Targeted sequencing identifies 91 neurodevelopmental-disorder risk genes with autism and developmental-disability biases

A de novo ZMYM2 gene variant associated to a Rett-like phenotype: Case report of a new phenotype and review of the literature

BACKGROUND

ZMYM2 heterozygous pathogenic variants cause an ultra-rare disease characterized by a broad clinical phenotype. This condition has been named neurodevelopmental-craniofacial syndrome with variable renal and cardiac abnormalities (NECRC, MIM#619522). Associated anomalies include congenital abnormalities of the kidney and urinary tract (CAKUT), non-specific facial, cardiac, and skeletal abnormalities, along with a variety of neurodevelopmental disorders. Other abnormalities reported in some patients include infantile hypotonia, poor growth, microcephaly, hypospadias, and motor stereotypies. Recently, one patient with cerebral palsy embedded in a complex phenotype was reported to carry a pathogenic ZMYM2 variant.

CASE PRESENTATION

This study presents the case of a 13-year-old girl carrying a de novo ZMYM2 heterozygous pathogenic variant. The patient displayed a Rett-like phenotype, associated with non-specific features such as precocious puberty, short stature, facial dysmorphisms, and spastic diplegia.

CONCLUSIONS

This case expands the known clinical phenotype associated with ZMYM2 pathogenic variants, suggesting for the first time a possible link to Rett-like syndromes.

Auts2 enhances neurogenesis and promotes expansion of the cerebral cortex

INTRODUCTION

The AUTS2 gene is associated with various neurodevelopmental and psychiatric disorders and has been suggested to play a role in acquiring human-specific traits. Functional analyses of Auts2 knockout mice have focused on postmitotic neurons, and the reported phenotypes do not faithfully recapitulate the whole spectrum of AUTS2-related human diseases.

OBJECTIVE

The objective of the study is to assess the role of AUTS2 in the biology of neural progenitor cells, cortical neurogenesis and expansion; and understand how its deregulation leads to neurological disorders.

METHODS

We screened the literature and conducted a time point analysis of AUTS2 expression during cortical development. We used in utero electroporation to acutely modulate the expression level of AUTS2 in the developing cerebral cortex in vivo, and thoroughly characterized cortical neurogenesis and morphogenesis using immunofluorescence, cell tracing and sorting, transcriptomic profiling, and gene ontology enrichment analyses.

RESULTS

In addition to its expression in postmitotic neurons, we showed that AUTS2 is also expressed in neural progenitor cells at the peak of neurogenesis. Upregulation of AUTS2 dramatically altered the differentiation program and fate determination of cortical progenitors. Notably, it increased the number of basal progenitors and neurons and changed the expression of hundreds of genes, among which 444 have not been implicated in mouse brain development or function.

CONCLUSION

The study provides evidence that AUTS2 is expressed in germinal zones and plays a key role in fate decision of neural progenitor cells with impact on corticogenesis. It also presents comprehensive lists of AUTS2 target genes thus advancing the molecular mechanisms underlying AUTS2-associated diseases and the evolutionary expansion of the cerebral cortex.

Natural History of NAA15 -Related Neurodevelopmental Disorder Through Adolescence

The NatA N-terminal acetyltransferase complex is composed of the NAA10 catalytic subunit and the auxiliary subunits NAA15 and HYPK. While those with variants in the enzymatic subunit develop Ogden Syndrome, individuals with variants in the NAA15 coding region develop NAA15-related neurodevelopmental syndrome, which presents with a wide array of manifestations that affect the heart, brain, musculoskeletal system, and behavioral and cognitive development. We tracked a cohort of 27 participants (9 females and 18 males) with pathogenic NAA15 variants over time and administered the Vineland-3 assessment to assess their adaptive functioning. We found that this cohort performed significantly worse compared to the normalized Vineland values. On average, females performed better than males, and they performed significantly better on the motor domain and fine motor sub-domain portions of the assessment. Over time, females showed a significant decrease in adaptive functioning, primarily in the daily living skills and motor domains. Males (after excluding one outlier) showed a moderate positive correlation between age and adaptive behavior composite (ABC) standard score. Despite a similar etiology caused by dysfunction in the NatA complex, NAA15-related neurodevelopmental disorder appears to have a weaker effect on adaptive behavior than Ogden Syndrome. However, these differences are based on comparisons to similar literature, as opposed to head-to-head testing. Lastly, comparisons between probands with loss of function variants in NAA15 and those with missense variants showed no significant differences in adaptive behavior metrics. Ultimately, additional longitudinal data should be collected to determine the validity of the between sex differences and to better understand the change in adaptive behavioral outcomes of individuals with NAA15-neurodevelopmental disorder as they age.

Androgens mediate sexual dimorphism in Pilarowski-Bjornsson Syndrome

Sex-specific penetrance in autosomal dominant Mendelian conditions is largely understudied. The neurodevelopmental disorder Pilarowski-Bjornsson syndrome (PILBOS) was initially described in females. Here, we describe the clinical and genetic characteristics of the largest PILBOS cohort to date, showing that both sexes can exhibit PILBOS features, although males are overrepresented. A mouse model carrying a human-derived Chd1 missense variant (Chd1 R616Q/+) displays female-restricted phenotypes, including growth deficiency, anxiety and hypotonia. Orchiectomy unmasks a growth deficiency phenotype in male Chd1 R616Q/+ mice, while testosterone rescues the phenotype in females, implicating androgens in phenotype modulation. In the gnomAD and UK Biobank databases, rare missense variants in CHD1 are overrepresented in males, supporting a male protective effect. We identify 33 additional highly constrained autosomal genes with missense variant overrepresentation in males. Our results support androgen-regulated sexual dimorphism in PILBOS and open novel avenues to understand the mechanistic basis of sexual dimorphism in other autosomal Mendelian disorders.

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.

Discovery of a Novel CUL3 Variant: Unveiling Epilepsy and Newly Associated Dysmorphic Traits in a Turkish Patient

Introduction

Cullin-3, encoded by the CUL3, is a core component of the ubiquitin E3 ligase complex. Through binding to specific adapters, this scaffold protein mediates the ubiquitination of a number of substrates, targeting their proteasomal degradation. Pathogenic variations of the CUL3 are thought to cause autism and neurodevelopmental disorders, but so far, few studies have been associated with the phenotype "neurodevelopmental disorder with or without autism or seizures (NEDAUS, #OMIM: 619239)." This study aimed to present the first Turkish patient with a NEDAUS phenotype exhibiting novel clinical and genotypic findings.

Case Presentation

A 7-year-old patient with seizure, speech delay, decreased eye contact, and autistic behaviors was referred to our clinic. The patient was evaluated through clinical examination, laboratory tests, and imaging studies. Physical examination revealed extremity findings (brachydactyly, tapering fingers). Single whole-exome sequencing analysis was performed for clinical diagnosis. A novel missense variant, c.368T>A (p.Leu123Gln) in CUL3, was discovered in the patient. Additionally, computational studies were employed to gain structural and mechanistic insights into the putative damaging impact of the variant. Computational analyses indicated that the p.Leu123Gln substitution may affect the stability and binding behavior of cullin-3. The detected variant was confirmed by the Sanger method and screened in family members by the same method and was found to be de novo.

Conclusion

By presenting the first Turkish case of a novel missense variant with a CUL3-related NEDAUS phenotype, this study contributes to the expansion of the genotypic and phenotypic spectrum of the disease.

Genomic analysis of 11,555 probands identifies 60 dominant congenital heart disease genes

Congenital heart disease (CHD) is a leading cause of infant mortality. We analyzed de novo mutations (DNMs) and very rare transmitted/unphased damaging variants in 248 prespecified genes in 11,555 CHD probands. The results identified 60 genes with a significant burden of heterozygous damaging variants. Variants in these genes accounted for CHD in 10.1% of probands with similar contributions from de novo and transmitted variants in parent-offspring trios that showed incomplete penetrance. DNMs in these genes accounted for 58% of the signal from DNMs. Thirty-three genes were linked to a single CHD subtype while 12 genes were associated with 2 to 4 subtypes. Seven genes were only associated with isolated CHD, while 37 were associated with 1 or more extracardiac abnormalities. Genes selectively expressed in the cardiomyocyte lineage were associated with isolated CHD, while those widely expressed in the brain were also associated with neurodevelopmental delay (NDD). Missense variants introducing or removing cysteines in epidermal growth factor (EGF)-like domains of NOTCH1 were enriched in tetralogy of Fallot and conotruncal defects, unlike the broader CHD spectrum seen with loss of function variants. Transmitted damaging missense variants in MYH6 were enriched in multiple CHD phenotypes and account for ~1% of all probands. Probands with characteristic mutations causing syndromic CHD were frequently not diagnosed clinically, often due to missing cardinal phenotypes. CHD genes that were positively or negatively associated with development of NDD suggest clinical value of genetic testing. These findings expand the understanding of CHD genetics and support the use of molecular diagnostics in CHD.

Gonadal Mosaicism for an ASH1L Intragenic Deletion Makes a Bridge Between MRD52 and 1q22 Microdeletion

ASH1L gene encodes a histone lysine methyltransferase, highly expressed in both embryonic and adult human brain. De novo loss-of-function variants in ASH1L are described in an ultrarare monogenic neurodevelopmental disorder, previously called mental retardation type 52 (MRD52). At the same time, a few cases are reported in the literature and DECIPHER with 1q22 microdeletions spanning ASH1L. We report three siblings presenting non-syndromic intellectual disability (ID) and an ASH1L intragenic deletion extending from exons 2 to 12 detected at SNP-array. Both parents resulted noncarrier suggesting gonadal/gonosomal mosaicism in one of the parents. This observation restricted the smallest region of overlap of the 1q22 microdeletion to ASH1L, and allowed to consider MRD52 and 1q22 microdeletion the same ASH1L-related neurodevelopmental disorder. We also reported the first example of gonadal/gonosomal mosaicism for an ASH1L deleterious variant, a fact that should generate the suspicion of recurrence also in sporadic cases of ASH1L-related neurodevelopmental disorder.

Evolutionary divergence in CTCF-mediated chromatin topology drives transcriptional innovation in humans

Chromatin topology can impact gene regulation, but how evolutionary divergence in chromatin topology has shaped gene regulatory landscapes for distinctive human traits remains poorly understood. CTCF sites determine chromatin topology by forming domains and loops. Here, we show evolutionary divergence in CTCF-mediated chromatin topology at the domain and loop scales during primate evolution, elucidating distinct mechanisms for shaping regulatory landscapes. Human-specific divergent domains lead to a broad rewiring of transcriptional landscapes. Divergent CTCF loops concord with species-specific enhancer activity, influencing enhancer connectivity to target genes in a concordant yet constrained manner. Under this concordant mechanism, we establish the role of human-specific CTCF loops in shaping transcriptional isoform diversity, with functional implications for disease susceptibility. Furthermore, we validate the function of these human-specific CTCF loops using human forebrain organoids. This study advances our understanding of genetic evolution from the perspective of genome architecture.

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

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

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

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

The application of population data linkage to capture sibling health outcomes among children and young adults with neurodevelopmental conditions. A scoping review

Introduction

Siblings of children with neurodevelopmental conditions have unique experiences and challenges related to their sibling role. Some develop mental health concerns as measured by self-reported surveys or parent report. Few data are available at the population level, owing to difficulties capturing wide-scale health data for siblings. Data linkage is a technique that can facilitate such research.

Objective

To explore the application of population data linkage as a research method to capture health outcomes of siblings of children with neurodevelopmental conditions.

Inclusion criteria

Peer reviewed papers that captured health outcomes for siblings of children and young adults with neurodevelopmental conditions using population data linkage.

Methods

JBI Scoping review methods were followed. Papers were searched within CINAHL, Ovid, Scopus, and Web of Science from 2000 to 2024 using search terms relating to 'data linkage' 'neurodevelopmental conditions' 'siblings' and 'health outcomes'.

Results

The final data extraction included 31 papers. The neurodevelopmental conditions of index children were autism, attention deficit hyperactivity disorder, intellectual disability, cerebral palsy and developmental delay. The mean follow-up time was 31 years, and the majority of studies originated from Scandinavia. Sibling health outcomes observed were psychiatric diagnoses, self-harm and suicide, other neurodevelopmental conditions, and medical conditions such as atopic disease, cancer and obesity.

Conclusion

Data linkage can help capture sibling health outcomes quickly across large cohorts with a range of neurodevelopmental conditions. Future research could be enhanced by focusing on siblings as the primary group of interest, increased integration of genealogical data, and comparisons between diagnostic groups and severity levels. Adoption of established rigorous reporting methods will increase the replicability of this type of research, and provide a stronger evidence-base from which to inform sibling supports.

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

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

Drosophila WDFY3/Bchs overexpression impairs neural function

Pathogenic variants in WDFY3, a gene encoding for an autophagy adaptor termed ALFY, are linked to neurodevelopmental delay and altered brain size in human probands. While the role of WDFY3 loss-of-function is extensively studied in neurons, little is known about the effects of WDFY3 upregulation in different cell types of the central nervous system (CNS). We show that overexpression of the Drosophila melanogaster WDFY3 ortholog, Bchs, in either glia or neurons impaired autophagy and locomotion. Bchs glial overexpression also increased VNC size and glial nuclei number significantly, whereas neuronal Bchs overexpression affected wing and thorax morphology. We identified 79 genes that were differentially expressed and overlapped in flies that overexpress Bchs in glial and neuronal cells, respectively. Additionally, upon neuronal Bchs overexpression differentially expressed genes clustered in gene ontology categories associated with autophagy and mitochondrial function. Our data indicate that glial as well as neuronal Bchs upregulation can have detrimental outcomes on neural function.

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

BACKGROUND

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

METHODS

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

RESULTS

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

CONCLUSION

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

The chromatin remodeler ADNP regulates neurodevelopmental disorder risk genes and neocortical neurogenesis

Although chromatin remodelers are among the most important risk genes associated with neurodevelopmental disorders (NDDs), the roles of these complexes during brain development are in many cases unclear. Here, we focused on the recently discovered ChAHP chromatin remodeling complex. The zinc finger and homeodomain transcription factor ADNP is a core subunit of this complex, and de novo ADNP mutations lead to intellectual disability and autism spectrum disorder. However, germline Adnp knockout mice were previously shown to exhibit early embryonic lethality, obscuring subsequent roles for the ChAHP complex in neurogenesis. To circumvent this early developmental arrest, we generated a conditional Adnp mutant allele. Using single-cell transcriptomics, cut&run-seq, and histological approaches, we show that during neocortical development, Adnp orchestrates the production of late-born, upper-layer neurons through a two-step process. First, Adnp is required to sustain progenitor proliferation specifically during the developmental window for upper-layer cortical neurogenesis. Accordingly, we found that Adnp recruits the ChAHP subunit Chd4 to genes associated with progenitor proliferation. Second, in postmitotic differentiated neurons, we define a network of risk genes linked to NDDs that are regulated by Adnp and Chd4. Taken together, these data demonstrate that ChAHP is critical for driving the expansion of upper-layer cortical neurons and for regulating neuronal gene expression programs, suggesting that these processes may potentially contribute to NDD etiology.

Naa15 Haploinsufficiency and De Novo Missense Variants Associate With Neurodevelopmental Disorders and Interfere With Neurogenesis and Neuron Development

Neurodevelopmental disorders (NDDs) encompass a group of conditions that impact brain development and function, exhibiting significant genetic and clinical heterogeneity. NAA15, the auxiliary subunit of the N-terminal acetyltransferase complex, has garnered attention due to its association with NDDs. However, the precise role of NAA15 in cortical development and its contribution to NDDs remain elusive. By employing targeted sequencing on a large Chinese cohort affected by ASD and conducting an extensive literature review, we have compiled 64 distinct variants in the NAA15 gene identified among individuals with neurodevelopmental disorders. Our research demonstrates that loss of NAA15 leads to a substantial increase in neuronal count, potentially resulting in aberrant brain development and triggering repetitive as well as anxious behaviors in mice models. Furthermore, disorder-associated variants within NAA15 impair axon and synapse formation processes crucial for neural connectivity establishment. These findings shed light on the consequences of NAA15 deficiency along with its de novo mutations on brain development while unraveling the cellular mechanisms underlying NDDs.

Unraveling Copper Imbalance in Autism Spectrum Disorder: Mechanistic Insights from the Valproic Acid Mouse Model

Abnormal copper (Cu) levels are often closely associated with neurological disorders including neurodevelopmental conditions, such as autism spectrum disorder (ASD). However, the mechanisms underlying the disruption of Cu homeostasis in critical organs, such as the brain, remain unclear. In this study, we elucidated the molecular mechanisms of Cu imbalance in the brain of a valproic acid (VPA) mouse model along with the changes in specific metabolites. Significant alterations occurred in proteins associated with primary Cu-related metabolism in specific regions of the brain (prefrontal cortex, amygdala, cerebellum, and hippocampus), resulting in a direct elevation of Cu ions within the brain tissues (control: 5.05 ± 0.61 μg/g vs model: 6.28 ± 0.81 μg/g, p = 0.015). Furthermore, the brain metabolic profiles revealed significant upregulation of lipids, particularly phospholipid metabolites. Typical neurotransmitters, for example, dopamine (DA) (p < 0.0001) and serotonin (5-HT) (p = 0.02) were upregulated in amygdala. Other small metabolites like glutathione (GSH) (p = 0.0004) also exhibited notable variation in brain. The potential impact of Cu toxicity on the signaling pathways of key metabolites was then evaluated, providing new insights into the role of Cu in metabolism of neurotransmitters in the brain. Our finding sheds molecular aberrations associated with essential element metabolism in the brain, providing new elemental perspectives for understanding the pathogenic mechanisms underlying ASD.

SETD1B variants associated with absence seizures

AIM

Exploring the association between SETD1B variants and absence seizures (ASs).

METHODS

We engaged a small cohort of four pediatric epilepsy patients with identified SETD1B variants and conducted a comprehensive review of 50 documented instances. Clinical profiles were meticulously compiled, and genetic screening was executed via trio-based whole-exome sequencing. Our literature survey centered on AS manifestations linked to SETD1B alterations, utilizing descriptive statistics for analysis.

RESULTS

The quartet of new cases presented with developmental impediments, cognitive deficits, and epileptic manifestations. Pathogenicity was established in the detected SETD1B variants. Among the 54 individuals, 26 (accounting for 48.1 %) presented with AS during the course of the disease. The median seizure onset age stood at 44.8 months, with a majority displaying cognitive challenges and autistic traits. Anti-epileptic drug therapies proved efficacious in 70.8 % of the instances. Notably, variants within the N-SET, SET, and post-SET domains of SETD1B were prevalent in 46.2 % of the AS-afflicted cohort.

DISCUSSION

Our findings accentuate the potential influence of SETD1B variants in AS pathogenesis, these variants may perturb neuronal excitability, possibly via modulation of histone methylation landscapes. The insights garnered here deepen our grasp of AS's genetic architecture.

CONCLUSION

Our study identified four novel SETD1B variants, highlighting that the importance of AS as part of the phenotype among individuals with SETD1B, demonstrated by 3 novel cases, and supported by review of the literature. Our findings also suggest that the SET domains may play a potential role in the pathogenesis of AS, providing a clue for future mechanistic research.

Chemogenetic Inhibition of Prefrontal Cortex Ameliorates Autism-Like Social Deficits and Absence-Like Seizures in a Gene-Trap Ash1l Haploinsufficiency Mouse Model

BACKGROUND

ASH1L (absent, small, or homeotic-like 1), a histone methyltransferase, has been identified as a high-risk gene for autism spectrum disorder (ASD). We previously showed that postnatal Ash1l severe deficiency in the prefrontal cortex (PFC) of male and female mice caused seizures. However, the synaptic mechanisms underlying autism-like social deficits and seizures need to be elucidated.

OBJECTIVE

The goal of this study is to characterize the behavioral deficits and reveal the synaptic mechanisms in an Ash1l haploinsufficiency mouse model using a targeted gene-trap knockout (gtKO) strategy.

METHOD

A series of behavioral tests were used to examine behavioral deficits. Electrophysiological and chemogenetic approaches were used to examine and manipulate the excitability of pyramidal neurons in the PFC of Ash1l+/GT mice.

RESULTS

Ash1l+/GT mice displayed social deficits, increased self-grooming, and cognitive impairments. Epileptiform discharges were found on electroencephalograms (EEGs) of Ash1l+/GT mice, indicating absence-like seizures. Ash1l haploinsufficiency increased the susceptibility for convulsive seizures when Ash1l+/GT mice were challenged by pentylenetetrazole (PTZ, a competitive GABAA receptor antagonist). Whole-cell patch-clamp recordings showed that Ash1l haploinsufficiency increased the excitability of pyramidal neurons in the PFC by altering intrinsic neuronal properties, enhancing glutamatergic synaptic transmission, and diminishing GABAergic synaptic inhibition. Chemogenetic inhibition of pyramidal neurons in the PFC of Ash1l+/GT mice ameliorated autism-like social deficits and abolished absence-like seizures.

CONCLUSIONS

We demonstrated that increased neural activity in the PFC contributed to the autism-like social deficits and absence-like seizures in Ash1l+/GT mice, which provides novel insights into the therapeutic strategies for patients with ASH1L-associated ASD and epilepsy.

Rapid effects of valproic acid on the fetal brain transcriptome: implications for brain development and autism

There is an increased incidence of autism among the children of women who take the anti-epileptic, mood-stabilizing drug, valproic acid (VPA) during pregnancy; moreover, exposure to VPA in utero causes autistic-like symptoms in rodents and non-human primates. Analysis of RNA-seq data obtained from E12.5 fetal mouse brains 3 hours after VPA administration to the pregnant dam revealed that VPA rapidly and significantly increased or decreased the expression of approximately 7,300 genes. No significant sex differences in VPA-induced gene expression were observed. Expression of 399 autism risk genes was significantly altered by VPA as was expression of 258 genes that have been reported to modulate fetal brain development but are not otherwise linked to autism. Expression of genes associated with intracellular signaling pathways, neurogenesis, and excitation-inhibition balance as well as synaptogenesis, neuronal fate determination, axon and dendritic development, neuroinflammation, circadian rhythms, and epigenetic modulation of gene expression was dysregulated by VPA. Notably, at least 40 genes that are known to regulate embryonic neurogenesis were dysregulated by VPA. The goal of this study was to identify mouse genes that are: (a) significantly up- or downregulated by VPA in the fetal brain and (b) associated with autism and/or known to play a role in embryonic neurodevelopmental processes, perturbation of which has the potential to alter brain connectivity and, consequently behavior, in the adult. The genes meeting these criteria provide potential targets for future hypothesis-driven studies to elucidate the proximal causes of errors in brain connectivity underlying neurodevelopmental disorders such as autism.

Dynamic Regulation OF The Chromatin Environment By Ash1L Modulates Human Neuronal Structure And Function

Precise regulation of the chromatin environment through post-translational histone modification modulates transcription and controls brain development. Not surprisingly, mutations in a large number of histone-modifying enzymes underlie complex brain disorders. In particular, the histone methyltransferase ASH1L modifies histone marks linked to transcriptional activation and has been implicated in multiple neuropsychiatric disorders. However, the mechanisms underlying the pathobiology of ASH1L-asociated disease remain underexplored. We generated human isogenic stem cells with a mutation in ASH1L's catalytic domain. We find that ASH1L dysfunction results in reduced neurite outgrowth, which correlates with alterations in the chromatin profile of activating and repressive histone marks, as well as the dysregulation of gene programs important for neuronal structure and function implicated in neuropsychiatric disease. We also identified a novel regulatory node implicating both the SP and Krüppel -like families of transcription factors and ASH1L relevant to human neuronal development. Finally, we rescue cellular defects linked to ASH1L dysfunction by leveraging two independent epigenetic mechanisms that promote transcriptional activation. In summary, we identified an ASH1L-driven epigenetic and transcriptional axis essential for human brain development and complex brain disorders that provide insights into future therapeutic strategies for ASH1L-related disorders.

Combining Off-flow, a Nextflow-coded program, and whole genome sequencing reveals unintended genetic variation in CRISPR/Cas-edited iPSCs

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas nucleases and human induced pluripotent stem cell (iPSC) technology can reveal deep insight into the genetic and molecular bases of human biology and disease. Undesired editing outcomes, both on-target (at the edited locus) and off-target (at other genomic loci) hinder the application of CRISPR-Cas nucleases. We developed Off-flow, a Nextflow-coded bioinformatic workflow that takes a specific guide sequence and Cas protein input to call four separate off-target prediction programs (CHOPCHOP, Cas-Offinder, CRISPRitz, CRISPR-Offinder) to output a comprehensive list of predicted off-target sites. We applied it to whole genome sequencing (WGS) data to investigate the occurrence of unintended effects in human iPSCs that underwent repair or insertion of disease-related variants by homology-directed repair. Off-flow identified a 3-base-pair-substitution and a mono-allelic genomic deletion at the target loci, KCNQ2, in 2 clones. Unbiased WGS analysis further identified off-target missense variants and a mono-allelic genomic deletion at the targeted locus, GNAQ, in 10 clones. On-target substitution and deletions had escaped standard PCR and Sanger sequencing analysis, while missense variants at other genomic loci were not detected by Off-flow. We used these results to filter out iPSC clones for subsequent functional experiments. Off-flow, which we make publicly available, works for human and mouse genomes currently and can be adapted for other genomes. Off-flow and WGS analysis can improve the integrity of studies using CRISPR/Cas-edited cells and animal models.

Generation of a human induced pluripotent stem cell line (FDIBSi001-A) from a patient with ADNP syndrome carrying ADNP mutation (c. 2059 T>C)

ADNP syndrome is a neurodevelopmental disorder characterized by autism, intellectual disability, and other physical and behavioral health manifestations. Mutations in ADNP gene is responsible for ADNP syndrome. A human iPSC line with a de novo heterozygous ADNP mutation (ADNP c. 2059 T>C) was generated from peripheral blood mononuclear cells of a patient with ADNP syndrome. This iPSC line showed typical human embryonic stem cell-like morphology, normal karyotype, pluripotency, and ability to differentiate into three germ layers. This iPSC line provides a useful resource to study the pathogenesis and drug screening of ADNP syndrome.

Clinical and Genetic Characterization of Adolescent-Onset Epilepsy: A Single-Center Experience in Republic of Korea

OBJECTIVES

This study investigated the characteristics of adolescent-onset epilepsy (AOE) and conducted genetic tests on a cohort of 76 Korean patients to identify variants and expand the spectrum of mutations associated with AOE.

METHODS

Clinical exome sequencing after routine karyotyping and chromosomal microarray was performed to identify causative variants and expand the spectrum of mutations associated with AOE.

RESULTS

In cases of AOE without neurodevelopmental delay (NDD), this study identified four likely pathogenic variants (LPVs) or variants of uncertain significance (VUS) and two copy number variations (CNVs). To explore the unique features of AOE; clinical manifestations were compared between patients with and without NDD. The analysis revealed statistically significant differences in the prevalence of males and the yield of genetic testing results. AOE without NDD had a lower prevalence in males (49%) compared to AOE with NDD (60%) (p = 0.007). Genetic alterations: AOE with NDD exhibited a higher frequency of genetic alterations (35%) compared to AOE without NDD (12%) (p = 0.011). Thorough evaluation of AOE can be particularly challenging in adolescent patients. Some individuals may display genetic variations due to a phenomenon known as locus heterogeneity, where different genetic causes lead to similar clinical presentations.

CONCLUSIONS

Implementing a robust genetic workflow is crucial for accurately diagnosing AOE, even in cases with complex genetic underpinnings. This study underscores the importance of genetic testing as an essential diagnostic tool for AOE. Identifying genetic variants and understanding their clinical correlations can aid in improving diagnostic accuracy and optimizing treatment approaches for adolescent patients with epilepsy.

Deficiency of DDX3X results in neurogenesis defects and abnormal behaviors via dysfunction of the Notch signaling

The molecular mechanisms underlying the neurodevelopmental disorders (NDDs) caused by DDX3X variants remain poorly understood. In this study, we validated that de novo DDX3X variants are enriched in female developmental delay (DD) patients and mainly affect the evolutionarily conserved amino acids based on a meta-analysis of 46,612 NDD trios. We generated a ddx3x deficient zebrafish allele, which exhibited reduced survival rate, DD, microcephaly, adaptation defects, anxiolytic behaviors, social interaction deficits, and impaired spatial recognitive memory. As revealed by single-nucleus RNA sequencing and biological validations, ddx3x deficiency leads to reduced neural stem cell pool, decreased total neuron number, and imbalanced differentiation of excitatory and inhibitory neurons, which are responsible for the behavioral defects. Indeed, the supplementation of L-glutamate or glutamate receptor agonist ly404039 could partly rescue the adaptation and social deficits. Mechanistically, we reveal that the ddx3x deficiency attenuates the stability of the crebbp mRNA, which in turn causes downregulation of Notch signaling and defects in neurogenesis. Our study sheds light on the molecular pathology underlying the abnormal neurodevelopment and behavior of NDD patients with DDX3X mutations, as well as providing potential therapeutic targets for the precision treatment.

Loss of DOT1L function disrupts neuronal transcription, animal behavior, and leads to a novel neurodevelopmental disorder

Individuals with monoallelic pathogenic variants in the histone lysine methyltransferase DOT1L display global developmental delay and varying congenital anomalies. However, the impact of monoallelic loss of DOT1L remains unclear. Here, we present a largely female cohort of 11 individuals with DOT1L variants with developmental delays and dysmorphic facial features. We found that DOT1L variants include missense variants clustered in the catalytic domain, frameshift, and stop-gain variants. We demonstrate that specific variants cause loss of methyltransferase activity and therefore sought to define the effects of decreased DOT1L function. Using RNA-sequencing of cultured neurons and single nucleus RNA-sequencing of mouse cortical tissue, we found that partial Dot1l depletion causes sex-specific transcriptional responses and disrupts transcription of synaptic genes. Further, Dot1l loss alters neuron branching and expression of synaptic proteins. Lastly using zebrafish and mouse models, we found behavioral disruptions that include sex-specific deficits in mice. Overall, we define how DOT1L loss leads to neurological dysfunction by demonstrating that partial Dot1l loss impacts transcription, neuron morphology, and behavior across multiple models and systems.

Targeting epigenetic dysregulation in autism spectrum disorders

Autism spectrum disorders (ASD) comprise a range of neurodevelopmental pathologies characterized by deficits in social interaction and repetitive behaviors, collectively affecting almost 1% of the worldwide population. Deciphering the etiology of ASD has proven challenging due to the intricate interplay of genetic and environmental factors and the variety of molecular pathways affected. Epigenomic alterations have emerged as key players in ASD etiology. Their research has led to the identification of biomarkers for diagnosis and pinpointed specific gene targets for therapeutic interventions. This review examines the role of epigenetic alterations, resulting from both genetic and environmental influences, as a central causative factor in ASD, delving into its contribution to pathogenesis and treatment strategies.

Comprehensive reanalysis for CNVs in ES data from unsolved rare disease cases results in new diagnoses

We report the results of a comprehensive copy number variant (CNV) reanalysis of 9171 exome sequencing datasets from 5757 families affected by a rare disease (RD). The data reanalysed was extremely heterogeneous, having been generated using 28 different enrichment kits by 42 different research groups across Europe partnering in the Solve-RD project. Each research group had previously undertaken their own analysis of the data but failed to identify disease-causing variants. We applied three CNV calling algorithms to maximise sensitivity, and rare CNVs overlapping genes of interest, provided by four partner European Reference Networks, were taken forward for interpretation by clinical experts. This reanalysis has resulted in a molecular diagnosis being provided to 51 families in this sample, with ClinCNV performing the best of the three algorithms. We also identified partially explanatory pathogenic CNVs in a further 34 individuals. This work illustrates the value of reanalysing ES cold cases for CNVs.

Autism Spectrum Disorder Pathogenesis-A Cross-Sectional Literature Review Emphasizing Molecular Aspects

The etiology of autism spectrum disorder (ASD) has not yet been completely elucidated. Through time, multiple attempts have been made to uncover the causes of ASD. Different theories have been proposed, such as being caused by alterations in the gut-brain axis with an emphasis on gut dysbiosis, post-vaccine complications, and genetic or even autoimmune causes. In this review, we present data covering the main streams that focus on ASD etiology. Data collection occurred in many countries covering ethnically diverse subjects. Moreover, we aimed to show how the progress in genetic techniques influences the explanation of medical White Papers in the ASD area. There is no single evidence-based pathway that results in symptoms of ASD. Patient management has constantly only been symptomatic, and there is no ASD screening apart from symptom-based diagnosis and parent-mediated interventions. Multigene sequencing or epigenetic alterations hold promise in solving the disjointed molecular puzzle. Further research is needed, especially in the field of biogenetics and metabolomic aspects, because young children constitute the patient group most affected by ASD. In summary, to date, molecular research has confirmed multigene dysfunction as the causative factor of ASD, the multigene model with metabolomic influence would explain the heterogeneity in ASD, and it is proposed that ion channel dysfunction could play a core role in ASD pathogenesis.

Molecular diagnosis of patients with syndromic short stature identified by trio whole-exome sequencing

Background

Short stature is a complex disorder with phenotypic and genetic heterogeneity. This study aimed to investigate clinical phenotypes and molecular basis of a cohort of patients with short stature.

Methods

Trio whole-exome sequencing (Trio-WES) was performed to explore the genetic aetiology and obtain a molecular diagnosis in twenty Chinese probands with syndromic and isolated short stature.

Results

Of the twenty probands, six (6/20, 30%) patients with syndromic short stature obtained a molecular diagnosis. One novel COMP pathogenic variant c.1359delC, p.N453fs*62 and one LZTR1 likely pathogenic variant c.509G>A, p.R170Q were identified in a patient with short stature and skeletal dysplasia. One novel de novo NAA15 pathogenic variant c.63T>G, p.Y21X and one novel de novo KMT2A pathogenic variant c.3516T>A, p.N1172K was identified in two probands with short stature, intellectual disability and abnormal behaviours, respectively. One patient with short stature, cataract, and muscle weakness had a de novo POLG pathogenic variant c.2863 T>C, p.Y955H. One PHEX pathogenic variant c.1104G>A, p.W368X was identified in a patient with short stature and rickets. Maternal uniparental disomy 7 (mUPD7) was pathogenic in a patient with pre and postnatal growth retardation, wide forehead, triangular face, micrognathia and clinodactyly. Thirteen patients with isolated short stature had negative results.

Conclusion

Trio-WES is an important strategy for identifying genetic variants and UPD in patients with syndromic short stature, in which dual genetic variants are existent in some individuals. It is important to differentiate between syndromic and isolated short stature. Genetic testing has a high yield for syndromic patients but low for isolated patients.

Cognitive behavioral phenotyping of DSCAM heterozygosity as a model for autism spectrum disorder

It is estimated that 1 in 36 children are affected by autism spectrum disorder (ASD) in the United States, which is nearly a twofold increase from a decade ago. Recent genetic studies have identified de novo loss-of-function (dnLoF) mutations in the Down Syndrome Cell Adhesion Molecule (DSCAM) as a strong risk factor for ASD. Previous research has shown that DSCAM ablation confers social interaction deficits and perseverative behaviors in mouse models. However, it remains unknown to what extent DSCAM underexpression captures the full range of behaviors, specifically cognitive phenotypes, presented in ASD. Here, we conducted a comprehensive cognitive behavioral phenotyping which revealed that loss of one copy of DSCAM, as in the DSCAM2J+/-, that is, DSCAM heterozygous mice, displayed hyperactivity, increased anxiety-like behavior, and motor coordination deficits. Additionally, hippocampal-dependent learning and memory was affected, including impairments in working memory, long-term memory, and contextual fear learning. Interestingly, implicit learning processes remained intact. Therefore, DSCAM LoF produces autistic-like behaviors that are similar to those observed in human cases of ASD. These findings further support a role for DSCAM dnLoF mutations in ASD and suggest DSCAM2J+/- as a suitable model for ASD research.

Use of biomarkers in the diagnosis of Alzheimer's disease in adults with intellectual disability

People with intellectual disability are a vulnerable cohort who face challenges accessing health care. Compared with the general population, people with intellectual disability have an elevated risk of developing dementia, which often presents at a younger age and with atypical symptoms. The lifelong cognitive and functional difficulties faced by people with intellectual disability further complicate the diagnostic process. Specialised intellectual disability memory services and evaluation using reliable biomarkers of neurodegeneration are needed to improve diagnostic and prognostic certainty in this group. Inadequate specialist services and paucity of research on biomarkers in this population hinders progress and impedes the delivery of adequate health care. Although cerebrospinal fluid-based biomarkers and radiological biomarkers are used routinely in the evaluation of Alzheimer's disease in the general population, biological variation within the clinically heterogenous group of people with intellectual disability could affect the clinical utility of existing biomarkers. As disease-modifying therapies become available for the treatment of early Alzheimer's disease, and hopefully other neurodegenerative conditions in the future, biomarkers will serve as gatekeepers to establish the eligibility for such therapies. Inadequate representation of adults with intellectual disability in biomarker research will result in their exclusion from treatment with disease-modifying therapies, thus perpetuating the inequity in health care that is already faced by this group. The aim of this Series paper is to summarise current evidence on the application of biomarkers for Alzheimer's disease in a population with intellectual disability (that is not attributable to Down syndrome) and suspected cognitive decline.

Expanding the molecular landscape of childhood apraxia of speech: evidence from a single-center experience

Background

Childhood apraxia of speech (CAS) is a genetically heterogeneous pediatric motor speech disorder. The advent of whole exome sequencing (WES) and whole genome sequencing techniques has led to increased identification of pathogenic variants in CAS genes. In an as yet uncharacterized Italian cohort, we aimed both to identify new pathogenic gene variants associated with CAS, and to confirm the disease-related role of genes already reported by others. We also set out to refine the clinical and neurodevelopmental characterization of affected children, with the aim of identifying specific, gene-related phenotypes.

Methods

In a single-center study aiming to explore the genetic etiology of CAS in a cohort of 69 Italian children, WES was performed in the families of the 34 children found to have no copy number variants. Each of these families had only one child affected by CAS.

Results

High-confidence (HC) gene variants were identified in 7/34 probands, in two of whom they affected KAT6A and CREBBP, thus confirming the involvement of these genes in speech impairment. The other probands carried variants in low-confidence (LC) genes, and 20 of these variants occurred in genes not previously reported as associated with CAS. UBA6, ZFHX4, and KAT6A genes were found to be more enriched in the CAS cohort compared to control individuals. Our results also showed that most HC genes are involved in epigenetic mechanisms and are expressed in brain regions linked to language acquisition processes.

Conclusion

Our findings confirm a relatively high diagnostic yield in Italian patients.

Impact of KDM6B mosaic brain knockout on synaptic function and behavior

Autism spectrum disorders (ASD) are complex neurodevelopmental conditions characterized by impairments in social communication, repetitive behaviors, and restricted interests. Epigenetic modifications serve as critical regulators of gene expression playing a crucial role in controlling brain function and behavior. Lysine (K)-specific demethylase 6B (KDM6B), a stress-inducible H3K27me3 demethylase, has emerged as one of the highest ASD risk genes, but the precise effects of KDM6B mutations on neuronal activity and behavioral function remain elusive. Here we show the impact of KDM6B mosaic brain knockout on the manifestation of different autistic-like phenotypes including repetitive behaviors, social interaction, and significant cognitive deficits. Moreover, KDM6B mosaic knockout display abnormalities in hippocampal excitatory synaptic transmission decreasing NMDA receptor mediated synaptic transmission and plasticity. Understanding the intricate interplay between epigenetic modifications and neuronal function may provide novel insights into the pathophysiology of ASD and potentially inform the development of targeted therapeutic interventions.

Elucidating genetic and molecular basis of altered higher-order brain structure-function coupling in major depressive disorder

Previous studies have shown that major depressive disorder (MDD) patients exhibit structural and functional impairments, but few studies have investigated changes in higher-order coupling between structure and function. Here, we systematically investigated the effect of MDD on higher-order coupling between structural connectivity (SC) and functional connectivity (FC). Each brain region was mapped into embedding vector by the node2vec algorithm. We used support vector machine (SVM) with the brain region embedding vector to distinguish MDD patients from health controls (HCs) and identify the most discriminative brain regions. Our study revealed that MDD patients had decreased higher-order coupling in connections between the most discriminative brain regions and local connections in rich-club organization and increased higher-order coupling in connections between the ventral attentional network and limbic network compared with HCs. Interestingly, transcriptome-neuroimaging association analysis demonstrated the correlations between regional rSC-FC coupling variations between MDD patients and HCs and α/β-hydrolase domain-containing 6 (ABHD6), β 1,3-N-acetylglucosaminyltransferase-9(β3GNT9), transmembrane protein 45B (TMEM45B), the correlation between regional dSC-FC coupling variations and retinoic acid early transcript 1E antisense RNA 1(RAET1E-AS1), and the correlations between regional iSC-FC coupling variations and ABHD6, β3GNT9, katanin-like 2 protein (KATNAL2). In addition, correlation analysis with neurotransmitter receptor/transporter maps found that the rSC-FC and iSC-FC coupling variations were both correlated with neuroendocrine transporter (NET) expression, and the dSC-FC coupling variations were correlated with metabotropic glutamate receptor 5 (mGluR5). Further mediation analysis explored the relationship between genes, neurotransmitter receptor/transporter and MDD related higher-order coupling variations. These findings indicate that specific genetic and molecular factors underpin the observed disparities in higher-order SC-FC coupling between MDD patients and HCs. Our study confirmed that higher-order coupling between SC and FC plays an important role in diagnosing MDD. The identification of new biological evidence for MDD etiology holds promise for the development of innovative antidepressant therapies.

Visual and auditory attention in individuals with DYRK1A and SCN2A disruptive variants

This preliminary study sought to assess biomarkers of attention using electroencephalography (EEG) and eye tracking in two ultra-rare monogenic populations associated with autism spectrum disorder (ASD). Relative to idiopathic ASD (n = 12) and neurotypical comparison (n = 49) groups, divergent attention profiles were observed for the monogenic groups, such that individuals with DYRK1A (n = 9) exhibited diminished auditory attention condition differences during an oddball EEG paradigm whereas individuals with SCN2A (n = 5) exhibited diminished visual attention condition differences noted by eye gaze tracking when viewing social interactions. Findings provide initial support for alignment of auditory and visual attention markers in idiopathic ASD and neurotypical development but not monogenic groups. These results support ongoing efforts to develop translational ASD biomarkers within the attention domain.

A Natural History of NAA15 -related Neurodevelopmental Disorder Through Adolescence

NAA15 is a member of the NatA N-terminal acetyltransferase complex, which also includes the NAA10 enzymatic sub-unit. Individuals with variants in the NAA15 coding region develop NAA15 -related neurodevelopmental syndrome, which presents with a wide array of manifestations that affect the heart, brain, musculoskeletal system, and behavioral and cognitive development. We tracked a cohort of 27 participants (9 females and 18 males) over time, each with a pathogenic NAA15 variant, and administered the Vineland-3 assessment to assess their adaptive functioning. We found that the cohort performed significantly worse compared to the normalized Vineland values. On average, females performed better than males, and they performed significantly better on the Motor Domain and Fine Motor Sub-Domain portions of the assessment. Over time, females showed a decrease in adaptive functioning, with the decline being especially correlated at the Coping, Domestic, and Fine motor sub-domains. Males (after excluding one outlier) showed a moderate positive correlation between age and ABC standard score. Ultimately, additional longitudinal data should be collected to determine the validity of the between sex-differences and to better understand the change in adaptive behavioral outcomes of individuals with NAA15 -neurodevelopmental disorder as they age.

Loss of the polarity protein Par3 promotes dendritic spine neoteny and enhances learning and memory

The Par3 polarity protein is critical for subcellular compartmentalization in different developmental processes. Variants of PARD3, encoding PAR3, are associated with intelligence and neurodevelopmental disorders. However, the role of Par3 in glutamatergic synapse formation and cognitive functions in vivo remains unknown. Here, we show that forebrain-specific Par3 conditional knockout leads to increased long, thin dendritic spines in vivo. In addition, we observed a decrease in the amplitude of miniature excitatory postsynaptic currents. Surprisingly, loss of Par3 enhances hippocampal-dependent spatial learning and memory and repetitive behavior. Phosphoproteomic analysis revealed proteins regulating cytoskeletal dynamics are significantly dysregulated downstream of Par3. Mechanistically, we found Par3 deletion causes increased Rac1 activation and dysregulated microtubule dynamics through CAMSAP2. Together, our data reveal an unexpected role for Par3 as a molecular gatekeeper in regulating the pool of immature dendritic spines, a rate-limiting step of learning and memory, through modulating Rac1 activation and microtubule dynamics in vivo.

Targeted sequencing for hereditary breast and ovarian cancer in BRCA1/2-negative families reveals complex genetic architecture and phenocopies

Approximately 20% of breast cancer cases are attributed to increased family risk, yet variation in BRCA1/2 can only explain 20%-25% of cases. Historically, only single gene or single variant testing were common in at-risk family members, and further sequencing studies were rarely offered after negative results. In this study, we applied an efficient and inexpensive targeted sequencing approach to provide molecular diagnoses in 245 human samples representing 134 BRCA mutation-negative (BRCAX) hereditary breast and ovarian cancer (HBOC) families recruited from 1973 to 2019 by Dr. Henry Lynch. Sequencing identified 391 variants, which were functionally annotated and ranked based on their predicted clinical impact. Known pathogenic CHEK2 breast cancer variants were identified in five BRCAX families in this study. While BRCAX was an inclusion criterion for this study, we still identified a pathogenic BRCA2 variant (p.Met192ValfsTer13) in one family. A portion of BRCAX families could be explained by other hereditary cancer syndromes that increase HBOC risk: Li-Fraumeni syndrome (gene: TP53) and Lynch syndrome (gene: MSH6). Interestingly, many families carried additional variants of undetermined significance (VOUSs) that may further modify phenotypes of syndromic family members. Ten families carried more than one potential VOUS, suggesting the presence of complex multi-variant families. Overall, nine BRCAX HBOC families in our study may be explained by known likely pathogenic/pathogenic variants, and six families carried potential VOUSs, which require further functional testing. To address this, we developed a functional assay where we successfully re-classified one family's PMS2 VOUS as benign.

Recurrent gene flow between Neanderthals and modern humans over the past 200,000 years

Although it is well known that the ancestors of modern humans and Neanderthals admixed, the effects of gene flow on the Neanderthal genome are not well understood. We develop methods to estimate the amount of human-introgressed sequences in Neanderthals and apply it to whole-genome sequence data from 2000 modern humans and three Neanderthals. We estimate that Neanderthals have 2.5 to 3.7% human ancestry, and we leverage human-introgressed sequences in Neanderthals to revise estimates of Neanderthal ancestry in modern humans, show that Neanderthal population sizes were significantly smaller than previously estimated, and identify two distinct waves of modern human gene flow into Neanderthals. Our data provide insights into the genetic legacy of recurrent gene flow between modern humans and Neanderthals.

A guide to selecting high-performing antibodies for Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform (PPP2R5D) for use in Western Blot, immunoprecipitation and immunofluorescence

Protein phosphatase 2A is a serine/threonine phosphatase with activity dependent on an associated regulatory subunit, serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta (δ) isoform (PPP2R5D). PPP2R5D is the δ isoform in the B56 family of regulatory subunits. Abundantly expressed in the brain and involved in a broad range of cellular processes, PPP2R5D plays an essential role in modulating key neuronal pathways and signalling. Pathogenic mutations in the PPP2R5D gene are linked to clinical symptoms characterized by neurodevelopmental delay, intellectual disability, and autism spectrum disorders. The etiology of these genetic disorders remains unknown, which can partly be due to the lack of independently characterized antibodies. Here we have characterized six PPP2R5D commercial antibodies for Western Blot, immunoprecipitation, and immunofluorescence using a standardized experimental protocol based on comparing read-outs in knockout cell lines and isogenic parental controls. These studies are part of a larger, collaborative initiative seeking to address antibody reproducibility by characterizing commercially available antibodies for human proteins and publishing the results openly as a resource for the scientific community. While use of antibodies and protocols vary between laboratories, we encourage readers to use this report as a guide to select the most appropriate antibodies for their specific needs.

Pathogenic variants in autism gene KATNAL2 cause hydrocephalus and disrupt neuronal connectivity by impairing ciliary microtubule dynamics

Enlargement of the cerebrospinal fluid (CSF)-filled brain ventricles (cerebral ventriculomegaly), the cardinal feature of congenital hydrocephalus (CH), is increasingly recognized among patients with autism spectrum disorders (ASD). KATNAL2, a member of Katanin family microtubule-severing ATPases, is a known ASD risk gene, but its roles in human brain development remain unclear. Here, we show that nonsense truncation of Katnal2 (Katnal2Δ17) in mice results in classic ciliopathy phenotypes, including impaired spermatogenesis and cerebral ventriculomegaly. In both humans and mice, KATNAL2 is highly expressed in ciliated radial glia of the fetal ventricular-subventricular zone as well as in their postnatal ependymal and neuronal progeny. The ventriculomegaly observed in Katnal2Δ17 mice is associated with disrupted primary cilia and ependymal planar cell polarity that results in impaired cilia-generated CSF flow. Further, prefrontal pyramidal neurons in ventriculomegalic Katnal2Δ17 mice exhibit decreased excitatory drive and reduced high-frequency firing. Consistent with these findings in mice, we identified rare, damaging heterozygous germline variants in KATNAL2 in five unrelated patients with neurosurgically treated CH and comorbid ASD or other neurodevelopmental disorders. Mice engineered with the orthologous ASD-associated KATNAL2 F244L missense variant recapitulated the ventriculomegaly found in human patients. Together, these data suggest KATNAL2 pathogenic variants alter intraventricular CSF homeostasis and parenchymal neuronal connectivity by disrupting microtubule dynamics in fetal radial glia and their postnatal ependymal and neuronal descendants. The results identify a molecular mechanism underlying the development of ventriculomegaly in a genetic subset of patients with ASD and may explain persistence of neurodevelopmental phenotypes in some patients with CH despite neurosurgical CSF shunting.

Insulin-Like Growth Factor 1 Has the Potential to Be Used as a Diagnostic Tool and Treatment Target for Autism Spectrum Disorders

Autism spectrum disorder (ASD), a heterogeneous group of neurodevelopmental disorders, is characterized by social impairment and repetitive and stereotypic behaviors. Because of the lack of approved laboratory diagnostic markers and effective therapeutic medications, it is one of the most challenging diseases. Therefore, it is urgent to explore potential diagnosis markers or therapeutic targets. Insulin-like growth factor 1 (IGF-1) is a neurotrophic growth factor that enhances brain development. IGF-1 levels in body fluids are lower in preschool children with ASD than in typically developing children, which may serve as a potential diagnostic marker. In various ASD models associated with genetic or environmental exposure, IGF-1 treatment can improve core symptoms or pathological changes, including neuronal development, neural cell survival, balance of synaptic excitation and inhibition, neuroimmunology, and oxidative stress status. In March 2023 an IGF-1 derivative was approved as the first drug for treating Rett syndrome, an ASD-related neurodevelopmental disorder, to improve fundamental symptoms such as social communication. Thus, in this review, we present accumulating evidence of altered IGF-1 levels in ASD patients and the possible mechanisms, as well as evidence that IGF-1 treatment improves the pathophysiology in various ASD models. IGF-1 has the potential to be an early diagnosis marker and an effective therapeutic for ASD.

Cognitive behavioral phenotyping of DSCAM heterozygosity as a model for autism spectrum disorder

It is estimated that 1 in 36 children are affected by autism spectrum disorder (ASD) in the United States, which is nearly a twofold increase from a decade ago. Recent genetic studies have identified de novo loss-of-function (dnLoF) mutations in the Down Syndrome Cell Adhesion Molecule (DSCAM) as a strong risk factor for ASD. Previous research has shown that DSCAM ablation confers social interaction deficits and perseverative behaviors in mouse models. However, it remains unknown to what extent DSCAM underexpression captures the full range of behaviors, specifically cognitive phenotypes, presented in ASD. Here, we conducted a comprehensive cognitive behavioral phenotyping which revealed that loss of one copy of DSCAM , as in the DSCAM 2J +/- mice, displayed hyperactivity, increased anxiety, and motor coordination impairments. Additionally, hippocampal-dependent learning and memory was affected, including working memory, long-term memory, and contextual fear learning. Interestingly, implicit learning processes remained intact. Therefore, DSCAM LoF produces autistic-like behaviors that are similar to human cases of ASD. These findings further support a role for DSCAM dnLoF mutations in ASD and suggest DSCAM 2J +/- as a suitable model for ASD research.

Summary Statement

Autism spectrum disorder represents a growing patient population. Loss of one copy of the DSCAM gene provides a promising mouse model that reproduces autistic-like behaviors for research and therapeutic testing.

Biallelic variants in CSMD1 are implicated in a neurodevelopmental disorder with intellectual disability and variable cortical malformations

CSMD1 (Cub and Sushi Multiple Domains 1) is a well-recognized regulator of the complement cascade, an important component of the innate immune response. CSMD1 is highly expressed in the central nervous system (CNS) where emergent functions of the complement pathway modulate neural development and synaptic activity. While a genetic risk factor for neuropsychiatric disorders, the role of CSMD1 in neurodevelopmental disorders is unclear. Through international variant sharing, we identified inherited biallelic CSMD1 variants in eight individuals from six families of diverse ancestry who present with global developmental delay, intellectual disability, microcephaly, and polymicrogyria. We modeled CSMD1 loss-of-function (LOF) pathogenesis in early-stage forebrain organoids differentiated from CSMD1 knockout human embryonic stem cells (hESCs). We show that CSMD1 is necessary for neuroepithelial cytoarchitecture and synchronous differentiation. In summary, we identified a critical role for CSMD1 in brain development and biallelic CSMD1 variants as the molecular basis of a previously undefined neurodevelopmental disorder.

Treatability of the KMT2-Associated Neurodevelopmental Disorders Using Antisense Oligonucleotide-Based Treatments

Neurodevelopmental disorders (NDDs) of genetic origin are a group of early-onset neurological diseases with highly heterogeneous etiology and a symptomatic spectrum that includes intellectual disability, autism spectrum disorder, and learning and language disorders. One group of rare NDDs is associated with dysregulation of the KMT2 protein family. Members of this family share a common methyl transferase function and are involved in the etiology of rare haploinsufficiency disorders. For each of the KMT2 genes, at least one distinct disorder has been reported, yet clinical manifestations often overlap for multiple of these individually very rare disorders. Clinical care is currently focused on the management of symptoms with no targeted treatments available, illustrating a high unmet medical need and the urgency of developing disease-modifying therapeutic strategies. Antisense oligonucleotides (ASOs) are one option to treat some of these rare genetic disorders. ASOs are RNA-based treatments that can be employed to modulate gene expression through various mechanisms. In this work, we discuss the phenotypic features across the KMT2-associated NDDs and which ASO approaches are most suited for the treatment of each associated disorder. We hereby address variant-specific strategies as well as options applicable to larger groups of patients.

Srcap haploinsufficiency induced autistic-like behaviors in mice through disruption of Satb2 expression

Mutations in the SRCAP gene are among the genetic alterations identified in autism spectrum disorders (ASD). However, the pathogenic mechanisms remain unclear. In this study, we demonstrate that Srcap+/- mice manifest deficits in social novelty response, as well as increased repetitive behaviors, anxiety, and impairments in learning and memory. Notably, a reduction in parvalbumin-positive neurons is observed in the retrosplenial cortex (RSC) and dentate gyrus (DG) of these mice. Through RNA sequencing, we identify dysregulation in 27 ASD-related genes in Srcap+/- mice. Specifically, we find that Srcap regulates expression of Satb2 via H2A.z in the promoter. Therapeutic intervention via retro-orbital injection of adeno-associated virus (AAV)-Satb2 in neonatal Srcap+/- mice leads to amelioration of the neurodevelopmental and ASD-like abnormalities. Furthermore, the expression of Satb2 only in the RSC of adolescent mice rectifies social novelty impairments. These results underscore the pivotal role of Srcap in neurodevelopment, by regulating Satb2, providing valuable insights for the pathophysiology of ASD.

Embryonic origin of two ASD subtypes of social symptom severity: the larger the brain cortical organoid size, the more severe the social symptoms

BACKGROUND

Social affective and communication symptoms are central to autism spectrum disorder (ASD), yet their severity differs across toddlers: Some toddlers with ASD display improving abilities across early ages and develop good social and language skills, while others with "profound" autism have persistently low social, language and cognitive skills and require lifelong care. The biological origins of these opposite ASD social severity subtypes and developmental trajectories are not known.

METHODS

Because ASD involves early brain overgrowth and excess neurons, we measured size and growth in 4910 embryonic-stage brain cortical organoids (BCOs) from a total of 10 toddlers with ASD and 6 controls (averaging 196 individual BCOs measured/subject). In a 2021 batch, we measured BCOs from 10 ASD and 5 controls. In a 2022 batch, we  tested replicability of BCO size and growth effects by generating and measuring an independent batch of BCOs from 6 ASD and 4 control subjects. BCO size was analyzed within the context of our large, one-of-a-kind social symptom, social attention, social brain and social and language psychometric normative datasets ranging from N = 266 to N = 1902 toddlers. BCO growth rates were examined by measuring size changes between 1- and 2-months of organoid development. Neurogenesis markers at 2-months were examined at the cellular level. At the molecular level, we measured activity and expression of Ndel1; Ndel1 is a prime target for cell cycle-activated kinases; known to regulate cell cycle, proliferation, neurogenesis, and growth; and known to be involved in neuropsychiatric conditions.

RESULTS

At the BCO level, analyses showed BCO size was significantly enlarged by 39% and 41% in ASD in the 2021 and 2022 batches. The larger the embryonic BCO size, the more severe the ASD social symptoms. Correlations between BCO size and social symptoms were r = 0.719 in the 2021 batch and r = 0. 873 in the replication 2022 batch. ASD BCOs grew at an accelerated rate nearly 3 times faster than controls. At the cell level, the two largest ASD BCOs had accelerated neurogenesis. At the molecular level, Ndel1 activity was highly correlated with the growth rate and size of BCOs. Two BCO subtypes were found in ASD toddlers: Those in one subtype had very enlarged BCO size with accelerated rate of growth and neurogenesis; a profound autism clinical phenotype displaying severe social symptoms, reduced social attention, reduced cognitive, very low language and social IQ; and substantially altered growth in specific cortical social, language and sensory regions. Those in a second subtype had milder BCO enlargement and milder social, attention, cognitive, language and cortical differences.

LIMITATIONS

Larger samples of ASD toddler-derived BCO and clinical phenotypes may reveal additional ASD embryonic subtypes.

CONCLUSIONS

By embryogenesis, the biological bases of two subtypes of ASD social and brain development-profound autism and mild autism-are already present and measurable and involve dysregulated cell proliferation and accelerated neurogenesis and growth. The larger the embryonic BCO size in ASD, the more severe the toddler's social symptoms and the more reduced the social attention, language ability, and IQ, and the more atypical the growth of social and language brain regions.