Mechanistic insights into human disease may enable the development of treatments that are effective in broad patient populations. The confluence of gene-editing technologies, induced pluripotent stem ...cells, and genome-wide association as well as DNA sequencing studies is enabling new approaches for illuminating the molecular basis of human disease. We discuss the opportunities and challenges of combining these technologies and provide a workflow for interrogating the contribution of disease-associated candidate genetic variants to disease-relevant phenotypes. Finally, we discuss the potential utility of human pluripotent stem cells for placing disease-associated genetic variants into molecular pathways.
This Perspective discusses opportunities and challenges for using iPSCs in modeling human disease and provides a workflow for using emerging technologies to interrogate the contribution of genetic variants to disease.
Most vertebrate cells, including mammalian postmitotic neurons, have fingerlike primary cilia that protrude from the cell body and act as specialized ‘signalling antennae’ enriched with specific ...receptors.Primary cilia length (PCL) can substantially change within minutes to hours in response to physiological changes such as circadian rhythms and metabolic state, and secreted factors such as neurotransmitters and hormones.The functional consequences of changes in PCL are still poorly understood, but are likely to affect cellular responses to exogenous signals across many cell types and processes.
Primary cilia protrude from most vertebrate cell bodies and act as specialized ‘signalling antennae’ that can substantially lengthen or retract in minutes to hours in response to specific stimuli. Here, we review the conditions and mechanisms responsible for regulating primary cilia length (PCL) in mammalian nonsensory neurons, and propose four models of how they could affect ciliary signalling and alter cell state and suggest experiments to distinguish between them. These models include (i) the passive indicator model, where changes in PCL have no consequence; (ii) the rheostat model, in which a longer cilium enhances signalling; (iii) the local concentration model, where ciliary shortening increases the local protein concentration to facilitate signalling; and (iv) the altered composition model where changes in PCL skew signalling.
The in vivo potential of neural stem cells in the postnatal mouse brain is not known, but because they produce many different types of neurons, they must be either very versatile or very diverse. By ...specifically targeting stem cells and following their progeny in vivo, we showed that postnatal stem cells in different regions produce different types of neurons, even when heterotopically grafted or grown in culture. This suggests that rather than being plastic and homogeneous, neural stem cells are a restricted and diverse population of progenitors.
Human pluripotent stem cells are a powerful tool for modeling brain development and disease. The human cortex is composed of two major neuronal populations: projection neurons and local interneurons. ...Cortical interneurons comprise a diverse class of cell types expressing the neurotransmitter GABA. Dysfunction of cortical interneurons has been implicated in neuropsychiatric diseases, including schizophrenia, autism, and epilepsy. Here, we demonstrate the highly efficient derivation of human cortical interneurons in an NKX2.1::GFP human embryonic stem cell reporter line. Manipulating the timing of SHH activation yields three distinct GFP+ populations with specific transcriptional profiles, neurotransmitter phenotypes, and migratory behaviors. Further differentiation in a murine cortical environment yields parvalbumin- and somatostatin-expressing neurons that exhibit synaptic inputs and electrophysiological properties of cortical interneurons. Our study defines the signals sufficient for modeling human ventral forebrain development in vitro and lays the foundation for studying cortical interneuron involvement in human disease pathology.
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•Inhibition of WNT signaling enhances forebrain induction from hPSCs•Differences in timing of SHH exposure induce distinct ventral forebrain fates•hESC-derived cortical interneurons exhibit characteristic migratory properties•In vitro coculture yields SST+ and PV+ interneurons with mature physiology
Combination of timed SHH signaling and coculture maturation yields distinct populations of cortical interneurons from human pluripotent cells.
Throughout life, neural stem cells (NSCs) in different domains of the ventricular-subventricular zone (V-SVZ) of the adult rodent brain generate several subtypes of interneurons that regulate the ...function of the olfactory bulb. The full extent of diversity among adult NSCs and their progeny is not known. Here, we report the generation of at least four previously unknown olfactory bulb interneuron subtypes that are produced in finely patterned progenitor domains in the anterior ventral V-SVZ of both the neonatal and adult mouse brain. Progenitors of these interneurons are responsive to sonic hedgehog and are organized into microdomains that correlate with the expression domains of the Nkx6.2 and Zic family of transcription factors. This work reveals an unexpected degree of complexity in the specification and patterning of NSCs in the postnatal mouse brain.
Studying the function of common genetic variants in primary human tissues and during development is challenging. To address this, we use an efficient multiplexing strategy to differentiate 215 human ...induced pluripotent stem cell (iPSC) lines toward a midbrain neural fate, including dopaminergic neurons, and use single-cell RNA sequencing (scRNA-seq) to profile over 1 million cells across three differentiation time points. The proportion of neurons produced by each cell line is highly reproducible and is predictable by robust molecular markers expressed in pluripotent cells. Expression quantitative trait loci (eQTL) were characterized at different stages of neuronal development and in response to rotenone-induced oxidative stress. Of these, 1,284 eQTL colocalize with known neurological trait risk loci, and 46% are not found in the Genotype-Tissue Expression (GTEx) catalog. Our study illustrates how coupling scRNA-seq with long-term iPSC differentiation enables mechanistic studies of human trait-associated genetic variants in otherwise inaccessible cell states.
The CRISPR-Cas9 system has the potential to revolutionize genome editing in human pluripotent stem cells (hPSCs), but its advantages and pitfalls are still poorly understood. We systematically tested ...the ability of CRISPR-Cas9 to mediate reporter gene knockin at 16 distinct genomic sites in hPSCs. We observed efficient gene targeting but found that targeted clones carried an unexpectedly high frequency of insertion and deletion (indel) mutations at both alleles of the targeted gene. These indels were induced by Cas9 nuclease, as well as Cas9-D10A single or dual nickases, and often disrupted gene function. To overcome this problem, we designed strategies to physically destroy or separate CRISPR target sites at the targeted allele and developed a bioinformatic pipeline to identify and eliminate clones harboring deleterious indels at the other allele. This two-pronged approach enables the reliable generation of knockin hPSC reporter cell lines free of unwanted mutations at the targeted locus.
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•Cas9 dual nickase mediates efficient reporter-gene insertion in human stem cells•Deleterious mutations at the targeted locus are unexpectedly common•Rational design and bioinformatic selection enable efficient reporter generation
Gene editing with CRISPR-Cas9 holds great promise. Merkle et al. show highly efficient reporter-gene insertion at many genomic loci but observe common “on-target” mutations. These mutations can be effectively mitigated by rational targeting-strategy design and bioinformatic screening.
Hypothalamic neurons orchestrate many essential physiological and behavioral processes via secreted neuropeptides, and are relevant to human diseases such as obesity, narcolepsy and infertility. We ...report the differentiation of human pluripotent stem cells into many of the major types of neuropeptidergic hypothalamic neurons, including those producing pro-opiolemelanocortin, agouti-related peptide, hypocretin/orexin, melanin-concentrating hormone, oxytocin, arginine vasopressin, corticotropin-releasing hormone (CRH) or thyrotropin-releasing hormone. Hypothalamic neurons can be generated using a 'self-patterning' strategy that yields a broad array of cell types, or via a more reproducible directed differentiation approach. Stem cell-derived human hypothalamic neurons share characteristic morphological properties and gene expression patterns with their counterparts in vivo, and are able to integrate into the mouse brain. These neurons could form the basis of cellular models, chemical screens or cellular therapies to study and treat common human diseases.
In adult rodents, subventricular zone (SVZ) astrocytes (B cells) function as primary progenitors in the generation of new neurons that migrate to the olfactory bulb (OB), where they differentiate ...into multiple types of interneurons. It has been generally considered that individual adult SVZ stem cells are capable of generating different types of neurons and glial cells. However, recent studies indicate that these adult SVZ primary progenitors are heterogeneous and predetermined to generate specific types of neurons. Surprisingly, OB interneurons are generated by stem cells not only in the walls of the lateral ventricle facing the striatum but also in the rostral migratory stream and walls of the lateral ventricle facing the cortex and the septum. SVZ B cells in different locations within this extensive germinal region generate different kinds of interneurons. General physiological characteristics of major classes of OB interneurons have begun to emerge, but the functional contribution of each subtype remains unknown. The mosaic organization of the SVZ offers a unique opportunity to understand the origin of interneuron diversity and how this assortment of neurons contributes to plasticity of postnatal olfactory circuits.
Neural stem cells (NSCs) are primary progenitors that give rise to neurons and glia in the embryonic, neonatal and adult brain. In recent years, we have learned three important things about these ...cells. First, NSCs correspond to cells previously thought to be committed glial cells. Second, embryonic and adult NSCs are lineally related: they transform from neuroepithelial cells into radial glia, then into cells with astroglial characteristics. Third, NSCs divide asymmetrically and often amplify the number of progeny they generate via symmetrically dividing intermediate progenitors. These advances challenge our traditional perceptions of glia and stem cells, and provide the foundation for understanding the molecular basis of mammalian NSC behavior.
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