Single-cell analysis of West Nile virus infection in brain organoids identified a serine synthesis enzyme as a determinant of viral neural tropism and a druggable antiviral target

Abstract

The cellular and molecular determinants of human neuroinvasive West Nile virus (WNV) disease are currently poorly defined. Previous studies of WNV neural infection relied on rodent models and immortalised cell lines that diverge from human brain tissue. Herein, we established a reproducible human cerebral organoid model of WNV infection and profiled it by virus-inclusive single-cell RNA sequencing (scRNA-Seq) to obtain an understanding of WNV-host interactions in the context of human neural tissue. We found that WNV showed preferential tropism to progenitor cells, immature neurons, and astrocytes, while the mature neurons were largely resistant to infection. Astrocytes were identified as the principal source of interferon (IFN) and the main hub of IFN-signalling, whereas mature neurons expressed little viral RNA-sensing machinery or STAT1 and responded weakly to infection and to IFN. The differential gene expression analysis between WNV-permissive and nonpermissive cells demonstrated that virus-susceptible cells had high baseline expression of the serine synthesis and one-carbon metabolism genes PHGDH, SHMT2, and MTHFD2, which were not induced by infection. RNA-interference and pharmacological inhibition of phosphoglycerate dehydrogenase (PHGDH) restricted WNV replication, confirming the requirement of this gene for WNV infection. In addition, the FDA-approved drug disulfiram, known to inhibit PHGDH, also reduced viral replication in neural progenitors and cerebral organoids. Overall, these results provide the first comprehensive single-cell-level characterisation of WNV neural infection in human neural tissue. They identify de novo serine synthesis as a metabolic dependency of WNV in human neural cells that can be targeted as a host-directed antiviral therapy.