Broadly neutralizing human antibodies against dengue virus identified by single B cell transcriptomics
- Chan Zuckerberg Biohub, United States
- Stanford University, United States
- Integral Molecular, Inc, United States
- Fundación Valle del Lili, Colombia
- Fred Hutchinson Cancer Research Center, United States
Abstract
Eliciting broadly neutralizing antibodies (bNAbs) against the four dengue virus serotypes (DENV1-4) that are spreading into new territories is an important goal of vaccine design. To define bNAb targets, we characterized 28 antibodies belonging to expanded and hypermutated clonal families identified by transcriptomic analysis of single plasmablasts from DENV-infected individuals. Among these, we identified J9 and J8, two somatically related bNAbs that potently neutralized DENV1-4. Mutagenesis studies showed that the major recognition determinants of these bNAbs are in E protein domain I, distinct from the only known class of human bNAbs against DENV with a well-defined epitope. B cell repertoire analysis from acute-phase peripheral blood suggested that J9 and J8 followed divergent somatic hypermutation pathways, and that a limited number of mutations was sufficient for neutralizing activity. Our study suggests multiple B cell evolutionary pathways leading to DENV bNAbs targeting a new epitope that can be exploited for vaccine design.
Data availability
All data generated or analysed during this study are included in the manuscript and supporting files. Source data files have been provided for Figures 2, 4, and 6.
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In vivo molecular signatures of severe dengue infection revealed by viscRNA-SeqNCBI Gene Expression Omnibus, GSE116672.
Article and author information
Author details
Funding
Chan Zuckerberg Biohub
- Natasha D Durham
- Aditi Agrawal
- Eric Waltari
- Fabio Zanini
- Olivia Smith
- Esteban Carabajal
- John E Pak
- Stephen R Quake
- Krista M McCutcheon
- Leslie Goo
Fred Hutchinson Cancer Research Center
- Leslie Goo
National Institutes of Health (HHSN272201400058C)
- Benjamin J Doranz
NSF Graduate Research Fellowship
- Derek Croote
Kou-I Yeh Stanford Graduate Fellowship
- Derek Croote
Catalyst Award from Dr Ralph and Marian Falk Medical Research Trust
- Shirit Einav
Stanford Bio-X Interdisciplinary Initiatives Seed Grants Program
- Shirit Einav
Stanford Advanced Residency Training at Stanford Fellowship Program
- Makeda Robinson
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Ethics
Human subjects: The study was approved by the Stanford University Administrative Panel on Human Subjects in Medical Research (Protocol #35460) and the Fundación Valle del Lili Ethics committee in biomedical research (Cali, Colombia). All subjects, their parents, or legal guardians provided written informed consent, and subjects between 6 to 17 years of age and older provided assent.
Reviewing Editor
- Sara L Sawyer, University of Colorado Boulder, United States
Version history
- Received: October 3, 2019
- Accepted: December 9, 2019
- Accepted Manuscript published: December 10, 2019 (version 1)
- Version of Record published: December 23, 2019 (version 2)
Copyright
© 2019, Durham et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Broadly neutralizing human antibodies against dengue virus identified by single B cell transcriptomics
eLife 8:e52384.
https://doi.org/10.7554/eLife.52384
Further reading
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Infection with Influenza A virus (IAV) causes the well-known symptoms of the flu, including fever, loss of appetite, and excessive sleepiness. These responses, mediated by the brain, will normally disappear once the virus is cleared from the system, but a severe respiratory virus infection may cause long-lasting neurological disturbances. These include encephalitis lethargica and narcolepsy. The mechanisms behind such long lasting changes are unknown. The hypothalamus is a central regulator of the homeostatic response during a viral challenge. To gain insight into the neuronal and non-neuronal molecular changes during an IAV infection, we intranasally infected mice with an H1N1 virus and extracted the brain at different time points. Using single-nucleus RNA sequencing (snRNA-seq) of the hypothalamus, we identify transcriptional effects in all identified cell populations. The snRNA-seq data showed the most pronounced transcriptional response at 3 days past infection, with a strong downregulation of genes across all cell types. General immune processes were mainly impacted in microglia, the brain resident immune cells, where we found increased numbers of cells expressing pro-inflammatory gene networks. In addition, we found that most neuronal cell populations downregulated genes contributing to the energy homeostasis in mitochondria and protein translation in the cytosol, indicating potential reduced cellular and neuronal activity. This might be a preventive mechanism in neuronal cells to avoid intracellular viral replication and attack by phagocytosing cells. The change of microglia gene activity suggest that this is complemented by a shift in microglia activity to provide increased surveillance of their surroundings.
