Pooled genetic perturbation screens with image-based phenotypes

Abstract

Discovery of the genetic components underpinning fundamental and disease-related processes is being rapidly accelerated by combining efficient, programmable genetic engineering with phenotypic readouts of high spatial, temporal, and/or molecular resolution. Microscopy is a fundamental tool for studying cell biology, but its lack of high-throughput sequence readouts hinders integration in large-scale genetic screens. Optical pooled screens using in situ sequencing provide massively scalable integration of barcoded lentiviral libraries (e.g., CRISPR perturbation libraries) with high-content imaging assays, including dynamic processes in live cells. The protocol uses standard lentiviral vectors and molecular biology, providing single-cell resolution of phenotype and engineered genotype, scalability to millions of cells, and accurate sequence reads sufficient to distinguish >10 6 perturbations. In situ amplification takes ~2 days, while sequencing can be performed in ~1.5 hours per cycle. The image analysis pipeline provided enables fully parallel automated sequencing analysis using a cloud or cluster computing environment.

Pooled image-base screening of mitochondria with microraft isolation distinguishes pathogenic mitofusin 2 mutations

“…Several other technologies can perform pooled screening for imageable phenotypes 46 , and these screening-imaging systems are listed in Table 1 for comparison. The quality of imaging varies by system (Table 1a ).…”

Pooled genetic screens with image‐based profiling

“…In this section, we propose a roadmap for the integration of new perturbation modalities and phenotypic measurements, the extension of approaches to new biological model systems, and improvements in workflows to enable greater scale and dissemination of technologies. While some aspects we discuss apply to the broader set of microscopy-based screening technologies, we focus our discussion on future implementations of pooled profiling technologies, in particular, ISS-based optical pooled profiling screens of mammalian cells (Feldman et al, 2019(Feldman et al, , 2022Funk et al, 2022).…”

“…Following amplification, barcodes are sequenced in situ , as demonstrated by several groups, with sequencing‐by‐synthesis (SBS) or sequencing‐by‐ligation chemistry (Fig 2C; Ke et al , 2013; Payne, 2017; Chen et al , 2018; Feldman et al , 2019). We describe the experimental procedure for ISS using SBS at length in a recent protocol publication (Feldman et al , 2022). In our initial demonstration, we studied 952 gene knockouts, measuring p65 localization in about 6 million cells in a series of screens and taking time course measurements of live cells for over 400,000 cells in targeted downstream screening (Feldman et al , 2019).…”

“…Pooled screening approaches facilitate the deployment of these assays across large libraries of genetic perturbations and multiple cellular models. We have demonstrated in situ genotyping of sgRNAs in tens of cancer cell lines, with effective genotyping typically possible using a single, standard protocol (Feldman et al , 2022).…”

High-content CRISPR screening in tumor immunology

“…Pooled CRISPR screens can additionally be linked to singlecell optical phenotypes in fixed and live cells (Table 1). Initial work done by Feldman et al (121,127) details the use of barcoded single gRNA libraries as well as non-barcoded CROP-seq libraries for this purpose (Figure 2A). Following a pooled CRISPR screen, immunostaining and microscopy is employed to delineate single cells in a region of interest prior to in situ amplification and sequencing.…”