a lifelong infection due to its ability to establish latent infection, with one characterized viral reservoir being hematopoietic cells. Although reactivation from latency causes serious disease in immunocompromised individuals, our molecular understanding of latency is limited. Here, we delineate viral gene expression during natural HCMV persistent infection by analyzing the massive transcriptome RNA sequencing (RNA-seq) atlas generated by the Genotype-Tissue Expression (GTEx) project. This systematic analysis reveals that HCMV persistence in vivo is prevalent in diverse tissues. Notably, we find only viral transcripts that resemble gene expression during various stages of lytic infection with no evidence of any highly restricted latency-associated viral gene expression program. To further define the transcriptional landscape during HCMV latent infection, we also used single-cell RNA-seq and a tractable experimental latency model. In contrast to some current views on latency, we also find no evidence for any highly restricted latency-associated viral gene expression program. Instead, we reveal that latency-associated gene expression largely mirrors a late lytic viral program, albeit at much lower levels of expression. Overall, our work has the potential to revolutionize our understanding of HCMV persistence and suggests that latency is governed mainly by quantitative changes, with a limited number of qualitative changes, in viral gene expression. IMPORTANCE Human cytomegalovirus is a prevalent pathogen, infecting most of the population worldwide and establishing lifelong latency in its hosts. Although reactivation from latency causes significant morbidity and mortality in immunocompromised hosts, our molecular understanding of the latent state remains limited. Here, we examine the viral gene expression during natural and experimental latent HCMV infection on a transcriptome-wide level. In contrast to the classical views on herpesvirus latency, we find no evidence for a restricted latency-associated viral gene expression program. Instead, we reveal that latency gene expression largely resembles a late lytic viral profile, albeit at much lower levels of expression. Taken together, our data transform the current view of HCMV persistence and suggest that latency is mainly governed by quantitative rather than qualitative changes in viral gene expression.

Original languageEnglish
Article numbere00013-18
JournalmBio
Volume9
Issue number2
DOIs
StatePublished - 13 Mar 2018
Externally publishedYes

Bibliographical note

Publisher Copyright:
© 2018 Shnayder et al.

Funding

This research was supported by the EU-FP7-PEOPLE career integration grant, the Israeli Science Foundation (1073/14; N.S.-G.), Infect-ERA (TANKACY; N.S.-G.), the European Research Council starting grant (StG-2014-638142; N.S.-G.), the British Medical Research Programme (grant G0701279; J.S.), a Wellcome Research Studentship Grant (B.K.), and the Cambridge NIHR BRC Cell Phenotyping Hub. N.S.-G. is incumbent of the Skirball career development chair in new scientist. We thank Yosef Shaul, Schraga Schwartz, Igor Ulitsky, Rotem Sorek, Ian Mohr, and Stern-Ginossar lab members for critical reading of the manuscript. We thank Eain A. Murphy for the TB40E-GFP virus strain. We thank Elad Chomsky, Yaara Arkin, Hadas Keren-Shaul, and Efrat Hagai for technical assistance. This research was supported by the EU-FP7-PEOPLE career integration grant, the Israeli Science Foundation (1073/14; N.S.-G.), Infect-ERA (TANKACY; N.S.-G.), the European Research Council starting grant (StG-2014-638142; N.S.-G.), the British Medical Research Programme (grant G0701279; J.S.), a Wellcome Research Studentship Grant (B.K.), and the Cambridge NIHR BRC Cell Phenotyping Hub. N.S.-G. is incumbent of the Skirball career development chair in new scientist.

FundersFunder number
British Medical Research Programme
Cambridge NIHR BRC
Israeli Science Foundation1073/14
Wellcome Trust
Horizon 2020 Framework Programme638142
Medical Research CouncilG0701279, MR/K021087/1
European Research CouncilStG-2014-638142
Israel Science Foundation

    Keywords

    • Cytomegalovirus
    • Gene expression
    • Latency
    • Single-cell RNA-seq
    • Transcriptome

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