Epigenetic regulation during human cortical development: Seq-ing answers from the brain to the organoid

Abstract

Epigenetic regulation plays an important role in controlling gene expression during complex processes, such as development of the human brain. Mutations in genes encoding chromatin modifying proteins and in the non-protein coding sequences of the genome can potentially alter transcription factor binding or chromatin accessibility. Such mutations can frequently cause neurodevelopmental disorders, therefore understanding how epigenetic regulation shapes brain development is of particular interest. While epigenetic regulation of neural development has been extensively studied in murine models, significant species-specific differences in both the genome sequence and in brain development necessitate human models. However, access to human fetal material is limited and these tissues cannot be grown or experimentally manipulated ex vivo. Therefore, models that recapitulate particular aspects of human fetal brain development, such as the in vitro differentiation of human pluripotent stem cells (hPSCs), are instrumental for studying the epigenetic regulation of human neural development. Here, we examine recent studies that have defined changes in the epigenomic landscape during fetal brain development. We compare these studies with analogous data derived by in vitro differentiation of hPSCs into specific neuronal cell types or as three-dimensional cerebral organoids. Such comparisons can be informative regarding which aspects of fetal brain development are faithfully recapitulated by in vitro differentiation models and provide a foundation for using experimentally tractable in vitro models of human brain development to study neural gene regulation and the basis of its disruption to cause neurodevelopmental disorders.

Keywords: Chromatin; Epigenetic regulation; Human brain development; Neuron; Organoid; Pluripotent stem cells.

Fig. 1.

Three models for studying epigenetic regulation of human brain development. High-throughput sequencing approaches such as ATAC-seq or ChIP-seq have been used to interrogate changes in the epigenetic landscape throughout human cortical development. Disruption of epigenetic regulation during embryonic development can contribute to neurodevelopmental disorders such as autism spectrum disorder (ASD). Human brain cells or tissues for use in these assays can be harvested from the developing fetus or produced by in vitro differentiation of human pluripotent stem cells into cortical neurons or cerebral organoids. Figure created using BioRender.com.

Fig. 2.

In vivo-derived human fetal cells and tissues. (A) Studies have performed epigenetic assays such as ChIP-seq, ATAC-seq, RNA-seq, and DNA methylation by using materials derived from human fetuses from 7 to 38 post-conceptional weeks (PCW). The data shown and other related information can be retrieved using accession numbers from the NCBI-GEO and PsychENCODE databases, shown in pink text and described in more detail in Supplementary Table 1. (B) Bulk brain tissue, dissected regions, or single cells have been assayed. The cerebral cortex is a particular focus of this review. Figure created using BioRender.com.

Fig. 3.

In vitro-derived cortical neurons from human pluripotent stem cells. Human pluripotent stem cells (hPSCs) can be derived from reprogramming of somatic cells (induced pluripotent stem cells; iPSCs) or from the inner cell mass of a blastocyst-stage embryo (human embryonic stem cells; hESCs). Directed differentiation with small molecules or recombinant proteins (via an intermediate neural progenitor cell (NPC) stage) or direct conversion via transcription factor overexpression can be used to produce cortical neurons. (B) Epigenetic assays have been performed on cells at varying stages of differentiation; these can be utilized to analyze epigenetic modifications occurring during directed differentiation or conversion of hESCs/iPSCs to NPCs and NPCs to cortical neurons. Dataset accession numbers are shown in pink text, with additional information for each dataset in Supplementary Table 1. Figure created using BioRender.com.

Fig. 4.

In vitro-derived cerebral organoids from human pluripotent stem cells. Human pluripotent stem cells (hPSCs) can be differentiated into cerebral organoids using unguided methods that allow for self-organization or into region-specific (e.g. cortex or medial ganglionic eminence; MGE) organoids using guided methods with patterning factors. hPSCs are formed into embryoid bodies (EBs) and are induced into neurons prior to being embedded in Matrigel to provide a scaffold, and then matured on a shaker. (B) Epigenetic assays have been performed on organoids at varying stages of neural induction and maturation, from day (D) 0 to 600. Dataset accession numbers are shown in pink, with additional information for each dataset in Supplementary Table 1. Figure created using BioRender.com.