Genetics of human brain development

Abstract

Brain development in humans is achieved through precise spatiotemporal genetic control, the mechanisms of which remain largely elusive. Recently, integration of technological advances in human stem cell-based modelling with genome editing has emerged as a powerful platform to establish causative links between genotypes and phenotypes directly in the human system. Here, we review our current knowledge of complex genetic regulation of each key step of human brain development through the lens of evolutionary specialization and neurodevelopmental disorders and highlight the use of human stem cell-derived 2D cultures and 3D brain organoids to investigate human-enriched features and disease mechanisms. We also discuss opportunities and challenges of integrating new technologies to reveal the genetic architecture of human brain development and disorders.

Fig. 1 ∣. Key processes of human brain development.

a, A summary of the major processes and their timing during human brain development, including neurulation and neural epithelial cell proliferation, neural stem cell-mediated neurogenesis, radial and tangential migration of neural precursor cells to their destination, neuronal differentiation and maturation to achieve lamination and establish areal identity, generation of neurites and synapses^,, and gliogenesis, as well as some processes that largely occur during human postnatal periods, including continuous synaptic pruning and oligodendrocyte myelination^,. Age timeline and brain size are not depicted to scale. b, Stepwise processes during human cortical development. Cellular features enriched in primates are included, such as outer radial glial cells (oRGCs, comprising the outer subventricular zone (SVZ)), an enlarged subplate (SP), an enlarged and more complex cortical plate (CP), pre-oligodendrocyte precursor cells (pre-OPCs) and truncated RGCs (tRGCs). APC, astrocyte precursor cell; BV, blood vessel; C–R, Cajal–Retzius; DL, deep layer; IPC, intermediate progenitor cell; IZ, intermediate zone; MZ, marginal zone; NB, neuroblast; NEC, neuroepithelial cell; pcw, post-conception week; UL, upper layer; VZ, ventricular zone.

Fig. 2 ∣. Applications of human pluripotent stem cell-based systems for studying human brain development.

Genetic studies of individuals with disrupted brain development and genome-wide association studies can be used to identify causative genetic mutations and risk genes, respectively. Human pluripotent stem cell-based models derived from patients or through genetic engineering — including 2D cell culture and 3D organoids — allow establishment of causality between genotypes and phenotypes and facilitate investigations of neuropathological examination, disease mechanisms, and drug or toxin responses. They can also be used to screen risk genes to study causal genetic (mal)functions. Although 2D induced pluripotent stem (IPS) cell culture provides a homogenous, reproducible, scalable platform, advanced 3D organoid culture has the unique advantage of modelling spatiotemporal features and functions of the developing human brain and can start to recapitulate cell interactions and circuit formation events despite room for improvement, such as reducing organoid-to-organoid variability. APC, astrocyte precursor cell; NPC, neuronal precursor cell to excitatory neuron; NPC’: neuronal precursor cell to inhibitory interneuron; OPC, oligodendrocyte precursor cell.

Fig. 3 ∣. Human-specific genetic modulation of brain development.

a, Examples of human-enriched genetic features that modulate neural stem cell-mediated neurogenesis, resulting in cortical expansion, that were modelled in mice and pluripotent stem cell-based systems. These genetic features can regulate the neural progenitor cell cycle (FZD8 (ref. 61), PPP1R17 (ref. 60) and ZEB2 (ref. 29)), regulate signalling pathways (mTOR^,, Notch (for example, NOTCH2NL)^,, PDGF and Robo) or specifically regulate outer radial glial cell (oRGC) behaviours (ARHGAP11B^-, CROCCP2 (ref. 66), TBC1D3 (refs. 74,75), TKTL1 (ref. 77) and TMEM14B). b, Examples of human-enriched genetic features that modulate neuron development processes, resulting in protracted neuron maturation (which is indicated by the ‘hourglass’ icon) and changes in neurite development, synapse plasticity and connectivity, that were mostly studied using humanized mouse models. These genetic features include CBLN2 (ref. 86), EPHA7 (ref. 88), FOXP2 (refs. 45,79,80), OSTN, PLXNA1 (ref. 87) and SRGAP2C^-. DL, deep layer; IPC, intermediate progenitor cell; NB, neuroblast; UL, upper layer; WT, wild type.

Fig. 4 ∣. Genetic basis of human brain development uncovered using hPS cell models by studying traits led by evolution, diseases and environmental exposure.

a, Evolutionary features modelled in human pluripotent stem cell (hPS cell)-derived organoid system. An illustrative study is depicted that compares ape and human cortical organoids and identified differential cellular and molecular features, including ZEB2 as a genetic driver that modulates the transition of neuroepithelial cells (NECs) to radial glial cells (RGCs) in humans. b, Neurodevelopmental and neuropsychiatric disorders modelled in hPS cell-derived systems derived from patients or genetically engineered. Depicted is a study that examined the consequences of mutations in three autism spectrum disorder risk genes, SUV420H1, ARID1B and CHD8, in their respective cortical organoids and found cell type-specific developmental abnormalities, including excessive interneuron differentiation and premature differentiation of deep-layer cortical neurons. The ‘hourglass’ icons in parts a and b indicate alterations of developmental tempo. c, Environmental exposure modelled in hPS cell-derived systems. Represented are studies^-,- that infected brain organoids with Zika virus and demonstrated substantial disruption in cellular architecture and further identified its genetic causes, including centrosomal and adherens junction genes. The microcephaly phenotypes identified and modelled in the dish were observed and validated in human patients, including aberrant adherens junctions. DL, deep layer; IPC, intermediate progenitor cell; NB, neuroblast; oRGC, outer RGC; UL, upper layer.

Fig. 4 ∣. Genetic basis of human brain development uncovered using hPS cell models by studying traits led by evolution, diseases and environmental exposure.

a, Evolutionary features modelled in human pluripotent stem cell (hPS cell)-derived organoid system. An illustrative study is depicted that compares ape and human cortical organoids and identified differential cellular and molecular features, including ZEB2 as a genetic driver that modulates the transition of neuroepithelial cells (NECs) to radial glial cells (RGCs) in humans. b, Neurodevelopmental and neuropsychiatric disorders modelled in hPS cell-derived systems derived from patients or genetically engineered. Depicted is a study that examined the consequences of mutations in three autism spectrum disorder risk genes, SUV420H1, ARID1B and CHD8, in their respective cortical organoids and found cell type-specific developmental abnormalities, including excessive interneuron differentiation and premature differentiation of deep-layer cortical neurons. The ‘hourglass’ icons in parts a and b indicate alterations of developmental tempo. c, Environmental exposure modelled in hPS cell-derived systems. Represented are studies^-,- that infected brain organoids with Zika virus and demonstrated substantial disruption in cellular architecture and further identified its genetic causes, including centrosomal and adherens junction genes. The microcephaly phenotypes identified and modelled in the dish were observed and validated in human patients, including aberrant adherens junctions. DL, deep layer; IPC, intermediate progenitor cell; NB, neuroblast; oRGC, outer RGC; UL, upper layer.

Fig. 4 ∣. Genetic basis of human brain development uncovered using hPS cell models by studying traits led by evolution, diseases and environmental exposure.

a, Evolutionary features modelled in human pluripotent stem cell (hPS cell)-derived organoid system. An illustrative study is depicted that compares ape and human cortical organoids and identified differential cellular and molecular features, including ZEB2 as a genetic driver that modulates the transition of neuroepithelial cells (NECs) to radial glial cells (RGCs) in humans. b, Neurodevelopmental and neuropsychiatric disorders modelled in hPS cell-derived systems derived from patients or genetically engineered. Depicted is a study that examined the consequences of mutations in three autism spectrum disorder risk genes, SUV420H1, ARID1B and CHD8, in their respective cortical organoids and found cell type-specific developmental abnormalities, including excessive interneuron differentiation and premature differentiation of deep-layer cortical neurons. The ‘hourglass’ icons in parts a and b indicate alterations of developmental tempo. c, Environmental exposure modelled in hPS cell-derived systems. Represented are studies^-,- that infected brain organoids with Zika virus and demonstrated substantial disruption in cellular architecture and further identified its genetic causes, including centrosomal and adherens junction genes. The microcephaly phenotypes identified and modelled in the dish were observed and validated in human patients, including aberrant adherens junctions. DL, deep layer; IPC, intermediate progenitor cell; NB, neuroblast; oRGC, outer RGC; UL, upper layer.

Fig. 5 ∣. Genetic basis of human brain development revealed by brain disorders.

An illustration showing examples of neurodevelopmental and neuropsychiatric disorders that have helped to determine how causal genetic variants (Table 1) impact specific neurodevelopmental processes. Some diseases commonly considered to be monogenic have overlapping phenotypes, highlighting genotype–phenotype disease manifestations, such as models for microcephaly and polymicrogyria, and focal cortical dysplasia displaying deficits in radial glial cell proliferation and neuron differentiation. ACC, agenesis of the corpus callosum.

Fig. 6 ∣. Current and future approaches for studying the genetics of human brain development.

a, Each section of the circle depicts a different biotechnology domain that empowers the investigation of the genetics of human brain development, including human phenotyping studies (such as patient genetics and functional imaging), multidimensional molecular detection and manipulation tools (such as single-cell multi-omics, genome-wide association studies (GWAS), CRISPR-based tools and prime editing), animal and human pluripotent stem cell (hPS cell)-based model systems (such as primate models, induced pluripotent stem cells (iPS cells) and 3D human brain organoids), and therapeutic development (such as compound screening, safety testing and efficacy testing). The lines in the centre indicate that different biotechnology domains can integrate to generate synergistic effects. For each biotechnology domain, the outermost part of the figure depicts several future technology developments that we believe will lead to substantial improvements. Notably, all technology use and advancement in the biomedicine space ought to be supervised and guided by proper ethics. b, An overview of a multidisciplinary study, using the DISC1 gene as an example. We first examined the role of DISC1 in animal models and utilized human models based on patient mutations and isogenic iPS cell lines to determine the causative roles in specific neural developmental phenotypes. This was followed by mechanistic studies to identify druggable targets and drug testing, and we finally tested efficacy at functional and behavioural levels in a humanized mouse model with the same patient mutation (see the main text for details). AI, artificial intelligence; fMRI, functional magnetic resonance imaging. Structure of DISC1 protein adapted from ref. , Springer Nature Limited.

Fig. 6 ∣. Current and future approaches for studying the genetics of human brain development.

a, Each section of the circle depicts a different biotechnology domain that empowers the investigation of the genetics of human brain development, including human phenotyping studies (such as patient genetics and functional imaging), multidimensional molecular detection and manipulation tools (such as single-cell multi-omics, genome-wide association studies (GWAS), CRISPR-based tools and prime editing), animal and human pluripotent stem cell (hPS cell)-based model systems (such as primate models, induced pluripotent stem cells (iPS cells) and 3D human brain organoids), and therapeutic development (such as compound screening, safety testing and efficacy testing). The lines in the centre indicate that different biotechnology domains can integrate to generate synergistic effects. For each biotechnology domain, the outermost part of the figure depicts several future technology developments that we believe will lead to substantial improvements. Notably, all technology use and advancement in the biomedicine space ought to be supervised and guided by proper ethics. b, An overview of a multidisciplinary study, using the DISC1 gene as an example. We first examined the role of DISC1 in animal models and utilized human models based on patient mutations and isogenic iPS cell lines to determine the causative roles in specific neural developmental phenotypes. This was followed by mechanistic studies to identify druggable targets and drug testing, and we finally tested efficacy at functional and behavioural levels in a humanized mouse model with the same patient mutation (see the main text for details). AI, artificial intelligence; fMRI, functional magnetic resonance imaging. Structure of DISC1 protein adapted from ref. , Springer Nature Limited.