Insights into Autism Spectrum Disorder Genomic Architecture and Biology from 71 Risk Loci

Sex-biased zinc responses modulate ribosomal protein expression, protein synthesis and social defects in Cttnbp2 mutant mice

Autism spectrum disorders (ASD) are neurodevelopmental conditions influenced by genetic mutations, dietary factors, and sex-specific mechanisms, yet the interplay of these factors remains elusive. Here, we investigate the sex-biased responses of mutant mice carrying an ASD-associated mutation in Cttnbp2 to dietary zinc supplementation using behavioral assays, proteomic and bioinformatic analyses, and puromycin pulse labeling to assess protein synthesis. Our results demonstrate that zinc supplementation enhances ribosomal protein expression and protein synthesis and increases the density and size of dendritic spines in male Cttnbp2 mutant mice, alleviating male-biased social deficits. Analyses of neuronal cultures further revealed that neurons, not astrocytes, respond to zinc to enhance protein synthesis. In contrast, female Cttnbp2 mutants exhibit resilience to differential zinc intake, even under zinc deprivation. Elevated mTOR phosphorylation and increased protein levels of translational initiation factors in female brains may provide a protective mechanism, reducing their sensitivity to zinc deficiency. Cttnbp2 mutations heighten male vulnerability to zinc deprivation, impairing social behaviors. These findings highlight zinc-regulated ribosomal protein expression and protein synthesis as critical mediators of sex-specific ASD phenotypes, offering new insights into dietary interventions.

Phenotypic Expansion of Knobloch Syndrome Type 2 in an Individual With a De Novo PAK2 Variant

P21-activated kinase 2 (PAK2) is a serine/threonine kinase essential for a variety of cellular processes including signal transduction, cellular survival, proliferation, and migration. A recent report proposed monoallelic PAK2 variants cause Knobloch syndrome type 2 (KNO2)-a developmental disorder primarily characterized by ocular anomalies. Here, we identified a novel de novo heterozygous missense variant in PAK2, NM_002577.4:c.1273G>A, p.(D425N), by genome sequencing in an individual with features consistent with KNO2. Notable clinical phenotypes observed in this individual were global developmental delay, congenital retinal detachment, mild cerebral ventriculomegaly, hypotonia, failure to thrive, pyloric stenosis, feeding intolerance, patent ductus arteriosus, and mild facial dysmorphism. The p.(D425N) variant lies within the protein kinase domain and is predicted to be functionally damaging by in silico analysis. Previous clinical genetic testing did not report this variant due to unknown relevance of PAK2 variants at the time of testing, highlighting the importance of reanalysis. Our findings substantiate the candidacy of PAK2 variants in KNO2 and expand the KNO2 clinical phenotypic spectrum.

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.

Genomics of schizophrenia, bipolar disorder and major depressive disorder

Schizophrenia, bipolar disorder and major depressive disorder - which are the most common adult disorders requiring psychiatric care - contribute substantially to premature mortality and morbidity globally. Treatments for these disorders are suboptimal, there are no diagnostic pathologies or biomarkers and their pathophysiologies are poorly understood. Novel therapeutic and diagnostic approaches are thus badly needed. Given the high heritability of psychiatric disorders, psychiatry has potentially much to gain from the application of genomics to identify molecular risk mechanisms and to improve diagnosis. Recent large-scale, genome-wide association studies and sequencing studies, together with advances in functional genomics, have begun to illuminate the genetic architectures of schizophrenia, bipolar disorder and major depressive disorder and to identify potential biological mechanisms. Genomic findings also point to the aetiological relationships between different diagnoses and to the relationships between adult psychiatric disorders and childhood neurodevelopmental conditions.

Autism Spectrum Disorder Across the Lifespan

Autism is a neurodevelopmental condition that affects individuals worldwide throughout their lives. Copious advances in research have enhanced our understanding of autism significantly since Dr. Leo Kanner's first description of the condition in 1943. This review aims to provide an overview of our current knowledge of autism, examining its manifestations across age, race, gender, and co-occurring conditions (e.g., intellectual disability) from childhood through adulthood. We also focus on the identification and diagnosis of autism, long-term outcomes with a spotlight on adulthood, and appropriate supports and interventions across different developmental stages for autistic individuals and their families. We stress the importance of a lifespan perspective that considers the evolving needs of individuals with autism as they age, and we highlight the role of longitudinal research.

Presymptomatic Biological, Structural, and Functional Diagnostic Biomarkers of Autism Spectrum Disorder

Autism spectrum disorder (ASD) is a common neurodevelopmental disorder clinically diagnosed by persistent deficits in three areas of social communication and interaction, plus at least two of four types of restricted repetitive behaviors. ASD has been shown to be caused by genetic predisposition and environmental factors; however, the heterogeneity of ASD complicates its diagnosis and treatment. Early behavioral interventions have shown significant benefits, emphasizing the urgent need for reliable diagnostic biomarkers to enhance long-term outcomes. Here we provide a systematic review that outlines current findings on genetic and neurological biomarkers for presymptomatic ASD diagnoses, assessed prior to the observation of behavioral manifestations. Specifically, we offer insights into the mechanisms of presymptomatic neurological, biological, structural, and functional markers for ASD, compare outcomes across studies, and critically assess their limitations and implications. Recent findings highlight genotype-guided therapeutic strategies in animal models, such as dietary zinc supplementation for reversing ASD-associated behaviors by synaptic deficits. However, the differential efficacy based on underlying genotypes, along with challenges in identifying reliable genomic biomarkers prior to symptom onset, indicates the need for further research. Notably, recent advancements in imaging technologies like magnetic resonance imaging, electroencephalography, and pupillometry have shown promising markers in neonates, and at 3 and 9 months old, respectively. Newer developments in magnetoencephalography hardware can facilitate the much-needed infant ASD studies. It is important to note that many of these biomarker findings are preliminary, and further validation for clinical use is required. Continued research is needed to advance the practicality, reliability, and acceptability of these biomarkers to improve ASD diagnosis and treatment strategies.

Review of structural neuroimaging and genetic findings in autism spectrum disorder - a clinical perspective

Autism spectrum disorders (ASDs) are neurodevelopmental conditions characterized by deficits in social relationships and communication and restrictive, repetitive behaviors and interests. ASDs form a heterogeneous group from a clinical and genetic perspective. Currently, ASDs diagnosis is based on the clinical observation of the individual's behavior. The subjective nature of behavioral diagnoses, in the context of ASDs heterogeneity, contributes to significant variation in the age at ASD diagnosis. Early detection has been proved to be critical in ASDs, as early start of appropriate therapeutic interventions greatly improve the outcome for some children. Structural magnetic resonance imaging (MRI) is widely used in the diagnostic work-up of neurodevelopmental conditions, including ASDs, mostly for brain malformations detection. Recently, the focus of brain imaging shifted towards quantitative MRI parameters, aiming to identify subtle changes that may establish early detection biomarkers. ASDs have a strong genetic component; deletions and duplications of several genomic loci have been strongly associated with ASDs risk. Consequently, a multitude of neuroimaging and genetic findings emerged in ASDs in the recent years. The association of gross or subtle changes in brain morphometry and volumes with different genetic defects has the potential to bring new insights regarding normal development and pathomechanisms of various disorders affecting the brain. Still, the clinical implications of these discoveries and the impact of genetic abnormalities on brain structure and function are unclear. Here we review the literature on brain imaging correlated with the most prevalent genomic imbalances in ASD, and discuss the potential clinical impact.

Autism Spectrum Disorder: Genetic Mechanisms and Inheritance Patterns

Autism spectrum disorder (ASD) is a neurodevelopmental disorder that first develops in early childhood and is characterized by restricted interests, activities, and behaviors, as well as difficulties with social interactions and communication. ASD arises from a complex interaction between environmental factors and genetic inheritance, influenced by epigenetic mechanisms. With an estimated heritability of 70-90%, ASD is highly familial, indicating that genetic factors play a significant role in its development. This shows how hundreds of genetic variants contribute to ASD, whose risk effects are highly variable and are often related to other conditions; these genetic alterations are at different levels, which include single gene mutations, monogenic disorders, genomic variants, and chromosomal abnormalities. Copy number variants (CNVs) appear to contribute significantly to understanding the pathogenesis of this complex disease. In some cases, single CNVs in genomic DNA are pathogenic and causative, supporting the hypothesis that some sporadic cases of ASD may result from rare mutations with significant clinical impact. However, in many cases, there are common genomic variants that increase the risk of developing ASD but are insufficient by themselves to determine an ASD phenotype, and rare genomic variants, of various sizes, inherited from a parent or de novo, that can be associated with the ASD phenotype. Therefore, the aim of this review is to deepen the concept of ASD inheritance through the two-hit theory of CNVs, in which the concomitant presence of two alterations could determine the clinical phenotypes, the concept of incomplete penetrance for inherited CNVs with pathogenic clinical significance, and the presence of compound heterozygosity. These aspects represent important mechanisms underlying the pathogenesis of autism, contributing to a better elucidation for the understanding of the genetic contribution to the ASD phenotype.

Molecular genetic testing and cohort analysis of 32 twin pairs with neurodevelopmental disorders-Reporting a novel de novo variant of TET3

Neurodevelopmental disorders (NDDs) pose significant challenges due to their impact on cognitive, social and motor abilities, often rooted in genetic factors such as copy number variations (CNVs) and single nucleotide variantions (SNVs). Molecular genetic testing, advanced due to sequencing technologies, is instrumental in diagnosing NDDs, with twins offering unique perspectives in detecting novel de novo CNVs and SNVs. The study enrolled 32 pairs of twins that underwent molecular genetic testing and comprehensive clinical data collection. Additionally, we analyzed the potential deleterious effects of a novel de novo TET methylcytosine dioxygenase 3 (TET3) variant (c.4927G > A) using western blotting, immunofluorescence assay and enzymatic activity assay. Analyzing simultaneously, the overall detection yield of molecular genetic testing was 17.2% (11/64). Children with disease-related genetic variants had lower total developmental quotients (DQ) than children without disease-related genetic variants. One pair of monozygotic twins carried a novel de novo TET3 variant. Immunostaining assay revealed that while the wildtype TET3 protein was evenly distributed in the nucleus, the variant was concentrated around the nucleus. Anenzymatic assay using corresponding TET2 mutants suggested that the variant has a significantly reduced activity. Taken together, our study elaborated molecular genetic testing results of 32 pairs of twins and found that children with lower developmental levels are prone to possessing identifiable genetic variants. We reported the clinical phenotype of a pair of monozygotic twins carrying a novel de novo TET3 variant and confirmed the detrimental effects of this variant in vitro.

Cortical differences across psychiatric disorders and associated common and rare genetic variants

Genetic studies have identified common and rare variants increasing the risk for neurodevelopmental and psychiatric disorders (NPDs). These risk variants have also been shown to influence the structure of the cerebral cortex. However, it is unknown whether cortical differences associated with genetic variants are linked to the risk they confer for NPDs. To answer this question, we analyzed cortical thickness (CT) and surface area (SA) for common and rare variants associated with NPDs, in ~33000 individuals from the general population and clinical cohorts, as well as ENIGMA summary statistics for 8 NPDs. Rare and common genetic variants increasing risk for NPDs were preferentially associated with total SA, while NPDs were preferentially associated with mean CT. Larger effects on mean CT, but not total SA, were observed in NPD medicated subgroups. At the regional level, genetic variants were preferentially associated with effects in sensorimotor areas, while NPDs showed higher effects in association areas. We show that schizophrenia- and bipolar-disorder-associated SNPs show positive and negative effect sizes on SA suggesting that their aggregated effects cancel out in additive polygenic models. Overall, CT and SA differences associated with NPDs do not relate to those observed across individual genetic variants and may be linked with critical non-genetic factors, such as medication and the lived experience of the disorder.

Integrated multi-omic characterizations of the synapse reveal RNA processing factors and ubiquitin ligases associated with neurodevelopmental disorders

The molecular composition of the excitatory synapse is incompletely defined due to its dynamic nature across developmental stages and neuronal populations. To address this gap, we apply proteomic mass spectrometry to characterize the synapse in multiple biological models, including the fetal human brain and human induced pluripotent stem cell (hiPSC)-derived neurons. To prioritize the identified proteins, we develop an orthogonal multi-omic screen of genomic, transcriptomic, interactomic, and structural data. This data-driven framework identifies proteins with key molecular features intrinsic to the synapse, including characteristic patterns of biophysical interactions and cross-tissue expression. The multi-omic analysis captures synaptic proteins across developmental stages and experimental systems, including 493 synaptic candidates supported by proteomics. We further investigate three such proteins that are associated with neurodevelopmental disorders-Cullin 3 (CUL3), DEAD-box helicase 3 X-linked (DDX3X), and Y-box binding protein-1 (YBX1)-by mapping their networks of physically interacting synapse proteins or transcripts. Our study demonstrates the potential of an integrated multi-omic approach to more comprehensively resolve the synaptic architecture.

Genetic modulation of brain dynamics in neurodevelopmental disorders: the impact of copy number variations on resting-state EEG

Research has shown that many copy number variations (CNVs) increase the risk of neurodevelopmental disorders (e.g., autism, ADHD, schizophrenia). However, little is known about the effects of CNVs on brain development and function. Resting-state electroencephalography (EEG) is a suitable method to study the disturbances of neuronal functioning in CNVs. We aimed to determine whether there are resting-state EEG signatures that are characteristic of children with pathogenic CNVs. EEG resting-state brain activity of 109 CNV carriers (66 deletion carriers, 43 duplication carriers) aged 3 to 17 years was recorded for 4 minutes. To better account for developmental variations, EEG indices (power spectral density and functional connectivity) were corrected with a normative model estimated from 256 Healthy Brain Network controls. Results showed a decreased exponent of the aperiodic activity and a reduced alpha peak frequency in CNV carriers. Additionally, the study showed altered periodic components and connectivity in several frequency bands. Deletion and duplication carriers exhibited a similar overall pattern of deviations in spectral and connectivity measures, although the significance and effect sizes relative to the control group varied across frequency bands. Deletion and duplication carriers can be differentiated by their periodic power in the gamma band and connectivity in the low alpha band, with duplication carriers showing more disrupted alterations than deletion carriers. The distinctive alterations in spectral patterns were found to be most prominent during adolescence. The results suggest that CNV carriers show electrophysiological alterations compared to neurotypical controls, regardless of the gene dosage effect and their affected genomic region. At the same time, while duplications and deletions share common electrophysiological alterations, each exhibits distinct brain alteration signatures that reflect gene dosage-specific effects.

Endothelial PD-1 Regulates Vascular Homeostasis and Oligodendrogenesis during Brain Development

Appropriate vascular and neural development is essential for central nervous system (CNS). Although programmed cell death receptor 1 (PD-1) mediates neurogenesis, its role in cerebrovascular development remains poorly understood. Here, a correlation between cerebral vessels and oligodendrocyte precursor cells (OPCs) is revealed during brain development. The ablation of endothelial PD-1 triggers cortical hypervascularization through excessive angiogenic sprouting, concomitantly driving OPC differentiation. These alterations disrupt blood brain barrier (BBB) maturation, induce dysmyelination, and ultimately result in abnormal behavior in mice. Mechanistically, the loss of endothelial PD-1 suppresses the activity of the Wnt/β-catenin signaling pathway, thereby disrupting normal angiogenesis. Concurrently, it activates the MEK1/2-ERK1/2-GLI1 pathway, leading to increased GREMLIN1 (GREM1) expression. Elevated GREM1 secretion inhibits the BMP/SMAD1/5/SMAD4 signaling cascade in OPCs, which inhibits oligodendrogenesis and myelination. These findings indicate the importance of endothelial cell-intrinsic PD-1 in regulating the oligovascular niche, and suggest potential therapeutic implications for neurological disorders associated with disrupted vascular development.

Deciphering the Role of Shank3 in Dendritic Morphology and Synaptic Function Across Postnatal Developmental Stages in the Shank3B KO Mouse

Autism Spectrum Disorder (ASD) is marked by early-onset neurodevelopmental anomalies, yet the temporal dynamics of genetic contributions to these processes remain insufficiently understood. This study aimed to elucidate the role of the Shank3 gene, known to be associated with monogenic causes of autism, in early developmental processes to inform the timing and mechanisms for potential interventions for ASD. Utilizing the Shank3B knockout (KO) mouse model, we examined Shank3 expression and its impact on neuronal maturation through Golgi staining for dendritic morphology and electrophysiological recordings to measure synaptic function in the anterior cingulate cortex (ACC) across different postnatal stages. Our longitudinal analysis revealed that, while Shank3B KO mice displayed normal neuronal morphology at one week postnatal, significant impairments in dendritic growth and synaptic activity emerged by two to three weeks. These findings highlight the critical developmental window during which Shank3 is essential for neuronal and synaptic maturation in the ACC.

Genetic advances in neurodevelopmental disorders

Neurodevelopmental disorders (NDDs) are a group of highly heterogeneous diseases that affect children's social, cognitive, and emotional functioning. The etiology is complicated with genetic factors playing an important role. During the past decade, large-scale whole exome sequencing (WES) and whole genome sequencing (WGS) have vastly advanced the genetic findings of NDDs. Various forms of variants have been reported to contribute to NDDs, such as de novo mutations (DNMs), copy number variations (CNVs), rare inherited variants (RIVs), and common variation. By far, over 200 high-risk NDD genes have been identified, which are involved in biological processes including synaptic function, transcriptional and epigenetic regulation. In addition, monogenic, oligogenic, polygenetic, and omnigenic models have been proposed to explain the genetic architecture of NDDs. However, the majority of NDD patients still do not have a definitive genetic diagnosis. In the future, more types of risk factors, as well as noncoding variants, are await to be identified, and including their interplay mechanisms are key to resolving the etiology and heterogeneity of NDDs.

Genomic and Transcriptomic Signatures of SETD1A Disruption in Human Excitatory Neuron Development and Psychiatric Disease Risk

Genetic disruption of SETD1A markedly increases the risk for schizophrenia. To elucidate the underlying mechanisms, we generated isogenic organoid models of the developing human cerebral cortex harboring a SETD1A loss-of-function schizophrenia risk mutation. Employing chromatin profiling combined with RNA sequencing, we identified high-confidence SETD1A target genes, analyzed the impact of the mutation on SETD1A binding and transcriptional regulation and validated key findings with orthogonal approaches. Disruption of SETD1A function disturbs the finely tuned temporal gene expression in the excitatory neuron lineage, yielding an aberrant transcriptional program that compromises key regulatory and metabolic pathways essential for neurodevelopmental transitions. Although overall SETD1A binding remains unchanged in mutant neurons, we identified localized alterations in SETD1A binding that correlate with shifts in H3K4me3 levels and gene expression. These changes are enriched at enhancer regions, suggesting that enhancer-regulated genes are especially vulnerable to SETD1A reduction. Notably, target genes with enhancer-bound SETD1A are primarily linked to neuronal functions while those with promoter-bound SETD1A are enriched for basic cellular functions. By mapping the SETD1A binding landscape in excitatory neurons of the human fetal frontal cortex and integrating multimodal neuroimaging and genetic datasets, we demonstrate that the genomic context of SETD1A binding differentially correlates with macroscale brain organization and establish a link between SETD1A-bound enhancers, schizophrenia-associated brain alterations and genetic susceptibility. Our study advances our understanding of the role of SETD1A binding patterns in schizophrenia pathogenesis, offering insights that may guide future therapeutic strategies.

Cullin-RING Ubiquitin Ligases in Neurodevelopment and Neurodevelopmental Disorders

Ubiquitination is a dynamic and tightly regulated post-translational modification essential for modulating protein stability, trafficking, and function to preserve cellular homeostasis. This process is orchestrated through a hierarchical enzymatic cascade involving three key enzymes: the E1 ubiquitin-activating enzyme, the E2 ubiquitin-conjugating enzyme, and the E3 ubiquitin ligase. The final step of ubiquitination is catalyzed by the E3 ubiquitin ligase, which facilitates the transfer of ubiquitin from the E2 enzyme to the substrate, thereby dictating which proteins undergo ubiquitination. Emerging evidence underscores the critical roles of ubiquitin ligases in neurodevelopment, regulating fundamental processes such as neuronal polarization, axonal outgrowth, synaptogenesis, and synaptic function. Mutations in genes encoding ubiquitin ligases and the consequent dysregulation of these pathways have been increasingly implicated in a spectrum of neurodevelopmental disorders, including autism spectrum disorder, intellectual disability, and attention-deficit/hyperactivity disorder. This review synthesizes current knowledge on the molecular mechanisms underlying neurodevelopment regulated by Cullin-RING ubiquitin ligases-the largest subclass of ubiquitin ligases-and their involvement in the pathophysiology of neurodevelopmental disorders. A deeper understanding of these mechanisms holds significant promise for informing novel therapeutic strategies, ultimately advancing clinical outcomes for individuals affected by neurodevelopmental disorders.

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.

Neurobiological Relationships Between Neurodevelopmental Disorders and Mood Disorders

According to the Diagnostic and Statistical Manual of Mental Disorders (DSM-5), neurodevelopmental disorders (NDDs) are a group of conditions that arise early in development and are characterized by deficits in personal, social, academic, or occupational functioning. These disorders frequently co-occur and include conditions such as autism spectrum disorder (ASD) and attention-deficit/hyperactivity disorder (ADHD). Mood disorders (MDs), such as major depressive disorder and bipolar disorder, also pose significant global health challenges due to their high prevalence and substantial impact on quality of life. Emerging evidence highlights overlapping neurobiological mechanisms between NDDs and MDs, including shared genetic susceptibilities, neurotransmitter dysregulation (e.g., dopaminergic and serotonergic pathways), neuroinflammation, and hypothalamic-pituitary-adrenal (HPA) axis dysfunction. Environmental factors such as early-life adversity further exacerbate these vulnerabilities, contributing to the complexity of their clinical presentation and comorbidity. Functional neuroimaging studies reveal altered connectivity in brain regions critical for emotional regulation and executive function, such as the prefrontal cortex and amygdala, across these disorders. Despite these advances, integrative diagnostic frameworks and targeted therapeutic strategies remain underexplored, limiting effective intervention. This review synthesizes current knowledge on the shared neurobiological underpinnings of NDDs and MDs, emphasizing the need for multidisciplinary research, including genetic, pharmacological, and psychological approaches, for unified diagnosis and treatment. Addressing these intersections can improve clinical outcomes and enhance the quality of life for individuals affected by these disorders.

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.

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.

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.

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.

Metal Dyshomeostasis as a Driver of Gut Pathology in Autism Spectrum Disorders

Despite being classified as neurodevelopmental disorders, in recent years, there has been a growing interest in the association between autism spectrum disorders (ASDs) and gut pathology. This comprehensive and systematic review explores a potential mechanism underlying gut pathology in ASDs, including alterations in gut microbiota, intestinal permeability, immune dysregulation, and gastrointestinal (GI) symptoms. Specifically, it delves into the role of toxic and essential metals and their interplay, affecting the development and function of the GI tract. The review also discusses the potential implications of this gut pathology in the development and management of ASDs. Studies have shown that heavy metal exposure, whether through environmental sources or dietary intake, can disrupt the delicate balance of trace elements in the gut. This disruption can adversely affect zinc homeostasis, potentially exacerbating gut pathology in individuals with ASDs. The impaired zinc absorption resulting from heavy metal exposure may contribute to the immune dysregulation, oxidative stress, and inflammation observed in the gut of individuals with ASDs. By shedding light on the multifaceted nature of gut pathology, including the impact of metal dyshomeostasis as a non-genetic factor in ASD, this review underscores the significance of the gut-brain axis in the etiology and management of ASDs.

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.

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.

Differential links in 16p11.2 deletion carriers reveal aberrant connections between large-scale networks

Qualitatively different topographical patterns of connections are thought to underlie individual differences in thought and behavior, particularly at heteromodal association areas. As such, we hypothesized that connections unique to 16p11.2 deletion carriers compared to controls, rather than hyper- or hypo-connectivity, would serve as a better model to explain the cognitive and behavioral changes observed in individuals carrying this autism-risk copy number variation. Using a spatially-unbiased, data-driven approach we found that differential links clustered non-uniformly across the cortex-particularly at the superior temporal gyrus and sulcus, posterior insula, cingulate sulcus, and inferior parietal lobule bilaterally. At these hotspots, altered local connectivity that spanned across the borders of cortical large-scale networks coincided with aberrant distant interconnectivity between large-scale networks. This was most evident between the auditory and the dorsomedial default (DNb) networks-such that greater between-network interconnectivity was associated with greater communication and social impairment. Entangled connectivity between large-scale networks may preclude each network from having the necessary fidelity to operate properly, particularly when the 2 networks have opposing organization principles-namely, local specialization (segregation) versus global coherency (integration).

Signaling in autism: Relevance to nutrients and sex

Autism spectrum disorders (ASD) are substantially heterogeneous neuropsychiatric conditions with over a thousand associated genetic factors and various environmental influences, such as infection and nutrition. Additionally, males are four times more likely than females to be affected. This heterogeneity underscores the need to uncover common molecular features within ASD. Recent studies have revealed interactions among genetic predispositions, environmental factors, and sex that may be critical to ASD etiology. This review focuses on emerging evidence for the impact of nutrients-particularly zinc and amino acids-on ASD, as demonstrated in mouse models and human studies. These nutrients have been shown to influence synaptic signaling, dendritic spine formation, and behaviors linked to autism. Furthermore, sex-based differences in nutritional requirements, especially for zinc and amino acids, may contribute to the observed male bias in autism, indicating that interactions between nutrients and genetic factors could be integral to understanding and potentially mitigating ASD symptoms.

Mapping the Landscape of Autism Research: A Scientometric Review (2011-2023)

This scientometric analysis maps the landscape of autism spectrum disorder (ASD) research between 2011 and 2023. By exploring patterns in publication growth, geographic distribution and institutional involvement, this study highlights evolving research themes, key contributors and collaborative networks. Our findings reveal a marked rise in ASD publications, particularly from 2020 onwards, with the United States, United Kingdom and China leading in contributions and collaborations. Scientometric analysis identifies a shift towards advanced machine learning techniques and neuroimaging in ASD studies, reflecting technological integration in research. Institutional analysis uncovers Vanderbilt University and Yale University as major contributors, with significant citation impacts across their publications. Furthermore, prominent funding sources, including the National Institutes of Health, underscore the critical role of funding in shaping research priorities. This comprehensive scientometric overview not only consolidates current knowledge but also serves as a resource to inform future research directions, enhancing interdisciplinary approaches to ASD understanding and intervention.

Behavioral Phenotypes and Comorbidity in 3q29 Deletion Syndrome: Results from the 3q29 Registry

3q29 deletion syndrome (3q29del) is associated with a significantly increased risk for neurodevelopmental and neuropsychiatric disorders. However, the full spectrum of behavioral phenotypes associated with 3q29del is still evolving. Individuals with 3q29del (n = 96, 60.42% male) or their guardian completed the Achenbach Child or Adult Behavior Checklist (CBCL/ABCL) via the online 3q29 registry (3q29deletion.org). Typically developing controls (n = 57, 49.12% male) were ascertained as a comparison group. We analyzed mean performance on the CBCL/ABCL for individuals with 3q29del and controls across composite, DSM-keyed, and developmental scales; and the relationship between CBCL/ABCL performance and clinical and developmental phenotypes for individuals with 3q29del. Individuals with 3q29del showed significantly elevated behavioral and developmental impairment relative to controls across CBCL/ABCL domains. A substantial proportion of study participants with 3q29del scored in the Borderline or Clinical range for composite and DSM-keyed scales, indicating significant behavioral problems that may require clinical evaluation. We found that the preschool CBCL DSM-keyed autism spectrum problems scale is a potential screening tool for autism spectrum disorder (ASD) for individuals with 3q29del; CBCL/ABCL DSM-keyed scales were not accurate screeners for anxiety disorders or attention-deficit/hyperactivity disorder (ADHD) in our study sample. We identified a high degree of psychiatric comorbidity in individuals with 3q29del, with 60.42% (n = 58) of individuals with 3q29del scoring in the Borderline or Clinical range on two or more DSM-keyed CBCL/ABCL scales. Finally, we found that the degree of developmental delay in participants with 3q29del does not explain the increased behavioral problems observed on the CBCL/ABCL. The CBCL/ABCL can be used as screening tools in populations such as 3q29del, even in the presence of substantial psychiatric comorbidity. These results expand our understanding of the phenotypic spectrum of 3q29del and demonstrate an effective method for recruiting and phenotyping a large sample of individuals with a rare genetic disorder.

Astrocytic-supplied cholesterol drives synaptic gene expression programs in developing neurons and downstream astrocytic transcriptional programs

Astrocytes participate in neuronal synaptic programs that are enriched for genetic associations in schizophrenia and autism spectrum disorders (ASD). To better understand how these co-regulated cellular programs are induced during early neuronal development, we studied astrocytes and iPSC-derived neurons in co-cultures and mono-cultures at 16 time points spanning 0.5 hours to 8 days. We found that upregulation in astrocytes of genes involved in cholesterol biosynthesis preceded the activation of synaptic gene programs in neurons and upregulation of the astrocytic Nrxn1. Neuronal knockdown of key cholesterol receptors led to downregulation of neuronal synaptic genes and induced a robust transcriptional response in the astrocytes, including further upregulation of Nrxn1. This suggests that astrocyte-supplied cholesterol drives these neuronal changes and that bi-directional signalling is occuring. The genes upregulated in neurons were enriched for deleterious variants in schizophrenia and neurodevelopmental disorders, suggesting that their pathogenic effect may be, in part, mediated by reduced buffering capacity for changes in the astrocyte cholesterol supply to neurons. These findings highlight the critical role of astrocyte-neuron interactions in psychiatric and neurodevelopmental disorders, particularly in relation to lipid metabolism and synaptic plasticity.

Diversity and consequences of structural variation in the human genome

The biomedical community is increasingly invested in capturing all genetic variants across human genomes, interpreting their functional consequences and translating these findings to the clinic. A crucial component of this endeavour is the discovery and characterization of structural variants (SVs), which are ubiquitous in the human population, heterogeneous in their mutational processes, key substrates for evolution and adaptation, and profound drivers of human disease. The recent emergence of new technologies and the remarkable scale of sequence-based population studies have begun to crystalize our understanding of SVs as a mutational class and their widespread influence across phenotypes. In this Review, we summarize recent discoveries and new insights into SVs in the human genome in terms of their mutational patterns, population genetics, functional consequences, and impact on human traits and disease. We conclude by outlining three frontiers to be explored by the field over the next decade.

Convergence of autism proteins at the cilium

Hundreds of high-confidence autism genes have been identified, yet the relevant etiological mechanisms remain unclear. Gene ontology analyses have repeatedly identified enrichment of proteins with annotated functions in gene expression regulation and neuronal communication. However, proteins are often pleiotropic and these annotations are inherently incomplete. Our recent autism functional genetics work has suggested that these genes may share a common mechanism at the cilium, a membrane-bound organelle critical for neurogenesis, brain patterning, and neuronal activity-all processes strongly implicated in autism. Moreover, autism commonly co-occurs with conditions that are known to involve ciliary-related pathologies, including congenital heart disease, hydrocephalus, and blindness. However, the role of autism genes at the cilium has not been systematically investigated. Here we demonstrate that autism proteins spanning disparate functional annotations converge in expression, localization, and function at cilia, and that patients with pathogenic variants in these genes have cilia-related co-occurring conditions and biomarkers of disrupted ciliary function. This degree of convergence among genes spanning diverse functional annotations strongly suggests that cilia are relevant to autism, as well as to commonly co-occurring conditions, and that this organelle should be explored further for therapeutic potential.

Generation and Characterization of a Knockout Mouse of an Enhancer of EBF3

Genomic studies of autism and other neurodevelopmental disorders have identified several relevant protein-coding and noncoding variants. One gene with an excess of protein-coding de novo variants is EBF3 that also is the gene underlying the Hypotonia, Ataxia, and Delayed Development Syndrome (HADDS). In previous work, we have identified noncoding de novo variants in an enhancer of EBF3 called hs737 and further showed that there was an enrichment of deletions of this enhancer in individuals with neurodevelopmental disorders. In this present study, we generated a novel mouse line that deletes the highly conserved, orthologous mouse region of hs737 within the Rr169617 regulatory region, and characterized the molecular and phenotypic aspects of this mouse model. This line contains a 1,160 bp deletion within Rr169617 and through heterozygous crosses we found a deviation from Mendelian expectation (p = 0.02) with a significant depletion of the deletion allele (p = 5.8 × 10-4). Rr169617 +/- mice had a reduction of Ebf3 expression by 10% and Rr169617 -/- mice had a reduction of Ebf3 expression by 20%. Differential expression analyses in E12.5 forebrain, midbrain, and hindbrain in Rr169617 +/+ versus Rr169617 -/- mice identified dysregulated genes including histone genes (i.e., Hist1h1e, Hist1h2bk, Hist1h3i, Hist1h2ao) and other brain development related genes (e.g., Chd5, Ntng1). A priori phenotyping analysis (open field, hole board and light/dark transition) identified sex-specific differences in behavioral traits when comparing Rr169617 -/- males versus females; whereby, males were observed to be less mobile, move slower, and spend more time in the dark. Furthermore, both sexes when homozygous for the enhancer deletion displayed body composition differences when compared to wild-type mice. Overall, we show that deletion within Rr169617 reduces the expression of Ebf3 and results in phenotypic outcomes consistent with potential sex specific behavioral differences. This enhancer deletion line provides a valuable resource for others interested in noncoding regions in neurodevelopmental disorders and/or those interested in the gene regulatory network downstream of Ebf3.

The zinc-finger protein POGZ associates with Polycomb repressive complex 1 to regulate bone morphogenetic protein signaling during neuronal differentiation

Polycomb Repressive Complex 1 (PRC1) is a family of epigenetic regulators critical for mammalian development. Elucidating PRC1 composition and function across cell types and developmental stages is key to understanding the epigenetic regulation of cell fate determination. In this study, we discovered POGZ, a prominent Autism Spectrum Disorder (ASD) risk factor, as a novel component of PRC1.6, forming the PRC1.6-POGZ complex. Functional assays revealed that POGZ elicits transcriptional repression that is dependent on RING1B expression. Analysis of publicly available ChIP-Seq data showed that POGZ highly colocalizes with RING1B and HP1γ, two PRC1.6 components, at genes involved in multiple aspects of transcriptional regulation in the embryonic mouse cortex. Although Pogz knockout (KO) does not compromise stem cell pluripotency, Pogz ablation in neuronal progenitor cells (NPCs) led to widespread transcriptomic dysregulation with failed activation of key neuronal genes. Finally, we demonstrated that PRC1.6-POGZ regulates neuronal differentiation by repressing the bone morphogenetic protein (BMP) signaling pathway. These findings reveal a mechanism by which PRC1 and POGZ coordinate transcriptional regulation during neuronal differentiation, which offers insights into how disruptions in this pathway may contribute to neurodevelopmental disorders such as ASD.

Shared rare genetic variants in multiplex autism families suggest a social memory gene under selection

Autism spectrum disorder (ASD) affects up to 1 in 59 children, and is one of the most common neurodevelopmental disorders. Recent genomic studies have highlighted the role of rare variants in ASD. This study aimed to identify genes affected by rare variants shared by siblings with ASD and validate the function of a candidate gene FRRS1L. By integrating the whole genome sequencing data of 866 multiplex families from the Hartwell Foundation's Autism Research and Technology Initiative and Autism Speaks MSSNG project, we identified rare variants shared by two or more siblings with ASD. Using shared rare variants (SRVs), we selected candidate genes for ASD. Gene prioritization by evolutionary features and expression alterations on autism identified FRRS1L in two families, including one with impaired social behaviors. One variant in this family was 6 bp away from human-specific trinucleotide fixation. Additionally, CRISPR/Cas9 experiments demonstrated downregulation by a family variant and upregulation by a fixed site. Population genetics further demonstrated that upregulation of this gene has been favored during human evolution. Various mouse behavioral tests showed that Frrs1l knockout specifically impairs social novelty recognition without altering other behavioral phenotypes. Furthermore, we constructed humanized mice by introducing human sequences into a mouse genome. These knockin mice showed improved abilities to retain social memory over time. The results of our population genetic and evolutionary analyses, behavior experiments, and genome editing propose a molecular mechanism that may confer a selective advantage through social memory enhancement and may cause autism-related social impairment when disrupted in humans. These findings highlight the role of FRRS1L, the AMPA receptor subunit, in social behavior and evolution.

Examining Diagnostic Trends and Gender Differences in the ADOS-II

Approximately 3-4 boys for every girl meet the clinical criteria for autism in studies of community diagnostic patterns and studies of autism using samples of convenience. However, girls with autism have been hypothesized to be underdiagnosed, possibly because they may present with differing symptom profiles as compared to boys. This secondary data analysis used the National Database of Autism Research (NDAR) to examine how gender and symptom profiles are associated with one another in a gold standard assessment of autism symptoms, the Autism Diagnostic Observation Schedule II (ADOS-II; Lord, C., Luyster, R., Guthrie, W., & Pickles A. (2012a). Patterns of developmental trajectories in toddlers with autism spectrum disorder. Journal of Consulting and Clinical Psychology, 80(3):477-489. https://doi.org/10.1037/a0027214 . Epub 2012 Apr 16. PMID: 22506796, PMCID: PMC3365612). ADOS-II scores from 6183 children ages 6-14 years from 78 different studies in the NDAR indicated that gender was a significant predictor of total algorithm, restrictive and repetitive behavioral, and social communicative difficulties composite severity scores. These findings suggest that gender differences in ADOS scores are common in many samples and may reflect on current diagnostic practices.

Hybrid deep learning method to identify key genes in autism spectrum disorder

Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder with a strong genetic component. This research aims to identify key genes associated with autism spectrum disorder using a hybrid deep learning approach. To achieve this, a protein-protein interaction network is constructedand analyzed through a graph convolutional network, which extracts features based on gene interactions. Logistic regression is then employed to predict potential key regulatorgenes using probability scores derived from these features. To evaluate the infection ability of these potential key regulator genes, a susceptible-infected (SI) model, is performed, which reveals the higher infection ability for the genes identified by the proposed method, highlighting its effectiveness in pinpointing key genetic factors associated with ASD. The performance of the proposed method is compared with centrality methods, showing significantly improved results. Identified key genes are further compared with the SFARI gene database and the Evaluation of Autism Gene Link Evidence (EAGLE) framework, revealing commongenes that are strongly associated with ASD. This reinforces the validity of the method in identifying key regulator genes. The proposed method aligns with advancements in therapeutic systems, diagnostics, and neural engineering, providing a robust framework for ASD research and other neurodevelopmental disorders.

Transcriptomic Evidence Reveals the Dysfunctional Mechanism of Synaptic Plasticity Control in ASD

BACKGROUND/OBJECTIVES

A prominent endophenotype in Autism Spectrum Disorder (ASD) is the synaptic plasticity dysfunction, yet the molecular mechanism remains elusive. As a prototype, we investigate the postsynaptic signal transduction network in glutamatergic neurons and integrate single-cell nucleus transcriptomics data from the Prefrontal Cortex (PFC) to unveil the malfunction of translation control.

METHODS

We devise an innovative and highly dependable pipeline to transform our acquired signal transduction network into an mRNA Signaling-Regulatory Network (mSiReN) and analyze it at the RNA level. We employ Cell-Specific Network Inference via Integer Value Programming and Causal Reasoning (CS-NIVaCaR) to identify core modules and Cell-Specific Probabilistic Contextualization for mRNA Regulatory Networks (CS-ProComReN) to quantitatively reveal activated sub-pathways involving MAPK1, MKNK1, RPS6KA5, and MTOR across different cell types in ASD.

RESULTS

The results indicate that specific pivotal molecules, such as EIF4EBP1 and EIF4E, lacking Differential Expression (DE) characteristics and responsible for protein translation with long-term potentiation (LTP) or long-term depression (LTD), are dysregulated. We further uncover distinct activation patterns causally linked to the EIF4EBP1-EIF4E module in excitatory and inhibitory neurons.

CONCLUSIONS

Importantly, our work introduces a methodology for leveraging extensive transcriptomics data to parse the signal transduction network, transforming it into mSiReN, and mapping it back to the protein level. These algorithms can serve as potent tools in systems biology to analyze other omics and regulatory networks. Furthermore, the biomarkers within the activated sub-pathways, revealed by identifying convergent dysregulation, illuminate potential diagnostic and prognostic factors in ASD.

HERVs Endophenotype in Autism Spectrum Disorder: Human Endogenous Retroviruses, Specific Immunoreactivity, and Disease Association in Different Family Members

Increasing evidence indicates that human endogenous retroviruses (HERVs) are important to human health and are an underexplored component of many diseases. Certain HERV families show unique expression patterns and immune responses in autism spectrum disorder (ASD) patients compared to healthy controls, suggesting their potential as biomarkers. Despite these interesting findings, the role of HERVs in ASD needs to be further investigated. In this review, we discuss recent advances in genetic research on ASD, with a particular emphasis on the implications of HERVs on neurodevelopment and future genomic initiatives aimed at discovering ASD-related genes through Artificial Intelligence. Given their pro-inflammatory and autoimmune characteristics, the existing literature suggests that HERVs may contribute to the onset or worsening of ASD in individuals with a genetic predisposition. Therefore, we propose that investigating their fundamental properties could not only improve existing therapies but also pave the way for new therapeutic strategies.

Genetic Variant Analyses Identify Novel Candidate Autism Risk Genes from a Highly Consanguineous Cohort of 104 Families from Oman

Deficits in social communication, restricted interests, and repetitive behaviours are hallmarks of autism spectrum disorder (ASD). Despite high genetic heritability, the majority of clinically diagnosed ASD cases have unknown genetic origins. We performed genome sequencing on mothers, fathers, and affected individuals from 104 families with ASD in Oman, a Middle Eastern country underrepresented in international genetic studies. This approach identified 48 novel candidate genes significantly associated with ASD in Oman. In particular, 35 of these genes have been previously implicated in neurodevelopmental disorders (NDDs) in other populations, underscoring the conserved genetic basis of ASD across ethnicities. Genetic variants within these candidate genes that would impact the encoded protein included 1 insertion, 4 frameshift, 6 splicing, 12 nonsense, and 67 missense changes. Notably, 61% of the SNVs were homozygous, suggesting a prominent recessive genetic architecture for ASD in this unique population. The scarcity of genetic studies on ASD in the Arabian Peninsula has impeded the understanding of the unique genetic landscape of ASD in this region. These findings help bridge this knowledge gap and provide valuable insights into the complex genetic basis of ASD in Oman.

Copy Number Variations and Human Well-Being: Integrating Psychiatric, Physical, and Socioeconomic Perspectives

Copy number variations (CNVs) have emerged as crucial genetic factors that influence a wide spectrum of human health outcomes, with particularly strong associations to psychiatric disorders. In this review, we present a synthesis of diverse impacts of psychiatric disorder-associated CNVs on neurodevelopment, brain function, and physical health across the lifespan. Large-scale studies have revealed that CNV carriers exhibit an increased risk for psychiatric disorders, cognitive deficits, sleep disturbances, neurological disorders, and other physical conditions, including cardiovascular diseases, diabetes, and renal disease, highlighting the wide-ranging impact of CNVs beyond the brain. Neuroimaging studies have revealed substantial CNV effects on brain structure, from cortical and subcortical alterations to white matter microstructure, with effect sizes often exceeding those observed in idiopathic psychiatric disorders. Cellular and animal models have begun to elucidate dynamic CNV effects on neurodevelopment, neuronal function, and cellular energy metabolism, while revealing complex CNV-environment interactions and cell type-specific responses, particularly in studies of 22q11.2 deletion syndrome. This review also explores the complex interplay between psychiatric and physical health conditions in CNV carriers and how these interactions contribute to adverse socioeconomic outcomes, including reduced educational attainment and income levels, creating a feedback loop that further impacts health outcomes. Finally, in this review, we also highlight research limitations and propose key priorities for clinical implementation, including the need for longitudinal studies, standardized guidelines for CNV result reporting and genetic counseling, and integrated care networks to provide a foundation for advancing the field of precision psychiatry.

Molecular diagnosis of 405 individuals with autism spectrum disorder

Autism spectrum disorder (ASD) is caused by combined genetic and environmental factors. Genetic heritability in ASD is estimated as 60-90%, and genetic investigations have revealed many monogenic factors. We analyzed 405 patients with ASD using family-based exome sequencing to detect disease-causing single-nucleotide variants (SNVs), small insertions and deletions (indels), and copy number variations (CNVs) for molecular diagnoses. All candidate variants were validated by Sanger sequencing or quantitative polymerase chain reaction and were evaluated using the American College of Medical Genetics and Genomics/Association for Molecular Pathology guidelines for molecular diagnosis. We identified 55 disease-causing SNVs/indels in 53 affected individuals and 13 disease-causing CNVs in 13 affected individuals, achieving a molecular diagnosis in 66 of 405 affected individuals (16.3%). Among the 55 disease-causing SNVs/indels, 51 occurred de novo, 2 were compound heterozygous (in one patient), and 2 were X-linked hemizygous variants inherited from unaffected mothers. The molecular diagnosis rate in females was significantly higher than that in males. We analyzed affected sibling cases of 24 quads and 2 quintets, but only one pair of siblings shared an identical pathogenic variant. Notably, there was a higher molecular diagnostic rate in simplex cases than in multiplex families. Our simulation indicated that the diagnostic yield is increasing by 0.63% (range 0-2.5%) per year. Based on our simple simulation, diagnostic yield is improving over time. Thus, periodical reevaluation of ES data should be strongly encouraged in undiagnosed ASD patients.

MYT1L deficiency impairs excitatory neuron trajectory during cortical development

Mutations reducing the function of MYT1L, a neuron-specific transcription factor, are associated with a syndromic neurodevelopmental disorder. MYT1L is used as a pro-neural factor in fibroblast-to-neuron transdifferentiation and is hypothesized to influence neuronal specification and maturation, but it is not clear which neuron types are most impacted by MYT1L loss. In this study, we profile 412,132 nuclei from the forebrains of wild-type and MYT1L-deficient mice at three developmental stages: E14 at the peak of neurogenesis, P1 when cortical neurons have been born, and P21 when neurons are maturing, to examine the role of MYT1L levels on neuronal development. MYT1L deficiency disrupts cortical neuron proportions and gene expression, primarily affecting neuronal maturation programs. Effects are mostly cell autonomous and persistent through development. While MYT1L can both activate and repress gene expression, the repressive effects are most sensitive to haploinsufficiency, likely mediating MYT1L syndrome. These findings illuminate MYT1L's role in orchestrating gene expression during neuronal development, providing insights into the molecular underpinnings of MYT1L syndrome.

Large-scale metagenomic analysis of oral microbiomes reveals markers for autism spectrum disorders

The link between the oral microbiome and neurodevelopmental disorders remains a compelling hypothesis, still requiring confirmation in large-scale datasets. Leveraging over 7000 whole-genome sequenced salivary samples from 2025 US families with children diagnosed with autism spectrum disorders (ASD), our cross-sectional study shows that the oral microbiome composition can discriminate ASD subjects from neurotypical siblings (NTs, AUC = 0.66), with 108 differentiating species (q < 0.005). The relative abundance of these species is highly correlated with cognitive impairment as measured by Full-Scale Intelligence Quotient (IQ). ASD children with IQ < 70 also exhibit lower microbiome strain sharing with parents (p < 10-6) with respect to NTs. A two-pronged functional enrichment analysis suggests the contribution of enzymes from the serotonin, GABA, and dopamine degradation pathways to the distinct microbial community compositions observed between ASD and NT samples. Although measures of restrictive eating diet and proxies of oral hygiene show relatively minor effects on the microbiome composition, the observed associations with ASD and IQ may still represent unaccounted-for underlying differences in lifestyle among groups. While causal relationships could not be established, our study provides substantial support to the investigation of oral microbiome biomarkers in ASD.

Modeling antisense oligonucleotide therapy in MECP2 duplication syndrome human iPSC-derived neurons reveals gene expression programs responsive to MeCP2 levels

Genomic copy-number variations (CNVs) that can cause neurodevelopmental disorders often encompass many genes, which complicates our understanding of how individual genes within a CNV contribute to pathology. MECP2 duplication syndrome (MDS or MRXSL in OMIM; OMIM#300260) is one such CNV disorder caused by duplications spanning methyl CpG-binding protein 2 (MECP2) and other genes on Xq28. Using an antisense oligonucleotide (ASO) to normalize MECP2 dosage is sufficient to rescue abnormal neurological phenotypes in mouse models overexpressing MECP2 alone, implicating the importance of increased MECP2 dosage within CNVs of Xq28. However, because MDS CNVs span MECP2 and additional genes, we generated human neurons from multiple MDS patient-derived induced pluripotent cells (iPSCs) to evaluate the benefit of using an ASO against MECP2 in a MDS human neuronal context. Importantly, we identified a signature of genes that is partially and qualitatively modulated upon ASO treatment, pinpointed genes sensitive to MeCP2 function, and altered in a model of Rett syndrome, a neurological disorder caused by loss of MeCP2 function. Furthermore, the signature contained genes that are aberrantly altered in unaffected control human neurons upon MeCP2 depletion, revealing gene expression programs qualitatively sensitive to MeCP2 levels in human neurons. Lastly, ASO treatment led to a partial rescue of abnormal neuronal morphology in MDS neurons. All together, these data demonstrate that ASOs targeting MECP2 benefit human MDS neurons. Moreover, our study establishes a paradigm by which to evaluate the contribution of individual genes within a CNV to pathogenesis and to assess their potential as a therapeutic target.

The pleiotropic spectrum of proximal 16p11.2 CNVs

Recurrent genomic rearrangements at 16p11.2 BP4-5 represent one of the most common causes of genomic disorders. Originally associated with increased risk for autism spectrum disorder, schizophrenia, and intellectual disability, as well as adiposity and head circumference, these CNVs have since been associated with a plethora of phenotypic alterations, albeit with high variability in expressivity and incomplete penetrance. Here, we comprehensively review the pleiotropy associated with 16p11.2 BP4-5 rearrangements to shine light on its full phenotypic spectrum. Illustrating this phenotypic heterogeneity, we expose many parallels between findings gathered from clinical versus population-based cohorts, which often point to the same physiological systems, and emphasize the role of the CNV beyond neuropsychiatric and anthropometric traits. Revealing the complex and variable clinical manifestations of this CNV is crucial for accurate diagnosis and personalized treatment strategies for carrier individuals. Furthermore, we discuss areas of research that will be key to identifying factors contributing to phenotypic heterogeneity and gaining mechanistic insights into the molecular pathways underlying observed associations, while demonstrating how diversity in affected individuals, cohorts, experimental models, and analytical approaches can catalyze discoveries.