Transcriptomic Landscape and Functional Characterization of Induced Pluripotent Stem Cell–Derived Cerebral Organoids in Schizophrenia

Abstract

IMPORTANCE Three-dimensional cerebral organoids generated from patient-derived induced pluripotent stem cells (iPSCs) may be used to interrogate cellular-molecular underpinnings of schizophrenia.OBJECTIVE To determine transcriptomic profiles and functional characteristics of cerebral organoids from patients with schizophrenia using gene expression studies, complemented with investigations of mitochondrial function through measurement of real-time oxygen consumption rate, and functional studies of neuronal firing with microelectrode arrays. DESIGN, SETTING, AND PARTICIPANTSThis case-control study was conducted at Massachusetts General Hospital between 2017 and 2019. Transcriptomic profiling of iPSC-derived cerebral organoids from 8 patients with schizophrenia and 8 healthy control individuals was undertaken to identify cellular pathways that are aberrant in schizophrenia. Induced pluripotent stem cells and cerebral organoids were generated from patients who had been diagnosed as having schizophrenia and from heathy control individuals.MAIN OUTCOMES AND MEASURES Transcriptomic analysis of iPSC-derived cerebral organoids from patients with schizophrenia show differences in expression of genes involved in synaptic biology and neurodevelopment and are enriched for genes implicated in schizophrenia genome-wide association studies (GWAS). RESULTSThe study included iPSC lines generated from 11 male and 5 female white participants, with a mean age of 38.8 years. RNA sequencing data from iPSC-derived cerebral organoids in schizophrenia showed differential expression of genes involved in synapses, in nervous system development, and in antigen processing. The differentially expressed genes were enriched for genes implicated in schizophrenia, with 23% of GWAS genes showing differential expression in schizophrenia and control organoids: 10 GWAS genes were upregulated in schizophrenia organoids while 15 GWAS genes were downregulated. Analysis of the gene expression profiles suggested dysregulation of genes involved in mitochondrial function and those involved in modulation of excitatory and inhibitory pathways. Studies of mitochondrial respiration showed lower basal consumption rate, adenosine triphosphate production, proton leak, and nonmitochondrial oxygen consumption in schizophrenia cerebral organoids, without any differences in the extracellular acidification rate. Microelectrode array studies of cerebral organoids showed no differences in baseline electrical activity in schizophrenia but revealed a diminished response to stimulation and depolarization.CONCLUSIONS AND RELEVANCE Investigations of patient-derived cerebral organoids in schizophrenia revealed gene expression patterns suggesting dysregulation of a number of pathways in schizophrenia, delineated differences in mitochondrial function, and showed deficits in response to stimulation and depolarization in schizophrenia.

Transcriptome analysis and functional characterization of cerebral organoids in bipolar disorder

“…iPSCs can be readily differentiated to a wide variety of neuronal and glial cell types, enabling the study of cell types that are relevant to disease biology [26,[68][69][70][71][72][73]. While the use of iPSC-based cellular models to study the neurobiology of BPI has been limited to the use of two-dimensional neuronal cultures, methods to grow brain organoids provide ways to study the disease biology in complex threedimensional structures that comprise a large number of cell types [74,75].…”

Modeling neurodegenerative diseases with cerebral organoids and other three-dimensional culture systems: focus on Alzheimer’s disease

“…There are also sex-specific trends in AD indicated by transcriptomic alterations in particular cell types [130], which may lend an important insight to the selection of iPSC donors for AD CO models. Novel diseasespecific deficits in neuronal differentiation, neurodevelopment and neurotransmission have been identified via scRNA-Seq in CO models for bipolar disorder, schizophrenia and autism spectrum disorder (ASD) [131][132][133]. Although these studies may not be directly generalizable to neurodegenerative conditions, they exemplify an ideal strategy to detect disease-specific transcriptomic changes at the cellular level, which may be of great benefit to further our understanding of ND mechanisms.…”

“…Compared to 2D cultures, COs reproduce human conditions like AD more closely [35,36,45,138]. Single cell transcriptomics of patient derived COs have shown considerable promise in identifying novel biomarker candidates [15,132,[171][172][173]. β and γ-secretase inhibitors decrease Aβ and pTau accumulation in COs [35,36,45,138].…”

The Role of Brain Microvascular Endothelial Cell and Blood-Brain Barrier Dysfunction in Schizophrenia

“…Human induced pluripotent stem cells (iPSC) provide us with the opportunity to develop physiologically relevant models of psychiatric disorders such as schizophrenia and bipolar disorder [28][29][30]. The use of iPSC-derived models to investigate schizophrenia pathophysiology has revealed disease-related changes in gene expression as well as deficits in specific neuronal subtypes [31,32]. Recent technical advances that enable efficient differentiation of iPSC to BMEC provide an opportunity to culture and study BMEC with disease-specific genetic backgrounds.…”