PPARGC1A coding variation may initiate impaired NEFA clearance during glucose challenge.

AIMS/HYPOTHESIS: The peroxisome proliferator-activated receptor gamma coactivator 1-alpha protein, encoded by the PPARGC1A gene, transcriptionally activates a complex pathway of lipid and glucose metabolism and is expressed primarily in tissues of high metabolic activity such as liver, heart and exercising oxidative skeletal muscle fibre. Ppargc1a-null mice develop systemic dyslipidaemia and hepatic steatosis. In humans, NEFAs downregulate PPARGC1A expression in skeletal muscle. Furthermore, a common non-synonymous coding variant at PPARGC1A (Gly482Ser, rs8192678) is associated with decreased PPARGC1A mRNA levels and increased type 2 diabetes risk. MATERIALS AND METHODS: In a population-based sample of 691 healthy middle-aged Europids we assessed whether Gly482Ser is associated with levels of NEFA when fasting and in response to an oral glucose challenge. We also assessed the potential effect-modifying role of adipose tissue mass on these phenotypes. RESULTS: After adjustment for age, sex, fat mass and fat-free mass, the Ser482 allele associated with higher NEFA at 30 min and 2 h and with NEFA AUC (all values p0.6). CONCLUSIONS/INTERPRETATION: Our observations indicate that NEFA clearance is blunted following a glucose load in carriers of the PPARCG1A Ser482 allele. This association is augmented by obesity.

Meta-analysis of the Gly482Ser variant in PPARGC1A in type 2 diabetes and related phenotypes.

AIMS/HYPOTHESIS: Peroxisome proliferator-activated receptor-gamma co-activator-1alpha (PPARGC1A) is a transcriptional co-activator with a central role in energy expenditure and glucose metabolism. Several studies have suggested that the common PPARGC1A polymorphism Gly482Ser may be associated with risk of type 2 diabetes, with conflicting results. To clarify the role of Gly482Ser in type 2 diabetes and related human metabolic phenotypes we genotyped this polymorphism in a case-control study and performed a meta-analysis of relevant published data. MATERIALS AND METHODS: Gly482Ser was genotyped in a type 2 diabetes case-control study (N=1,096) using MassArray technology. A literature search revealed publications that examined Gly482Ser for association with type 2 diabetes and related metabolic phenotypes. Meta-analysis of the current study and relevant published data was undertaken. RESULTS: In the pooled meta-analysis, including data from this study and seven published reports (3,718 cases, 4,818 controls), there was evidence of between-study heterogeneity (p<0.1). In the fixed-effects meta-analysis, the pooled odds ratio for risk of type 2 diabetes per Ser482 allele was 1.07 (95% CI 1.00-1.15, p=0.044). Elimination of one of the studies from the meta-analysis gave a summary odds ratio of 1.11 (95% CI 1.04-1.20, p=0.004), with no between-study heterogeneity (p=0.475). For quantitative metabolic traits in normoglycaemic subjects, we also found significant between-study heterogeneity. However, no significant association was observed between Gly482Ser and BMI, fasting glucose or fasting insulin. CONCLUSIONS/INTERPRETATION: This meta-analysis of data from the current and published studies supports a modest role for the Gly482Ser PPARGC1A variant in type 2 diabetes risk.

Genetic variants of insulin receptor substrate-1 (IRS-1) in syndromes of severe insulin resistance. Functional analysis of Ala513Pro and Gly1158Glu IRS-1.

AIMS: To define further the role of IRS-1 mutations in human syndromes of severe insulin resistance. METHODS: The IRS-1 gene was scanned for mutations in 83 unrelated affected subjects and 47 unaffected individuals using fluorescent single-strand conformation polymorphism (fSSCP) analysis. A novel heterozygous mutation, Gly1158Glu, was found in one affected subject. Four and two subjects were heterozygous for the previously reported variants Gly972Arg and Ala513Pro, respectively. The previously identified variant Gly819Arg was found in one affected and one unaffected subject. While Gly972Arg has been described to alter the signalling properties of IRS-1, no functional studies of Ala513Pro or Gly1158Glu have been reported. RESULTS: Chinese hamster ovary (CHO) cells stably over-expressing the insulin receptor were transiently transfected with vectors expressing either wild-type, Glu1158 or Pro513 IRS-1. A modest increase in insulin-stimulated tyrosine phosphorylation of Glu1158 IRS-1 was observed. However, this did not result in any significant change in the association of Grb2 or the p85 alpha subunit of PI3-kinase or of PI3-kinase activity. In parallel studies, the Pro513 IRS-1 variant was indistinguishable from wild-type IRS-1. CONCLUSIONS: While subtle effects of these variants cannot be excluded in this system, it is unlikely that these variants are responsible for the extreme insulin resistance seen in the subjects harbouring them. Although IRS proteins play a central role in insulin signalling, functionally significant mutations in the IRS-1 gene are a rare cause of human syndromes of severe insulin resistance.

Compound effects of point mutations causing campomelic dysplasia/autosomal sex reversal upon SOX9 structure, nuclear transport, DNA binding, and transcriptional activation.

Human mutations in the transcription factor SOX9 cause campomelic dysplasia/autosomal sex reversal. Here we identify and characterize two novel heterozygous mutations, F154L and A158T, that substitute conserved "hydrophobic core" amino acids of the high mobility group domain at positions thought to stabilize SOX9 conformation. Circular dichroism studies indicated that both mutations disrupt alpha-helicity within their high mobility group domain, whereas tertiary structure is essentially maintained as judged by fluorescence spectroscopy. In cultured cells, strictly nuclear localization was observed for wild type SOX9 and the F154L mutant; however, the A158T mutant showed a 2-fold reduction in nuclear import efficiency. Importin-beta was demonstrated to be the nuclear transport receptor recognized by SOX9, with both mutant proteins binding importin-beta with wild type affinity. Whereas DNA bending was unaffected, DNA binding was drastically reduced in both mutants (to 5% of wild type activity in F154L, 17% in A158T). Despite this large effect, transcriptional activation in cultured cells was only reduced to 26% in F154L and 62% in A158T of wild type activity, suggesting that a small loss of SOX9 transactivation activity could be sufficient to disrupt proper regulation of target genes during bone and testis formation. Thus, clinically relevant mutations of SOX9 affect protein structure leading to compound effects of reduced nuclear import and reduced DNA binding, the net effect being loss of transcriptional activation.

Intonational disambiguation in sentence production and comprehension.

Speakers' prosodic marking of syntactic constituency is often measured in sentence reading tasks that lack realistic situational constraints on speaking. Results from such studies can be criticized because the pragmatic goals of readers differ dramatically from those of speakers in typical conversation. On the other hand, recordings of unscripted speech do not readily yield the carefully controlled contrasts required for many research purposes. Our research employs a cooperative game task, in which two speakers use utterances from a predetermined set to negotiate moves around gameboards. Results from a set of early versus late closure ambiguities suggest that speakers signal this syntactic difference with prosody even when the utterance context fully disambiguates the structure. Phonetic and phonological analyses show reliable prosodic disambiguation in speakers' productions; results of a comprehension task indicate that listeners can successfully use prosodic cues to categorize syntactically ambiguous fragments as portions of early or late closure utterances.

Detection of polymorphism in the RING3 gene by high-throughput fluorescent SSCP analysis.

We describe the use of a high-throughput, fluorescent, polymorphism-detection system, based on single-strand conformation polymorphism to screen for polymorphism in the RING3 gene. This is the first extensive mutation screen of this major histocompatibility complex-linked gene, and the entire coding region and intron-exon junctions were examined by multiplexing over 3000 polymerase chain reaction products. These techniques should be applicable for analysis of variation in other human genes. Investigation of DNA from acute lymphoblastic leukemia (ALL) and chronic myeloid leukemia (CML) patients, as well as healthy individuals revealed low levels of polymorphism across the RING3 gene. Comparison of the distribution of genotypes at each polymorphic site between patients and healthy individuals revealed a single site which significantly deviates from Hardy-Weinberg proportions.

Analysis and occurrence of estrogenic hormones and their glucuronides in surface water and waste water in The Netherlands.

An analytical procedure was developed that enables routine analysis of four estrogenic hormones in concentrations below 1 ng/l in surface water and waste water. The recovery was 88-98% with a limit of detection of 0.1-2.4 ng/l depending on the compound and the matrix measured. This method was used to determine the occurrence of 17 beta-estradiol, 17 alpha-estradiol, estrone and 17 alpha-ethinylestradiol in the aquatic environment in The Netherlands. The data show that estrogenic hormones can be detected at low concentrations (up to 6 ng/l) at some locations in surface water. In selected effluents of waste water treatment plants estrone and 17 beta-estradiol were detected in concentrations in the ng/l range. Concentrations of 17 alpha-estradiol and the contraceptive 17 alpha-ethinylestradiol were in most of these samples below the limit of detection. Hormone glucuronides were not detected in most surface water and effluents.

Dominant negative mutations in human PPARgamma associated with severe insulin resistance, diabetes mellitus and hypertension.

Thiazolidinediones are a new class of antidiabetic agent that improve insulin sensitivity and reduce plasma glucose and blood pressure in subjects with type 2 diabetes. Although these agents can bind and activate an orphan nuclear receptor, peroxisome proliferator-activated receptor gamma (PPARgamma), there is no direct evidence to conclusively implicate this receptor in the regulation of mammalian glucose homeostasis. Here we report two different heterozygous mutations in the ligand-binding domain of PPARgamma in three subjects with severe insulin resistance. In the PPARgamma crystal structure, the mutations destabilize helix 12 which mediates transactivation. Consistent with this, both receptor mutants are markedly transcriptionally impaired and, moreover, are able to inhibit the action of coexpressed wild-type PPARgamma in a dominant negative manner. In addition to insulin resistance, all three subjects developed type 2 diabetes mellitus and hypertension at an unusually early age. Our findings represent the first germline loss-of-function mutations in PPARgamma and provide compelling genetic evidence that this receptor is important in the control of insulin sensitivity, glucose homeostasis and blood pressure in man.

DNA variation and the future of human genetics.

The use of DNA variants in the mapping of the human genome and in the positional cloning of monogenic disease genes is well established. Determining the genetic bases of the more common "multifactorial" diseases, however, presents a major challenge. The genetics of these diseases are complicated by the interplay between many genes and the environment. These investigations will require large numbers of DNA markers and the technology to screen large populations with these markers. The systematic identification of the common DNA polymorphisms in the human genome coupled with the development of high throughput screening methods should allow ultimately the elucidation of the genetic component of most clinical and nonclinical phenotypes.

Sex determination in humans.

In mammals, the Y chromosome induces testis formation and thus male sexual development; in the absence of a Y chromosome, gonads differentiate into ovaries and female development ensues. Molecular genetic studies have identified the Y-located testis determining gene SRY as well as autosomal and X-linked genes necessary for gonadal development. The phenotypes resulting from mutation of these genes, together with their patterns of expression, provide the basis for establishing a hierarchy of genes and their interactions in the mammalian sex determination pathway.

Linkage analysis of a kindred with inherited 46,XY partial gonadal dysgenesis.

We have reported a kindred in which 46,XY gonadal dysgenesis was inherited in an X-linked (or autosomal dominant sex-limited) manner and in which affected subjects did not have a large duplication of the short arm of the X-chromosome. In the present study we used linkage and sequence analyses to test the role of X-linked and various autosomal genes in the etiology of the familial 46,XY partial gonadal dysgenesis. For analysis of X-linkage, 28 microsatellite polymorphisms and 1 restriction fragment length polymorphism were studied. The genotypes of informative family members were determined at each locus, and data were analyzed. Despite the large number of loci tested, our studies did not establish linkage between the trait and an X-chromosomal locus. With respect to the study of autosomal genes, linkage analysis using a polymorphism within the 3'-untranslated region of the WT1 gene excluded involvement of WT-1 in the etiology of the abnormal gonadal differentiation of the family in this study. Similarly, linkage analysis using four microsatellites on the distal short arm of chromosome 9 was not consistent with linkage. Linkage analysis of a locus close to the SOX9 gene as well as analysis of the coding region of the SOX9 gene suggested that this gene was not associated with the trait in the affected subjects we studied. Our data suggest the role of an autosomal gene in the abnormal gonadal differentiation in the family in the study, but do not formally exclude the role of an X-chromosome gene.

A high-resolution whole genome radiation hybrid map of human chromosome 17q22-q25.3 across the genes for GH and TK.

We have constructed a whole genome radiation hybrid (WG-RH) map across a region of human chromosome 17q, from growth hormone (GH) to thymidine kinase (TK). A panel of 128 WG-RH hybrid cell lines generated by X-irradiation and fusion has been tested for the retention of 39 sequence-tagged site (STS) markers by the polymerase chain reaction. This genome mapping technique has allowed the integration of existing VNTR and microsatellite markers with additional new markers and existing STS markers previously mapped to this region by other means. The WG-RH map includes eight expressed sequence tag (EST) and three anonymous markers developed for this study, together with 23 anonymous microsatellites and five existing ESTs. Analysis of these data resulted in a high-density comprehensive map across this region of the genome. A subset of these markers has been used to produce a framework map consisting of 20 loci ordered with odds greater than 1000:1. The markers are of sufficient density to build a YAC contig across this region based on marker content. We have developed sequence tags for both ends of a 2.1-Mb YAC and mapped these using the WG-RH panel, allowing a direct comparison of cRay6000 to physical distance.

The role of SOX9 in autosomal sex reversal and campomelic dysplasia.

In eutherian mammals, the Y-chromosome gene SRY is required for induction of testis development. Although the Y chromosome is sex determining, loci located elsewhere in the genome participate in the complex cascade of genetic interactions required to form a testis. Male to female sex reversal (46,XY females) occurs at a high frequency in individuals afflicted with the skeletal malformation syndrome campomelic dysplasia. Chromosomal translocations in individuals with both syndromes had localized an autosomal sex reversal locus (SRA1) and a campomelic dysplasia locus (CMPD1) to the long arm of human chromosome 17. The molecular cloning of a translocation breakpoint in a sex reversed campomelic dysplasia patient revealed its proximity to SOX9, a gene which is related to SRY. Analysis of SO X9 in patients without chromosomal rearrangements demonstrated single allele mutations in sex reversed campomelic individuals, linking this gene with both bone formation and control of testis development. Identification of SO X9 as SRA1/CMPD1 and the role of SO X9 mutations in sex reversal and campomelic dysplasia are discussed.

Tissue-specific extinguisher loci in the murine genome: a screening study based on a rat/mouse microcell hybrid panel.

Extinction of tissue-specific traits in intertypic somatic cell hybrids is a well-known phenomenon. In the past few years, microcell hybrids have been used in attempts to dissect this phenotype genetically, and tissue-specific extinguisher loci have been mapped to two different mouse chromosomes. When transferred from fibroblast into hepatoma cells by microcell fusion, these loci down-regulate expression of specific liver genes in trans. However, other liver genes that are extinguished in genotypically complete hybrids seem not to be extinguished in monochromosomal hybrids. To assess the generality of monochromosomal extinction phenotypes, we assembled a collection of rat hepatoma/mouse fibroblast microcell hybrids that represent most of the mouse chromosome complement, and we screened them for expression of a large number of liver-specific genes. Phosphoenolpyruvate carboxykinase gene expression was down-regulated in hybrids containing mouse chromosome 7 or mouse chromosome 11, but other extinction phenotypes were not readily apparent. These results indicate that extinction of many liver genes may be a polygenic trait.

The human SRY transcript.

SRY encodes the Y-linked testis-determining factor in humans. A predominant 900 bp transcript originates from a single exon and encompasses the putative SRY coding sequence. We show that in human adult testis SRY transcription involves multiple start sites. In addition to a previously defined major initiation site, transcripts originating at least 410 bp upstream of this site were detected. Using a cDNA specific RT-PCR assay, embryonic and adult human tissues were screened for SRY expression. In humans, SRY transcription is not restricted to the presumptive and the mature gonadal tissues in the embryo and the adult respectively but can be detected in a range of other locations. Two human cell lines, NTERA-2 cl.D1 (NT2/D1) and Hep G2, have been identified which express SRY at similar levels to adult testis. The NT2/D1 SRY transcripts appear to have the same structure as those in adult testis. HMBA-induced differentiation of NT2/D1 cells results in a diminution of SRY mRNA, while transcription of SRY in retinoic acid differentiated NT2/D1 is unaffected.

Multiple elements regulate phosphoenolpyruvate carboxykinase gene expression in hepatoma hybrid cells.

The phosphoenolpyruvate carboxykinase (PEPCK) gene is highly expressed in cultured rat hepatoma cells, but extinguished in hepatoma x fibroblast hybrids. Extinction of PEPCK gene expression in hybrids is a polygenic process that involves several fibroblast loci, only one of which (tissue-specific extinguisher-1, TSE1) has been characterized to date. To identify sequence elements of the PEPCK gene that are involved both in TSE1-mediated extinction and in TSE1-independent processes, we assayed expression of chimeric PEPCK transgenes in transiently and stably transfected hybrid cells. We report that TSE1 responsiveness mapped to the PEPCK CRE (cAMP response element), as shown previously for the tyrosine aminotransferase gene. This was expected from the recent identification of the TSE1 gene product as a regulatory subunit of protein kinase A. However, none of the transgenes we assayed were responsive to TSE1-independent extinction mechanisms, suggesting that these controls require DNA sequences and/or chromatin structures that were not present in the transfected reporters. The implications of these findings are discussed.

Physical mapping of human chromosome 17 using fragment-containing microcell hybrids.

Hybrid cell lines were generated by microcell-mediated transfer of human chromosome 17 into rat recipient cells. The genotypes of 36 such lines were analyzed using a set of human chromosome 17-derived sequences to probe the structural integrity of the chromosome. Four classes of hybrids were obtained: clones with an apparently intact chromosome 17, clones containing large fragments of the chromosome including both the centromere and the selected marker, clones containing only the selected marker and flanking sequences, and clones containing two 17-derived fragments--the pericentric region plus the region of the selected marker. Data from these hybrids were used in conjunction with published regional localization information to obtain a provisional linear map of the chromosome. Results of this analysis are compared to the gene maps predicted from recent linkage studies and from other somatic cell hybrid experiments.