
A comprehensive library of human transcription factors for cell fate engineering
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ABSTRACT Human pluripotent stem cells (hPSCs) offer an unprecedented opportunity to model diverse cell types and tissues. To enable systematic exploration of the programming landscape
mediated by transcription factors (TFs), we present the Human TFome, a comprehensive library containing 1,564 TF genes and 1,732 TF splice isoforms. By screening the library in three hPSC
lines, we discovered 290 TFs, including 241 that were previously unreported, that induce differentiation in 4 days without alteration of external soluble or biomechanical cues. We used four
of the hits to program hPSCs into neurons, fibroblasts, oligodendrocytes and vascular endothelial-like cells that have molecular and functional similarity to primary cells. Our
cell-autonomous approach enabled parallel programming of hPSCs into multiple cell types simultaneously. We also demonstrated orthogonal programming by including oligodendrocyte-inducible
hPSCs with unmodified hPSCs to generate cerebral organoids, which expedited in situ myelination. Large-scale combinatorial screening of the Human TFome will complement other strategies for
cell engineering based on developmental biology and computational systems biology. Access through your institution Buy or subscribe This is a preview of subscription content, access via your
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Instant access to full article PDF Buy now Prices may be subject to local taxes which are calculated during checkout ADDITIONAL ACCESS OPTIONS: * Log in * Learn about institutional
subscriptions * Read our FAQs * Contact customer support SIMILAR CONTENT BEING VIEWED BY OTHERS EFFICIENT GENERATION OF FUNCTIONAL NEURONS FROM MOUSE EMBRYONIC STEM CELLS VIA NEUROGENIN-2
EXPRESSION Article 18 August 2023 IDENTIFICATION OF ASCL1 AS A DETERMINANT FOR HUMAN IPSC-DERIVED DOPAMINERGIC NEURONS Article Open access 15 November 2021 ESSENTIAL TRANSCRIPTION FACTORS
FOR INDUCED NEURON DIFFERENTIATION Article Open access 15 December 2023 DATA AVAILABILITY. Next-generation sequencing data that support the findings of the study are available in the Gene
Expression Omnibus using accession code GSE159786. CODE AVAILABILITY The code that supports the findings of this study is available from the corresponding authors upon reasonable request.
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1143–1154 (2015). Article CAS PubMed Google Scholar Download references ACKNOWLEDGEMENTS We thank J. Aach, M. O. Karl, R. Kalhor, N. Ostrov and H. Lee for critical feedback and the
Church and Busskamp laboratories for support. We acknowledge technical support from the Harvard Biopolymers Facility, the Harvard Division of Immunology Flow Cytometry Core Facility, the
Beth Israel Deaconess Medical Center Flow Cytometry Core, the Wyss Flow Cytometry and Microscopy Core, M. Ericsson and P. Coughlin at the Harvard Medical School Electron Microscopy Facility,
M. T. Gianatasio at the Dana-Farber/Harvard Cancer Center Specialized Histopathology Core and Rodent Histopathology Core (both supported, in part, by National Cancer Institute Cancer Center
Support grant NIH 5 P30 CA06516) and Harvard Medical School Orchestra Research Computing. We also thank the TU Dresden Center for Molecular and Cellular Bioengineering Advanced Imaging,
Deep Sequencing, Flow Cytometry and Stem Cell Engineering core facilities. We would also like to thank J. Gray’s laboratory for electrophysiology support, S. Jeanty and J. Lee (Church lab,
Harvard Medical School) for the PGP1 Sendai virus hiPSC line, G. Sheynkman and W. Glindmeyer for helpful discussions, A. Jolma, K. Nitta and K. Said for technical assistance and M. Lemieux
and J. McDade for their support in depositing the library to Addgene. A.H.M.N. was supported by an NSERC Postgraduate Fellowship and a Peter and Carolyn Lynch Foundation Fellowship. J.E.R.A.
was supported by the DIGS-BB program. S.L.S. is a Shurl and Kay Curci Foundation Fellow of the Life Sciences Research Foundation. The Ellison Foundation and Institute Sponsored Research
funds from the DFCI Strategic Initiative supported M.V. and D.E.H. The project was supported by the Volkswagen Foundation (Freigeist - A110720), the European Research Council (ERC-StG-678071
- ProNeurons) and the Deutsche Forschungsgemeinschaft (SPP2127, EXC-2068-390729961 - Cluster of Excellence - Physics of Life at TU Dresden and EXC-2151-390873048 – Cluster of Excellence –
ImmunoSensation2 at the University of Bonn) to V.B. G.M.C. acknowledges funding from National Human Genome Research Institute grants P50 HG005550 ‘Center for Casual Variation’, RM1 HG008525
‘Center for Genomically Engineered Organs’, the Simons Foundation for Autism Research Initiative (368485), the Blavatnik Biomedical Accelerator at Harvard University, the FunGCAT program
from the Office of the Director of National Intelligence Intelligence Advanced Research Projects Activity, via the Army Research Office, under federal award no. W911NF-17-2-0089 and research
funding from R. Merkin and the Merkin Family Foundation. AUTHOR INFORMATION Author notes * Jesus Eduardo Rojo Arias Present address: Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey
Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK * These authors contributed equally: Alex H. M. Ng, Parastoo Khoshakhlagh. AUTHORS AND
AFFILIATIONS * Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA Alex H. M. Ng, Parastoo Khoshakhlagh, Evan Appleton, Kiavash Kiaee, Richie E. Kohman,
Matthew Dysart, Kathleen Leeper, Wren Saylor, Jeremy Y. Huang, David E. Hill, Marc Vidal & George M. Church * Wyss Institute for Biologically Inspired Engineering at Harvard University,
Boston, MA, USA Alex H. M. Ng, Parastoo Khoshakhlagh, Evan Appleton, Kiavash Kiaee, Richie E. Kohman, Andyna Vernet, Matthew Dysart, Kathleen Leeper, Wren Saylor, Jeremy Y. Huang, Amanda
Graveline & George M. Church * GC Therapeutics, Inc, Cambridge, MA, USA Alex H. M. Ng, Parastoo Khoshakhlagh, Evan Appleton, Kiavash Kiaee & George M. Church * Technische Universität
Dresden, Center for Molecular and Cellular Bioengineering (CMCB), Center for Regenerative Therapies Dresden (CRTD), Dresden, Germany Jesus Eduardo Rojo Arias, Giovanni Pasquini, Anka
Swiersy & Volker Busskamp * Department of Cardiac Surgery, Boston Children’s Hospital, Boston, MA, USA Kai Wang & Juan M. Melero-Martin * Department of Surgery, Harvard Medical
School, Boston, MA, USA Kai Wang & Juan M. Melero-Martin * Gladstone Institutes and University of California, San Francisco, San Francisco, CA, USA Seth L. Shipman * Department of
Biochemistry, University of Cambridge, Cambridge, UK Jussi Taipale * Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden Jussi Taipale * Applied Tumor
Genomics Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland Jussi Taipale * Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA David
E. Hill & Marc Vidal * Department of Ophthalmology, Medical Faculty, University of Bonn, Bonn, Germany Volker Busskamp Authors * Alex H. M. Ng View author publications You can also
search for this author inPubMed Google Scholar * Parastoo Khoshakhlagh View author publications You can also search for this author inPubMed Google Scholar * Jesus Eduardo Rojo Arias View
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author publications You can also search for this author inPubMed Google Scholar * Jussi Taipale View author publications You can also search for this author inPubMed Google Scholar * David
E. Hill View author publications You can also search for this author inPubMed Google Scholar * Marc Vidal View author publications You can also search for this author inPubMed Google Scholar
* Juan M. Melero-Martin View author publications You can also search for this author inPubMed Google Scholar * Volker Busskamp View author publications You can also search for this author
inPubMed Google Scholar * George M. Church View author publications You can also search for this author inPubMed Google Scholar CONTRIBUTIONS A.H.M.N., P.K., V.B. and G.M.C. conceived the
idea, led the study and designed all experiments. A.H.M.N. and P.K. performed most of the experiments and analyses, with significant technical contributions from J.E.R.A, G.P., K.W., A.S.,
S.L.S., E.A., K.K., R.E.K., A.V., M.D., K.L., W.S., J.Y.H., A.G., J.T., D.E.H., M.V. and J.M.M.-M. V.B. and G.M.C. oversaw the study. A.H.M.N., P.K. and V.B. wrote the manuscript with input
and feedback from all authors. CORRESPONDING AUTHORS Correspondence to Volker Busskamp or George M. Church. ETHICS DECLARATIONS COMPETING INTERESTS A.H.M.N., P.K., V.B. and G.M.C. are
inventors on patents filed by the Presidents and Fellows of Harvard College. Full disclosure for G.M.C. is available at http://arep.med.harvard.edu/gmc/tech.html. A.H.M.N., P.K. and G.M.C.
are co-founders of and have equity in GC Therapeutics, Inc. No reagents or funding from GC Therapeutics were used in this study. ADDITIONAL INFORMATION PUBLISHER’S NOTE Springer Nature
remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. SUPPLEMENTARY INFORMATION SUPPLEMENTARY INFORMATION Supplementary Figs. 1–7 REPORTING
SUMMARY SUPPLEMENTARY TABLE 1 TFs in the Human TFome SUPPLEMENTARY TABLE 2 TFome screen sequencing statistics SUPPLEMENTARY TABLE 3 TFome screen differentiation scores SUPPLEMENTARY TABLE 4
Novelty and tissue expression of 290 TF hits SUPPLEMENTARY TABLE 5 RNA-seq statistics and expression profiles SUPPLEMENTARY TABLE 6 TFs involved in oligodendrocyte development SUPPLEMENTARY
TABLE 7 Exact _P_ values for statistical tests RIGHTS AND PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE Ng, A.H.M., Khoshakhlagh, P., Rojo Arias, J.E. _et al._ A
comprehensive library of human transcription factors for cell fate engineering. _Nat Biotechnol_ 39, 510–519 (2021). https://doi.org/10.1038/s41587-020-0742-6 Download citation * Received:
03 November 2019 * Accepted: 19 October 2020 * Published: 30 November 2020 * Issue Date: April 2021 * DOI: https://doi.org/10.1038/s41587-020-0742-6 SHARE THIS ARTICLE Anyone you share the
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