3D brain Organoids derived from pluripotent stem cells: promising experimental models for brain development and neurodegenerative disorders

Three-dimensional (3D) brain organoids derived from human pluripotent stem cells (hPSCs), including embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), appear to recapitulate the brain’s 3D cytoarchitectural arrangement and provide new opportunities to explore disease pathogenesis in the human brain. Human iPSC (hiPSC) reprogramming methods, combined with 3D brain organoid tools, may allow patient-derived organoids to serve as a preclinical platform to bridge the translational gap between animal models and human clinical trials. Studies using patient-derived brain organoids have already revealed novel insights into molecular and genetic mechanisms of certain complex human neurological disorders such as microcephaly, autism, and Alzheimer’s disease. Furthermore, the combination of hiPSC technology and small-molecule high-throughput screening (HTS) facilitates the development of novel pharmacotherapeutic strategies, while transcriptome sequencing enables the transcriptional profiling of patient-derived brain organoids. Finally, the addition of CRISPR/Cas9 genome editing provides incredible potential for personalized cell replacement therapy with genetically corrected hiPSCs. This review describes the history and current state of 3D brain organoid differentiation strategies, a survey of applications of organoids towards studies of neurodevelopmental and neurodegenerative disorders, and the challenges associated with their use as in vitro models of neurological disorders.

[1]  R. Lanciotti,et al.  Pathology of congenital Zika syndrome in Brazil: a case series , 2016, The Lancet.

[2]  F. Ginhoux,et al.  Fate Mapping Analysis Reveals That Adult Microglia Derive from Primitive Macrophages , 2010, Science.

[3]  Peter Kirwan,et al.  Human cerebral cortex development from pluripotent stem cells to functional excitatory synapses , 2012, Nature Neuroscience.

[4]  Mustafa Tekin,et al.  Next generation sequencing: implications in personalized medicine and pharmacogenomics. , 2016, Molecular bioSystems.

[5]  D. Howells,et al.  Can Animal Models of Disease Reliably Inform Human Studies? , 2010, PLoS medicine.

[6]  M. Gill,et al.  Common polygenic variation enhances risk prediction for Alzheimer's disease. , 2015, Brain : a journal of neurology.

[7]  R. Nowakowski,et al.  Cdk5rap2 exposes the centrosomal root of microcephaly syndromes. , 2011, Trends in cell biology.

[8]  B. Dubois,et al.  Early-onset autosomal dominant Alzheimer disease: prevalence, genetic heterogeneity, and mutation spectrum. , 1999, American journal of human genetics.

[9]  B. Zuckerman,et al.  Neonatal Neurobehavioral and Neuroanatomic Correlates of Prenatal Cocaine Exposure: Problems of Dose and Confounding , 1998, Annals of the New York Academy of Sciences.

[10]  P. Carmeliet,et al.  Relief of hypoxia by angiogenesis promotes neural stem cell differentiation by targeting glycolysis , 2016, The EMBO journal.

[11]  R. de Kanter,et al.  Species differences between mouse, rat, dog, monkey and human CYP-mediated drug metabolism, inhibition and induction , 2006, Expert opinion on drug metabolism & toxicology.

[12]  R. Hammer,et al.  CDK5RAP2 regulates centriole engagement and cohesion in mice. , 2010, Developmental cell.

[13]  T. Rana,et al.  Zika Virus Depletes Neural Progenitors in Human Cerebral Organoids through Activation of the Innate Immune Receptor TLR3. , 2016, Cell stem cell.

[14]  Marko Kolenc,et al.  Zika Virus Associated with Microcephaly. , 2016, The New England journal of medicine.

[15]  R. Pearce,et al.  Directed Differentiation of Dopaminergic Neuronal Subtypes from Human Embryonic Stem Cells , 2005, Stem cells.

[16]  D. Maric,et al.  Differentiation of human and murine induced pluripotent stem cells to microglia-like cells , 2017, Nature Neuroscience.

[17]  Madeline A. Lancaster,et al.  Human cerebral organoids recapitulate gene expression programs of fetal neocortex development , 2015, Proceedings of the National Academy of Sciences.

[18]  A. Pinto,et al.  Exploiting the potential of next-generation sequencing in genomic medicine , 2016, Expert review of molecular diagnostics.

[19]  Peng Jin,et al.  Zika Virus Infects Human Cortical Neural Progenitors and Attenuates Their Growth. , 2016, Cell stem cell.

[20]  D. Geschwind,et al.  Advances in autism genetics: on the threshold of a new neurobiology , 2008, Nature Reviews Genetics.

[21]  Takanori Takebe,et al.  Vascularized and Complex Organ Buds from Diverse Tissues via Mesenchymal Cell-Driven Condensation. , 2015, Cell stem cell.

[22]  Peter M Visscher,et al.  Large-scale genomics unveils the genetic architecture of psychiatric disorders , 2014, Nature Neuroscience.

[23]  John R. Yates,et al.  Isogenic Human iPSC Parkinson’s Model Shows Nitrosative Stress-Induced Dysfunction in MEF2-PGC1α Transcription , 2013, Cell.

[24]  S. Engle,et al.  Small Molecule Screening in Human Induced Pluripotent Stem Cell-derived Terminal Cell Types* , 2013, The Journal of Biological Chemistry.

[25]  P. Levitt,et al.  Prenatal exposure to drugs: effects on brain development and implications for policy and education , 2009, Nature Reviews Neuroscience.

[26]  Thomas Hartung,et al.  Toward a 3D model of human brain development for studying gene/environment interactions , 2013, Stem Cell Research & Therapy.

[27]  P. Garcez,et al.  Zika virus impairs growth in human neurospheres and brain organoids , 2016, Science.

[28]  M. Eiraku,et al.  Self-organization of axial polarity, inside-out layer pattern, and species-specific progenitor dynamics in human ES cell–derived neocortex , 2013, Proceedings of the National Academy of Sciences.

[29]  E. Ostrea,et al.  Prenatal cocaine and neonatal outcome: evaluation of dose-response relationship. , 1996, Pediatrics.

[30]  S. Cavallaro,et al.  Copy number variability in Parkinson’s disease: assembling the puzzle through a systems biology approach , 2016, Human Genetics.

[31]  Nicholas Lange,et al.  Longitudinal changes in cortical thickness in autism and typical development. , 2014, Brain : a journal of neurology.

[32]  Wieland B Huttner,et al.  Neural progenitors, neurogenesis and the evolution of the neocortex , 2014, Development.

[33]  N. Low,et al.  Zika Virus Infection as a Cause of Congenital Brain Abnormalities and Guillain–Barré Syndrome: Systematic Review , 2016, bioRxiv.

[34]  G. Malinger,et al.  Zika virus intrauterine infection causes fetal brain abnormality and microcephaly: tip of the iceberg? , 2016, Ultrasound in obstetrics & gynecology : the official journal of the International Society of Ultrasound in Obstetrics and Gynecology.

[35]  S. Chauhan,et al.  Recurrent Shoulder Dystocia: A Review , 2010, Obstetrical & gynecological survey.

[36]  D. Amaral,et al.  Neuroanatomy of autism , 2008, Trends in Neurosciences.

[37]  D. Missé,et al.  Biology of Zika Virus Infection in Human Skin Cells , 2015, Journal of Virology.

[38]  W. Freed,et al.  Cocaine causes deficits in radial migration and alters the distribution of glutamate and GABA neurons in the developing rat cerebral cortex , 2011, Synapse.

[39]  Huaxi Xu,et al.  Proteolytic processing of Alzheimer’s β‐amyloid precursor protein , 2012, Journal of neurochemistry.

[40]  M. Maia,et al.  Zika virus in Brazil and macular atrophy in a child with microcephaly , 2016, The Lancet.

[41]  M. Tomishima,et al.  Highly efficient neural conversion of human ES and iPS cells by dual inhibition of SMAD signaling , 2009, Nature Biotechnology.

[42]  L. Gallagher,et al.  Copy-number variants in neurodevelopmental disorders: promises and challenges. , 2009, Trends in genetics : TIG.

[43]  Yechiel Elkabetz,et al.  Human ES cell-derived neural rosettes reveal a functionally distinct early neural stem cell stage. , 2008, Genes & development.

[44]  Carlos G Schrago,et al.  Detection and sequencing of Zika virus from amniotic fluid of fetuses with microcephaly in Brazil: a case study. , 2016, The Lancet. Infectious diseases.

[45]  E. Hashino,et al.  Organoid technologies meet genome engineering , 2017, EMBO reports.

[46]  S. Hyman,et al.  Progress in the Genetics of Polygenic Brain Disorders: Significant New Challenges for Neurobiology , 2013, Neuron.

[47]  P. Wong,et al.  Amyloid precursor protein processing and Alzheimer's disease. , 2011, Annual review of neuroscience.

[48]  G. Uhl,et al.  Functional consequences of 17q21.31/WNT3-WNT9B amplification in hPSCs with respect to neural differentiation. , 2015, Cell reports.

[49]  J. Carpten,et al.  Translating RNA sequencing into clinical diagnostics: opportunities and challenges , 2016, Nature Reviews Genetics.

[50]  R. Tanzi,et al.  The genetic epidemiology of neurodegenerative disease. , 2005, The Journal of clinical investigation.

[51]  S. Antonarakis,et al.  Modelling and rescuing neurodevelopmental defect of Down syndrome using induced pluripotent stem cells from monozygotic twins discordant for trisomy 21 , 2013, EMBO molecular medicine.

[52]  Marius Wernig,et al.  In vitro differentiation of transplantable neural precursors from human embryonic stem cells , 2001, Nature Biotechnology.

[53]  E. Courchesne,et al.  Neuron number and size in prefrontal cortex of children with autism. , 2011, JAMA.

[54]  M. Behnke,et al.  Prenatal Substance Abuse: Short- and Long-term Effects on the Exposed Fetus , 2013, Pediatrics.

[55]  Simon K Warfield,et al.  Volumetric MRI Study of Brain in Children With Intrauterine Exposure to Cocaine, Alcohol, Tobacco, and Marijuana , 2008, Pediatrics.

[56]  J. Nabekura,et al.  Microglia: actively surveying and shaping neuronal circuit structure and function , 2013, Trends in Neurosciences.

[57]  U. Müller,et al.  Shaping Our Minds: Stem and Progenitor Cell Diversity in the Mammalian Neocortex , 2013, Neuron.

[58]  N. Socci,et al.  Directed Differentiation and Transplantation of Human Embryonic Stem Cell‐Derived Motoneurons , 2007, Stem cells.

[59]  Hyejung Won,et al.  The road to precision psychiatry: translating genetics into disease mechanisms , 2016, Nature Neuroscience.

[60]  Christa Lese Martin,et al.  A Cross-Disorder Method to Identify Novel Candidate Genes for Developmental Brain Disorders. , 2016, JAMA psychiatry.

[61]  Madeline A. Lancaster,et al.  Cerebral organoids model human brain development and microcephaly , 2013, Nature.

[62]  CNVs in neurodevelopmental disorders , 2015, Oncotarget.

[63]  Daniel H. Geschwind,et al.  Systems biology and gene networks in neurodevelopmental and neurodegenerative disorders , 2015, Nature Reviews Genetics.

[64]  W. Freed,et al.  A new technique for modeling neuronal connectivity using human pluripotent stem cells , 2015, Restorative neurology and neuroscience.

[65]  F. Ginhoux,et al.  Origin and differentiation of microglia , 2013, Front. Cell. Neurosci..

[66]  Christopher P Austin,et al.  High-throughput screening assays for the identification of chemical probes. , 2007, Nature chemical biology.

[67]  David W. Nauen,et al.  Brain-Region-Specific Organoids Using Mini-bioreactors for Modeling ZIKV Exposure , 2016, Cell.

[68]  John T. Dimos,et al.  The timing of cortical neurogenesis is encoded within lineages of individual progenitor cells , 2006, Nature Neuroscience.

[69]  S. Nishikawa,et al.  A ROCK inhibitor permits survival of dissociated human embryonic stem cells , 2007, Nature Biotechnology.

[70]  Arnold Kriegstein,et al.  A stem cell niche for intermediate progenitor cells of the embryonic cortex. , 2009, Cerebral cortex.

[71]  E. Mohammadi,et al.  Barriers and facilitators related to the implementation of a physiological track and trigger system: A systematic review of the qualitative evidence , 2017, International journal for quality in health care : journal of the International Society for Quality in Health Care.

[72]  W. Freed,et al.  An in vitro model of human neocortical development using pluripotent stem cells: cocaine-induced cytoarchitectural alterations , 2014, Disease Models & Mechanisms.

[73]  Linzhao Cheng,et al.  Genome Editing in Human Pluripotent Stem Cells. , 2016, Cold Spring Harbor protocols.

[74]  D. Selkoe Alzheimer's disease. , 2011, Cold Spring Harbor perspectives in biology.

[75]  C. Walsh,et al.  Cdk5rap2 regulates centrosome function and chromosome segregation in neuronal progenitors , 2010, Development.

[76]  Amadou Alpha Sall,et al.  Zika virus and microcephaly: why is this situation a PHEIC? , 2016, The Lancet.

[77]  Li-Huei Tsai,et al.  Efficient derivation of microglia-like cells from human pluripotent stem cells , 2016, Nature Medicine.

[78]  B. Stevens,et al.  New insights on the role of microglia in synaptic pruning in health and disease , 2016, Current Opinion in Neurobiology.

[79]  R. Lanciotti,et al.  Notes from the Field: Evidence of Zika Virus Infection in Brain and Placental Tissues from Two Congenitally Infected Newborns and Two Fetal Losses--Brazil, 2015. , 2016, MMWR. Morbidity and mortality weekly report.

[80]  S. Beggs,et al.  Sublime Microglia: Expanding Roles for the Guardians of the CNS , 2014, Cell.

[81]  V. Paz-Soldan,et al.  Maternal dengue and pregnancy outcomes: a systematic review. , 2010, Obstetrical & gynecological survey.

[82]  D. Geschwind,et al.  Altered proliferation and networks in neural cells derived from idiopathic autistic individuals , 2016, Molecular Psychiatry.

[83]  Lisle W. Blackbourn,et al.  Modeling ALS with iPSCs reveals that mutant SOD1 misregulates neurofilament balance in motor neurons. , 2014, Cell stem cell.

[84]  Carlos S. Moreno,et al.  Relative Burden of Large CNVs on a Range of Neurodevelopmental Phenotypes , 2011, PLoS genetics.

[85]  J. Bradbury Molecular Insights into Human Brain Evolution , 2005, PLoS biology.

[86]  Basavaraj Hooli,et al.  A three-dimensional human neural cell culture model of Alzheimer’s disease , 2014, Nature.

[87]  Robert A Pearce,et al.  Specification of motoneurons from human embryonic stem cells , 2005, Nature Biotechnology.

[88]  Jeffrey M Karp,et al.  Engineering Stem Cell Organoids. , 2016, Cell stem cell.

[89]  J. Rubenstein,et al.  Compartment-specific transcription factors orchestrate angiogenesis gradients in the embryonic brain , 2008, Nature Neuroscience.

[90]  Ben A. Barres,et al.  Microglia Sculpt Postnatal Neural Circuits in an Activity and Complement-Dependent Manner , 2012, Neuron.

[91]  D. Geschwind,et al.  Functional cortical neurons and astrocytes from human pluripotent stem cells in 3D culture , 2015, Nature Methods.

[92]  Amadou A. Sall,et al.  The Brazilian Zika virus strain causes birth defects in experimental models , 2016, Nature.

[93]  M. Potenza,et al.  Prenatal Cocaine Exposure and Gray Matter Volume in Adolescent Boys and Girls: Relationship to Substance Use Initiation , 2013, Biological Psychiatry.

[94]  C. Woods,et al.  Autosomal recessive primary microcephaly (MCPH): a review of clinical, molecular, and evolutionary findings. , 2005, American journal of human genetics.

[95]  Chad A. Cowan,et al.  Genome Editing in Human Pluripotent Stem Cells: Approaches, Pitfalls, and Solutions. , 2016, Cell stem cell.

[96]  Young Hye Kim,et al.  A 3D human neural cell culture system for modeling Alzheimer's disease , 2015, Nature Protocols.

[97]  F. Pereyra-Bonnet,et al.  iPSCs: A Minireview from Bench to Bed, including Organoids and the CRISPR System , 2016, Stem cells international.

[98]  A. Salvator,et al.  Cognitive and motor outcomes of cocaine-exposed infants. , 2002, JAMA.

[99]  Tuan Leng Tay,et al.  Microglia across the lifespan: from origin to function in brain development, plasticity and cognition , 2017, The Journal of physiology.

[100]  B. Zuckerman,et al.  Late dose-response effects of prenatal cocaine exposure on newborn neurobehavioral performance. , 1996, Pediatrics.

[101]  Clive N. Svendsen,et al.  Human stem cells and drug screening: opportunities and challenges , 2010, Nature Reviews Drug Discovery.

[102]  Mahmood Rasool,et al.  Molecular genetics of human primary microcephaly: an overview , 2015, BMC Medical Genomics.

[103]  P. Rakic Evolution of the neocortex: Perspective from developmental biology , 2010 .

[104]  Ben A. Barres,et al.  Complement and microglia mediate early synapse loss in Alzheimer mouse models , 2016, Science.

[105]  A. Kriegstein,et al.  Development and Evolution of the Human Neocortex , 2011, Cell.

[106]  Yoshiki Sasai,et al.  Self-organized formation of polarized cortical tissues from ESCs and its active manipulation by extrinsic signals. , 2008, Cell stem cell.

[107]  D. Mash,et al.  CYP3A5 Mediates Effects of Cocaine on Human Neocorticogenesis: Studies using an In Vitro 3D Self-Organized hPSC Model with a Single Cortex-Like Unit , 2017, Neuropsychopharmacology.

[108]  L. Kuhn,et al.  Prenatal cocaine exposures and dose-related cocaine effects on infant tone and behavior. , 2007, Neurotoxicology and teratology.

[109]  D. Missé,et al.  Dengue virus replication in infected human keratinocytes leads to activation of antiviral innate immune responses. , 2011, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[110]  M. Gerstein,et al.  FOXG1-Dependent Dysregulation of GABA/Glutamate Neuron Differentiation in Autism Spectrum Disorders , 2015, Cell.

[111]  C. David Page,et al.  Human pluripotent stem cell-derived neural constructs for predicting neural toxicity , 2015, Proceedings of the National Academy of Sciences.

[112]  V. Martínez‐Cerdeño,et al.  Microglia Regulate the Number of Neural Precursor Cells in the Developing Cerebral Cortex , 2013, The Journal of Neuroscience.

[113]  W. Hauser,et al.  Dose–Response Effect of Fetal Cocaine Exposure on Newborn Neurologic Function , 1999, Pediatrics.

[114]  Fred H. Gage,et al.  Modelling schizophrenia using human induced pluripotent stem cells , 2011, Nature.

[115]  L. Tsai,et al.  Self-Organizing 3D Human Neural Tissue Derived from Induced Pluripotent Stem Cells Recapitulate Alzheimer’s Disease Phenotypes , 2016, PloS one.

[116]  Eric Courchesne,et al.  Patches of disorganization in the neocortex of children with autism. , 2014, The New England journal of medicine.

[117]  J. Anthony,et al.  Severity of Prenatal Cocaine Exposure and Child Language Functioning Through Age Seven Years: A Longitudinal Latent Growth Curve Analysis , 2004, Substance use & misuse.

[118]  S. Minnes,et al.  Prenatal Tobacco, Marijuana, Stimulant, and Opiate Exposure: Outcomes and Practice Implications , 2011, Addiction science & clinical practice.

[119]  H. M. Geller,et al.  A Mechanism for the Inhibition of Neural Progenitor Cell Proliferation by Cocaine , 2008, PLoS medicine.

[120]  A. Ko,et al.  Zika Virus Infection and Stillbirths: A Case of Hydrops Fetalis, Hydranencephaly and Fetal Demise , 2016, PLoS neglected tropical diseases.

[121]  K. Mizuseki,et al.  Directed differentiation of telencephalic precursors from embryonic stem cells , 2005, Nature Neuroscience.

[122]  David W. Nauen,et al.  Synaptic dysregulation in a human iPS cell model of mental disorders , 2014, Nature.