Zohreh Talebizadeh

Subset of individuals with autism spectrum disorders and extreme macrocephaly associated with germline PTEN tumour suppressor gene mutations

The genetic aetiology of autism remains elusive. Occasionally, individuals with Cowden syndrome (a cancer syndrome) and other related hamartoma disorders such as Bannayan-Riley-Ruvalcaba syndrome, Proteus syndrome, and Proteus-like conditions, are characterised by germline PTEN mutations, and may have neurobehavioural features resembling autism as well as overgrowth and macrocephaly. Therefore, we undertook PTEN gene mutation analysis in 18 subjects mainly prospectively ascertained with autism spectrum disorder and macrocephaly. Of these 18 autistic subjects (13 males and five females; ages 3.1–18.4 years) with a head circumference range from 2.5 to 8.0 standard deviations above the mean, three males (17%) carried germline PTEN mutations. These three probands had previously undescribed PTEN mutations: H93R (exon 4), D252G (exon 7), and F241S (exon 7). They had the larger head circumference measurements amongst all our study subjects. The three residues altered in our patients were highly evolutionarily conserved. We suggest that PTEN gene testing be considered for patients with autistic behaviour and extreme macrocephaly. The gene findings may impact on recurrence risks as well as medical management for the patient.

Novel splice isoforms for NLGN3 and NLGN4 with possible implications in autism

Objective: To screen cDNA for NLGN3 and NLGN4 from lymphoblastoid cells from autistic subjects. Methods and results: 10 young autistic females and 30 non-autistic subjects were studied for alterations in two X linked genes, NLGN3 and NLGN4. A novel NLGN4 isoform lacking exon 4, which occurred de novo on the paternal allele, was identified in one of the autistic females. Monoallelic expression of NLGN4 was seen in this subject and in 11 of 14 informative autistic and non-autistic females using a single nucleotide polymorphism found at 3′ UTR. Additionally, the NLGN3 transcript was present in two isoforms (with and without exon 7) in nine of 10 autistic females and in 30 non-autistic subjects, including parents of the autistic female having only the complete transcript with exon 7, and from the whole brain of a control. The novel truncated NLGN3 product may have a regulatory role, as reported in other proteins (for example, vasopressin receptor) by attenuating the function of the full length isoform, resulting in a reduction of the mature protein. Three dimensional protein structures were characterised using comparative modelling, and significant changes were suggested in the protein cores for these two neuroligin isoforms. Conclusions: Splice variants may lead to potentially abnormal neuroligins in the causation of autism spectrum disorders.

Body Composition and Fatness Patterns in Prader-Willi Syndrome: Comparison with Simple Obesity

Objective: To characterize the body composition of Prader‐Willi syndrome (PWS) subjects and compare with simple obesity.

Comparison of X-chromosome inactivation patterns in multiple tissues from human females

Background: X-chromosome inactivation (XCI) is the mechanism by which gene dosage uniformity is achieved between female mammals with two X chromosomes and male mammals with a single X chromosome, and is thought to occur randomly. For molecular genetic testing, accessible tissues (eg blood) are commonly studied, but the relationship with inaccessible tissues (eg brain) is poorly understood. For accessible tissues to be informative for genetic analysis, a high degree of concordance of genetic findings among tissue types is required. Objective: To determine the relationship among multiple tissues within females at different ages (fetus to 82 years). Methods: XCI patterns were analysed using the polymorphic androgen receptor (AR) gene assay. DNA was isolated from 26 different human females without history of malignancy, using 34 autopsy tissues representing the three embryonic germ layers. Results: 33 of the 280 tissue samples analysed from 13 of the 26 females showed skewed XCI values (>80:20%). Average XCI value was not significantly different among the tissues, but a trend for increasing XCI variability was observed with age in blood and other tissues studied (eg the SD for all tissues studied for the 0–2 years group was 9.9% compared with 14.8% in the >60 years group). We found a significant correlation (rs = 0.51, p = 0.035) between XCI values for blood and/or spleen and brain tissue, and in most other tissues representing the three embryonic germ layers. Conclusions: In our study, XCI data were comparable among accessible (eg blood) and inaccessible tissues (eg brain) in females at various ages, and may be useful for genetic testing. A trend was seen for greater XCI variability with increasing age, particularly in older women (>60 years).

X chromosome gene expression in human tissues: Male and female comparisons

About 25% of X-linked genes may escape inactivation at least to some degree. However, in vitro results from somatic cell hybrids may not reflect what happens in vivo. Therefore, we analyzed the female/male (F/M) gene fold expression ratio for 299 X-linked and 7795 autosomal genes from 11 different tissues from an existing in vivo microarray database. On average 5.1 and 4.9% of genes showed higher expression in females compared with 7.4 and 7.9% in males, respectively, for X-linked and autosomal genes. A trend was found for F/M gene fold ratios greater than 1.5 for several X-linked genes indicating overexpression in females among multiple tissues. Nine X-linked genes showed overexpression in females in at least 3 of the 11 studied tissues. Of the 9 genes, 6 were located on the short arm and 3 on the long arm of the X chromosome. Six of the 9 genes have previously been reported to escape X inactivation. However, in general, no consistent pattern was seen for the expression of X-linked genes between in vitro and in vivo systems. This study indicates that factors other than the X-inactivation process may impact on the expression of X-linked genes resulting in an overall similar gender expression for both X-linked and autosomal genes.

Microarray analysis of gene/transcript expression in Prader-Willi syndrome: deletion versus UPD

Background: Prader-Willi syndrome (PWS), the most common genetic cause of marked obesity, is caused by genomic imprinting and loss of expression of paternal genes in the 15q11–q13 region. There is a paucity of data examining simultaneous gene expression in this syndrome. Methods: We generated cDNA microarrays representing 73 non-redundant genes/transcripts from the 15q11–q13 region, the majority within the PWS critical region and others distally on chromosome 15. We used our custom microarrays to compare gene expression from actively growing lymphoblastoid cell lines established from nine young adult males (six with PWS (three with deletion and three with UPD) and three controls). Results: There was no evidence of expression of genes previously identified as paternally expressed in the PWS cell lines with either deletion or UPD. We detected no difference in expression of genes with known biallelic expression located outside the 15q11–q13 region in all cell lines studied. There was no difference in expression levels of biallelically expressed genes (for example, OCA2) from within 15q11–q13 when comparing UPD cell lines with controls. However, two genes previously identified as maternally expressed (UBE3A and ATP10C) showed a significant increase in expression in UPD cell lines compared with control and PWS deletion subjects. Several genes/transcripts (for example, GABRA5, GABRB3) had increased expression in UPD cell lines compared with deletion, but less than controls indicating paternal bias. Conclusions: Our results suggest that differences in expression of candidate genes may contribute to phenotypic differences between PWS subjects with deletion or UPD and warrant further investigations.

Plasma Peptide YY and Ghrelin Levels in Infants and Children with Prader-Willi Syndrome

An insatiable appetite is a cardinal feature of Prader-Willi syndrome (PWS) with stomach rupturing as a reported consequence. Peptide YY, secreted by the intestine and released post-prandially, inhibits appetite, while ghrelin, secreted by the stomach during mealtime hunger, stimulates appetite. Both peptide YY and ghrelin act at the brain level, particularly the hypothalamus. Recently, plasma ghrelin levels were reported to be elevated in children and adults with PWS but peptide YY levels have not been studied in this syndrome or ghrelin in infants with PWS. To further address the abnormal eating behavior in PWS, we obtained fasting plasma peptide YY and ghrelin levels in 12 infants and children with PWS ranging in age from 2.5 months to 13.3 years and compared them with values from normal populations reported in the literature. Plasma ghrelin levels in our patients with PWS were similar to those of other children with PWS and were significantly higher than those reported in obese children without PWS. Our infants with PWS had similar plasma ghrelin levels compared with our children with PWS but peptide YY levels in our children and infants with PWS were lower than reported in similarly aged individuals without PWS. In addition, we performed preliminary gene expression analysis of ghrelin and peptide YY and their receptors in patients with PWS using established lymphoblastoid cell lines but gene expression did not correlate with plasma ghrelin or peptide YY levels.

Autism genetic database (AGD): a comprehensive database including autism susceptibility gene-CNVs integrated with known noncoding RNAs and fragile sites

BackgroundAutism is a highly heritable complex neurodevelopmental disorder, therefore identifying its genetic basis has been challenging. To date, numerous susceptibility genes and chromosomal abnormalities have been reported in association with autism, but most discoveries either fail to be replicated or account for a small effect. Thus, in most cases the underlying causative genetic mechanisms are not fully understood. In the present work, the Autism Genetic Database (AGD) was developed as a literature-driven, web-based, and easy to access database designed with the aim of creating a comprehensive repository for all the currently reported genes and genomic copy number variations (CNVs) associated with autism in order to further facilitate the assessment of these autism susceptibility genetic factors.DescriptionAGD is a relational database that organizes data resulting from exhaustive literature searches for reported susceptibility genes and CNVs associated with autism. Furthermore, genomic information about human fragile sites and noncoding RNAs was also downloaded and parsed from miRBase, snoRNA-LBME-db, piRNABank, and the MIT/ICBP siRNA database. A web client genome browser enables viewing of the features while a web client query tool provides access to more specific information for the features. When applicable, links to external databases including GenBank, PubMed, miRBase, snoRNA-LBME-db, piRNABank, and the MIT siRNA database are provided.ConclusionAGD comprises a comprehensive list of susceptibility genes and copy number variations reported to-date in association with autism, as well as all known human noncoding RNA genes and fragile sites. Such a unique and inclusive autism genetic database will facilitate the evaluation of autism susceptibility factors in relation to known human noncoding RNAs and fragile sites, impacting on human diseases. As a result, this new autism database offers a valuable tool for the research community to evaluate genetic findings for this complex multifactorial disorder in an integrated format. AGD provides a genome browser and a web based query client for conveniently selecting features of interest. Access to AGD is freely available at http://wren.bcf.ku.edu/.

Genetic studies of complex human diseases: Characterizing SNP-disease associations using Bayesian networks

BackgroundDetecting epistatic interactions plays a significant role in improving pathogenesis, prevention, diagnosis, and treatment of complex human diseases. Applying machine learning or statistical methods to epistatic interaction detection will encounter some common problems, e.g., very limited number of samples, an extremely high search space, a large number of false positives, and ways to measure the association between disease markers and the phenotype.ResultsTo address the problems of computational methods in epistatic interaction detection, we propose a score-based Bayesian network structure learning method, EpiBN, to detect epistatic interactions. We apply the proposed method to both simulated datasets and three real disease datasets. Experimental results on simulation data show that our method outperforms some other commonly-used methods in terms of power and sample-efficiency, and is especially suitable for detecting epistatic interactions with weak or no marginal effects. Furthermore, our method is scalable to real disease data.ConclusionsWe propose a Bayesian network-based method, EpiBN, to detect epistatic interactions. In EpiBN, we develop a new scoring function, which can reflect higher-order epistatic interactions by estimating the model complexity from data, and apply a fast Branch-and-Bound algorithm to learn the structure of a two-layer Bayesian network containing only one target node. To make our method scalable to real data, we propose the use of a Markov chain Monte Carlo (MCMC) method to perform the screening process. Applications of the proposed method to some real GWAS (genome-wide association studies) datasets may provide helpful insights into understanding the genetic basis of Age-related Macular Degeneration, late-onset Alzheimers disease, and autism.

No association between HOXA1 and HOXB1 genes and autism spectrum disorders (ASD)

Autism (MIM 209850) is an early onset neurodevelopmental disorder with a prevalence rate of at least 5 in 10 000 people1–3 and belongs to a group of heterogeneous diseases known as autism spectrum disorders (ASD), including autism, Asperger syndrome, and the prototypical pervasive development disorder-not otherwise specified (PDD-NOS).4 Affected subjects have impairment in reciprocal communication and social interaction which are accompanied by repetitive and stereotyped behaviours and interests. Twin and family studies have shown a strong underlying genetic predisposition for autism5–8 with linkage to regions 2q, 7q, 16p,9–12 and 15q.13–15 The greatest linkage is to 7q31.9,16,17 However, to date no single gene has been identified as being responsible for autism and it is suggested that as many as 15 loci are likely to contribute to its aetiology.18,19 Because autism is a neurodevelopmental disorder, genes involved in early formation of the brain and nervous system are good candidates to study for this complex disorder. HOX genes encode a class of transcription factors known as homeobox genes which are involved in regulating neural migration during embryogenesis.20,21 Furthermore, analysis of mice mutants have shown that HOX genes, specifically HOXA1 and HOXB1 , function together in the development of the hindbrain.22,23 HOXA1 and HOXB1 are located on chromosomes 7p24,25 and 17q25 in humans, respectively. Recently, Ingram et al 26 investigated the frequency of HOXA1 and HOXB1 variants in 57 white autistic probands from singleton or multiplex families and 119 unrelated adults as controls. They studied a variant of the HOXA1 gene (A218G) which changes the codon for one histidine in a series of histidine repeats to an arginine (H73R). They also studied a common variant in the HOXB1 gene which includes a 9 …