Comparative RNAi Screens in Isogenic Human Stem Cells Reveal SMARCA4 as a Differential Regulator

Abstract

Summary: Large-scale RNAi screens are a powerful approach to identify functions of genes in a cell-type-specific manner. For model organisms, genetically identical (isogenic) cells from different cell types are readily available, making comparative studies meaningful. However, large-scale screens in isogenic human primary cells remain challenging. Here, we show that RNAi screens are possible in genetically identical human stem cells, using induced pluripotent stem cells as intermediates. The screens revealed SMARCA4 (SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4) as a stemness regulator, while balancing differentiation distinctively for each cell type. SMARCA4 knockdown in hematopoietic stem and progenitor cells caused impaired self-renewal in vitro and in vivo with skewed myeloid differentiation; whereas, in neural stem cells, it impaired self-renewal while biasing differentiation toward neural lineage, through combinatorial SWI/SNF subunit assembly. Our findings pose a powerful approach for deciphering human stem cell biology and attribute distinct roles to SMARCA4 in stem cell maintenance. : Güneş et al. show that RNAi screens on genetically identical (isogenic) human stem cells can dissect epigenetic factors important for self-renewal versus differentiation. By using iPSCs as a bridging cell type, the comparative RNAi screens in HSPCs and NSCs identify SMARCA4 as an important regulator of self-renewal and differentiation with cell-type-specific functions. Keywords: RNAi, comparative functional profiling, isogenic, hematopoiesis, self-renewal, neural differentiation, SMARCA4, SWI/SNF