A divergent and complementary transcriptional response in poxvirus-infected and bystander inflammatory monocytes is partly dictated by interferon [iMO_Bcells_ECTV]

Inflammatory monocytes (iMO) and B-cells are the main targets of the poxvirus ectromelia virus (ECTV) in the lymph nodes of mice and play distinct roles in surviving the infection. Infected and bystander iMO control ECTV’s systemic spread, preventing early death, while B-cells make antibodies that eliminate ECTV. Our work demonstrates that within an infected animal that survives ECTV infection, intrinsic and bystander infection of iMO and B-cells differentially control the transcription of genes important for immune cell function and, perhaps, cell identity. Bystander cells upregulate metabolism, antigen presentation, and interferon-stimulated genes. Infected cells downregulate many cell-type-specific genes and upregulate transcripts typical of non-immune cells. Bys and Inf iMO non-redundantly contribute to the cytokine milieu and the interferon response. Furthermore, we uncovered how IFN-I or IFN-γ signaling differentially regulates immune pathways in Inf and Bys iMO and, that at steady state, IFN-I primes iMO for rapid IFN-I production and antigen presentation. Bystander and infected iMO and B-cells were sorted from popliteal draining lymph nodes of ectromelia virus-infected mice at 3 days post-infection. GFP-expressing ectromelia virus was used for sorting Bystander and Infected cells. As controls, Naïve iMO were sorted from spleen and Naïve B-cells sorted from lymph node of uninfected animals. 3 biological replicates were sequenced for all groups, except for Inf iMO for which only 2 biological replicates were sequenced.