Immunological landscape of human lymphoid explants during measles virus infection [scRNA-seq]

In humans, lymph nodes are the primary site of measles virus (MeV) replication. To understand the immunological events that occur at this site, we infected human lymphoid tissue explants using a pathogenic strain of MeV that expresses GFP. We found that MeV infected between 5-15% of cells across donors. Using single cell RNA-Seq (scRNA-Seq) and flow cytometry, we found that while most of the 29 cell populations identified in the lymphoid culture were susceptible to MeV, there was a broad preferential infection of B cells and reduced infection of T cells. Further subsetting of T cells revealed that this reduction may be driven by the decreased infection of naïve T cells. Transcriptional changes in infected B cells were dominated by an interferon stimulated gene (ISG) signature. To determine which of these ISGs were most substantial, we evaluated the proteome of MeV-infected Raji cells by mass spectrometry. We found that IFIT1, IFIT2, IFIT3, ISG15, CXCL10, MX2, and XAF1 proteins were the most highly induced, and positively correlated with their expression in the transcriptome. These data provide insight into the immunological events that occur in lymph nodes during infection and may lead to the development of therapeutic interventions. Overall design: Human tonsilar explants were infected with measles virus (IC323-eGFP). After 8 days of infection, tissues were homogenized with collagenase and single cell suspensions were generated. Infected (GFP+), Bystander (GFP- from infected explants) and donor matched uninfected cells (GFP- from uninfected explants) were isolated by FACS, and analyzed by single cell RNA sequencing. This study included one tonsil donor for analysis.