Deciphering spatial patterns of immune response in fruit fly larvae*

Strong cellular variability in gene expression is a hallmark of innate immune responses and can steer infection outcomes. Variability can occur for many reasons, including stochastic gene expression and spatial microenvironments. However, it is difficult to know which mechanisms are relevant in vivo due to a lack of spatial and dynamical information. A better understanding of in vivo cellular variability will help us identify failure modes of the immune system in infectious disease. To this end, we established precision bacterial infection experiments in fruit fly larvae. Using live, light sheet fluorescence microscopy, we obtained organism-scale readouts of immune response gene expression at single-cell resolution. We discovered a robust U-shaped pattern of antimicrobial peptide expression along the animal's anterior-posterior axis. Preliminary experiments in heartless animals suggest this pattern is driven by blood flow, which causes bacterial aggregation and accumulation of activating ligands at the animal's poles. This work highlights the role of physical processes in driving immune variability. More broadly, the combination of live imaging and genetic perturbations possible in our fly system enables novel studies of in vivo immune responses in space and time.