SEUSS: A scalable screening platform to assess transcriptomic and fitness effects of transcription factor overexpression

Understanding the complex effects of genetic perturbations on cellular state and fitness in human pluripotent stem cells (hPSCs) has been challenging using traditional pooled screening techniques which typically rely on unidimensional phenotypic readouts. Here, we use barcoded open reading frame (ORF) overexpression libraries with a coupled single-cell RNA sequencing (scRNA-seq) and fitness screening approach, a technique we call SEUSS (ScalablE fUnctional Screening by Sequencing), to establish a comprehensive assaying platform. Using this system, we perturbed hPSCs with a library of developmentally critical transcription factors (TFs), and assayed the impact of TF overexpression on fitness and transcriptomic cell state across multiple media conditions. We further leveraged the versatility of the ORF library approach to systematically assay mutant gene libraries and also whole gene families. From the transcriptomic responses, we built genetic co-perturbation networks to identify key altered gene modules. Strikingly, we found that KLF4 and SNAI2 have opposing effects on the pluripotency gene module, highlighting the power of our method to characterize the effects of genetic perturbations. From the fitness responses, we identified ETV2 as a driver of reprogramming towards an endothelial-like state. Pooled transcription factor overexpression screens with scRNA-seq in ~35,000 cells across ten screens: 61 pluripotency/lineage TFs in hPSC media with five replicates, endothelial media with one replicate, multilineage media with two replicates; MYC mutant overexpression in hPSC media with one replicate; KLF family TF overexpression in hPSC media with one replicate.