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Virus-inclusive single-cell RNA sequencing reveals the molecular signature of progression to severe dengue
Dengue virus (DENV) infection can result in severe complications. However, the understanding of the molecular correlates of severity is limited, partly due to difficulties in defining the peripheral blood mononuclear cells (PBMCs) that contain DENV RNA in vivo. Accordingly, there are currently no bi...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
National Academy of Sciences
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6310786/ https://www.ncbi.nlm.nih.gov/pubmed/30530648 http://dx.doi.org/10.1073/pnas.1813819115 |
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author | Zanini, Fabio Robinson, Makeda L. Croote, Derek Sahoo, Malaya Kumar Sanz, Ana Maria Ortiz-Lasso, Eliana Albornoz, Ludwig Luis Rosso, Fernando Montoya, Jose G. Goo, Leslie Pinsky, Benjamin A. Quake, Stephen R. Einav, Shirit |
author_facet | Zanini, Fabio Robinson, Makeda L. Croote, Derek Sahoo, Malaya Kumar Sanz, Ana Maria Ortiz-Lasso, Eliana Albornoz, Ludwig Luis Rosso, Fernando Montoya, Jose G. Goo, Leslie Pinsky, Benjamin A. Quake, Stephen R. Einav, Shirit |
author_sort | Zanini, Fabio |
collection | PubMed |
description | Dengue virus (DENV) infection can result in severe complications. However, the understanding of the molecular correlates of severity is limited, partly due to difficulties in defining the peripheral blood mononuclear cells (PBMCs) that contain DENV RNA in vivo. Accordingly, there are currently no biomarkers predictive of progression to severe dengue (SD). Bulk transcriptomics data are difficult to interpret because blood consists of multiple cell types that may react differently to infection. Here, we applied virus-inclusive single-cell RNA-seq approach (viscRNA-Seq) to profile transcriptomes of thousands of single PBMCs derived early in the course of disease from six dengue patients and four healthy controls and to characterize distinct leukocyte subtypes that harbor viral RNA (vRNA). Multiple IFN response genes, particularly MX2 in naive B cells and CD163 in CD14(+) CD16(+) monocytes, were up-regulated in a cell-specific manner before progression to SD. The majority of vRNA-containing cells in the blood of two patients who progressed to SD were naive IgM B cells expressing the CD69 and CXCR4 receptors and various antiviral genes, followed by monocytes. Bystander, non-vRNA–containing B cells also demonstrated immune activation, and IgG1 plasmablasts from two patients exhibited clonal expansions. Lastly, assembly of the DENV genome sequence revealed diversity at unexpected sites. This study presents a multifaceted molecular elucidation of natural dengue infection in humans with implications for any tissue and viral infection and proposes candidate biomarkers for prediction of SD. |
format | Online Article Text |
id | pubmed-6310786 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | National Academy of Sciences |
record_format | MEDLINE/PubMed |
spelling | pubmed-63107862019-01-04 Virus-inclusive single-cell RNA sequencing reveals the molecular signature of progression to severe dengue Zanini, Fabio Robinson, Makeda L. Croote, Derek Sahoo, Malaya Kumar Sanz, Ana Maria Ortiz-Lasso, Eliana Albornoz, Ludwig Luis Rosso, Fernando Montoya, Jose G. Goo, Leslie Pinsky, Benjamin A. Quake, Stephen R. Einav, Shirit Proc Natl Acad Sci U S A PNAS Plus Dengue virus (DENV) infection can result in severe complications. However, the understanding of the molecular correlates of severity is limited, partly due to difficulties in defining the peripheral blood mononuclear cells (PBMCs) that contain DENV RNA in vivo. Accordingly, there are currently no biomarkers predictive of progression to severe dengue (SD). Bulk transcriptomics data are difficult to interpret because blood consists of multiple cell types that may react differently to infection. Here, we applied virus-inclusive single-cell RNA-seq approach (viscRNA-Seq) to profile transcriptomes of thousands of single PBMCs derived early in the course of disease from six dengue patients and four healthy controls and to characterize distinct leukocyte subtypes that harbor viral RNA (vRNA). Multiple IFN response genes, particularly MX2 in naive B cells and CD163 in CD14(+) CD16(+) monocytes, were up-regulated in a cell-specific manner before progression to SD. The majority of vRNA-containing cells in the blood of two patients who progressed to SD were naive IgM B cells expressing the CD69 and CXCR4 receptors and various antiviral genes, followed by monocytes. Bystander, non-vRNA–containing B cells also demonstrated immune activation, and IgG1 plasmablasts from two patients exhibited clonal expansions. Lastly, assembly of the DENV genome sequence revealed diversity at unexpected sites. This study presents a multifaceted molecular elucidation of natural dengue infection in humans with implications for any tissue and viral infection and proposes candidate biomarkers for prediction of SD. National Academy of Sciences 2018-12-26 2018-12-07 /pmc/articles/PMC6310786/ /pubmed/30530648 http://dx.doi.org/10.1073/pnas.1813819115 Text en Copyright © 2018 the Author(s). Published by PNAS. https://creativecommons.org/licenses/by-nc-nd/4.0/ This open access article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND) (https://creativecommons.org/licenses/by-nc-nd/4.0/) . |
spellingShingle | PNAS Plus Zanini, Fabio Robinson, Makeda L. Croote, Derek Sahoo, Malaya Kumar Sanz, Ana Maria Ortiz-Lasso, Eliana Albornoz, Ludwig Luis Rosso, Fernando Montoya, Jose G. Goo, Leslie Pinsky, Benjamin A. Quake, Stephen R. Einav, Shirit Virus-inclusive single-cell RNA sequencing reveals the molecular signature of progression to severe dengue |
title | Virus-inclusive single-cell RNA sequencing reveals the molecular signature of progression to severe dengue |
title_full | Virus-inclusive single-cell RNA sequencing reveals the molecular signature of progression to severe dengue |
title_fullStr | Virus-inclusive single-cell RNA sequencing reveals the molecular signature of progression to severe dengue |
title_full_unstemmed | Virus-inclusive single-cell RNA sequencing reveals the molecular signature of progression to severe dengue |
title_short | Virus-inclusive single-cell RNA sequencing reveals the molecular signature of progression to severe dengue |
title_sort | virus-inclusive single-cell rna sequencing reveals the molecular signature of progression to severe dengue |
topic | PNAS Plus |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6310786/ https://www.ncbi.nlm.nih.gov/pubmed/30530648 http://dx.doi.org/10.1073/pnas.1813819115 |
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