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

Maternal-infant probiotic transmission mitigates early-life stress-induced autism in mice

Autism, a disorder influenced by both genetic and environmental factors, presents significant challenges for prevention and treatment. While maternal-infant gut microbiota has been a focus in autism research, preventive strategies targeting maternal gut microbiota remain underexplored. This study demonstrates that prenatal probiotic intake can effectively prevent maternal separation-induced autistic-like behaviors in offspring without altering the embryonic neurodevelopment in mice. Using specific PCR primers and cross-fostering experiments, we traced the vertical transmission of probiotics, primarily via fecal/vaginal contamination. Early probiotic colonization conferred resilience against stress-induced gut pathogenic microbes and Th17-mediated peripheral inflammation while significantly inhibiting hypermyelination and neuroinflammation linked to systemic inflammation. Microbial metabolites like tyrosol and xanthurenic acid alleviated neuroinflammation and hypermyelination in vitro, though the causal relationship among neuroinflammation, hypermyelination, and autism in vivo requires further validation. These findings underscore the importance of the maternal-infant microbiota transmission window in autism prevention and highlight the clinical potential of prenatal probiotic interventions.

Unraveling genetic risk contributions to nonverbal status in autism spectrum disorder probands

Autism spectrum disorder (ASD) presents a wide range of cognitive and language impairments. In this study, we investigated the genetic basis of non-verbal status in ASD using a comprehensive genomic approach. We identified a novel common variant, rs1944180 in CNTN5, significantly associated with non-verbal status through family-based Transmission Disequilibrium Testing. Polygenic risk score (PRS) analysis further showed that higher ASD PRS was significantly linked to non-verbal status (p = 0.034), specific to ASD and not related to other conditions such as bipolar disorder, schizophrenia and three language-related traits. Using structural equation modeling (SEM), we found two causal SNPs, rs1247761 located in KCNMA1 and rs2524290 in RAB3IL1, linking ASD with language traits. The model indicated a unidirectional effect, with ASD driving language impairments. Additionally, de novo mutations (DNMs) were found to be related with ASD and interaction between common variants and DNMs significantly impacted non-verbal status (p = 0.038). Our findings also identified 5 high-risk ASD genes, and DNMs were enriched in glycosylation-related pathways. These results offer new insights into the genetic mechanisms underlying language deficits in ASD.

Identifying associations of de novo noncoding variants with autism through integration of gene expression, sequence, and sex information

BACKGROUND

Whole-genome sequencing (WGS) data has facilitated genome-wide identification of rare noncoding variants. However, elucidating these variants' associations with complex diseases remains challenging. A previous study utilized a deep-learning-based framework and reported a significant brain-related association signal of autism spectrum disorder (ASD) detected from de novo noncoding variants in the Simons Simplex Collection (SSC) WGS cohort.

RESULTS

We revisit the reported significant brain-related ASD association signal attributed to deep-learning and show that local GC content can capture similar association signals. We further show that the association signal appears driven by variants from male proband-female sibling pairs that are upstream of assigned genes. We then develop Expression Neighborhood Sequence Association Study (ENSAS), which utilizes gene expression correlations and sequence information, to more systematically identify phenotype-associated variant sets. Applying ENSAS to the same set of de novo variants, we identify gene expression-based neighborhoods showing significant ASD association signal, enriched for synapse-related gene ontology terms. For these top neighborhoods, we also identify chromatin state annotations of variants that are predictive of the proband-sibling local GC content differences.

CONCLUSIONS

Overall, our work simplifies a previously reported ASD signal and provides new insights into associations of noncoding de novo mutations in ASD. We also present a new analytical framework for understanding disease impact of de novo mutations, applicable to other phenotypes.

Cognitive and Synaptic Impairment Induced by Deficiency of Autism Risk Gene Smarcc2 and its Rescue by Histone Deacetylase Inhibition

SMARCC2 , which encodes BAF170, a core subunit of chromatin remodeling BAF complex, is one of the top-ranking risk genes for autism spectrum disorder (ASD). However, the mechanisms linking SMARCC2 haploinsufficiency to ASD remain poorly understood. Genome-wide RNA-seq analysis revealed that SMARCC2 was significantly diminished in iPSC-derived neurons from idiopathic ASD patients. ChIP-seq of SMARCC2 demonstrated its binding to many other ASD risk genes involved in transcriptional regulation. Smarcc2 deficiency in prefrontal cortex (PFC) of adolescent mice led to impaired working memory, with largely intact social and anxiety-like behaviors. Significant downregulation of genes enriched in synaptic transmission were found in PFC of S marcc2 -deficient mice by RNA-seq and qPCR profiling. In parallel, electrophysiological recordings uncovered the significant impairment of GABAergic and glutamatergic synaptic currents in S marcc2 -deficient PFC pyramidal neurons. Smarcc2 bound to HDAC2, and Smarcc2 deficiency led to the reduced global histone acetylation and H3K9ac enrichment at synaptic gene Slc1a3 (EAAT1), Slc6a1 (GAT1), and Slc32a1 (VGAT) promoters. Treatment of S marcc2 -deficient mice with romidepsin, a class I HDAC inhibitor, restored histone acetylation, working memory and some synaptic gene expression. These findings highlight the critical role of Smarcc2 in regulating cognitive and synaptic function, suggesting that targeting HDAC could alleviate deficits in Smarcc2-associated neurodevelopmental disorders.

A common computational and neural anomaly across mouse models of autism

Computational psychiatry studies suggest that individuals with autism spectrum disorder (ASD) inflexibly update their expectations. Here we leveraged high-yield rodent psychophysics, extensive behavioral modeling and brain-wide single-cell extracellular recordings to assess whether mice with different genetic perturbations associated with ASD show this same computational anomaly, and if so, what neurophysiological features are shared across genotypes. Mice harboring mutations in Fmr1, Cntnap2 or Shank3B show a blunted update of priors during decision-making. Compared with mice that flexibly updated their priors, inflexible updating of priors was associated with a shift in the weighting of prior encoding from sensory to frontal cortices. Furthermore, frontal areas in mouse models of ASD showed more units encoding deviations from the animals' long-run prior, and sensory responses did not differentiate between expected and unexpected observations. These findings suggest that distinct genetic instantiations of ASD may yield common neurophysiological and behavioral phenotypes.

Preface to the Special Issue "Autism Spectrum Disorder: From Genes to Therapies"

Autism spectrum disorder (ASD) is a complex neurodevelopmental condition characterized by repetitive behaviors and deficits in social interaction and communication. While its exact etiology remains unclear, both genetic and environmental factors contribute to its development. The following preface provides a synthesis of six review articles and five original research studies published in this issue that explore various mechanisms potentially underlying ASD pathology. These publications collectively investigate a range of potential mechanisms underlying ASD pathology, including altered neural connectivity, synaptic dysfunction, immune dysregulation, and epigenetic modifications.

No more nonsense: evaluating poison exons as therapeutic targets in neurodevelopmental disorders

Alternative splicing of pre-mRNA generates multiple transcripts from a single gene, contributing to transcriptomic diversity. Alternative splicing can result in inclusion of poison exons (PEs), which contain a premature stop codons (PTC) that target transcripts for nonsense-mediated decay (NMD). PE-containing transcripts are prevalent in the brain, where they can play roles in fine-tuning mRNA and protein levels. Antisense, or splice-switching, oligonucleotides (ASOs/SSOs) are used to target PEs to reduce their inclusion and treat neurodevelopmental disorders. ASOs/SSOs address the genetic causes of disease and are precision therapies that can provide a cure rather than only address disease symptoms. This review explores the role of PEs in the brain, therapeutic targeting of PEs, and current challenges in our understanding of PEs.

Alternative splicing in autism spectrum disorder: Recent insights from mechanisms to therapy

Alternative splicing (AS) is a vital and highly dynamic RNA regulatory mechanism that allows a single gene to generate multiple mRNA and protein isoforms. Dysregulation of AS has been identified as a key contributor to the pathogenesis of autism spectrum disorders (ASD). A comprehensive understanding of aberrant splicing mechanisms and their functional consequences in ASD can help uncover the molecular basis of the disorder and facilitate the development of therapeutic strategies. This review focuses on the major aberrant splicing events and key splicing regulators associated with ASD, highlighting their roles in linking defective splicing to ASD pathogenesis. In addition, a discussion of how emerging technologies, such as long-read sequencing, single-cell sequencing, spatial transcriptomics and CRISPR-Cas systems are offering novel insights into the role and mechanisms of AS in ASD is presented. Finally, the RNA splicing-based therapeutic strategies are evaluated, emphasizing their potential to address unmet clinical needs in ASD treatment.

Precision medicine in the pediatric and neonatal intensive care units through genomics

PURPOSE OF REVIEW

Genome-wide sequencing technologies have revolutionized the understanding of human disorders and advanced precision medicine, especially for pediatric disorders. Here, we discuss the utility of genomic technologies in advancing the care of children admitted to the pediatric and neonatal intensive care units.

RECENT FINDINGS

Rapid molecular diagnosis permitted by genomic medicine has yielded clinically actionable findings that influence decision-making and facilitate timely therapeutic interventions. Identifying a genetic association provides a causal anchor to understanding disease biology at the single nucleotide resolution, revealing hidden biological heterogeneity that may be obscured by traditional imaging, laboratory, and pathological workup. The importance of a genetic diagnosis is further highlighted by the promise of gene therapy to correct the underlying genetic perturbation, as evidenced by the recent emergence of FDA-approved gene therapies for childhood genetic conditions.

SUMMARY

We predict that whole-genome sequencing, in conjunction with other omic technologies, will become critical diagnostic adjuncts in the clinical workup of critically ill children.

Auditory processing deficits in autism spectrum disorder: mechanisms, animal models, and therapeutic directions

Auditory processing abnormalities are a prominent feature of Autism Spectrum Disorder (ASD), significantly affecting sensory integration, communication, and social interaction. This review delves into the neurobiological mechanisms underlying these deficits, including structural and functional disruptions in the auditory cortex, imbalances in excitatory and inhibitory signaling, and synaptic dysfunction. Genetic contributions from mutations in CNTNAP2, SHANK3, FMR1, and FOXP2 are explored, highlighting their roles in auditory abnormalities. Animal models, such as BTBRT+tf/J mice (BTBR) and valproic acid (VPA)-exposed rodents, provide critical insights into the sensory abnormalities observed in ASD. In addition, the review discusses current pharmacological strategies and emerging interventions targeting neurotransmitter systems and synaptic plasticity. Notably, future directions are emphasized, highlighting the need for integrated pharmacological and auditory-specific therapies to enhance sensory processing and communication outcomes in ASD. Overall, this review aims to bridge the gap between basic neurobiological research and clinical application, guiding future studies and therapeutic developments in ASD-related auditory processing deficits.

Understanding autism: Causes, diagnosis, and advancing therapies

Autism Spectrum Disorder (ASD) is a neurodevelopmental condition marked by difficulties in social communication, languages, and repetitive behaviors. Its rising prevalence has made it a critical global public health issue. ASD is believed to arise from a combination of genetic and environmental influences. While some gene mutations associated with ASD have been identified, most cases lack clear genetic explanations. Evidence increasingly points to early-life environmental factors as key contributors to ASD, including advanced parental age, maternal diabetes during pregnancy, infections, hormonal imbalances, certain medications, and exposure to air pollution. Currently, ASD diagnosis relies on behavioral assessments, but the absence of specific molecular biomarkers poses significant obstacles to early detection and targeted therapies. Encouragingly, research has identified potential biomarkers, such as neuroimaging classifiers, electroencephalography patterns, eye-tracking data, digital analytics, gene expression profiles, inflammatory and chemokine markers, proteomic and metabolomic profiles, and gut microbiota characteristics. Potential therapeutical strategies under investigation include digital therapies, non-invasive brain stimulation, antioxidants, oxytocin, AVPR1a antagonists, PPAR agonists, and mTOR inhibitors. This review explores ASD across five areas: epidemiological trends, genetic mechanisms, early-life environmental factors and their potential roles, diagnostic biomarkers, and therapeutic approaches.

The distribution of highly deleterious variants across human ancestry groups

A major focus of human genetics is to map severe disease mutations. Increasingly, that goal is understood as requiring huge numbers of people to be sequenced from every broadly defined genetic ancestry group, so as not to miss "ancestry-specific variants." Here, we consider whether this focus is warranted. We start from first principles considerations, based on models of mutation-drift-selection balance, which suggest that since severe disease mutations tend to be strongly deleterious, and thus evolutionarily young, they will be kept at relatively constant frequency through recurrent mutation. Therefore, highly pathogenic alleles should be shared identically by descent within extended families, not broad ancestry groups, and sequencing more people should yield similar numbers regardless of ancestry. We test the model predictions using gnomAD genetic ancestry groupings and show that they provide a good fit to the classes of variants most likely to be highly pathogenic, notably sets of loss of function alleles at strongly constrained genes. These findings clarify that strongly deleterious alleles will be found at comparable rates in people of all ancestries, and the information they provide about human biology is shared across ancestries.

Duplication of the autism-related gene Chd8 leads to behavioral hyperactivity and neurodevelopmental defects in mice

Mutations in the gene encoding chromodomain helicase DNA-binding protein 8 (CHD8) are strongly associated with autism spectrum disorder (ASD). Although duplications of the chromosomal locus including CHD8 have also been detected in individuals with neurodevelopmental disorders, the contribution of CHD8 duplication to clinical phenotypes and the underlying mechanisms have remained unknown. Here we show that Chd8 knock-in (KI) mice that overexpress CHD8 as a model of human CHD8 duplication manifest growth retardation, microcephaly, impaired neuronal differentiation, and behavioral abnormalities including hyperactivity and reduced anxiety-like behavior. Chd8 overexpression affects the transcription and chromatin accessibility of genes related to neurogenesis, with these changes being associated with aberrant binding of CHD8 to enhancer regions. Furthermore, pharmacological intervention partially ameliorates the hyperactivity of Chd8 KI mice. Our results thus indicate that Chd8 KI mice recapitulate key features of CHD8 duplication syndrome in humans, providing insight into pathogenic mechanisms underlying neurodevelopmental disorders.

Early establishment and life course stability of sex biases in the human brain transcriptome

To elaborate on the origins of the established male-female differences in several brain-related phenotypes, we assessed the patterns of transcriptomic sex biases in the developing and adult human forebrain. We find an abundance of sex differences in expression (sex-DEs) in the prenatal brain, driven by both hormonal and sex-chromosomal factors, and considerable consistency in the sex effects between the developing and adult brain, with little sex-DE exclusive to the adult forebrain. Sex-DE was not enriched in genes associated with brain disorders, consistent with systematic differences in the characteristics of these genes (e.g., constraint). Yet, the genes with persistent sex-DE across the lifespan were overrepresented in disease gene co-regulation networks, pointing to their potential to mediate sex biases in brain phenotypes. Altogether, our work highlights prenatal development as a crucial time point for the establishment of brain sex differences.

Spatiotemporal 3D chromatin organization across multiple brain regions during human fetal development

Elucidating the regulatory mechanisms underlying the development of different brain regions in humans is essential for understanding advanced cognition and neuropsychiatric disorders. However, the spatiotemporal organization of three-dimensional (3D) chromatin structure and its regulatory functions across different brain regions remain poorly understood. Here, we generated an atlas of high-resolution 3D chromatin structure across six developing human brain regions, including the prefrontal cortex (PFC), primary visual cortex (V1), cerebellum (CB), subcortical corpus striatum (CS), thalamus (TL), and hippocampus (HP), spanning gestational weeks 11-26. We found that the spatial and temporal dynamics of 3D chromatin organization play a key role in regulating brain region development. We also identified H3K27ac-marked super-enhancers as key contributors to shaping brain region-specific 3D chromatin structures and gene expression patterns. Finally, we uncovered hundreds of neuropsychiatric GWAS SNP-linked genes, shedding light on critical molecules in various neuropsychiatric disorders. In summary, our findings provide important insights into the 3D chromatin regulatory mechanisms governing brain region-specific development and can serve as a valuable resource for advancing our understanding of neuropsychiatric disorders.

"Teaching the biology of neurodiversity for social change"

The scientific understanding of autism spectrum disorder (ASD) is historically rooted in the diagnosis of children with divergent behavior and socialization within Western societies. Increased activism and visibility of ASD individuals has helped popularize the neurodiversity movement, which proposes that autism falls within the natural spectrum of human behavior and is not always pathological. The increased interest in neurodiversity has coincided with rapid advances in the field of psychiatric genetics, particularly in understanding the underlying genetic causes of ASD. Identified genes linked to ASD have highlighted mid-fetal cortical development as a nexus when many of these genes are co-expressed. New discoveries in the genetics of ASD present a unique opportunity in teaching developmental biology and especially brain development to engage students with the biology underlying ASD and neurodiversity in general. Informed and inclusive language, engagement with the neurodiversity community, and awareness of the complexity of the issues are good practices in teaching the biology of neurodiversity.

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.

Multimodal analyses reveal genes driving electrophysiological maturation of neurons in the primate prefrontal cortex

The prefrontal cortex (PFC) is critical for myriad high-cognitive functions and is associated with several neuropsychiatric disorders. Here, using Patch-seq and single-nucleus multiomic analyses, we identified genes and regulatory networks governing the maturation of distinct neuronal populations in the PFC of rhesus macaque. We discovered that specific electrophysiological properties exhibited distinct maturational kinetics and identified key genes underlying these properties. We unveiled that RAPGEF4 is important for the maturation of resting membrane potential and inward sodium current in both macaque and human. We demonstrated that knockdown of CHD8, a high-confidence autism risk gene, in human and macaque organotypic slices led to impaired maturation, via downregulation of key genes, including RAPGEF4. Restoring the expression of RAPGEF4 rescued the proper electrophysiological maturation of CHD8-deficient neurons. Our study revealed regulators of neuronal maturation during a critical period of PFC development in primates and implicated such regulators in molecular processes underlying autism.

ASiDentify (ASiD): a machine learning model to predict new autism spectrum disorder risk genes

Autism spectrum disorder (ASD) is a neurodevelopmental disorder that affects nearly 3% of children and has a strong genetic component. While hundreds of ASD risk genes have been identified through sequencing studies, the genetic heterogeneity of ASD makes identifying additional risk genes using these methods challenging. To predict candidate ASD risk genes, we developed a simple machine learning model, ASiDentify (ASiD), using human genomic, RNA- and protein-based features. ASiD identified over 1,300 candidate ASD risk genes, over 300 of which have not been previously predicted. ASiD made accurate predictions of ASD risk genes using 6 features predictive of ASD risk gene status, including mutational constraint, synapse localization and gene expression in neurons, astrocytes and non-brain tissues. Particular functional groups of proteins found to be strongly implicated in ASD include RNA-binding proteins (RBPs) and chromatin regulators. We constructed additional logistic regression models to make predictions and assess informative features specific to RBPs, including mutational constraint, or chromatin regulators, for which both expression level in excitatory neurons and mutational constraint were informative. The fact that RBPs and chromatin regulators had informative features distinct from all protein-coding genes suggests that specific biological pathways connect risk genes with different molecular functions to ASD.

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.

Highly demarcated structural alterations in the brain and impaired social incentive learning in Tbx1 heterozygous mice

Copy number variants (CNVs) are robustly associated with psychiatric disorders and changes in brain structures. However, because CNVs contain many genes, the precise gene-phenotype relationship remains unclear. Although various volumetric alterations in the brains of 22q11.2 CNV carriers have been identified in humans and mouse models, it is unknown how each gene encoded in the 22q11.2 region contributes to structural alterations, associated mental illnesses, and their dimensions. Our previous studies identified Tbx1, a T-box family transcription factor encoded in the 22q11.2 CNV, as a driver gene for social interaction and communication, spatial and working memory, and cognitive flexibility. However, it remains unclear how TBX1 impacts the volumes of various brain regions and their functionally linked behavioral dimensions. In this study, we used volumetric magnetic resonance imaging analysis to comprehensively evaluate brain region volumes and behavioral alterations relevant to affected structures in congenic Tbx1 heterozygous mice. Our data showed that the volumes of the anterior and posterior portions of the amygdaloid complex and its surrounding cortical regions were most robustly reduced in Tbx1 heterozygous mice. In an amygdala-dependent task, Tbx1 heterozygous mice were impaired in their ability to learn the incentive value of a social partner. The volumes of the primary and secondary auditory cortexes were increased, and acoustic, but not non-acoustic, sensorimotor gating was impaired in Tbx1 heterozygous mice. Our findings identify the brain's regional volume alterations and their relevant behavioral dimensions associated with Tbx1 heterozygosity.

m6A-mRNA Reader YTHDF2 Identified as a Potential Risk Gene in Autism With Disproportionate Megalencephaly

Among autistic individuals, a subphenotype of disproportionate megalencephaly (ASD-DM) seen at three years of age is associated with co-occurring intellectual disability and poorer prognoses later in life. However, many of the genes contributing to ASD-DM have yet to be delineated. In this study, we identified additional ASD-DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD-DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection, totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD-DM genes harboring de novo protein-impacting variants. Our findings include 14 high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM, including CHD8 and PTEN. By performing functional network analysis, we expanded to additional candidate genes, including one previously implicated in ASD-DM (PIK3CA) as well as 184 additional genes connected with ASD or DM alone. Using zebrafish, we modeled a de novo tandem duplication impacting YTHDF2, encoding an N6-methyladenosine (m6A)-mRNA reader, in an ASD-DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size, while overexpressing YTHDF2 resulted in increased head/brain size matching that of the proband. Single-cell transcriptomes of YTHDF2 gain-of-function larvae point to reduced expression of Fragile-X-syndrome-associated FMRP-target genes globally and in the developing brain, providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader, YTHDC1, in our ASD-DM cohort. Though we highlight only two cases to date, our study provides support for the m6A-RNA modification pathway as potentially contributing to this severe form of autism.

Impact of a Genetic Diagnosis for a Child's Autism on Parental Perceptions

Genetic testing is recommended as part of an autism assessment, and most parents support genetic testing for their minor children. However, the impact on parents of receiving a monogenetic/ copy number variant diagnosis for autism in their child is not well understood. To explore this, we surveyed and interviewed parents of children in the SPARK study, a study of autism that includes genetic testing. Surveys were administered one month before and one and 12 months after parents received their child's genetic result. Interviews were conducted approximately one month after results disclosure. A genetic diagnosis (GD) for their child appeared to reduce parents' sense of self-blame and feelings of guilt, and this impact was relatively stable. The data also indicate a modest impact on parents' actions related to the condition, perceptions of themselves, and some aspects of life planning for their child, as measured by quantitative instruments at one month and 12 months after receipt of results. Other measures of parental identity and expectations for their child, in contrast, showed little change following receipt of genetic findings. Overall, parents who were told that no GD was identified showed minimal changes in their responses over time. These results suggest a discernable but relatively limited impact of genetic test results on parents of children with autism. These results should be reassuring to clinicians caring for children with autism and are consistent with studies in other areas of medicine that have suggested that genetic results tend to have fewer effects-negative or positive-than were anticipated.

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.

Detailed phenotyping of Tbr1-2A-CreER knock-in mice demonstrates significant impacts on TBR1 protein levels and axon development

Cre recombinase knock-in mouse lines have served as invaluable genetic tools for understanding key developmental processes altered in autism. However, insertion of exogenous DNA into the genome can have unintended effects on local gene regulation or protein function that must be carefully considered. Here, we analyze a recently generated Tbr1-2A-CreER knock-in mouse line, where a 2A-CreER cassette was inserted in-frame before the stop codon of the transcription factor gene Tbr1. Heterozygous TBR1 mutations in humans and mice are known to cause autism or autism-like behavioral phenotypes accompanied by structural brain malformations, most frequently a reduction of the anterior commissure (AC). Thus, it is critical for modified versions of Tbr1 to exhibit true wild-type-like activity. We evaluated the Tbr1-2A-CreER allele for its potential impact on Tbr1 function and complementation to Tbr1 loss-of-function alleles. In mice with one copy of the Tbr1-2A-CreER allele, we identified reduction of TBR1 protein in early postnatal cortex along with thinning of the AC, suggesting hypersensitivity of this structure to TBR1 dosage. Comparing Tbr1-2A-CreER and Tbr1-null mice to Tbr1-null complementation crosses showed reductions of TBR1 dosage ranging from 20% to 100%. Using six combinatorial genotypes, we found that moderate to severe TBR1 reductions (≥44%) were associated with cortical layer 5 expansion, while only the complete absence of TBR1 was associated with reeler-like "inverted" cortical layering. In total, these results strongly support the conclusion that Tbr1-2A-CreER is a hypomorphic allele. We advise caution when interpreting experiments using this allele, considering the sensitivity of various corticogenic processes to TBR1 dosage and the association of heterozygous TBR1 mutations with complex neurodevelopmental disorders.

Crosstalk Between Mitochondrial DNA and Immune Response: Focus on Autism Spectrum Disorder

Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by multiple dysfunctions in behavior, the nervous system, and the immune system. Increasing evidence suggests that mitochondrial DNA (mtDNA) plays a crucial role in the pathology of ASD. In clinical practice, altered mtDNA levels have been observed in various tissues of individuals with ASD. Mutation or oxidation of mtDNA is also closely related to the immune response associated with the pathology of autism. With mtDNA identified as a causal factor, much interest has focused on how its production affects neurodevelopment and neurophysiology. Here, we review how mtDNA leads to dysfunction of cellular mitochondria and immune response. We also illustrate the relationship between mtDNA alterations and the pathology of autism. Finally, we discuss the existing evidence on cell-free mtDNA associated with ASD and look forward to its application in clinical diagnosis and treatment.

Monoallelic loss-of-function variants in GSK3B lead to autism and developmental delay

De novo variants adjacent to the canonical splicing sites or in the well-defined splicing-related regions are more likely to impair splicing but remain under-investigated in autism spectrum disorder (ASD). By analyzing large, recent ASD genome sequencing cohorts, we find a significant burden of de novo potential splicing-disrupting variants (PSDVs) in 5048 probands compared to 4090 unaffected siblings. We identified 55 genes with recurrent de novo PSDVs that were highly intolerant to variation. Forty-six of these genes have not been strongly implicated in ASD or other neurodevelopmental disorders previously, including GSK3B. Through international, multicenter collaborations, we assembled genotype and phenotype data for 15 individuals with GSK3B variants and identified common phenotypes including developmental delay, ASD, sleeping disturbance, and aggressive behavior. Using available single-cell transcriptomic data, we show that GSK3B is enriched in dorsal progenitors and intermediate forms of excitatory neurons in the developing brain. We showed that Gsk3b knockdown in mouse excitatory neurons interferes with dendrite arborization and spine maturation which could not be rescued by de novo missense variants identified from affected individuals. In summary, our findings suggest that PSDVs may play an important role in the genetic etiology of ASD and allow for the prioritization of new ASD candidate genes. Importantly, we show that genetic variation resulting in GSK3B loss-of-function can lead to a neurodevelopmental disorder with core features of ASD and developmental delay.

Protein-truncating variants and deletions of SHANK2 are associated with autism spectrum disorder and other neurodevelopmental concerns

BACKGROUND

SHANK2 disorder is a rare neurodevelopmental disorder caused by a deletion or pathogenic sequence variant of the SHANK2 gene and is associated with autism spectrum disorder (ASD), intellectual disability (ID), and developmental delay. To date, research in SHANK2 has focused on laboratory-based in vivo and in vitro studies with few prospective clinical studies in humans.

METHODS

A remote assessment battery was comprised of caregiver interviews with a psychiatrist, psychologists, and a genetic counselor, caregiver-reports, and review of records. Results from this cohort were reported using descriptive statistics. An age-matched sample of participants with SHANK3 haploinsufficiency (Phelan-McDermid syndrome, PMS) was used to compare adaptive behavior between the two groups.

RESULTS

All ten participants demonstrated delays in adaptive behavior, with most motor skills preserved and a weakness in communication. According to parent report, 90% of participants carried a formal diagnosis of ASD, 50% of participants carried a diagnosis of attention-deficit/hyperactivity disorder (ADHD), and mild-to-moderate developmental delays were noted. Sensory hyperreactivity and seeking behaviors were more pronounced than sensory hyporeactivity. Medical features included hypotonia, recurrent ear infections, and gastrointestinal abnormalities. No similar facial dysmorphic features were observed. Compared to PMS participants, individuals with SHANK2 disorder had significantly higher adaptive functioning.

CONCLUSIONS

Consistent with previous studies of SHANK2 disorder, these results indicate mild to moderate developmental impairment. Overall, SHANK2 disorder is associated with developmental and adaptive functioning delays, high rates of autism, including sensory symptoms and repetitive behaviors, and ADHD. This study was limited by its remote nature, diverse age range, and the homogeneous racial and ethnic sample. Future studies should examine larger, diverse cohorts, add cognitive testing, capture longitudinal data, and include in-person assessments.

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.

Psychopharmacology in children with genetic disorders of epigenetic and chromatin regulation

OBJECTIVE

Hundreds of rare genetic variants associated with autism or intellectual disability have been identified, and many impact genes known to have a primary epigenetic/chromatin regulatory function. The objective of this study was to examine and compare behavioural profiles and longitudinal psychotropic treatment patterns in children with epigenetic/chromatin variants, other rare variants impacting neurodevelopment, or no known genetic condition.

METHODS

Using electronic medical records from a pediatric psychopharmacology program for children with autism or intellectual disability, we compared clinical characteristics, longitudinal psychotropic medication profiles and side effects between those with and without a rare genetic variant, and by variant subtype [epigenetic/chromatin regulation or other variant].

RESULTS

A total of 331 children attended 2724 unique medical visits between 2019 and 2022, with a mean of 8 follow-up visits over 3.4 years. Nine children (3%) had variants in epigenetic/chromatin regulatory genes (EC), twenty-three children (7%) had other rare genetic variants (OTH), and the rest had no reported variant (NR, n = 299, 90%). Those with a rare genetic variant (EC or OTH) were more likely to have an intellectual disability and had a greater number of co-occurring physical health conditions (p < 0.01). Overall, 66% of psychotropic medications were continued for ≥ 3 visits, while 26% were discontinued. Rates of psychotropic polypharmacy, medication patterns, behavioural challenges, and co-occurring developmental diagnoses were similar between genetic groups. Analyses uncorrected for multiple comparisons suggested those with genetic variants were more likely to experience drowsiness/sedation as a side effect (EC 33%, OTH 35%, NR 16%, p < 0.05); weight gain as a side effect was also higher in the epigenetic/chromatin group (EC 50% vs OTH 11%).

CONCLUSION

Genetic classification of neurodevelopmental disorders (NDDs) may help anticipate treatment tolerability; additional prescribing considerations may be needed for those with rare variants. Current psychotropic prescribing practices do not differ across rare genetic NDD subgroups.

Do Influential Articles on the Genetics of Autism Show Evidence of Engagement With the Autistic Community?

Investigations into the etiology and genetic basis of autism continue to drive much autism research, yet reports are emerging of this research not aligning with priorities of autistic people. Engagement of autistic people in the research process is a key way to take their perspectives on board. We investigated whether influential genetic autism research shows evidence of engagement with the autistic community via indicators in published article texts. Through text mining of the abstracts of articles mentioning the words "autism" or "autistic," we found minimal prevalence of progressive terminology associated with autism. We also devised a novel rating system to assess three hallmarks of autistic community engagement: presence of non-stigmatizing language, referencing community priorities, and the use of participatory methods. We reviewed 149 articles within leading autism and genetic journals. Minimal evidence of engagement with the autistic community was found within all three hallmarks. Genetics researchers focused on autism should embrace opportunities to engage with the autistic community to bring their work into closer alignment with their priorities, yielding scientific and moral benefits.

Advancing autism research: Insights from brain organoid modeling

Autism Spectrum Disorders (ASD) are characterized by a variety of behavioral symptoms and a complex genetic architecture, posing significant challenges in understanding the mechanistic processes underlying their pathology. Despite extensive research, the mechanisms linking genetic variations to the phenotypic outcomes associated with ASD remain elusive. Consistent evidence indicates disruptions in early brain development among individuals with ASD. The advent of brain organoids offers a unique opportunity for uncovering, how brain development changes in ASD patients. Brain organoids are three-dimensional in vitro model systems derived from pluripotent stem cells that recapitulate early human brain development across multiple biological levels. They have become an invaluable tool for studying human-specific brain development processes and neurodevelopmental disorders. In this review, we discuss recent findings using brain organoid technologies to model ASD and discuss, how these new technologies can enhance our understanding of ASD genetics and pathology at the molecular, cellular, and tissue levels.

Requirements for the neurodevelopmental disorder-associated gene ZNF292 in human cortical interneuron development and function

Pathogenic mutation of the zinc-finger transcription factor ZNF292 is a recently defined contributor to human neurodevelopmental disorders (NDDs). However, the gene's roles in cortical development and regulatory networks under its control were previously undefined. Here, human stem cell models of ZNF292 deficiency, resembling pathogenic haploinsufficiency, are used to derive cortical inhibitory neuron progenitors and neurons. ZNF292-deficient progenitors undergo precocious differentiation but subsequently exhibit compromised interneuron maturation and function. In progenitors, genome-wide occupancy and transcriptomic analyses identify direct target genes controlling neuronal differentiation and synapse formation that are upregulated upon ZNF292 deficiency. By contrast, deficiency in interneurons compromises ZNF292 genome-wide association with and causes downregulation of direct target genes promoting interneuron maturation and function, including other NDD genes. ZNF292-deficient interneurons also exhibit altered channel activities, elevated GABA responsiveness, and hallmarks of neuronal hyperactivity. Together, the results of this work define neurodevelopmental requirements for ZNF292, some of which may contribute to pathogenic ZNF292 mutation-related NDDs.

Simultaneous CRISPR screening and spatial transcriptomics reveal intracellular, intercellular, and functional transcriptional circuits

Pooled optical screens have enabled the study of cellular interactions, morphology, or dynamics at massive scale, but they have not yet leveraged the power of highly plexed single-cell resolved transcriptomic readouts to inform molecular pathways. Here, we present a combination of imaging spatial transcriptomics with parallel optical detection of in situ amplified guide RNAs (Perturb-FISH). Perturb-FISH recovers intracellular effects that are consistent with single-cell RNA-sequencing-based readouts of perturbation effects (Perturb-seq) in a screen of lipopolysaccharide response in cultured monocytes, and it uncovers intercellular and density-dependent regulation of the innate immune response. Similarly, in three-dimensional xenograft models, Perturb-FISH identifies tumor-immune interactions altered by genetic knockout. When paired with a functional readout in a separate screen of autism spectrum disorder risk genes in human-induced pluripotent stem cell (hIPSC) astrocytes, Perturb-FISH shows common calcium activity phenotypes and their associated genetic interactions and dysregulated molecular pathways. Perturb-FISH is thus a general method for studying the genetic and molecular associations of spatial and functional biology at single-cell resolution.

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.

Convergent depression of activity-dependent bulk endocytosis in rodent models of autism spectrum disorder

BACKGROUND

The key pathological mechanisms underlying autism spectrum disorder (ASD) remain relatively undetermined, potentially due to the heterogenous nature of the condition. Targeted studies of a series of monogenic ASDs have revealed postsynaptic dysfunction as a central conserved mechanism. Presynaptic dysfunction is emerging as an additional disease locus in neurodevelopmental disorders; however, it is unclear whether this dysfunction drives ASD or is an adaptation to the altered brain microenvironment.

METHODS

To differentiate between these two competing scenarios, we performed a high content analysis of key stages of the synaptic vesicle lifecycle in primary neuronal cultures derived from a series of preclinical rat models of monogenic ASD. These five independent models (Nrxn1+/-, Nlgn3-/y, Syngap+/-, Syngap+/Δ-GAP, Pten+/-) were specifically selected to have perturbations in a diverse palette of genes that were expressed either at the pre- or post-synapse. Synaptic vesicle exocytosis and cargo trafficking were triggered via two discrete trains of activity and monitored using the genetically-encoded reporter synaptophysin-pHluorin. Activity-dependent bulk endocytosis was assessed during intense neuronal activity using the fluid phase marker tetramethylrhodamine-dextran.

RESULTS

Both synaptic vesicle fusion events and cargo trafficking were unaffected in all models investigated under all stimulation protocols. However, a key convergent phenotype across neurons derived from all five models was revealed, a depression in activity-dependent bulk endocytosis.

LIMITATIONS

The study is exclusively conducted in primary cultures of hippocampal neurons; therefore, the impact on neurons from other brain regions or altered brain microcircuitry was not assessed. No molecular mechanism has been identified for this depression.

CONCLUSION

This suggests that depression of activity-dependent bulk endocytosis is a presynaptic homeostatic mechanism to correct for intrinsic dysfunction in ASD neurons.

Minding the synapse: A multi-omic approach reveals hidden regulators of neurodevelopment

Synapses are fundamental for neural communication, yet their molecular architecture remains incompletely defined. Now, Mei et al. generate proteomic data from multiple biological systems and combine these data with other multi-omics datasets to identify over 1,000 high-confidence synaptic proteins.1 Characterizing three such proteins-DDX3X, YBX1, and CUL3-uncovers mechanisms underlying neurodevelopmental disorders.

An integrative scoring approach for prioritization of rare autism spectrum disorder candidate variants from whole exome sequencing data

Discerning clinically relevant autism spectrum disorder (ASD) candidate variants from whole-exome sequencing (WES) data is complex, time-consuming, and labor-intensive. To this end, we developed AutScore, an integrative prioritization algorithm of ASD candidate variants from WES data and assessed its performance to detect clinically relevant variants. We studied WES data from 581 ASD probands, and their parents registered in the Azrieli National Center database for Autism and Neurodevelopment Research. We focused on rare allele frequency (< 1%) and high-quality proband-specific variants affecting genes associated with ASD or other neurodevelopmental disorders (NDDs). We developed AutScore and AutScore.r and assigned each variant based on their pathogenicity, clinical relevance, gene-disease association, and inheritance patterns. Finally, we compared the performance of both AutScore versions with the rating of clinical experts and the NDD variant prioritization algorithm, AutoCaSc. Overall, 1161 rare variants distributed in 687 genes in 441 ASD probands were evaluated by AutScore with scores ranging from - 4 to 25, with a mean ± SD of 5.89 ± 4.18. AutScore.r cut-off of ≥ 0.335 performs better than AutoCaSc and AutScore in detecting clinically relevant ASD variants, with a detection accuracy rate of 85% and an overall diagnostic yield of 10.3%. Five variants with AutScore.r of ≥ 0.335 were distributed in five novel ASD candidate genes. AutScore.r is an effective automated ranking system for ASD candidate variants that could be implemented in ASD clinical genetics pipelines.

γ-Aminobutyric Acid Transporter Mutation GAT1 (S295L) Substantially Impairs Neurogenesis in Dentate Gyrus

Background: GABAergic signaling plays a crucial role in modulating neuronal proliferation, migration, and the formation of neural network connections. The termination of GABA transmission primarily occurs through the action of GABA transporter 1 (GAT1), encoded by the SLC6A1 gene. Multiple SLC6A1 mutations have been implicated in neurodevelopmental disorders, but their effects on the nervous system are unclear. Methods: We estimated the expression pattern of the GAT1 (S295L) protein using the Slc6a1S295L/S295L mouse model via RT-PCR, Western blotting, and confocal immunofluorescence. The effect of GAT1 (S295L) on hippocampal neurogenesis was investigated by neuronal marker staining (Sox2, Tbr2, NeuroD1, DCX, NeuN) and BrdU label experiments. The dendritic complexity was mapped through Sholl analysis. RNA-Seq was utilized to explore the signaling pathways and molecules associated with neurodevelopmental disorders. Results: We detected a remarkable decline in the quantity of type-2b intermediate progenitor cells, neuroblasts, and immature neurons in the dentate gyrus (DG) of Slc6a1S295L/S295L mice at 4 weeks. These abnormalities were exacerbated in adulthood, as evidenced by compromised dendritic length and height as well as the complexity of immature neurons. Immunofluorescence staining showed the abnormal aggregation of GAT1 (S295L) protein in neurons. RNA-seq analysis identified pathways associated with neurodevelopment, neurological disorders, protein homeostasis, and neuronutrition. The neurotrophin Bdnf decreased at all ages in the Slc6a1S295L/S295L mice. Conclusions: Our data provide new evidence that GAT1 (S295L) causes impaired neurogenesis in the DG. GAT1 mutation not only disrupts GABA homeostasis but also impairs the neurotrophic support necessary for normal hippocampal development, which may be one of the factors contributing to impaired neurogenesis.

Biogenic Amine Metabolism and Its Genetic Variations in Autism Spectrum Disorder: A Comprehensive Overview

Autism spectrum disorder (ASD) is a genetically heterogeneous syndrome characterized by repetitive, restricted, and stereotyped behaviors, along with persistent difficulties with social interaction and communication. Despite its increasing prevalence globally, the underlying pathogenic mechanisms of this complex neurodevelopmental disorder remain poorly understood. Therefore, the identification of reliable biomarkers could play a crucial role in enabling early screening and more precise classification of ASD subtypes, offering valuable insights into its physiopathology and aiding the customization of treatment or early interventions. Biogenic amines, including serotonin, histamine, dopamine, epinephrine, norepinephrine, and polyamines, are a class of organic compounds mainly produced by the decarboxylation of amino acids. A substantial portion of the genetic variation observed in ASD has been linked to genes that are either directly or indirectly involved in the metabolism of biogenic amines. Their potential involvement in ASD has become an area of growing interest due to their pleiotropic activities in the central nervous system, where they act as both neurotransmitters and neuromodulators or hormones. This review examines the role of biogenic amines in ASD, with a particular focus on genetic alterations in the enzymes responsible for their synthesis and degradation.

CRISPRi-based screen of autism spectrum disorder risk genes in microglia uncovers roles of ADNP in microglia endocytosis and synaptic pruning

Autism Spectrum Disorders (ASD) are a set of neurodevelopmental disorders with complex biology. The identification of ASD risk genes from exome-wide association studies and de novo variation analyses has enabled mechanistic investigations into how ASD-risk genes alter development. Most functional genomics studies have focused on the role of these genes in neurons and neural progenitor cells. However, roles for ASD risk genes in other cell types are largely uncharacterized. There is evidence from postmortem tissue that microglia, the resident immune cells of the brain, appear activated in ASD. Here, we used CRISPRi-based functional genomics to systematically assess the impact of ASD risk gene knockdown on microglia activation and phagocytosis. We developed an iPSC-derived microglia-neuron coculture system and high-throughput flow cytometry readout for synaptic pruning to enable parallel CRISPRi-based screening of phagocytosis of beads, synaptosomes, and synaptic pruning. Our screen identified ADNP, a high-confidence ASD risk genes, as a modifier of microglial synaptic pruning. We found that microglia with ADNP loss have altered endocytic trafficking, remodeled proteomes, and increased motility in coculture.

PPP5C pathogenic variant identified: a potential key to gaining insight into developmental and epileptic encephalopathy?

BACKGROUND

Emerging evidence suggesting a possible link between the PPP5C gene (protein phosphatase 5 catalytic subunit; OMIM#600658) and developmental and epileptic encephalopathy (DEE, OMIM#308350), although the clinical significance of pathogenic variants in this gene remains unclear. PPP5C is a member of the protein phosphatase catalytic subunit family, which is involved in various signaling pathways governing cell growth, differentiation, and responses to hormonal signals or cellular stress. To date, only one case with a PPP5C variant has been reported, associated with a severe neurological phenotype, including microcephaly, failure to thrive, and early-onset seizures.

RESULTS

We report a 12-year-old girl affected by epilepsy and learning disorders. At the age of five, she presented convulsive status epilepticus with respiratory failure at onset and she started anticonvulsant therapy with Levetiracetam with a significant improvement. Genetic analysis revealed a de novo heterozygous missense variant of PPP5C gene (c.202 C > T: p.Arg68Cys), which had not been previously described in the literature.

CONCLUSION

This case expands the phenotypic spectrum associated with PPP5C variants, highlighting the potential role of this gene inneurological disorders. Our findings may provide some valuable insights into the spectrum of phenotypic manifestations linked to this gene less investigated in neuropediatrics.

Germline mosaicism in TCF20-associated neurodevelopmental disorders: a case study and literature review

Autosomal dominant variants in transcription factor 20 (TCF20) can result in TCF20-associated neurodevelopmental disorder (TAND), a condition characterized by developmental delay and intellectual disability, autism, dysmorphisms, dystonia, and variable other neurological features. To date, a total of 91 individuals with TAND have been reported; ~67% of cases arose de novo, while ~10% were inherited, and, intriguingly, ~8% were either confirmed or suspected to have arisen via germline mosaicism. Here, we describe two siblings with a developmental condition characterized by intellectual disability, autism, a circadian rhythm sleep disorder, and attention deficit hyperactivity disorder (ADHD) caused by a novel heterozygous single nucleotide deletion in the TCF20 gene, NM_001378418.1:c.4737del; NP_001365347.1:p.Lys1579Asnfs*36 (GRCh38/hg38). The variant was not detected in DNA extracted from peripheral blood in either parent by Sanger sequencing of PCR-generated amplicons, or by deep sequencing of PCR amplicons using MiSeq and MinION. However, droplet digital PCR (ddPCR) of DNA derived from early morning urine detected the variation in 3.2% of the father's urothelial cells, confirming germline mosaicism. This report is only the second to confirm with physical evidence TCF20 germline mosaicism and discusses germline mosaicism as a likely under-detected mode of inheritance in neurodevelopmental conditions.

Kynurenic Acid and Promotion of Activity-Dependent Synapse Elimination in Schizophrenia

OBJECTIVE

Schizophrenia is a neurodevelopmental disorder characterized by an excessive loss of synapses. Kynurenic acid (KYNA), a neuroactive metabolite of tryptophan along the kynurenine pathway, can induce schizophrenia-related phenotypes in rodents, and clinical studies have revealed elevated KYNA levels in the CNS of individuals with schizophrenia. However, the factors that cause elevated KYNA levels in schizophrenia, and the mechanisms by which KYNA contributes to pathophysiology, remain largely elusive. The authors used patient-derived cellular modeling to test the hypothesis that KYNA can induce microglia-mediated synapse engulfment by reducing neuronal activity.

METHODS

Patient-derived induced pluripotent stem cells were used to generate 2D cultures of neurons and microglia-like cells, as well as forebrain organoids with innately developing microglia, to study how KYNA influences synaptic activity and microglial uptake of synaptic structures. To verify the experimental data in a clinical context, large-scale developmental postmortem brain tissue and genetic datasets were used to study coexpression networks for the KYNA-producing kynurenine aminotransferases (KATs) regarding enrichment for common schizophrenia genetic risk variants and functional annotations.

RESULTS

In these patient-derived experimental models, KYNA induced uptake of synaptic structures in microglia, and inhibition of the endogenous KYNA production led to a decrease in the internalization of synapses in microglia. The integrated large-scale transcriptomic and genetic datasets showed that KYNA-producing KATs enriched for genes governing synaptic activity and genetic risk variants for schizophrenia.

CONCLUSIONS

Together, these results link genetic risk variants for schizophrenia to elevated production of KYNA and excessive and activity-dependent internalization of synaptic material in microglia, while implicating pharmacological inhibition of KATs as a strategy to avoid synapse loss in schizophrenia.

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.

Mapping medically relevant RNA isoform diversity in the aged human frontal cortex with deep long-read RNA-seq

Determining whether the RNA isoforms from medically relevant genes have distinct functions could facilitate direct targeting of RNA isoforms for disease treatment. Here, as a step toward this goal for neurological diseases, we sequenced 12 postmortem, aged human frontal cortices (6 Alzheimer disease cases and 6 controls; 50% female) using one Oxford Nanopore PromethION flow cell per sample. We identified 1,917 medically relevant genes expressing multiple isoforms in the frontal cortex where 1,018 had multiple isoforms with different protein-coding sequences. Of these 1,018 genes, 57 are implicated in brain-related diseases including major depression, schizophrenia, Parkinson's disease and Alzheimer disease. Our study also uncovered 53 new RNA isoforms in medically relevant genes, including several where the new isoform was one of the most highly expressed for that gene. We also reported on five mitochondrially encoded, spliced RNA isoforms. We found 99 differentially expressed RNA isoforms between cases with Alzheimer disease and controls.

In silico toxicology investigation of μ-conotoxin KIIIA on human Na+ channel Nav1.2

Conotoxins(CTXs) can specifically act on multiple ion channels, which are crucial for the development of neurobiology and novel targeted drug development. At present, >10,000 kinds of CTXs have been sequenced, it would be extremely laborious to conduct experiments for each. μ-CTX KIIIA is a type of substance that can selectively recognize voltage-gated sodium ion channels. This article constructs four derivatives of KIIIA and predicts their 3D structures; afterwards, their molecular orbital arrangements and physicochemical properties were calculated using DFT; then, predicted their toxicokinetic parameters such as absorption, distribution, metabolism, excretion (ADME) and toxicity (T) through Machine Learning (ML); finally, molecular docking and molecular dynamics are used to investigate the interaction modes and binding affinity. The results indicate that the toxicity of KIIIA and its derivatives (KIIIA-1 -KIIIA-4) to the human body is mainly concentrated in the liver and respiratory tract. Among four derivatives, KIIIA-2 (5 Ser → Arg) has better toxicokinetics properties and its binding energy to Nav1.2 is -65.32 kcal/mol, which is higher than that of wild type(-32.13 kcal/mol). This study indicate that computational toxicology can facilitate the druggability research of CTXs, and KIIIA-2 can be developed as a potential antiepileptic drug.

Rare mutations implicate CGE interneurons as a vulnerable axis of cognitive deficits across psychiatric disorders

Neuropsychiatric disorders such as autism spectrum disorder (ASD) and schizophrenia (SCZ) share genetic risk factors, including rare high penetrance single nucleotide variants and copy number variants (CNVs), and exhibit both overlapping and distinct clinical phenotypes. Cognitive deficits and intellectual disability-critical predictors of long-term outcomes-are common to both conditions. To investigate shared and disorder-specific neurobiological impact of highly penetrant rare mutations in ASD and SCZ, we analyzed human single-nucleus whole-brain sequencing data to identify strongly affected brain cell types. Our analysis revealed Caudal Ganglionic Eminence (CGE)-derived GABAergic interneurons as a key nexus for cognitive deficits across these disorders. Notably, genes within 22q11.2 deletions, known to confer a high risk of SCZ, ASD, and cognitive impairment, showed a strong expression bias toward vasoactive intestinal peptide-expressing cells (VIP+) among CGE subtypes. To explore VIP+ GABAergic interneuron perturbations in the 22q11.2 deletion syndrome in vivo , we examined their activity in the Df(16)A +/- mouse model during a spatial navigation task and observed reduced activity along with altered responses to random rewards. At the population level, VIP+ interneurons exhibited impaired spatial encoding and diminished subtype-specific activity suggesting deficient disinhibition in CA1 microcircuits in the hippocampus, a region essential for learning and memory. Overall, these results demonstrate the crucial role of CGE-derived interneurons in mediating cognitive processes that are disrupted across a range of psychiatric and neurodevelopmental disorders.

Oxytocin and autism: Insights from clinical trials and animal models

Autism spectrum disorder is a highly heritable and heterogeneous neurodevelopmental disorder, characterized by impaired social interactions and repetitive behaviors. Despite its complex etiology, increasing evidence has linked autism to the oxytocin system. The oxytocin peptide has long been known as the "social hormone," and has been shown to increase attention to social cues, elevate salience of socially relevant stimuli, and increase learning and reward in social situations. Reduced oxytocin levels and mutations in the oxytocin system have been reported in autism patients, while exogenously delivered oxytocin has been shown to alleviate social interaction deficits in both patients and animal models. Here, we summarize the results of recent clinical trials using oxytocin nasal spray to treat individuals with autism, as well as studies of autism animal models with oxytocin system deficits, and the rescue of their social behavior deficits by oxytocin. Finally, we discuss factors influencing clinical outcomes and reflect on future directions.

Alternative splicing analysis in a Spanish ASD (Autism Spectrum Disorders) cohort: in silico prediction and characterization

Autism Spectrum Disorders (ASD) are complex and genetically heterogeneous neurodevelopmental conditions. Although alternative splicing (AS) has emerged as a potential contributor to ASD pathogenesis, its role in large-scale genomic studies has remained relatively unexplored. In this comprehensive study, we utilized computational tools to identify, predict, and validate splicing variants within a Spanish ASD cohort (360 trios), shedding light on their potential contributions to the disorder. We utilized SpliceAI, a newly developed machine-learning tool, to identify high-confidence splicing variants in the Spanish ASD cohort and applied a stringent threshold (Δ ≥ 0.8) to ensure robust confidence in the predictions. The in silico validation was then conducted using SpliceVault, which provided compelling evidence of the predicted splicing effects, using 335,663 reference RNA-sequencing (RNA-seq) datasets from GTEx v8 and the sequence read archive (SRA). Furthermore, ABSplice was employed for additional orthogonal in silico confirmation and to elucidate the tissue-specific impacts of the splicing variants. Notably, our analysis suggested the contribution of splicing variants within CACNA1I, CBLB, CLTB, DLGAP1, DVL3, KIAA0513, OFD1, PKD1, SLC13A3, and SCN2A. Complementary datasets, including more than 42,000 ASD cases, were employed for gene validation and gene ontology (GO) analysis. These analyses revealed potential tissue-specific effects of the splicing variants, particularly in adipose tissue, testis, and the brain. These findings suggest the involvement of these tissues in ASD etiology, which opens up new avenues for further functional testing. Enrichments in molecular functions and biological processes imply the presence of separate pathways and mechanisms involved in the progression of the disorder, thereby distinguishing splicing genes from other ASD-related genes. Notably, splicing genes appear to be predominantly associated with synaptic organization and transmission, in contrast to non-splicing genes (i.e., genes harboring de novo and inherited coding variants not predicted to alter splicing), which have been mainly implicated in chromatin remodeling processes. In conclusion, this study advances our comprehension of the role of AS in ASD and calls for further investigations, including in vitro validation and integration with multi-omics data, to elucidate the functional roles of the highlighted genes and the intricate interplay of the splicing process with other regulatory mechanisms and tissues in ASD.