Molecular Autism

A large subset of ASD associated genes, almost 50% of the highest confidence risk genes listed on the Simons Foundation Autism Research Institute database, are epigenetic modifiers. This suggests that the organization of sensory biology and its coupling to underlying genetic control are an important element underpinning this discord. Furthermore, sensory processing changes in individuals with autism spectrum disorder (ASD) has been a growing area of study in recent years. C. elegans have robust readouts for both developmental and sensory biology allowing these signatures of ASD to be systematically modelled. 52 epigenetic modifiers (65 strains) were selected for study in C. elegans based on gene function, presence of orthologues in C. elegans and the availability of viable putative null strains. This highlighted significant changes to reproduction, gross development and sensory processing across the range of epigenetic modifiers. Each strain was filtered against selective criteria for significant sensory and developmental phenotypes allowing for selective phenotypic profiles to emerge. These were three primary groups, those with sensory perturbations but unaffected gross development (6), developmentally affected genes with intact sensory function (10) and finally genes with impaired gross development and sensory function (11). Thus, this study provides a link between sensory and developmental outcomes in ASD associated mutant strains and suggests that more regular sensory testing should be performed in human cohorts to further refine sub-categorisation of ASD cohorts.

Mutations in the synaptic scaffold protein SHANK3 represent one of the most frequent genetic causes of autism spectrum disorder (ASD), yet the circuit mechanisms through which SHANK3 dysfunction leads to behavioral alterations remain incompletely understood. The anterior insular cortex (aINS) is a key integrative hub involved in socio-emotional processing, anxiety regulation, and social cognition, a group of behaviors frequently disrupted in ASD. Here, we investigated whether selective deletion of SHANK3 signaling in glutamatergic neurons of the aINS is sufficient to produce ASD-relevant behavioral and circuit phenotypes. Using conditional Shank3flox4-22 mice combined with stereotaxic viral delivery of Cre recombinase under the CaMKII promoter, we selectively deleted Shank3 in glutamatergic neurons of the aINS. Behavioral phenotyping revealed increased anxiety-like behavior, enhanced repetitive behavior, and impaired social memory, while sociability and locomotor activity were largely preserved. These behavioral alterations were accompanied by genotype-dependent differences in neuronal activity revealed by calcium imaging, indicating disrupted activity dynamics in insular glutamatergic neurons following Shank3 deletion. To assess the broader relevance of these findings, we evaluated the behavioral profile of BTBR T+ Itpr3tf/J mice, a model of idiopathic ASD, in the same battery of behavioral tests. Several behavioral alterations observed following insular Shank3 deletion partially overlapped with those present in BTBR mice, supporting the relevance of aINS Shank3 in ASD-related phenotypes. Together, these findings identify glutamatergic neurons of the aINS as a critical locus through which Shank3 dysfunction can disrupt socio-emotional, cognitive, and repetitive behaviors. Our results highlight the aINS as a key circuit node contributing to ASD-related behavioral alterations and provide mechanistic insight into how synaptic scaffold disruption leads to circuit dysfunction and produces behavioral alterations.

Abstract Background & Aims: Language development in autism is heterogeneous and strongly predicts later functioning. The balance between receptive and expressive abilities and their developmental trajectories, however, remains poorly understood. While some autistic children exhibit a relative expressive advantage (ExpAdv), others show receptive advantage (RecAdv) or a balanced profile. Prior studies report inconsistent findings and are often limited by cross-sectional designs and small samples. The present study aimed to (1) describe longitudinal trajectories of receptive and expressive language in autistic and typically developing (TD) children; (2) classify children into ExpAdv, Balanced, and RecAdv profiles across early childhood; and (3) examine the stability and transitions of these profiles over time, including associated clinical features. Methods: We analyzed 1,174 longitudinal time points from 318 autistic children and 294 time points from 108 TD children (1.2-5.8 years) from the Geneva Autism Cohort. Receptive and expressive language were assessed with the Mullen Scales of Early Learning. Receptive-expressive balance was quantified as the ratio of receptive to expressive age equivalent scores, classifying children into ExpAdv, Balanced, and RecAdv profiles using adapted cut-offs. Mixed-effects models examined developmental trajectories, and Sankey diagrams visualized profile transitions. Autism features and adaptive behavior were compared across profiles. Results: Autistic children displayed lower expressive and receptive language than TD peers, with receptive abilities exceeding expressive skills in both groups. Overall, 30-35% of autistic children were classified as ExpAdv at 18-36 months, declining to ~12% by 48-54 months, while Balanced and RecAdv profiles became more prevalent with age. ExpAdv was associated with slower verbal and non-verbal developmental gains. Stability was highest for Balanced and RecAdv profiles (50-60%), whereas ExpAdv often transitioned to Balanced. Autistic children with stable ExpAdv profiles were more often female, less likely to receive early intervention, and showed weaker adaptive communication. Conclusions: Receptive-expressive language profiles in autistic children are dynamic. ExpAdv profile is more frequent in younger autistic children, less stable, and linked to slower verbal and non-verbal development and higher autism severity. Implications: ExpAdv may represent an early marker of autism associated with slower expressive and receptive language growth. Longitudinal monitoring of receptive and expressive skills is essential, as transitions toward Balanced or RecAdv profiles are associated with improved developmental outcomes. Early intervention before age three may facilitate transitions toward Balanced or RecAdv profiles, supporting more favorable language development and long-term outcomes. Keywords: autism; early childhood; longitudinal design; expressive language; receptive language; language profile; early intervention; language gap; discrepant profiles

Background: Female individuals tend to be diagnosed with autism later. One factor suggested to contribute to diagnostic timing is verbal ability, in which autistic females may show strengths relative to male peers. Social drivers of health (SDOH) predict higher verbal skills, yet access to resources may facilitate diagnosis; thus, SDOH likely contributes to diagnostic timing in complex ways. We use data from two autism cohorts with substantial representation of those assigned female at birth (AFAB) to examine interactions among assigned sex at birth (sex), verbal IQ (VIQ), and SDOH in predicting autism diagnostic timing. Methods: We used multiple linear regression to examine sex assigned at birth and VIQ as predictors of diagnostic timing in an assigned-sex-balanced research sample (N=164, AFAB: 71) and an independent clinical sample (N=641, AFAB: 177). We hypothesized VIQ would positively predict diagnostic age, particularly among AFAB. Available data in the clinical sample also permitted us to explore the contributions of SDOH and inclusion criteria to model fit in this cohort. Results: In the research sample, VIQ, but not sex, positively predicted diagnostic age. In the clinical sample, VIQ and VIQ x SDOH, but not sex, predicted diagnostic age. Fitting the same model in a subsample of the clinical cohort formed by applying exclusion criteria used in the research sample (N=484, AFAB: 110), VIQ x SDOH x Sex became significant. For AFAB, higher VIQ and lower SDOH together were associated with later diagnosis in the clinical subsample, while for AMAB the opposite was true. Conclusions: Autistic youth with strong verbal ability may experience diagnostic delays. SDOH interacts with VIQ in a complex fashion, with lower SDOH generally exacerbating the tendency for VIQ to be associated with later diagnosis across a large clinical sample. However, among autistic youth without complicating medical factors or intellectual disability, this relationship is dependent upon sex.

BackgroundPhelan McDermid syndrome (PMS), caused by SHANK3 haploinsufficiency, is a genetic form of autism spectrum disorder (ASD) that provides a genetically defined model for studying ASD-related circuit dysfunction. SHANK3 mutations disrupt synaptic organization and cortical synchrony, leading to attenuated gamma-band auditory steady-state responses (ASSRs). We investigated whether PMS-related electrophysiological signatures could be identified using machine learning and whether similar patterns are present in a subset of individuals with idiopathic ASD (iASD). MethodsEEG recorded during a 40-Hz ASSR paradigm was collected from 123 participants (42 TD aged 2-30, 56 iASD aged 3-31, 25 PMS aged 2-26). We extracted time-series, ERSP, FOOOF-derived spectral, and intertrial phase coherence (ITPC) features. XGBoost models with leave-one-out cross-validation classified PMS versus TD; the best age/sex-adjusted ITPC model was then applied to iASD participants to derive a Synchrony Atypicality Index (SAI). Unsupervised clustering of high-dimensional ITPC features was also performed. ResultsITPC-based models showed the strongest discrimination between TD and PMS participants (AUROC = 0.83). When applied to iASD participants, 35.7% exhibited elevated SAI, indicating a PMS-like gamma-band phase-locking profile. Classification of iASD versus PMS performed poorly in the full sample but improved markedly after excluding high-SAI iASD individuals, consistent with substantial heterogeneity within iASD. Unsupervised clustering of ITPC features identified PMS-enriched clusters that also captured high-SAI iASD participants. Results were consistent after controlling for age in sensitivity analyses. ConclusionsReduced 40-Hz ITPC is a mechanistically interpretable electrophysiological signature of PMS and identifies a biologically meaningful PMS-like subgroup within iASD, supporting biomarker-guided stratification.

Autism spectrum disorder (ASD) is a complex neurodevelopmental condition with symptoms spanning cognitive, social and behavioral domains and leading to lifelong challenges. Autism is heritable but specific genetic and environmental factors that shape its early neurodevelopmental trajectory remain unknown. Despite the clinical variability, neuroimaging findings from Enhancing Neuro Imaging Genetics through Meta Analysis (ENIGMA)-ASD consortium identified stable and replicable patterns of cortical and subcortical differences that were consistent with those reported by an independent consortium, the Cognitive Genetics Collaborative Research Organization (COCORO) in Japan. Here we developed and evaluated a regional vulnerability index (RVI), a similarity metric that quantifies how closely a persons brain resembles the specific pattern of an individual with autism. RVI-ASD is based on combining the regional effect sizes for regional brain measurements published by the ENIGMA-ASD group with microstructural white matter integrity differences reported by COCORO. RVI-ASD showed significantly higher effect size for case-control differences relative to any individual brain measure (d=0.30 vs. d=0.01-0.21) in individuals with autism, particularly in the adolescent-to-adult sample (N=2,577; Mean age = 16.1; SD=5.0). We next calculated RVI-ASD in the baseline and follow-up (ages 10 and 12) data from normally developing participants of the ABCD study (N=4,201). We tested the longitudinal stability, heritability, genotype-by-age interaction and sensitivity of RVI-ASD to known factors and cognitive measurements. RVI-ASD were stable on the 2-year follow up (ICC=0.76-0.92); showed significant heritability (h{superscript 2}=0.55-0.83, p<10-16) but was not affected by gene-by-age interaction. RVI-ASD showed significant positive correlation with paternal age, while correlation with maternal age was non-significant. Baseline and follow-up RVI-ASD were negatively correlated with cognitive measures including total, fluid and crystallized intelligence (r=-0.09 to -0.11, p<10-6). RVI-ASD scores tracked with core autism phenotypes including poor eye contact and rigid routines (p < .01). In a sub-sample of children with symptoms of autism (N=20), we found that earlier age of symptom onset was strongly correlated with higher White Matter RVI (r = -0.61), linking early behavioral emergence to the neuroanatomical signature. Longitudinal changes in subcortical RVI-ASD are significantly correlated with change in social functioning. The RVI-ASD is a neuroimaging-based biomarker linked to stable and reproducible brain patterns in autism. RVI-ASD allows researchers to study associations with factors associated with the likelihood for autism and cognition across large and inclusive non-clinical samples, thus moving beyond simple case-control models to understand the biological pathways of autism.

Atypical sensory experiences are highly prevalent in autistic children and include both hyper- and hypo-responsivity, often accompanied by sensory overload. Alpha oscillations (7-13 Hz), which dynamically regulate cortical excitability, represent a plausible neural mechanism underlying these phenomena: reduced alpha activity is associated with enhanced sensory responsiveness, whereas increased alpha supports suppression of external input. Although decreased alpha power has been repeatedly reported in autism, it remains unclear whether this reduction reflects lower oscillatory amplitude or reduced temporal stability of alpha rhythms, two mechanisms with distinct neurophysiological implications. To better characterize alpha activity in autism, we examined resting-state alpha dynamics in non-autistic children (NA; n = 39), autistic children (AU; n = 52), and siblings of autistic children (SIB; n = 26), aged 8-14 years. We combined traditional broadband measures of relative alpha power, parametric separation of periodic and aperiodic activity, and single-event analyses that quantify the temporal structure of alpha oscillations. Both broadband relative alpha power and periodic alpha power were reduced in autism over parietal regions, replicating prior findings. Importantly, ordinal analyses revealed an intermediate profile in siblings, supporting a liability-related gradient of alpha alterations. However, single-event analyses demonstrated that the average amplitude of individual alpha bursts did not differ between groups. Instead, autistic children showed significantly shorter alpha burst duration and reduced alpha abundance (i.e., proportion of time occupied by rhythmic alpha episodes), with siblings again exhibiting intermediate values. Linear regression analyses confirmed that reductions in relative and periodic alpha power were primarily driven by decreased alpha abundance rather than diminished burst amplitude. These findings indicate that altered alpha activity in autism reflects reduced temporal stability and density of alpha events rather than weaker oscillatory amplitude per se. Reduced persistence of alpha rhythms may therefore represent a neural marker of altered cortical excitability and sensory regulation in autism. Lay summaryAutistic children often experience the world differently at the sensory level, including being more easily overwhelmed by sounds, lights, or other stimuli. In this study, we looked at a type of brain activity called alpha rhythms, which help regulate how strongly the brain responds to incoming information. We found that, in autistic children, these alpha rhythms were not weaker when they occurred, but they lasted for a shorter time and happened less often. Siblings of autistic children showed an intermediate pattern. These results suggest that sensory differences in autism may be linked to less stable brain rhythms that normally help control sensory input. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=158 SRC="FIGDIR/small/716324v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@1be733dorg.highwire.dtl.DTLVardef@7fea49org.highwire.dtl.DTLVardef@1ee9124org.highwire.dtl.DTLVardef@17af139_HPS_FORMAT_FIGEXP M_FIG C_FIG

Background Autism is characterized by social-communicative difficulties, with sex differences in symptom presentation. Social functioning is inherently dynamic, however, many neuroimaging studies rely on static, time-averaged approaches that obscure time-varying network interactions, potentially limiting our ability to capture the dynamic processes underlying social cognition. The fusiform gyrus (FFG), central to face and social perception, shows differences in functional connectivity in autism, yet is rarely examined dynamically or as a spatially heterogeneous structure. Here, we investigate the dynamic functional connectivity of FFG subregions in terms of their large-scale network configurations as a function of diagnosis and sex. Methods We applied micro co-activation patterns analysis (CAPs) to resting-state fMRI data from 286 autistic individuals (208:78 males:females) and 228 non-autistic individuals (146:82 males:females), aged 6-30 years, from the EU-AIMS LEAP dataset. CAPs were identified using k-means clustering with FFG as the seed, and connectopic mapping positioned each CAP along the principal connectivity gradient. We quantified CAPs occurrence and further examined dwell time, transition probabilities, and spatial extent, along with associations with social functioning. Results Six CAPs mapped onto distinct FFG subregions along a posterior-anterior axis. A significant sex-by-diagnosis interaction emerged for a default mode network (DMN)-related CAP. Non-autistic females exhibited significantly more frequent occurrences, longer dwell times and distinct transition dynamics compared to males, while no sex difference was observed in autism. The spatial extent of this CAP showed a reversal of typical sex effects. Conclusions Autism is associated with an attenuation and reversal of typical sex differences in the functional configuration and spatial extent of FFG-DMN coupling, indicating that neural signatures of social-cognitive functions are sex-specific and dynamic. These findings suggest that sex is a neurobiologically meaningful dimension of heterogeneity in autism, expressed in dynamic network organization.

Delayed onset of canonical babbling and first words is often reported in infants later diagnosed with autism spectrum disorder. Identifying the neural mechanisms underlying language acquisition in autism is therefore critical to inform early diagnosis, prognosis, and intervention strategies. In this study, we investigated two speech processing mechanisms previously identified as atypical in children and adults with autism: the neural ability to track syllables; and statistical learning, the capacity to detect speech regularities beneath surface variability. We recorded 83 longitudinal high-density EEGs from 44 infants (2.5-22.6 months) at high (HL) and low (LL) likelihood for autism and assessed their verbal outcomes at 20 months. Neural entrainment was measured at syllable and word frequencies during exposure to a multi-speaker stream of concatenated tri-syllabic words, followed by a word recognition test using ERP recording. Our findings revealed reduced tracking abilities at the syllabic level in HL infants, a measure that correlated with verbal outcomes. While HL infants did not exhibit deficits in statistical learning itself, they displayed reduced novelty orientation during the word recognition test, indicated by a reduced late ERP. By contrast, multi-talker variability temporarily disrupted word segmentation around 12 months in LL infants, but not in HL infants, potentially reflecting decreased sensitivity to human voices variability in the HL group. These results emphasize the importance of longitudinal protocols employing online, implicit measures to track the hierarchical stages of speech processing in both HL and LL infants.

The mechanistic role of the third visual pathway in autism spectrum disorder (ASD) remains unknown. We previously developed a neurofeedback therapy for autism targeting the posterior superior temporal sulcus (pSTS), a region in this network that underlies the perception and imagery of emotional facial expressions, resulting in improvements in adaptive behavior and recognition of fear in facial expressions. Here, we investigated the impact of this 5-session therapy on the functional connectivity of that core region of the third visual pathway. We found evidence for a profound reorganization of this network with treatment-induced decreases in connectivity between low-level visual areas, the pSTS, and the posterior occipital face area (OFA), and increased connectivity with higher-level visual regions (fusiform face area - FFA), right middle STS (mSTS), and parietal cortex. These changes, suggesting the restoration of connectivity in regions known to be underconnected in ASD, such as mSTS and pSTS, and in a set of regions belonging to the temporoparietal junction and the ventral attention network, which are known to be involved in broader aspects of social cognition, were positively associated with clinical improvements. The demonstration of treatment response associated with network reconfiguration paves the way for multicentric trials to probe this observed reorganization as a treatment target.

Autism spectrum disorder (ASD) is frequently accompanied by sensory and motor abnormalities, including impaired balance, postural control, and spatial orientation, that are often attributed largely to altered central circuitry. Emerging evidence, however, suggests that peripheral sensory dysfunction can also shape ASD related behavioral phenotypes. Here, we tested whether loss of the ASD associated gene Cntnap2/Caspr2 alters vestibular signaling in Cntnap2-/- mice. Developmental transcriptomic analysis showed that Cntnap2 is expressed in vestibular sensory organs and increases during the first postnatal month, coincident with vestibular pathway maturation. Vestibular sensory evoked potentials revealed reduced response amplitudes and prolonged latencies in Cntnap2-/- mice, indicating impaired peripheral afferent responses to transient linear acceleration. Cntnap2-/- mice also showed delayed contact righting, reduced ocular counter roll, and increased hindlimb slips and compensatory tail excursions during balance beam walking, whereas rotational vestibulo-ocular reflex gain and phase were preserved. These vestibular and balance abnormalities were accompanied by reduced novel arm preference in the Y maze and severe impairment of Barnes maze acquisition, consistent with impaired spatial learning. Together, these findings identify Cntnap2/Caspr2 as a regulator of vestibular sensory signaling and support a model in which disrupted peripheral vestibular input, likely acting together with central effects of Cntnap2 loss, contributes to sensorimotor and spatial cognitive phenotypes relevant to ASD.

Previously we found that female autistic youth (Aut-F) showed reduced brain response in dorsal striatum (putamen) when viewing human motion, alongside larger rare copy number variants that included genes expressed in early striatal development. Thus, striatal differences may characterize Aut-F, but broader systems-level and behavioral implications of these differences remain unexplored. We conducted secondary data analysis of the sex-balanced cohort (8-17y) in which we first discovered these patterns, in order to: 1) understand how functional connectivity between putamen and frontal targets might vary from the non-autistic population, and differ by sex; and 2) explore which brain connectivity and phenotypic features best predicted executive function. Using psychophysiological interaction analysis (N=184), we found that Aut-F youth (n=45) showed reduced functional connectivity between left anterior putamen (Pa) and dorsal premotor cortex/pre-supplementary motor area versus matched non-autistic female peers (NAut-F; n=45), suggesting reduced engagement of a typical Pa-frontal pathway for attentional regulation. Best subsets regression (N=200) indicated that left Pa-left dorsolateral prefrontal functional connectivity explained significant variance in executive functioning across all participants, controlling for neurotype. These results suggest that striatal differences in Aut-F may have adaptive consequences in part due to impacts on connectivity between Pa and frontal regions important for attentional control. Lay summaryWe previously found that female autistic people show differences in a part of the brain called the striatum. Some parts of the striatum connect to the frontal lobe of the brain, and may help people control their attention and behavior. We studied how the striatum "talked to" the frontal lobe in autistic girls. We found out that this communication is lower in autistic than non-autistic girls. We also found out that how much striatum "talks to" frontal lobe helps explain differences in how well both autistic and non-autistic youth of both sexes control their attention and behavior.

Atypical processing of emotional faces has been proposed as a characteristic of Autism Spectrum Disorder (ASD), but functional neuroimaging research has yielded inconsistent findings. Prior work is limited in generalizability due to methodological heterogeneity, imbalanced or small sample sizes, and underrepresentation of females. The present study examined functional brain activation during the Hariri Emotional Face-Matching Task (EFMT) in a large, sex-balanced sample of both typically developing and ASD participants (n=295, 8-18 years old) from the multi-site Autism Center of Excellence GENDAAR project. Using an ROI-driven approach, we targeted the right FFA, right OFA, right pSTS, and bilateral amygdala, we investigated whether ASD diagnosis was associated with atypical regional activation when viewing emotional faces, and if these differences were generalizable across sexes. Results revealed a group-by-sex interaction in the right FFA, driven by divergence of ASD males from the ASD female and typically developing participants. Generally, ASD females did not diverge greatly from typically developing populations. These findings suggest that atypical face processing is present, but meaningfully modulated by sex, underscoring the importance of sex-balanced, well-powered developmental samples in autism.

Autism spectrum disorder (ASD) is increasingly conceptualized as a condition rooted in altered prenatal neurodevelopment, yet in vivo evidence from fetal brain imaging remains limited. Using retrospective fetal MRI and surface-based morphometry, we investigated cortical development in 15 fetuses later diagnosed with ASD (77%; mean gestational age [GA] = 26.7 weeks) without major structural brain abnormalities and compared them with 60 typically developing controls (57% male; mean GA = 28.4 weeks). Fetuses later diagnosed with ASD showed significantly reduced whole-brain inner cortical plate surface area compared with controls ({beta} = -0.08 {+/-} 0.02 SE, p = 0.002, partial {superscript 2} = 0.13), corresponding to an estimated [~]7.7% reduction (predicted at GA = 28.1 weeks). Lobar mixed-effects analyses demonstrated broadly distributed reductions across all cortical lobes (FDR-corrected p = <0.001-0.024; Cohens d = -0.06 to -0.10), with modest regional heterogeneity indicating relatively greater frontal and insular involvement (groupxlobe: F = 19.31, p = 0.002, {superscript 2} = 0.08). Surface area findings remained directionally stable across sensitivity analyses, including restriction to neurodevelopmentally confirmed controls and models accounting for image quality variability, although effect sizes were attenuated after quality adjustment. Normative modeling further demonstrated subtle negative deviations from typical prenatal cortical surface area trajectories in ASD (mean Z = -0.27, p = 0.018). These findings suggest that aspects of cortical morphogenesis may diverge prenatally in individuals later diagnosed with ASD and suggest the feasibility of fetal MRI-based surface morphometry for studying early neurodevelopmental variation associated with ASD risk.

Meiotic recombination is an important means of increasing genetic diversity by generating novel haplotypes in a population. Recombination separates linked loci extremely slowly in some regions, therefore genetic variants in high linkage disequilibrium may become co-adapted. Reciprocal recombination that separates co-adapted variants may generate a deleterious de novo haplotype that contributes to disease. We developed statistical methods to detect genomic regions of recombination excess in two different family-based study designs. We identified recombination in the Simons Simplex Collection in 273 simplex families with one child with autism spectrum disorder (ASD) and at least two unaffected children, in which recombinations can be mapped to the proband and contrasted with the recombination counts in unaffected siblings; and in 1,802 families with two children, where the number of recombinations identified can be contrasted with the expectation from a reference recombination map. Both strategies revealed a tail of low p-values for loci of interest that contrasted with the rest of the distribution. Permutation and bootstrap tests did not identify genome-wide primary findings in either cohort, but the most significant three-child cohort locus of recombination excess (between cadherin genes CDH4 and CDH26) replicated in the two-child cohort (p=0.01). While this replication strategy was not defined a priori, five of the most recombination enriched bins identified candidate ASD genes (p=0.02; WWOX, ADAMTS16, INSR, ADARB2, and HS6ST1). Since the six identified loci were not identified as regions of high de novo copy number variation in the study cohort and no CNVs were detected in any of the recombinant probands in the identified regions, they represent candidates for reciprocal recombinations generating unfavourable haplotypes for these genes. This study highlights a previously unidentified source of clinical genetic variability contributing to the molecular aetiology of ASD. AUTHOR SUMMARYAutism spectrum disorder (ASD) is a constellation of neurodevelopmental disabilities characterised by deficits in social communication and repetitive patterns of behaviour. While ASD is highly heritable, its genetic basis is complex and poorly understood. While some highly penetrant types of genetic variation have been identified, most people with ASD carry a large number of variants that each contribute a small amount to their overall phenotype. In addition to mutations in individual genes, changes in the configuration of genes along a chromosome may contribute to ASD. Here, we describe a method for identifying regions where such new configurations have occurred through recombination and attempt to find regions where such changes are more common in autistic children than in their non-autistic siblings. We explore recombination as a source of genetic variation contributing to autism, which has potential to inform clinicians in providing services to autistic people and their families.

The brain generates predictions to prepare for upcoming events. Because the environment is not perfectly predictable, the brain also estimates the certainty of these predictions and adjusts preparatory processes accordingly. Given that autistic individuals often resist even small changes to everyday routines, we hypothesized altered tuning of prediction certainty in autism. To test this, EEG was recorded from adolescents and young autistic adults (n = 20) and from age- and IQ-matched non-autistic adults (n = 19) during a probabilistic cued target identification task during which cue validity was systematically varied across four levels: 100%, 84%, 67%, and 33%. Participants were not informed of the cue-target validity nor when it changed. We focused on two neural signatures of anticipatory readiness, contingent negative variation (CNV) and alpha-band event-related desynchronization (-ERD), and one of cognitive updating: the P3 to targets and to invalid (e.g., a non-target in place of the target) stimuli. Across groups, preparatory activity increased as contextual certainty decreased, with larger CNV amplitudes and stronger -ERD preceding targets in lower-probability contexts, suggesting enhanced preparatory engagement under greater uncertainty. Furthermore, larger CNV amplitudes predicted faster reaction times, indicating functionally significant anticipatory dynamics. However, modulation of both neural preparation and response times as a function of cue-target probability was significantly reduced in the autistic group. In addition, autistic participants showed diminished probability-dependent modulation of the P3b to both targets and invalid stimuli, and coupling between anticipatory activity (CNV) and subsequent updating (P3b) was observed in non-autistic participants whereas it was absent in autism. Together, these findings suggest that while predictive mechanisms are present in autism, anticipatory processes are less flexibly tuned to contextual uncertainty and less effectively linked to subsequent cognitive updating. This reduced adaptability may reflect difficulty adjusting internal predictive models to changing environmental contingencies, potentially contributing to core features of autism such as resistance to change and insistence on sameness. HighlightsO_LIAnticipatory brain mechanisms (CNV and alpha desynchronization) are present in autism and are behaviorally relevant, predicting faster responses. C_LIO_LIAutistic individuals exhibit reduced modulation of anticipatory CNV and alpha activity as a function of cue-target validity. C_LIO_LIP3b responses to both targets and invalid stimuli show diminished sensitivity to contextual probability in autism, consistent with altered prior updating. C_LIO_LIThe link between anticipatory activity and cognitive updating (i.e., CNV to P3b) is disrupted in autism. C_LIO_LIP3a amplitude to invalid stimuli is reduced in autism, suggesting diminished engagement of violation-sensitive processes. C_LIO_LITogether, findings point to less flexible tuning of predictive mechanisms and reduced adaptation to contextual uncertainty in autism. C_LI

Autism spectrum disorder (ASD) is a heterogeneous neurodevelopmental condition shaped by contributions from hundreds of genes, many of which remain poorly characterized. This largely uncharacterized genomic landscape may therefore hold critical insight into how diverse molecular disruptions converge on shared social phenotypes. Here, we investigated KIAA0232 (mouse orthologue D5Ertd579e), an uncharacterized locus lacking known functional domains, using a global null knockout mouse model. While loss of D5Ertd579e did not overtly disrupt cortical progenitor dynamics, laminar organization, or gross brain morphology, D5Ertd579e null mutants exhibited selective behavioral deficits in vocalization, sociability, and novelty preference, while anxiety- and memory-related behaviors remained preserved. These behavioral phenotypes were accompanied by attenuated long-term plasticity, despite normal basal synaptic transmission. Together, our findings indicate that D5Ertd579e loss selectively alters neurodevelopment, preferentially impacting neural systems involved in social and motivational processing while preserving hippocampal-dependent networks. We propose that D5Ertd579e functions as a regionally specific regulator of neurodevelopment, whose disruption may contribute to ASD through distinct genetic pathways. More broadly, this study underscores the importance of interrogating uncharacterized loci to refine mechanistic models of the social brain in ASD.

BackgroundAutism Spectrum Disorder (ASD) and Attention-Deficit/Hyperactivity Disorder (ADHD) share substantial clinical and physiological overlap. While naturalistic and sensory-driven paradigms increasingly capture evoked neurophysiological responses, the intrinsic baseline physiology of these conditions remains poorly defined. We aimed to characterize resting-state autonomic arousal and oculomotor stability across the ASD-ADHD spectrum using both continuous (RDoC) and categorical (DSM-5) analytical frameworks. MethodsWe analyzed resting-state eye-tracking data from a large pediatric cohort (N = 2,640) from the Healthy Brain Network. During an unconstrained baseline, we extracted Pupil Relative Volatility (Coefficient of Variation [CV]) to index intrinsic autonomic arousal, and the Bivariate Contour Ellipse Area (BCEA) to index spatial gaze instability. Data were evaluated using continuous dimensional regressions against the Social Responsiveness Scale (SRS) and SWAN inventories, followed by 2x2 factorial ANCOVAs based on clinical diagnoses. Sensitivity analyses accounted for clinical collinearity, spatial outliers, and psychostimulant medication. ResultsDimensional models revealed that Pupil CV was significantly and uniquely associated with continuous autistic traits (q = 0.0043, joint model), exhibiting a strong statistical suppression effect when controlling for ADHD trait covariance. However, this pupillary biomarker lost significance in binary categorical models. Conversely, spatial gaze instability (BCEA) demonstrated robust categorical threshold effects; isolated ASD and ADHD diagnoses significantly impaired baseline gaze stability. Furthermore, comorbid ASD+ADHD produced a distinct, sub-additive interaction for BCEA (q = 0.005) that remained robust to extreme spatial outliers. Both physiological phenotypes were independent of active psychostimulant use. LimitationsWhile this study included a large and diverse group of children, the eye-tracking data were collected during a brief resting period -- watching a simple cross on a screen -- which may not capture how children behave in everyday, real-world situations. Because holding still for eye-tracking can be difficult, particularly for children with more severe symptoms, some data were lost; however, we statistically accounted for how much data each child contributed. Finally, while we confirmed that ADHD medication taken on the day of testing did not explain our findings, complete medication records were not available for every participant in this large observational study. ConclusionsPupillary dynamics and oculomotor stability associate with the ASD-ADHD spectrum through differing analytical patterns during resting states. Baseline autonomic volatility is more strongly captured by dimensional models of autistic trait severity, whereas baseline gaze instability is more clearly differentiated across categorical diagnostic groups, exhibiting a sub-additive interaction in comorbidity. Integrating both dimensional and categorical frameworks provides a more comprehensive understanding of these physiological variations, establishing a necessary foundation for future naturalistic and sensory-evoked research.

PurposeNavigational ability develops throughout childhood alongside the maturation of brain regions supporting egocentric and allocentric processing. In Autism Spectrum Disorder (ASD), atypical hippocampal development may impact flexible spatial memory; however, findings on navigational ability in autistic children remain inconsistent. This study aimed to compare both objective and perceived navigation ability in children with ASD and typically developing (TD) peers. MethodTwenty-six children with high-functioning ASD and twenty-five age- and gender-matched TD children (M_age = 12.04 years, SD = 1.64) completed a battery of navigational tasks from the Spatial Performance Assessment for Cognitive Evaluation (SPACE), including Path Integration, Egocentric Pointing, Mapping, Associative Memory, and Perspective Taking. Perceived navigation ability was assessed using the Santa Barbara Sense of Direction (SBSOD) scale. ResultsNo significant group differences were observed across any objective navigation tasks. However, children with ASD reported significantly lower perceived navigation ability compared to TD peers. ConclusionThese findings suggest a dissociation between perceived and actual navigational ability in ASD. By early adolescence, objective navigation performance appears intact, potentially reflecting sufficient maturation of underlying neural systems or the presence of compensatory mechanisms. The results underscore the importance of incorporating objective, task-based measures when assessing cognitive abilities in autistic populations.

Autism spectrum disorder and subclinical variation along the autism continuum are characterized by in sensory processing and cognitive integration, phenomena increasingly linked to atypical large-scale communication across cortical hierarchies. While structural and functional connectivity differences have been extensively documented, whether autistic traits are associated with a reorganization of the directional properties of ongoing cortical activity remains less understood. Here, we recorded resting-state EEG from 201 young adults selected from the lower and upper terciles of the Autism Quotient distribution and analyzed traveling-wave dynamics over parieto-frontal lines. Individuals with higher autistic traits showed a selective shift in left-hemisphere alpha-band traveling-wave directionality, driven primarily by reduced backward-dominant propagation and accompanied by a reciprocal shift toward forward dominance. This effect was anatomically specific, absent in an occipito-central control line set, and not accompanied by a matching pattern of group differences in oscillatory power, aperiodic spectral parameters, or peak alpha frequency. These findings identify resting-state alpha traveling waves as a candidate physiological signature of altered directional organization across the autism continuum, with potential relevance as a trait-sensitive neural marker.