Using Stem Cell Models to Explore the Genetics Underlying Psychiatric Disorders: Linking Risk Variants, Genes, and Biology in Brain Disease
Abstract
There is an urgent and unmet need to advance our ability to translate genetic studies of psychiatric disorders into clinically actionable information, which could transform diagnostics and even one day lead to novel (and potentially presymptomatic) therapeutic interventions. Today, although there are hundreds of significant loci associated with psychiatric disorders, resolving the target gene(s) and pathway(s) impacted by each is a major challenge. Integrating human induced pluripotent stem cell–based approaches with CRISPR-mediated genomic engineering strategies makes it possible to study the impact of patient-specific variants within the cell types of the brain. As the scale and scope of functional genomic studies expands, so does our ability to resolve the complex interplay of the many risk variants linked to psychiatric disorders. In this review, the author discusses some of the technological advances that make it possible to ask exciting questions that are fundamental to our understanding of psychiatric disorders. How do distinct risk variants converge and interact with each other (and the environment) across the diverse cell types that comprise the human brain? Can clinical trajectories and/or therapeutic response be predicted from genetic profiles? Just as critically, by spreading the message that genetic risk for psychiatric disorders is biological and fundamentally no different than for other human conditions, we can dispel the stigma associated with mental illness.
Over 50 million (one in five) Americans are affected by psychiatric disorders, which include diverse conditions that vary in symptoms, severity, outcomes, and treatment responsiveness. These polygenic disorders arise from a combination of variants that contribute to risk with differing frequencies and penetrance. The extreme clinical heterogeneity among patients with the same diagnosis, coupled with the frequent overlap in clinical presentation across disorders, can delay accurate diagnosis, which remains highly subjective (1). Despite a substantial investment in genetic studies that have now cataloged hundreds of disease-associated variants, findings have not translated into clinical insights. Why is this important? A better understanding of the molecular underpinning of disease will make possible the prediction of clinical outcomes years before the onset of symptoms and facilitate the discovery of drugs that might delay, mitigate, or reverse disease pathophysiology.
Precision Medicine: Preventing Disease Before It Arises
Large genetic studies can identify rare “genetic heroes,” carriers of Mendelian mutations without clinical manifestation of disease (2). For example, and with relevance to the brain, case reports include one such genetic hero for Alzheimer’s disease: an autosomal dominant PSEN1 mutation carrier, which results in early disease onset (at 30–50 years of age), who also happens to be homozygous for the protective APOE3 Christchurch mutation (R136S) and has shown no evidence of early-onset Alzheimer’s disease for three decades (3). More commonly, although APOE4/4 carriers have a 15-fold increased risk for Alzheimer’s disease (4), 1 in 10 “resilient” individuals do not develop symptoms. In either case, the variable penetrance of PSEN1 and APOE4/4 variants can be reframed as evidence of naturalistic “cures” that can prevent disease in individuals with otherwise high genetic predispositions. In the widely accepted additive risk model for genetic disease, does there exist a discrete “tipping point” between health and disease? Can ameliorative early interventions “untip” genetic disease risk?
Even for highly penetrant conditions with no current treatment strategies, a spectrum of phenotypes are possible. Individuals with Down syndrome have IQs ranging from <40 to 120 (5), and symptoms of Huntington’s disease can onset from 2 to 79 years of age (6, 7). This vast heterogeneity reflects complex interactions between genes, circuits, and environments. Understanding the contexts that buffer genetic risk will allow individuals to achieve their greatest phenotypic potential and improve life outcomes.
Stem Cell Models: Resolving Cell-Type-Specific and Context-Dependent Effects of Genetic Risk
Many psychiatric disorders, notably schizophrenia, include a long prodromal period prior to the onset of symptoms. In order to study the molecular mechanisms underlying disease initiation prior to diagnosis, physicians and scientists have historically tracked high-risk individuals for decades, waiting for symptom onset in a small subset of their cohort. Instead, using stem cell models, it is possible to recapitulate neurodevelopment in vitro, essentially observing risk in a laboratory dish. We and others have repeatedly observed that neurons and glia derived from human induced pluripotent stem cells (hiPSCs) most resemble their prenatal in vivo counterparts (8–13), and so are particularly well suited to test the neurodevelopmental impact of the many psychiatric risk variants predicted to influence fetal cortical development (14). Put simply, these risk-in-a-dish models make it possible to observe cellular phenotypes related to disease, uncover molecular mechanisms driving these perturbations, and screen for drug and/or gene therapies with which to prevent or reverse them.
The first human embryonic stem cell lines were grown in 1998, with the theoretical capability to differentiate to every cell type in the human body, and so they represented a nearly limitless source of material for studies of human disease (15). Research into the patterning of these cells, toward understanding the molecular networks regulating pluripotency—their unique ability to differentiate into all cell lineages—uncovered four genes that, when overexpressed, were sufficient to reprogram adult somatic cells into hiPSCs (16). This transformative discovery made it possible to generate stem cells from any individual, and therefore to make the precise cell types affected by any disease, in order to observe disease-associated processes in real time. Unfortunately, the results have been anything but clear-cut. For example, in schizophrenia hiPSC-based studies, phenotypes have been reported in each of glutamatergic neurons (17), GABAergic neurons (18), dopaminergic neurons (19), neural progenitor cells (8), astrocytes (20), oligodendrocytes (21), and microglia (22). Moreover, as the case-control hiPSC experiments of schizophrenia grew larger, it became clear that patients did not all differ from control subjects in the same way (23), and also that there was substantial variation between individual control subjects (13). In hindsight, the field’s earliest experiments proved naive. But why?
Genetics and Genomics: The (Increasingly) Complex Risk Architecture of Psychiatric Disorders
Over the past decade, our understanding of the complex genetics of psychiatric disorders has exploded, although admittedly, there is much more yet to learn. Ten years ago, the largest-ever genome-wide association study (GWAS) of schizophrenia identified seven loci associated with disease risk (24). Today, with over 10-fold more individuals analyzed, there are 270 loci (25), with no clear estimate as to how many variants will ultimately be implicated in disease risk (26, 27). There are now hundreds of significant loci associated with psychiatric (28–31) and neurodegenerative disease risk (32, 33). Risk variants linked to schizophrenia (28, 34–36), autism spectrum disorder (ASD) (37–39), and more broadly across the neuropsychiatric disorder spectrum (14, 40–43) are enriched for genes involved in synaptic biology and gene regulation (39, 44–48) and for those expressed during fetal cortical development (14, 44, 49, 50). Although highly penetrant rare mutations underlie a fraction of cases (51), psychiatric disorders more frequently arises from risk variants that each confer only a tiny increase of risk and are common in the population at large (25). Thus, individually small risk effects combine to yield much larger impacts in aggregate, although the precise mechanisms involved remain unclear (for a review, see reference 52).
CRISPR: Engineering Risk for Psychiatric Disorders
Fortuitously, in parallel with these genetic advances were substantial developments in genome engineering (53). CRISPR-associated proteins (Cas) use short and easily synthesized “clustered regularly interspaced short palindromic repeats” (CRISPR) sequences as guide RNAs to recognize specific complementary strands of DNA. Together, they form the basis of a technology known as CRISPR-Cas, which can be used to efficiently edit DNA to introduce variants or rescue mutations (54), and also to alter the epigenome—for example, manipulating histone modifications (55, 56), DNA methylation (57), and chromatin interactions (58), directly activating or repressing expression of target genes (59), and cleaving RNA (60). Engineering can be multiplexed (61), parallelized (62), and conducted at near genome-wide scale (63). Thus, it is now theoretically possible to introduce, or reverse, the myriad risk loci associated with psychiatric disorders, alone or in combination, in specific neuronal cell types.
Many hiPSC-based studies of psychiatric risk genes recruit patients with highly penetrant rare mutations (e.g., MECP2 [64], FMR1 [65], CACNA1C [66], SHANK3 [67], NRXN1 [68], NLGN4 [69], 22q11.2 [70], and DISC1 [71]), observing phenotypes such as altered neuronal development and/or synaptic function. Likewise, engineered deletions of FMR1 (65), SHANK3 (72), NRXN1 (73), and many more genes (74) revealed similar impacts. Although the common risk variants identified through GWAS are predicted to result in relatively more subtle phenotypic effects, several such risk loci have successfully been explored within case-control cohort designs (e.g., C4 [22], CACNA1C [75]). To improve our ability to resolve the small effect sizes associated with common variants (termed single-nucleotide polymorphisms or SNPs), CRISPR engineering can be used to make comparisons across a shared genetic (“isogenic”) background. This strategy has demonstrated the causal role of schizophrenia-associated GWAS SNPs in gene regulation through enhancer-promoter looping (CACNA1C [76]), 3D-genome folding (PCDHα [77]), miRNA abundance (miR-137 [78]), and mRNA levels (FURIN [79]). In fact, CRISPR-based isogenic comparisons of one such noncoding SNP (rs4702) produced genotype-dependent transcriptomic and neuronal activity differences that were not just cell-type-specific but also microRNA-dependent (79). Likewise, for two predicted target genes of schizophrenia GWAS (SNAP91, TSNARE1), CRISPR-based approaches to activate and repress endogenous gene expression resolved distinct pre- and postsynaptic perturbations (79).
While CRISPR-based approaches can manipulate a handful of variants or genes, higher-throughput methods are necessary to comprehensively survey all of the loci associated with psychiatric disorders (for a review, see reference 80). Toward this, massively parallel reporter assays (MPRAs) can evaluate the regulatory activity of the thousands of loci associated with human cortical development (81, 82) and psychiatric disorder risk (83–85). Additionally, CRISPR expression quantitative trait loci (eQTL) mapping can identify SNPs that differentially regulate proximal (e.g., crisprQTL [86]) and distal (e.g., CRISPRi-FlowFISH [87]) target gene expression. Finally, population-scale “village-in-a-dish” experiments, whereby single-cell RNAseq is applied to pooled populations of hiPSC-derived neurons or glia from dozens of genotyped donors (e.g., Census-seq [88–91]) are extremely well powered to link SNPs to gene expression and phenotypic effects.
Traditional functional genomic approaches generally involved one-gene-at-a-time “genotype-to-phenotype” studies, applying prior knowledge in a hypothesis-driven manner to test the causal role of specific genes. By contrast, large-scale screens are “phenotype-to-genotype” approaches, broadly manipulating many variants or genes at once in order to characterize those that result in specific changes. Although traditionally conducted in an arrayed format that requires a substantial time and resource investment, state-of-the-art CRISPR or village-in-a-dish screens incorporate a pooled design. Coupling CRISPR-based perturbations to single-cell RNA sequencing for analytical readouts (e.g., Perturb-seq [92] and ECCITE-seq [93]) further expands the breadth of biological questions that can be tested in each pooled screen. Altogether, this makes possible the comprehensive interrogation of candidate disease genes (94) or unbiased gene lists (95–97) in a single-tissue culture well, dramatically reducing the time and financial costs involved.
Fundamental Questions Lacking Answers
A major challenge in the field is connecting disease-associated risk variants (the vast majority of which fall in noncoding sequences) to their respective target gene(s), pathway(s), and causal cellular phenotype(s) (52), and in doing so, translating genetic findings into disease-relevant cell biology. Given that a spectrum of developmental and neuropsychiatric phenotypes share overlapping genetic architectures (52), there is great value in exploring their shared heritability.
Rare and common variants underlying risk for psychiatric disorders show evidence of cumulative effects (98, 99) and are predicted to converge at the pathway level (100). Toward this, we recently perturbed a dozen schizophrenia risk genes in isogenic glutamatergic neurons, observing convergence on a subset of genes and subnetworks involved in synaptic function (101). Recent studies likewise queried an overlapping set of ASD genes in vitro in human neural progenitor cells (27 genes) (94) and human brain organoids (three genes) (102), and in vivo in fetal mouse brains (35 genes) (103) and Xenopus tropicalis (10 genes) (104). Using hypothesis-free pooled (manipulating many genes at once in the same “chimeric” cell culture experiment or animal) and/or parallelized (manipulating many genes one at a time in “arrayed” format across cell culture wells or animals) approaches, the studies reporting convergence of ASD genes impacting neurogenesis (94, 102–104), Wnt signaling (an important neurodevelopmental pathway that controls cell fate decisions and tissue patterning) (94) and gene expression (102, 103). Moreover, in one report, two subgroups of ASD genes were resolved, which correlated with abnormal Wnt signaling: one that inhibited and one that enhanced spontaneous cortical neurogenesis (94). Do these points of convergence represent novel points of therapeutic intervention?
It follows that we must also resolve how the effects of risk variants combine to yield much larger impacts in aggregate. Within individual patients, it is possible that genetic risk factors sum in different patterns depending on whether their target genes are expressed in the same cell types and/or converge within the same biological pathways. Individual risk variants may sum linearly (105, 106) or be amplified (107) or buffered (108) by epistatic effects. We previously uncovered an unexpected combinatorial effect between risk genes that was not predicted from single gene perturbations, one that concentrated on synaptic function and linked the rare and common variant genes implicated in psychiatric disorders (79). Likewise, a single GWAS risk locus that regulates expression of more than one target gene can result in highly significant gene×gene interaction terms, suggesting that they synergistically contribute to the molecular and synaptic phenotypes observed (109). Does understanding the combinatorial interactions between risk variants improve genetic diagnosis and/or indicate new drug targets?
The task is complicated in that many of the genes regulated by disease-associated variants are most likely expressed and regulated in cell-type-specific and context-dependent manners. To date, efforts to explain psychiatric disorder risk through annotation of GWAS signals with functional genomics have not accounted for the impact of environment or stressors. This failure to incorporate gene-by-environment interactions may be especially critical in studies of those psychiatric disorders that require or include specific stressors (e.g., posttraumatic stress disorder) or exposures (e.g., substance use disorders, anorexia nervosa) among the diagnostic criteria, or that count exposure to illicit substances or extreme stress as among the critical risk factors for disease (e.g., schizophrenia). Glucocorticoid receptor signaling is highly associated with trauma response (110); therefore, understanding the genetic basis for dysregulated stress response may yield novel therapeutic targets. Studies of in vitro brain organoids generated from healthy control subjects suggest that excessive glucocorticoid exposure could interfere with neuronal maturation (111). Furthermore, we observed robust glucocorticoid hypersensitivity in hiPSC neurons derived from individuals with posttraumatic stress disorder (112). How do risk variants interact with the environment across the diverse cell types that comprise the human brain?
Whereas every current antipsychotic drug targets dopaminergic signaling, genetic risk for schizophrenia is enriched for genes expressed by glutamatergic and subsets of GABAergic neurons (113), suggesting that disease etiology reflects cell types distinct from observed pharmacology. Consistent with this, studies of neuronal convergence of ASD genes in brain organoids reveal asynchronous development of inhibitory GABAergic neurons and deep-layer glutamatergic projection neurons through distinct molecular pathways (102). In fact, the mechanisms underlying psychiatric disorders are thought to drive symptoms through iterative pathological changes in circuit function (114). Thus, the challenge is to assemble in vitro models that capture neuronal circuitry (115, 116), glial support (117–119), vasculature (120, 121), and blood-brain-barrier functions (122) while retaining the capacity to deconvolve cell-type-specific effects. For example, mutations in CACNA1C associated with Timothy syndrome cause deficits in calcium signaling in both glutamatergic (66, 115) and GABAergic (115) neurons, which specifically lead to perturbations in interneuron migration into cortical brain organoids (123). How do risk variants impact cellular function within circuits?
Finally, the extent to which clinical drug responsiveness is heritable and/or stable throughout the lifetime, across the spectrum of neuropsychiatric disease, needs further investigation, but promising examples such as lithium-responsive bipolar disorder (124) have been identified. We helped to show that hyperexcitability in hippocampal neurons derived from lithium-responsive, but not nonresponsive, patients with bipolar disorder is ameliorated after lithium treatment (125). In an independent follow-up, a similar phenotypic analysis was capable of predicting with 92% accuracy whether hippocampal neurons were derived from a patient with or without clinical responsiveness to lithium (126). Is clinical treatment response predictable? Future genomic approaches will provide the means to stratify patients with overlapping risk combinations into “genetically defined” cohorts. An improved drug screening strategy would better recapitulate disease pathophysiology and integrate advances in psychiatric genetics. Toward this, we described a proof-of-concept application of transcriptomic drug screening to hiPSC-based models, demonstrating that drug-induced differences (including many known antipsychotics) in patient-derived neural progenitor cells were capable of reversing postmortem schizophrenia transcriptional signatures and were enriched for genes related to schizophrenia biology (127). Altogether, these studies reveal major advantages of incorporating cell type and patient-specific platforms in drug discovery.
Conclusions
Each person’s distinct genetic, epigenetic, and environmental risk profile predisposes them to some brain disorders and confers resilience to others. There will be no one-size-fits-all cure for psychiatric disorders. Each patient represents a unique aggregation of risk factors, which may converge on different pathways, interact in dissimilar cell types, and impact distinct developmental windows. Pursuing a functional genomics approach that integrates stem cell models and genome engineering will help to resolve the impact of patient-specific variants across cell types, genetic backgrounds, and environmental conditions. Striving to translate risk “variants to genes,” “genes to pathways,” and “pathways to circuits” will reveal the convergent, additive, and synergistic relationships between risk factors within and between the cell types of the brain. These insights could identify therapeutics tailored to an individual’s specific risk profile, and so springboard the development of novel, personalized approaches to treat disease.
1. : Can mental health diagnoses in administrative data be used for research? A systematic review of the accuracy of routinely collected diagnoses. BMC Psychiatry 2016; 16:263Crossref, Medline, Google Scholar
2. : Analysis of 589,306 genomes identifies individuals resilient to severe Mendelian childhood diseases. Nat Biotechnol 2016; 34:531–538Crossref, Medline, Google Scholar
3. : Resistance to autosomal dominant Alzheimer’s disease in an APOE3 Christchurch homozygote: a case report. Nat Med 2019; 25:1680–1683Crossref, Medline, Google Scholar
4. : Effects of age, sex, and ethnicity on the association between apolipoprotein E genotype and Alzheimer disease: a meta-analysis. APOE and Alzheimer Disease Meta Analysis Consortium. JAMA 1997; 278:1349–1356Crossref, Medline, Google Scholar
5. : Clinical and cardiorespiratory assessment in children with Down syndrome without congenital heart disease. Arch Pediatr Adolesc Med 2000; 154:408–410Crossref, Medline, Google Scholar
6. : Late onset Huntington disease: clinical and genetic characteristics of 34 cases. J Neurol Sci 2009; 276:159–162Crossref, Medline, Google Scholar
7. : Biological and clinical manifestations of juvenile Huntington’s disease: a retrospective analysis. Lancet Neurol 2018; 17:986–993Crossref, Medline, Google Scholar
8. : Phenotypic differences in hiPSC NPCs derived from patients with schizophrenia. Mol Psychiatry 2015; 20:361–368Crossref, Medline, Google Scholar
9. : Modeling human cortical development in vitro using induced pluripotent stem cells. Proc Natl Acad Sci USA 2012; 109:12770–12775Crossref, Medline, Google Scholar
10. : Functional cortical neurons and astrocytes from human pluripotent stem cells in 3D culture. Nat Methods 2015; 12:671–678Crossref, Medline, Google Scholar
11. : Brain-region-specific organoids using mini-bioreactors for modeling ZIKV exposure. Cell 2016; 165:1238–1254Crossref, Medline, Google Scholar
12. : Functional maturation of hPSC-derived forebrain interneurons requires an extended timeline and mimics human neural development. Cell Stem Cell 2013; 12:573–586Crossref, Medline, Google Scholar
13. : Transcriptional signatures of schizophrenia in hiPSC-derived NPCs and neurons are concordant with post-mortem adult brains. Nat Commun 2017; 8:2225Crossref, Medline, Google Scholar
14. : A genome-wide association study of shared risk across psychiatric disorders implicates gene regulation during fetal neurodevelopment. Nat Neurosci 2019; 22:353–361Crossref, Medline, Google Scholar
15. : Embryonic stem cell lines derived from human blastocysts. Science 1998; 282:1145–1147Crossref, Medline, Google Scholar
16. : Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 2007; 131:861–872Crossref, Medline, Google Scholar
17. : Modeling hippocampal neurogenesis using human pluripotent stem cells. Stem Cell Reports 2014; 2:295–310Crossref, Medline, Google Scholar
18. : Dysregulated protocadherin-pathway activity as an intrinsic defect in induced pluripotent stem cell-derived cortical interneurons from subjects with schizophrenia. Nat Neurosci 2019; 22:229–242Crossref, Medline, Google Scholar
19. : Human iPSC neurons display activity-dependent neurotransmitter secretion: aberrant catecholamine levels in schizophrenia neurons. Stem Cell Reports 2014; 3:531–538Crossref, Medline, Google Scholar
20. : Human iPSC glial mouse chimeras reveal glial contributions to schizophrenia. Cell Stem Cell 2017; 21:195–208.e6Crossref, Medline, Google Scholar
21. : Oligodendrocyte differentiation of induced pluripotent stem cells derived from subjects with schizophrenias implicate abnormalities in development. Transl Psychiatry 2018; 8:230Crossref, Medline, Google Scholar
22. : Increased synapse elimination by microglia in schizophrenia patient-derived models of synaptic pruning. Nat Neurosci 2019; 22:374–385Crossref, Medline, Google Scholar
23. : Dysregulation of miRNA-9 in a subset of schizophrenia patient-derived neural progenitor cells. Cell Rep 2016; 15:1024–1036Crossref, Medline, Google Scholar
24. Genome-wide association study identifies five new schizophrenia lociNat Genet 2011; 43:969–976Crossref, Medline, Google Scholar
25. : Mapping genomic loci prioritises genes and implicates synaptic biology in schizophrenia. medRxiv 2020
26. : Common disease is more complex than implied by the core gene omnigenic model. Cell 2018; 173:1573–1580Crossref, Medline, Google Scholar
27. . An expanded view of complex traits: from polygenic to omnigenic. Cell 2017; 169:1177–1186Crossref, Medline, Google Scholar
28. : Common schizophrenia alleles are enriched in mutation-intolerant genes and in regions under strong background selection. Nat Genet 2018; 50:381–389Crossref, Medline, Google Scholar
29. : Identification of common genetic risk variants for autism spectrum disorder. Nat Genet 2019; 51:431–444Crossref, Medline, Google Scholar
30. : Genome-wide association study identifies 30 loci associated with bipolar disorder. Nat Genet 2019; 51:793–803Crossref, Medline, Google Scholar
31. : Genome-wide association study identifies eight risk loci and implicates metabo-psychiatric origins for anorexia nervosa. Nat Genet 2019; 51:1207–1214Crossref, Medline, Google Scholar
32. : Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer’s disease risk. Nat Genet 2019; 51:404–413Crossref, Medline, Google Scholar
33. : Identification of novel risk loci, causal insights, and heritable risk for Parkinson’s disease: a meta-analysis of genome-wide association studies. Lancet Neurol 2019; 18:1091–1102Crossref, Medline, Google Scholar
34. : A polygenic burden of rare disruptive mutations in schizophrenia. Nature 2014; 506:185–190Crossref, Medline, Google Scholar
35. : De novo mutations in schizophrenia implicate synaptic networks. Nature 2014; 506:179–184Crossref, Medline, Google Scholar
36. : Contribution of copy number variants to schizophrenia from a genome-wide study of 41,321 subjects. Nat Genet 2017; 49:27–35Crossref, Medline, Google Scholar
37. : Large-scale exome sequencing study implicates both developmental and functional changes in the neurobiology of autism. Cell 2020; 180:568–584.e23Crossref, Medline, Google Scholar
38. : Insights into autism spectrum disorder genomic architecture and biology from 71 risk loci. Neuron 2015; 87:1215–1233Crossref, Medline, Google Scholar
39. : Synaptic, transcriptional, and chromatin genes disrupted in autism. Nature 2014; 515:209–215Crossref, Medline, Google Scholar
40. : Genome wide meta-analysis identifies genomic relationships, novel loci, and pleiotropic mechanisms across eight psychiatric disorders. bioRxiv 2019
41. : A computational tool (H-MAGMA) for improved prediction of brain-disorder risk genes by incorporating brain chromatin interaction profiles. Nat Neurosci 2020; 23:583–593Crossref, Medline, Google Scholar
42. : A global overview of pleiotropy and genetic architecture in complex traits. Nat Genet 2019; 51:1339–1348Crossref, Medline, Google Scholar
43. : Genomic relationships, novel loci, and pleiotropic mechanisms across eight psychiatric disorders. Cell 2019; 179:1469–1482.e11Crossref, Medline, Google Scholar
44. : Sequencing chromosomal abnormalities reveals neurodevelopmental loci that confer risk across diagnostic boundaries. Cell 2012; 149:525–537Crossref, Medline, Google Scholar
45. : Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature 2012; 485:242–245Crossref, Medline, Google Scholar
46. : Multiplex targeted sequencing identifies recurrently mutated genes in autism spectrum disorders. Science 2012; 338:1619–1622Crossref, Medline, Google Scholar
47. : De novo mutations revealed by whole-exome sequencing are strongly associated with autism. Nature 2012; 485:237–241Crossref, Medline, Google Scholar
48. : Recurrent de novo mutations implicate novel genes underlying simplex autism risk. Nat Commun 2014; 5:5595Crossref, Medline, Google Scholar
49. : Genome-wide burden of deleterious coding variants increased in schizophrenia. Nat Commun 2015; 6:7501Crossref, Medline, Google Scholar
50. : Spatial and temporal mapping of de novo mutations in schizophrenia to a fetal prefrontal cortical network. Cell 2013; 154:518–529Crossref, Medline, Google Scholar
51. : Exome sequencing identifies rare coding variants in 10 genes which confer substantial risk for schizophrenia. medRxiv 2020
52. : Defining the genetic, genomic, cellular, and diagnostic architectures of psychiatric disorders. Cell 2019; 177:162–183Crossref, Medline, Google Scholar
53. : Development and applications of CRISPR-Cas9 for genome engineering. Cell 2014; 157:1262–1278Crossref, Medline, Google Scholar
54. : Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 2019; 576:149–157Crossref, Medline, Google Scholar
55. : Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements. Nat Methods 2015; 12:1143–1149Crossref, Medline, Google Scholar
56. : Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers. Nat Biotechnol 2015; 33:510–517Crossref, Medline, Google Scholar
57. : Rescue of fragile X syndrome neurons by DNA methylation editing of the FMR1 gene. Cell 2018; 172:979–992.e6Crossref, Medline, Google Scholar
58. : CRISPR-based chromatin remodeling of the endogenous Oct4 or Sox2 locus enables reprogramming to pluripotency. Cell Stem Cell 2018; 22:252–261.e4Crossref, Medline, Google Scholar
59. : Evaluating synthetic activation and repression of neuropsychiatric-related genes in hiPSC-derived NPCs, neurons, and astrocytes. Stem Cell Reports 2017; 9:615–628Crossref, Medline, Google Scholar
60. : Transcriptome engineering with RNA-targeting type VI-D CRISPR effectors. Cell 2018; 173:665–676.e14Crossref, Medline, Google Scholar
61. : Inducible and multiplex gene regulation using CRISPR-Cpf1-based transcription factors. Nat Methods 2017; 14:1163–1166Crossref, Medline, Google Scholar
62. : Parallelized engineering of mutational models using piggyBac transposon delivery of CRISPR libraries. bioRxiv 2020
63. : Optimized libraries for CRISPR-Cas9 genetic screens with multiple modalities. Nat Commun 2018; 9:5416Crossref, Medline, Google Scholar
64. : A model for neural development and treatment of Rett syndrome using human induced pluripotent stem cells. Cell 2010; 143:527–539Crossref, Medline, Google Scholar
65. : The fragile X mutation impairs homeostatic plasticity in human neurons by blocking synaptic retinoic acid signaling. Sci Transl Med 2018; 10:eaar4338Crossref, Medline, Google Scholar
66. : Using iPSC-derived neurons to uncover cellular phenotypes associated with Timothy syndrome. Nat Med 2011; 17:1657–1662Crossref, Medline, Google Scholar
67. : SHANK3 and IGF1 restore synaptic deficits in neurons from 22q13 deletion syndrome patients. Nature 2013; 503:267–271Crossref, Medline, Google Scholar
68. : Neuronal impact of patient-specific aberrant NRXN1α splicing. Nat Genet 2019; 51:1679–1690Crossref, Medline, Google Scholar
69. : Neuroligin-4 regulates excitatory synaptic transmission in human neurons. Neuron 2019; 103:617–626.e6Crossref, Medline, Google Scholar
70. : Neuronal defects in a human cellular model of 22q11.2 deletion syndrome. Nat Med 2020; 26:1888–1898Crossref, Medline, Google Scholar
71. : Synaptic dysregulation in a human iPS cell model of mental disorders. Nature 2014; 515:414–418Crossref, Medline, Google Scholar
72. : Autism-associated SHANK3 haploinsufficiency causes Ih channelopathy in human neurons. Science 2016; 352:aaf2669Crossref, Medline, Google Scholar
73. : Human neuropsychiatric disease modeling using conditional deletion reveals synaptic transmission defects caused by heterozygous mutations in NRXN1. Cell Stem Cell 2015; 17:316–328Crossref, Medline, Google Scholar
74. : Complete disruption of autism-susceptibility genes by gene editing predominantly reduces functional connectivity of isogenic human neurons. Stem Cell Reports 2018; 11:1211–1225Crossref, Medline, Google Scholar
75. : Functional implications of a psychiatric risk variant within CACNA1C in induced human neurons. Mol Psychiatry 2015; 20:162–169Crossref, Medline, Google Scholar
76. : A role for noncoding variation in schizophrenia. Cell Rep 2014; 9:1417–1429Crossref, Medline, Google Scholar
77. : Neuron-specific signatures in the chromosomal connectome associated with schizophrenia risk. Science 2018; 362:eaat4311Crossref, Medline, Google Scholar
78. : Open chromatin profiling in hiPSC-derived neurons prioritizes functional noncoding psychiatric risk variants and highlights neurodevelopmental loci. Cell Stem Cell 2017; 21:305–318.e8Crossref, Medline, Google Scholar
79. : Synergistic effects of common schizophrenia risk variants. Nat Genet 2019; 51:1475–1485Crossref, Medline, Google Scholar
80. : Massively parallel techniques for cataloguing the regulome of the human brain. Nat Neurosci 2020; 23:1509–1521Crossref, Medline, Google Scholar
81. : Identification and massively parallel characterization of regulatory elements driving neural induction. Cell Stem Cell 2019; 25:713–727.e10Crossref, Medline, Google Scholar
82. : Massively parallel disruption of enhancers active during human corticogenesis. bioRxiv 2019
83. : Massively parallel discovery of human-specific substitutions that alter enhancer activity. Proc Natl Acad Sci USA 2021; 118:e2007049118Crossref, Medline, Google Scholar
84. : A screen of 1,049 schizophrenia and 30 Alzheimer’s-associated variants for regulatory potential. Am J Med Genet B Neuropsychiatr Genet 2020; 183:61–73Crossref, Medline, Google Scholar
85. : Transcriptional-regulatory convergence across functional MDD risk variants identified by massively parallel reporter assays. Transl Psychiatry 2021; 11:403Crossref, Medline, Google Scholar
86. : A genome-wide framework for mapping gene regulation via cellular genetic screens. Cell 2019; 176:1516Crossref, Medline, Google Scholar
87. : Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations. Nat Genet 2019; 51:1664–1669Crossref, Medline, Google Scholar
88. : Single cell eQTL analysis identifies cell type-specific genetic control of gene expression in fibroblasts and reprogrammed induced pluripotent stem cells. bioRxiv 2020
89. : Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression. Nat Commun 2020; 11:810Crossref, Medline, Google Scholar
90. : Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation. Nat Genet 2021; 53:304–312Crossref, Medline, Google Scholar
91. : Mapping genetic effects on cellular phenotypes with “cell villages”. bioRxiv 2020
92. : Perturb-Seq: dissecting molecular circuits with scalable single-cell RNA profiling of pooled genetic screens. Cell 2016; 167:1853–1866.e17Crossref, Medline, Google Scholar
93. : Multiplexed detection of proteins, transcriptomes, clonotypes, and CRISPR perturbations in single cells. Nat Methods 2019; 16:409–412Crossref, Medline, Google Scholar
94. : A multiplex human pluripotent stem cell platform defines molecular and functional subclasses of autism-related genes. Cell Stem Cell 2020; 27:35–49.e6Crossref, Medline, Google Scholar
95. : Overexpression of NEUROG2 and NEUROG1 in human embryonic stem cells produces a network of excitatory and inhibitory neurons. FASEB J 2019; 33:5287–5299Crossref, Medline, Google Scholar
96. : CRISPR activation screens systematically identify factors that drive neuronal fate and reprogramming. Cell Stem Cell 2018; 23:758–771.e8Crossref, Medline, Google Scholar
97. : CRISPR interference-based platform for multimodal genetic screens in human iPSC-derived neurons. Neuron 2019; 104:239–255.e12Crossref, Medline, Google Scholar
98. : Polygenic transmission disequilibrium confirms that common and rare variation act additively to create risk for autism spectrum disorders. Nat Genet 2017; 49:978–985Crossref, Medline, Google Scholar
99. : Common alleles contribute to schizophrenia in CNV carriers. Mol Psychiatry 2016; 21:1153Crossref, Medline, Google Scholar
100. : Strength of functional signature correlates with effect size in autism. Genome Med 2017; 9:64Crossref, Medline, Google Scholar
101. Townsley KG, Li A, Deans PJM, et al: Convergent impact of schizophrenia risk genes. bioRxiv 2022. doi: 10.1101/2022.03.29.486286Google Scholar
102. : Autism genes converge on asynchronous development of shared neuron classes. Nature 2022; 602:268–273Crossref, Medline, Google Scholar
103. : In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with autism risk genes. Science 2020; 370:eaaz6063Crossref, Medline, Google Scholar
104. : Parallel in vivo analysis of large-effect autism genes implicates cortical neurogenesis and estrogen in risk and resilence. Neuron 2021; 109:788–804.e8Crossref, Medline, Google Scholar
105. : Recovery of trait heritability from whole genome sequence data. bioRxiv 2019
106. : Large-scale analyses provide no evidence for gene-gene interactions influencing type 2 diabetes risk. Diabetes 2020; 69:2518–2522Crossref, Medline, Google Scholar
107. : Trans effects on gene expression can drive omnigenic inheritance. Cell 2019; 177:1022–1034.e6Crossref, Medline, Google Scholar
108. : A polygenic resilience score moderates the genetic risk for schizophrenia. Mol Psychiatry 2021; 26:800–815Crossref, Medline, Google Scholar
109. Zhang S, Zhang H, Forrest MP, et al: Multiple genes in cis mediate the effects of a single chromatin accessibility variant on aberrant synaptic development and function in human neurons. BioRxiv 2021. doi: 10.1101/2021.12.11.472229Google Scholar
110. : Expression profiling associates blood and brain glucocorticoid receptor signaling with trauma-related individual differences in both sexes. Proc Natl Acad Sci USA 2014; 111:13529–13534Crossref, Medline, Google Scholar
111. : Cell-type-specific impact of glucocorticoid receptor activation on the developing brain: a cerebral organoid study. Am J Psychiatry 2022; 179:375–387Link, Google Scholar
112. : Modeling gene x environment interactions in PTSD using glucocorticoid-induced transcriptomics in human neurons. Eur Neuropsychopharmacol 2021; 51:e30Crossref, Google Scholar
113. : Genetic identification of brain cell types underlying schizophrenia. Nat Genet 2018; 50:825–833Crossref, Medline, Google Scholar
114. : Molecular neuroscience in the 21st century: a personal perspective. Neuron 2017; 96:536–541Crossref, Medline, Google Scholar
115. : Assembly of functionally integrated human forebrain spheroids. Nature 2017; 545:54–59Crossref, Medline, Google Scholar
116. : hESC-derived thalamic organoids form reciprocal projections when fused with cortical organoids. Cell Stem Cell 2019; 24:487–497.e7Crossref, Medline, Google Scholar
117. : Derivation of functional human astrocytes from cerebral organoids. Sci Rep 2017; 7:45091Crossref, Medline, Google Scholar
118. : Differentiation and maturation of oligodendrocytes in human three-dimensional neural cultures. Nat Neurosci 2019; 22:484–491Crossref, Medline, Google Scholar
119. : iPSC-derived human microglia-like cells to study neurological diseases. Neuron 2017; 94:278–293.e9Crossref, Medline, Google Scholar
120. : An in vivo model of functional and vascularized human brain organoids. Nat Biotechnol 2018; 36:432–441Crossref, Medline, Google Scholar
121. : Engineering of human brain organoids with a functional vascular-like system. Nat Methods 2019; 16:1169–1175Crossref, Medline, Google Scholar
122. : Human iPSC-derived blood-brain barrier chips enable disease modeling and personalized medicine applications. Cell Stem Cell 2019; 24:995–1005.e6Crossref, Medline, Google Scholar
123. : Dissecting the molecular basis of human interneuron migration in forebrain assembloids from Timothy syndrome. Cell Stem Cell 2022; 29:248–264.e7Crossref, Medline, Google Scholar
124. : Genetic variants associated with response to lithium treatment in bipolar disorder: a genome-wide association study. Lancet 2016; 387:1085–1093Crossref, Medline, Google Scholar
125. : Differential responses to lithium in hyperexcitable neurons from patients with bipolar disorder. Nature 2015; 527:95–99Crossref, Medline, Google Scholar
126. : Prediction of response to drug therapy in psychiatric disorders. Open Biol 2018; 8:180031Crossref, Medline, Google Scholar
127. : Expression-based drug screening of neural progenitor cells from individuals with schizophrenia. Nat Commun 2018; 9:4412Crossref, Medline, Google Scholar