Genes for cognitive function: developments on the X

Challenges in molecular diagnosis of X-linked Intellectual disability

BACKGROUND

Intellectual disability (ID) affects 1-3% of the Western population and is heterogeneous in origin. Mutations in X-linked genes represent 5-10% of ID in males. Fragile X syndrome, due to the silencing of the FMR1 gene, is the most common form of ID, with a prevalence of around 1:5000 males. Females are usually non- or mildly affected carriers, and in a few rare cases, the only gender affected. Array comparative genome hybridization (aCGH) and next-generation sequencing (NGS) have dramatically changed the nature of human genome analysis leading to the identification of new X-linked intellectual disability syndromes and disease-causing genes.

SOURCES OF DATA

Original papers, reviews, guidelines and experiences of the diagnostic laboratories.

AREAS OF AGREEMENT

Family history and clinical examination still are essential to choose the appropriate diagnostic tests, including, a disease-specific genetic test, aCGH or FMR1 molecular analysis. If negative, NGS approaches like well-defined gene panels, whole exome, or even whole genome sequencing, are increasingly being used, improving diagnostics and leading to the identification of novel disease mechanisms.

AREAS OF CONTROVERSY

The main challenge in the era of NGS is filtering and interpretation of the data generated by the analysis of a single individual. In X-linked cases, assessing pathogenicity is particularly challenging, even more when the variant is found to be inherited from a healthy carrier mother or when a heterozygous X-linked mutation is found in an impaired female.

GROWING POINTS

At present, variant interpretation remains a challenging task, especially in X-linked disorders. We review the main difficulties and propose a comprehensive overview that might aid in variant interpretation. Establishing a genetic diagnosis facilitates counseling and allows better delineation of clinical phenotypes.

AREAS TIMELY FOR DEVELOPING RESEARCH

To improve variant interpretation, there is need to refine in silico predictions with specific criteria for each gene, and to develop cost-effective functional tools, which can be easily transferred to diagnostics.

Body iron and lead status in early childhood and its effects on development and cognition: a longitudinal study from urban Vellore

OBJECTIVE

Early childhood factors can have persisting effects on development and cognition in children. We propose to explore the trends of Fe deficiency and Pb toxicity in early childhood and their association with child development at 2 years of age and cognition at 5 years.

DESIGN

Longitudinal birth cohort study.

SETTING

Urban slum, Vellore, India.

PARTICIPANTS

Children enrolled at birth were followed up regularly in the first 2 years with developmental and cognitive assessments at 2 and 5 years of age, respectively.

RESULTS

The birth cohort enrolled 251 children with 228 children followed up at 2 years and 212 at 5 years of age. Fe deficiency (ID) was highest at 15 months of age and improved subsequently at 24 months. Blood Pb levels (BLL) remained high at all age groups with an increasing trend with age; 97 % at 36 months having high BLL. Persistent high mean BLL at 15 and 24 months had negative association with both cognition and expressive language raw scores of 24 months, while high mean BLL at 15, 24 and 36 months had no significant association with any of the domains of cognition at 5 years of age. Early childhood cumulative body Fe status at 7, 15 and 24 months did not show any association with child development at 2 years, but was associated with verbal, performance and processing speed components of cognition at 5 years.

CONCLUSIONS

Optimising body Fe status and limiting Pb exposure in early childhood can augment child development and school entry cognition.

Prenatal Exposure to Methamphetamine: Up-Regulation of Brain Receptor Genes

Methamphetamine (METH) is a widespread illicit drug. If it is taken by pregnant women, it passes through the placenta and just as it affects the mother, it can impair the development of the offspring. The aim of our study was to identify candidates to investigate for changes in the gene expression in the specific regions of the brain associated with addiction to METH in rats. We examined the various areas of the central nervous system (striatum, hippocampus, prefrontal cortex) for signs of impairment in postnatal day 80 in experimental rats, whose mothers had been administered METH (5 mg/kg/day) during the entire gestation period. Changes in the gene expression at the mRNA level were determined by two techniques, microarray and real-time PCR. Results of two microarray trials were evaluated by LIMMA analysis. The first microarray trial detected either up-regulated or down-regulated expression of 2189 genes in the striatum; the second microarray trial detected either up-regulated or down-regulated expression of 1344 genes in the hippocampus of prenatally METH-exposed rats. We examined the expression of 10 genes using the real-time PCR technique. Differences in the gene expression were counted by the Mann–Whitney U-test. Significant changes were observed in the cocaine- and amphetamine-regulated transcript prepropeptide, tachykinin receptor 3, dopamine receptor D3 gene expression in the striatum regions, in the glucocorticoid nuclear receptor Nr3c1 gene expression in the prefrontal cortex and in the carboxylesterase 2 gene expression in the hippocampus of prenatally METH-exposed rats. The microarray technique also detected up-regulated expression of trace amine-associated receptor 7 h gene in the hippocampus of prenatally METH-exposed rats. We have identified susceptible genes; candidates for the study of an impairment related to methamphetamine addiction in the specific regions of the brain.

Early childhood cognitive development is affected by interactions among illness, diet, enteropathogens and the home environment: findings from the MAL-ED birth cohort study

Background

Millions of children in low-income and middle-income countries (LMICs) are at risk of not reaching their full cognitive potential. Malnutrition and enteric infections in early life are implicated as risk factors; however, most studies on these risks and their associations with cognitive development have failed to adequately account for confounding factors or the accumulation of putative insults. Here, we examine the interaction between infections and illness on cognitive development in LMIC community settings.

Methods

As part of the Etiology, Risk Factors, and Interactions of Enteric Infections and Malnutrition and the Consequences for Child Health and Development (MAL-ED) longitudinal birth cohort study, children from eight LMICs were followed from birth to 24 months to understand the influence of repeated enteric infections on child growth and development. Here, data from six sites were employed to evaluate associations between infection, illness, the home environment, micronutrient intake and status, maternal reasoning, and cognitive development at 24 months.

Results

Higher rates of enteropathogen detection and days with illness were associated with lower haemoglobin concentrations, which in turn were associated with lower cognitive scores at 24 months. Children with lower environmental health/safety scores and lower intakes of vitamin B₆ and folate had more enteropathogen detections and illness. Strength of associations varied by weight-for-age in the first 17 days of life; lower weight infants were more susceptible to the negative effects of enteropathogens and illness.

Conclusions

Enteropathogens were negatively related to child cognitive development. However, other factors were more strongly associated with child cognition. Targeting of interventions to improve cognitive development should include a focus on reducing frequency of illness, improving the safety and healthfulness of the child’s environment, and improving dietary intake.

A Role for the X Chromosome in Sex Differences in Variability in General Intelligence?

There is substantial evidence that males are more variable than females in general intelligence. In recent years, researchers have presented this as a reason that, although there is little, if any, mean sex difference in general intelligence, males tend to be overrepresented at both ends of its overall distribution. Part of the explanation could be the presence of genes on the X chromosome related both to syndromal disorders involving mental retardation and to population variation in general intelligence occurring normally. Genes on the X chromosome appear overrepresented among genes with known involvement in mental retardation, which is consistent with a model we developed of the population distribution of general intelligence as a mixture of two normal distributions. Using this model, we explored the expected ratios of males to females at various points in the distribution and estimated the proportion of variance in general intelligence potentially due to genes on the X chromosome. These estimates provide clues to the extent to which biologically based sex differences could be manifested in the environment as sex differences in displayed intellectual abilities. We discuss these observations in the context of sex differences in specific cognitive abilities and evolutionary theories of sexual selection.

Dietary patterns in pregnancy and effects on nutrient intake in the Mid-South: the Conditions Affecting Neurocognitive Development and Learning in Early Childhood (CANDLE) study

Dietary patterns are sensitive to differences across socio-economic strata or cultural habits and may impact programing of diseases in later life. The purpose of this study was to identify distinct dietary patterns during pregnancy in the Mid-South using factor analysis. Furthermore, we aimed to analyze the differences in the food groups and in macro- and micronutrients among the different food patterns. The study was a cross-sectional analysis of 1155 pregnant women (mean age 26.5 ± 5.4 years; 62% African American, 35% Caucasian, 3% Other; and pre-pregnancy BMI 27.6 ± 7.5 kg/m(2)). Using food frequency questionnaire data collected from participants in the Conditions Affecting Neurocognitive Development and Learning in Early Childhood (CANDLE) study between 16 and 28 weeks of gestation, dietary patterns were identified using factor analysis. Three major dietary patterns, namely, Healthy, Processed, and US Southern were identified among pregnant women from the Mid-South. Further analysis of the three main patterns revealed four mixed dietary patterns, i.e., Healthy-Processed, Healthy-US Southern, Processed-US Southern, and overall Mixed. These dietary patterns were different (p < 0.001) from each other in almost all the food items, macro- and micro nutrients and aligned across socioeconomic and racial groups. Our study describes unique dietary patterns in the Mid-South, consumed by a cohort of women enrolled in a prospective study examining the association of maternal nutritional factors during pregnancy that are known to affect brain and cognitive development by age 3.

[Progresses on autosomal recessive nonsyndromic mental retardation related genes]

Some autosomal genes are associated with development and function of nervous system. Mutations of these genes can lead to nonsyndromic mental retardation. This paper reviews recent progresses on autosomal recessive nonsyndromic mental retardation related genes, including localization, expression, biological function and pathogenesis after mutations. The prospect in this field is also discussed.

Letter to the Editor: The Relative Contribution of the X Chromosome to Ocular Phenotypes

The X chromosome is unique, both in terms of functional expression and evolutionary history. Population frequencies for a minority of conditions, such as mental retardation, are directly related to the X chromosome. To explore these ideas, we investigated the general role of the X chromosome in ocular genetics through bioinformatic analysis of the distribution of eye-related genes in the human genome. The proportion of eye-disease loci located on the X chromosome compared to those eye diseases with an autosomal locus was calculated. The resultant figure (3.47) is lower than that calculated for mental retardation (9.74). A comparison between the number of X chromosome genes expressed in the eye compared to the number of autosomal genes expressed in the eye also did not reveal significant differences. Of all genes expressed in the eye, 2.9% are thought to be located on the X chromosome, fewer than found for the larger autosomes (which range from 10.1% to 3.6%). The eye's functional genetic components appear to be dispersed throughout the human genome, possibly to ensure survival in the event of significant cytogenetic derangement.

Positive association of neuroligin-4 gene with nonspecific mental retardation in the Qinba Mountains Region of China

OBJECTIVE

Neuroligin-4 is essential for proper brain function. Some studies indicate a close relationship between neuroligin-4 and several human psychiatric conditions.

METHODS

The case-control method was used to study the association between nonspecific mental retardation (NSMR) and genetic variants of neuroligin-4 gene (NLGN4). Five single nucleotide polymorphisms (SNPs: rs5916271, rs7049300, rs6638575, rs3810686, and rs1882260) were genotyped by PCR-RFLP/SSCP method in the NLGN4.

RESULTS

Individual SNP analysis shows significant differences at SNPs rs3810686 and rs1882260 for allele frequency when NSMR cases and controls [odds ratio (OR)=1.589, 95% confidence interval (CI)=1.035-2.438, chi2=4.53, df=1, P=0.033; OR=2.050, 95% CI=1.211-3.470, chi2=7.38, df=1, P=0.007, respectively] were compared. Further haplotype analysis indicates that there are two haplotype sets, rs3810686-rs1882260 and rs6638575-rs3810686-rs1882260, which show statistical differences between NSMR cases and controls (chi2=6.79, df=2, global P=0.034; chi2=9.29, df=2, global P=0.0096, respectively).

CONCLUSION

The results suggest a positive association between the genetic variants of the NLGN4 and NSMR in the Chinese children from Qinba Mountains Region.

Forty Years From Markers to Genes

There have been incredible advances made in human genetics over the past 40 years. I have set out in the next few pages to describe just some of these changes and to illustrate how they unfolded through my own experiences.

Positive association of the FTSJ1 gene polymorphisms with nonsyndromic X-linked mental retardation in young Chinese male subjects

To investigate the possible genetic association of nonsyndromic X-linked mental retardation (NS-XLMR) with FTSJ1 gene polymorphisms, a case-control association study was performed focusing on the Chinese Han population in the Qinba mountain region. Three common single nucleotide polymorphisms (SNPs) (rs2268954, rs2070991, rs5905692) in the gene were selected and genotyped using the polymerase chain reaction single-strand confirmation polymorphism (PCR-SSCP) method. Pairwise linkage disequilibrium (LD) analysis showed that the three SNPs were in strong LD (all D' > 0.8). There were significant differences between cases and controls in allele frequency distribution of rs2268954 (P = 0.036), rs2070991 (P = 0.043), and rs5905692 (P = 0.014) and in the distributions of common haplotypes combined by these SNPs (global P = 0.01236) in male subjects. In female subjects, however, no positive results were found. Our results suggest a positive association between the genetic variants of the FTSJ1 gene and NS-XLMR in young male subjects in the Chinese Han population in the Qinba region.

Mutations in UPF3B, a member of the nonsense-mediated mRNA decay complex, cause syndromic and nonsyndromic mental retardation

Nonsense-mediated mRNA decay (NMD) is of universal biological significance. It has emerged as an important global RNA, DNA and translation regulatory pathway. By systematically sequencing 737 genes (annotated in the Vertebrate Genome Annotation database) on the human X chromosome in 250 families with X-linked mental retardation, we identified mutations in the UPF3 regulator of nonsense transcripts homolog B (yeast) (UPF3B) leading to protein truncations in three families: two with the Lujan-Fryns phenotype and one with the FG phenotype. We also identified a missense mutation in another family with nonsyndromic mental retardation. Three mutations lead to the introduction of a premature termination codon and subsequent NMD of mutant UPF3B mRNA. Protein blot analysis using lymphoblastoid cell lines from affected individuals showed an absence of the UPF3B protein in two families. The UPF3B protein is an important component of the NMD surveillance machinery. Our results directly implicate abnormalities of NMD in human disease and suggest at least partial redundancy of NMD pathways.

Scope for more genetic testing in learning disability. Case report of an inherited duplication on the X-chromosome

There have been major advances in the past few years in our understanding of the X-linked learning disabilities. The most common of these is the fragile-X syndrome, but the number of other gene defects that are now recognised to be linked with learning disability is increasing year on year. We describe one family displaying a family displaying a rare X-linked abnormality. Repeat genetic testing was requested for a family member with mild learning disability when, following chromosomal analysis for her brother, it became known that he had a genetic defect. The genetic defect 46, Xdup(X) (p22.13 p22.31) was identified. To our knowledge this is the first time this precise configuration has been demonstrated. We conclude that genetic testing for individuals with learning disability is worthwhile, even when there may be only a low index of suspicion.

Investigating cognitive genetics and its implications for the treatment of cognitive deficit

Cognitive impairment in the elderly, caused by either normal ageing process or dementia, is an increasing problem in developed countries that has enormous social and economic considerations. Research investigating the genetic basis of cognition is a new and rapidly developing field that may aid in the development of new treatments for age-related cognitive deficit. Over the past 6 years, a number of quantitative trait loci (QTLs) have been associated with cognitive functioning in humans including loci within the genes catechol-o-methyltransferase, brain-derived neurotrophic factor, muscle segment homeobox 1, serotonin transporter 2A (HTR2A), cholinergic muscarinic receptor 2, cathepsin D, metabotrophic glutamate receptor and most recently the class II human leukocyte antigens. Unfortunately, inconsistency within the literature, which is a hallmark of almost all association studies investigating complex diseases and traits, is casting doubt as to which genes are truly associated with cognition and which are a result of Type 2 error. This review will highlight implicated intelligence QTLs, examine the probable reasons for the current discrepancies between reports and discuss the potential advantages that may be procured from the study of cognitive genetics.

Disruption of DMD and deletion of ACSL4 causing developmental delay, hypotonia, and multiple congenital anomalies

We have studied a male patient with significant developmental delay, growth failure, hypotonia, girdle weakness, microcephaly, and multiple congenital anomalies including atrial (ASD) and ventricular (VSD) septal defects. Detailed cytogenetic and molecular analyses revealed three de novo X chromosome aberrations and a karyotype 46,Y,der(X)inv(X) (p11.4q11.2)inv(X)(q11.2q21.32 approximately q22.2)del(X)(q22.3q22.3) was determined. The three X chromosome aberrations in the patient include: a pericentric inversion (inv 1) that disrupted the Duchenne muscular dystrophy (DMD) gene, dystrophin, at Xp11.4; an Xq11.2q21.32 approximately q22.2 paracentric inversion (inv 2) putatively affecting no genes; and an interstitial deletion at Xq22.3 that results in functional nullisomy of several known genes, including a gene previously associated with X-linked nonsyndromic mental retardation, acyl-CoA synthetase long chain family member 4 (ACSL4). These findings suggest that the disruption of DMD and the absence of ACSL4 in the patient are responsible for neuromuscular disease and cognitive impairment.

Loss of ZDHHC15 expression in a woman with a balanced translocation t(X;15)(q13.3;cen) and severe mental retardation

X-linked mental retardation (XLMR) affects one in 600 males and is highly heterogeneous. We describe here a 29-year-old woman with severe nonsyndromic mental retardation and a balanced reciprocal translocation between chromosomes X and 15 [46,XX,t(X;15)(q13.3;cen)]. Methylation studies showed a 100% skewed X-inactivation in patient-derived lymphocytes indicating that the normal chromosome X is retained inactive. Physical mapping of the breakpoints localised the Xq13.3 breakpoint to within 3.9 kb of the first exon of the ZDHHC15 gene encoding a zinc-finger and a DHHC domain containing product. Expression analysis revealed that different transcript variants of the gene are expressed in brain. ZDHHC15-specific RT-PCR analysis on lymphocytes from the patient revealed an absence of ZDHHC15 transcript variants, detected in control samples. We suggest that the absence of the ZDHHC15 transcripts in this patient contributes to her phenotype, and that the gene is a strong candidate for nonsyndromic XLMR.

X linked mental retardation: a clinical guide

Mental retardation is more common in males than females in the population, assumed to be due to mutations on the X chromosome. The prevalence of the 24 genes identified to date is low and less common than expansions in FMR1, which cause Fragile X syndrome. Systematic screening of all other X linked genes in X linked families with mental retardation is currently not feasible in a clinical setting. The phenotypes of genes causing syndromic and non-syndromic mental retardation (NLGN3, NLGN4, RPS6KA3(RSK2), OPHN1, ATRX, SLC6A8, ARX, SYN1, AGTR2, MECP2, PQBP1, SMCX, and SLC16A2) are first discussed, as these may be the focus of more targeted mutation analysis. Secondly, the relative prevalence of genes causing only non-syndromic mental retardation (IL1RAPL1, TM4SF2, ZNF41, FTSJ1, DLG3, FACL4, PAK3, ARHGEF6, FMR2, and GDI) is summarised. Thirdly, the problem of recurrence risk where a molecular genetics diagnosis has not been made and what proportion of the male excess of mental retardation is due to monogenic disorders of the X chromosome are discussed.

X chromosome array-CGH for the identification of novel X-linked mental retardation genes

Array-CGH technology for the detection of submicroscopic copy number changes in the genome has recently been developed for the identification of novel disease-associated genes. It has been estimated that submicroscopic genomic deletions or duplications will be present in 5-7% of patients with idiopathic mental retardation (MR). Since 30% more males than females are diagnosed with MR, we have developed a full coverage X chromosome array-CGH with a theoretical resolution of 82 kb, for the detection of copy number alterations in patients with suspected X-linked mental retardation (XLMR). First, we have validated the genomic location of X-derived clones through male versus female hybridisations. Next, we validated our array for efficient and reproducible detection of known alterations in XLMR patients. In all cases, we were able to detect the deletions and duplications in males as well as females. Due to the high resolution of our X-array, the boundaries of the genomic aberrations could clearly be identified making genotype-phenotype studies more reliable. Here, we describe the production and validation of a full coverage X-array-CGH, which will allow for fast and easy screening of submicroscopic copy number alterations in XLMR patients with the aim to identify novel MR genes or mechanisms involved in a deranged cognitive development.

Monogenic X-linked mental retardation: is it as frequent as currently estimated? The paradox of the ARX (Aristaless X) mutations

Mental retardation affects 30 to 50% more males than females, and X-linked mental retardation (XLMR) is thought to account for the major part of this sex bias. Nonsyndromic XLMR is very heterogeneous, with more than 15 genes identified to date, each of them accounting for a very small proportion of nonsyndromic families. The Aristaless X (ARX) gene is an exception since it was found mutated in 11 of 136 such families, with a highly recurrent mutation (dup24) leading to an expansion of a polyalanine tract in the protein. The rather high frequency of dup24 reported in families with clear X-linked MR (6.6%) contrasts with the very low prevalence of this mutation observed in sporadic male MR (0.13%). We conclude that monogenic XLMR has much lower prevalence in male MR (< 10%) than the 23% that would be required to account for a 30% male excess of mental retardation.

Mirror writing ability is genetic and probably transmitted as a sex-linked dominant trait: it is hypothesised that mirror writers have bilateral language centres with a callosal interconnection

Mirror writing is the ability to write from right to left, reversing each letter so that when held to a mirror the script appears normal. There is no information on the prevalence of this trait but a suggestion was received that it may be hereditary. A newspaper survey was carried out to discover the approximate prevalence and whether a hereditary factor is involved. The results indicated a prevalence of 1 in 6500. There is strong evidence that the trait is hereditary and is associated with non-right-handedness'. It is hypothesised that mirror writers may comprise a very small group of people who not only have bilateral language centres but also have an interconnecting pathway between these centres via the corpus callosum. The surprising genetic nature of a trait with no obvious evolutionary consequences is discussed. The data can best be explained on the basis of the trait being the phenotypic expression of an X-linked dominant gene, which does have evolutionary consequences. Similarities are noted between the proposed genetics of mirror writing and those of synaesthesia and of a few pathological X-linked dominant syndromes such as Rett syndrome. Other similarities and contrasts between mirror writing and synaesthesia are noted.

Mutations in the FTSJ1 gene coding for a novel S-adenosylmethionine-binding protein cause nonsyndromic X-linked mental retardation

Nonsyndromic X-linked mental retardation (NSXLMR) is a very heterogeneous condition, and most of the underlying gene defects are still unknown. Recently, we have shown that approximately 30% of these genes cluster on the proximal Xp, which prompted us to perform systematic mutation screening in brain-expressed genes from this region. Here, we report on a novel NSXLMR gene, FTSJ1, which harbors mutations in three unrelated families--one with a splicing defect, one with a nonsense mutation, and one with a deletion of one nucleotide. In two families, subsequent expression studies showed complete absence or significant reduction of mutant FTSJ1 transcripts. FTSJ1 protein is a homolog of Escherichia coli RNA methyltransferase FtsJ/RrmJ and may play a role in the regulation of translation. Further studies aim to elucidate the function of human FTSJ1 and its role during brain development.

A comparative expression analysis of four MRX genes regulating intracellular signalling via small GTPases

The X chromosomal mental retardation genes have attained high interest in the past. A rough classification distinguishes syndromal mental retardation (MRXS) and nonsyndromal mental retardation (MRX) conditions. The latter are suggested to be responsible for human specific development of cognitive abilities. These genes have been shown to be engaged in chromatin remodelling or in intracellular signalling. During this analysis, we have compared the expression pattern in the mouse of four genes from the latter class of MRX genes: Ophn1, Arhgef6 (also called alphaPix), Pak3, and Gdi1. Ophn1, Pak3, and Gdi1 show a specific neuronal expression pattern with a certain overlap that allows to assign these signalling molecules to the same functional context. We noticed the highest expression of these genes in the dentate gyrus and cornu ammonis of the hippocampus, in structures engaged in learning and memory. A completely different expression pattern was observed for Arhgef6. In the CNS, it is expressed in ventricular zones, where neuronal progenitor cells are located. But Arhgef6 expression is also found in other non-neural tissues. Our analysis provides evidence that these signalling molecules are involved in different spatio-temporal expression domains of common signalling cascades and that for most tissues considerable functional redundancy of Rho-mediated signalling pathways exists.

Genetic services for people with intellectual disability and their families

This paper reviews the advances in molecular genetics over the recent years and discusses the impact it may have on those with intellectual disability and their families. The aim is not to present a comprehensive scientific treatise but rather to use illustrations from genetics to highlight our current thinking and draw attention to areas of uncertainty and misinformation. As our knowledge and understanding of the genetic basis of disease increases over the years, there may be significant benefits to some families, but the potential for discrimination against individuals on genetic grounds will also increase.

Localization of a non-syndromic X-linked mental retardation gene (MRX80) to Xq22-q24

Isolated mental retardation is clinically and genetically heterogenous and may be inherited in an autosomal dominant, autosomal recessive, or X-linked manner. We report here a linkage analysis in a large family including 15 members, 6 of whom presenting X-linked non-syndromic mental retardation (MRX). Two-point linkage analysis using 23 polymorphic markers covering the entire X chromosome demonstrated significant linkage between the causative gene and DXS8055 with a maximum LOD score of 2.98 at theta = 0.00. Haplotype analysis indicated location for the disease gene in a 23.1 cM interval between DXS1106 and DXS8067. This MRX localization overlaps with 7 XLMR loci (MRX23, MRX27, MRX30, MRX35, MRX47, MRX53, and MRX63). This interval contains two genes associated with non-syndromic mental retardation (NSMR), namely the PAK3 gene, encoding a p21-activated kinase (MRX30 and MRX47) and the FACL4 gene encoding a fatty acyl-CoA ligase (MRX63). As skewed X-inactivation, an apparently constant feature in FACL4 carrier females was not observed in an obligate carrier belonging to the MRX family presented here, the PAK3 gene should be considered as the strongest candidate for this MRX locus.

X-linked mild non-syndromic mental retardation with neuropsychiatric problems and the missense mutation A365E in PAK3

We describe a family of 19 males in five generations with mild to borderline non-syndromic X-linked mental retardation (MRX). There were no clinical manifestations in the affected males other than mental impairment and relatively long ears, with neuropsychiatric problems in some cases. Linkage analysis carried out on part of the pedigree using 34 markers spanning the X chromosome localized the gene between DXS454 and DXS1001 in Xq23. The maximum two-point lod score was 3.21 at DXS1059. PAK3 is a known MRX gene mapping to the same region. The affected males and obligate carrier females were found to have a missense mutation c.1094C > A in exon 10 causing an A365E substitution in a highly conserved region of the protein. The C to A base change abolishes a PvuII restriction enzyme site providing the basis for a simple test, if required, for carrier detection and prenatal diagnosis in the extended family.

Nonsyndromic X-linked mental retardation: where are the missing mutations?

Analysis of linkage intervals from 125 unrelated families with nonsyndromic X-linked mental retardation (NS-XLMR) has revealed that the respective gene defects are conspicuously clustered in defined regions of the human X-chromosome, with approximately 30% of all mutations being located on the proximal Xp. In 83% of these families, underlying gene defects are not yet known. Our observations should speed up the search for mutations that are still missing and pave the way for the molecular diagnosis of this common disorder.

Syndromic form of X-linked mental retardation with marked hypotonia in early life, severe mental handicap, and difficult adult behavior maps to Xp22

An X-linked recessive syndromic form of mental retardation is described in a family in which 10 males in four generations were affected. The main manifestations were severe to profound intellectual disability, muscular hypotonia in childhood, delayed walking, and difficult, aggressive behavior. There was a moderate reduction both in occipitofrontal circumference (OFC) and height and a similar facial appearance, triangular in shape with a high forehead, prominent ears, and a small pointed chin. Linkage analysis located the gene at Xp22 with maximum lod scores of 4.8 at theta = 0.0 for markers mapping between the closest recombination points at DXS7104 and DXS418. The physical length of this region is approximately 6 Mb. Mutations in the GRPR gene and M6b genes were excluded by sequence analysis. Nearby genes in which mutations are known to be associated with mental retardation (RPS6KA3, STK9, and VCXA, B and C), were excluded by position.

X-linked mental retardation: vanishing boundaries between non-specific (MRX) and syndromic (MRXS) forms

This review covers the history and nosology of X-linked mental retardation (XLMR) in which the following, largely clinically based, subclassification was used: fragile X syndrome (FRAXA), syndromic forms (MRXS) and non-specific forms (MRX). After the discovery of the FMR2 gene at the FRAXE site, 10 MRX genes have been identified in the last 6 years. A short description is given of the strategies used to identify the genes that cause mental retardation (MR). Furthermore, their potential functions and the association with MR will be discussed. It is emphasized that mutations in several of these MR genes can result in non-specific, as well as in syndromic forms of XLMR. Present findings stress the importance of accurate clinical evaluation. Most considerably, genotype-phenotype correlation studies of affected individuals in XLMR families with MRX gene mutations are necessary to define the criteria of MRX vs MRXS subclassification.

The apolipoprotein E gene, attention, and brain function

The epsilon4 allele of the apolipoprotein E (ApoE) gene is associated with alterations in brain function and is a risk factor for Alzheimer's disease (AD). Changes in components of visuospatial attention with ApoE-epsilon4, aging, and AD are described. Healthy middle-aged adults without dementia who have the ApoE-epsilon4 gene show deficits in spatial attention and working memory that are qualitatively similar to those seen in clinically diagnosed AD patients. The findings support an association between ApoE polymorphism and specific components of visuospatial attention. Molecular mechanisms that may mediate the ApoE-attention link by modulating cholinergic neurotransmission to the posterior parietal cortex are discussed. Studies of attention and brain function in ApoE-epsilon4 carriers without dementia can advance knowledge of the genetics of visual attention, may enhance understanding of the preclinical phase of AD, and may lead to better methods for early AD detection.

The novel Rho-GTPase activating gene MEGAP/ srGAP3 has a putative role in severe mental retardation

In the last few years, several genes involved in X-specific mental retardation (MR) have been identified by using genetic analysis. Although it is likely that additional genes responsible for idiopathic MR are also localized on the autosomes, cloning and characterization of such genes have been elusive so far. Here, we report the isolation of a previously uncharacterized gene, MEGAP, which is disrupted and functionally inactivated by a translocation breakpoint in a patient who shares some characteristic clinical features, such as hypotonia and severe MR, with the 3p(-) syndrome. By fluorescence in situ hybridization and loss of heterozygosity analysis, we demonstrated that this gene resides on chromosome 3p25 and is deleted in 3p(-) patients that present MR. MEGAP/srGAP3 mRNA is predominantly and highly expressed in fetal and adult brain, specifically in the neurons of the hippocampus and cortex, structures known to play a pivotal role in higher cognitive function, learning, and memory. We describe several MEGAP/srGAP3 transcript isoforms and show that MEGAP/srGAP3a and -b represent functional GTPase-activating proteins (GAP) by an in vitro GAP assay. MEGAP/srGAP3 has recently been shown to be part of the Slit-Robo pathway regulating neuronal migration and axonal branching, highlighting the important role of MEGAP/srGAP3 in mental development. We propose that haploinsufficiency of MEGAP/srGAP3 leads to the abnormal development of neuronal structures that are important for normal cognitive function.

The apolipoprotein E gene, attention, and brain function

The epsilon4 allele of the apolipoprotein E (ApoE) gene is associated with alterations in brain function and is a risk factor for Alzheimer's disease (AD). Changes in components of visuospatial attention with ApoE-epsilon4, aging, and AD are described. Healthy middle-aged adults without dementia who have the ApoE-epsilon4 gene show deficits in spatial attention and working memory that are qualitatively similar to those seen in clinically diagnosed AD patients. The findings support an association between ApoE polymorphism and specific components of visuospatial attention. Molecular mechanisms that may mediate the ApoE-attention link by modulating cholinergic neurotransmission to the posterior parietal cortex are discussed. Studies of attention and brain function in ApoE-epsilon4 carriers without dementia can advance knowledge of the genetics of visual attention, may enhance understanding of the preclinical phase of AD, and may lead to better methods for early AD detection.

Nutritional status, brain development and scholastic achievement of Chilean high-school graduates from high and low intellectual quotient and socio-economic status

The objective of the present study was to investigate the inter-relationships between nutritional status (past and current nutrition), brain development, and scholastic achievement (SA) of Chilean high-school graduates from high and low intellectual quotient (IQ) and socio-economic status (SES) (mean age 18.0 (SD 0.9) years). Results showed that independently of SES, high-school graduates with similar IQ have similar nutritional, brain development and SA variables. Multiple regression analysis between child IQ (dependent variable) and age, sex, SES, brain volume (BV), undernutrition during the first year of life, paternal and maternal IQ (independent variables) revealed that maternal IQ (P<0.0001), BV (P<00387) and severe undernutrition during the first year of life (P<0.0486), were the independent variables with the greatest explanatory power for child IQ variance (r2 0.707), without interaction with age, sex or SES. Child IQ (P<0.0001) was the only independent variable that explained both SA variance (r2 0.848) and academic aptitude test variance (r2 0.876) without interaction with age, sex or SES. These results confirm the hypotheses formulated for this study that: (1) independently of SES, high-school graduates with similar IQ have similar variables of nutritional status, brain development and SA; (2) past nutritional status, brain development, child IQ and SA are strongly and significantly inter-related. These findings are relevant in explaining the complex interactions between variables that affect IQ and SA and can be useful for nutritional and educational planning.

Novel mental retardation-epilepsy syndrome linked to Xp21.1-p11.4

We evaluated a kindred with X-linked mental retardation and epilepsy. Seven affected males with mild to moderate mental retardation developed seizures (primarily generalized, tonic-clonic, and atonic) that began on average at 6.8 months of age (range, 4 to 14 months). These patients did not have a history of infantile spasms. There were no dysmorphic features. Other than mental retardation, the neurological examination was unremarkable, with exception of 2 affected subjects who had mild generalized rigidity and ataxia. We identified tight linkage to a group of markers on Xp21.1-p11.4. A maximum two-point LOD score of +3.83 at straight theta = 0 was obtained for markers DXS8090, DXS1069, DXS8102, and DXS8085. This locus spans 7.7cM between DXS1049 and DXS8054 and does not overlap the locus for X-linked West syndrome. The tetraspanin gene, implicated in nonspecific mental retardation, is mapped to this region. We sequenced the tetraspanin coding sequence in subjects with X-linked mental retardation and epilepsy and did not identify disease-specific mutations. The syndrome we describe, designated X-linked mental retardation and epilepsy, is clinically and genetically distinct from X-linked West syndrome and other X-linked mental retardation-epilepsy syndromes.

A high density of X-linked genes for general cognitive ability: a run-away process shaping human evolution?

The incidence of mental disability is 30% higher in males than in females. We have examined entries in the OMIM database that are associated with mental disability and for several other common defects. Our findings indicate that compared with the autosomes, the X chromosome contains a significantly higher number of genes that, when mutated, cause mental impairment. We propose that these genes are involved in the development of cognitive abilities and thus exert a large X-chromosome effect on general intelligence in humans. We discuss these conclusions with regard to the conservation of the vertebrate X-chromosomal linkage group and to human evolution.

In search of the MRX genes

Mental retardation (MR) is one of the most common human disorders. MR may be just one of the clinical signs of a complex syndrome or it may be associated with metabolic disorders or with disorders of brain development, but in many patients [nonspecific MR (NSMR)], it is the only consistent clinical manifestation. It is expected that NSMR is caused by alterations in molecular pathways important for cognitive functions. Insights into NSMR have recently come from the study of X-linked MR as eight genes were identified during the last few years. This development has represented a fundamental breakthrough in our understanding of NSMR and of cognitive functions and has opened new perspectives in the study of MR. The new genes identified are a heterogeneous group, but it is very intriguing that they are all directly or indirectly involved in signaling pathways and that the majority are proteins that regulate members of the Ras superfamily of small GTP binding proteins.

IL1RAPL2 maps to Xq22 and is specifically expressed in the central nervous system

We report the identification and characterization of a homologue of the IL1RAPL transcript which is responsible for a form of X-linked mental retardation (MRX34). This new transcript was cloned by analysis of genomic sequences from the Xq22 region and was named IL1RAPL2 (Interleukin 1 Receptor Accessory Protein-Like-2). The two X-linked genes share the same domains, the same exon-intron organization and a high degree of similarity at the protein level (70.4% similarity). RNA in situ expression studies on mouse embryo tissue section at different developmental stages show that Il1rapl2 is specifically expressed in the nervous system from embryonic day 12.5. The homologies together with the pattern of expression render ILRAPL2 a candidate gene for disorders displaying involvement of the CNS, including the MRX loci for which the gene has not been identified yet.

NXF5, a novel member of the nuclear RNA export factor family, is lost in a male patient with a syndromic form of mental retardation

BACKGROUND

Although X-linked mental retardation (XLMR) affects 2%-3% of the human population, little is known about the underlying molecular mechanisms. Recent interest in this topic led to the identification of several genes for which mutations result in the disturbance of cognitive development.

RESULTS

We identified a novel gene that is interrupted by an inv(X)(p21.1;q22) in a male patient with a syndromic form of mental retardation. Molecular analysis of both breakpoint regions did not reveal an interrupted gene on Xp, but identified a novel nuclear RNA export factor (NXF) gene cluster, Xcen-NXF5-NXF2-NXF4-NXF3-Xqter, in which NXF5 is split by the breakpoint, leading to its functional nullisomy. The predicted NXF5 protein shows high similarity with the central part of the presumed mRNA nuclear export factor TAP/NXF1. Functional analysis of NXF5 demonstrates binding to RNA as well as to the RNA nuclear export-associated protein p15/NXT. In contrast to TAP/NXF1, overexpression studies localized NXF5 in the form of granules in the cell body and neurites of mature hippocampal neurons, suggesting a role in mRNA transport. The two newly identified mouse nxf homologs, nxf-a and nxf-b, which also map on X, show highest mRNA levels in the brain.

CONCLUSIONS

A novel member of the nuclear RNA export factor family is absent in a male patient with a syndromic form of mental retardation. Although we did not find direct evidence for the involvement of NXF5 in MR, the gene could be involved in development, possibly through a process in mRNA metabolism in neurons.

Linkage mapping of a nonspecific form of X-linked mental retardation (MRX53) in a large Pakistani family

Nonspecific X-linked mental retardation is a nonprogressive, genetically heterogeneous condition that affects cognitive function in the absence of other distinctive clinical manifestations. We report here linkage data on a large Pakistani family affected by a form of X-linked nonspecific mental retardation. X chromosome genotyping of family members and linkage analysis allowed the identification of a new disease locus, MRX53. The defined critical region spans approximately 15 cM between DXS1210 and DXS1047 in Xq22.2-26. A LOD score value of 3.34 at no recombination was obtained with markers DXS1072 and DXS8081.

Some problems in the genetics of X-linked mental retardation

X-linked mental retardation has recently become one of the most interesting genetic anomalies. Studying this group of conditions has led to many insights into the mechanisms involved in normal and abnormal gene actions in humans. Since the early 1980s, the number of disease entities for which the responsible genes could be localized on the X chromosome has increased from year to year; at the Ninth International Workshop on Fragile-X-Syndrome and X-linked Mental Retardation, 199 such disease units were counted (Hamel, 1999). Conventionally, these units were subdivided into two groups: syndromal and non-syndromal types. The syndro- mal types are characterized by external features, neurological signs, and/or metabolic anomalies. The non-syndromal types do not show such specific features; here, the X-linked mode of inheritance is the only indicator. Due to the reduced reproduction of mentally severely retarded males, a relatively high fraction of new mutants among cases of a specific type must be expected. It cannot be the purpose of the present short article to review sufficiently well the entire field; this would require a complete book. Rather, it is our intention to point to some open problems and possible ways for their solution.

Do the constraints of human speciation cause expression of the same set of genes in brain, testis, and placenta?

Evolution appears to be especially rapid during speciation, and the genes involved in speciation should be evident in species such as humans that have recently speciated or are presently in the process of speciation. Haldane's rule is that when one sex is sterile or inviable in interspecific F(1) hybrids, it is usually the heterogametic sex. For mammals, this implicates genes on the X chromosome as those particularly responsible for speciation. A preponderance of sex- and reproduction-related genes on the X chromosome has been shown repeatedly, but also mental retardation genes are more frequent on the X chromosome. We argue that brain, testis, and placenta are those organs most responsible for human speciation. Furthermore, the high degree of complexity of the vertebrate genome demands coordinate evolution of new characters. This coordination is best attained when the same set of genes is redeployed for these new characters in the brain, testis, and placenta.

Genes responsible for nonspecific mental retardation

Mental retardation (MR) is a group of heterogeneous clinical conditions. There are more than 900 genetic disorders associated with MR and it affects around 3% of the general population. MR can be subdivided into syndromic, if it is characterized by consistent and distinctive clinical findings, and nonspecific, if mental retardation is the only primary symptom among affected individuals. Many MR conditions described are syndromic, fragile X syndrome being the most common clinical entity among them. In the past years, knowledge of the molecular basis of mental retardation has increased remarkably. Eight genes involved in nonspecific X-linked MR have been identified so far, including FMR2, OPHN1, GDI1, PAK3, IL1RAPL, TM4SF2, VCX-A, and ARHGEF6. Two other genes also located on the X chromosome have been involved both in syndromic and in MRX forms (RSK2 and XNP/ATR-X). New insights into the pathogenesis of mental retardation are being provided by the discovery of these genes involved in different cellular signaling pathways in the central nervous system although many others remain to be identified.

A member of a gene family on Xp22.3, VCX-A, is deleted in patients with X-linked nonspecific mental retardation

X-linked nonspecific mental retardation (MRX) has a frequency of 0.15% in the male population and is caused by defects in several different genes on the human X chromosome. Genotype-phenotype correlations in male patients with a partial nullisomy of the X chromosome have suggested that at least one locus involved in MRX is on Xp22.3. Previous deletion mapping has shown that this gene resides between markers DXS1060 and DXS1139, a region encompassing approximately 1.5 Mb of DNA. Analyzing the DNA of 15 males with Xp deletions, we were able to narrow this MRX critical interval to approximately 15 kb of DNA. Only one gene, VCX-A (variably charged, X chromosome mRNA on CRI-S232A), was shown to reside in this interval. Because of a variable number of tandem 30-bp repeats in the VCX-A gene, the size of the predicted protein is 186-226 amino acids. VCX-A belongs to a gene family containing at least four nearly identical paralogues on Xp22.3 (VCX-A, -B, -B1, and -C) and two on Yq11.2 (VCY-D, VCY-E), suggesting that the X and Y copies were created by duplication events. We have found that VCX-A is retained in all patients with normal intelligence and is deleted in all patients with mental retardation. There is no correlation between the presence or absence of VCX-B1, -B, and VCX-C and mental status in our patients. These results suggest that VCX-A is sufficient to maintain normal mental development.