#73 Single Cell RNA Sequencing of Zika Infection in Neural Tissues Reveals an Astrocyte-Driven Innate Immune Response Governed by Interferon Beta.

Abstract

Abstract Background Congenital infection with Zika virus (ZIKV) has been linked to severe of fetal brain disruption and other developmental anomalies referred to collectively as congenital Zika syndrome (CZS). Long-term follow up of ZIKV-exposed infants has shown that even those without overt findings of CZS can have significant cognitive and developmental difficulties. However, the pathogenesis of ZIKV-related microcephaly and cognitive dysfunction remain poorly understood. To begin answering these questions, we sought to define the consequences of ZIKV infection on specific cell types in the developing brain. Method We have used primary human fetal brain cultures and human induced pluripotent stem cell-derived neural progenitor cell lines to probe innate immune signaling to ZIVK infection in vitro. We used single-cell RNA sequencing (10x Genomics) to identify the cell type-specific transcriptional changes induced by ZIKV infection. Results We found that neural progenitor cells (NPCs) support higher ZIKV RNA copy number than do differentiated neural cells. Moreover, while IFN-β is the predominant cytokine released by differentiated cells in response to ZIKV infection, NPCs do not produce IFN-β. By additionally characterizing the transcriptional response to IFN-β treatment, we have been able to distinguish virus-stimulated genes (VSGs) from interferon-stimulated genes (ISGs) across cell types. We find extensive heterogeneity in cell type-specific VSG and ISG profiles. Astrocytes undergo the largest transcriptional changes in response to infection and are the main producers of IFN-β. Our findings also identify genes whose expression is altered during viral infection specifically in NPCs and neurons, providing candidate pathways that may underlie neural dysfunction. Conclusion Across cell types, the response to Zika infection closely matches the response to IFN-β, arguing that astrocyte-derived IFN-β is the main driver of the innate immune response to ZIKV in the developing brain. Our findings provide insight into the pathogenesis of CZS and offer novel targets for improving developmental outcomes after fetal ZIKV infection.