A novel hybrid CRISPR tool for gene network perturbation and hiPSC engineering

Stem cell-based applications benefit from an ability to generate specific cell types. That is because therapeutic cell replacement or diagnostics work best if they use only the very specific cell types required. But current methods for generating cells are often only able to make approximately the cells required. And they often generate of a mix of both desired and undesired cells. Furthermore, these methods are often labor-intensive and require much trial-and-error experimentation. There is thus a major need for methods that improve and standardize the process for making specific cell types from stem cells. In this project, we have developed such a method. We refer to our method as a unified workflow for data-driven precision cell fate engineering. Our workflow consists of two parts – computation and execution. The computation part consists of our new computer model that uses publicly available big biological datasets as input. The model predicts which combination of genes should be simultaneously turned on or off in a starting cell type to convert it into a desired target cell type. To execute this multi-gene “command” in stem cells, we developed a suite of molecular tools capable of simultaneously turning many genes on and off, which has not been feasible before. When combined, this computation-execution workflow enabled us to convert stem cells into one desired cell type while simultaneously blocking the formation of undesired cell types that are normally difficult to get rid of. Such data-driven cell programming, and such deliberate exclusion of undesired cell types, has previously been unfeasible. In future work, we will apply our new technology to making therapeutically relevant cells that could find uses in both cell-replacement therapies, diagnostics, and drug testing.