scholarly journals Transcriptional signatures of participant-derived neural progenitor cells and neurons implicate altered Wnt signaling in Phelan McDermid syndrome and autism

2019 ◽  
Author(s):  
Michael S. Breen ◽  
Andrew Browne ◽  
Gabriel E. Hoffman ◽  
Sofia Stathopoulos ◽  
Kristen Brennand ◽  
...  
Keyword(s):  
Intellectual Disability ◽  
Wnt Signaling ◽  
Progenitor Cells ◽  
Rna Sequencing ◽  
Neural Progenitor Cells ◽  
Genetic Disorder ◽  
Protein Translation ◽  
Neural Progenitor ◽  
Autism Spectrum ◽  
Genome Wide

ABSTRACTBackgroundPhelan-McDermid syndrome (PMS) is a rare genetic disorder with high risk of autism spectrum disorder (ASD), intellectual disability and language delay, and is caused by 22q13.3 deletions or mutations in the SHANK3 gene. To date, the molecular and pathway changes resulting from SHANK3 haploinsufficiency in PMS remain poorly understood. Uncovering these mechanisms is critical for understanding pathobiology of PMS and, ultimately, for the development of new therapeutic interventions.MethodsWe developed human induced pluripotent stem cell (hiPSC)-based models of PMS by reprogramming peripheral blood samples from individuals with PMS (n=7) and their unaffected siblings (n=6). For each participant, up to three hiPSC clones were generated and differentiated into induced neural progenitor cells (iNPCs; n=32) and induced forebrain neurons (iNeurons; n=42). Genome-wide RNA-sequencing was applied to explore transcriptional differences between PMS probands and unaffected siblings.ResultsTranscriptome analyses identified 391 differentially expressed genes (DEGs) in iNPCs and 82 DEGs in iNeurons, when comparing cells from PMS probands and unaffected siblings (FDR <5%). Genes under-expressed in PMS were implicated in Wnt signaling, embryonic development and protein translation, while over-expressed genes were enriched for pre- and post-synaptic density genes, regulation of synaptic plasticity, and G-protein-gated potassium channel activity. Gene co-expression network analysis identified two modules in iNeurons that were over-expressed in PMS, implicating postsynaptic signaling and GDP binding, and both modules harbored a significant enrichment of genetic risk loci for developmental delay and intellectual disability. Finally, PMS-associated genes were integrated with other ASD iPSC transcriptome findings and several points of convergence were identified, indicating altered Wnt signaling, extracellular matrix and glutamatergic synapses.LimitationsGiven the rarity of the condition, we could not carry out experimental validation in independent biological samples. In addition, functional and morphological phenotypes caused by loss of SHANK3 were not characterized here.ConclusionsThis is the largest human neural sample analyzed in PMS. Genome-wide RNA-sequencing in hiPSC-derived neural cells from individuals with PMS revealed both shared and distinct transcriptional signatures across iNPCs and iNeurons, including many genes implicated in risk for ASD, as well as specific neurobiological pathways, including the Wnt pathway.

scholarly journals Genome-wide screens in accelerated human stem cell-derived neural progenitor cells identify Zika virus host factors and drivers of proliferation

2018 ◽  
Author(s):  
Michael F. Wells ◽  
Max R. Salick ◽  
Federica Piccioni ◽  
Ellen J. Hill ◽  
Jana M. Mitchell ◽  
...  
Keyword(s):  
Stem Cell ◽  
Progenitor Cells ◽  
Zika Virus ◽  
Large Scale ◽  
Neural Progenitor Cells ◽  
Neural Progenitor ◽  
Autism Spectrum ◽  
Host Factors ◽  
Protein Markers ◽  
Genome Wide

SUMMARYNeural progenitor cells (NPCs) are essential to brain development and their dysfunction is linked to several disorders, including autism, Zika Virus Congenital Syndrome, and cancer. Understanding of these conditions has been improved by advancements with stem cell-derived NPC models. However, current differentiation methods require many days or weeks to generate NPCs and show variability in efficacy among cell lines. Here, we describe humanStem cell-derivedNGN2-acceleratedProgenitor cells (SNaPs), which are produced in only 48 hours. SNaPs express canonical forebrain NPC protein markers, are proliferative, multipotent, and like other human NPCs, are susceptible to Zika-mediated death. We further demonstrate SNaPs are valuable for large-scale investigations of genetic and environmental influencers of neurodevelopment by deploying them for genome-wide CRISPR-Cas9 screens. Our studies expand knowledge of NPCs by identifying known and novel Zika host factors, as well as new regulators of NPC proliferation validated by re-identification of the autism spectrum genePTEN.

scholarly journals TSC patient-derived isogenic neural progenitor cells reveal altered early neurodevelopmental phenotypes and rapamycin-induced MNK-eIF4E signaling

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Pauline Martin ◽  
Vilas Wagh ◽  
Surya A. Reis ◽  
Serkan Erdin ◽  
Roberta L. Beauchamp ◽  
...  
Keyword(s):  
Progenitor Cells ◽  
Large Scale ◽  
Neural Progenitor Cells ◽  
Neurodevelopmental Disorder ◽  
Protein Translation ◽  
Neural Progenitor ◽  
Autism Spectrum ◽  
Patient Specific ◽  
Dependent Manner ◽  
Multiple Organs

Abstract Background Tuberous sclerosis complex (TSC) is a neurodevelopmental disorder with frequent occurrence of epilepsy, autism spectrum disorder (ASD), intellectual disability (ID), and tumors in multiple organs. The aberrant activation of mTORC1 in TSC has led to treatment with mTORC1 inhibitor rapamycin as a lifelong therapy for tumors, but TSC-associated neurocognitive manifestations remain unaffected by rapamycin. Methods Here, we generated patient-specific, induced pluripotent stem cells (iPSCs) from a TSC patient with a heterozygous, germline, nonsense mutation in exon 15 of TSC1 and established an isogenic set of heterozygous (Het), null and corrected wildtype (Corr-WT) iPSCs using CRISPR/Cas9-mediated gene editing. We differentiated these iPSCs into neural progenitor cells (NPCs) and examined neurodevelopmental phenotypes, signaling and changes in gene expression by RNA-seq. Results Differentiated NPCs revealed enlarged cell size in TSC1-Het and Null NPCs, consistent with mTORC1 activation. TSC1-Het and Null NPCs also revealed enhanced proliferation and altered neurite outgrowth in a genotype-dependent manner, which was not reversed by rapamycin. Transcriptome analyses of TSC1-NPCs revealed differentially expressed genes that display a genotype-dependent linear response, i.e., genes upregulated/downregulated in Het were further increased/decreased in Null. In particular, genes linked to ASD, epilepsy, and ID were significantly upregulated or downregulated warranting further investigation. In TSC1-Het and Null NPCs, we also observed basal activation of ERK1/2, which was further activated upon rapamycin treatment. Rapamycin also increased MNK1/2-eIF4E signaling in TSC1-deficient NPCs. Conclusion MEK-ERK and MNK-eIF4E pathways regulate protein translation, and our results suggest that aberrant translation distinct in TSC1/2-deficient NPCs could play a role in neurodevelopmental defects. Our data showing upregulation of these signaling pathways by rapamycin support a strategy to combine a MEK or a MNK inhibitor with rapamycin that may be superior for TSC-associated CNS defects. Importantly, our generation of isogenic sets of NPCs from TSC patients provides a valuable platform for translatome and large-scale drug screening studies. Overall, our studies further support the notion that early developmental events such as NPC proliferation and initial process formation, such as neurite number and length that occur prior to neuronal differentiation, represent primary events in neurogenesis critical to disease pathogenesis of neurodevelopmental disorders such as ASD.

scholarly journals Cellular and molecular characterization of multiplex autism in human induced pluripotent stem cell-derived neurons

2019 ◽  
Author(s):  
Emily M.A. Lewis ◽  
Kesavan Meganathan ◽  
Dustin Baldridge ◽  
Paul Gontarz ◽  
Bo Zhang ◽  
...  
Keyword(s):  
Progenitor Cells ◽  
Neural Progenitor Cells ◽  
Phenotypic Expression ◽  
Neural Progenitor ◽  
Autism Spectrum ◽  
Cellular Systems ◽  
Transcriptomic Analysis ◽  
Unrelated Control ◽  
Altered Expression ◽  
Induced Pluripotent

AbstractBackgroundAutism spectrum disorder (ASD) is a neurodevelopmental disorder with pronounced heritability in the general population. This is largely attributable to effects of polygenic susceptibility, with inherited liability exhibiting distinct sex differences in phenotypic expression. Attempts to model ASD in human cellular systems have principally involved rarede novomutations associated with ASD phenocopies. However, by definition, these models are not representative of polygenic liability, which accounts for the vast share of population-attributable risk.MethodsHere, we performed what is, to our knowledge, the first attempt to model multiplex autism using patient-derived induced pluripotent stem cells (iPSCs) in a family manifesting incremental degrees of phenotypic expression of inherited liability (absent, intermediate, severe). The family members share an inherited variant of unknown significance inGPD2, a gene that was previously associated with developmental disability but here is insufficient by itself to cause ASD. iPSCs from three first-degree relatives and an unrelated control were differentiated into both cortical excitatory (cExN) and cortical inhibitory (cIN) neurons, and cellular phenotyping and transcriptomic analysis were conducted.ResultscExN neurospheres from the two affected individuals were reduced in size, compared to those derived from unaffected related and unrelated individuals. This reduction was, at least in part, due to increased apoptosis of cells from affected individuals upon initiation of cExN neural induction. Likewise, cIN neural progenitor cells from affected individuals exhibited increased apoptosis, compared to both unaffected individuals. Transcriptomic analysis of both cExN and cIN neural progenitor cells revealed distinct molecular signatures associated with affectation, including misregulation of suites of genes associated with neural development, neuronal function, and behavior, as well as altered expression of ASD risk-associated genes.ConclusionsWe have provided evidence of morphological, physiological, and transcriptomic signatures of polygenic liability to ASD from an analysis of cellular models derived from a multiplex autism family. ASD is commonly inherited on the basis of additive genetic liability. Therefore, identifying convergent cellular and molecular phenotypes resulting from polygenic and monogenic susceptibility may provide a critical bridge for determining which of the disparate effects of rare highly deleterious mutations might also apply to common autistic syndromes.

scholarly journals Cellular and molecular characterization of multiplex autism in human induced pluripotent stem cell-derived neurons

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Emily M. A. Lewis ◽  
Kesavan Meganathan ◽  
Dustin Baldridge ◽  
Paul Gontarz ◽  
Bo Zhang ◽  
...  
Keyword(s):  
Progenitor Cells ◽  
Neural Progenitor Cells ◽  
Phenotypic Expression ◽  
Neural Progenitor ◽  
Autism Spectrum ◽  
Cellular Systems ◽  
Transcriptomic Analysis ◽  
Unrelated Control ◽  
Altered Expression ◽  
Induced Pluripotent

Abstract Background Autism spectrum disorder (ASD) is a neurodevelopmental disorder with pronounced heritability in the general population. This is largely attributable to the effects of polygenic susceptibility, with inherited liability exhibiting distinct sex differences in phenotypic expression. Attempts to model ASD in human cellular systems have principally involved rare de novo mutations associated with ASD phenocopies. However, by definition, these models are not representative of polygenic liability, which accounts for the vast share of population-attributable risk. Methods Here, we performed what is, to our knowledge, the first attempt to model multiplex autism using patient-derived induced pluripotent stem cells (iPSCs) in a family manifesting incremental degrees of phenotypic expression of inherited liability (absent, intermediate, severe). The family members share an inherited variant of uncertain significance (VUS) in GPD2, a gene that was previously associated with developmental disability but here is insufficient by itself to cause ASD. iPSCs from three first-degree relatives and an unrelated control were differentiated into both cortical excitatory (cExN) and cortical inhibitory (cIN) neurons, and cellular phenotyping and transcriptomic analysis were conducted. Results cExN neurospheres from the two affected individuals were reduced in size, compared to those derived from unaffected related and unrelated individuals. This reduction was, at least in part, due to increased apoptosis of cells from affected individuals upon initiation of cExN neural induction. Likewise, cIN neural progenitor cells from affected individuals exhibited increased apoptosis, compared to both unaffected individuals. Transcriptomic analysis of both cExN and cIN neural progenitor cells revealed distinct molecular signatures associated with affectation, including the misregulation of suites of genes associated with neural development, neuronal function, and behavior, as well as altered expression of ASD risk-associated genes. Conclusions We have provided evidence of morphological, physiological, and transcriptomic signatures of polygenic liability to ASD from an analysis of cellular models derived from a multiplex autism family. ASD is commonly inherited on the basis of additive genetic liability. Therefore, identifying convergent cellular and molecular phenotypes resulting from polygenic and monogenic susceptibility may provide a critical bridge for determining which of the disparate effects of rare highly deleterious mutations might also apply to common autistic syndromes.

scholarly journals Transcriptional signatures of participant-derived neural progenitor cells and neurons implicate altered Wnt signaling in Phelan-McDermid syndrome and autism

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Michael S. Breen ◽  
Andrew Browne ◽  
Gabriel E. Hoffman ◽  
Sofia Stathopoulos ◽  
Kristen Brennand ◽  
...  
Keyword(s):  
Wnt Signaling ◽  
Progenitor Cells ◽  
Neural Progenitor Cells ◽  
Neural Progenitor

scholarly journals Transcriptional Signatures of Participant-Derived Neural Progenitor Cells and Neurons Implicate Altered WNT Signaling in Phelan-McDermid Syndrome and Autism

2020 ◽  
Vol 87 (9) ◽  
pp. S456-S457
Author(s):  
Michael Breen ◽  
Andrew Browne ◽  
Gabriel Hoffman ◽  
Sofia Stathopoulous ◽  
Kristen Brennand ◽  
...  
Keyword(s):  
Wnt Signaling ◽  
Progenitor Cells ◽  
Neural Progenitor Cells ◽  
Neural Progenitor

scholarly journals Genome-Wide Gene Amplification during Differentiation of Neural Progenitor Cells In Vitro

PLoS ONE ◽  
2012 ◽  
Vol 7 (5) ◽  
pp. e37422 ◽  
Author(s):  
Ulrike Fischer ◽  
Andreas Keller ◽  
Meike Voss ◽  
Christina Backes ◽  
Cornelius Welter ◽  
...  
Keyword(s):  
Progenitor Cells ◽  
Gene Amplification ◽  
Neural Progenitor Cells ◽  
Neural Progenitor ◽  
Genome Wide

scholarly journals Transcriptome analysis of MBD5-associated neurodevelopmental disorder (MAND) neural progenitor cells reveals dysregulation of autism-associated genes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sureni V. Mullegama ◽  
Steven D. Klein ◽  
Stephen R. Williams ◽  
Jeffrey W. Innis ◽  
Frank J. Probst ◽  
...  
Keyword(s):  
Progenitor Cells ◽  
Behavioral Problems ◽  
Transcriptome Analysis ◽  
Neural Progenitor Cells ◽  
Neurodevelopmental Disorder ◽  
Neural Progenitor ◽  
Autism Spectrum ◽  
Hippo Signaling ◽  
Biological Processes ◽  
Speech Impairment

AbstractMBD5-associated neurodevelopmental disorder (MAND) is an autism spectrum disorder (ASD) characterized by intellectual disability, motor delay, speech impairment and behavioral problems; however, the biological role of methyl-CpG-binding domain 5, MBD5, in neurodevelopment and ASD remains largely undefined. Hence, we created neural progenitor cells (NPC) derived from individuals with chromosome 2q23.1 deletion and conducted RNA-seq to identify differentially expressed genes (DEGs) and the biological processes and pathways altered in MAND. Primary skin fibroblasts from three unrelated individuals with MAND and four unrelated controls were converted into induced pluripotent stem cell (iPSC) lines, followed by directed differentiation of iPSC to NPC. Transcriptome analysis of MAND NPC revealed 468 DEGs (q < 0.05), including 20 ASD-associated genes. Comparison of DEGs in MAND with SFARI syndromic autism genes revealed a striking significant overlap in biological processes commonly altered in neurodevelopmental phenotypes, with TGFβ, Hippo signaling, DNA replication, and cell cycle among the top enriched pathways. Overall, these transcriptome deviations provide potential connections to the overlapping neurocognitive and neuropsychiatric phenotypes associated with key high-risk ASD genes, including chromatin modifiers and epigenetic modulators, that play significant roles in these disease states.

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