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Genomic and transcriptomic profiles underlying the effect of SETD1A disruption on human neurodevelopmental trajectories (scRNA-Seq)

ABSTRACT: To dissect, in more detail, cell population alterations and examine in situ genotypic differences in transcriptomic and regulatory profiles during neurogenesis and neuronal differentiation, we used single cell RNA sequencing (scRNA-seq) to profile cell type composition and molecular signatures of FOs derived from mutant and control iPSC lines at DIV70

ORGANISM(S): Homo sapiens

PROVIDER: GSE239864 | GEO | 2025/04/17

REPOSITORIES: GEO

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Genomic and transcriptomic profiles underlying the effect of SETD1A disruption on human neurodevelopmental trajectories

Project description:To examine the transcriptomic alteration by SETD1A deficiency, combining CRISPR/CAS9 genome editing and 3-Dimentional Cell Culture technology, we generated organoid models of the developing human cerebral cortex derived from isogenic human induced pluripotent stem cells (hiPSCs) modified to carry a SETD1A LoF schizophrenia risk mutation. We then performed gene expression profiling analysis using data obtained from RNA-seq of WT and mutant cortical neurons at DIV70.

2025-04-17 | GSE237165 | GEO

Genomic and transcriptomic profiles underlying the effect of SETD1A disruption on human neurodevelopmental trajectories [ChIP-seq]

Project description:To examine the genomic alteration by SETD1A deficiency, combining CRISPR/CAS9 genome editing and 3-Dimentional Cell Culture technology, we generated organoid models of the developing human cerebral cortex derived from isogenic human induced pluripotent stem cells (hiPSCs) modified to carry a SETD1A LoF schizophrenia risk mutation. We then performed genomic profiling analysis using data obtained from CUT&Tag of WT and mutant cortical neurons at DIV70.

2025-04-17 | GSE237297 | GEO

Genomic and transcriptomic profiles underlying the effect of SETD1A disruption on human neurodevelopmental trajectories

Project description:Genomic and transcriptomic profiles underlying the effect of SETD1A disruption on human neurodevelopmental trajectories

| PRJNA994099 | ENA

Genomic and transcriptomic profiles underlying the effect of SETD1A disruption on human neurodevelopmental trajectories [ChIP-seq]

Project description:Genomic and transcriptomic profiles underlying the effect of SETD1A disruption on human neurodevelopmental trajectories [ChIP-seq]

| PRJNA994538 | ENA

Genomic and transcriptomic profiles underlying the effect of SETD1A disruption on human neurodevelopmental trajectories (scRNA-Seq)

Project description:Genomic and transcriptomic profiles underlying the effect of SETD1A disruption on human neurodevelopmental trajectories (scRNA-Seq)

| PRJNA1001298 | ENA

SETD1A Mediated H3K4 Methylation and Its Role in Neurodevelopmental and Neuropsychiatric Disorders.

Project description:Posttranslational modification of histones and related gene regulation are shown to be affected in an increasing number of neurological disorders. SETD1A is a chromatin remodeler that influences gene expression through the modulation of mono- di- and trimethylation marks on Histone-H3-Lysine-4 (H3K4me1/2/3). H3K4 methylation is predominantly described to result in transcriptional activation, with its mono- di- and trimethylated forms differentially enriched at promoters or enhancers. Recently, dominant mostly de novo variants in SETD1A have clinically been linked to developmental delay, intellectual disability (DD/ID), and schizophrenia (SCZ). Affected individuals often display both developmental and neuropsychiatric abnormalities. The primary diagnoses are mainly dependent on the age at which the individual is assessed. Investigations in mouse models of SETD1A dysfunction have been able to recapitulate key behavioral features associated with ID and SCZ. Furthermore, functional investigations suggest disrupted synaptic and neuronal network function in these mouse models. In this review, we provide an overview of pre-clinical studies on the role of SETD1A in neuronal development. A better understanding of the pathobiology underlying these disorders may provide novel opportunities for therapeutic intervention. As such, we will discuss possible strategies to move forward in elucidating the genotype-phenotype correlation in SETD1A associated disorders.

| S-EPMC8595121 | biostudies-literature

E-GEOD-60548

Project description:Rapid neurogenesis through transcriptional activation in human stem cell (RNA-Seq)

2025-01-24 | E-GEOD-60548 | ExpressionAtlas

De novo variant of SETD1A causes neurodevelopmental disorder with dysmorphic facies: A case report.

Project description: Not available

| S-EPMC9300109 | biostudies-literature

Metabolic contributions to neuronal deficits caused by genomic disruption of schizophrenia risk gene SETD1A.

Project description:Regulation of neuronal metabolism during early brain development is crucial for directing synaptic plasticity and proper circuit formation. Alterations in neuronal glycolysis or mitochondrial function are associated with several neuropsychiatric disorders, including schizophrenia. Recently, loss-of-function mutations in SETD1A, a histone methyltransferase, have been linked to increased schizophrenia risk and global developmental delay. Here, we show that heterozygous disruption of SETD1A in human induced pluripotent stem cell (hiPSC)-derived neurons results in reduced neurite outgrowth and spontaneous activity, two phenotypes commonly associated with schizophrenia, as well as alterations in metabolic capacity. Furthermore, supplementing culture media with metabolic intermediates ameliorated changes in neurite outgrowth and spontaneous activity, suggesting that metabolic dysfunction contributes to neuronal phenotypes caused by SETD1A haploinsufficiency. These findings highlight a previously unknown connection between SETD1A function, metabolic regulation, and neuron development, and identifies alternative avenues for therapeutic development.

| S-EPMC9800576 | biostudies-literature

Developmental disruption to the cortical transcriptome and synaptosome in a model of SETD1A loss-of-function.

Project description:Large-scale genomic studies of schizophrenia implicate genes involved in the epigenetic regulation of transcription by histone methylation and genes encoding components of the synapse. However, the interactions between these pathways in conferring risk to psychiatric illness are unknown. Loss-of-function (LoF) mutations in the gene encoding histone methyltransferase, SETD1A, confer substantial risk to schizophrenia. Among several roles, SETD1A is thought to be involved in the development and function of neuronal circuits. Here, we employed a multi-omics approach to study the effects of heterozygous Setd1a LoF on gene expression and synaptic composition in mouse cortex across five developmental timepoints from embryonic day 14 to postnatal day 70. Using RNA sequencing, we observed that Setd1a LoF resulted in the consistent downregulation of genes enriched for mitochondrial pathways. This effect extended to the synaptosome, in which we found age-specific disruption to both mitochondrial and synaptic proteins. Using large-scale patient genomics data, we observed no enrichment for genetic association with schizophrenia within differentially expressed transcripts or proteins, suggesting they derive from a distinct mechanism of risk from that implicated by genomic studies. This study highlights biological pathways through which SETD1A LOF may confer risk to schizophrenia. Further work is required to determine whether the effects observed in this model reflect human pathology.

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