The generation and maintenance of differentiated cell types in the intestine depends on genetic networks that remain poorly understood. The Drosophila midgut is a powerful model for studying these regulatory circuits. Its biology is conserved across species, and its genetic accessibility allows targeted perturbation of individual genes at scale.
Our research investigates how intestinal stem cells (ISCs) give rise to distinct cell types in the Drosophila midgut. We use single-cell transcriptomic data from in vivo CRISPR knockdown experiments targeting ISCs in healthy adult animals. Our goal is to explore how single gene perturbations affect cellular behaviour across the tissue. The dataset comprises scRNA-seq profiles of ~620 000 cells from 127 replicate experiments covering 49 unique genetic perturbations.
We perform an exploratory analysis to uncover molecular relationships between perturbation conditions. We group conditions based on similarity in cell type abundance shifts, particularly among differentiated enterocyte populations, identifying 6 phenotypically coherent clusters. For each cluster, we examine expression changes to detect shared molecular responses. We assess common pathways, transcription factors, and differentially expressed genes across perturbations and cell types to characterize convergent regulatory signatures in the intestinal tissue.
This analysis reveals candidate genetic network modules and generates testable hypotheses about how distinct perturbations converge on shared cellular outcomes.

Co-authors: Siamak Redhai, Michael Boutros, Stefan Peidli, Wolfgang Huber