Hardy, C. S. C. | Search bioRxiv

bioRxiv2026

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

BackgroundDengue 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. MethodsWe 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. FindingsAcross 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. InterpretationThese 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 ContextO_ST_ABSEvidence for this studyC_ST_ABSDengue 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 studyThis 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 evidenceThese 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.

immunology↗

bioRxiv2024

Antibody-dependent DENV infection induces distinct transcriptomic responses in infected and bystander human macrophages

Dengue virus (DENV) is a mosquito-borne flavivirus which coexists as four genetically and immunologically distinct serotypes (DENV1-4). In secondary heterologous DENV infection, pre-existing immunity is believed to contribute to severe disease through antibody dependent enhancement (ADE). Although the elevated pathology observed in ADE conditions has been described, the cell intrinsic mechanisms governing this process remain unclear. Using scRNAseq, we investigated the transcriptomic profiles of human monocyte-derived macrophages infected by DENV via ADE compared to conventional infection conditions. Unsupervised analysis of scRNAseq data enabled the identification and differentiation of infected and bystander/uninfected cells in a heterogeneous cell culture. Differential gene expression and Ingenuity Pathway analyses revealed a number of significantly up- and down-regulated genes and gene networks between cells infected by ADE compared to conventional infection. Specifically, these pathways indicated mechanisms such as suppressed interferon signaling and inflammatory chemokine transcription in cells infected via ADE. Further analysis revealed that transcriptomic changes were independent of viral RNA within infected cells, suggesting that the observed changes are reflective of cell-intrinsic responses and not simply a function of per-cell viral burden. Bystander cells in ADE conditions also demonstrated distinct profiles, indicating an immunologically activated phenotype enriched for the expression of gene networks involved with protein translation, cytokine production, and antigen presentation. Together, these findings support the concept that DENV infection via ADE induces a qualitatively different transcriptomic response in infected and bystander cells, contributing to our understanding of ADE as a mechanistic driver of disease and pathogenesis. IMPORTANCEDengue virus (DENV) is a mosquito-borne human pathogen with a significant and growing global health burden. Although correlates of severe dengue disease are poorly understood, pre-existing immunity to DENV has been associated with severe disease risk and known to contribute to an alternative route of viral entry termed antibody-dependent enhancement (ADE). Using single cell RNA sequencing, we identified distinct transcriptomic processes involved in antibody-mediated DENV entry compared to conventional receptor mediated entry. These data provide meaningful insight into the discrete processes contributing to DENV pathogenesis in ADE conditions.

immunology↗