The Cellular Diversity and Transcription Factor Code of Drosophila Enteroendocrine Cells

Enteroendocrine cells (EEs) in the intestinal epithelium have important endocrine functions, yet this cell lineage exhibits great local and regional variations that have hampered detailed characterization of EE subtypes. Through single-cell RNA-sequencing analysis, combined with a collection of peptide hormone and receptor knockin strains, here we provide a comprehensive analysis of cellular diversity, spatial distribution, and transcription factor (TF) code of EEs in adult Drosophila midgut. We identify 10 major EE subtypes that totally produced approximately 14 different classes of hormone peptides. Each EE on average co-produces approximately 2–5 different classes of hormone peptides. Functional screen with subtype-enriched TFs suggests a combinatorial TF code that controls EE cell diversity; class-specific TFs Mirr and Ptx1 respectively define two major classes of EEs, and regional TFs such as Esg, Drm, Exex, and Fer1 further define regional EE identity. Our single-cell data should greatly facilitate Drosophila modeling of EE differentiation and function. [Display omitted] •Single-cell analysis reveals 10 EE subtypes in Drosophila midgut•Most EEs produce approximately 2–5 peptide hormone classes•The spatial distribution of EE subtypes along the length of midgut is determined•TF code analysis and functional screens identify EE subtype regulators Through single-cell RNA-sequencing analysis and functional screens, Guo et al. provide a comprehensive characterization of the cellular diversity, spatial distribution, and transcription factor code of enteroendocrine cells in adult Drosophila midgut.