The proteomic architecture of schizophrenia iPSC-derived cerebral organoids reveals alterations in GWAS and neuronal development factors

Abstract

Schizophrenia (Scz) is a brain disorder that has a typical onset in early adulthood but otherwise maintains unknown disease origins. Unfortunately, little progress has been made in understanding the molecular mechanisms underlying neurodevelopment of Scz due to ethical and technical limitations in accessing developing human brain tissue. To overcome this challenge, we have previously utilized patient-derived Induced Pluripotent Stem Cells (iPSCs) to generate self-developing, self-maturating, and self-organizing 3D brain-like tissue known as cerebral organoids. As a continuation of this prior work, here we provide an architectural map of the developing Scz organoid proteome. Utilizing iPSCs from n = 25 human donors (n = 8 healthy Ctrl donors, and n = 17 Scz patients), we generated 3D cerebral organoids, employed 16-plex isobaric sample-barcoding chemistry, and simultaneously subjected samples to comprehensive high-throughput liquid-chromatography/mass-spectrometry (LC/MS) quantitative proteomics. Of 3,705 proteins identified by high-throughput proteomic profiling, we identified that just ~2.62% of the organoid global proteomic landscape was differentially regulated in Scz organoids. In sum, just 43 proteins were up-regulated and 54 were down-regulated in Scz patient-derived organoids. Notably, a range of neuronal factors were depleted in Scz organoids (e.g., MAP2, TUBB3, SV2A, GAP43, CRABP1, NCAM1 etc.). Based on global enrichment analysis, alterations in key pathways that regulate nervous system development (e.g., axonogenesis, axon development, axon guidance, morphogenesis pathways regulating neuronal differentiation, as well as substantia nigra development) were perturbed in Scz patient-derived organoids. We also identified prominent alterations in two novel GWAS factors, Pleiotrophin (PTN) and Podocalyxin (PODXL), in Scz organoids. In sum, this work serves as both a report and a resource that researchers can leverage to compare, contrast, or orthogonally validate Scz factors and pathways identified in observational clinical studies and other model systems.

Genetic and Epigenetic Regulation of Brain Organoids

“…Schizophrenia organoids were also subjected to quantitative proteomic analysis. Similar defects were observed in axon and neuronal differentiation at protein level (Notaras et al, 2021b), which is consistent with transcriptome and genome researches.…”

Ventral forebrain organoids derived from individuals with schizophrenia recapitulate perturbed striatal gene expression dynamics of the donor’s brains

“…3e) and downregulation of genes such as CRABP1, POU3F2 and NOVA1 (Fig. 3f) whose dysregulation was linked to the SCZ risk [50-53]. Gene ontology (GO) analysis identified the remarkable upregulation of synaptic transmission-related genes and downregulation of genes regulating translation (Fig.…”

Human-Induced Pluripotent Stem Cell Technology: Toward the Future of Personalized Psychiatry

“…Notaras et al observed that in SZ BO, about 2.62% of global proteome was differentially regulated, with a depletion of factors that support neuronal development, differentiation, and/or function [ 48 ]. Moreover, the differential regulation of two novel specific disease candidates identified through genome-wide association study (GWAS) arrays (namely, Pleiotrophin and Podocalyxin) was observed [ 48 ]. The SZ organoids exhibited altered progenitor survival and disrupted neurogenesis, yielding fewer neurons within developing cortical areas [ 49 ].…”

“…This approach supports the neurodevelopmental hypothesis of SZ, stating that the disruption of early brain development increases the risk of later manifest psychotic symptoms. Patient-derived iPSCs have proven to be a powerful tool in identifying SZ early neurodevelopmental defects, having revealed alterations in neuronal differentiation [ 45 , 48 , 49 ], migration capacity [ 39 , 43 ], neurite number and length [ 38 , 66 ], synaptic biology [ 47 , 49 , 50 ], connectivity [ 38 ], and neuronal activity [ 41 , 42 , 50 ].…”