Directed Evolution of Reprogramming Factors by Cell Selection and Sequencing

Abstract

Summary: Directed biomolecular evolution is widely used to tailor and enhance enzymes, fluorescent proteins, and antibodies but has hitherto not been applied in the reprogramming of mammalian cells. Here, we describe a method termed directed evolution of reprogramming factors by cell selection and sequencing (DERBY-seq) to identify artificially enhanced and evolved reprogramming transcription factors. DERBY-seq entails pooled screens with libraries of positionally randomised genes, cell selection based on phenotypic readouts, and genotyping by amplicon sequencing for candidate identification. We benchmark this approach using pluripotency reprogramming with libraries based on the reprogramming factor SOX2 and the reprogramming incompetent endodermal factor SOX17. We identified several SOX2 variants outperforming the wild-type protein in three- and four-factor cocktails. The most effective variants were discovered from the SOX17 library, demonstrating that this factor can be converted into a highly potent inducer of pluripotency with a range of diverse modifications. We propose DERBY-seq as a broad-based approach to discover reprogramming factors for any donor/target cell combination applicable to direct lineage reprogramming in vitro and in vivo. : Transcription factor-driven cell-fate conversions are powerful methods to turn one cell type into another but are typically slow and inefficient. In this article Jauch and Veerapandian et al. showed that naturally occurring factors are not optimally adapted for this feat but can be profoundly improved by artificially evolving the way they read and translate regulatory information stored in the genome. Keywords: directed evolution, protein engineering, cellular reprogramming, synthetic biology, deep mutational scanning, synthetic transcription factors, SOX2, SOX17, OCT4