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

Stem Cell Reports. 2019 May 14;12(5):1084-1098. doi: 10.1016/j.stemcr.2019.03.012. Epub 2019 Apr 25.


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.

Keywords: RNAi; SMARCA4; SWI/SNF; comparative functional profiling; hematopoiesis; isogenic; neural differentiation; self-renewal.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cell Differentiation / genetics
  • Cell Self Renewal / genetics
  • Cells, Cultured
  • DNA Helicases / genetics*
  • Hematopoietic Stem Cells / cytology
  • Hematopoietic Stem Cells / metabolism
  • High-Throughput Screening Assays / methods*
  • Humans
  • Induced Pluripotent Stem Cells / cytology
  • Induced Pluripotent Stem Cells / metabolism*
  • Mice
  • Neural Stem Cells / cytology
  • Neural Stem Cells / metabolism*
  • Nuclear Proteins / genetics*
  • RNA Interference*
  • Stem Cell Transplantation / methods
  • Stem Cells / cytology
  • Stem Cells / metabolism
  • Transcription Factors / genetics*


  • Nuclear Proteins
  • Transcription Factors
  • SMARCA4 protein, human
  • DNA Helicases