Brain Organoids


Recent developments in stem cell technologies are extending the boundaries forward to produce not only specific cell types but also even complex 3D structures, such as organoids, ‘mini organs in dish’. One such type is brain organoids derived from human pluripotent stem cells. Brain organoids consist of various cell types of ectodermal lineage and self‐assemble into organised structures resembling early human brain. Brain organoids exhibit ventricular zones (VZs) consisting of highly proliferative neural stem cells. During neurogenesis, neural stem cells differentiate and migrate from the VZ to the marginal zone of the organoid to form a primitive cortical plate by differentiating to neurons.

Brain organoids provide novel insights into human brain development and give new opportunities to study neurodevelopmental disorders such as microcephaly in vitro. In future, brain organoids can serve as a useful tool to model neurodegenerative disorders in humans and for therapeutic screening and drug testing in high‐throughput assays.

Key Concepts

  • Human 3D cell culture models are an alternative to animal models to study developmental diseases in humans.
  • Pluripotent stem cells can differentiate into complex 3D organoids.
  • Differentiating cells self‐assemble to form tissue‐like structures.
  • Brain organoids recapitulate important aspects of human brain development.
  • Brain organoids recapitulate early events in human brain development.
  • Brain organoids serve as a tool to model neurodevelopmental and neurodegenerative diseases.
  • Brain organoids can be used in high‐throughput assays for drug screening and toxicity testing.

Keywords: brain organoids; pluripotent stem cells; human iPSC; neurodevelopment; neural stem cells; primitive cortical plate; neurogenesis; microcephaly; in vitro differentiation

Figure 1. Human brain organoids derived from iPS cells of a healthy donor (wild type) and of a microcephaly (MCPH) patient. (a) Macroscopic view of 14‐day‐old human brain organoids generated from wild‐type human iPS cells. (i) Organoids are relatively homogenous in size and shape. (ii) An organoid in higher magnification harbouring fluid‐filled cavities (arrow) and resembling human embryonic brain. (b) Upper panel shows 14‐day‐old human brain organoids from healthy donor iPS cells. Bottom panel shows age‐matched human brain organoids derived from a MCPH patient. (c) Immunofluorescent images of 14‐day‐old human brain organoids cryosectioned in 20‐µm‐thin sections. (i) Organoid from a healthy donor with Pax6‐positive neural stem cells residing in the VZ (magenta) nearby the lumen (L). TUJ1‐positive neurons (green) are forming the primitive cortical plate in the periphery of the organoid. (ii) Immunofluorescent staining of a cryosectioned 14‐day‐old organoid generated from a MCPH patient. Note the larger lumen (L), lesser number of Pax6‐positive cells in the thus thinner VZ and the thinner cortical area containing TUJ1‐positive neurons (green) compared to organoid from healthy donor. Reproduced with permission from Gabriel et al. © EMBO.
Figure 2. Symmetrically and asymmetrically dividing aRG cells in the VZ. (a) Overview of a ventricular zone (VZ) containing dividing aRG cells at the apical side of the VZ labelled by phospho‐vimentin (pVim; magenta) towards the lumen (L), which is surrounded by Arl13b‐positive cilia from aRG cells (green). Right‐side image illustrates a symmetrically dividing aRG (bottom) with division plane horizontal to the luminar surface and an asymmetrically dividing aRG (upper) with a vertically oriented division plane. (b) High magnification of the symmetrically dividing aRG. Note that the division plane is clearly visible as this cell is in anaphase of mitosis. Right schematic shows the horizontal division plane parallel to the luminar surface. (c) High magnification of the asymmetrically diving aRG in anaphase of mitosis. Right schematic shows vertical division plane perpendicular to the luminar surface. Reproduced from Gabriel et al. © Elsevier.
Figure 3. Modelling Zika virus‐induced microcephaly (MCPH) during early human brain development. (a) Model of how Zika virus might cause MCPH during early human brain development. (i) Blue area is the ventricular zone (VZ) with mainly symmetrically dividing radial glial (RG) cells. White area is the intermediate zone through which differentiating cells migrate to form the newly born neurons (magenta) in the primitive cortical plate (yellow area). Red colour indicates the primary cilium of the apical RG cells protruding into the lumen of the VZ inside the organoid. (ii) Zika virus (green) infects and replicates preferably in apical RG cells. Infected RG cells then prematurely differentiate from symmetric to asymmetric cell division, illustrated by newly born neurons (magenta) within the VZ. This leads to a reduced thickness of VZ and cortical plate compared to noninfected left panel. Zika virus‐infected differentiated cells then show enhanced apoptosis when they reach primitive cortical plate. (b) Immunofluorescent staining of an 11‐day‐old human brain organoid derived from human‐induced pluripotent stem cells infected for 2 days with a recent Zika virus isolate. In (i), all channels are shown as merged. Proliferating aRG cells in the VZ are preferably targeted by Zika virus (ii, green) and start differentiation and migration towards the cortical plate upon (iii, magenta) where they undergo apoptosis eventually (iv, yellow). Reproduced from Gabriel et al. © Elsevier.


Al‐Dosari MS, Shaheen R, Colak D and Alkuraya FS (2010) Novel CENPJ mutation causes Seckel syndrome. Journal of Medical Genetics 47: 411–414.

de Araujo TV, Rodrigues LC, de Alencar Ximenes RA, et al. (2016) Association between Zika virus infection and microcephaly in Brazil, January to May, 2016: preliminary report of a case–control study. Lancet Infectious Diseases 16: 1356–1363.

Barbelanne M and Tsang WY (2014) Molecular and cellular basis of autosomal recessive primary microcephaly. BioMed Research International 2014: 547986.

Bartfeld S and Clevers H (2017) Stem cell‐derived organoids and their application for medical research and patient treatment. Journal of Molecular Medicine (Berlin, Germany) 95 (7): 729–738.

Bershteyn M, Nowakowski TJ, Pollen AA, et al. (2017) Human iPSC‐derived cerebral organoids model cellular features of lissencephaly and reveal prolonged mitosis of outer radial glia. Cell Stem Cell 20: 435–449.e434.

Bhat V, Girimaji SC, Mohan G, et al. (2011) Mutations in WDR62, encoding a centrosomal and nuclear protein, in Indian primary microcephaly families with cortical malformations. Clinical Genetics 80: 532–540.

Bond J, Roberts E, Springell K, et al. (2005) A centrosomal mechanism involving CDK5RAP2 and CENPJ controls brain size. Nature Genetics 37: 353–355.

Buchman JJ, Tseng HC, Zhou Y, et al. (2010) Cdk5rap2 interacts with pericentrin to maintain the neural progenitor pool in the developing neocortex. Neuron 66: 386–402.

Camp JG, Badsha F, Florio M, et al. (2015) Human cerebral organoids recapitulate gene expression programs of fetal neocortex development. Proceedings of the National Academy of Sciences of the United States of America 112: 15672–15677.

Carpenter MK, Inokuma MS, Denham J, et al. (2001) Enrichment of neurons and neural precursors from human embryonic stem cells. Experimental Neurology 172: 383–397.

Dicke U and Roth G (2016) Neuronal factors determining high intelligence. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 371: 20150180.

Eiraku M, Watanabe K, Matsuo‐Takasaki M, et al. (2008) Self‐organized formation of polarized cortical tissues from ESCs and its active manipulation by extrinsic signals. Cell Stem Cell 3: 519–532.

Farkas LM and Huttner WB (2008) The cell biology of neural stem and progenitor cells and its significance for their proliferation versus differentiation during mammalian brain development. Current Opinion in Cell Biology 20: 707–715.

Feng Y and Walsh CA (2004) Mitotic spindle regulation by Nde1 controls cerebral cortical size. Neuron 44: 279–293.

Fernandez V, Llinares‐Benadero C and Borrell V (2016) Cerebral cortex expansion and folding: what have we learned? EMBO Journal 35: 1021–1044.

Fish JL, Kosodo Y, Enard W, Paabo S and Huttner WB (2006) Aspm specifically maintains symmetric proliferative divisions of neuroepithelial cells. Proceedings of the National Academy of Sciences of the United States of America 103: 10438–10443.

Florio M, Albert M, Taverna et al. (2015) Human‐specific gene ARHGAP11B promotes basal progenitor amplification and neocortex expansion. Science 347: 1465–1470.

Frith C and Frith U (2005) Theory of mind. Current Biology 15: R644–R646.

Gabriel E, Wason A, Ramani A, et al. (2016) CPAP promotes timely cilium disassembly to maintain neural progenitor pool. EMBO Journal 35: 803–819.

Gabriel E and Gopalakrishnan J (2017) Generation of iPSC‐derived human brain organoids to model early neurodevelopmental disorders. Journal of Visualized Experiments. DOI: 10.3791/55372.

Gabriel E, Ramani A, Karow U, et al. (2017) Recent zika virus isolates induce premature differentiation of neural progenitors in human brain organoids. Cell Stem Cell 20: 397–406.e395.

Gotz M and Huttner WB (2005) The cell biology of neurogenesis. Nature Reviews Molecular Cell Biology 6: 777–788.

Guemez‐Gamboa A, Coufal NG and Gleeson JG (2014) Primary cilia in the developing and mature brain. Neuron 82: 511–521.

Guernsey DL, Jiang H, Hussin J, et al. (2010) Mutations in centrosomal protein CEP152 in primary microcephaly families linked to MCPH4. American Journal of Human Genetics 87: 40–51.

Higginbotham H, Guo J, Yokota Y, et al. (2013) Arl13b‐regulated cilia activities are essential for polarized radial glial scaffold formation. Nature Neuroscience 16: 1000–1007.

Hussain MS, Baig SM, Neumann S, et al. (2012) A truncating mutation of CEP135 causes primary microcephaly and disturbed centrosomal function. American Journal of Human Genetics 90: 871–878.

Huttner WB and Kosodo Y (2005) Symmetric versus asymmetric cell division during neurogenesis in the developing vertebrate central nervous system. Current Opinion in Cell Biology 17: 648–657.

Ivanov DP and Grabowska AM (2017) Spheroid arrays for high‐throughput single‐cell analysis of spatial patterns and biomarker expression in 3D. Scientific Reports 7: 41160.

Jo J, Xiao Y, Sun AX, et al. (2016) Midbrain‐like organoids from human pluripotent stem cells contain functional dopaminergic and neuromelanin‐producing neurons. Cell Stem Cell 19: 248–257.

Kadoshima T, Sakaguchi H, Nakano T, et al. (2013) Self‐organization of axial polarity, inside‐out layer pattern, and species‐specific progenitor dynamics in human ES cell‐derived neocortex. Proceedings of the National Academy of Sciences of the United States of America 110: 20284–20289.

Kumar A, Girimaji SC, Duvvari MR and Blanton SH (2009) Mutations in STIL, encoding a pericentriolar and centrosomal protein, cause primary microcephaly. American Journal of Human Genetics 84: 286–290.

Lancaster MA, Renner M, Martin CA, et al. (2013) Cerebral organoids model human brain development and microcephaly. Nature 501: 373–379.

Lindborg BA, Brekke JH, Vegoe AL, et al. (2016) Rapid induction of cerebral organoids from human induced pluripotent stem cells using a chemically defined hydrogel and defined cell culture medium. Stem Cells Translational Medicine 5: 970–979.

Mariani J, Coppola G, Zhang P, et al. (2015) FOXG1‐dependent dysregulation of GABA/glutamate neuron differentiation in autism spectrum disorders. Cell 162: 375–390.

Mochida GH (2008) Molecular genetics of lissencephaly and microcephaly. Brain and Nerve 60: 437–444.

Mora‐Bermudez F and Huttner WB (2015) Novel insights into mammalian embryonic neural stem cell division: focus on microtubules. Molecular Biology of the Cell 26: 4302–4306.

Nadarajah B and Parnavelas JG (2002) Modes of neuronal migration in the developing cerebral cortex. Nature Reviews Neuroscience 3: 423–432.

Nat R, Cretoiu D and Popescu LM (2001) In vitro differentiation of human embryonic neural stem cells. Journal of Cellular and Molecular Medicine 5: 324–325.

Passemard S, Kaindl AM and Verloes A (2013) Microcephaly. Handbook of Clinical Neurology 111: 129–141.

Qian X, Nguyen HN, Song MM, et al. (2016) Brain‐region‐specific organoids using mini‐bioreactors for modeling ZIKV exposure. Cell 165: 1238–1254.

Quadrato G, Brown J and Arlotta P (2016) The promises and challenges of human brain organoids as models of neuropsychiatric disease. Nature Medicine 22: 1220–1228.

Rauch A, Thiel CT, Schindler D, et al. (2008) Mutations in the pericentrin (PCNT) gene cause primordial dwarfism. Science 319: 816–819.

Reubinoff BE, Itsykson P, Turetsky T, et al. (2001) Neural progenitors from human embryonic stem cells. Nature Biotechnology 19: 1134–1140.

Ryan KJ (2000) The politics and ethics of human embryo and stem cell research. Womens Health Issues 10: 105–110.

Sadler TW (2005) Embryology of neural tube development. American Journal of Medical Genetics. Part C, Seminars in Medical Genetics 135C: 2–8.

Sun AX, Yuan Q, Tan S, et al. (2016) Direct induction and functional maturation of forebrain GABAergic neurons from human pluripotent stem cells. Cell Reports 16: 1942–1953.

Swistowski A, Peng J, Liu Q, et al. (2010) Efficient generation of functional dopaminergic neurons from human induced pluripotent stem cells under defined conditions. Stem Cells 28: 1893–1904.

Takahashi K and Yamanaka S (2006) Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126: 663–676.

Thomson JA, Itskovitz‐Eldor J, Shapiro SS, et al. (1998) Embryonic stem cell lines derived from human blastocysts. Science 282: 1145–1147.

Toro R, Perron M, Pike B, et al. (2008) Brain size and folding of the human cerebral cortex. Cerebral Cortex 18: 2352–2357.

Verloes A, Drunat S, Gressens P and Passemard S (1993) Primary autosomal recessive microcephalies and seckel syndrome spectrum disorders. In: Pagon RA, Adam MP, Ardinger HH, Wallace SE, Amemiya A, Bean LJH, Bird TD, Ledbetter N, Mefford HC, Smith RJH, et al. (eds) GeneReviews(R). Seattle, WA: University of Washington.

Wilson PG and Stice SS (2006) Development and differentiation of neural rosettes derived from human embryonic stem cells. Stem Cell Reviews 2: 67–77.

Zhang SC, Wernig M, Duncan ID, Brustle O and Thomson JA (2001) In vitro differentiation of transplantable neural precursors from human embryonic stem cells. Nature Biotechnology 19: 1129–1133.

Zhang Y, Pak C, Han Y, et al. (2013) Rapid single‐step induction of functional neurons from human pluripotent stem cells. Neuron 78: 785–798.

Further Reading

Daley GQ, Hyun I, Apperley JF, et al. (2016) Setting global standards for stem cell research and clinical translation: the 2016 ISSCR guidelines. Stem Cell Reports 6: 787–797. DOI: 10.1016/j.stemcr.2016.05.001.

Kelava I and Lancaster MA (2016) Dishing out mini‐brains: current progress and future prospects in brain organoid research. Developmental Biology 420: 199–209.

Lancaster MA and Knoblich JA (2014) Generation of cerebral organoids from human pluripotent stem cells. Nature Protocols 9: 2329–2340.

Russell WMS and Burch RL (1959) The Principles of Humane Experimental Technique. London: Methuen.

Shi Y, Inoue H, Wu JC and Yamanaka S (2017) Induced pluripotent stem cell technology: a decade of progress. Nature Reviews Drug Discovery 16: 115–130. DOI: 10.1038/nrd.2016.245.

Thornton GK and Woods CG (2009) Primary microcephaly: do all roads lead to Rome? Trends in Genetics 25: 501–510.

Toselli F, Dodd PR and Gillam EM (2016) Emerging roles for brain drug‐metabolizing cytochrome P450 enzymes in neuropsychiatric conditions and responses to drugs. Drug Metabolism Reviews 48: 379–404. DOI: 10.1080/03602532.2016.1221960.

Wollnik B (2010) A common mechanism for microcephaly. Nature Genetics 42: 923–924.

Yumlu S et al. (2017) Gene editing and clonal isolation of human induced pluripotent stem cells using CRISPR/Cas9. Methods 121–122: 29–44. DOI: 10.1016/j.ymeth.2017.05.009.

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Gabriel, Elke, and Gopalakrishnan, Jay(Nov 2017) Brain Organoids. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0027186]