Single cell immune profiling of dengue virus patients reveals intact immune responses to Zika virus with enrichment of innate immune signatures

Abstract

The genus Flavivirus contains many mosquito-borne human pathogens of global epidemiological importance such as dengue virus, West Nile virus, and Zika virus, which has recently emerged at epidemic levels. Infections with these viruses result in divergent clinical outcomes ranging from asymptomatic to fatal. Myriad factors influence infection severity including exposure, immune status and pathogen/host genetics. Furthermore, pre-existing infection may skew immune pathways or divert immune resources. We profiled immune cells from dengue virus-infected individuals by multiparameter mass cytometry (CyTOF) to define functional status. Elevations in IFNβ were noted in acute patients across the majority of cell types and were statistically elevated in 31 of 36 cell subsets. We quantified response to in vitro (re)infection with dengue or Zika viruses and detected a striking pattern of upregulation of responses to Zika infection by innate cell types which was not noted in response to dengue virus. Significance was discovered by statistical analysis as well as a neural network-based clustering approach which identified unusual cell subsets overlooked by conventional manual gating. Of public health importance, patient cells showed significant enrichment of innate cell responses to Zika virus indicating an intact and robust anti-Zika response despite the concurrent dengue infection.

Design and implementation of a prospective cohort study of persons living with and without HIV infection who are initiating medication treatment for opioid use disorder

“…The antibody panel for phenotyping has been validated for lineage markers to define immune cell subsets as well as shared markers of cellular activation. We have processed whole blood samples from study subjects for immune profiling [ 39 ].…”

“…Multivariable linear regressions will be fit to the outcomes of cell proportions and cytokine expression using predictors of group, stimulation type, and their interaction, with age and gender included as covariates. We conduct this detailed analysis using both manual gating and an unsupervised deep learning model following our recent methods [ 39 ]. Data from immune profiles will be integrated with other immune elements in the study for a full understanding of factors associated with MOUD and HIV status.…”

“…Profiling of immune cell frequency and functional status is determined by multiparameter immune profiling using cytometry by time-of-flight (CyTOF) according to our established methods [ 38 , 39 ]. Surface markers on freshly isolated heparinized blood are labeled with metal-conjugated antibodies (Fluidigm, South San Francisco, CA) prior to fixation for optimal labeling.…”

Progress and applications of mass cytometry in sketching immune landscapes

“…Viral infections pose a constant challenge to the hosts' immune system. Researchers have applied CyTOF to explore the immune alterations of patients infected with influenza, 124 HIV, [125][126][127][128][129][130][131][132][133] Japanese Encephalitis, 134 Ebola, 135 Gammaherpesvirus, 136 chikungunya, 137 hepatitis B, 138,139 as well as the mosquito-borne human viral pathogens, including dengue [140][141][142] and Zika, 143,144 and elucidated the fates of immune cells across viral infections. The use of CyTOF has also supported recent findings in COVID-19 pathogenesis and immune perturbations, 145,146 where the results showed immunosuppression and dysfunction in PBMCs of COVID-19-infected patients.…”

The Role of Single-Cell Technology in the Study and Control of Infectious Diseases

“…Going beyond traditional flow cytometry, mass spectrometry, or cytometry by time-of-flight (CyTOF) offers vastly increased numbers of parameters that can be investigated simultaneously, exponentially increasing the depth of the dataset collected. For instance, to investigate the effect of a precedent dengue virus infection on the outcome of subsequent Zika infections, PBMCs derived from patients with either acute dengue infection or health individuals were incubated with dengue virus or Zika virus, and the treated PBMCs were assessed by multiparameter CyTOF [37]. CyTOF in this study allowed the simultaneous detection of changes in the frequency of immune cell subpopulations and quantification of functional activation markers and cytokines in distinct cell subsets.…”