Biological implications of genetic variations in autism spectrum disorders from genomics studies

Exploring key genes and pathways associated with sex differences in autism spectrum disorder: integrated bioinformatic analysis

Autism spectrum disorder (ASD) is a heterogenous neurodevelopmental disorder marked by functional abnormalities in brain that causes social and linguistic difficulties. The incidence of ASD is more prevalent in males compared to females, but the underlying mechanism, as well as molecular indications for identifying sex-specific differences in ASD symptoms remain unknown. Thus, impacting the development of personalized strategy towards pharmacotherapy of ASD. The current study employs an integrated bioinformatic approach to investigate the genes and pathways uniquely associated with sex specific differences in autistic individuals. Based on microarray dataset (GSE6575) extracted from the gene expression omnibus, the dysregulated genes between the autistic and the neurotypical individuals for both sexes were identified. Gene set enrichment analysis was performed to ascertain biological activities linked to the dysregulated genes. Protein-protein interaction network analysis was carried out to identify hub genes. The identified hub genes were examined to determine their functions and involvement in the associated pathways using Enrichr. Additionally, hub genes were validated from autism-associated databases and the potential small molecules targeting the hub genes were identified. The present study utilized whole blood transcriptomic gene expression analysis data and identified 2211 and 958 differentially expressed unique genes in males and females respectively. The functional enrichment analysis revealed that male hub genes were functionally associated with RNA polymerase II mediated transcriptional regulation whereas female hub genes were involved in intracellular signal transduction and cell migration. The top male hub genes exhibited functional enrichment in tyrosine kinase signalling pathway. The pathway enrichment analysis of male hub genes indicates the enrichment of papillomavirus infection. Female hub genes were enriched in androgen receptor signalling pathway and functionally enriched in focal adhesion specific excision repair. Identified drug like candidates targeting these genes may serve as a potential sex specific therapeutics. Wortmannin for males, 5-Fluorouracil for females had the highest scores. Targeted and sex-specific pharmacotherapies may be created for the management of ASD. The current investigation identifies sex-specific molecular signatures derived from whole blood which may serve as a potential peripheral sex-specific biomarkers for ASD. The study also uncovers the possible pharmacological interventions against the selected genes/pathway, providing support in development of therapeutic strategies to mitigate ASD. However, experimental proofs on biological systems are warranted.

Inhibitory dysfunction and social processing difficulties in autism: A comprehensive narrative review

The primary inhibitory neurotransmitter γ-aminobutyric acid (GABA) has a prominent role in regulating neural development and function, with disruption to GABAergic signalling linked to behavioural phenotypes associated with neurodevelopmental disorders, particularly autism. Such neurochemical disruption, likely resulting from diverse genetic and molecular mechanisms, particularly during early development, can subsequently affect the cellular balance of excitation and inhibition in neuronal circuits, which may account for the social processing difficulties observed in autism and related conditions. This comprehensive narrative review integrates diverse streams of research from several disciplines, including molecular neurobiology, genetics, epigenetics, and systems neuroscience. In so doing it aims to elucidate the relevance of inhibitory dysfunction to autism, with specific focus on social processing difficulties that represent a core feature of this disorder. Many of the social processing difficulties experienced in autism have been linked to higher levels of the excitatory neurotransmitter glutamate and/or lower levels of inhibitory GABA. While current therapeutic options for social difficulties in autism are largely limited to behavioural interventions, this review highlights the psychopharmacological studies that explore the utility of GABA modulation in alleviating such difficulties.

Behavioural deficits of autism spectrum disorder and associations with different gene clusters: a study with the whole-genome transmission disequilibrium test

BACKGROUND

Autism spectrum disorder (ASD) is a diverse neurodevelopmental disease primarily distinguished by limited and stereotyped activities as well as impaired social interaction. Due to the high heritability of ASD, research on the disorder has emphasised on identifying the underlying genetic and epigenetic aetiology. Many ASD loci have been identified by genome-wide association studies (GWASs). However, GWASs are more susceptible to bias due to population stratification. Moreover, GWASs barely reflect the genetic aetiology of subtypes of behavioural deficits.

METHODS

We applied whole-genome transmission disequilibrium test (TDT) to reveal the gene sets that are significantly associated with the four behavioural subtypes of restricted repetitive behaviours in 334 ASD trios. We further mapped the clustered genes to pathways and enriched the SFARI genes in these pathways.

RESULTS

Four unique gene clusters (181 genes in total) that are related to four different behavioural subtypes in ASD were identified. 23 SFARI genes were enriched in these four clusters. Through pathway analysis, nine non-SFARI genes (CNDP1, ETNK1, ITPKB, KCNQ5, PDE4D, PDGFRA, PPARGC1A, ULK2, SYNJ2) were found to be linked to the SFARI genes, which may contribute to the development of ASD. Furthermore, we found that the mTOR pathway enriched with the CNDP1, PDE4D, ULK2 genes is associated with neurodevelopment.

CONCLUSIONS

Whole-genome TDT test is a unique tool in clustering genes related to ASD subtypes of behavioural deficits. Several new candidate genes for ASD are revealed by pathway analysis of the clustered genes. These findings are useful for understanding the underlying mechanism of ASD.

Shorter telomere length in children with autism spectrum disorder is associated with oxidative stress

Objective

Autism spectrum disorder (ASD) is a highly heterogeneous neurodevelopmental disorder caused by a complex interaction between genetic and environmental risk factors. The balance between antioxidant capacity and oxidative stress (OS) induced free radicals may be crucial during the pathophysiological development of ASD.

Methods

In this study, 96 children with ASD who met the diagnostic and statistical manual of mental disorders were collected, and the number of children in the typical development (TD) group was matched by 1:1. Digital PCR (dPCR) for telomere length (TL) expression in ASD in peripheral blood leukocytes. Urine levels of 8-hydroxy-2-deoxyguanosine (8-OHdG) content were measured by tandem triple quadrupole mass spectrometry and corrected by urinary creatinine levels. The levels of superoxide dismutase (SOD), catalase (CAT), and capacity (AOC) were detected by kits.

Results

The TL of the ASD group was shorter than the TD group (p < 0.01) and had some accurate predictive significance for the identification of ASD (AUC = 0.632, 95% CI: 0.533-0.710, p = 0.002). Both 8-OHdG content and SOD activity in the ASD group were significantly higher than those in the TD group (p < 0.05). Shortened TL (Monofactor: 2.20 (1.22, 3.96), p = 0.009; Multifactor: 2.22 (1.22, 4.00), p = 0.008) and reduced CAT activity (Monofactor: 2.31 (1.28, 4.17), p = 0.006; Multifactor: 2.31 (1.28, 4.18), p = 0.006) are risk factors for the development of ASD, while reduced 8-OHdG content (Monofactor: 0.29 (0.14, 0.60), p = 0.001; Multifactor: 0.27 (0.13, 0.57), p = 0.001) and reduced SOD activity (Monofactor: 0.55 (0.31, 0.98), p = 0.042; Multifactor: 0.54 (0.30, 0.98), p = 0.042) are protective factors for the development of ASD.

Conclusion

In this study, TL and OS were significantly different between the ASD group and the TD group. As guanine-rich telomere sequences were likely damaged by oxygen free radicals, creating OS, which is a factor in the incidence and progression of ASDs. In conclusion, oxidative damage occurs in the bodies of children with ASD, which may lead to sustained disease progression and severe clinical manifestations. We assume that timely supplementation of antioxidants is very likely to be a potential treatment for early intervention in children with ASD. Identification and detection of OS-related biomarkers may contribute to early diagnosis and timely interventions in young patients with ASD.

Abnormal Brain Structure Is Associated with Social and Communication Deficits in Children with Autism Spectrum Disorder: A Voxel-Based Morphometry Analysis

Structural magnetic resonance imaging (sMRI) studies have shown abnormalities in the brain structure of ASD patients, but the relationship between structural changes and social communication problems is still unclear. This study aims to explore the structural mechanisms of clinical dysfunction in the brain of ASD children through voxel-based morphometry (VBM). After screening T1 structural images from the Autism Brain Imaging Data Exchange (ABIDE) database, 98 children aged 8-12 years old with ASD were matched with 105 children aged 8-12 years old with typical development (TD). Firstly, this study compared the differences in gray matter volume (GMV) between the two groups. Then, this study evaluated the relationship between GMV and the subtotal score of communications and social interaction on the Autism Diagnostic Observation Schedule (ADOS) in ASD children. Research has found that abnormal brain structures in ASD include the midbrain, pontine, bilateral hippocampus, left parahippocampal gyrus, left superior temporal gyrus, left temporal pole, left middle temporal gyrus and left superior occipital gyrus. In addition, in ASD children, the subtotal score of communications and social interaction on the ADOS were only significantly positively correlated with GMV in the left hippocampus, left superior temporal gyrus and left middle temporal gyrus. In summary, the gray matter structure of ASD children is abnormal, and different clinical dysfunction in ASD children is related to structural abnormalities in specific regions.

Genetics of autism spectrum disorders and future direction

Autism spectrum disorders (ASDs) have been increasing in prevalence. ASD is a complex human genetic disorder with high heredity and involves interactions between genes and the environment. A significant inheritance pattern in ASD involves a rare genetic mutation; common copy number variants refer to duplication or deletion of stretches of chromosomal loci or protein-disrupting single-nucleotide variants. Haploinsufficiency is one of the more common single-gene causes of ASD, explaining at least 0.5% of cases. Epigenetic mechanisms, such as DNA methylation, act at an interface of genetic and environmental risk and protective factors. Advances in genome-wide sequencing have broadened the view of the human methylome and have revealed the organization of the human genome into large-scale methylation domains with a footprint over neurologically important genes involved in embryonic development. Psychiatric disorders, including ASD, are expected to be diagnosed based on their genetically regulated pathophysiology and to be linked to their treatment.

Genetic diagnostic yields of 354 Chinese ASD children with rare mutations by a pipeline of genomic tests

Purpose: To establish an effective genomic diagnosis pipeline for children with autism spectrum disorder (ASD) for its genetic etiology and intervention. Methods: A cohort of 354 autism spectrum disorder patients were obtained from Beijing Children's Hospital, Capital Medical University. Peripheral blood samples of the patients were collected for whole genome sequencing (WGS) and RNA sequencing (RNAseq). Sequencing data analyses were performed for mining the single nucleotide variation (SNV), copy number variation (CNV) and structural variation (SV). Sanger sequencing and quantitative PCR were used to verify the positive results. Results: Among 354 patients, 9 cases with pathogenic/likely pathogenic copy number variation and 10 cases with pathogenic/likely pathogenic single nucleotide variations were detected, with a total positive rate of 5.3%. Among these 9 copy number variation cases, 5 were de novo and 4 were inherited. Among the 10 de novo single nucleotide variations, 7 were previously unreported. The pathological de novo mutations account for 4.2% in our cohort. Conclusion: Rare mutations of copy number variations and single nucleotide variations account for a relatively small proportion of autism spectrum disorder children, which can be easily detected by a genomic testing pipeline of combined whole genome sequencing and RNA sequencing. This is important for early etiological diagnosis and precise management of autism spectrum disorder with rare mutations.

Loss-of-function of KMT5B leads to neurodevelopmental disorder and impairs neuronal development and neurogenesis

Autism spectrum disorder (ASD) is a group of neurodevelopmental disorders that cause severe social, communication and behavioral problems. Recent studies show that the variants of a histone methyltransferase gene KMT5B, cause neurodevelopmental disorders (NDDs), including ASD and the knockout of Kmt5b in mice is embryonic lethal. However, the detailed genotype-phenotype correlations and functional effects of KMT5B in neurodevelopment are unclear. By targeted sequencing of a large Chinese ASD cohort, analyzing published genome-wide sequencing data, and mining literature, we curated 39 KMT5B variants identified from NDD individuals. A genotype-phenotype correlation analysis for ten individuals with KMT5B pathogenic variants reveals common symptoms, including ASD, intellectual disability, languages problem and macrocephaly. In vitro knockdown of the expression of Kmt5b in cultured mouse primary cortical neurons leads to a decrease in neuronal dendritic complexity and an increase in dendritic spine density, which can be rescued by expression of human KMT5B but not that of pathogenic de novo missense mutants. In vivo knockdown of the Kmt5b expression in the mouse embryonic cerebral cortex by in utero electroporation results in decreased proliferation and accelerated migration of neural progenitor cells. Our findings reveal essential roles of histone methyltransferase KMT5B in neuronal development, prenatal neurogenesis, and neuronal migration.