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.