Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism

Autism spectrum disorder risk genes have convergent effects on transcription and neuronal firing patterns in primary neurons

Autism spectrum disorder (ASD) is a highly heterogenous neurodevelopmental disorder with numerous genetic risk factors. Notably, a disproportionate number of risk genes encode transcription regulators including transcription factors and proteins that regulate chromatin. Here, we tested the function of nine such ASD-linked transcription regulators by depleting them in primary cultured neurons. We then defined the resulting gene expression disruptions using RNA-sequencing and tested effects on neuronal firing using multielectrode array recordings. We identified shared gene expression signatures across many ASD risk genes that converged on disruption of critical synaptic genes. Fitting with this, we detected drastic disruptions to neuronal firing throughout neuronal maturation. Together, these findings provide evidence that multiple ASD-linked transcriptional regulators disrupt transcription of synaptic genes and have convergent effects on neuronal firing that may contribute to enhanced ASD risk.

Development of the rodent prefrontal cortex: circuit formation, plasticity, and impacts of early life stress

The prefrontal cortex (PFC), located at the anterior region of the cerebral cortex, is a multimodal association cortex essential for higher-order brain functions, including decision-making, attentional control, memory processing, and regulation of social behavior. Structural, circuit-level, and functional abnormalities in the PFC are often associated with neurodevelopmental disorders. Here, we review recent findings on the postnatal development of the PFC, with a particular emphasis on rodent studies, to elucidate how its structural and circuit properties are established during critical developmental windows and how these processes influence adult behaviors. Recent evidence also highlights the lasting effects of early life stress on the PFC structure, connectivity, and function. We explore potential mechanisms underlying these stress-induced alterations, with a focus on epigenetic regulation and its implications for PFC maturation and neurodevelopmental disorders. By integrating these insights, this review provides an overview of the developmental processes shaping the PFC and their implications for brain health and disease.

Upregulated inwardly rectifying K + current-mediated hypoactivity of parvalbumin interneuron underlies autism-like deficits in Bod1-deficient mice

Parvalbumin-positive (PV +) interneuron dysfunction is believed to be linked to autism spectrum disorder (ASD), a neurodevelopmental disorder, characterized by social deficits and stereotypical behaviors. However, the underlying mechanisms of PV + interneuron dysfunction remain largely unclear. Here, we found that a deficiency of biorientation defective 1 ( Bod1) in PV + interneuron led to an ASD-like phenotype in Pvalb-Cre; Bod1 f/f mice. Mechanistically, we identified that Bod1 deficiency induced hypoactivity of PV + interneuron and hyperactivity of calcium/calmodulin-dependent protein kinase Ⅱ alpha (CaMKⅡα) neurons in the medial prefrontal cortex (mPFC), as determined by whole-cell patch-clamp recording. Additionally, it concurrently decreased the power of high gamma oscillation, as assessed by in vivo multi-channel electrophysiological recording. Furthermore, we found that Bod1 deficiency enhanced inwardly rectifying K + current, leading to an increase in the resting membrane potential of PV + interneurons. Importantly, the gain-of-function of Bod1 improved social deficits and stereotypical behaviors in Pvalb-Cre; Bod1 f/f mice. These findings provide mechanistic insights into the PV + interneuron dysfunction and suggest new strategies for developing PV + interneuron therapies for ASD.

Cell-type-specific roles of FOXP1 in the excitatory neuronal lineage during early neocortical murine development

Forkhead box protein P1 (FOXP1), a transcription factor enriched in the neocortex, is associated with autism spectrum disorders (ASDs) and FOXP1 syndrome. Emx1Cre/+;Foxp1fl/fl conditional deletion (Foxp1 conditional knockout [cKO]) in the mouse cortex leads to overall reduced cortex thickness, alterations in cortical lamination, and changes in the relative thickness of cortical layers. However, the developmental and cell-type-specific mechanisms underlying these changes remained unclear. We find that Foxp1 deletion results in accelerated pseudo-age during early neurogenesis, increased cell cycle exit during late neurogenesis, altered gene expression and chromatin accessibility, and selective migration deficits in a subset of upper-layer neurons. These data explain the postnatal differences observed in cortical layers and relative cortical thickness. We also highlight genes regulated by FOXP1 and their enrichment with high-confidence ASD or synaptic genes. Together, these results underscore a network of neurodevelopmental-disorder-related genes that may serve as potential modulatory targets for postnatal modification relevant to ASDs and FOXP1 syndrome.

A CHD8-TRRAP axis facilitates MYC and E2F target gene regulation in human neural stem cells

Mutations in ATP-dependent chromatin remodeler CHD8 cause one of the most frequent monogenetic forms of autism and are associated with brain overgrowth. Nevertheless, the activities of CHD8 in autism-relevant cell types are still poorly understood. Here, we purify the CHD8 protein from human neural stem cells and determine its interaction partners using mass spectrometry. We identify the TRRAP complex, a coactivator of MYC and E2F transcription factors, as a prominent CHD8 interaction partner. CHD8 colocalizes genome-wide with TRRAP and binds together at MYC and E2F target gene promoters in human neural stem cells. Depletion of CHD8 or TRRAP in human neural stem cells shows downregulation of MYC and E2F target genes as the most prominent gene-regulatory events. Depletion of CHD8 diminishes cell-cycle entry into S-phase. MYC and E2F transcription factors are established oncogenes and regulate cell growth. Our results link CHD8 to TRRAP in facilitating the regulation of MYC and E2F target genes in human neural stem cells.

Elucidating neuroepigenetic mechanisms to inform targeted therapeutics for brain disorders

The evolving field of neuroepigenetics provides important insights into the molecular foundations of brain function. Novel sequencing technologies have identified patient-specific mutations and gene expression profiles involved in shaping the epigenetic landscape during neurodevelopment and in disease. Traditional methods to investigate the consequences of chromatin-related mutations provide valuable phenotypic insights but often lack information on the biochemical mechanisms underlying these processes. Recent studies, however, are beginning to elucidate how structural and/or functional aspects of histone, DNA, and RNA post-translational modifications affect transcriptional landscapes and neurological phenotypes. Here, we review the identification of epigenetic regulators from genomic studies of brain disease, as well as mechanistic findings that reveal the intricacies of neuronal chromatin regulation. We then discuss how these mechanistic studies serve as a guideline for future neuroepigenetics investigations. We end by proposing a roadmap to future therapies that exploit these findings by coupling them to recent advances in targeted therapeutics.

Characterizing Rare DNA Copy-Number Variants in Pediatric Obsessive-Compulsive Disorder

OBJECTIVE

Pediatric obsessive-compulsive disorder (OCD) is a common neuropsychiatric disorder in which genetic factors play an important role. Recent studies have demonstrated an enrichment of rare de novo DNA single-nucleotide variants in persons with OCD compared to controls, and larger studies have examined copy-number variants (CNVs) using microarray data. Our study examines rare de novo CNVs using whole-exome sequencing (WES) data to provide additional insight into genetic factors and biological processes underlying OCD.

METHOD

We detected CNVs using whole-exome DNA sequencing (WES) data from 183 OCD trio families (unaffected parents and children with OCD) and 771 control families to test the hypothesis that rare de novo CNVs are enriched in persons with OCD compared to controls. Our primary analysis used the eXome-Hidden Markov Model (XHMM) to identify CNVs in silico. We performed burden analyses comparing persons with OCD vs controls and downstream biological systems analyses of CNVs in probands with OCD. We then used a second algorithm (GATK-gCNV) to confirm our primary analysis.

RESULTS

Our findings demonstrate a higher rate of rare de novo CNVs detected by WES in persons with OCD (0.07 CNVs per proband) compared to controls (0.005) (corrected rate ratio = 11.7 95% CI = 3.6-50.0, p = 4.00×10-6). We confirmed this enrichment using GATK-gCNV. The majority of these rare de novo CNVs in persons with OCD are predicted to be pathogenic or likely pathogenic, and an examination of genes disrupted by rare de novo CNVs in persons with OCD finds enrichment of several Gene Ontology sets.

CONCLUSION

This study shows for the first time an enrichment of rare de novo CNVs detected by WES in OCD, complementing previous, larger CNV studies and providing additional insight into genetic factors underlying OCD risk.

The interplay between genomic copy number variants, sleep, and cognition in the general population

Genomic Copy Number variants (CNVs) increase risk for neurodevelopmental disorders (NDDs) and affect cognition, but their impact on sleep remains understudied despite the well-established link between sleep disturbances, NDDs, and cognition. We investigated the relationship between CNVs, sleep traits, cognitive ability, and executive function in 498,852 individuals from an unselected population in the UK Biobank. We replicated the U-shape relationship between measures of cognitive ability and sleep duration. The effects of CNVs on sleep duration were evident at the genome-wide level; CNV-burden analyses showed that overall, CNVs with an increasing number of intolerant genes were associated with increased or decreased sleep duration in a U-shape pattern (p < 2e-16), but did not increase risk of insomnia. Sleep duration only marginally mediated the robust association between CNVs and poorer cognitive performance, suggesting that sleep and cognitive phenotypes may result from pleiotropic effects of CNVs with minimal causal relationship.

Is There a Core Deficit in Autism Spectrum Disorder? An Analysis of CPEP-3 Assessment Data from 543 Children With Autism

Identifying a "core deficit" is essential for early detection and intervention in developmental disorders among children. However, the presence of a core deficit within autism spectrum disorder (ASD) continues to be unclear. Therefore, the purpose of this study was to examine the possibility of the core deficit in autism spectrum disorders. This study evaluated 543 children diagnosed with ASD by using Chinese version of the Psychoeducational Profile-Third Edition (CPEP-3). Structural equation modeling (SEM) was used to construct single-factor models (assuming the presence of a core deficit) and a multi-factor model (assuming the absence of core deficits) based on the assessed data, and then to compare the fit of the two types of models. Assessments revealed developmental delays and adaptive challenges among the children with ASD. The single-factor model assuming the "motor" domain as the "core deficit" showed a superior fit (CFI = 0.86, AIC = 356.47, ECVI = 0.66) than other single-factor models. The multi-factor model, which assumes no core deficit, provided a better fit and greater predictive accuracy (CFI = 0.87, AIC = 351.94, ECVI = 0.65) than all single-factor models. ASD is characterized by widespread developmental delays and adaptive challenges. While motor impairment may serve as an effective predictor of these issues, it does not fully account for the diverse and complex symptomatology observed in children with ASD. The symptoms in these children likely arise from multiple factors, which are not adequately explained by a single core deficit model.

Kismet/CHD7/CHD8 affects gut microbiota, mechanics, and the gut-brain axis in Drosophila melanogaster

The gut microbiome affects brain and neuronal development and may contribute to the pathophysiology of neurodevelopmental disorders. However, it is unclear how risk genes associated with such disorders affect gut physiology in a manner that could impact microbial colonization and how the mechanical properties of the gut tissue might play a role in gut-brain bidirectional communication. To address this, we used Drosophila melanogaster with a null mutation in the gene kismet, an ortholog of chromodomain helicase DNA-binding protein (CHD) family members CHD7 and CHD8. In humans, these are risk genes for neurodevelopmental disorders with co-occurring gastrointestinal symptoms. We found that kismet mutant flies have a significant increase in gastrointestinal transit time, indicating the functional homology of kismet with CHD7/CHD8 in vertebrates. Rheological characterization of dissected gut tissue revealed significant changes in the mechanics of kismet mutant gut elasticity, strain stiffening behavior, and tensile strength. Using 16S rRNA metagenomic sequencing, we also found that kismet mutants have reduced diversity and abundance of gut microbiota at every taxonomic level. To investigate the connection between the gut microbiome and behavior, we depleted gut microbiota in kismet mutant and control flies and quantified the flies' courtship behavior. Depletion of gut microbiota rescued courtship defects of kismet mutant flies, indicating a connection between gut microbiota and behavior. In striking contrast, depletion of the gut microbiome in the control strain reduced courtship activity, demonstrating that antibiotic treatment can have differential impacts on behavior and may depend on the status of microbial dysbiosis in the gut prior to depletion. We propose that Kismet influences multiple gastrointestinal phenotypes that contribute to the gut-microbiome-brain axis to influence behavior. We also suggest that gut tissue mechanics should be considered as an element in the gut-brain communication loop, both influenced by and potentially influencing the gut microbiome and neurodevelopment.

Shank3 modulates Rpl3 expression and protein synthesis via mGlu5: implications for Phelan McDermid syndrome

Mutations or deletions in the SHANK3 gene have been identified in up to 1% of autism spectrum disorder cases and are considered the primary cause of neuropsychiatric symptoms in Phelan McDermid syndrome (PMS). While synaptic dysfunctions have been extensively documented in the absence of Shank3, other mechanisms through which Shank3 may regulate neuronal functions remain unclear. In this study, we report that the ribosomal protein Rpl3 and overall protein synthesis are downregulated in the cortex and striatum of Shank3 knockout (KO) mice and in neurons differentiated from human-induced pluripotent stem cells (hiPSCs) derived from a PMS patient. Moreover, restoring Rpl3 expression in the striatum of Shank3 KO mice was sufficient to rescue protein synthesis and mitigate excessive grooming, suggesting that the behavioral alterations observed in Shank3 KO mice might be, at least in part, caused by Rpl3 downregulation and consequent impaired protein synthesis. Furthermore, we demonstrated that chronic inhibition of mGlu5 is sufficient to reduce Rpl3 expression, which in turn impairs global protein synthesis. Consequently, chronic treatment with VU0409551, a potent and selective mGlu5 positive allosteric modulator, rescues Rpl3 expression and the resulting reduction in protein synthesis, leading to long-lasting improvements in behavioral deficits in Shank3 KO mice Altogether, we propose a new role for Shank3 in modulating Rpl3 protein expression, ribosomal function, and protein synthesis by downregulating mGlu5 receptor activity.

Synaptic-dependent developmental dysconnectivity in 22q11.2 deletion syndrome

Chromosome 22q11.2 deletion increases the risk of neuropsychiatric disorders like autism and schizophrenia. Disruption of large-scale functional connectivity in 22q11 deletion syndrome (22q11DS) has been widely reported, but the biological factors driving these changes remain unclear. We used a cross-species design to uncover the developmental trajectory and neural underpinnings of brain dysconnectivity in 22q11DS. In LgDel mice, a model for 22q11DS, we found age-specific patterns of brain dysconnectivity, with widespread fMRI hyperconnectivity in juvenile mice reconfiguring to hippocampal hypoconnectivity over puberty. These changes correlated with developmental alterations in dendritic spine density, and both were transiently normalized by GSK3β inhibition, suggesting a synaptic origin for this phenomenon. Notably, analogous pubertal hyperconnectivity-to-hypoconnectivity reconfiguration occurs in human 22q11DS, affecting cortical regions enriched for GSK3β-associated synaptic genes and autism-relevant transcripts. This dysconnectivity also predicts age-dependent social alterations in 22q11DS individuals. These results suggest that synaptic mechanisms underlie developmental brain dysconnectivity in 22q11DS.

Cntnap2 loss drives striatal neuron hyperexcitability and behavioral inflexibility

Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by two major diagnostic criteria - persistent deficits in social communication and interaction, and the presence of restricted, repetitive patterns of behavior (RRBs). Evidence from both human and animal model studies of ASD suggest that alteration of striatal circuits, which mediate motor learning, action selection, and habit formation, may contribute to the manifestation of RRBs. CNTNAP2 is a syndromic ASD risk gene, and loss of function of Cntnap2 in mice is associated with RRBs. How loss of Cntnap2 impacts striatal neuron function is largely unknown. In this study, we utilized Cntnap2 -/- mice to test whether altered striatal neuron activity contributes to aberrant motor behaviors relevant to ASD. We find that Cntnap2 -/- mice exhibit increased cortical drive of direct pathway striatal projection neurons (dSPNs). This enhanced drive is likely due to increased intrinsic excitability of dSPNs, which make them more responsive to cortical inputs. We find that Cntnap2 -/- mice exhibit spontaneous repetitive behaviors, increased motor routine learning, perseveration, and cognitive inflexibility. Increased corticostriatal drive of the direct pathway may therefore contribute to the acquisition of repetitive, inflexible behaviors in Cntnap2 mice.

SOX7: Autism Associated Gene Identified by Analysis of Multi-Omics Data

Genome-wide association studies and next generation sequencing data analyses based on DNA information have identified thousands of mutations associated with autism spectrum disorder (ASD). However, more than 99% of identified mutations are non-coding. Thus, it is unclear which of these mutations might be functional and thus potentially causal variants. Transcriptomic profiling using total RNA-sequencing has been one of the most utilized approaches to link protein levels to genetic information at the molecular level. The transcriptome captures molecular genomic complexity that the DNA sequence solely does not. Some mutations alter a gene's DNA sequence but do not necessarily change expression and/or protein function. To date, few common variants reliably associated with the diagnosis status of ASD despite consistently high estimates of heritability. In addition, reliable biomarkers used to diagnose ASD or molecular mechanisms to define the severity of ASD do not exist. Therefore, it is necessary to integrate DNA and RNA testing together to identify true causal genes and propose useful biomarkers for ASD. We performed gene-based association studies with adaptive test using genome-wide association studies (GWAS) summary statistics with two large GWAS datasets (ASD 2019 data: 18,382 ASD cases and 27,969 controls [discovery data]; ASD 2017 data: 6,197 ASD cases and 7,377 controls [replication data]) which were obtained from the Psychiatric Genomics Consortium (PGC). In addition, we investigated differential expression between ASD cases and controls for genes identified in gene-based GWAS with two RNA-seq datasets (GSE211154: 20 cases and 19 controls; GSE30573: 3 cases and 3 controls). We identified 5 genes significantly associated with ASD in ASD 2019 data (KIZ-AS1, p=8.67×10-10; KIZ, p=1.16×10-9; XRN2, p=7.73×10-9; SOX7, p=2.22×10-7; LOC101929229 also known as PINX1-DT, p=2.14×10-6). Among these 5 genes, gene SOX7 (p=0.00087) and LOC101929229 (p=0.009) were replicated in ASD 2017 data. KIZ-AS1 (p=0.059) and KIZ (p=0.06) were close to the boundary of replication in ASD 2017 data. Genes SOX7 (p=0.036 in all samples; p=0.044 in white samples) indicated significant expression differences between cases and controls in the GSE211154 RNA-seq data. Furthermore, gene SOX7 was upregulated in cases than in controls in the GSE30573 RNA-seq data (p=0.0017; Benjamini-Hochberg adjusted p=0.0085). SOX7 encodes a member of the SOX (SRY-related HMG-box) family of transcription factors pivotally contributing to determining of the cell fate and identity in many lineages. The encoded protein may act as a transcriptional regulator after forming a protein complex with other proteins leading to autism. Gene SOX7 in the transcription factor family could be associated with ASD. This finding may provide new diagnostic and therapeutic strategies for ASD.

Perirhinal cortex abnormalities impair hippocampal plasticity and learning in Scn2a, Fmr1, and Cdkl5 autism mouse models

Learning and memory deficits, including spatial navigation difficulties, are common in autism spectrum disorder (ASD). Several ASD mouse models (Scn2a+/-, Fmr1-/-, Cdkl5-/-) exhibit impaired spatial learning, with these deficits often attributed to hippocampal dysfunction. However, we identify the perirhinal cortex (PRC) as a critical driver of these deficits. Cortical-wide Scn2a reduction in excitatory neurons replicated the spatial learning and long-term potentiation (LTP) impairments-a cellular correlate of learning-seen in Scn2a+/- mice, while hippocampal-wide reduction did not. PRC-specific viral-mediated Scn2a reduction in excitatory neurons decreased release probability, which consequently disrupted synaptic transmission and LTP in the hippocampus, as well as spatial learning. As PRC activity was reduced, chemogenetic activation of the PRC reversed these deficits in Scn2a+/- mice and rescued spatial learning and LTP impairments in Fmr1 and Cdkl5 knockout mice. Thus, in several genetic models of ASD, PRC abnormalities may disrupt hippocampal function to impair learning and memory.

Heterozygosity for neurodevelopmental disorder-associated TRIO variants yields distinct deficits in behavior, neuronal development, and synaptic transmission in mice

Genetic variants in TRIO are associated with neurodevelopmental disorders (NDDs) including schizophrenia (SCZ), autism spectrum disorder (ASD) and intellectual disability. TRIO uses its two guanine nucleotide exchange factor (GEF) domains to activate GTPases (GEF1: Rac1 and RhoG; GEF2: RhoA) that control neuronal development and connectivity. It remains unclear how discrete TRIO variants differentially impact these neurodevelopmental events. Here, we investigate how heterozygosity for NDD-associated Trio variants - +/K1431M (ASD), +/K1918X (SCZ), and +/M2145T (bipolar disorder, BPD) - impact mouse behavior, brain development, and synapse structure and function. Heterozygosity for different Trio variants impacts motor, social, and cognitive behaviors in distinct ways that model clinical phenotypes in humans. Trio variants differentially impact head and brain size, with corresponding changes in dendritic arbors of motor cortex layer 5 pyramidal neurons (M1 L5 PNs). Although neuronal structure was only modestly altered in the Trio variant heterozygotes, we observe significant changes in synaptic function and plasticity. We also identified distinct changes in glutamate synaptic release in +/K1431M and +/M2145T cortico-cortical synapses. The TRIO K1431M GEF1 domain has impaired ability to promote GTP exchange on Rac1, but +/K1431M mice exhibit increased Rac1 activity, associated with increased levels of the Rac1 GEF Tiam1. Acute Rac1 inhibition with NSC23766 rescued glutamate release deficits in +/K1431M variant cortex. Our work reveals that discrete NDD-associated Trio variants yield overlapping but distinct phenotypes in mice, demonstrates an essential role for Trio in presynaptic glutamate release, and underscores the importance of studying the impact of variant heterozygosity in vivo.

Genome-wide prediction of dominant and recessive neurodevelopmental disorder-associated genes

Despite great progress, thousands of neurodevelopmental disorder (NDD) risk genes remain to be discovered. We present a computational approach that accelerates NDD risk gene identification using machine learning. First, we demonstrate that models trained solely on single-cell RNA sequencing data can robustly predict genes implicated in autism spectrum disorder (ASD), developmental and epileptic encephalopathy (DEE), and developmental delay (DD). Notably, we find differences in gene expression patterns of genes with monoallelic and bi-allelic inheritance patterns in the developing human cortex. We then integrate expression data with 300 orthogonal features, including intolerance metrics, protein-protein interaction data, and others, in a semi-supervised machine learning framework (mantis-ml) to train inheritance-specific models for these disorders. The models have high predictive power (area under the receiver operator curves [AUCs]: 0.84-0.95), and the top-ranked genes were up to 2-fold (monoallelic models) and 6-fold (bi-allelic models) more enriched for high-confidence NDD risk genes compared to genic intolerance metrics alone. Additionally, genes ranking in the top decile were 45 to 180 times more likely to have literature support than those in the bottom decile. Collectively, this work provides robust NDD risk gene predictions that can complement large-scale gene discovery efforts and underscores the importance of considering inheritance in gene risk prediction.

Autism gene variants disrupt enteric neuron migration and cause gastrointestinal dysmotility

The co-occurrence of autism and gastrointestinal distress is well-established, yet the molecular underpinnings remain unknown. The identification of high-confidence, large-effect autism genes offers the opportunity to identify convergent, underlying biology by studying these genes in the context of the gastrointestinal system. Here we show that the expression of these genes is enriched in human prenatal gut neurons and their migratory progenitors, suggesting that the development and/or function of these neurons may be disrupted by autism-associated genetic variants, leading to gastrointestinal dysfunction. Here we document the prevalence of gastrointestinal issues in patients with large-effect variants in sixteen autism genes, highlighting dysmotility, consistent with potential enteric neuron dysfunction. Using Xenopus tropicalis, we individually target five of these genes (SYNGAP1, CHD8, SCN2A, CHD2, and DYRK1A) and observe disrupted enteric neuronal progenitor migration for each. Further analysis of DYRK1A reveals that perturbation causes gut dysmotility in vivo, which can be ameliorated by treatment with either of two serotonin signaling modulators, identified by in vivo drug screening. This work suggests that atypical development of enteric neurons contributes to the gastrointestinal distress commonly seen in individuals with autism and that serotonin signaling may be a productive therapeutic pathway.

Molecular signature of primate astrocytes reveals pathways and regulatory changes contributing to human brain evolution

Astrocytes contribute to the development and regulation of the higher-level functions of the brain, the critical targets of evolution. However, how astrocytes evolve in primates is unsettled. Here, we obtain human, chimpanzee, and macaque induced pluripotent stem-cell-derived astrocytes (iAstrocytes). Human iAstrocytes are bigger and more complex than the non-human primate iAstrocytes. We identify new loci contributing to the increased human astrocyte. We show that genes and pathways implicated in long-range intercellular signaling are activated in the human iAstrocytes and partake in controlling iAstrocyte complexity. Genes downregulated in human iAstrocytes frequently relate to neurological disorders and were decreased in adult brain samples. Through regulome analysis and machine learning, we uncover that functional activation of enhancers coincides with a previously unappreciated, pervasive gain of "stripe" transcription factor binding sites. Altogether, we reveal the transcriptomic signature of primate astrocyte evolution and a mechanism driving the acquisition of the regulatory potential of enhancers.

Contribution of autosomal rare and de novo variants to sex differences in autism

Autism is four times more prevalent in males than females. To study whether this reflects a difference in genetic predisposition attributed to autosomal rare variants, we evaluated sex differences in effect size of damaging protein-truncating and missense variants on autism predisposition in 47,061 autistic individuals using a liability model with differing thresholds. Given the sex differences in the rates of cognitive impairment among autistic individuals, we also compared effect sizes of rare variants between individuals with and without cognitive impairment or motor delay. Although these variants mediated different likelihoods of autism with versus without cognitive or motor difficulties, their effect sizes on the liability scale did not differ significantly by sex exome wide or in genes sex-differentially expressed in the cortex. De novo mutations were enriched in genes with male-biased expression in the adult cortex, but these genes did not show a significant sex difference on the liability scale, nor did the liability conferred by these genes differ significantly from other genes with similar loss-of-function intolerance and sex-averaged cortical expression. Exome-wide female bias in de novo protein-truncating mutation rates on the observed scale was driven by high-confidence and syndromic autism-predisposition genes. In summary, autosomal rare and damaging coding variants confer similar liability for autism in females and males.

Structural pathways related to the subventricular zone are decreased in volume with altered microstructure in young adult males with autism spectrum disorder

Autism spectrum disorder is a neurodevelopmental condition characterized by reduced social communication and repetitive behaviors. Altered neurogenesis, including disturbed neuronal migration, has been implicated in autism spectrum disorder. Using diffusion MRI, we previously identified neuronal migration pathways in the human fetal brain and hypothesized that similar pathways persist into adulthood, with differences in volume and microstructural characteristics between individuals with autism spectrum disorder and controls. We analyzed diffusion MRI-based tractography of subventricular zone-related pathways in 15 young adult men with autism spectrum disorder and 18 controls at Massachusetts General Hospital, with validation through the Autism Imaging Data Exchange II dataset. Participants with autism spectrum disorder had reduced subventricular zone pathway volumes and fractional anisotropy compared to controls. Furthermore, subventricular zone pathway volume was positively correlated (r: 0.68; 95% CI: 0.25 to 0.88) with symptom severity, suggesting that individuals with more severe symptoms tended to have larger subventricular zone pathway volumes, normalized by brain size. Analysis of the Autism Imaging Data Exchange cohort confirmed these findings of reduced subventricular zone pathway volumes in autism spectrum disorder. While some of these pathways may potentially include inaccurately disconnected pathways that go through the subventricular zone, our results suggest that diffusion MRI-based tractography pathways anatomically linked to the periventricular region are associated with certain symptom types in adult males with autism spectrum disorder.

Restoration of excitation/inhibition balance enhances neuronal signal-to-noise ratio and rescues social deficits in autism-associated Scn2a-deficiency

Social behavior is critical for survival and adaptation, which is profoundly disrupted in autism spectrum disorders (ASD). Social withdrawal due to information overload was often described in ASD, and it was suspected that increased basal noise, i.e., excessive background neuronal activities in the brain could be a disease mechanism. However, experimental test of this hypothesis is limited. Loss-of-function mutations (deficiency) in SCN2A, which encodes the voltage-gated sodium channel NaV1.2, have been revealed as a leading monogenic cause of profound ASD. Here, we revealed that Scn2a deficiency results in robust and multifaceted social impairments in mice. Scn2a-deficient neurons displayed an increased excitation-inhibition (E/I) ratio, contributing to elevated basal neuronal noise and diminished signal-to-noise ratio (SNR) during social interactions. Notably, the restoration of Scn2a expression in adulthood is able to rescue both SNR and social deficits. By balancing the E/I ratio and reducing basal neuronal firing, an FDA-approved GABAA receptor-positive allosteric modulator improves sociability in Scn2a-deficient mice and normalizes neuronal activities in translationally relevant human brain organoids carrying autism-associated SCN2A nonsense mutation. Collectively, our findings revealed a critical role of the NaV1.2 channel in the regulation of social behaviors, and identified molecular, cellular, and circuitry mechanisms underlying SCN2A-associated disorders.

Biological subtyping of autism via cross-species fMRI

It is frequently assumed that the phenotypic heterogeneity in autism spectrum disorder reflects underlying pathobiological variation. However, direct evidence in support of this hypothesis is lacking. Here, we leverage cross-species functional neuroimaging to examine whether variability in brain functional connectivity reflects distinct biological mechanisms. We find that fMRI connectivity alterations in 20 distinct mouse models of autism (n=549 individual mice) can be clustered into two prominent hypo- and hyperconnectivity subtypes. We show that these connectivity profiles are linked to distinct signaling pathways, with hypoconnectivity being associated with synaptic dysfunction, and hyperconnectivity reflecting transcriptional and immune-related alterations. Extending these findings to humans, we identify analogous hypo- and hyperconnectivity subtypes in a large, multicenter resting state fMRI dataset of n=940 autistic and n=1036 neurotypical individuals. Remarkably, hypo- and hyperconnectivity autism subtypes are replicable across independent cohorts (accounting for 25.1% of all autism data), exhibit distinct functional network architecture, are behaviorally dissociable, and recapitulate synaptic and immune mechanisms identified in corresponding mouse subtypes. Our cross-species investigation, thus, decodes the heterogeneity of fMRI connectivity in autism into distinct pathway-specific etiologies, offering a new empirical framework for targeted subtyping of autism.

CTCF regulates global chromatin accessibility and transcription during rod photoreceptor development

Chromatin architecture facilitates accurate transcription at a number of loci, but it remains unclear how much chromatin architecture is involved in global transcriptional regulation. Previous work has shown that rapid depletion of the architectural protein CTCF in cell culture alters global chromatin organization but results in surprisingly limited gene expression changes. This discrepancy has also been observed when other architectural proteins are depleted, and one possible explanation is that full transcriptional changes are masked by cellular heterogeneity. We tested this idea by performing multiomics analyses with sorted juvenile postmitotic mouse rods, which undergo synchronized development, and we identified CTCF-dependent regulation of global chromatin accessibility and gene expression. CTCF depletion leads to dysregulation of ~20% of the entire transcriptome (>3,000 genes) and ~41% of genome accessibility (>27,000 sites) before any prominent cellular or physiological phenotypes arise. Importantly, these changes are highly enriched for CTCF occupancy at euchromatin, suggesting direct CTCF binding and transcriptional regulation at these active loci. CTCF mainly promotes chromatin accessibility and frequently inhibits expression of these direct binding targets, which are enriched for binding motifs of transcription repressors. These findings provide different and sometimes opposite conclusions from previous studies, emphasizing the need to consider cellular heterogeneity and cell-type specificity when performing multiomics analyses. CTCF knockout rods undergo complete degeneration by adulthood, indicating an essential role for their viability. We conclude that the architectural protein CTCF binds chromatin and regulates global chromatin accessibility and transcription during rod development.

A Mutation in the ANK2 Gene Causing ASD and a Review of the Literature

OBJECTIVE

To investigate the clinical and genetic characteristics of patients with ANK2(HGNC:493)-associated autism spectrum disorders (ASDs) and epilepsy (EP).

METHODS

We identified a novel ANK2 variant in a patient with ASD and EP and summarized the clinical and genetic characteristics of ANK2 gene variants in this patient and those in previous reports.

RESULTS

A novel nonsense variant, ANK2 (NM_001148.6):c.3007C>T/p.R1003* in exon 27, was identified in one patient. We described the clinical features and molecular genetics of this patient and previously reported patients. This was discovered at a follow-up visit to the pediatric neurology department where genetic testing based on condition identified this rare genetic variant. He mainly presents with language delay, intellectual disability, limited learning, and communication skills, and later develops seizures, combined with common childhood neurological disorders such as hyperactivity, behavioral abnormalities, and even self-injury. The patient cohort included 16 patients with a complex array of neurological disabilities: ASD (9 patients); EP (10 patients); ASD with EP (4 patients); intellectual disability and developmental delay (5 patients); poor language communication (11 patients); language and learning impairment (11 patients); anxiety/agitation mood disorder (6 patients); attention-deficit/hyperactivity disorder (5 patients); cognitive, memory, and adaptability deficits (1 patient); tic disorder (1 patient); electrocardiogram and cardiac damage (1 patient); and abnormal electroencephalography (EEG) (9 patients).

CONCLUSION

For the first time, we identified a novel variant of the ANK2 gene in China, broadening the genetic spectrum of the ANK2 gene. ANK2 gene mutations can cause ASD, EP, ASD with EP, developmental delay and intellectual disability, poor language communication skills, language and learning disorders, anxiety/agitation mood disorder, and attention-deficit/hyperactivity disorder. Clinical ASD, EP, common EP should consider the ANK2 gene mutation.

Genetic variants and phenotypic data curated for the CAGI6 intellectual disability panel challenge

Neurodevelopmental disorders (NDDs) are common conditions including clinically diverse and genetically heterogeneous diseases, such as intellectual disability, autism spectrum disorders, and epilepsy. The intricate genetic underpinnings of NDDs pose a formidable challenge, given their multifaceted genetic architecture and heterogeneous clinical presentations. This work delves into the intricate interplay between genetic variants and phenotypic manifestations in neurodevelopmental disorders, presenting a dataset curated for the Critical Assessment of Genome Interpretation (CAGI6) ID Panel Challenge. The CAGI6 competition serves as a platform for evaluating the efficacy of computational methods in predicting phenotypic outcomes from genetic data. In this study, a targeted gene panel sequencing has been used to investigate the genetic causes of NDDs in a cohort of 415 paediatric patients. We identified 60 pathogenic and 49 likely pathogenic variants in 102 individuals that accounted for 25% of NDD cases in the cohort. The most mutated genes were ANKRD11, MECP2, ARID1B, ASH1L, CHD8, KDM5C, MED12 and PTCHD1 The majority of pathogenic variants were de novo, with some inherited from mildly affected parents. Loss-of-function variants were the most common type of pathogenic variant. In silico analysis tools were used to assess the potential impact of variants on splicing and structural/functional effects of missense variants. The study highlights the challenges in variant interpretation especially in cases with atypical phenotypic manifestations. Overall, this study provides valuable insights into the genetic causes of NDDs and emphasises the importance of understanding the underlying genetic factors for accurate diagnosis, and intervention development in neurodevelopmental conditions.

Multi-omic analysis of the ciliogenic transcription factor RFX3 reveals a role in promoting activity-dependent responses via enhancing CREB binding in human neurons

Heterozygous loss-of-function (LoF) variants in RFX3, a transcription factor known to play key roles in ciliogenesis, result in autism spectrum disorder (ASD) and neurodevelopmental delay. RFX binding motifs are also enriched upstream of genes found to be commonly dysregulated in transcriptomic analyses of brain tissue from individuals with idiopathic ASD. Still, the precise functions of RFX3 in the human brain is unknown. Here, we studied the impact of RFX3 deficiency using human iPSC-derived neurons and forebrain organoids. Biallelic loss of RFX3 disrupted ciliary gene expression and delayed neuronal differentiation, while monoallelic loss of RFX3 did not. Instead, transcriptomic and DNA binding analyses demonstrated that monoallelic RFX3 loss disrupted synaptic target gene expression and diminished neuronal activity-dependent gene expression. RFX3 binding sites co-localized with CREB binding sites near activity-dependent genes, and RFX3 deficiency led to decreased CREB binding and impaired induction of CREB targets in response to neuronal depolarization. This study demonstrates a novel role of the ASD-associated gene RFX3 in shaping neuronal synaptic development and plasticity.

A Hypothesis: Metabolic Contributions to 16p11.2 Deletion Syndrome

16p11.2 deletion syndrome is a severe genetic disorder associated with the deletion of 27 genes from a Copy Number Variant region on human chromosome 16. Symptoms associated include cognitive impairment, language and motor delay, epilepsy or seizures, psychiatric disorders, autism spectrum disorder (ASD), changes in head size and body weight, and dysmorphic features, with a crucial need to define genes and mechanisms responsible for symptomatology. In this review, we analyze the clinical associations and biological pathways of 16p11.2 locus genes and identify that a majority of 16p11.2 genes relate to metabolic processes. We present a hypothesis in which changes in the dosage of 16p11.2 metabolic genes contribute to pathology through direct or indirect alterations in pathways that include amino acids or proteins, DNA, RNA, catabolism, lipid, energy (carbohydrate). This hypothesis suggests that research into the specific roles of each metabolic gene will help identify useful therapeutic targets.

Mechanistic insights into retinoic-acid treatment for autism in the improvement of social behavior: Evidence from a multi omics study in rats

BACKGROUND

Autism spectrum disorder (ASD) is a lifelong condition. It is characterized by complex etiologies, including disruptions in exogenous retinoic acid (RA) signaling, which may serve as an environmental risk factor. Targeting the RA pathway presents a promising therapeutic avenue, though the precise mechanisms remain to be elucidated.

METHODS

Female Sprague-Dawley rats were treated with valproic acid (VPA) during pregnancy to induce an ASD model in their offspring. Some offspring received RA treatment postnatally. Social behavior and brain-functional connectivity were assessed using behavioral tests and functional magnetic resonance imaging (fMRI), respectively. Transcriptomics analysis and proteomics analysis of the hypothalamus identified differentially expressed genes (DEGs) and differentially expressed proteins (DEPs). These were intersected with ASD pathogenic genes (APGs) and ASD pathogenic proteins (APPs) to identify differentially expressed APGs (DE-APGs) and differentially expressed APPs (DE-APPs), which were validated by real-time reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and western blotting. Analyses of enrichment of signaling pathways were done using the Kyoto Encyclopedia of Genes and Genomes database.

RESULTS

RA treatment significantly improved social behaviors and revealed distinct patterns of hypo- and hyper-connectivity across various brain regions, with notable changes involving the hypothalamus and facial nerve. Differential analysis revealed 4165 DEGs (DEG 1) and 329 DEPs (DEP 1) between control and VPA groups, and 1610 DEGs (DEG 2) and 197 DEPs (DEP 2) between VPA and RA supplementation (RAS) groups. Twenty-two DE-APGs and five DE-APPs were identified, with key associations found between proteins such as Tbl1xr1 and Myo5a and >13 genes including Nrxn1, Cacna1e, and Gabrb2. Significant alterations in DE-APGs, including Grin2b, Nrxn1, Cacna1e, and Gabrb2, were confirmed via real-time RT-PCR and western blotting. In addition, 22 key signaling pathways were enriched in DEPs and DEGs.

CONCLUSION

RA supplementation in ASD rats induced by VPA may ameliorate social deficits and modulated functional connectivity, especially in the hypothalamus and facial nerve regions. This suggests potential therapeutic benefits for neural circuitry dysregulation in ASD. Additionally, RA altered critical gene and protein expressions in hypothalamus, implicating its role in modulating key signaling pathways to mitigate social deficits in ASD. This study provides new insights into the molecular mechanisms of ASD and supports the development of novel therapeutic strategies.

Association Analysis of Rare CNTN5 Variants With Autism Spectrum Disorder in a Japanese Population

BACKGROUND

Contactin-5 (CNTN5), a neural adhesion molecule involved in synaptogenesis and synaptic maturation in the auditory pathway, has been associated with the pathophysiology of autism spectrum disorder (ASD), particularly hyperacusis. To investigate the role of rare CNTN5 variants in ASD susceptibility, we performed resequencing and association analysis in a Japanese population.

METHODS

We resequenced the CNTN5 coding regions in 302 patients with ASD and prioritized rare putatively damaging variants. The prioritized variants were then genotyped in 313 patients with ASD and 1065 controls. Subsequently, we conducted an association study of selected variants with ASD in 614 patients with ASD and 61 057 controls. Clinical data were reviewed for patients carrying prioritized variants.

RESULTS

Through resequencing, we prioritized three rare putatively damaging missense variants (W69G, I227L, and L1000S) in patients with ASD. Although we found a nominally significant association between the I227L variant and ASD, it did not remain significant after post hoc correction. Hyperacusis was found in three out of nine patients carrying prioritized variants.

CONCLUSION

This study does not provide evidence for the contribution of rare CNTN5 variants to the genetic etiology of ASD in the Japanese population.

Cortical Thickness Differences in Autistic Children With and Without Intellectual Disability

Of the 1 in 36 individuals in the United States who are diagnosed with autism spectrum disorder, nearly 40% also have intellectual disability (ID). The cortex has been widely implicated in neural processes underlying autistic behaviors as well as intellectual ability. Thus, neuroimaging features such as cortical thickness are of particular interest as a possible biomarkers of the condition. However, neuroimaging studies often fail to include autistic individuals with ID. As a result, there are few studies of cortical thickness in autistic individuals across the entire range of intellectual abilities. This study used MRI to evaluate cortical thickness in young autistic children (n = 88, mean age 5.37 years) with a large range of intellectual ability (IQ 19-133) as well as nonautistic, nondevelopmentally delayed (referred to here as typically developing [TD]) peers (n = 53, mean age 5.29 years). We first investigated associations between full scale IQ and cortical thickness in both autistic and TD children. Autistic children had significant negative associations (i.e., thinner cortex, higher IQ) in bilateral entorhinal cortex, right fusiform gyrus, superior, middle and inferior temporal gyri, and right temporal pole that were not present in TD children. Significantly thicker cortex was also observed in these regions for autistic children with ID (i.e., IQ ≤ 70) compared with those without. Last, given the reported correspondence between the severity of autism symptoms and intellectual ability, we compared cortical thickness associations with both IQ and ADOS Calibrated Severity Scores and found these patterns overlapped to a significant degree across the cortex.

Untangling the Molecular Mechanisms Contributing to Autism Spectrum Disorder Using Stem Cells

Autism spectrum disorder (ASD) is a complex neuro developmental condition characterized by significant genetic and phenotypic variability, making diagnosis and treatment challenging. The heterogeneity of ASD-associated genetic variants and the absence of clear causal factors in many cases complicate personalized care. Traditional models, such as postmortem brain tissue and animal studies, have provided valuable insights but are limited in capturing the dynamic processes and human-specific aspects of ASD pathology. Recent advances in human induced pluripotent stem cell (iPSC) technology have transformed ASD research by enabling the generation of patient-derived neural cells in both two-dimensional cultures and three-dimensional brain organoid models. These models retain the donor's genetic background, allowing researchers to investigate disease-specific cellular and molecular mechanisms while identifying potential therapeutic targets tailored to individual patients. This commentary highlights how stem cell-based approaches are advancing our understanding of ASD and paving the way for more personalized diagnostic and therapeutic strategies.

Whole-genome sequencing analysis of Japanese autism spectrum disorder trios

AIM

Autism spectrum disorder (ASD) is a genetically and phenotypically heterogeneous neurodevelopmental disorder with a strong genetic basis. Conducting the first comprehensive whole-genome sequencing (WGS) analysis of Japanese ASD trios, this study aimed to elucidate the clinical significance of pathogenic variants and enhance the understanding of ASD pathogenesis.

METHODS

WGS was performed on 57 Japanese patients with ASD and their parents, investigating variants ranging from single-nucleotide variants to structural variants (SVs), short tandem repeats (STRs), mitochondrial variants, and polygenic risk score (PRS).

RESULTS

Potentially pathogenic variants that could explain observed phenotypes were identified in 18 patients (31.6%) overall and in 10 of 23 patients (43.5%) with comorbid intellectual developmental disorder (IDD). De novo variants in PTEN, CHD7, and HNRNPH2 were identified in patients referred for genetic counseling who exhibited previously reported phenotypes, including one patient with ASD who had profound IDD and macrocephaly with PTEN L320S. Analysis of the AlphaFold3 protein structure indicated potential inhibition of intramolecular interactions within PTEN. SV analysis identified deletions in ARHGAP11B and TMLHE. A pathogenic de novo mitochondrial variant was identified in a patient with ASD who had a history of encephalitis and cognitive decline. GO enrichment analysis of genes with nonsense variants and missense variants (Missense badness, PolyPhen-2, and Constraint >1) showed associations with regulation of growth and ATP-dependent chromatin remodeler activity. No reportable results were obtained in the analysis of STR and PRS.

CONCLUSION

Characterizing the comprehensive genetic architecture and phenotypes of ASD is a fundamental step towards unraveling its complex biology.

Review: Dopamine, Serotonin, and the Translational Neuroscience of Aggression in Autism Spectrum Disorder

Objective

Autism spectrum disorder (ASD) is a neurodevelopmental disorder with a 1% to 2% prevalence in children. In addition to social communication deficits and restricted or repetitive behavior, ASD is often characterized by a heightened propensity for aggression. In fact, aggressive behavior is the primary reason for hospitalization in children with ASD, and current treatment options, despite some efficacy, are often associated with prominent side effects. Despite such high clinical toll, the neurobiology of aggression in ASD remains poorly understood.

Method

The neural circuits linked to both ASD and aggression were reviewed, with the goal of identifying overlapping components to help guide future treatment development. In discussing the clinical phenotype of aggression in ASD, some of the triggers and risk factors were noted to differ from those that cause aggression in neurotypical children. Preclinical and clinical studies on the neurobiology of aggression and ASD were synthesized to combine evidence from genetics, neuroimaging, pharmacology, and circuit manipulations. Dopamine and serotonin, 2 neuromodulators that contribute to development and behavioral control, were specifically studied.

Results

The literature indicates that the intricate interplay of the dopamine and serotonin systems has a pivotal role in shaping behavior, including the expression of aggression.

Conclusion

Understanding the balance between dopamine as an accelerator and serotonin as a brake may provide insights into the mechanisms of aggression in children with ASD. Although much work remains to be done, new perspectives promise to bridge the gap between human and animal studies and pinpoint the neurobiology of aggression in ASD.

Diversity & Inclusion Statement

One or more of the authors of this paper self-identifies as a member of one or more historically underrepresented sexual and/or gender groups in science. We actively worked to promote sex and gender balance in our author group.

PTEN mutations impair CSF dynamics and cortical networks by dysregulating periventricular neural progenitors

Enlargement of the cerebrospinal fluid (CSF)-filled brain ventricles (ventriculomegaly) is a defining feature of congenital hydrocephalus (CH) and an under-recognized concomitant of autism. Here, we show that de novo mutations in the autism risk gene PTEN are among the most frequent monogenic causes of CH and primary ventriculomegaly. Mouse Pten-mutant ventriculomegaly results from aqueductal stenosis due to hyperproliferation of periventricular Nkx2.1+ neural progenitor cells (NPCs) and increased CSF production from hyperplastic choroid plexus. Pten-mutant ventriculomegalic cortices exhibit network dysfunction from increased activity of Nkx2.1+ NPC-derived inhibitory interneurons. Raptor deletion or postnatal everolimus treatment corrects ventriculomegaly, rescues cortical deficits and increases survival by antagonizing mTORC1-dependent Nkx2.1+ NPC pathology. Thus, PTEN mutations concurrently alter CSF dynamics and cortical networks by dysregulating Nkx2.1+ NPCs. These results implicate a nonsurgical treatment for CH, demonstrate a genetic association of ventriculomegaly and ASD, and help explain neurodevelopmental phenotypes refractory to CSF shunting in select individuals with CH.

Advancing Mental Health Research Through Strategic Integration of Transdiagnostic Dimensions and Genomics

Genome-wide studies are yielding a growing catalog of common and rare variants that confer risk for psychopathology. However, despite representing unprecedented progress, emerging data also indicate that the full promise of psychiatric genetics-including understanding pathophysiology and improving personalized care-will not be fully realized by targeting traditional dichotomous diagnostic categories. The current article provides reflections on themes that emerged from a 2021 National Institute of Mental Health-sponsored conference convened to address strategies for the evolving field of psychiatric genetics. As anticipated by the National Institute of Mental Health's Research Domain Criteria framework, multilevel investigations of dimensional and transdiagnostic phenotypes, particularly when integrated with biobanks and big data, will be critical to advancing knowledge. The path forward will also require more diverse representation in source studies. Additionally, progress will be catalyzed by a range of converging approaches, including capitalizing on computational methods, pursuing biological insights, working within a developmental framework, and engaging health care systems and patient communities.

Autism spectrum disorder related phenotypes in a mouse model lacking the neuronal actin binding protein profilin 2

Introduction

Profilin 2 (PFN2) is an actin binding protein highly expressed in the brain that participates in actin dynamics. It has been shown in vitro and in vivo that in neurons it functions both post-synaptically to shape and maintain dendritic arborizations and spine density and plasticity, as well as pre-synaptically to regulate vesicle exocytosis. PFN2 was also found in protein complexes with proteins that have been implicated in or are causative of autism spectrum disorder.

Methods

We employ a genetically engineered knock-out mouse line for Pfn2 that we previously generated to study the mouse social, vocal and motor behavior in comparison to wild type control littermates. We also study neuronal physiology in the knock-out mouse model by means of cellular and field electrophysiological recordings in cerebellar Purkinje cells and in the Schaffer collaterals. Lastly, we study anatomical features of the cerebellum using immunofluorescence stainings.

Results

We show that PFN2 deficiency reproduces a number of autistic-like phenotypes in the mouse, such as social behavior impairment, stereotypic behavior, altered vocal communication, and deficits in motor performance and coordination. Our studies correlate the behavioral phenotypes with increased excitation/inhibition ratio in the brain, due to brain-wide hyperactivity of glutamatergic neurons and increased glutamate release not compensated by enhanced GABAergic neurotransmission. Consequently, lack of PFN2 caused seizures behavior and age-dependent loss of cerebellar Purkinje cells, comorbidities observed in a subset of autistic patients, which can be attributed to the effect of excessive glutamatergic neurotransmission.

Discussion

Our data directly link altered pre-synaptic actin dynamics to autism spectrum disorder in the mouse model and support the hypothesis that synaptic dysfunctions that asymmetrically increase the excitatory drive in neuronal circuits can lead to autistic-like phenotypes. Our findings inspire to consider novel potential pathways for therapeutic approaches in ASD.

Clinical and genetic findings in autism spectrum disorders analyzed using exome sequencing

Autism spectrum disorder (ASD) refers to a group of complex neurodevelopmental disorders and is characterized by impaired reciprocal social interaction and communication, as well as the presence of restricted interests and stereotyped and repetitive behaviors. As a complex neurodevelopmental disorder, the phenotype and severity of autism are extremely heterogeneous, with differences from one patient to another. Chromosome microarray (CMA) and fragile X syndrome analyses has been used as a powerful tool to identify new candidate genes for ASD.

METHODS

In the present study, CMA was first used to scan for genome-wide copy number variants in the patient, and no clinically significant copy number variants were found. Exome sequencing (ES) was used for further genetic testing.

RESULTS

ES was performed on 20 subjects. Eighty percent of our sample presented intellectual disability. Other co-occurring clinical conditions included speech disorders, psychomotor delay, the presence of dysmorphic features and medical co-morbidities. A pathogenic variant was identified in 10 patients (ADNP, FBN1, WAC, ASXL3, NR4A2, ALX4, ANKRD1, POGZ, SHANK3 and BPTF). Patients with a positive finding in ES were more likely to present a dysmorphic trunk, more than three dysmorphic features, hypotonia, psychomotor delay and strabismus.

CONCLUSIONS

ES offers expanded diagnostic options for patients with ASD who are negative on CMA. However, further studies are needed for a better understanding of ASD etiology and also the different phenotypes.

Polygenic scores for autism are associated with reduced neurite density in adults and children from the general population

Genetic variants linked to autism are thought to change cognition and behaviour by altering the structure and function of the brain. Although a substantial body of literature has identified structural brain differences in autism, it is unknown whether autism-associated common genetic variants are linked to changes in cortical macro- and micro-structure. We investigated this using neuroimaging and genetic data from adults (UK Biobank, N = 31,748) and children (ABCD, N = 4928). Using polygenic scores and genetic correlations we observe a robust negative association between common variants for autism and a magnetic resonance imaging derived phenotype for neurite density (intracellular volume fraction) in the general population. This result is consistent across both children and adults, in both the cortex and in white matter tracts, and confirmed using polygenic scores and genetic correlations. There were no sex differences in this association. Mendelian randomisation analyses provide no evidence for a causal relationship between autism and intracellular volume fraction, although this should be revisited using better powered instruments. Overall, this study provides evidence for shared common variant genetics between autism and cortical neurite density.

Digenic impairments of haploinsufficient genes in patients with craniosynostosis

Craniosynostosis (CRS) is characterized by the development of abnormal cranial suture ossification and premature fusion. Despite the identification of several associated genetic disorders, the genetic determinants of CRS remain poorly understood. In this study, we conducted integrative analyses on 225 exomes, comprising 121 CRS probands and 104 parental exomes (52 trios). These analyses encompassed de novo and pathogenic variants, and digenic combinations within haploinsufficient genes harboring rare variants. Our analysis unveils a shared molecular network between genes associated with CRS and those linked to skeletal and neurodevelopmental disorders, with a notable enrichment of deleterious variants within haploinsufficient genes. Additionally, we identified a unique digenic pair (IL6ST and TRPS1) within haploinsufficient genes that was present in 2 patients with nonsyndromic CRS but absent in parents or 1,048 population controls. In vitro experiments provided evidence that the identified missense variants were hypomorphs, and accelerated bone mineralization could result from the additive effects of diminished IL6ST and TRPS1 activities in osteoblasts. Overall, our study underscores the important role of rare variations in haploinsufficient genes and suggests that in a subset of undiagnosed patients, the CRS phenotype may arise from multiple genetic variations.

Cell type-specific roles of FOXP1 in the excitatory neuronal lineage during early neocortical murine development

FOXP1, a transcription factor enriched in the neocortex, is associated with autism spectrum disorders (ASD) and FOXP1 syndrome. Emx1 Cre/+ ;Foxp1 fl/fl conditional deletion (Foxp1 cKO) in the mouse cortex leads to overall reduced cortex thickness, alterations in cortical lamination, and changes in the relative thickness of cortical layers. However, the developmental and cell type-specific mechanisms underlying these changes remained unclear. We find that Foxp1 deletion results in accelerated pseudo-age during early neurogenesis, increased cell cycle exit during late neurogenesis, altered gene expression and chromatin accessibility, and selective migration deficits in a subset of upper-layer neurons. These data explain the postnatal differences observed in cortical layers and relative cortical thickness. We also highlight genes regulated by FOXP1 and their enrichment with high-confidence ASD or synaptic genes. Together, these results underscore a network of neurodevelopmental disorder-related genes that may serve as potential modulatory targets for postnatal modification relevant to ASD and FOXP1 syndrome.

Single-cell multiomics of neuronal activation reveals context-dependent genetic control of brain disorders

Despite hundreds of genetic risk loci identified for neuropsychiatric disorders (NPD), most causal variants/genes remain unknown. A major hurdle is that disease risk variants may act in specific biological contexts, e.g., during neuronal activation, which is difficult to study in vivo at the population level. Here, we conducted a single-cell multiomics study of neuronal activation (stimulation) in human iPSC-induced excitatory and inhibitory neurons from 100 donors, and uncovered abundant neuronal stimulation-specific causal variants/genes for NPD. We surveyed NPD-relevant transcriptomic and epigenomic landscape of neuronal activation and identified thousands of genetic variants associated with activity-dependent gene expression (i.e., eQTL) and chromatin accessibility (i.e., caQTL). These caQTL explained considerably larger proportions of NPD heritability than the eQTL. Integrating the multiomic data with GWAS further revealed NPD risk variants/genes whose effects were only detected upon stimulation. Interestingly, multiple lines of evidence support a role of activity-dependent cholesterol metabolism in NPD. Our work highlights the power of cell stimulation to reveal context-dependent "hidden" genetic effects.

A Massively Parallel CRISPR-Based Screening Platform for Modifiers of Neuronal Activity

Understanding the complex interplay between gene expression and neuronal activity is crucial for unraveling the molecular mechanisms underlying cognitive function and neurological disorders. Here, we developed pooled screens for neuronal activity, using CRISPR interference (CRISPRi) and the fluorescent calcium integrator CaMPARI2. Using this screening method, we evaluated 1343 genes for their effect on excitability in human iPSC-derived neurons, revealing potential links to neurodegenerative and neurodevelopmental disorders. These genes include known regulators of neuronal excitability, such as TARPs and ion channels, as well as genes associated with autism spectrum disorder and Alzheimer's disease not previously described to affect neuronal excitability. This CRISPRi-based screening platform offers a versatile tool to uncover molecular mechanisms controlling neuronal activity in health and disease.

Autophosphorylation of the Tousled-like kinases TLK1 and TLK2 regulates recruitment to damaged chromatin via PCNA interaction

Tousled-like kinases 1 and 2 (TLK1 and 2) are cell cycle-regulated serine/threonine kinases that are involved in multiple biological processes. Mutation of TLK1 and 2 confer neurodegenerative diseases. Recent studies demonstrate that TLK1 and 2 are involved in DNA repair. However, there is no direct evidence that TLK1 and 2 function at DNA damage sites. Here, we show that both TLK1 and TLK2 are hyper-autophosphorylated at their N-termini, at least in part, mediated by their homo- or hetero- dimerization. We found that TLK1 and 2 hyper-autophosphorylation suppresses their recruitment to damaged chromatin. Furthermore, both TLK1 and 2 associate with PCNA specifically through their evolutionarily conserved non-canonical PCNA-interacting protein (PIP) box at the N-terminus, and mutation of the PIP-box abolishes their recruitment to DNA damage sites. Mechanistically, the TLK1 and 2 hyper-autophosphorylation masks the PIP-box and negatively regulates their recruitment to the DNA damage site. Overall, our study dissects the detailed genetic regulation of TLK1 and 2 at damaged chromatin, which provides important insights into their emerging roles in DNA repair.

A Robust and Comprehensive Study of the Molecular and Genetic Basis of Neurodevelopmental Delay in a Sample of 3244 Patients, Evaluated by Exome Analysis in a Latin Population

Background and Objectives: Neurodevelopmental disorders (NDDs), including developmental delay (DD), autism spectrum disorder (ASD), intellectual disability (ID), attention-deficit/hyperactivity disorder (ADHD), and specific learning disorders, affect 15% of children and adolescents worldwide. Advances in next-generation sequencing, particularly whole exome sequencing (WES), have improved the understanding of NDD genetics. Methodology: This study analyzed 3244 patients undergoing WES (single, duo, trio analyses), with 1028 meeting inclusion criteria (67% male; aged 0-50 years). Results: Pathogenic (P) or likely pathogenic (LP) variants were identified in 190 patients, achieving a diagnostic yield of 13.4% (singleton), 14% (duo), and 21.2% (trio). A total of 207 P/LP variants were identified in NDD-associated genes: 38% were missense (48 de novo), 29% frameshift (26 de novo), 21% nonsense (14 de novo), 11% splicing site (14 de novo), and 1% inframe (1 de novo). De novo variants accounted for 49.8% of cases, with 86 novels de novo variants and 27 novel non de novo variants unreported in databases like ClinVar or scientific literature. Conclusions: This is the largest study on WES in Colombian children with NDDs and one of the largest in Latino populations. It highlights WES as a cost-effective first-tier diagnostic tool in low-income settings, reducing diagnostic timelines and improving clinical care. These findings underscore the feasibility of implementing WES in underserved populations and contribute significantly to understanding NDD genetics, identifying novel variants with potential for further research and clinical applications.

A general principle of neuronal evolution reveals a human-accelerated neuron type potentially underlying the high prevalence of autism in humans

The remarkable ability of a single genome sequence to encode a diverse collection of distinct cell types, including the thousands of cell types found in the mammalian brain, is a key characteristic of multicellular life. While it has been observed that some cell types are far more evolutionarily conserved than others, the factors driving these differences in evolutionary rate remain unknown. Here, we hypothesized that highly abundant neuronal cell types may be under greater selective constraint than rarer neuronal types, leading to variation in their rates of evolution. To test this, we leveraged recently published cross-species single-nucleus RNA-sequencing datasets from three distinct regions of the mammalian neocortex. We found a strikingly consistent relationship where more abundant neuronal subtypes show greater gene expression conservation between species, which replicated across three independent datasets covering >106 neurons from six species. Based on this principle, we discovered that the most abundant type of neocortical neurons-layer 2/3 intratelencephalic excitatory neurons-has evolved exceptionally quickly in the human lineage compared to other apes. Surprisingly, this accelerated evolution was accompanied by the dramatic down-regulation of autism-associated genes, which was likely driven by polygenic positive selection specific to the human lineage. In sum, we introduce a general principle governing neuronal evolution and suggest that the exceptionally high prevalence of autism in humans may be a direct result of natural selection for lower expression of a suite of genes that conferred a fitness benefit to our ancestors while also rendering an abundant class of neurons more sensitive to perturbation.

Meta-analysis reveals transcription factors and DNA binding domain variants associated with congenital heart defect and orofacial cleft

Many structural birth defect patients lack genetic diagnoses because there are many disease genes as yet to be discovered. We applied a gene burden test incorporating de novo predicted-loss-of-function (pLoF) and likely damaging missense variants together with inherited pLoF variants to a collection of congenital heart defect (CHD) and orofacial cleft (OC) parent-offspring trio cohorts (n = 3,835 and 1,844, respectively). We identified 17 novel candidate CHD genes and 10 novel candidate OC genes, of which many were known developmental disorder genes. Shorter genes were more powered in a "de novo only" analysis as compared to analysis including inherited pLoF variants. TFs were enriched among the significant genes; 14 and 8 transcription factor (TF) genes showed significant variant burden for CHD and OC, respectively. In total, 30 affected children had a de novo missense variant in a DNA binding domain of a known CHD, OC, and other developmental disorder TF genes. Our results suggest candidate pathogenic variants in CHD and OC and their potentially pleiotropic effects in other developmental disorders.

Excitatory/Inhibitory imbalance as a mechanism linking autism and sleep problems

Sleep problems occur more frequently in individuals with autism spectrum disorder (ASD) than in typically developing individuals, and recent studies support a genetic link between ASD and sleep disturbances. However, it remains unclear how sleep problems may be mechanistically connected to ASD phenotypes. A longstanding hypothesis posits that an imbalance between excitatory and inhibitory (E/I) signaling in the brain underlies the behavioral characteristics of ASD. In recent years, emerging evidence has shown that regulation of the E/I ratio is coupled to sleep/wake states in wild-type animal models. In this review, we will explore the idea of altered E/I regulation over the sleep/wake cycle as a mechanism bridging sleep disruption and behavioral phenotypes in ASD.

Roles of ANK2/ankyrin-B in neurodevelopmental disorders: Isoform functions and implications for autism spectrum disorder and epilepsy

The ANK2 gene, encoding ankyrin-B, is a high-confidence risk factor for neurodevelopmental disorders (NDDs). Evidence from exome sequencing studies have repeatedly implicated rare variants in ANK2 in autism spectrum disorder. Recently, the functions of ankyrin-B isoforms on neuronal phenotypes have been investigated using a number of techniques including electrophysiology, proteomic screens and behavioral analysis using animal models with loss of distinct Ank2 isoforms or with targeted loss of Ank2 in different cell types and time points during brain development. ANK2 variants and their pathophysiology could provide valuable insights into the molecular mechanisms underlying NDDs. In this review, we focus on recently reported studies to help understand the pathological mechanisms of ANK2 loss and how it may facilitate the development of treatments for NDDs in the future.

Revisiting the genetic architecture of autism spectrum disorders in the genomic era: Insights from East Asian studies

This review delves into the genetic landscape of Autism Spectrum Disorder (ASD) in the genomic era, with a special focus on insights from East Asian populations. We analyze a spectrum of genetic research, including whole-exome and whole-genome sequencing, to elucidate both the challenges and advancements in comprehending the genetic foundations of ASD. Critical findings from this review highlight the identification of de novo variants, particularly noting the significant role of rare variants that differ from the common variants identified in earlier research. The review emphasizes the importance of large, diverse, and meticulously maintained ASD cohorts, which are essential for advancing genetic studies and developing potential therapeutic interventions. Through collaborative international efforts, we argue for a global perspective necessary to grasp the intricate genetic factors underlying ASD.