16p11.2 deletion is associated with hyperactivation of human iPSC-derived dopaminergic neuron networks and is rescued by RHOA inhibition in vitro

Sundberg, Maria; Pinson, Hannah; Smith, Richard; Winden, Kellen D.; Venugopal, Pooja; Tai, Derek J.C.; Gusella, James F.; Talkowski, Michael E.; Walsh, Christopher A.; Tegmark, Max; Şahin, Mustafa

doi:10.1038/s41467-021-23113-z

Cited by 42 publications

(42 citation statements)

References 96 publications

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“…To comprehensively investigate the maturity of spinal motor neurons, we utilized the CMOS-based HD-MEA platform, which is a high-throughput and high-resolution system containing 26,400 electrodes and 1,024 simultaneous recording channels (Muller et al, 2015; Sundberg et al, 2021; Yuan et al, 2020). We first scanned and analyzed the entire HD-MEA electrode array to examine spontaneous neural activities during spinal motor neuron differentiation.…”

Section: Resultsmentioning

confidence: 99%

Generation of functional posterior spinal motor neurons from hPSCs-derived human spinal cord neural progenitor cells

Yao

et al. 2022

Preprint

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SUMMARYSpinal motor neurons deficiency results in a series of devastating disorders such as amyotrophic lateral sclerosis (ALS), spinal muscular atrophy (SMA) and spinal cord injury (SCI). These disorders are currently incurable, while human pluripotent stem cells (hPSCs)-derived spinal motor neurons are promising but suffered from low-efficiency, functional immaturity and lacks of posterior cellular identity. In this study, we have established human spinal cord neural progenitor cells (hSCNPCs) via hPSCs differentiated neuromesodermal progenitors (NMPs) and demonstrated the hSCNPCs can be continuously expanded up to 40 passages. hSCNPCs can be rapidly differentiated into posterior spinal motor neurons with high efficiency. The functional maturity has been examined in detail. Moreover, a co-culture scheme which is compatible for both neural and muscular differentiation is developed to mimic the neuromuscular junction (NMJ) formation in vitro. Together, these studies highlight the potential avenues for generating clinically relevant spinal motor neurons and modeling neuromuscular diseases through our defined hSCNPCs.

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Section: Resultsmentioning

confidence: 99%

Generation of functional posterior spinal motor neurons from hPSCs-derived human spinal cord neural progenitor cells

Yao

et al. 2022

Preprint

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“…Together, the notable similarities and many differences in transcriptomic alterations between brain regions, peripheral tissues and human neuronal cells indicate that the CNV dosage changes of the same set of genes have impacts, both in terms of biological processes disrupted and in terms of the genes most significantly altered within those processes, that are context-specific. The importance of cellular context is reinforced by differences in the functional impact of the 16p11.2 CNV in our iNs (reduced numbers of neurites and branchpoints and electrical activity due to both deletion and duplication) compared to dopaminergic neurons (larger soma and hyperexcitability due to deletion and increased number of neurites due to duplication) derived from the same hiPSCs (Sundberg et al, 2021). Consequently, it is likely that multiple CNV genes and consequently disrupted biological processes contribute to the phenotypic features of the 16p11.2 RGD, potentially through a combination of different effects in different contributing cell types.…”

Section: Discussionmentioning

confidence: 96%

Tissue and cell-type specific molecular and functional signatures of 16p11.2 reciprocal genomic disorder across mouse brain and human neuronal models

Tai

Razaz

Erdin

et al. 2022

Preprint

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SUMMARYRecurrent deletion and duplication of ∼743 kilobases of unique genomic sequence and segmental duplications at chromosome 16p11.2 underlie a reciprocal genomic disorder (RGD; OMIM 611913 and 614671) associated with neurodevelopmental and psychiatric phenotypes, including intellectual disability, autism spectrum disorder (ASD), and schizophrenia (SCZ). To define molecular alterations associated with the 16p11.2 RGD, we performed transcriptome analyses of mice with reciprocal copy number variants (CNVs) of the syntenic chromosome 7qF3 region and human neuronal models derived from isogenic human induced pluripotent stem cells (hiPSCs) carrying CRISPR-engineered CNVs at 16p11.2. Analysis of differentially expressed genes (DEGs) in mouse cortex, striatum, cerebellum and three non-brain tissues, as well as in human neural stem cells and induced glutamatergic neurons revealed that the strongest and most consistent effects occurred within the CNV sequence, with notable instances of differential expression of genes in the immediate vicinity that could reflect position effect. While differential expression of genes outside of chromosome 16p11.2 was largely region, tissue, and cell type-specific, a small but significant minority of such DEGs was shared between brain regions or human cell types. Gene Ontology (GO) enrichment analyses to identify cellular processes dysregulated due to these CNVs found support in select circumstances for terms related to energy metabolism, RNA metabolism, and translation but did not reveal a single universally affected process. Weighted gene co-expression network analysis identified modules that showed significant correlation with reciprocal or individual CNV genotype and better captured shared effects, indicating that energy metabolism, RNA metabolism, translation and protein targeting were disrupted across all three brain regions. The first two of these processes also emerged in the human neural stem cell (NSC) data. A subset of co-expression modules that correlated with CNV genotype revealed significant enrichments for known neurodevelopmental disorder genes, loss-of-function constrained genes, FMRP targets, and chromatin modifiers. Intriguingly, neuronal differentiation of the hiPSCs revealed that both the deletion and duplication CNV resulted in similar deficits in neurite extension and branching and alterations in electrical activity. Finally, generation of cerebral organoid derivatives indicated that the CNVs reciprocally altered the ratio of excitatory and inhibitory GABAergic neurons generated during in vitro neurodevelopment, consistent with a major mechanistic hypothesis for ASD. Collectively, our data suggest that the 16p11.2 RGD involves disruption of multiple biological processes, with a relative impact that is context-specific. Perturbation of individual and multiple genes within the CNV region will be required to dissect single-gene effects, uncover regulatory interactions, and define how each contributes to abnormal neurodevelopment.

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“…We performed replication analysis using the published raw transcriptomic data of cellular models derived from hiPSC with 16p11.2del, including cortex neurons (Roth et al, 2020), dopaminergic neuron (Sundberg et al, 2021), and cortical organoids (1M and 3M refers to 1 Month and 3M organoid) (Urresti et al, 2021). For the neuron cell data (Roth et al, 2020), DAVID gene enrichment analysis showed MAPK3 was involved in 60 out of the 73 enrichment categories.…”

Section: Mapk3 Emerges As Driver Signal Related To Abnormal Developme...mentioning

confidence: 99%

Human iPSC-derived neuron of 16p11.2 deletion reveals haplotype-specific expression of MAPK3 and its contribution to variable NDD phenotypes

Liu

Liang

et al. 2022

Preprint

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Recurrent proximal 16p11.2 deletion (16p11.2del) is risk factor of diverse neurodevelopmental disorders (NDDs) with variable penetrance. Although previous human induced pluripotent stem cell (hiPSs) models of 16p11.2del confirmed disrupted neuron development, it is not known which gene(s) at this interval are mainly responsible for the abnormal cellular phenotypes and how the NDD penetrance is regulated. After haplotype phasing of 16p11.2 region, we generated hiPSCs for two 16p11.2del families with distinct residual haplotypes and variable NDD phenotypes. We also differentiated the hiPSCs to cortical neural cells and demonstrated MAPK3 as a driver signal of 16p11.2 region contributing to the dysfunctions in multiple pathways related to neuron development, which leads to altered morphological or electrophysiological properties in neuron cells. Furthermore, residual haplotype-specific MAPK3 expression was identified in 16p11.2del neuron cells, associating MAPK3 down-expression with the minor allele of the residual haplotype. Ten SNPs of the residual haplotype are mapped as enhancer SNPs (enSNPs) of MAPK3, eight enSNPs were functionally validated by luciferase assays, implying enSNPs contribute to residual haplotype-specific MAPK3 expression via cis-regulation. Finally, the analyses of three different patient cohorts showed that the residual haplotype of 16p11.2del is associated with variable NDD phenotypes.

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16p11.2 deletion is associated with hyperactivation of human iPSC-derived dopaminergic neuron networks and is rescued by RHOA inhibition in vitro

Cited by 42 publications

References 96 publications

Generation of functional posterior spinal motor neurons from hPSCs-derived human spinal cord neural progenitor cells

Generation of functional posterior spinal motor neurons from hPSCs-derived human spinal cord neural progenitor cells

Tissue and cell-type specific molecular and functional signatures of 16p11.2 reciprocal genomic disorder across mouse brain and human neuronal models

Human iPSC-derived neuron of 16p11.2 deletion reveals haplotype-specific expression of MAPK3 and its contribution to variable NDD phenotypes

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