Modeling neuronal consequences of autism-associated gene regulatory variants with human induced pluripotent stem cells

Silencing Trisomy 21 with XIST in Neural Stem Cells Promotes Neuronal Differentiation

(2020) Jan Tomasz Czermiński et al.   DEVELOPMENTAL CELL

Autism-Misregulated eIF4G Microexons Control Synaptic Translation and Higher Order Cognitive Functions

(2020) Thomas Gonatopoulos-Pournatzis et al.   MOLECULAR CELL

Pathological priming causes developmental gene network heterochronicity in autistic subject-derived neurons

(2019) Simon T. Schafer et al.   NATURE NEUROSCIENCE

The novel lncRNA lnc-NR2F1 is pro-neurogenic and mutated in human neurodevelopmental disorders

(2019) Cheen Euong Ang et al.   eLife

Enhancer Histone Acetylation Modulates Transcriptional Bursting Dynamics of Neuronal Activity-Inducible Genes

(2019) Liang-Fu Chen et al.   Cell Reports

SHANK2 mutations associated with autism spectrum disorder cause hyperconnectivity of human neurons

(2019) Kirill Zaslavsky et al.   NATURE NEUROSCIENCE

Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk

(2019) Jian Zhou et al.   NATURE GENETICS

CNTN5-/+or EHMT2-/+human iPSC-derived neurons from individuals with autism develop hyperactive neuronal networks

(2019) Eric Deneault et al.   eLife

Synaptic dysfunction in human neurons with autism-associated deletions in PTCHD1-AS

(2019) P. Joel Ross et al.   BIOLOGICAL PSYCHIATRY

The Translational Landscape of the Human Heart

(2019) Sebastiaan van Heesch et al.   CELL

Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes

(2019) Michael Song et al.   NATURE GENETICS

Neuroligin-4 Regulates Excitatory Synaptic Transmission in Human Neurons

(2019) Samuele G. Marro et al.   NEURON

A genome-wide scan statistic framework for whole-genome sequence data analysis

(2019) Zihuai He et al.   Nature Communications

Inherited and De Novo Genetic Risk for Autism Impacts Shared Networks

(2019) Elizabeth K. Ruzzo et al.   CELL

Getting to the Cores of Autism

(2019) Lilia M. Iakoucheva et al.   CELL

From enhanceropathies to the epigenetic manifold underlying human cognition

(2019) Alessandro Vitriolo et al.   HUMAN MOLECULAR GENETICS

Conserved cell types with divergent features in human versus mouse cortex

(2019) Rebecca D. Hodge et al.   NATURE

Synergistic effects of common schizophrenia risk variants

(2019) Nadine Schrode et al.   NATURE GENETICS

CRISPR Tools for Systematic Studies of RNA Regulation

(2019) Jesse Engreitz et al.   Cold Spring Harbor Perspectives in Biology

Complex Oscillatory Waves Emerging from Cortical Organoids Model Early Human Brain Network Development

(2019) Cleber A. Trujillo et al.   Cell Stem Cell

Neuronal network dysfunction in a model for Kleefstra syndrome mediated by enhanced NMDAR signaling

(2019) Monica Frega et al.   Nature Communications

Ranking of non-coding pathogenic variants and putative essential regions of the human genome

(2019) Alex Wells et al.   Nature Communications

A large data resource of genomic copy number variation across neurodevelopmental disorders

(2019) Mehdi Zarrei et al.   npj Genomic Medicine

Convergence of spectrums: neuronal gene network states in autism spectrum disorder

(2019) Josefa M Sullivan et al.   CURRENT OPINION IN NEUROBIOLOGY

Precision Health Resource of Control iPSC Lines for Versatile Multilineage Differentiation

(2019) Matthew R. Hildebrandt et al.   Stem Cell Reports

FUN-LDA: A Latent Dirichlet Allocation Model for Predicting Tissue-Specific Functional Effects of Noncoding Variation: Methods and Applications

(2018) Daniel Backenroth et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A Statistical Framework for Mapping Risk Genes from De Novo Mutations in Whole-Genome-Sequencing Studies

(2018) Yuwen Liu et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Modeling the Interplay Between Neurons and Astrocytes in Autism Using Human Induced Pluripotent Stem Cells

(2018) Fabiele Baldino Russo et al.   BIOLOGICAL PSYCHIATRY

An integrative analysis of non-coding regulatory DNA variations associated with autism spectrum disorder

(2018) Sarah M. Williams et al.   MOLECULAR PSYCHIATRY

New considerations for hiPSC-based models of neuropsychiatric disorders

(2018) Gabriel E. Hoffman et al.   MOLECULAR PSYCHIATRY

Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk

(2018) Jian Zhou et al.   NATURE GENETICS

Paternally inherited cis-regulatory structural variants are associated with autism

(2018) William M. Brandler et al.   SCIENCE

Functional changes of AMPA responses in human induced pluripotent stem cell–derived neural progenitors in fragile X syndrome

(2018) Venkat Swaroop Achuta et al.   Science Signaling

Functional changes of AMPA responses in human induced pluripotent stem cell–derived neural progenitors in fragile X syndrome

(2018) Venkat Swaroop Achuta et al.   Science Signaling

MicroRNA profiling during directed differentiation of cortical interneurons from human-induced pluripotent stem cells

(2018) Jiajie Tu et al.   FEBS Open Bio

Further evidence of a causal association between AGO1, a critical regulator of microRNA formation, and intellectual disability/autism spectrum disorder

(2018) Asami Sakaguchi et al.   European Journal of Medical Genetics

Rapid and efficient induction of functional astrocytes from human pluripotent stem cells

(2018) Isaac Canals et al.   NATURE METHODS

Joint profiling of chromatin accessibility and gene expression in thousands of single cells

(2018) Junyue Cao et al.   SCIENCE

Single-Cell Sequencing of iPSC-Dopamine Neurons Reconstructs Disease Progression and Identifies HDAC4 as a Regulator of Parkinson Cell Phenotypes

(2018) Charmaine Lang et al.   Cell Stem Cell

A placental mammal‐specific microRNA cluster acts as a natural brake for sociability in mice

(2018) Martin Lackinger et al.   EMBO REPORTS

Genetic Modulation of RNA Splicing with a CRISPR-Guided Cytidine Deaminase

(2018) Juanjuan Yuan et al.   MOLECULAR CELL

Partial loss of psychiatric risk gene Mir137 in mice causes repetitive behavior and impairs sociability and learning via increased Pde10a

(2018) Ying Cheng et al.   NATURE NEUROSCIENCE

Autism spectrum disorder: insights into convergent mechanisms from transcriptomics

(2018) Mathieu Quesnel-Vallières et al.   NATURE REVIEWS GENETICS

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

miRBase: from microRNA sequences to function

(2018) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Long noncoding RNA GM12371 acts as a transcriptional regulator of synapse function

(2018) Bindu L. Raveendra et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder

(2018) Michael J. Gandal et al.   SCIENCE

Genome-wide de novo risk score implicates promoter variation in autism spectrum disorder

(2018) Joon-Yong An et al.   SCIENCE

Comprehensive functional genomic resource and integrative model for the human brain

(2018) Daifeng Wang et al.   SCIENCE

Transcriptome and epigenome landscape of human cortical development modeled in organoids

(2018) Anahita Amiri et al.   SCIENCE

The Role of De Novo Noncoding Regulatory Mutations in Neurodevelopmental Disorders

(2018) Tychele N. Turner et al.   TRENDS IN NEUROSCIENCES

Complete Disruption of Autism-Susceptibility Genes by Gene Editing Predominantly Reduces Functional Connectivity of Isogenic Human Neurons

(2018) Eric Deneault et al.   Stem Cell Reports

Spatiotemporal Proteomic Profiling of Human Cerebral Development

(2017) Ugljesa Djuric et al.   MOLECULAR & CELLULAR PROTEOMICS

MeCP2-regulated miRNAs control early human neurogenesis through differential effects on ERK and AKT signaling

(2017) N Mellios et al.   MOLECULAR PSYCHIATRY

Molecular and functional variation in iPSC-derived sensory neurons

(2017) Jeremy Schwartzentruber et al.   NATURE GENETICS

Generation of pure GABAergic neurons by transcription factor programming

(2017) Nan Yang et al.   NATURE METHODS

Whole genome sequencing in psychiatric disorders: the WGSPD consortium

(2017) Stephan J. Sanders et al.   NATURE NEUROSCIENCE

Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder

(2017) Ryan K C Yuen et al.   NATURE NEUROSCIENCE

Mining for Micropeptides

(2017) Catherine A. Makarewich et al.   TRENDS IN CELL BIOLOGY

Transcriptional signatures of schizophrenia in hiPSC-derived NPCs and neurons are concordant with post-mortem adult brains

(2017) Gabriel E. Hoffman et al.   Nature Communications

The long non-coding RNA NEAT1 is responsive to neuronal activity and is associated with hyperexcitability states

(2017) Guy Barry et al.   Scientific Reports

Networks of Cultured iPSC-Derived Neurons Reveal the Human Synaptic Activity-Regulated Adaptive Gene Program

(2017) Priit Pruunsild et al.   Cell Reports

CRISPR/Cas9-mediated heterozygous knockout of the autism gene CHD8 and characterization of its transcriptional networks in cerebral organoids derived from iPS cells

(2017) Ping Wang et al.   Molecular Autism

Using Human iPSC-Derived Neurons to Uncover Activity-Dependent Non-Coding RNAs

(2017) Mainá Bitar et al.   Genes

Variable phenotype expression in a family segregating microdeletions of the NRXN1 and MBD5 autism spectrum disorder susceptibility genes

(2017) Marc Woodbury-Smith et al.   npj Genomic Medicine

Genome Sequencing of Autism-Affected Families Reveals Disruption of Putative Noncoding Regulatory DNA

(2016) Tychele N. Turner et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Mutations in Human Accelerated Regions Disrupt Cognition and Social Behavior

(2016) Ryan N. Doan et al.   CELL

cAMP/CREB-regulated LINC00473 marks LKB1-inactivated lung cancer and mediates tumor growth

(2016) Zirong Chen et al.   JOURNAL OF CLINICAL INVESTIGATION

Rapid Ngn2-induction of excitatory neurons from hiPSC-derived neural progenitor cells

(2016) Seok-Man Ho et al.   METHODS

Predicting the functional states of human iPSC-derived neurons with single-cell RNA-seq and electrophysiology

(2016) C Bardy et al.   MOLECULAR PSYCHIATRY

Altered proliferation and networks in neural cells derived from idiopathic autistic individuals

(2016) M C Marchetto et al.   MOLECULAR PSYCHIATRY

Genome-wide changes in lncRNA, splicing and regional gene expression patterns in autism

(2016) Neelroop N. Parikshak et al.   NATURE

A spectral approach integrating functional genomic annotations for coding and noncoding variants

(2016) Iuliana Ionita-Laza et al.   NATURE GENETICS

Engineering microdeletions and microduplications by targeting segmental duplications with CRISPR

(2016) Derek J C Tai et al.   NATURE NEUROSCIENCE

Evaluating cell reprogramming, differentiation and conversion technologies in neuroscience

(2016) Jerome Mertens et al.   NATURE REVIEWS NEUROSCIENCE

De Novo Synonymous Mutations in Regulatory Elements Contribute to the Genetic Etiology of Autism and Schizophrenia

(2016) Atsushi Takata et al.   NEURON

Autism-associated SHANK3 haploinsufficiency causes Ih channelopathy in human neurons

(2016) F. Yi et al.   SCIENCE

Whole-genome mutational burden analysis of three pluripotency induction methods

(2016) Kunal Bhutani et al.   Nature Communications

MECP2 Is Post-transcriptionally Regulated during Human Neurodevelopment by Combinatorial Action of RNA-Binding Proteins and miRNAs

(2016) Deivid C. Rodrigues et al.   Cell Reports

A Comparative Review of microRNA Expression Patterns in Autism Spectrum Disorder

(2016) Steven D. Hicks et al.   Frontiers in Psychiatry

Genome-wide characteristics of de novo mutations in autism

(2016) Ryan KC Yuen et al.   npj Genomic Medicine

Utility of Scalp Hair Follicles as a Novel Source of Biomarker Genes for Psychiatric Illnesses

(2015) Motoko Maekawa et al.   BIOLOGICAL PSYCHIATRY

FOXG1-Dependent Dysregulation of GABA/Glutamate Neuron Differentiation in Autism Spectrum Disorders

(2015) Jessica Mariani et al.   CELL

Human Neuropsychiatric Disease Modeling using Conditional Deletion Reveals Synaptic Transmission Defects Caused by Heterozygous Mutations in NRXN1

(2015) ChangHui Pak et al.   Cell Stem Cell

First glimpses of the neurobiology of autism spectrum disorder

(2015) Stephan J Sanders   CURRENT OPINION IN GENETICS & DEVELOPMENT

Two rare deletions upstream of the NRXN1 gene (2p16.3) affecting the non-coding mRNA AK127244 segregate with diverse psychopathological phenotypes in a family

(2015) Linh T.T. Duong et al.   European Journal of Medical Genetics

Analysis of conditional heterozygous STXBP1 mutations in human neurons

(2015) Christopher Patzke et al.   JOURNAL OF CLINICAL INVESTIGATION

Genes with de novo mutations are shared by four neuropsychiatric disorders discovered from NPdenovo database

(2015) Jinchen Li et al.   MOLECULAR PSYCHIATRY

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

MECP2e1 isoform mutation affects the form and function of neurons derived from Rett syndrome patient iPS cells

(2015) Ugljesa Djuric et al.   NEUROBIOLOGY OF DISEASE

Mechanisms of Long Non-coding RNAs in Mammalian Nervous System Development, Plasticity, Disease, and Evolution

(2015) James A. Briggs et al.   NEURON

Common and rare variants of microRNA genes in autism spectrum disorders

(2015) Claudio Toma et al.   WORLD JOURNAL OF BIOLOGICAL PSYCHIATRY

Predicting effective microRNA target sites in mammalian mRNAs

(2015) Vikram Agarwal et al.   eLife

MicroRNA Profiling of Neurons Generated Using Induced Pluripotent Stem Cells Derived from Patients with Schizophrenia and Schizoaffective Disorder, and 22q11.2 Del

(2015) Dejian Zhao et al.   PLoS One

Genome-wide Identification and Characterization of Fixed Human-Specific Regulatory Regions

(2014) Davide Marnetto et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A Highly Conserved Program of Neuronal Microexons Is Misregulated in Autistic Brains

(2014) Manuel Irimia et al.   CELL

Pathways Disrupted in Human ALS Motor Neurons Identified through Genetic Correction of Mutant SOD1

(2014) Evangelos Kiskinis et al.   Cell Stem Cell

An Evolutionarily Conserved Long Noncoding RNA TUNA Controls Pluripotency and Neural Lineage Commitment

(2014) Nianwei Lin et al.   MOLECULAR CELL

Modeling non-syndromic autism and the impact of TRPC6 disruption in human neurons

(2014) K Griesi-Oliveira et al.   MOLECULAR PSYCHIATRY

Synaptic, transcriptional and chromatin genes disrupted in autism

(2014) Silvia De Rubeis et al.   NATURE

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Transcriptional landscape of the prenatal human brain

(2014) Jeremy A. Miller et al.   NATURE

A promoter-level mammalian expression atlas

(2014)   NATURE

CORTECON: A Temporal Transcriptome Analysis of In Vitro Human Cerebral Cortex Development from Human Embryonic Stem Cells

(2014) Joyce van de Leemput et al.   NEURON

Regulation of histone H3K4 methylation in brain development and disease

(2014) E. Shen et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Defining functional DNA elements in the human genome

(2014) M. Kellis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The human splicing code reveals new insights into the genetic determinants of disease

(2014) H. Y. Xiong et al.   SCIENCE

Ribosome Profiling Reveals Pervasive Translation Outside of Annotated Protein-Coding Genes

(2014) Nicholas T. Ingolia et al.   Cell Reports

Considerations when investigating lncRNA function in vivo

(2014) Andrew R Bassett et al.   eLife

Identification of candidate intergenic risk loci in autism spectrum disorder

(2013) Susan Walker et al.   BMC GENOMICS

Widespread and extensive lengthening of 3' UTRs in the mammalian brain

(2013) P. Miura et al.   GENOME RESEARCH

Disruption of MBD5 contributes to a spectrum of psychopathology and neurodevelopmental abnormalities

(2013) J C Hodge et al.   MOLECULAR PSYCHIATRY

SHANK3 and IGF1 restore synaptic deficits in neurons from 22q13 deletion syndrome patients

(2013) Aleksandr Shcheglovitov et al.   NATURE

Activity-dependent neuronal signalling and autism spectrum disorder

(2013) Daniel H. Ebert et al.   NATURE

Multi-electrode array technologies for neuroscience and cardiology

(2013) Micha E. Spira et al.   Nature Nanotechnology

Rapid Single-Step Induction of Functional Neurons from Human Pluripotent Stem Cells

(2013) Yingsha Zhang et al.   NEURON

AKAPs integrate genetic findings for autism spectrum disorders

(2013) G Poelmans et al.   Translational Psychiatry

Genetic architecture in autism spectrum disorder

(2012) Bernie Devlin et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Activity-Dependent Human Brain Coding/Noncoding Gene Regulatory Networks

(2012) L. Lipovich et al.   GENETICS

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

A Noncoding RNA Antisense to Moesin at 5p14.1 in Autism

(2012) T. Kerin et al.   Science Translational Medicine

Synaptic Dysfunction in Neurodevelopmental Disorders Associated with Autism and Intellectual Disabilities

(2012) H. Y. Zoghbi et al.   Cold Spring Harbor Perspectives in Biology

Assessment of 2q23.1 Microdeletion Syndrome Implicates MBD5 as a Single Causal Locus of Intellectual Disability, Epilepsy, and Autism Spectrum Disorder

(2011) Michael E. Talkowski et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Copy number variation and selection during reprogramming to pluripotency

(2011) Samer M. Hussein et al.   NATURE

Transcriptomic analysis of autistic brain reveals convergent molecular pathology

(2011) Irina Voineagu et al.   NATURE

Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation

(2010) Tim R Mercer et al.   BMC NEUROSCIENCE

Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding

(2010) D. Schmidt et al.   SCIENCE

Disruption at the PTCHD1 Locus on Xp22.11 in Autism Spectrum Disorder and Intellectual Disability

(2010) A. Noor et al.   Science Translational Medicine

MicroRNAs Potentiate Neural Development

(2009) Sarah K. Fineberg et al.   NEURON

Heterogeneous dysregulation of microRNAs across the autism spectrum

(2008) Kawther Abu-Elneel et al.   NEUROGENETICS