Purita Ramos

The EXT2 multiple exostoses gene defines a family of putative tumour suppressor genes

Hereditary multiple exostoses (EXT) is an autosomal dominant condition characterized by short stature and the development of bony protuberances at the ends of all the long bones. Three genetic loci have been identified by genetic linkage analysis at chromosomes 8q24.1, 11p11–13 and 19p. The EXT1 gene on chromosome 8 was recently identified and characterized. Here, we report the isolation and characterization of the EXT2 gene. This gene shows striking sequence similarity to the EXT1 gene, and we have identified a four base deletion segregating with the phenotype. Both EXT1 and EXT2 show significant homology with one additional expressed sequence tag, defining a new multigene family of proteins with potential tumour suppressor activity.

Cognitive and motor development during childhood in boys with Klinefelter syndrome.

The goal of this study was to expand the description of the cognitive development phenotype in boys with Klinefelter syndrome (47,XXY). We tested neuropsychological measures of memory, attention, visual‐spatial abilities, visual‐motor skills, and language. We examined the influence of age, handedness, genetic aspects (parental origin of the extra X chromosome, CAGn repeat length, and pattern of X inactivation), and previous testosterone treatment on cognition. We studied 50 boys with KS (4.1–17.8 years). There was a significant increase in left‐handedness (P = 0.002). Specific language, academic, attentional, and motor abilities tended to be impaired. In the language domain, there was relative sparing of vocabulary and meaningful language understanding abilities but impairment of higher level linguistic competence. KS boys demonstrated an array of motor difficulties, especially in strength and running speed. Deficits in the ability to sustain attention without impulsivity were present in the younger boys. Neither genetic factors examined nor previous testosterone treatment accounted for variation in the cognitive phenotype in KS. The cognitive results from this large KS cohort may be related to atypical brain lateralization and have important diagnostic and psychoeducational implications. The difficulty in complex language processing, impaired attention and motor function in boys with KS may be missed. It is critical that boys with KS are provided with appropriate educational support that targets their learning challenges in school in addition to modifications that address their particular learning style. These findings would also be an important component of counseling clinicians and families about this disorder.

Effect of Ascertainment and Genetic Features on the Phenotype of Klinefelter Syndrome

OBJECTIVE To describe the Klinefelter Syndrome (KS) phenotype during childhood in a large cohort. STUDY DESIGN Clinical assessment, measurement of hormonal indices of testicular function, and parent of origin of extra X chromosome were assessed in a cross-sectional study of 55 boys with KS, aged 2.0 to 14.6 years, at an outpatient center. RESULTS Mean height and body mass index SD scores (SDS +/- SD) were 0.9 +/- 1.3 and 0.4 +/- 1.4, respectively. Mean penile length and testicular volume SDS were -0.5 +/- 0.9 and -0.9 +/- 1.4. Testosterone levels were in the lowest quartile of normal in 66% of the cohort. Other features included clinodactyly (74%), hypertelorism (69%), elbow dysplasia (36%), high-arched palate (37%), hypotonia (76%), and requirement for speech therapy (69%). Features were similar in boys in whom the diagnosis was made prenatally versus boys in whom the diagnosis was made postnatally. There was no evidence for a phenotypic effect of parent of origin of the extra X chromosome. CONCLUSIONS Boys with KS commonly have reduced penile length and small testes in childhood. The phenotype in boys with KS does not differ according to ascertainment or origin of the extra X chromosome. Boys with KS may be identified before puberty by tall stature, relatively decreased penile length, clinodactyly, hypotonia, and requirement for speech therapy.

A turner syndrome neurocognitive phenotype maps to Xp22.3

BackgroundTurner syndrome (TS) is associated with a neurocognitive phenotype that includes selective nonverbal deficits, e.g., impaired visual-spatial abilities. We previously reported evidence that this phenotype results from haploinsufficiency of one or more genes on distal Xp. This inference was based on genotype/phenotype comparisons of individual girls and women with partial Xp deletions, with the neurocognitive phenotype considered a dichotomous trait. We sought to confirm our findings in a large cohort (n = 47) of adult women with partial deletions of Xp or Xq, enriched for subjects with distal Xp deletions.MethodsSubjects were recruited from North American genetics and endocrinology clinics. Phenotype assessment included measures of stature, ovarian function, and detailed neurocognitive testing. The neurocognitive phenotype was measured as a quantitative trait, the Turner Syndrome Cognitive Summary (TSCS) score, derived from discriminant function analysis. Genetic analysis included karyotyping, X inactivation studies, fluorescent in situ hybridization, microsatellite marker genotyping, and array comparative genomic hybridization.ResultsWe report statistical evidence that deletion of Xp22.3, an interval containing 31 annotated genes, is sufficient to cause the neurocognitive phenotype described by the TSCS score. Two other cardinal TS features, ovarian failure and short stature, as well as X chromosome inactivation pattern and subjects age, were unrelated to the TSCS score.ConclusionDetailed mapping suggests that haploinsufficiency of one or more genes in Xp22.3, the distal 8.3 megabases (Mb) of the X chromosome, is responsible for a TS neurocognitive phenotype. This interval includes the 2.6 Mb Xp-Yp pseudoautosomal region (PAR1). Haploinsufficiency of the short stature gene SHOX in PAR1 probably does not cause this TS neurocognitive phenotype. Two genes proximal to PAR1 within the 8.3 Mb critical region, STS and NLGN4X, are attractive candidates for this neurocognitive phenotype.

Genetics and Bitter Taste Responses to Goitrin, a Plant Toxin Found in Vegetables

The perceived bitterness of cruciferous vegetables such as broccoli varies from person to person, but the functional underpinnings of this variation are not known. Some evidence suggests that it arises, in part, from variation in ability to perceive goitrin (5-vinyloxazolidine-2-thione), a potent antithyroid compound found naturally in crucifers. Individuals vary in ability to perceive synthetic compounds similar to goitrin, such as 6-propyl-2-thiouracil (PROP) and phenylthiocarbamide (PTC), as the result of mutations in the TAS2R38 gene, which encodes a bitter taste receptor. This suggests that taste responses to goitrin itself may be mediated by TAS2R38. To test this hypothesis, we examined the relationships between genetic variation in TAS2R38, functional variation in the encoded receptor, and threshold taste responses to goitrin, PROP, and PTC in 50 subjects. We found that threshold responses to goitrin were associated with responses to both PROP (P = 8.9 x 10(-4); r(s) = 0.46) and PTC (P = 7.5 x 10(-4); r(s) = 0.46). However, functional assays revealed that goitrin elicits a weaker response from the sensitive (PAV) allele of TAS2R38 (EC(50) = 65.0 μM) than do either PROP (EC(50) = 2.1 μM) or PTC (EC(50) = 1.1 μM) and no response at all from the insensitive (AVI) allele. Furthermore, goitrin responses were significantly associated with mutations in TAS2R38 (P = 9.3 × 10(-3)), but the same mutations accounted for a smaller proportion of variance in goitrin response (r(2) = 0.16) than for PROP (r(2) = 0.50) and PTC (r(2) = 0.57). These findings suggest that mutations in TAS2R38 play a role in shaping goitrin perception, but the majority of variance must be explained by other factors.

Genetic, Functional, and Phenotypic Diversity in TAS2R38-Mediated Bitter Taste Perception

Mutational polymorphism in the TAS2R38 bitter taste receptor is a key determinant of threshold taste detection of isolated compounds, such as phenylthiocarbamide (PTC) and propylthiouracil (PROP), as well as complex orosensation-mediated traits such as diet choice and smoking habits. These relationships are accounted for, in part, by 2 common alleles differing in functionality, TAS2R38-PAV and TAS2R38-AVI. However, TAS2R38 harbors extensive additional polymorphism whose functional significance remains unknown. To examine this variation, we ascertained genetic diversity in 56 Caucasian subjects via whole-gene sequencing, analyzed allele-specific responses to 5 TAS2R38 agonists (PTC, PROP, goitrin, methimazole, and sinigrin) using in vitro assays, and assessed genotypic associations with threshold detection phenotypes. Sequencing identified 3 single-nucleotide substitutions encoding 3 amino acid changes (C145G/P49A, C785T/A262V, and A886G/I296V), which combined to form 6 haplotypes in our sample. In vitro assays revealed a continuous range of response across alleles, and associations with threshold were significant for all single nucleotide polymorphisms (P < 0.002) and PAV/AVI haplotypes (P < 0.001). Haplotypes other than PAV and AVI did not exhibit phenotypic associations in our sample, possibly as a result of their low frequencies. However, prior studies have indicated that these alleles are common in some global regions, suggesting that alleles rare in our sample may be phenotypically relevant in other populations.

The glycine 90 to aspartate alteration in the Aβ subunit of PP2A (PPP2R1B) associates with breast cancer and causes a deficit in protein function

Mutations of the PPP2R1B gene, which encodes the Aβ scaffolding subunit of serine/threonine protein phosphatase 2A (PP2A), have been identified in several types of cancer including lung and breast carcinoma. One of these mutations results in an alteration of glycine 90 to aspartic acid (G90D), which has been found in both tumor and genomic DNA, raising the possibility that it is associated with an increased risk for cancer. A novel microarray‐based technology was used to screen for this single‐nucleotide polymorphism in 387 cancer patients and 329 control individuals. These data were used for case–control and family‐based comparisons in order to study the association of this polymorphism with susceptibility to lung carcinoma, breast carcinoma, and acute lymphoblastic leukemia. The frequency of the G90D polymorphism in breast cancer patients was significantly higher in cases (3%) than in controls (0.3%). The wild‐type Aβ subunit interacted with the B56γ (PPP2R5C), PR72 (PPP2R3A), and PR48 subunits of PP2A but did not interact with the B55α (PPP2R2A), B56α (PPP2R5A), or B56β (PPP2R5B) regulatory subunits in an in vitro binding assay. The G90D alteration inhibited the interaction of Aβ with the B56γ subunit but had no effect on binding to the PR72 subunit. These results provide evidence that the G90D alteration of the Aβ subunit of PP2A is associated with a low frequency of breast carcinoma and that the role of this alteration in transformation is likely to involve decreased interaction with the B56γ regulatory subunit.

Human balanced translocation and mouse gene inactivation implicate Basonuclin 2 in distal urethral development

We studied a man with distal hypospadias, partial anomalous pulmonary venous return, mild limb-length inequality and a balanced translocation involving chromosomes 9 and 13. To gain insight into the etiology of his birth defects, we mapped the translocation breakpoints by high-resolution comparative genomic hybridization (CGH), using chromosome 9- and 13-specific tiling arrays to analyze genetic material from a spontaneously aborted fetus with unbalanced segregation of the translocation. The chromosome 13 breakpoint was ∼400 kb away from the nearest gene, but the chromosome 9 breakpoint fell within an intron of Basonuclin 2 (BNC2), a gene that encodes an evolutionarily conserved nuclear zinc-finger protein. The BNC2/Bnc2 gene is abundantly expressed in developing mouse and human periurethral tissues. In all, 6 of 48 unrelated subjects with distal hypospadias had nine novel nonsynonymous substitutions in BNC2, five of which were computationally predicted to be deleterious. In comparison, two of 23 controls with normal penile urethra morphology, each had a novel nonsynonymous substitution in BNC2, one of which was predicted to be deleterious. Bnc2−/− mice of both sexes displayed a high frequency of distal urethral defects; heterozygotes showed similar defects with reduced penetrance. The association of BNC2 disruption with distal urethral defects and the genes expression pattern indicate that it functions in urethral development.

Expression in heterologous cells of the unusual cytoplasmic domain of rat brain 5B4/NCAM-ld

Monoclonal antibody 5B4 recognizes a carboxy-terminal epitope common to large (approximately 180 kDa) and short (approximately 140 kDa) forms of neural cell adhesion molecules (NCAM-ld and NCAM-sd, respectively). The deduced primary sequence of rat brain 5B4/NCAM-ld predicts a large cytoplasmic domain (390 amino acids, Mr 39,284) of striking amino acid composition (52% proline, alanine, serine and threonine) and little predicted alpha or beta secondary structure: its function is unknown. To directly test the deduced topology of the protein, and especially the solubility and stability of its unusual cytoplasmic domain, we have constructed a cDNA expression vector designed to express this domain independently as a soluble protein (designated 5B4cyt) in a heterologous cell system (simian Cos cells). 5B4cyt is indeed soluble, but migrates anomalously on SDS-PAGE under denaturing and reducing conditions as two species of approximately 77 and approximately 80 kDa. In pulse chase experiments, the approximately 77 kDa band chases into the approximately 80 kDa band with a t1/2 of approximately 1 h. The difference in mobility is apparently a consequence of the rapid phosphorylation of the approximately 77 kDa species. The approximately 88 kDa phospho-form is reasonably stable with a t1/2 of approximately 6 h. These results are consistent with the deduced topology of 5B4/NCAM-ld, and demonstrate the feasibility of this experimental approach for exploring the biochemistry and structure of its unusual cytoplasmic domain.

Reply to Benito-Sanz et al.

To the Editor: We applaud the thorough characterization by Benito-Sanz et al. (in this issue)1 of deletions encompassing the SHOX gene (MIM 312865) in patients with Leri-Weill dyschondrosteosis (MIM 127300). Benito-Sanz et al. suggest a founder effect to explain the apparent recombination hotspot we observed among our probands with SHOX deletions.2 Indeed, four of our five probands who shared both 5′ and 3′ breakpoints were Hispanic. However, the same 3′ breakpoint was present in four non-Hispanic white probands, only one of whom had the common 5′ breakpoint. Additional studies will be required to determine whether the common SHOX deletion we observed was recurrent or arose only once. Benito-Sanz et al.1 also propose that diagnosis of SHOX disorders should include testing for deletion of downstream Xp-Yp pseudoautosomal region 1 (PAR1) markers. It will be important to determine whether any of the SNP or microsatellite markers used in their study show deletion polymorphisms among unaffected individuals, since such variations could cause false-positive results in clinical testing. We agree with the statement by Benito-Sanz et al. that Xp deletions extending beyond PAR1 have important genetic counseling implications. Of the 49 deletions they mapped, 5 or 6 were large enough to be visible cytogenetically; our results were similar, but we excluded such deletions from our study. We suggest a low threshold for karyotyping patients with SHOX deletions, which may result not only from simple deletions but also from complex chromosomal rearrangements, such as unbalanced translocations or isodicentric chromosomes.3,4