In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with autism risk genes

The number of disease risk genes and loci identified through human genetic studies far outstrips the capacity to systematically study their functions. We applied a scalable genetic screening approach, in vivo Perturb-Seq, to functionally evaluate 35 autism spectrum disorder/neurodevelopmental delay (ASD/ND) de novo loss-of-function risk genes. Using CRISPR-Cas9, we introduced frameshift mutations in these risk genes in pools, within the developing mouse brain in utero, followed by single-cell RNA-sequencing of perturbed cells in the postnatal brain. We identified cell type–specific and evolutionarily conserved gene modules from both neuronal and glial cell classes. Recurrent gene modules and cell types are affected across this cohort of perturbations, representing key cellular effects across sets of ASD/ND risk genes. In vivo Perturb-Seq allows us to investigate how diverse mutations affect cell types and states in the developing organism.

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In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with Autism risk genes

10.1101/791525 ◽

2019 ◽

Cited By ~ 7

Author(s):

Xin Jin ◽

Sean K. Simmons ◽

Amy X. Guo ◽

Ashwin S. Shetty ◽

Michelle Ko ◽

...

Keyword(s):

De Novo ◽

Disease Risk ◽

Autism Spectrum ◽

Specific Gene ◽

Functional Evaluation ◽

Loss Of Function ◽

Risk Genes ◽

Biologically Relevant ◽

Relevant Context

AbstractThe thousands of disease risk genes and loci identified through human genetic studies far outstrip our current capacity to systematically study their functions. New experimental approaches are needed for functional investigations of large panels of genes in a biologically relevant context. Here, we developed a scalable genetic screen approach, in vivo Perturb-Seq, and applied this method to the functional evaluation of 35 autism spectrum disorder (ASD) de novo loss-of-function risk genes. Using CRISPR-Cas9, we introduced frameshift mutations in these risk genes in pools, within the developing brain in utero, and then performed single-cell RNA-Seq in the postnatal brain. We identified cell type-specific gene signatures from both neuronal and glial cell classes that are affected by genetic perturbations, and pointed at elements of both convergent and divergent cellular effects across this cohort of ASD risk genes. In vivo Perturb-Seq pioneers a systems genetics approach to investigate at scale how diverse mutations affect cell types and states in the biologically relevant context of the developing organism.

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Integrating de novo and inherited variants in over 42,607 autism cases identifies mutations in new moderate risk genes

10.1101/2021.10.08.21264256 ◽

2021 ◽

Author(s):

Xueya Zhou ◽

Pamela Feliciano ◽

Tianyun Wang ◽

Irina Astrovskaya ◽

Chang Shu ◽

...

Keyword(s):

Genetic Risk ◽

De Novo ◽

Meta Analysis ◽

Neurodevelopmental Disorder ◽

Autism Spectrum ◽

Loss Of Function ◽

Moderate Risk ◽

Full Spectrum ◽

Risk Genes ◽

Biological Parents

AbstractDespite the known heritable nature of autism spectrum disorder (ASD), studies have primarily identified risk genes with de novo variants (DNVs). To capture the full spectrum of ASD genetic risk, we performed a two-stage analysis of rare de novo and inherited coding variants in 42,607 ASD cases, including 35,130 new cases recruited online by SPARK. In the first stage, we analyzed 19,843 cases with one or both biological parents and found that known ASD or neurodevelopmental disorder (NDD) risk genes explain nearly 70% of the genetic burden conferred by DNVs. In contrast, less than 20% of genetic risk conferred by rare inherited loss-of-function (LoF) variants are explained by known ASD/NDD genes. We selected 404 genes based on the first stage of analysis and performed a meta-analysis with an additional 22,764 cases and 236,000 population controls. We identified 60 genes with exome-wide significance (p < 2.5e-6), including five new risk genes (NAV3, ITSN1, MARK2, SCAF1, and HNRNPUL2). The association of NAV3 with ASD risk is entirely driven by rare inherited LoFs variants, with an average relative risk of 4, consistent with moderate effect. ASD individuals with LoF variants in the four moderate risk genes (NAV3, ITSN1, SCAF1, and HNRNPUL2, n = 95) have less cognitive impairment compared to 129 ASD individuals with LoF variants in well-established, highly penetrant ASD risk genes (CHD8, SCN2A, ADNP, FOXP1, SHANK3) (59% vs. 88%, p= 1.9e-06). These findings will guide future gene discovery efforts and suggest that much larger numbers of ASD cases and controls are needed to identify additional genes that confer moderate risk of ASD through rare, inherited variants.

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Haploinsufficiency of autism candidate gene NUAK1 impairs cortical development and behavior

10.1101/262725 ◽

2018 ◽

Author(s):

Virginie Courchet ◽

Amanda J Roberts ◽

Peggy Del Carmine ◽

Tommy L. Lewis ◽

Franck Polleux ◽

...

Keyword(s):

Social Preference ◽

De Novo ◽

Sensorimotor Gating ◽

Learning Task ◽

Autism Spectrum ◽

Dominant Negative ◽

Loss Of Function ◽

Cortical Connectivity

SUMMARYRecently, numerous rare de novo mutations have been identified in children diagnosed with autism spectrum disorders (ASD). However, despite the predicted loss-of-function nature of some of these de novo mutations, the affected individuals are heterozygous carriers, which would suggest that most of these candidate genes are haploinsufficient and/or that these mutations lead to expression of dominant-negative forms of the protein. Here, we tested this hypothesis with the gene Nuak1, recently identified as a candidate ASD gene and that we previously identified for its role in the development of cortical connectivity. We report that Nuak1 is happloinsufficient in mice in regard to its function in cortical axon branching in vitro and in vivo. Nuak1+/− mice show a combination of abnormal behavioral traits ranging from defective memory consolidation in a spatial learning task, defects in social novelty (but not social preference) and abnormal sensorimotor gating and prepulse inhibition of the startle response. Overall, our results demonstrate that Nuak1 haploinsufficiency leads to defects in the development of cortical connectivity and a complex array of behavorial deficits compatible with ASD, intellectual disability and schizophrenia.

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Evolutionary conservation and divergence of human brain co-expression networks

10.1101/2020.06.04.100776 ◽

2020 ◽

Author(s):

WG Pembroke ◽

CL Hartl ◽

DH Geschwind

Keyword(s):

Human Brain ◽

Mouse Models ◽

Disease Modeling ◽

Disease Risk ◽

Sequence Divergence ◽

Cell Types ◽

Regulatory Sequence ◽

Loss Of Function ◽

Regional Patterns

AbstractMouse models have allowed for the direct interrogation of genetic effects on molecular, physiological and behavioral brain phenotypes. However, it is unknown to what extent neurological or psychiatric traits may be human or primate-specific and therefore, which components can be faithfully recapitulated in mouse models. We identify robust co-expression modules reflecting whole brain and regional patterns of gene expression and compare conservation of co-expression in 116 independent data sets derived from human, mouse and non-human primate representing more than 15,000 total samples. We observe greater co-expression changes occurring on the human lineage than mouse, and substantial regional variation that highlights cerebral cortex as the most diverged region. Cell type specific modules are the most divergent across the brain, compared with those that represent basic metabolic processes. Among these, glia are the most divergent, three times that of neurons. We show that regulatory sequence divergence explains a significant fraction of co-expression divergence. Similarly, protein coding sequence constraint parallels co-expression conservation, such that genes with loss of function intolerance are enriched in neuronal, rather than glial modules. We also identify dozens of human disease risk genes, such as COMT, PSEN-1, LRRK2, and SNCA, with highly divergent co-expression between mouse and primates or human. We show that 3D human brain organoids recapitulate in vivo co-expression modules representing several human cell types, which along with our analysis of human-mouse disease gene divergence, serve as a foundational resource to guide disease modeling and its interpretation.

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Single-cell transcriptome identifies molecular subtype of autism spectrum disorder impacted by de novo loss-of-function variants regulating glial cells

Human Genomics ◽

10.1186/s40246-021-00368-7 ◽

2021 ◽

Vol 15 (1) ◽

Author(s):

Nasna Nassir ◽

Asma Bankapur ◽

Bisan Samara ◽

Abdulrahman Ali ◽

Awab Ahmed ◽

...

Keyword(s):

Single Cell ◽

Large Scale ◽

De Novo ◽

Cell Types ◽

Brain Regions ◽

Autism Spectrum ◽

Loss Of Function ◽

Cell Transcriptome ◽

Single Cell Transcriptome ◽

Variant Genes

Abstract Background In recent years, several hundred autism spectrum disorder (ASD) implicated genes have been discovered impacting a wide range of molecular pathways. However, the molecular underpinning of ASD, particularly from the point of view of ‘brain to behaviour’ pathogenic mechanisms, remains largely unknown. Methods We undertook a study to investigate patterns of spatiotemporal and cell type expression of ASD-implicated genes by integrating large-scale brain single-cell transcriptomes (> million cells) and de novo loss-of-function (LOF) ASD variants (impacting 852 genes from 40,122 cases). Results We identified multiple single-cell clusters from three distinct developmental human brain regions (anterior cingulate cortex, middle temporal gyrus and primary visual cortex) that evidenced high evolutionary constraint through enrichment for brain critical exons and high pLI genes. These clusters also showed significant enrichment with ASD loss-of-function variant genes (p < 5.23 × 10–11) that are transcriptionally highly active in prenatal brain regions (visual cortex and dorsolateral prefrontal cortex). Mapping ASD de novo LOF variant genes into large-scale human and mouse brain single-cell transcriptome analysis demonstrate enrichment of such genes into neuronal subtypes and are also enriched for subtype of non-neuronal glial cell types (astrocyte, p < 6.40 × 10–11, oligodendrocyte, p < 1.31 × 10–09). Conclusion Among the ASD genes enriched with pathogenic de novo LOF variants (i.e. KANK1, PLXNB1), a subgroup has restricted transcriptional regulation in non-neuronal cell types that are evolutionarily conserved. This association strongly suggests the involvement of subtype of non-neuronal glial cells in the pathogenesis of ASD and the need to explore other biological pathways for this disorder.

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Biophysical classification of a CACNA1D de novo mutation as a high-risk mutation for a severe neurodevelopmental disorder

Molecular Autism ◽

10.1186/s13229-019-0310-4 ◽

2020 ◽

Vol 11 (1) ◽

Cited By ~ 10

Author(s):

Nadja T. Hofer ◽

Petronel Tuluc ◽

Nadine J. Ortner ◽

Yuliia V. Nikonishyna ◽

Monica L. Fernándes-Quintero ◽

...

Keyword(s):

High Risk ◽

Neurodevelopmental Disorders ◽

Developmental Disorder ◽

De Novo ◽

Disease Risk ◽

Neurodevelopmental Disorder ◽

Autism Spectrum ◽

De Novo Mutation ◽

Loss Of Function ◽

Gain Of Function

Abstract Background There is increasing evidence that de novo CACNA1D missense mutations inducing increased Cav1.3 L-type Ca2+-channel-function confer a high risk for neurodevelopmental disorders (autism spectrum disorder with and without neurological and endocrine symptoms). Electrophysiological studies demonstrating the presence or absence of typical gain-of-function gating changes could therefore serve as a tool to distinguish likely disease-causing from non-pathogenic de novo CACNA1D variants in affected individuals. We tested this hypothesis for mutation S652L, which has previously been reported in twins with a severe neurodevelopmental disorder in the Deciphering Developmental Disorder Study, but has not been classified as a novel disease mutation. Methods For functional characterization, wild-type and mutant Cav1.3 channel complexes were expressed in tsA-201 cells and tested for typical gain-of-function gating changes using the whole-cell patch-clamp technique. Results Mutation S652L significantly shifted the voltage-dependence of activation and steady-state inactivation to more negative potentials (~ 13–17 mV) and increased window currents at subthreshold voltages. Moreover, it slowed tail currents and increased Ca2+-levels during action potential-like stimulations, characteristic for gain-of-function changes. To provide evidence that only gain-of-function variants confer high disease risk, we also studied missense variant S652W reported in apparently healthy individuals. S652W shifted activation and inactivation to more positive voltages, compatible with a loss-of-function phenotype. Mutation S652L increased the sensitivity of Cav1.3 for inhibition by the dihydropyridine L-type Ca2+-channel blocker isradipine by 3–4-fold. Conclusions and limitations Our data provide evidence that gain-of-function CACNA1D mutations, such as S652L, but not loss-of-function mutations, such as S652W, cause high risk for neurodevelopmental disorders including autism. This adds CACNA1D to the list of novel disease genes identified in the Deciphering Developmental Disorder Study. Although our study does not provide insight into the cellular mechanisms of pathological Cav1.3 signaling in neurons, we provide a unifying mechanism of gain-of-function CACNA1D mutations as a predictor for disease risk, which may allow the establishment of a more reliable diagnosis of affected individuals. Moreover, the increased sensitivity of S652L to isradipine encourages a therapeutic trial in the two affected individuals. This can address the important question to which extent symptoms are responsive to therapy with Ca2+-channel blockers.

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BET Bromodomain Degradation As a Therapeutic Strategy in Multiple Myeloma

Blood ◽

10.1182/blood.v128.22.1062.1062 ◽

2016 ◽

Vol 128 (22) ◽

pp. 1062-1062 ◽

Cited By ~ 2

Author(s):

Geoffrey M. Matthews ◽

Sara Gandolfi ◽

Johanna Bruggentheis ◽

Ricardo De Matos Simoes ◽

Dennis L Buckley ◽

...

Keyword(s):

Multiple Myeloma ◽

Caspase 3 ◽

De Novo ◽

Critical Role ◽

Cell Types ◽

Drug Resistant ◽

Loss Of Function ◽

Treatment Naïve

Abstract Multiple myeloma (MM) remains an incurable malignancy with a clear need for novel therapeutic modalities. Moreover, acquired or de novo resistance to established or novel therapeutics remains a major challenge in this, and other, neoplasias. BET Bromodomain inhibitors (BBIs), including JQ1, have potent anti-MM activity in vitro and in in vivo, but do not provide curative outcome and do not induce apoptosis in many tumor cell types. Recently, a "next-generation" BBI, dBET, that causes degradation of BET Bromodomains (BRDs) through CRBN-mediated ubiquitination has been demonstrated to have potent activity in leukemia and myeloma. Here we sought to compare the mechanistic differences between BRD inhibition with BRD degradation in treatment-naive and drug-resistant MM. Additionally, we posited that resistance to dBET treatment could emerge through genetic perturbations and wished to uncover potential mechanisms prior to its clinical utilization. To address this, we compared effects of JQ1 with lead optimized compound dBET6, in a panel of human MM cell lines (± stromal cells), including clones resistant to JQ1, bortezomib and IMIDs, and assessed viability using CS-BLI/CTG assay. RNAseq and reverse phase protein arrays (RPPA) were employed to compare the transcriptional and translational effects of BRD degradation vs. inhibition. Using an open-ended unbiased genome-wide CRISPR (clustered regularly interspaced short palindromic repeats)-associated Cas9 approach, we examined whether we could uncover genes associated with resistance to dBET6. MM1.S cells were transduced with Cas9 and pooled lentiviral particles of the GeCKO library, consisting of 2 pooled sgRNA sub-libraries (~120,000 sgRNAs; targeting ~19,000 genes and ~1800 miRNAs). Using this CRISPR/Cas9-based approach we sought to expedite the isolation of MM cells resistant to dBET6. We treated the pool of cells thrice with dBET (250nM), allowing regrowth between treatments and maintaining a coverage of 1000 cells/sgRNA. dBET6-resistant cells were processed to quantify sgRNA enrichment or depletion, using deep sequencing. We observed dBET6 to have significantly greater potency against MM cells than JQ1, or its combination with lenalidomide, and that MM1S.CRBN-/- cells were resistant to dBET6. Resistance to neither JQ1 nor bortezomib conferred resistance to dBET6. We observed dBET6 to induce rapid and robust (<4hrs) degradation of BRD2, BRD3 and BRD4 and loss of c-MYC protein, compared with JQ1 which caused an apparent increase in BRD4 protein and significantly less c-MYC down-regulation. Interestingly, while dBET6 caused a time-dependent reduction in pro-survival Mcl-1 protein (among others) and increased cleavage of caspase-3/7, JQ1 caused Mcl-1 upregulation and did not induce cleavage of caspase-3/7. As predicted, our CRISPR/Cas9 screen identified significant enrichment of sgRNAs targeting CRBN, as well as several members of the Cullin-RING ligase (CRL) complex, known to play a critical role in E3 ubiquitin ligase activity. Preliminary experiments using individual sgRNAs appear to validate the role the CRL complex in dBET resistance. In summary, our data strongly support the development of dBET for the treatment of treatment-naive and drug-resistant MM. We demonstrate overlapping and distinct mechanisms of action between BRD inhibition vs. degradation and suggest that differential potencies of JQ1 vs. dBET is, at least in part, due to far greater loss of c-MYC and Mcl-1 expression, however further analysis is warranted. Additionally, our results demonstrate that loss of function of CRBN or the CRL complex induces dBET resistance by perturbing dBET-mediated BRD4 degradation. However, it is plausible that additional CRBN/CRL-independent mechanisms of dBET resistance exist that allow cells to survive despite complete degradation of BRDs and this will be a key question to be answered in future studies. Disclosures Bradner: Novartis Institutes for BioMedical Research: Employment.

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CHD8 Regulates Cellular Homeostasis and Neuronal Function Genes Across Multiple Models of CHD8 Haploinsufficiency

10.1101/375238 ◽

2018 ◽

Author(s):

A. Ayanna Wade ◽

Kenneth Lim ◽

Rinaldo Catta-Preta ◽

Alex S. Nord

Keyword(s):

Gene Expression ◽

Gene Regulation ◽

Chromatin Remodeling ◽

De Novo ◽

Autism Spectrum ◽

Loss Of Function ◽

Cell Functions ◽

High Affinity

ABSTRACTThe packaging of DNA into chromatin determines the transcriptional potential of cells and is central to eukaryotic gene regulation. Recent sequencing of patient mutations has linked de novo loss-of-function mutations to chromatin remodeling factors with specific, causal roles in neurodevelopmental disorders. Characterizing cellular and molecular phenotypes arising from haploinsufficiency of chromatin remodeling factors could reveal convergent mechanisms of pathology. Chromodomain helicase DNA binding protein 8 (CHD8) encodes a chromatin remodeling factor gene and has among the highest de novo loss-of-function mutations rates in patients with autism spectrum disorder (ASD). Mutations to CHD8 are expected to drive neurodevelopmental pathology through global disruptions to gene expression and chromatin state, however, mechanisms associated with CHD8 function have yet to be fully elucidated. We analyzed published transcriptomic and epigenomic data across CHD8 in vitro and in vivo knockdown and knockout models to identify convergent mechanisms of gene regulation by CHD8. We found reproducible high-affinity interactions of CHD8 near promoters of genes necessary for basic cell functions and gene regulation, especially chromatin organization and RNA processing genes. Overlap between CHD8 interaction and differential expression suggests that reduced dosage of CHD8 directly relates to decreased expression of these genes. In addition, genes important for neuronal development and function showed consistent dysregulation, though there was a reduced rate and decreased affinity for CHD8 interactions near these genes. This meta-analysis verifies CHD8 as a critical regulator of gene expression and reveals a consistent set of high affinity CHD8 interaction targets observed across human and mouse in vivo and in vitro studies. Our findings highlight novel core functions of CHD8 and indicate direct and downstream gene regulatory impacts that are likely to be associated with neuropathology underlying CHD8-associated neurodevelopmental disorder.

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Single cell transcriptome identifies molecular subtype of autism spectrum disorder impacted by de novo loss of function mutation genes regulating glial cells

10.21203/rs.3.rs-763046/v1 ◽

2021 ◽

Author(s):

Nasna Nassir ◽

Asma Bankapur ◽

Bisan Samara ◽

Abdulrahman Ali ◽

Awab Ahmed ◽

...

Keyword(s):

Autism Spectrum Disorder ◽

Single Cell ◽

Large Scale ◽

De Novo ◽

Cell Types ◽

Brain Regions ◽

Autism Spectrum ◽

Loss Of Function ◽

Cell Transcriptome ◽

Single Cell Transcriptome

Abstract Background In recent years, several hundred autism spectrum disorder (ASD) implicated genes have been discovered impacting a wide range of molecular pathways. However, the molecular underpinning of ASD, particularly from the point of view of ‘brain to behaviour’ pathogenic mechanisms, remains largely unknown. Methods We undertook a study to investigate patterns of spatiotemporal and cell type expression of ASD-implicated genes by integrating large-scale brain single cell transcriptomes (> million cells) and de novo loss of function (LOF) ASD mutations (impacting 852 genes from 40122 cases). Results We identified multiple single cell clusters from three distinct developmental human brain regions (anterior cingulate cortex, middle temporal gyrus and primary visual cortex) that evidenced high evolutionary constraint through enrichment for brain critical exons and high PLi genes. These clusters also showed significant enrichment with ASD loss of function mutation genes (p < 5.23 x 10− 11) that are transcriptionally highly active in prenatal brain regions (visual cortex and dorsolateral prefrontal cortex). Mapping ASD de novo LOF mutated genes into large scale human and mouse brain single cell transcriptome analysis demonstrate enrichment of such genes into neuronal subtypes and are also enriched for subtype of non-neuronal glial cell types (astrocyte, p < 6.40 x 10− 11; oligodendrocyte, p < 1.31 x 10− 09). Conclusion Among the ASD genes enriched with pathogenic de novo LOF mutations (i.e., KANK1, PLXNB1), a subgroup has restricted transcriptional regulation in non-neuronal cell types that are evolutionarily conserved. This association strongly suggests the involvement of subtype of non-neuronal glial cells in the pathogenesis of ASD, and the need to explore other biological pathways for this disorder.

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Cul3 regulates cytoskeleton protein homeostasis and cell migration during a critical window of brain development

10.1101/2020.01.10.902064 ◽

2020 ◽

Author(s):

Jasmin Morandell ◽

Lena A. Schwarz ◽

Bernadette Basilico ◽

Saren Tasciyan ◽

Armel Nicolas ◽

...

Keyword(s):

Neuronal Migration ◽

Motor Coordination ◽

De Novo ◽

Critical Role ◽

Autism Spectrum ◽

Cytoskeletal Proteins ◽

Inhibitory Neurons ◽

Loss Of Function ◽

Proteomic Approach

AbstractDe novo loss of function mutations in the ubiquitin ligase-encoding gene Cullin3 (CUL3) lead to autism spectrum disorder (ASD). Here, we used Cul3 mouse models to evaluate the consequences of Cul3 mutations in vivo. Our results show that Cul3 haploinsufficient mice exhibit deficits in motor coordination as well as ASD-relevant social and cognitive impairments. Cul3 mutant brain displays cortical lamination abnormalities due to defective neuronal migration and reduced numbers of excitatory and inhibitory neurons. In line with the observed abnormal columnar organization, Cul3 haploinsufficiency is associated with decreased spontaneous excitatory and inhibitory activity in the cortex. At the molecular level, employing a quantitative proteomic approach, we show that Cul3 regulates cytoskeletal and adhesion protein abundance in mouse embryos. Abnormal regulation of cytoskeletal proteins in Cul3 mutant neuronal cells results in atypical organization of the actin mesh at the cell leading edge, likely causing the observed migration deficits. In contrast to these important functions early in development, Cul3 deficiency appears less relevant at adult stages. In fact, induction of Cul3 haploinsufficiency in adult mice does not result in the behavioral defects observed in constitutive Cul3 haploinsufficient animals. Taken together, our data indicate that Cul3 has a critical role in the regulation of cytoskeletal proteins and neuronal migration and that ASD-associated defects and behavioral abnormalities are primarily due to Cul3 functions at early developmental stages.

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