Master Regulators and Cofactors of Human Neuronal Cell Fate Specification Identified by CRISPR Gene Activation Screens
Joshua B. Black,
Sean R. McCutcheon,
Shataakshi Dube,
Alejandro Barrera,
Tyler S. Klann,
Grayson A. Rice,
Shaunak S. Adkar,
Scott H. Soderling,
Timothy E. Reddy,
Charles A. Gersbach
Affiliations
Joshua B. Black
Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
Sean R. McCutcheon
Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
Shataakshi Dube
Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA
Alejandro Barrera
Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA; Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA
Tyler S. Klann
Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
Grayson A. Rice
Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
Shaunak S. Adkar
Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA; Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
Scott H. Soderling
Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA; Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
Timothy E. Reddy
Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA; Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA; Graduate Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA; University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA; Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708, USA
Charles A. Gersbach
Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA; Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA; Graduate Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA; University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA; Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA; Corresponding author
Summary: Technologies to reprogram cell-type specification have revolutionized the fields of regenerative medicine and disease modeling. Currently, the selection of fate-determining factors for cell reprogramming applications is typically a laborious and low-throughput process. Therefore, we use high-throughput pooled CRISPR activation (CRISPRa) screens to systematically map human neuronal cell fate regulators. We utilize deactivated Cas9 (dCas9)-based gene activation to target 1,496 putative transcription factors (TFs) in the human genome. Using a reporter of neuronal commitment, we profile the neurogenic activity of these factors in human pluripotent stem cells (PSCs), leading to a curated set of pro-neuronal factors. Activation of pairs of TFs reveals neuronal cofactors, including E2F7, RUNX3, and LHX8, that improve conversion efficiency, subtype specificity, and maturation of neuronal cell types. Finally, using multiplexed gene regulation with orthogonal CRISPR systems, we demonstrate improved neuronal differentiation with concurrent activation and repression of target genes, underscoring the power of CRISPR-based gene regulation for programming complex cellular phenotypes.
