Temporal specificity and heterogeneity of Drosophila immune cells

Immune cells provide defense against non‐self and have recently been shown to also play key roles in diverse processes such as development, metabolism, and tumor progression. The heterogeneity of Drosophila immune cells (hemocytes) remains an open question. Using bulk RNA sequencing, we find that the hemocytes display distinct features in the embryo, a closed and rapidly developing system, compared to the larva, which is exposed to environmental and metabolic challenges. Through single‐cell RNA sequencing, we identify fourteen hemocyte clusters present in unchallenged larvae and associated with distinct processes, e.g., proliferation, phagocytosis, metabolic homeostasis, and humoral response. Finally, we characterize the changes occurring in the hemocyte clusters upon wasp infestation, which triggers the differentiation of a novel hemocyte type, the lamellocyte. This first molecular atlas of hemocytes provides insights and paves the way to study the biology of the Drosophila immune cells in physiological and pathological conditions. Synopsis Single cell transcriptome analyses of control and challenged Drosophila hemocytes identify immune cell populations associated with distinct biological processes. The transcriptome of the fly immune cells undergoes a metabolic switch during development. A single‐cell atlas of fly immune cells in control and wasp‐infested larvae. Fourteen immune cell populations are identified that are associated with distinct cellular processes. Two additional populations appear upon immune challenge. Graphical Abstract Single cell RNAseq in normal and wasp infected flies reveals distinct immune cell populations associated with different biological processes.