20. CHROMATIN ACCESSIBILITY MAPPING REVEALS COMPOUND GENETIC EFFECTS AT A SCHIZOPHRENIA GWAS RISK LOCUS IMPAIRING NEURODEVELOPMENT AND SYNAPTIC FUNCTION IN HUMAN NEURONS

AbstractChromatin accessibility identifies active regions of the genome, often at transcription factor (TF) binding sites, enhancers, and promoters, and contains regulatory genetic variation. Functionally related accessible sites have been reported to be co-accessible; however, the prevalence and range of co-accessibility is unknown. We perform ATAC-seq in induced pluripotent stem cells from 134 individuals and integrate it with RNA-seq, WGS, and ChIP-seq, providing the first long-range chromosome-length analysis of co-accessibility. We show that co-accessibility is highly connected, with sites having a median of 24 co-accessible partners up to 250Mb away. We also show that co-accessibility can de novo identify known and novel co-expressed genes, and co-regulatory TFs and chromatin states. We perform a cis and trans-caQTL, a trans-eQTL, and examine allelic effects of co-accessibility, identifying tens of thousands of trans-caQTLs, and showing that trans genetic effects can be propagated through co-accessibility to gene expression for cell-type and disease relevant genes.

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SYNGAP1 Controls the Maturation of Dendrites, Synaptic Function, and Network Activity in Developing Human Neurons

Journal of Neuroscience ◽

10.1523/jneurosci.1367-20.2020 ◽

2020 ◽

Vol 40 (41) ◽

pp. 7980-7994

Author(s):

Nerea Llamosas ◽

Vineet Arora ◽

Ridhima Vij ◽

Murat Kilinc ◽

Lukasz Bijoch ◽

...

Keyword(s):

Synaptic Function ◽

Network Activity ◽

Human Neurons

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Ibuprofen enhances synaptic function and neural progenitors proliferation markers and improves neuropathology and motor coordination in Machado–Joseph disease models

Human Molecular Genetics ◽

10.1093/hmg/ddz097 ◽

2019 ◽

Vol 28 (22) ◽

pp. 3691-3703 ◽

Cited By ~ 5

Author(s):

Liliana S Mendonça ◽

Clévio Nóbrega ◽

Silvia Tavino ◽

Maximilian Brinkhaus ◽

Carlos Matos ◽

...

Keyword(s):

Stem Cells ◽

Motor Coordination ◽

Clinical Manifestations ◽

Cerebellar Atrophy ◽

Neural Progenitors ◽

Synaptic Function ◽

Spinocerebellar Ataxia Type ◽

Pharmacological Intervention ◽

Human Neurons ◽

Machado Joseph Disease

Abstract Machado–Joseph disease or spinocerebellar ataxia type 3 is an inherited neurodegenerative disease associated with an abnormal glutamine over-repetition within the ataxin-3 protein. This mutant ataxin-3 protein affects several cellular pathways, leading to neuroinflammation and neuronal death in specific brain regions resulting in severe clinical manifestations. Presently, there is no therapy able to modify the disease progression. Nevertheless, anti-inflammatory pharmacological intervention has been associated with positive outcomes in other neurodegenerative diseases. Thus, the present work aimed at investigating whether ibuprofen treatment would alleviate Machado–Joseph disease. We found that ibuprofen-treated mouse models presented a significant reduction in the neuroinflammation markers, namely Il1b and TNFa mRNA and IKB-α protein phosphorylation levels. Moreover, these mice exhibited neuronal preservation, cerebellar atrophy reduction, smaller mutant ataxin-3 inclusions and motor performance improvement. Additionally, neural cultures of Machado–Joseph disease patients’ induced pluripotent stem cells-derived neural stem cells incubated with ibuprofen showed increased levels of neural progenitors proliferation and synaptic markers such as MSI1, NOTCH1 and SYP. These findings were further confirmed in ibuprofen-treated mice that display increased neural progenitor numbers (Ki67 positive) in the subventricular zone. Furthermore, interestingly, ibuprofen treatment enhanced neurite total length and synaptic function of human neurons. Therefore, our results indicate that ibuprofen reduces neuroinflammation and induces neuroprotection, alleviating Machado–Joseph disease-associated neuropathology and motor impairments. Thus, our findings demonstrate that ibuprofen treatment has the potential to be used as a neuroprotective therapeutic approach in Machado–Joseph disease.

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Addiction associated N40D mu-opioid receptor variant modulates synaptic function in human neurons

10.1101/328898 ◽

2018 ◽

Author(s):

Apoorva Halikere ◽

Dina Popova ◽

Aula Hamod ◽

Mavis R. Swerdel ◽

Jennifer C. Moore ◽

...

Keyword(s):

Gene Expression ◽

Synaptic Transmission ◽

Opioid Receptor ◽

Cell Lines ◽

Synaptic Function ◽

Ips Cell ◽

Neuronal Marker ◽

Human Neurons ◽

Regulatory Effects ◽

In Cells

AbstractBackgroundThe OPRM1 A118G gene variant (N40D) encoding the µ-opioid receptor (MOR) has been associated with dependence on opiates and other abused drugs but its mechanism is unknown. With opioid abuse-related deaths rising at unprecedented rates, understanding these mechanisms may provide a path to therapy.MethodsSeven human induced pluripotent stem (iPS) cell lines from homozygous N40D subjects (4 with N40 and 3 with D40 variants) were generated and human induced neuronal cells (iNs) were derived from these iPS cell lines. Morphological, gene expression as well as synaptic physiology analyses were conducted in human iN cells carrying N40D MOR variants; Two pairs of isogenic pluripotent stem cells carrying N40D were generated using CRISPR/Cas9 genome-editing and iN cells derived from them were analyzed.ResultsInhibitory human neurons generated from subjects carrying N40D MOR gene variants show mature properties in morphological and functional analyses. Gene expression revealed that they express mature neuronal marker and MORs. Activation of MORs suppressed inhibitory synaptic transmission in human neurons carrying both N40 or D40 MOR variants but D40 show stronger effects. To mitigate the confounding effects of background genetic variation on neuronal function, the regulatory effects of MORs on synaptic transmission were validated in two sets of independently generated isogenic N40D iNs.ConclusionsActivations of N40D MOR variants show different regulatory effects on synaptic transmission in inhibitory human neurons. This study identifies neurophysiological differences between human MOR variants that may predict altered opioid responsivity and/or dependence in this subset of individuals.

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Addiction associated N40D mu-opioid receptor variant modulates synaptic function in human neurons

Molecular Psychiatry ◽

10.1038/s41380-019-0507-0 ◽

2019 ◽

Vol 25 (7) ◽

pp. 1406-1419 ◽

Cited By ~ 7

Author(s):

Apoorva Halikere ◽

Dina Popova ◽

Matthew S. Scarnati ◽

Aula Hamod ◽

Mavis R. Swerdel ◽

...

Keyword(s):

Opioid Receptor ◽

Mu Opioid Receptor ◽

Synaptic Function ◽

Mu Opioid ◽

Human Neurons

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Cohen Syndrome Patient iPSC-Derived Neurospheres and Forebrain-Like Glutamatergic Neurons Reveal Reduced Proliferation of Neural Progenitor Cells and Altered Expression of Synapse Genes

Journal of Clinical Medicine ◽

10.3390/jcm9061886 ◽

2020 ◽

Vol 9 (6) ◽

pp. 1886

Author(s):

You-Kyung Lee ◽

Su-Kyeong Hwang ◽

Soo-Kyung Lee ◽

Jung-eun Yang ◽

Ji-Hye Kwak ◽

...

Keyword(s):

Stem Cells ◽

Autosomal Recessive Disorder ◽

Synaptic Function ◽

Compound Heterozygous Mutation ◽

Heterozygous Mutation ◽

Compound Heterozygous ◽

Altered Expression ◽

Glutamatergic Neurons ◽

Cohen Syndrome ◽

Human Neurons

Cohen syndrome (CS), a rare autosomal recessive disorder, has been associated with genetic mutations in the VPS13B gene, which regulates vesicle-mediated protein sorting and transport. However, the cellular mechanism underlying CS pathogenesis in patient-derived human neurons remains unknown. We identified a novel compound heterozygous mutation, due to homozygous variation of biparental origin and heterozygous variation inherited from the father, in the VPS13B gene in a 20-month-old female patient. To understand the cellular pathogenic mechanisms, we generated induced pluripotent stem cells (iPSCs) from the fibroblasts of the CS patient. The iPSCs were differentiated into forebrain-like functional glutamatergic neurons or neurospheres. Functional annotation from transcriptomic analysis using CS iPSC-derived neurons revealed that synapse-related functions were enriched among the upregulated and downregulated genes in the CS neurons, whereas processes associated with neurodevelopment were enriched in the downregulated genes. The developing CS neurospheres were small in size compared to control neurospheres, likely due to the reduced proliferation of SOX2-positive neural stem cells. Moreover, the number of SV2B-positive puncta and spine-like structures was significantly reduced in the CS neurons, suggesting synaptic dysfunction. Taking these findings together, for the first time, we report a potential cellular pathogenic mechanism which reveals the alteration of neurodevelopment-related genes and the dysregulation of synaptic function in the human induced neurons differentiated from iPSCs and neurospheres of a CS patient.

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Genetic effects on liver chromatin accessibility identify disease regulatory variants

The American Journal of Human Genetics ◽

10.1016/j.ajhg.2021.05.001 ◽

2021 ◽

Author(s):

Kevin W. Currin ◽

Michael R. Erdos ◽

Narisu Narisu ◽

Vivek Rai ◽

Swarooparani Vadlamudi ◽

...

Keyword(s):

Chromatin Accessibility ◽

Genetic Effects ◽

Regulatory Variants ◽

Liver Chromatin

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Cross-Platform Validation of Neurotransmitter Release Impairments in Schizophrenia Patient-Derived NRXN1-Mutant Neurons

10.1101/2020.11.03.366617 ◽

2020 ◽

Author(s):

ChangHui Pak ◽

Tamas Danko ◽

Vincent R. Mirabella ◽

Jinzhao Wang ◽

Xianglong Zhang ◽

...

Keyword(s):

Stem Cells ◽

Drug Discovery ◽

Neurotransmitter Release ◽

Single Gene ◽

Embryonic Stem ◽

Synaptic Function ◽

Pathophysiological Mechanism ◽

Human Neurons ◽

Future Drug ◽

Induced Pluripotent

ABSTRACTHeterozygous NRXN1 deletions constitute the most prevalent currently known single-gene mutation predisposing to schizophrenia. Previous studies showed that engineered heterozygous NRXN1 deletions impaired neurotransmitter release in human neurons, suggesting a synaptic pathophysiological mechanism. Utilizing this observation for drug discovery, however, requires confidence in its robustness and validity. Here, we describe a multi-center effort to test the generality of this pivotal observation, using independent analyses at two laboratories of patient-derived and newly engineered human neurons with heterozygous NRXN1 deletions. We show that in neurons that were trans-differentiated from induced pluripotent stem cells derived from three NRXN1-deletion patients, the same impairment in neurotransmitter release was observed as in engineered NRXN1-deficient neurons. This impairment manifested as a decrease in spontaneous synaptic events and in evoked synaptic responses, and an alteration in synaptic paired-pulse depression. Nrxn1-deficient mouse neurons generated from embryonic stem cells by the same method as human neurons did not exhibit impaired neurotransmitter release, suggesting a human-specific phenotype. NRXN1 deletions produced a reproducible increase in the levels of CASK, an intracellular NRXN1-binding protein, and were associated with characteristic gene expression changes. Thus, heterozygous NRXN1 deletions robustly impair synaptic function in human neurons regardless of genetic background, enabling future drug discovery efforts.

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Single-cell dissection of schizophrenia reveals neurodevelopmental-synaptic axis and transcriptional resilience

10.1101/2020.11.06.20225342 ◽

2020 ◽

Author(s):

W. Brad Ruzicka ◽

Shahin Mohammadi ◽

Jose Davila-Velderrain ◽

Sivan Subburaju ◽

Daniel Reed Tso ◽

...

Keyword(s):

Single Cell ◽

Cell Types ◽

Synaptic Function ◽

Inhibitory Neurons ◽

Projection Neurons ◽

Cell Type ◽

Cortical Projection ◽

Human Neurons ◽

Small Effect Size ◽

Therapeutic Development

AbstractSchizophrenia is a devastating mental disorder with a high societal burden, complex pathophysiology, and diverse genetic and environmental risk factors. Its complexity, polygenicity, and small-effect-size and cell-type-specific contributors have hindered mechanistic elucidation and the search for new therapeutics. Here, we present the first single-cell dissection of schizophrenia, across 500,000+ cells from 48 postmortem human prefrontal cortex samples, including 24 schizophrenia cases and 24 controls. We annotate 20 cell types/states, providing a high-resolution atlas of schizophrenia-altered genes and pathways in each. We find neurons are the most affected cell type, with deep-layer cortico-cortical projection neurons and parvalbumin-expressing inhibitory neurons showing significant transcriptional changes converging on genetically-implicated regions. We discover a novel excitatory-neuron cell-state indicative of transcriptional resilience and enriched in schizophrenia subjects with less-perturbed transcriptional signatures. We identify key trans-acting factors as candidate drivers of observed transcriptional perturbations, including MEF2C, TCF4, SOX5, and SATB2, and map their binding patterns in postmortem human neurons. These factors regulate distinct gene sets underlying fetal neurodevelopment and adult synaptic function, bridging two leading models of schizophrenia pathogenesis. Our results provide the most detailed map to date for mechanistic understanding and therapeutic development in neuropsychiatric disorders.

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Loss-of-function variants in the schizophrenia risk gene SETD1A alter neuronal network activity in human neurons through cAMP/PKA pathway

10.1101/2021.05.25.445613 ◽

2021 ◽

Author(s):

Shan Wang ◽

Jon-Ruben van Rhijn ◽

Ibrahim A Akkouh ◽

Naoki Kogo ◽

Nadine Maas ◽

...

Keyword(s):

Neuronal Network ◽

Synaptic Function ◽

Network Activity ◽

Loss Of Function ◽

Functional Changes ◽

Neuronal Network Activity ◽

Camp Pathway ◽

Human Neurons ◽

Induced Pluripotent ◽

Pka Pathway

Heterozygous loss-of-function (LoF) mutations in SETD1A, which encodes a subunit of histone H3 lysine 4 methyltransferase, have been shown to cause a novel neurodevelopmental syndrome and increase the risk for schizophrenia. To study the effect of decreased SETD1A function in human cells, we generated excitatory/inhibitory neuronal networks from human induced pluripotent stem cells with a SETD1A heterozygous LoF mutation (SETD1A+/-). Our data show that SETD1A haploinsufficiency resulted in altered neuronal network activity, which was mainly characterized by an overly synchronized network. In individual neurons, this network phenotype was reflected by increased somatodendritic complexity and elevated synaptic connectivity. We found that this network phenotype was driven by SETD1A haploinsufficiency in glutamatergic neurons. In accordance with the functional changes, transcriptomic profiling revealed perturbations in gene sets associated with schizophrenia, synaptic transmission and glutamatergic synaptic function. At the molecular level, we identified specific changes in the cAMP/PKA pathway pointing toward a hyperactive cAMP pathway in SETD1A+/- neurons. Finally, using pharmacological experiments targeting the cAMP pathway we were able to rescue the network deficits in SETD1A+/- cultures. In conclusion, our results illuminate key molecular, cellular and network abnormalities caused by SETD1A haploinsufficiency and demonstrate a direct link between SETD1A and the cAMP-dependent pathway in human neurons.

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