Perturb-Multimodal pooled screening in intact tissues

Abstract

Imaging-based pooled genetic screening has been adopted to study genotype–phenotype relationships and expanded to multimodal measurements. Saunders et al. introduce an integrated approach known as Perturb-Multimodal (Perturb-Multi), which combines imaging and single-cell RNA sequencing for pooled genetic screens in intact tissues with multimodal phenotypic readouts. Perturb-Multi benefits from technological innovations to capture RNA–protein phenotypes and intact transcriptomes for in vivo screens. The unique feature is paired sequencing and imaging analysis of genetic perturbations in the same tissue, which enables the effects on both gene expression and subcellular morphology to be measured simultaneously, providing the potential to study genetic regulation of organ function at scale and in vivo. Applying Perturb-Multi to the mouse liver led to a systematic view of diverse gene perturbation effects on transcriptional state and tissue organization, and importantly, the identification of candidate genetic regulators of liver physiology related to hepatocyte zonation, cellular stress response and steatosis. Perturb-Multi provides training data for machine learning models, and may be expanded to other organs for functional genomics studies at the cellular and tissue levels under different physiological conditions.

Original reference: Cell https://doi.org/10.1016/j.cell.2025.05.022 (2025)