A comparative analysis of the immunotranscriptomic features of DENV-1, -3, and -4 human challenge models

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ABSTRACT Background Dengue virus (DENV) infections cause a range of clinical symptoms, from a mild febrile illness to severe disease. Higher levels of DENV RNAemia are associated with severe dengue, although this relationship is incompletely understood. Dengue Human Infection Models (DHIMs), in which volunteers are experimentally infected with underattenuated DENV strains, provide an invaluable tool for studying early virologic, transcriptional, and immunologic features of infection. DHIM studies using DENV-1, DENV-3, and DENV-4 have demonstrated qualitatively distinct clinical features, however, the contribution of RNAemia and serotype to divergent transcriptional and clinical profiles in these challenge models remains unclear. Methods We performed a comparative analysis of DHIM-1, DHIM-3, and DHIM-4 studies to determine shared and unique features of the transcriptional response to infection and their associations with RNAemia and clinical symptoms. We then exposed primary human PBMC in vitro to DENV-1 or DENV-3 at varying titers and performed bulk RNA sequencing. Findings Across DHIMs, we identified a set of conserved, upregulated genes at day of peak RNAemia, representing a core antiviral response independent of serotype. Further, a unique gene signature indicating downregulated cytoplasmic translation emerged in a subset of DHIM-3 participants with elevated RNAemia and symptomatology. In vitro PBMC exposure to DENV demonstrated that conserved and unique gene expression signatures varied as a function of viral dose rather than serotype. Interpretation These data show that viral burden correlates with transcriptional responses and clinical symptomatology following experimental DENV infection, contributing to our understanding of dengue pathogenesis and immunity. Research in Context Evidence for this study Dengue virus (DENV) infections are known to elicit a range of clinical symptoms. Previous studies have demonstrated the association of higher DENV RNAemia with more pronounced symptoms and elevated risk for severe disease. Understanding the molecular features associated with RNAemia kinetics may provide insight into disease immunologic and clinical pathogenesis. Three live virus human challenge model studies employing underattenuated DENV-1, DENV-3, and DENV-4 have been conducted which demonstrate variance in clinical and virologic features. These experimental DENV infections serve as a valuable model to study early kinetics of infection and immunotranscriptomic features associated with RNAemia irrespective of serotype. Added value of this study This study is the first to conduct a head-to-head comparison of the transcriptional features of DHIM-1, -3 and -4 models, and to provide an in-depth analysis of these signatures with respect to RNAemia kinetics. These unique datasets provide a rare opportunity to investigate the longitudinal transcriptional signatures associated with peak symptomatology, serotype and RNAemia kinetics. Implications of all the available evidence These data support the existence of conserved gene expression features of DENV infection, irrespective of serotype and dependent on RNAemia levels. These transcriptional signatures are relevant for our understanding of early events after DENV infection and their relationship to RNAemia as a correlate of disease severity.

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