Next-Generation Sequencing Reveals HIV-1-Mediated Suppression of T Cell Activation and RNA Processing and Regulation of Noncoding RNA Expression in a CD4<sup>+</sup> T Cell Line

ABSTRACT Next-generation sequencing (NGS) enables the highly sensitive measurement of whole transcriptomes. We report the first application to our knowledge of this technology to the analysis of RNA from a CD4+ T cell line infected with intact HIV. We sequenced the total mRNA from infected cells and...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Stewart T. Chang, Pavel Sova, Xinxia Peng, Jeffrey Weiss, G. Lynn Law, Robert E. Palermo, Michael G. Katze
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2011
Materias:	Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/4335629fcdcd4a7c9458980a08e6dea5
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:4335629fcdcd4a7c9458980a08e6dea5
record_format	dspace
spelling	oai:doaj.org-article:4335629fcdcd4a7c9458980a08e6dea52021-11-15T15:38:57ZNext-Generation Sequencing Reveals HIV-1-Mediated Suppression of T Cell Activation and RNA Processing and Regulation of Noncoding RNA Expression in a CD4<sup>+</sup> T Cell Line10.1128/mBio.00134-112150-7511https://doaj.org/article/4335629fcdcd4a7c9458980a08e6dea52011-11-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.00134-11https://doaj.org/toc/2150-7511ABSTRACT Next-generation sequencing (NGS) enables the highly sensitive measurement of whole transcriptomes. We report the first application to our knowledge of this technology to the analysis of RNA from a CD4+ T cell line infected with intact HIV. We sequenced the total mRNA from infected cells and detected differences in the expression of both host and viral mRNA. Viral reads represented a large portion of the total mapped sequencing reads: approximately 20% at 12 h postinfection (hpi) and 40% at 24 hpi. We also detected a small but significant suppression of T cell activation-related genes at 12 hpi. This suppression persisted and expanded by 24 hpi, providing new possible markers of virus-induced T cell cytopathology. By 24 hpi, the expression of over 50% of detectable host loci was also altered, indicating widespread alteration of host processes, including RNA processing, splicing, and transport to an extent not previously reported. In addition, next-generation sequencing provided insights into alternative viral RNA splice events and the expression of noncoding RNAs, including microRNA host genes. IMPORTANCE Recent advances in sequencing technology now allow the measurement of effectively all the RNA in a cell. This approach is especially useful for studying models of virus infection, as it allows the simultaneous measurement of both host and viral RNA. Using next-generation sequencing (NGS), we measured changes in total mRNA from a HIV-infected T cell line. To our knowledge, this is the first application of this technology to the investigation of HIV-host interactions involving intact HIV. We directly measured the amount of viral mRNA in infected cells and detected novel viral RNA splice variants and changes in the host expression of noncoding RNA species. We also detected small changes in T cell activation and other host processes during the early stages of viral replication that increased near the peak of viral replication, providing new candidate biomarkers of T cell death.Stewart T. ChangPavel SovaXinxia PengJeffrey WeissG. Lynn LawRobert E. PalermoMichael G. KatzeAmerican Society for MicrobiologyarticleMicrobiologyQR1-502ENmBio, Vol 2, Iss 5 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbiology QR1-502
spellingShingle	Microbiology QR1-502 Stewart T. Chang Pavel Sova Xinxia Peng Jeffrey Weiss G. Lynn Law Robert E. Palermo Michael G. Katze Next-Generation Sequencing Reveals HIV-1-Mediated Suppression of T Cell Activation and RNA Processing and Regulation of Noncoding RNA Expression in a CD4<sup>+</sup> T Cell Line
description	ABSTRACT Next-generation sequencing (NGS) enables the highly sensitive measurement of whole transcriptomes. We report the first application to our knowledge of this technology to the analysis of RNA from a CD4+ T cell line infected with intact HIV. We sequenced the total mRNA from infected cells and detected differences in the expression of both host and viral mRNA. Viral reads represented a large portion of the total mapped sequencing reads: approximately 20% at 12 h postinfection (hpi) and 40% at 24 hpi. We also detected a small but significant suppression of T cell activation-related genes at 12 hpi. This suppression persisted and expanded by 24 hpi, providing new possible markers of virus-induced T cell cytopathology. By 24 hpi, the expression of over 50% of detectable host loci was also altered, indicating widespread alteration of host processes, including RNA processing, splicing, and transport to an extent not previously reported. In addition, next-generation sequencing provided insights into alternative viral RNA splice events and the expression of noncoding RNAs, including microRNA host genes. IMPORTANCE Recent advances in sequencing technology now allow the measurement of effectively all the RNA in a cell. This approach is especially useful for studying models of virus infection, as it allows the simultaneous measurement of both host and viral RNA. Using next-generation sequencing (NGS), we measured changes in total mRNA from a HIV-infected T cell line. To our knowledge, this is the first application of this technology to the investigation of HIV-host interactions involving intact HIV. We directly measured the amount of viral mRNA in infected cells and detected novel viral RNA splice variants and changes in the host expression of noncoding RNA species. We also detected small changes in T cell activation and other host processes during the early stages of viral replication that increased near the peak of viral replication, providing new candidate biomarkers of T cell death.
format	article
author	Stewart T. Chang Pavel Sova Xinxia Peng Jeffrey Weiss G. Lynn Law Robert E. Palermo Michael G. Katze
author_facet	Stewart T. Chang Pavel Sova Xinxia Peng Jeffrey Weiss G. Lynn Law Robert E. Palermo Michael G. Katze
author_sort	Stewart T. Chang
title	Next-Generation Sequencing Reveals HIV-1-Mediated Suppression of T Cell Activation and RNA Processing and Regulation of Noncoding RNA Expression in a CD4<sup>+</sup> T Cell Line
title_short	Next-Generation Sequencing Reveals HIV-1-Mediated Suppression of T Cell Activation and RNA Processing and Regulation of Noncoding RNA Expression in a CD4<sup>+</sup> T Cell Line
title_full	Next-Generation Sequencing Reveals HIV-1-Mediated Suppression of T Cell Activation and RNA Processing and Regulation of Noncoding RNA Expression in a CD4<sup>+</sup> T Cell Line
title_fullStr	Next-Generation Sequencing Reveals HIV-1-Mediated Suppression of T Cell Activation and RNA Processing and Regulation of Noncoding RNA Expression in a CD4<sup>+</sup> T Cell Line
title_full_unstemmed	Next-Generation Sequencing Reveals HIV-1-Mediated Suppression of T Cell Activation and RNA Processing and Regulation of Noncoding RNA Expression in a CD4<sup>+</sup> T Cell Line
title_sort	next-generation sequencing reveals hiv-1-mediated suppression of t cell activation and rna processing and regulation of noncoding rna expression in a cd4<sup>+</sup> t cell line
publisher	American Society for Microbiology
publishDate	2011
url	https://doaj.org/article/4335629fcdcd4a7c9458980a08e6dea5
work_keys_str_mv	AT stewarttchang nextgenerationsequencingrevealshiv1mediatedsuppressionoftcellactivationandrnaprocessingandregulationofnoncodingrnaexpressioninacd4supsuptcellline AT pavelsova nextgenerationsequencingrevealshiv1mediatedsuppressionoftcellactivationandrnaprocessingandregulationofnoncodingrnaexpressioninacd4supsuptcellline AT xinxiapeng nextgenerationsequencingrevealshiv1mediatedsuppressionoftcellactivationandrnaprocessingandregulationofnoncodingrnaexpressioninacd4supsuptcellline AT jeffreyweiss nextgenerationsequencingrevealshiv1mediatedsuppressionoftcellactivationandrnaprocessingandregulationofnoncodingrnaexpressioninacd4supsuptcellline AT glynnlaw nextgenerationsequencingrevealshiv1mediatedsuppressionoftcellactivationandrnaprocessingandregulationofnoncodingrnaexpressioninacd4supsuptcellline AT robertepalermo nextgenerationsequencingrevealshiv1mediatedsuppressionoftcellactivationandrnaprocessingandregulationofnoncodingrnaexpressioninacd4supsuptcellline AT michaelgkatze nextgenerationsequencingrevealshiv1mediatedsuppressionoftcellactivationandrnaprocessingandregulationofnoncodingrnaexpressioninacd4supsuptcellline
_version_	1718427822496677888

Next-Generation Sequencing Reveals HIV-1-Mediated Suppression of T Cell Activation and RNA Processing and Regulation of Noncoding RNA Expression in a CD4<sup>+</sup> T Cell Line

Ejemplares similares