Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics

Dylan Kotliar; Aaron E Lin; James Logue; Travis K Hughes; Nadine M Khoury; Siddharth S Raju; Marc H Wadsworth 2nd; Han Chen; Jonathan R Kurtz; Bonnie Dighero-Kemp; Zach B Bjornson; Nilanjan Mukherjee; Brian A Sellers; Nancy Tran; Matthew R Bauer; Gordon C Adams; Ricky Adams; John L Rinn; Marta Melé; Stephen F Schaffner; Garry P Nolan; Kayla G Barnes; Lisa E Hensley; David R McIlwain; Alex K Shalek; Pardis C Sabeti; Richard S Bennett

doi:10.1016/j.cell.2020.10.002

Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics

Cell. 2020 Nov 25;183(5):1383-1401.e19. doi: 10.1016/j.cell.2020.10.002. Epub 2020 Nov 6.

Authors

Dylan Kotliar¹, Aaron E Lin², James Logue³, Travis K Hughes⁴, Nadine M Khoury⁵, Siddharth S Raju⁶, Marc H Wadsworth 2nd⁷, Han Chen⁸, Jonathan R Kurtz³, Bonnie Dighero-Kemp³, Zach B Bjornson⁸, Nilanjan Mukherjee⁸, Brian A Sellers⁹, Nancy Tran¹⁰, Matthew R Bauer⁵, Gordon C Adams⁵, Ricky Adams³, John L Rinn¹¹, Marta Melé¹², Stephen F Schaffner¹³, Garry P Nolan⁸, Kayla G Barnes¹⁴, Lisa E Hensley¹⁵, David R McIlwain¹⁶, Alex K Shalek⁴, Pardis C Sabeti¹⁷, Richard S Bennett³

Affiliations

¹ Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA. Electronic address: dylan_kotliar@hms.harvard.edu.
² FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Program in Virology, Harvard Medical School, Boston, MA 02115, USA. Electronic address: alin@broadinstitute.org.
³ Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA.
⁴ Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Chemistry, Institute for Medical Engineering and Sciences (IMES), and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02142, USA; Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA.
⁵ FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
⁶ Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
⁷ Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Chemistry, Institute for Medical Engineering and Sciences (IMES), and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02142, USA; Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA.
⁸ Department of Pathology, Stanford University, Stanford, CA 94305, USA.
⁹ Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation, National Institutes of Health, Bethesda, MD 20814, USA.
¹⁰ Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA.
¹¹ Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA.
¹² Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Catalonia 08034, Spain.
¹³ FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA.
¹⁴ Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA; MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK.
¹⁵ Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA. Electronic address: lisa.hensley@nih.gov.
¹⁶ Department of Pathology, Stanford University, Stanford, CA 94305, USA. Electronic address: mcilwain@stanford.edu.
¹⁷ FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.

Abstract

Ebola virus (EBOV) causes epidemics with high mortality yet remains understudied due to the challenge of experimentation in high-containment and outbreak settings. Here, we used single-cell transcriptomics and CyTOF-based single-cell protein quantification to characterize peripheral immune cells during EBOV infection in rhesus monkeys. We obtained 100,000 transcriptomes and 15,000,000 protein profiles, finding that immature, proliferative monocyte-lineage cells with reduced antigen-presentation capacity replace conventional monocyte subsets, while lymphocytes upregulate apoptosis genes and decline in abundance. By quantifying intracellular viral RNA, we identify molecular determinants of tropism among circulating immune cells and examine temporal dynamics in viral and host gene expression. Within infected cells, EBOV downregulates STAT1 mRNA and interferon signaling, and it upregulates putative pro-viral genes (e.g., DYNLL1 and HSPA5), nominating pathways the virus manipulates for its replication. This study sheds light on EBOV tropism, replication dynamics, and elicited immune response and provides a framework for characterizing host-virus interactions under maximum containment.

Keywords: CyTOF; Ebola virus; Seq-Well; bystander cells; host-virus interactions; interferon; monocytes; scRNA-Seq; single-cell; viral tropism.

Publication types

Research Support, N.I.H., Extramural
Research Support, N.I.H., Intramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, P.H.S.

MeSH terms

Animals
Antigens, CD / metabolism
Biomarkers / metabolism
Bystander Effect
Cell Differentiation
Cell Proliferation
Cytokines / metabolism
Ebolavirus / genetics
Ebolavirus / physiology*
Endoplasmic Reticulum Chaperone BiP
Gene Expression Profiling
Gene Expression Regulation
Gene Expression Regulation, Viral
Hemorrhagic Fever, Ebola / genetics*
Hemorrhagic Fever, Ebola / immunology
Hemorrhagic Fever, Ebola / pathology
Hemorrhagic Fever, Ebola / virology*
Histocompatibility Antigens Class II / metabolism
Host-Pathogen Interactions / genetics*
Interferons / genetics
Interferons / metabolism
Macaca mulatta
Macrophages / metabolism
Monocytes / metabolism
Myelopoiesis
RNA, Messenger / genetics
RNA, Messenger / metabolism
Single-Cell Analysis*
Time Factors
Transcriptome / genetics

Substances

Antigens, CD
Biomarkers
Cytokines
Endoplasmic Reticulum Chaperone BiP
HSPA5 protein, human
Histocompatibility Antigens Class II
RNA, Messenger
Interferons

Abstract

Publication types

MeSH terms

Substances

Grants and funding