Interactions between the lipidome and genetic and environmental factors in autism

Autism omics research has historically been reductionist and diagnosis centric, with little attention paid to common co-occurring conditions (for example, sleep and feeding disorders) and the complex interplay between molecular profiles and neurodevelopment, genetics, environmental factors and health. Here we explored the plasma lipidome (783 lipid species) in 765 children (485 diagnosed with autism spectrum disorder (ASD)) within the Australian Autism Biobank. We identified lipids associated with ASD diagnosis (n = 8), sleep disturbances (n = 20) and cognitive function (n = 8) and found that long-chain polyunsaturated fatty acids may causally contribute to sleep disturbances mediated by the FADS gene cluster. We explored the interplay of environmental factors with neurodevelopment and the lipidome, finding that sleep disturbances and unhealthy diet have a convergent lipidome profile (with potential mediation by the microbiome) that is also independently associated with poorer adaptive function. In contrast, ASD lipidome differences were accounted for by dietary differences and sleep disturbances. We identified a large chr19p13.2 copy number variant genetic deletion spanning the LDLR gene and two high-confidence ASD genes (ELAVL3 and SMARCA4) in one child with an ASD diagnosis and widespread low-density lipoprotein-related lipidome derangements. Lipidomics captures the complexity of neurodevelopment, as well as the biological effects of conditions that commonly affect quality of life among autistic people.

Autism-related dietary preferences mediate autism-gut microbiome associations

There is increasing interest in the potential contribution of the gut microbiome to autism spectrum disorder (ASD). However, previous studies have been underpowered and have not been designed to address potential confounding factors in a comprehensive way. We performed a large autism stool metagenomics study (n = 247) based on participants from the Australian Autism Biobank and the Queensland Twin Adolescent Brain project. We found negligible direct associations between ASD diagnosis and the gut microbiome. Instead, our data support a model whereby ASD-related restricted interests are associated with less-diverse diet, and in turn reduced microbial taxonomic diversity and looser stool consistency. In contrast to ASD diagnosis, our dataset was well powered to detect microbiome associations with traits such as age, dietary intake, and stool consistency. Overall, microbiome differences in ASD may reflect dietary preferences that relate to diagnostic features, and we caution against claims that the microbiome has a driving role in ASD.

Emerging Therapies and challenges for individuals with Angelman syndrome

PURPOSE OF REVIEW

This review describes current understandings in the search for therapies to support children with Angelman syndrome. There is a rapid progression in particular in genetic therapies in this disorder supported by the Angelman community.

RECENT FINDINGS

Recent papers shed light on the timing of therapies and novel genetic therapies coming to trial as well as potential therapies still in preclinical phases. Further understanding of UBE3A and its role in neuronal development and plasticity as well as other mechanisms contributing to the Angelman phenotype is offering an opportunity for novel therapeutics.

SUMMARY

Greater understanding of the pathophysiology of the different phenotypes will offer an opportunity for novel therapeutics and may well change the course of this disorder over time where previously there has been minimal ability to intervene.

Analysis of common genetic variation and rare CNVs in the Australian Autism Biobank

BACKGROUND

Autism spectrum disorder (ASD) is a complex neurodevelopmental condition whose biological basis is yet to be elucidated. The Australian Autism Biobank (AAB) is an initiative of the Cooperative Research Centre for Living with Autism (Autism CRC) to establish an Australian resource of biospecimens, phenotypes and genomic data for research on autism.

METHODS

Genome-wide single-nucleotide polymorphism genotypes were available for 2,477 individuals (after quality control) from 546 families (436 complete), including 886 participants aged 2 to 17 years with diagnosed (n = 871) or suspected (n = 15) ASD, 218 siblings without ASD, 1,256 parents, and 117 unrelated children without an ASD diagnosis. The genetic data were used to confirm familial relationships and assign ancestry, which was majority European (n = 1,964 European individuals). We generated polygenic scores (PGS) for ASD, IQ, chronotype and height in the subset of Europeans, and in 3,490 unrelated ancestry-matched participants from the UK Biobank. We tested for group differences for each PGS, and performed prediction analyses for related phenotypes in the AAB. We called copy-number variants (CNVs) in all participants, and intersected these with high-confidence ASD- and intellectual disability (ID)-associated CNVs and genes from the public domain.

RESULTS

The ASD (p = 6.1e-13), sibling (p = 4.9e-3) and unrelated (p = 3.0e-3) groups had significantly higher ASD PGS than UK Biobank controls, whereas this was not the case for height-a control trait. The IQ PGS was a significant predictor of measured IQ in undiagnosed children (r = 0.24, p = 2.1e-3) and parents (r = 0.17, p = 8.0e-7; 4.0% of variance), but not the ASD group. Chronotype PGS predicted sleep disturbances within the ASD group (r = 0.13, p = 1.9e-3; 1.3% of variance). In the CNV analysis, we identified 13 individuals with CNVs overlapping ASD/ID-associated CNVs, and 12 with CNVs overlapping ASD/ID/developmental delay-associated genes identified on the basis of de novo variants.

LIMITATIONS

This dataset is modest in size, and the publicly-available genome-wide-association-study (GWAS) summary statistics used to calculate PGS for ASD and other traits are relatively underpowered.

CONCLUSIONS

We report on common genetic variation and rare CNVs within the AAB. Prediction analyses using currently available GWAS summary statistics are largely consistent with expected relationships based on published studies. As the size of publicly-available GWAS summary statistics grows, the phenotypic depth of the AAB dataset will provide many opportunities for analyses of autism profiles and co-occurring conditions, including when integrated with other omics datasets generated from AAB biospecimens (blood, urine, stool, hair).

Cannabidiol and Neurodevelopmental Disorders in Children

Neurodevelopmental and neuropsychiatric disorders (such as autism spectrum disorder) have broad health implications for children, with no definitive cure for the vast majority of them. However, recently medicinal cannabis has been successfully trialled as a treatment to manage many of the patients' symptoms and improve quality of life. The cannabinoid cannabidiol, in particular, has been reported to be safe and well-tolerated with a plethora of anticonvulsant, anxiolytic and anti-inflammatory properties. Lately, the current consensus is that the endocannabinoid system is a crucial factor in neural development and health; research has found evidence that there are a multitude of signalling pathways involving neurotransmitters and the endocannabinoid system by which cannabinoids could potentially exert their therapeutic effects. A better understanding of the cannabinoids' mechanisms of action should lead to improved treatments for neurodevelopmental disorders.

Associations Between Sleep Hygiene and Sleep Problems in Adolescents With ADHD: A Cross-Sectional Study

Objective: To determine whether self-reported sleep hygiene practices are associated with self- and parent-reported behavioral sleep problems in adolescents with ADHD. Method: Participants included 79 adolescents with ADHD (13-17 years) and their parents. Adolescents were asked to report on their sleep hygiene (Adolescent Sleep Hygiene Scale) and sleep (Adolescent Sleep Wake Scale). Parents also reported on their adolescent's sleep (Sleep Disturbance Scale for Children). Results: Poorer sleep hygiene was associated with higher total self-reported behavioral sleep problems and most self-reported sleep problems: falling asleep, reinitiating sleep, and returning to wakefulness. The association was also apparent for total parent-reported behavioral sleep problems, problems with initiating and maintaining sleep, and excessive somnolence. Conclusion: This study demonstrates small-to-moderate relationships between poor sleep hygiene practices and sleep problems in adolescents with ADHD, by both self- and parent-report.

A case-control genome-wide association study of ADHD discovers a novel association with the tenascin R (TNR) gene

It is well-established that there is a strong genetic contribution to the aetiology of attention deficit hyperactivity disorder (ADHD). Here, we employed a hypothesis-free genome-wide association study (GWAS) design in a sample of 480 clinical childhood ADHD cases and 1208 controls to search for novel genetic risk loci for ADHD. DNA was genotyped using Illumina's Human Infinium PsychArray-24v1.2., and the data were subsequently imputed to the 1000 Genomes reference panel. Rigorous quality control and pruning of genotypes at both individual subject and single nucleotide polymorphism (SNP) levels was performed. Polygenic risk score (PGRS) analysis revealed that ADHD case-control status was explained by genetic risk for ADHD, but no other major psychiatric disorders. Logistic regression analysis was performed genome-wide to test the association between SNPs and ADHD case-control status. We observed a genome-wide significant association (p = 3.15E-08) between ADHD and rs6686722, mapped to the Tenascin R (TNR) gene. Members of this gene family are extracellular matrix glycoproteins that play a role in neural cell adhesion and neurite outgrowth. Suggestive evidence of associations with ADHD was observed for an additional 111 SNPs (⩽9.91E-05). Although intriguing, the association between DNA variation in the TNR gene and ADHD should be viewed as preliminary given the small sample size of this discovery dataset.

Sleep in children with neurodevelopmental difficulties

Sleep disorders in children with neurodevelopmental disorders are complex and reflect underlying genetic/biological and behavioural components. The sleep disorders are the same as in the typically developing child, although there may be some modifications to the presentation or the frequency depending on the phenotype. Consideration of the known phenotypes and environmental issues are important in defining management strategies. Despite this complexity, defined behavioural strategies with good sleep hygiene can have a significant effect on the sleep problem and on parental management of the behaviours.

Rare DNA variants in the brain-derived neurotrophic factor gene increase risk for attention-deficit hyperactivity disorder: a next-generation sequencing study

Attention-deficit hyperactivity disorder (ADHD) is a prevalent and highly heritable disorder of childhood with negative lifetime outcomes. Although candidate gene and genome-wide association studies have identified promising common variant signals, these explain only a fraction of the heritability of ADHD. The observation that rare structural variants confer substantial risk to psychiatric disorders suggests that rare variants might explain a portion of the missing heritability for ADHD. Here we believe we performed the first large-scale next-generation targeted sequencing study of ADHD in 152 child and adolescent cases and 188 controls across an a priori set of 117 genes. A multi-marker gene-level analysis of rare (<1% frequency) single-nucleotide variants (SNVs) revealed that the gene encoding brain-derived neurotrophic factor (BDNF) was associated with ADHD at Bonferroni corrected levels. Sanger sequencing confirmed the existence of all novel rare BDNF variants. Our results implicate BDNF as a genetic risk factor for ADHD, potentially by virtue of its critical role in neurodevelopment and synaptic plasticity.

An open-label pilot trial of minocycline in children as a treatment for Angelman syndrome

BACKGROUND

Minocycline, a member of the tetracycline family, has a low risk of adverse effects and an ability to improve behavioral performance in humans with cognitive disruption. We performed a single-arm open-label trial in which 25 children diagnosed with Angelman syndrome (AS) were administered minocycline to assess the safety and tolerability of minocycline in this patient population and determine the drug's effect on the cognitive and behavioral manifestations of the disorder.

METHODS

Participants, age 4-12 years old, were randomly selected from a pool of previously screened children for participation in this study. Each child received 3 milligrams of minocycline per kilogram of body weight per day for 8 weeks. Participants were assessed during 3 study visits: baseline, after 8-weeks of minocycline treatment and after an 8-week wash out period. The primary outcome measure was the Bayley Scales of Infant and Toddler Development 3rd Edition (BSID-III). Secondary outcome measures included the Clinical Global Impressions Scale (CGI), Vineland Adaptive Behavior Scales 2nd Edition (VABS-II), Preschool Language Scale 4th Edition (PLS-IV) and EEG scores. Observations were considered statistically significant if p < 0.05 using ANOVA and partial eta squared (η(2)) was calculated to show effect size. Multiple comparisons testing between time points were carried out using Dunnett's post hoc testing.

RESULTS

Significant improvement in the mean raw scores of the BSID-III subdomains communication and fine motor ability as well as the subdomains auditory comprehension and total language ability of the PLS-IV when baseline scores were compared to scores after the washout period. Further, improvements were observed in the receptive communication subdomain of the VABS-II after treatment with minocycline. Finally, mean scores of the BSID-III self-direction subdomain and CGI scale score were significantly improved both after minocycline treatment and after the wash out period.

CONCLUSION

The clinical and neuropsychological measures suggest minocycline was well tolerated and causes improvements in the adaptive behaviors of this sample of children with Angelman syndrome. While the optimal dosage and the effects of long-term use still need to be determined, these findings suggest further investigation into the effect minocycline has on patients with Angelman syndrome is warranted.

TRIAL REGISTRATION

NCT01531582 - clinicaltrials.gov.

A high density linkage disequilibrium mapping in 14 noradrenergic genes: evidence of association between SLC6A2, ADRA1B and ADHD

Pharmacological evidence suggests the importance of noradrenergic and other monoaminergic neurotransmitters in the aetiology and treatment of attention deficit hyperactivity disorder (ADHD). Until recently, the genes of the noradrenergic pathway were not intensively investigated in ADHD compared to dopaminergic and serotonergic candidates. In this study, 91 SNP markers of 14 noradrenergic genes (an average density of one SNP per 4.5 kbp) were examined in ADHD samples from Ireland and Australia. Although suggestive evidence of association (nominal p ≤ 0.05) with the genes SLC6A2, ADRA1A, ADRA1B and ADRA2B was observed, none remained significant after permutation adjustments. In contrast, haplotype analyses demonstrated a significant association between ADHD and a SLC6A2 haplotype comprising the markers rs36009, rs1800887, rs8049681, rs2242447 and rs9930182 (χ(2) = 9.39, p-corrected = 0.019, OR = 1.51). A rare ADRA1B haplotype made of six SNPs (rs2030373, rs6884105, rs756275, rs6892282, rs6888306 and rs13162302) was also associated (χ(2) = 7.79, p-corrected = 0.042 OR = 2.74) with the disorder. These findings provide evidence of a contribution of the noradrenaline system to the genetic aetiology of ADHD. The observed haplotype association signals may be driven by as yet unidentified functional risk variants in or around the associated regions. Functional genomic analysis is warranted to determine the biological mechanism of the observed association.

Plasma and urinary sulfate determination in a cohort with autism

Sulfate is important for mammalian development but is not routinely measured in clinical settings. The renal NaS1 sulfate transporter maintains circulating sulfate levels and is linked to renal sulfate wasting in mice. Some autistic individuals exhibit renal sulfate wasting, but the etiology is yet unknown. We measured plasma and urinary sulfate levels, calculated the fractional excretion index (FEI) of sulfate, and screened for two loss-of-function NaS1 sequence variants (R12X and N174S) in 23 autistic individuals. The FEI sulfate values ranged from 0.13 to 0.50. NaS1 variants were detected in 18 of the 23 individuals (11 heterozygous N174S, four homozygous N174S, two heterozygous R12X, and one individual carried both R12X and N174S). Those individuals with neither sequence variant had FEI sulfate ≤ 0.34, whereas FEI sulfate ≥ 0.35 was found in about 60 % (11 of 18) of individuals that had R12X and/or N174S. This study links renal sulfate wasting with loss-of-function NaS1 sequence variants in humans.

WITHDRAWN: NaS1 sulfate transporter is linked to hyposulfatemia and longevity

This article has been withdrawn at the request of the editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy.

Analysis of N- and O-linked protein glycosylation in children with Prader-Willi syndrome

BACKGROUND

Current genotype-phenotype correlations in Prader-Willi syndrome (PWS) are struggling to give an explanation of the diversity in phenotype and there is a need to move towards a molecular understanding of PWS. A range of functions related to glycoproteins are involved in the pathophysiology of PWS and it may be that abnormal glycosylation is contributing to the biological phenotype. The objective of this study was to investigate the state of N- and O-linked glycosylation in children with Prader-Willi syndrome.

METHODS

Twenty-three children with PWS and 20 non-PWS controls were included in the study. Protein N-linked glycosylation was assessed by analysing serum transferrin through mass spectrometry and protein O-linked through isoelectric focusing (IEF) of serum apolipoprotein C-III (apoC-III), confirmed by mass spectrometry.

RESULTS

The results of this analysis indicated that the N-linked glycosylation pathway in PWS is normal. A subgroup of PWS individuals was found to have a hyposialylated pattern of apoC-III isoforms. This was independent of the underlying genetic mechanism and is the first report of an apoC-III IEF abnormality in PWS.

CONCLUSIONS

This is the first report of apoC-III hyposialylation in PWS. As this field is in its infancy, additional study is required before these findings may be used in clinical settings.

Characteristics of sleep EEG power spectra in healthy infants in the first two years of life

OBJECTIVE

This study characterises and describes the maturational evolution of the healthy infant sleep electroencephalogram (EEG) longitudinally from 2 weeks to 24 months of age, by means of power spectral analysis.

METHODS

A prospective cohort of 34 healthy infants underwent overnight polysomnography (PSG) at 2 weeks, and at 3, 6, 12 and 24 months of age. Sleep epochs were scored as Active Sleep (AS) and Quiet Sleep (QS) at 2 weeks of age and as Rapid Eye Movement (REM) and Non-REM (NREM) stages from 3 months onwards. Representative epochs were used to generate the EEG power spectra, from the central C3 derivation. These were analysed visually and quantitatively in AS/REM and QS/NREM sleep in the following bandwidths: delta (0.5-4 Hz); theta (4-8 Hz); alpha (8-11 Hz); sigma (11-15 Hz) and 0.5-25 Hz.

RESULTS

Sleep EEG (central derivation) power spectra changed significantly in the different bandwidths as the infants matured. The emergence of a peak in the sigma bandwidth in NREM N2 sleep corresponded with the development of sleep spindles. Maturational changes were also seen in NREM N3 and in theta and alpha bandwidths in both AS/REM and QS/NREM.

CONCLUSIONS

Sleep EEG power spectra characteristics in healthy infants evolve in keeping with maturation and neurodevelopmental milestones.

SIGNIFICANCE

This study provides an atlas of healthy infant sleep EEG in the early years of life, providing a basis for association with other neurodevelopmental measures and a normative dataset on which disease may be discriminated.

Sleep disturbances in CHARGE syndrome: types and relationships with behavior and caregiver well-being

Children with CHARGE syndrome frequently develop moderate to severe behavior difficulties and are often diagnosed with obsessive-compulsive disorder, attention deficit disorder, Tourette syndrome, and autism. Anecdotal reports have indicated that sleep is also affected. However, the prevalence and types of sleep disturbance have not been identified. This study investigated sleep disturbances in 87 children with CHARGE syndrome, aged 6 to 18 years (mean 11y, SD 3y 8mo). There were 52 males and 35 females represented. Instruments included measures of sleep (Sleep Disturbances Scale for Children [SDSC]), behavior (Developmental Behaviour Checklist [DBC]), and carer well-being (Malaise Inventory). On the SDSC, 57.5% received scores considered significant for sleep disturbances, with disorders of initiating and maintaining sleep, sleep breathing, and sleep-wake transition being the most common. The SDSC was significantly correlated with the DBC (p=0.010) and the Malaise Inventory (p=0.003). Regression analysis found that both problem behavior and sleep disturbances contributed to the prediction of scores on the Malaise Inventory. Being both deaf and blind (p=0.001), experiencing frequent middle-ear infections (p=0.015), and starting to walk at an older age (p=0.007) were associated with more sleep disturbance. Craniofacial anomalies were not. The study highlights the importance of addressing the sleep difficulties associated with CHARGE syndrome relating both to airway management and to disorders of initiating sleep.

9. Common causes of sleep disruption and daytime sleepiness: childhood sleep disorders II

There are strong associations between childhood sleep disorders and behavioural, concentration and mood problems. Sleep disorders caused and maintained by behavioural factors (eg, sleep-onset association disorder) are common in young children, and have a significant impact on families. Evaluation should include a medical history, a physical, neurological and developmental examination, a description of any nocturnal events or daytime effects of the child's disturbed sleep, and a good understanding of the family situation and parental management of the child. Management involves recognising the developmental age of the child and the family dynamics, and educating and supporting families in applying behavioural techniques to establish good sleep hygiene. Children with parasomnias (eg, night terrors) also benefit from good sleep hygiene, while those with respiratory or neurological causes of sleep disturbance should be referred for specialist treatment.

Extreme variability of expression of a Sonic Hedgehog mutation: attention difficulties and holoprosencephaly

Holoprosencephaly (HPE) is a clinically variable and genetically heterogeneous central nervous system (CNS) malformation. Alobar HPE, which is its most severe form, is associated with a poor prognosis. At the milder end of the HPE spectrum microcephaly, hypotelorism, and single central maxillary incisor may be recognised. Currently, four genes have been identified for this condition. These include Sonic Hedgehog (SHH) on chromosome 7q36, which is thought to be responsible for a significant proportion of autosomal dominant HPE. We report an index case with alobar holoprosencephaly caused by an SHH mutation and six members of his family over two generations with this mutation, with a broad range of clinical presentation, including attention deficit hyperactivity disorder (ADHD). The combination of microcephaly, hypotelorism, subtle midline facial anomalies, and ADHD within a sibship should alert the physician to the possible diagnosis of HPE.