Characterization of myeloid cells in acute and chronic LCMV infection by scRNA-seq

The immune response to a chronic viral infection is uniquely tailored to balance viral control and immunopathology. The role of myeloid cells in shaping the response to chronic viral infection, however, is poorly understood. Single-cell RNA sequencing of myeloid cells during acute and chronic LCMV infection was performed to address this question. We discovered a cluster of suppressive neutrophils that is enriched in chronic versus acute infection. Furthermore, suppressive neutrophils highly expressed the gene encoding PIM1, a kinase known to promote mitochondrial fitness and cell survival. Pharmacological inhibition of PIM1 selectively diminished suppressive neutrophil-mediated immunosuppression without affecting the function of monocytic myeloid derived suppressor cells (M-MDSCs). Decreased accumulation of suppressive neutrophils led to increased CD8 T cell function and viral control. Mechanistically, PIM kinase activity was required for maintaining fused mitochondrial networks in suppressive neutrophils, but not in M-MDSCs, and loss of PIM kinase function caused increased apoptosis of suppressive neutrophils. Mice were infected with 200 or 2,000,000 PFU LCMV Clone 13 to establish acute and chronic infection, respectively. Spleens were harvested 7 days post-infection. Myeloid cells (B220- CD3- NK1.1- CD11b+) were purified by FACS sorting and subjected to the 10x Genomics scRNA-seq protocol.