Evidence for contribution of common genetic variants within chromosome 8p21.2-8p21.1 to restricted and repetitive behaviors in autism spectrum disorders

Characterizing subdomains of insistence on sameness in autistic youth

Insistence on sameness (IS) encompasses a range of behavioral patterns, including resistance to change, routines, and ritualized behaviors, that can be present across social and non-social contexts. Given the breadth of behaviors encompassed by IS, it is important to determine whether this domain is best conceptualized and measured as uni- or a multi-dimensional construct. Therefore, the current study aimed to characterize the structure of IS and explore potentially distinct of patterns of associations between identified IS factors and relevant correlates, including age, sex, IQ, anxiety, social abilities, emotional and behavioral dysregulation, and sensory hypersensitivity. Exploratory graph analysis was conducted using the dimensional assessment of restricted and repetitive behaviors to examine the structure of IS in a sample 1892 autistic youth (Mage  = 10.82, SDage  = 4.14; range: 3-18 years; 420 females) recruited from the Simons Foundation Powering Autism Research for Knowledge cohort. Three distinct IS subdomains labeled as IS-Ritualistic/sameness, IS-Routines, and IS-Others (referring to IS behaviors during interactions with others) were identified. Generalized additive models demonstrated that each of the IS subdomains showed a unique pattern of association with key variables. More specifically, while sensory hypersensitivity was significantly associated with IS-Ritualistic/sameness and IS-Routines, it was not associated with IS-Others. Further, while emotional dysregulation was a unique predictor of IS-Ritualistic/sameness (but not IS-Routines or IS-Others), social interaction abilities were a unique predictor of IS-Routines (but not IS-Ritualistic/sameness or IS-Others). Current findings provide preliminary evidence that the IS may encompass several distinct subdomains.

Implications of Cell Adhesion Molecules in Autism Spectrum Disorder Pathogenesis

Autism spectrum disorder (ASD) is a neurodevelopmental illness that leads to repetitive behavior and debilitates social communication. Genetic changes such as susceptible genes and environmental factors promote ASD pathogenesis. Mutations in neuroligins (NLGNs) and neurexin (NRXNs) complex which encode cell adhesion molecules have a significant part in synapses formation, transcription, and excitatory-inhibitory balance. The ASD pathogenesis could partly, at the least, be related to synaptic dysfunction. Here, the NRXNs and NLGNs genes and signaling pathways involved in the synaptic malfunction that causes ASD have been reviewed. Besides, a new insight of NLGNs and NRXNs genes in ASD will be conferred.

Arriving at the empirically based conceptualization of restricted and repetitive behaviors: A systematic review and meta-analytic examination of factor analyses

An empirically based understanding of the factor structure of the restricted and repetitive behaviors (RRB) domain is a prerequisite for interpreting studies attempting to understand the correlates and mechanisms underpinning RRB and for measurement development. Therefore, this study aimed to conduct a systematic review and meta-analysis of RRB factor analytic studies. Sets of meta-analyses were performed to examine (a) the factor structure of individual RRB instruments, (b) associations between RRB subdomains across instruments, and (c) the association between RRB factors and other variables. Searches for peer-reviewed articles evaluating the factor structure of the RRB domain were performed in PsycINFO (Ovid), Medline (Ovid), and Embase (Ovid). No age, measurement, or informant-type limits were imposed. Quality and risk of bias for individual studies were assessed using relevant COSMIN sections. Among the 53 studies retained for review, 41 examined RRB factor structures among individuals with autism spectrum disorder (ASD) and 12 among non-ASD samples. Meta-analysis of factor correlations provided evidence that the RRB domain encompasses the following eight specific factors: repetitive motor behaviors, insistence on sameness, restricted interests, unusual interests, sensory sensitivity, and repetitive, stereotyped language. Although interrelated, RRB factors were distinct, showing a unique pattern of associations with demographic, cognitive, and clinical correlates. Meta-analyses of the associations between RRB factors and specific correlates, specifically adaptive functioning and communication impairments, should be considered preliminary due to the limited number of studies. Despite limitations, this review provides important insights into the factor structure of the RRB domain and highlights critical conceptual, measurement, and methodological limitations of the current research that will need to be addressed in order to improve our understanding of RRB.

Longitudinal Changes in Cortical Thickness in Adolescents with Autism Spectrum Disorder and Their Association with Restricted and Repetitive Behaviors

The neuroanatomy of autism spectrum disorder (ASD) shows highly heterogeneous developmental trajectories across individuals. Mapping atypical brain development onto clinical phenotypes, and establishing their molecular underpinnings, is therefore crucial for patient stratification and subtyping. In this longitudinal study we examined intra- and inter-individual differences in the developmental trajectory of cortical thickness (CT) in childhood and adolescence, and their genomic underpinnings, in 33 individuals with ASD and 37 typically developing controls (aged 11-18 years). Moreover, we aimed to link regional atypical CT development to intra-individual variations in restricted and repetitive behavior (RRB) over a two-year time period. Individuals with ASD showed significantly reduced cortical thinning in several of the brain regions functionally related to wider autism symptoms and traits (e.g., fronto-temporal and cingulate cortices). The spatial patterns of the neuroanatomical differences in CT were enriched for genes known to be associated with ASD at a genetic and transcriptomic level. Further, intra-individual differences in CT correlated with within-subject variability in the severity of RRBs. Our findings represent an important step towards characterizing the neuroanatomical underpinnings of ASD across development based upon measures of CT. Moreover, our findings provide important novel insights into the link between microscopic and macroscopic pathology in ASD, as well as their relationship with different clinical ASD phenotypes.

Genetic contributions to autism spectrum disorder

Autism spectrum disorder (autism) is a heterogeneous group of neurodevelopmental conditions characterized by early childhood-onset impairments in communication and social interaction alongside restricted and repetitive behaviors and interests. This review summarizes recent developments in human genetics research in autism, complemented by epigenetic and transcriptomic findings. The clinical heterogeneity of autism is mirrored by a complex genetic architecture involving several types of common and rare variants, ranging from point mutations to large copy number variants, and either inherited or spontaneous (de novo). More than 100 risk genes have been implicated by rare, often de novo, potentially damaging mutations in highly constrained genes. These account for substantial individual risk but a small proportion of the population risk. In contrast, most of the genetic risk is attributable to common inherited variants acting en masse, each individually with small effects. Studies have identified a handful of robustly associated common variants. Different risk genes converge on the same mechanisms, such as gene regulation and synaptic connectivity. These mechanisms are also implicated by genes that are epigenetically and transcriptionally dysregulated in autism. Major challenges to understanding the biological mechanisms include substantial phenotypic heterogeneity, large locus heterogeneity, variable penetrance, and widespread pleiotropy. Considerable increases in sample sizes are needed to better understand the hundreds or thousands of common and rare genetic variants involved. Future research should integrate common and rare variant research, multi-omics data including genomics, epigenomics, and transcriptomics, and refined phenotype assessment with multidimensional and longitudinal measures.

Single cell RNA sequencing detects persistent cell type- and methylmercury exposure paradigm-specific effects in a human cortical neurodevelopmental model

The developing human brain is uniquely vulnerable to methylmercury (MeHg) resulting in lasting effects especially in developing cortical structures. Here we assess by single-cell RNA sequencing (scRNAseq) persistent effects of developmental MeHg exposure in a differentiating cortical human-induced pluripotent stem cell (hiPSC) model which we exposed to in vivo relevant and non-cytotoxic MeHg (0.1 and 1.0 μM) concentrations. The cultures were exposed continuously for 6 days either once only during days 4-10, a stage representative of neural epithelial- and radial glia cells, or twice on days 4-10 and days 14-20, a somewhat later stage which includes intermediate precursors and early postmitotic neurons. After the completion of MeHg exposure the cultures were differentiated further until day 38 and then assessed for persistent MeHg-induced effects by scRNAseq. We report subtle, but significant changes in the population size of different cortical cell types/stages and cell cycle. We also observe MeHg-dependent differential gene expression and altered biological processes as determined by Gene Ontology analysis. Our data demonstrate that MeHg results in changes in gene expression in human developing cortical neurons that manifest well after cessation of exposure and that these changes are cell type-, developmental stage-, and exposure paradigm-specific.

Using the big data approach to clarify the structure of restricted and repetitive behaviors across the most commonly used autism spectrum disorder measures

BACKGROUND

Restricted and repetitive behaviors (RRB) in autism spectrum disorder (ASD) encompass several distinct domains. However, commonly used general ASD measures provide broad RRB scores rather than assessing separate RRB domains. The main objective of the current investigation was to conduct a psychometric evaluation of the ability of the Social Responsiveness Scale (SRS-2), the Social Communication Questionnaire (SCQ), the Autism Diagnostic Interview-Revised (ADI-R) and the Autism Diagnostic Observation Schedule (ADOS) to capture different RRB constructs.

METHODS

Exploratory Structural Equation Modeling (ESEM) was conducted using individual item-level data from the SRS-2, SCQ, ADI-R and the ADOS. Data were obtained from five existing publicly available databases. For the SRS-2, the final sample consisted of N = 16,761 individuals (Mage = 9.43, SD = 3.73; 18.5% female); for the SCQ, of N = 15,840 (Mage = 7.99, SD = 4.06; 18.1% female); for the ADI-R, of N = 8985 (Mage = 8.86, SD = 4.68; 19.4% female); and for the ADOS, of N = 6314 (Mage = 12.29, SD = 6.79; 17.7% female).

RESULTS

The three-factor structure provided the most optimal and interpretable fit to data for all measures (comparative fit index ≥ .983, Tucker Lewis index ≥ .966, root mean square error of approximation ≤ .028). Repetitive-motor behaviors, insistence on sameness and unusual or circumscribed interests factors emerged across all instruments. No acceptable fit was identified for the ADOS.

LIMITATIONS

The five datasets used here afforded a large as well as wide distribution of the RRB item scores. However, measures used for establishing convergent and divergent validity were only available for a portion of the sample.

CONCLUSIONS

Reported findings offer promise for capturing important RRB domains using general ASD measures and highlight the need for measurement development.

Brief Report: Role of Parent-Reported Executive Functioning and Anxiety in Insistence on Sameness in Individuals with Germline PTEN Mutations

This study aimed to characterize the relationship between insistence on sameness (IS), executive functioning (EF) and anxiety among individuals with PTEN mutations and individuals with macrocephalic ASD. The sample included 38 individuals with PTEN mutation and ASD diagnosis (PTEN-ASD; M_age = 8.93 years, SD_age = 4.75), 23 with PTEN mutation without ASD (PTEN-no ASD; M_age = 8.94 years; SD_age = 4.85) and 25 with ASD and macrocephaly but with no PTEN mutation (Macro-ASD; M_age = 11.99 years; SD_age = 5.15). The final model accounted for 45.7% of variance in IS, with Set-Shifting EF subdomain as a unique independent predictor (t = 4.12, p < 0.001). This investigation provides the first preliminary evidence for the EF-anxiety-IS interrelationship in individuals with PTEN mutations and with macrocephalic ASD.

A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues

Background

Although considerable progress has been made towards annotating the noncoding portion of the human and mouse genomes, regulatory elements in other species, such as livestock, remain poorly characterized. This lack of functional annotation poses a substantial roadblock to agricultural research and diminishes the value of these species as model organisms. As active regulatory elements are typically characterized by chromatin accessibility, we implemented the Assay for Transposase Accessible Chromatin (ATAC-seq) to annotate and characterize regulatory elements in pigs and cattle, given a set of eight adult tissues.

Results

Overall, 306,304 and 273,594 active regulatory elements were identified in pig and cattle, respectively. 71,478 porcine and 47,454 bovine regulatory elements were highly tissue-specific and were correspondingly enriched for binding motifs of known tissue-specific transcription factors. However, in every tissue the most prevalent accessible motif corresponded to the insulator CTCF, suggesting pervasive involvement in 3-D chromatin organization. Taking advantage of a similar dataset in mouse, open chromatin in pig, cattle, and mice were compared, revealing that the conservation of regulatory elements, in terms of sequence identity and accessibility, was consistent with evolutionary distance; whereas pig and cattle shared about 20% of accessible sites, mice and ungulates only had about 10% of accessible sites in common. Furthermore, conservation of accessibility was more prevalent at promoters than at intergenic regions.

Conclusions

The lack of conserved accessibility at distal elements is consistent with rapid evolution of enhancers, and further emphasizes the need to annotate regulatory elements in individual species, rather than inferring elements based on homology. This atlas of chromatin accessibility in cattle and pig constitutes a substantial step towards annotating livestock genomes and dissecting the regulatory link between genome and phenome.

Quantitative genome-wide association study of six phenotypic subdomains identifies novel genome-wide significant variants in autism spectrum disorder

Autism spectrum disorders (ASD) are highly heritable and are characterized by deficits in social communication and restricted and repetitive behaviors. Twin studies on phenotypic subdomains suggest a differing underlying genetic etiology. Studying genetic variation explaining phenotypic variance will help to identify specific underlying pathomechanisms. We investigated the effect of common variation on ASD subdomains in two cohorts including >2500 individuals. Based on the Autism Diagnostic Interview-Revised (ADI-R), we identified and confirmed six subdomains with a SNP-based genetic heritability h²_SNP = 0.2-0.4. The subdomains nonverbal communication (NVC), social interaction (SI), and peer interaction (PI) shared genetic risk factors, while the subdomains of repetitive sensory-motor behavior (RB) and restricted interests (RI) were genetically independent of each other. The polygenic risk score (PRS) for ASD as categorical diagnosis explained 2.3-3.3% of the variance of SI, joint attention (JA), and PI, 4.5% for RI, 1.2% of RB, but only 0.7% of NVC. We report eight genome-wide significant hits-partially replicating previous findings-and 292 known and novel candidate genes. The underlying biological mechanisms were related to neuronal transmission and development. At the SNP and gene level, all subdomains showed overlap, with the exception of RB. However, no overlap was observed at the functional level. In summary, the ADI-R algorithm-derived subdomains related to social communication show a shared genetic etiology in contrast to restricted and repetitive behaviors. The ASD-specific PRS overlapped only partially, suggesting an additional role of specific common variation in shaping the phenotypic expression of ASD subdomains.

Erythrocyte deformability in children with autism spectrum disorder: correlation with clinical features

Biomechanical properties of erythrocytes play an important role in health and disease. Deformability represents intrinsic property of erythrocytes to undergo deformation that is crucial for their passage through the narrow capillaries. The erythrocyte damage can lead to compromised tissue perfusion and consequently play a role in the pathogenesis of various diseases including neurological ones. Data available in databases indicate that erythrocytes in autism spectrum disorder (ASD) are altered. This may affect the clinical symptoms of ASD. The aim of our study was to determine erythrocyte deformability in 54 children with ASD and correlate it with clinical symptoms. We found significant negative correlation between erythrocyte deformability and score in C domain of the Autism Diagnostic Interview-Revised (ADI-R) diagnostic tool describing the measure of restrictive, repetitive, and stereotyped behaviors and interests, mainly observable in C1 and C2, but not in C3 and C4 subdomains. This supports the findings of other authors and suggest that behavioral domain C comprises of more subcategories with different underlying etiology. Our results also indicate that abnormalities in erythrocyte deformability may be involved in ASD pathomechanisms and contribute to its clinical manifestation. Further research is necessary to bring more data and identify erythrocyte deformability as prognostic biomarker in ASD.

Social and non-social autism symptoms and trait domains are genetically dissociable

The core diagnostic criteria for autism comprise two symptom domains - social and communication difficulties, and unusually repetitive and restricted behaviour, interests and activities. There is some evidence to suggest that these two domains are dissociable, though this hypothesis has not yet been tested using molecular genetics. We test this using a genome-wide association study (N = 51,564) of a non-social trait related to autism, systemising, defined as the drive to analyse and build systems. We demonstrate that systemising is heritable and genetically correlated with autism. In contrast, we do not identify significant genetic correlations between social autistic traits and systemising. Supporting this, polygenic scores for systemising are significantly and positively associated with restricted and repetitive behaviour but not with social difficulties in autistic individuals. These findings strongly suggest that the two core domains of autism are genetically dissociable, and point at how to fractionate the genetics of autism.

Assessing subtypes of restricted and repetitive behaviour using the Adult Repetitive Behaviour Questionnaire-2 in autistic adults

Background

The majority of previous research into restricted and repetitive behaviours (RRBs) has focussed on children, partly due to a lack of suitable measures for RRBs in adults. This study aimed to explore the psychometric properties of the Adult Repetitive Behaviour Questionnaire-2 (RBQ-2A) in a large sample of autistic adults using a self-report questionnaire method.

Methods

The RBQ-2A and Autism-Spectrum Quotient (AQ) were administered online. Data from 275 autistic adults aged 18-66 (M = 36.56, SD = 12.24; 100 men and 171 women) were analysed using polychoric principal components analysis (PCA). Reliability and validity were assessed using Cronbach's alpha and correlation analyses.

Results

PCA resulted in two components of the RBQ-2A, interpretable as repetitive sensory and motor behaviours (RSMB) and insistence on sameness (IS). Both components showed acceptable internal consistency (α = .70 and .81 respectively) and were significantly moderately correlated with scores on the AQ (r _s  = .25 and .42). Participants' scores on IS were higher than their scores on RSMB. RSMB, but not IS, was negatively associated with age, particularly in older adults (≥ 50 years). There were no gender differences.

Conclusions

The RBQ-2A is a reliable and valid self-report measure of RRBs in the present sample of autistic adults. As one of the few measures of RRBs aimed at adults, it is suitable for adults with the ability to read and complete a self-report questionnaire. Results build on previous work with children using the Repetitive Behaviour Questionnaire-2 (RBQ-2).

Bivariate genome-wide association analysis strengthens the role of bitter receptor clusters on chromosomes 7 and 12 in human bitter taste

Background

Human perception of bitter substances is partially genetically determined. Previously we discovered a single nucleotide polymorphism (SNP) within the cluster of bitter taste receptor genes on chromosome 12 that accounts for 5.8% of the variance in the perceived intensity rating of quinine, and we strengthened the classic association between TAS2R38 genotype and the bitterness of propylthiouracil (PROP). Here we performed a genome-wide association study (GWAS) using a 40% larger sample (n = 1999) together with a bivariate approach to detect previously unidentified common variants with small effects on bitter perception.

Results

We identified two signals, both with small effects (< 2%), within the bitter taste receptor clusters on chromosomes 7 and 12, which influence the perceived bitterness of denatonium benzoate and sucrose octaacetate respectively. We also provided the first independent replication for an association of caffeine bitterness on chromosome 12. Furthermore, we provided evidence for pleiotropic effects on quinine, caffeine, sucrose octaacetate and denatonium benzoate for the three SNPs on chromosome 12 and the functional importance of the SNPs for denatonium benzoate bitterness.

Conclusions

These findings provide new insights into the genetic architecture of bitter taste and offer a useful starting point for determining the biological pathways linking perception of bitter substances.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5058-2) contains supplementary material, which is available to authorized users.

ASD restricted and repetitive behaviors associated at 17q21.33: genes prioritized by expression in fetal brains

Autism spectrum disorder (ASD) is a behaviorally defined condition that manifests in infancy or early childhood as deficits in communication skills and social interactions. Often, restricted and repetitive behaviors (RRBs) accompany this disorder. ASD is polygenic and genetically complex, so we hypothesized that focusing analyses on intermediate core component phenotypes, such as RRBs, can reduce genetic heterogeneity and improve statistical power. Applying this approach, we mined Caucasian genome-wide association studies (GWAS) data from two of the largest ASD family cohorts, the Autism Genetics Resource Exchange and Autism Genome Project (AGP). Of the 12 RRBs measured by the Autism Diagnostic Interview-Revised, seven were found to be significantly familial and substantially variable, and hence, were tested for genome-wide association in 3104 ASD-affected children from 2045 families. Using a stringent significance threshold (P<7.1 × 10-9), GWAS in the AGP revealed an association between 'the degree of the repetitive use of objects or interest in parts of objects' and rs2898883 (P<6.8 × 10-9), which resides within the sixth intron of PHB. To identify the candidate target genes of the associated single-nucleotide polymorphisms at that locus, we applied chromosome conformation studies in developing human brains and implicated three additional genes: SLC35B1, CALCOCO2 and DLX3. Gene expression, brain imaging and fetal brain expression quantitative trait locus studies prioritize SLC35B1 and PHB. These analyses indicate that GWAS of single heritable features of genetically complex disorders followed by chromosome conformation studies in relevant tissues can be successful in revealing novel risk genes for single core features of ASD.

Common Genetic Variants Found in HLA and KIR Immune Genes in Autism Spectrum Disorder

The "common variant-common disease" hypothesis was proposed to explain diseases with strong inheritance. This model suggests that a genetic disease is the result of the combination of several common genetic variants. Common genetic variants are described as a 5% frequency differential between diseased vs. matched control populations. This theory was recently supported by an epidemiology paper stating that about 50% of genetic risk for autism resides in common variants. However, rare variants, rather than common variants, have been found in numerous genome wide genetic studies and many have concluded that the "common variant-common disease" hypothesis is incorrect. One interpretation is that rare variants are major contributors to genetic diseases and autism involves the interaction of many rare variants, especially in the brain. It is obvious there is much yet to be learned about autism genetics. Evidence has been mounting over the years indicating immune involvement in autism, particularly the HLA genes on chromosome 6 and KIR genes on chromosome 19. These two large multigene complexes have important immune functions and have been shown to interact to eliminate unwanted virally infected and malignant cells. HLA proteins have important functions in antigen presentation in adaptive immunity and specific epitopes on HLA class I proteins act as cognate ligands for KIR receptors in innate immunity. Data suggests that HLA alleles and KIR activating genes/haplotypes are common variants in different autism populations. For example, class I allele (HLA-A2 and HLA-G 14 bp-indel) frequencies are significantly increased by more than 5% over control populations (Table 2). The HLA-DR4 Class II and shared epitope frequencies are significantly above the control populations (Table 2). Three activating KIR genes: 3DS1, 2DS1, and 2DS2 have increased frequencies of 15, 22, and 14% in autism populations, respectively. There is a 6% increase in total activating KIR genes in autism over control subjects. And, more importantly there is a 12% increase in activating KIR genes and their cognate HLA alleles over control populations (Torres et al., 2012a). These data suggest the interaction of HLA ligand/KIR receptor pairs encoded on two different chromosomes is more significant as a ligand/receptor complex than separately in autism.