A Pooled Cell Painting CRISPR Screening Platform Enables de novo Inference of Gene Function by Self-supervised Deep Learning

Pooled CRISPR screening has emerged as a powerful method of mapping gene functions thanks to its scalability, affordability, and robustness against well or plate-specific confounders present in array-based screening^1–6. Most pooled CRISPR screens assay for low dimensional phenotypes (e.g. fitness, fluorescent markers). Higher-dimensional assays such as perturb-seq are available but costly and only applicable to transcriptomics readouts^7–11. Recently, pooled optical screening, which combines pooled CRISPR screening and microscopy-based assays, has been demonstrated in the studies of the NFkB pathway, essential human genes, cytoskeletal organization and antiviral response^12–15. While the pooled optical screening methodology is scalable and information-rich, the applications thus far employ hypothesis-specific assays. Here, we enable hypothesis-free reverse genetic screening for generic morphological phenotypes by re-engineering the Cell Painting¹⁶technique to provide compatibility with pooled optical screening. We validated this technique using well-defined morphological genesets (124 genes), compared classical image analysis and self-supervised learning methods using a mechanism-of-action (MoA) library (300 genes), and performed discovery screening with a druggable genome library (1640 genes)¹⁷. Across these three experiments we show that the combination of rich morphological data and deep learning allows gene networks to emerge without the need for target-specific biomarkers, leading to better discovery of gene functions.