Transcriptional programs regulating neuronal differentiation are disrupted in DLG2 knockout human embryonic stem cells and enriched for schizophrenia and related disorders risk variants

Bret Sanders,Derek J Blake,Daniel D’Andrea,Adrian J Harwood,Gareth Chapman,Daniel J Whitcomb,Elliott Rees,Antonio F Pardiñas,Mark O Collins,Eunju Shin,William P Gray,Sophie E Legge,Michael J Owen,Ying Zhu,Adam C Errington,Michael C O’Donovan,Tom G J Steward,Andrew J Pocklington

doi:10.1038/s41467-021-27601-0

Abstract

Coordinated programs of gene expression drive brain development. It is unclear which transcriptional programs, in which cell-types, are affected in neuropsychiatric disorders such as schizophrenia. Here we integrate human genetics with transcriptomic data from differentiation of human embryonic stem cells into cortical excitatory neurons. We identify transcriptional programs expressed during early neurogenesis in vitro and in human foetal cortex that are down-regulated in DLG2−/− lines. Down-regulation impacted neuronal differentiation and maturation, impairing migration, morphology and action potential generation. Genetic variation in these programs is associated with neuropsychiatric disorders and cognitive function, with associated variants predominantly concentrated in loss-of-function intolerant genes. Neurogenic programs also overlap schizophrenia GWAS enrichment previously identified in mature excitatory neurons, suggesting that pathways active during prenatal cortical development may also be associated with mature neuronal dysfunction. Our data from human embryonic stem cells, when combined with analysis of available foetal cortical gene expression data, de novo rare variants and GWAS statistics for neuropsychiatric disorders and cognition, reveal a convergence on transcriptional programs regulating excitatory cortical neurogenesis.

Highlights

Coordinated programs of gene expression drive brain development
Two DLG2−/− lines were created from H7 human embryonic stem cells (hESCs) using the CRISPR/Cas9-D10A nickase system targeting the first PDZ domain, generating a frameshift and premature stop codon in both alleles (Supplementary Fig. 1)
DLG2−/− and WT lines were differentiated into cortical excitatory neurons using a modified dual SMAD inhibition protocol[28,29]; RNA was extracted in triplicate from each line at 4 timepoints spanning cortical excitatory neuron development and gene expression quantified (Fig. 1b, Supplementary Fig. 3)

Summary

Introduction

Coordinated programs of gene expression drive brain development. It is unclear which transcriptional programs, in which cell-types, are affected in neuropsychiatric disorders such as schizophrenia. Down-regulation impacted neuronal differentiation and maturation, impairing migration, morphology and action potential generation Genetic variation in these programs is associated with neuropsychiatric disorders and cognitive function, with associated variants predominantly concentrated in loss-of-function intolerant genes. Supporting a neurodevelopmental role for SZ common variants, there is growing evidence that many such risk factors impact gene expression in the fetal brain[17,18,19,20] and are enriched in cell-types at multiple stages of cortical excitatory neuron development[21]. This raises the question: do SZ common variants converge on specific gene expression programs that are normally activated or repressed during fetal cortical excitatory neuron development? We explored whether disease-associated neurogenic programs identified in vitro possessed a similar profile of expression across neurodevelopmental cell-types in human fetal cortex

Methods

Results

Conclusion