SAMHD1 Knockout hiPSC model enables high lenti-viral transduction in myeloid cell types

Huinan Li ^1* Maliha Afroze ² Gunisha Arora ² Scot Federman ¹ Kaivalya Shevade ¹ Yeqing Angela Yang ² Phuong Nguyen ¹ Rustam Esanov ² Laralynne Przybyla ¹ Adam Litterman ¹ Shawn Shafer ^2*

• ¹ Laboratory for Genomics Research, University of California, San Francisco, San Francisco, United States
• ² GlaxoSmithKline (United States), Philadelphia, Pennsylvania, United States

Recent advances in functional genomics tools have ushered in a new era of genetic editing to identify molecular pathways relevant to developmental and disease biology. However, limited model systems are available that adequately mimic cell states and phenotypes associated with human disease pathways. Here, we quantitatively analyzed the founder population bottleneck effect and demonstrated how the population changes from human induced pluripotent stem cells (hiPSCs) to hematopoietic stem cells and to the final induced macrophage population. We then engineered a key gene encoding an enzyme in the myeloid cell antiviral pathway-SAMHD1knockout (KO) hiPSCs and characterized the hiPSCs line with RNA Seq, and induced macrophages from two distinct protocols with functional analysis. We then generated SAMHD1 KO CRISPR-dCAS9 KRAB hiPSCs through lenti-viral transduction aiming to increase the efficiency of lentiviral mediated gene transfer. We demonstrated increased lenti-viral transduction efficiency in induced macrophage, as well as microglia induced with two distinct protocols. This model allows for efficient gene knock down, as well as large-scale functional genomics screens in mature hiPSC-derived macrophages or microglia with applications in innate immunity and chronic inflammatory disease biology. These experiments highlight the broad applicability of this platform for disease-relevant target identification and may improve our ability to run large-scale screens in hiPSC-derived myeloid model systems.