Individual brain organoids reproducibly form cell diversity of the human cerebral cortex.

Silvia Velasco, Amanda J Kedaigle, Sean K Simmons, Allison Nash, Marina Rocha, Giorgia Quadrato, Bruna Paulsen, Lan Nguyen, Xian Adiconis, Aviv Regev, Joshua Z Levin, Paola Arlotta
Author Information
  1. Silvia Velasco: Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
  2. Amanda J Kedaigle: Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
  3. Sean K Simmons: Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  4. Allison Nash: Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
  5. Marina Rocha: Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
  6. Giorgia Quadrato: Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
  7. Bruna Paulsen: Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
  8. Lan Nguyen: Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  9. Xian Adiconis: Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  10. Aviv Regev: Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  11. Joshua Z Levin: Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
  12. Paola Arlotta: Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA. paola_arlotta@harvard.edu.

Abstract

Experimental models of the human brain are needed for basic understanding of its development and disease. Human brain organoids hold unprecedented promise for this purpose; however, they are plagued by high organoid-to-organoid variability. This has raised doubts as to whether developmental processes of the human brain can occur outside the context of embryogenesis with a degree of reproducibility that is comparable to the endogenous tissue. Here we show that an organoid model of the dorsal forebrain can reliably generate a rich diversity of cell types appropriate for the human cerebral cortex. We performed single-cell RNA-sequencing analysis of 166,242 cells isolated from 21 individual organoids, finding that 95% of the organoids generate a virtually indistinguishable compendium of cell types, following similar developmental trajectories and with a degree of organoid-to-organoid variability comparable to that of individual endogenous brains. Furthermore, organoids derived from different stem cell lines show consistent reproducibility in the cell types produced. The data demonstrate that reproducible development of the complex cellular diversity of the central nervous system does not require the context of the embryo, and that establishment of terminal cell identity is a highly constrained process that can emerge from diverse stem cell origins and growth environments.

References

  1. Proc Natl Acad Sci U S A. 2015 Dec 22;112(51):15672-7 [PMID: 26644564]
  2. Nat Methods. 2019 Jan;16(1):75-78 [PMID: 30573846]
  3. Cell. 2018 Aug 9;174(4):1015-1030.e16 [PMID: 30096299]
  4. Cell Stem Cell. 2017 Sep 7;21(3):383-398.e7 [PMID: 28757360]
  5. PLoS One. 2011;6(10):e26203 [PMID: 22022567]
  6. Nature. 2013 Sep 19;501(7467):373-9 [PMID: 23995685]
  7. Nat Rev Neurosci. 2013 Nov;14(11):755-69 [PMID: 24105342]
  8. Science. 2017 Dec 8;358(6368):1318-1323 [PMID: 29217575]
  9. Nature. 2017 May 4;545(7652):48-53 [PMID: 28445462]
  10. Cell Stem Cell. 2017 Apr 6;20(4):435-449.e4 [PMID: 28111201]
  11. Proc Natl Acad Sci U S A. 2015 Jun 9;112(23):7285-90 [PMID: 26060301]
  12. Cell. 2015 Sep 24;163(1):55-67 [PMID: 26406371]
  13. Nat Biotechnol. 2017 Jul;35(7):659-666 [PMID: 28562594]
  14. Proc Natl Acad Sci U S A. 2014 Oct 21;111(42):E4468-77 [PMID: 25294932]
  15. J Neurosci. 2009 Sep 30;29(39):12343-54 [PMID: 19793993]
  16. Nat Commun. 2017 Jan 16;8:14049 [PMID: 28091601]
  17. Cell Res. 2018 Jul;28(7):730-745 [PMID: 29867213]
  18. J Neurosci. 2007 Jun 27;27(26):6878-91 [PMID: 17596436]
  19. Nat Methods. 2017 Jul;14(7):743-751 [PMID: 28504681]
  20. Annu Rev Cell Dev Biol. 2015;31:699-720 [PMID: 26359774]
  21. Neuron. 2016 Jan 20;89(2):248-68 [PMID: 26796689]
  22. Nat Methods. 2017 Oct;14(10):979-982 [PMID: 28825705]
  23. Cell. 2019 Feb 7;176(4):743-756.e17 [PMID: 30735633]
  24. Nat Med. 2016 Nov;22(11):1220-1228 [PMID: 27783065]
  25. Proc Natl Acad Sci U S A. 2013 Dec 10;110(50):20284-9 [PMID: 24277810]
  26. Stem Cell Reports. 2016 Jun 14;6(6):993-1008 [PMID: 27304920]
  27. Neuron. 2005 Jan 20;45(2):207-21 [PMID: 15664173]
  28. Nat Biotechnol. 2018 Jun;36(5):411-420 [PMID: 29608179]
  29. Neuron. 2016 Jan 6;89(1):37-53 [PMID: 26687838]
  30. Cell. 2016 Aug 25;166(5):1308-1323.e30 [PMID: 27565351]
  31. Mol Syst Biol. 2005;1:2005.0030 [PMID: 16729065]
  32. Cell. 2016 May 19;165(5):1238-1254 [PMID: 27118425]
  33. Nature. 2017 May 4;545(7652):54-59 [PMID: 28445465]
  34. Nat Methods. 2017 Oct;14(10):955-958 [PMID: 28846088]
  35. Cell Syst. 2019 Apr 24;8(4):281-291.e9 [PMID: 30954476]

Grants

  1. R01 MH112940/NIMH NIH HHS
  2. U01 MH115727/NIMH NIH HHS
  3. /Howard Hughes Medical Institute
  4. P50 MH094271/NIMH NIH HHS

MeSH Term

Cell Line
Cerebral Cortex
Female
Fetus
Humans
Induced Pluripotent Stem Cells
Male
Organoids
Prosencephalon
RNA-Seq
Reproducibility of Results
Single-Cell Analysis
Time Factors
Tissue Culture Techniques
Transcriptome