A Quantitative Framework to Evaluate Modeling of Cortical Development by Neural Stem Cells

Neural stem cells have been adopted to model a wide range of neuropsychiatric conditions in vitro. However, how well such models correspond to in vivo brain has not been evaluated in an unbiased, comprehensive manner. We used transcriptomic analyses to compare in vitro systems to developing human fetal brain and observed strong conservation of in vivo gene expression and network architecture in differentiating primary human neural progenitor cells (phNPCs). Conserved modules are enriched in genes associated with ASD, supporting the utility of phNPCs for studying neuropsychiatric disease. We also developed and validated a machine learning approach called CoNTExT that identifies the developmental maturity and regional identity of in vitro models. We observed strong differences between in vitro models, including hiPSC-derived neural progenitors from multiple laboratories. This work provides a systems biology framework for evaluating in vitro systems and supports their value in studying the molecular mechanisms of human neurodevelopmental disease.

[1]  R. Stevenson,et al.  Fragile X and X-linked intellectual disability: four decades of discovery. , 2012, American journal of human genetics.

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

[3]  Kenny Q. Ye,et al.  De Novo Gene Disruptions in Children on the Autistic Spectrum , 2012, Neuron.

[4]  Steffen Jung,et al.  Control of microglial neurotoxicity by the fractalkine receptor , 2006, Nature Neuroscience.

[5]  D. Geschwind,et al.  Functional and Evolutionary Insights into Human Brain Development through Global Transcriptome Analysis , 2009, Neuron.

[6]  J. Rubenstein,et al.  Deriving Excitatory Neurons of the Neocortex from Pluripotent Stem Cells , 2011, Neuron.

[7]  D. Volk,et al.  Increased density of microtubule associated protein 2-immunoreactive neurons in the prefrontal white matter of schizophrenic subjects , 1996, Schizophrenia Research.

[8]  J. Kleinman,et al.  Spatiotemporal transcriptome of the human brain , 2011, Nature.

[9]  D. Price,et al.  Role of Pax6 in forebrain regionalization , 2005, Brain Research Bulletin.

[10]  P. Penzes,et al.  Dendritic spine pathology in neuropsychiatric disorders , 2011, Nature Neuroscience.

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

[12]  Charles A. Vacanti,et al.  Stimulus-triggered fate conversion of somatic cells into pluripotency , 2014, Nature.

[13]  Allan R. Jones,et al.  Transcriptional Landscape of the Prenatal Human Brain , 2014, Nature.

[14]  S. Grant,et al.  Molecular characterization and comparison of the components and multiprotein complexes in the postsynaptic proteome , 2006, Journal of neurochemistry.

[15]  Jianxin Shi,et al.  Copy number variants in schizophrenia: confirmation of five previous findings and new evidence for 3q29 microdeletions and VIPR2 duplications. , 2011, The American journal of psychiatry.

[16]  Grigorios Tsoumakas,et al.  Multi-Label Classification: An Overview , 2007, Int. J. Data Warehous. Min..

[17]  H. Ropers,et al.  Genetics of intellectual disability. , 2008, Current opinion in genetics & development.

[18]  J. Hutsler,et al.  Increased dendritic spine densities on cortical projection neurons in autism spectrum disorders , 2010, Brain Research.

[19]  Zohar Mukamel,et al.  Modeling the functional genomics of autism using human neurons , 2011, Molecular Psychiatry.

[20]  Evan T. Geller,et al.  Patterns and rates of exonic de novo mutations in autism spectrum disorders , 2012, Nature.

[21]  Kristopher L. Nazor,et al.  Probing sporadic and familial Alzheimer’s disease using induced pluripotent stem cells , 2012, Nature.

[22]  M. Giustetto,et al.  Synaptic Pruning by Microglia Is Necessary for Normal Brain Development , 2011, Science.

[23]  S. Horvath,et al.  Functional organization of the transcriptome in human brain , 2008, Nature Neuroscience.

[24]  C. Englund,et al.  Pax6, Tbr2, and Tbr1 Are Expressed Sequentially by Radial Glia, Intermediate Progenitor Cells, and Postmitotic Neurons in Developing Neocortex , 2005, The Journal of Neuroscience.

[25]  Daniele Linaro,et al.  Pyramidal Neurons Derived from Human Pluripotent Stem Cells Integrate Efficiently into Mouse Brain Circuits In Vivo , 2013, Neuron.

[26]  Marie-Christine Chaboissier,et al.  The Sox9 transcription factor determines glial fate choice in the developing spinal cord. , 2003, Genes & development.

[27]  Susan Lindquist,et al.  Generation of Isogenic Pluripotent Stem Cells Differing Exclusively at Two Early Onset Parkinson Point Mutations , 2011, Cell.

[28]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[29]  Allan R. Jones,et al.  An anatomically comprehensive atlas of the adult human brain transcriptome , 2012, Nature.

[30]  Jennifer E. Chubb,et al.  DISC1 and PDE4B Are Interacting Genetic Factors in Schizophrenia That Regulate cAMP Signaling , 2005, Science.

[31]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[32]  Christopher Baum,et al.  Lentiviral vector design and imaging approaches to visualize the early stages of cellular reprogramming. , 2011, Molecular therapy : the journal of the American Society of Gene Therapy.

[33]  Michael E. Greenberg,et al.  Activity-dependent neuronal signalling and autism spectrum disorder , 2013, Nature.

[34]  Ryoichiro Kageyama,et al.  Dynamic Notch signaling in neural progenitor cells and a revised view of lateral inhibition , 2008, Nature Neuroscience.

[35]  D. Geschwind,et al.  Using iPS cell-derived neurons to uncover cellular phenotypes associated with Timothy Syndrome , 2011, Nature Medicine.

[36]  Thomas Wisniewski,et al.  Differences Between the Pattern of Developmental Abnormalities in Autism Associated With Duplications 15q11.2-q13 and Idiopathic Autism , 2012, Journal of neuropathology and experimental neurology.

[37]  Arnold Kriegstein,et al.  The glial nature of embryonic and adult neural stem cells. , 2009, Annual review of neuroscience.

[38]  Stefan Wagner,et al.  Generation of induced pluripotent stem cells from human cord blood. , 2009, Cell stem cell.

[39]  R. Hume,et al.  Glial and neuronal differentiation in the human fetal brain 9–23 weeks of gestation , 1990, Neuropathology and applied neurobiology.

[40]  Jennifer K Inlow,et al.  Molecular and comparative genetics of mental retardation. , 2004, Genetics.

[41]  P. Arlotta,et al.  Neuronal subtype specification in the cerebral cortex , 2007, Nature Reviews Neuroscience.

[42]  Pasko Rakic,et al.  Developmental and evolutionary adaptations of cortical radial glia. , 2003, Cerebral cortex.

[43]  Hossein Baharvand,et al.  Comprehensive Gene Expression Analysis of Human Embryonic Stem Cells during Differentiation into Neural Cells , 2011, PloS one.

[44]  Stephen S. Taylor,et al.  Kinetochore Localization of Murine Bub1 Is Required for Normal Mitotic Timing and Checkpoint Response to Spindle Damage , 1997, Cell.

[45]  S. Grant,et al.  Targeted tandem affinity purification of PSD-95 recovers core postsynaptic complexes and schizophrenia susceptibility proteins , 2009, Molecular systems biology.

[46]  Bradley P. Coe,et al.  Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations , 2012, Nature.

[47]  K. Eggan,et al.  Modeling human disease with pluripotent stem cells: from genome association to function. , 2013, Cell stem cell.

[48]  A. Zimmerman,et al.  Neuroglial activation and neuroinflammation in the brain of patients with autism , 2005, Annals of neurology.

[49]  Y. Benjamini,et al.  THE CONTROL OF THE FALSE DISCOVERY RATE IN MULTIPLE TESTING UNDER DEPENDENCY , 2001 .

[50]  Michael F. Walker,et al.  De novo mutations revealed by whole-exome sequencing are strongly associated with autism , 2012, Nature.

[51]  Robert V Farese,et al.  Functional Genomic Analyses Identify Pathways Dysregulated by Progranulin Deficiency, Implicating Wnt Signaling , 2011, Neuron.

[52]  A. Packer,et al.  SFARI Gene: an evolving database for the autism research community , 2010, Disease Models & Mechanisms.

[53]  S. Andersen.  Trajectories of brain development: point of vulnerability or window of opportunity? , 2003, Neuroscience & Biobehavioral Reviews.

[54]  K. Eggan,et al.  Opportunities and challenges of pluripotent stem cell neurodegenerative disease models , 2013, Nature Neuroscience.

[55]  R. Taschereau,et al.  Rank–rank hypergeometric overlap: identification of statistically significant overlap between gene-expression signatures , 2010, Nucleic acids research.

[56]  S. Pääbo,et al.  Extension of cortical synaptic development distinguishes humans from chimpanzees and macaques. , 2012, Genome research.

[57]  Fred H. Gage,et al.  Cell culture: Progenitor cells from human brain after death , 2001, Nature.

[58]  T. Graf.  Faculty Opinions recommendation of Induction of pluripotent stem cells from adult human fibroblasts by defined factors. , 2007 .

[59]  T. Ichisaka,et al.  Induction of Pluripotent Stem Cells from Adult Human Fibroblasts by Defined Factors , 2007, Cell.

[60]  Henry Kennedy,et al.  Precursor Diversity and Complexity of Lineage Relationships in the Outer Subventricular Zone of the Primate , 2013, Neuron.

[61]  Fred H. Gage,et al.  A Model for Neural Development and Treatment of Rett Syndrome Using Human Induced Pluripotent Stem Cells , 2010, Cell.

[62]  Daniel H. Geschwind,et al.  The Human Brain in a Dish: The Promise of iPSC-Derived Neurons , 2011, Cell.

[63]  A. Kriegstein,et al.  Neurogenic radial glia in the outer subventricular zone of human neocortex , 2010, Nature.

[64]  Rui Luo,et al.  Is My Network Module Preserved and Reproducible? , 2011, PLoS Comput. Biol..

[65]  박찬영.  Using iPSC-derived neurons to uncover cellular phenotypes associated with Timothy syndrome , 2012 .

[66]  Kathryn Roeder,et al.  Multiple Recurrent De Novo CNVs, Including Duplications of the 7q11.23 Williams Syndrome Region, Are Strongly Associated with Autism , 2011, Neuron.

[67]  M. Rosenfeld,et al.  Transcriptional Regulation of Cortical Neuron Migration by POU Domain Factors , 2002, Science.

[68]  Richard M. Page,et al.  Microglial Cx3cr1 knockout prevents neuron loss in a mouse model of Alzheimer's disease , 2010, Nature Neuroscience.

[69]  S. Horvath,et al.  Integrative Functional Genomic Analyses Implicate Specific Molecular Pathways and Circuits in Autism , 2013, Cell.

[70]  J. Fish,et al.  OSVZ progenitors of human and ferret neocortex are epithelial-like and expand by integrin signaling , 2010, Nature Neuroscience.

[71]  D. Geschwind,et al.  Genome-Wide Analysis of a Wnt1-Regulated Transcriptional Network Implicates Neurodegenerative Pathways , 2011, Science Signaling.

[72]  Hans van Bokhoven,et al.  Genetic and epigenetic networks in intellectual disabilities. , 2011, Annual review of genetics.

[73]  Paola Arlotta,et al.  Neuronal Subtype-Specific Genes that Control Corticospinal Motor Neuron Development In Vivo , 2005, Neuron.

[74]  J. Rubenstein,et al.  Functional maturation of hPSC-derived forebrain interneurons requires an extended timeline and mimics human neural development. , 2013, Cell stem cell.

[75]  Jesse Read,et al.  Scalable Multi-label Classification , 2010 .

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

[77]  D. Licatalosi,et al.  FMRP Stalls Ribosomal Translocation on mRNAs Linked to Synaptic Function and Autism , 2011, Cell.

[78]  Fumio Nakamura,et al.  Collapsin-induced growth cone collapse mediated by an intracellular protein related to UNC-33 , 1995, Nature.

[79]  R. Ozawa,et al.  Identification and Classification of Genes Regulated by Phosphatidylinositol 3-kinase-and Trkb-mediated Signalling Pathways during Neuronal Differentiation in Two Subtypes of the Human Neuroblastoma Cell Line Sh-sy5y , 2022 .

[80]  Matthew Trotter,et al.  Capture of Neuroepithelial-Like Stem Cells from Pluripotent Stem Cells Provides a Versatile System for In Vitro Production of Human Neurons , 2012, PloS one.

[81]  S. Nelson,et al.  Molecular taxonomy of major neuronal classes in the adult mouse forebrain , 2006, Nature Neuroscience.

[82]  Tamas L. Horvath,et al.  Modeling human cortical development in vitro using induced pluripotent stem cells , 2012, Proceedings of the National Academy of Sciences.

[83]  V. Carey,et al.  Mixed-Effects Models in S and S-Plus , 2001 .

[84]  D. G. Clark,et al.  Common variants in MS4A4/MS4A6E, CD2uAP, CD33, and EPHA1 are associated with late-onset Alzheimer’s disease , 2011, Nature Genetics.

[85]  L. Siever,et al.  Spatial and Temporal Mapping of De Novo Mutations in Schizophrenia to a Fetal Prefrontal Cortical Network , 2013, Cell.

[86]  F. Gage,et al.  Phenotypic differences in hiPSC NPCs derived from patients with schizophrenia , 2014, Molecular Psychiatry.

[87]  R. Gronostajski,et al.  Sox9 and NFIA Coordinate a Transcriptional Regulatory Cascade during the Initiation of Gliogenesis , 2012, Neuron.

[88]  J. Frahm,et al.  Chromatin regulation by BAF170 controls cerebral cortical size and thickness. , 2013, Developmental cell.

[89]  Cheng Li,et al.  Adjusting batch effects in microarray expression data using empirical Bayes methods. , 2007, Biostatistics.

[90]  Janet Rossant,et al.  The International Stem Cell Initiative: toward benchmarks for human embryonic stem cell research , 2005, Nature Biotechnology.

[91]  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.

[92]  Simon C. Potter,et al.  Genome-wide Association Analysis Identifies 14 New Risk Loci for Schizophrenia , 2013, Nature Genetics.

[93]  Allissa Dillman,et al.  Edinburgh Research Explorer Integration of GWAS SNPs and tissue specific expression profiling reveal discrete eQTLs for human traits in blood and brain , 2022 .

[94]  Geoff Holmes,et al.  Classifier chains for multi-label classification , 2009, Machine Learning.

[95]  Steve Horvath,et al.  WGCNA: an R package for weighted correlation network analysis , 2008, BMC Bioinformatics.

[96]  Y. Xing,et al.  A Transcriptome Database for Astrocytes, Neurons, and Oligodendrocytes: A New Resource for Understanding Brain Development and Function , 2008, The Journal of Neuroscience.

[97]  S. Horvath,et al.  Transcriptomic Analysis of Autistic Brain Reveals Convergent Molecular Pathology , 2011, Nature.

[98]  E. G. Jones,et al.  Maldistribution of interstitial neurons in prefrontal white matter of the brains of schizophrenic patients. , 1996, Archives of general psychiatry.

[99]  G. Fishell,et al.  Sonic hedgehog functions through dynamic changes in temporal competence in the developing forebrain. , 2010, Current opinion in genetics & development.

[100]  R. McKay,et al.  Dopamine neurons derived from embryonic stem cells function in an animal model of Parkinson's disease , 2002, Nature.

[101]  D. Stephan,et al.  Recessive symptomatic focal epilepsy and mutant contactin-associated protein-like 2. , 2006, The New England journal of medicine.

[102]  Tobias Wittkop,et al.  Genetic correction of Huntington's disease phenotypes in induced pluripotent stem cells. , 2012, Cell stem cell.

[103]  S. Grant,et al.  Characterization of the proteome, diseases and evolution of the human postsynaptic density , 2011, Nature Neuroscience.

[104]  Jan H Lui,et al.  Non-epithelial stem cells and cortical interneuron production in the human ganglionic eminences , 2013, Nature Neuroscience.

[105]  Wei Niu,et al.  Coexpression Networks Implicate Human Midfetal Deep Cortical Projection Neurons in the Pathogenesis of Autism , 2013, Cell.

[106]  J. Leek,et al.  Temporal dynamics and genetic control of transcription in the human prefrontal cortex , 2011, Nature.

[107]  P. Rakic,et al.  Origin of GABAergic neurons in the human neocortex , 2002, Nature.

[108]  C. Walsh,et al.  Doublecortin Is a Microtubule-Associated Protein and Is Expressed Widely by Migrating Neurons , 1999, Neuron.

[109]  Chris T. A. Evelo,et al.  Bioinformatics Applications Note Databases and Ontologies Go-elite: a Flexible Solution for Pathway and Ontology Over-representation , 2022 .