scIVNL-seq resolves in vivo single-cell RNA dynamics of immune cells during Salmonella infection

The immune response against pathogens involves multiple cell state transitions and complex gene expression changes. Here, we establish a single-cell in vivo new RNA labeling sequencing method (scIVNL-seq) and apply it to survey time-resolved RNA dynamics during immune response to acute enteric infection with Salmonella. We show that the detection of new RNA synthesis reflects more realistic information on cell activation and gene transcription than total RNA level. Interplay of RNA synthesis and degradation modulates the dynamics of total RNA. The bone marrow macrophages are first primed at a very early stage upon Salmonella infection. In contrast, the innate immune response of macrophages in intestine is limited. Notably, intestinal CD8⁺ T cells and plasma cells are rapidly and specifically activated at the early stage post infection. Intestinal late enterocytes quickly express MHC-I molecules and present Salmonella antigen to CD8⁺ T cells for their activation, serving as antigen presenting cells for the initiation of adaptive immunity. Our findings reveal the RNA control strategies and the dynamic activation rules of immune cells in response to Salmonella infection, challenging the doctrine boundary between innate immunity and adaptive immunity against bacterial infection.