Dataset Information

Functional Genomic Profiling of Schizophrenia-Associated Genes Reveals Key Microglial Regulators

ABSTRACT: Microglia are increasingly recognized as key regulators of neural circuit development and putative contributors to the pathophysiology of neuropsychiatric disorders such as schizophrenia (SCZ). However, the functional impact of SCZ-associated genes in microglia remains largely unexplored. Here, we performed an arrayed CRISPR targeting screen of 30 schizophrenia-associated genes predicted to be differentially expressed in human microglia-like cells. Target genes were prioritized based on post-mortem transcriptomic relevance and predicted ontology-based roles in phagocytosis pathways. We quantified phagocytic activity and morphological changes following gene targeting using high-content confocal imaging. Key targets, including CYFIP1, MSR1, TREM2, SYK, ITGB2, ITGAM and IRF8, modulated phagocytosis and altered morphological properties consistent with activation states, validating their functional roles in microglia. To elucidate transcriptional impact, we further applied a multiplexed RNA sequencing platform across gene targets. These analyses revealed gene-specific transcriptional signatures, implicating divergent pathways related to phagocytic, activation, cytoskeletal, and lysosomal function. Together, these findings demonstrate the utility of CRISPR-based functional genomics in characterizing microglia function and identifying new target genes and mechanisms that may underlie their contributions to schizophrenia pathophysiology.

ORGANISM(S): Homo sapiens

PROVIDER: GSE319209 | GEO | 2026/04/13

REPOSITORIES: GEO

ACCESS DATA

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Project description:Molecular mechanisms underlying dorsolateral prefrontal cortex (dlPFC) dysfunction in schizophrenia (SCZ) are poorly understood. dlPFC cell types are spatially organized across the six layers into functional microcircuits, which regulate cognitive and emotional processes that are implicated in SCZ. While regional specificity across cortical layers and cell types has been demonstrated for some SCZ-linked genes, spatially-resolved transcriptomics (SRT) can more definitively map molecular associations of disease. We investigated spatial gene expression changes in the human dlPFC from neurotypical control (n=31) and SCZ (n=32) brain donors using the Visium platform with incorporation of immunostaining to label perineuronal nets, neurons and vasculature. SCZ-associated DEGs were then mapped across these labeled cellular microenvironments and cortical layers. Major transcriptional alterations were identified in synaptic and neuroimmune pathways, which we localized to neuropil and glia-enriched domains. Integrative analysis with bulk and single-cell RNA studies highlighted distinct roles for spatially-localized glial cell populations, and identified enrichment of novel DEGs in endothelial cells and microglia. These findings were supported by enrichment of SCZ genetic risk across similar domains, and association of laminae-specific transcription factors to SCZ risk variants. Cellular resolution SRT using Xenium extended laminar disease associations to spatially-organized cell types. The findings highlight unique advantages of SRT to identify novel SCZ-related biology, particularly for cellular populations and compartments that may be missed with alternative technologies. We provide data resources to enable sample-level visualization of the spatial transcriptomics data (Samui) and to explore SCZ-associated DEGs across spatial domains (iSEE-layer adjusted) and cellular microenvironments (iSEE-Neuropil, iSEE-Neuron, iSEE-vasculature, iSEE-PNNs). The primary goal of the Xenium experiments was to cross-validate layer-adjusted schizophrenia-associated differentially expressed genes previously identified by Visium spatial transcriptomics at enhanced cellular resolution, along with a select set of previously reported SCZ-associated genes and risk factors.

Project description:Background: Widescale evidence points to the involvement of glia and immune pathways in the progression of Alzheimer’s disease (AD). AD-associated iPSC-derived glial cells show a diverse range of AD-related phenotypic states encompassing cytokine/chemokine release, phagocytosis and morphological profiles, but to date studies are limited to cells derived from PSEN1, APOE and APP mutations or sporadic patients. The aim of the current study was to successfully differentiate iPSC-derived microglia and astrocytes from patients harbouring an AD-causative PSEN2 (N141I) mutation and characterise the inflammatory and morphological profile of these cells. Methods: iPSCs from three healthy control individuals and three familial AD patients harbouring a heterozygous PSEN2 (N141I) mutation were used to derive astrocytes and microglia-like cells and cell identity and morphology were characterised through immunofluorescent microscopy. Cellular characterisation involved the stimulation of these cells by LPS and Aβ42 and analysis of cytokine/chemokine release was conducted through ELISAs and multi-cytokine arrays. The phagocytic capacity of these cells was then indexed by the uptake of fluorescently labelled fibrillar Aβ42. Results: AD-derived astrocytes and microglia-like cells exhibited an atrophied and less complex morphological appearance than healthy controls. AD-derived astrocytes showed increased basal expression of GFAP, S100β and increased secretion and phagocytosis of Aβ42 while AD-derived microglia-like cells showed decreased IL-8 secretion compared to healthy controls. Upon immunological challenge AD-derived astrocytes and microglia-like cells show exaggerated secretion of the pro-inflammatory IL-6, CXCL1, ICAM-1 and IL-8 from astrocytes and IL-18 and MIF from microglia.Conclusion: Our study showed, for the first time, the differentiation and characterisation of iPSC-derived astrocytes and microglia-like cells harbouring a PSEN2 (N141I) mutation. PSEN2 (N141I)-mutant astrocytes and microglia-like cells presented with a ‘primed’ phenotype characterised by reduced morphological complexity, exaggerated pro-inflammatory cytokine secretion and altered Aβ42 production and phagocytosis.

Dataset Information

Functional Genomic Profiling of Schizophrenia-Associated Genes Reveals Key Microglial Regulators

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets