Shprintzen-Goldberg syndrome: fourteen new patients and a clinical analysis

The Shprintzen-Goldberg syndrome (SGS) is a disorder of unknown cause comprising craniosynostosis, a marfanoid habitus and skeletal, neurological, cardiovascular, and connective-tissue anomalies. There are no pathognomonic signs of SGS and diagnosis depends on recognition of a characteristic combination of anomalies. Here, we describe 14 persons with SGS and compare their clinical findings with those of 23 previously reported individuals, including two families with more than one affected individual. Our analysis suggests that there is a characteristic facial appearance, with more than two thirds of all individuals having hypertelorism, down-slanting palpebral fissures, a high-arched palate, micrognathia, and apparently low-set and posteriorly rotated ears. Other commonly reported manifestations include hypotonia in at least the neonatal period, developmental delay, and inguinal or umbilical hernia. The degree of reported intellectual impairment ranges from mild to severe. The most common skeletal manifestations in SGS were arachnodactyly, pectus deformity, camptodactyly, scoliosis, and joint hypermobility. None of the skeletal signs alone is specific for SGS. Our study includes 14 mainly German individuals with SGS evaluated over a period of 10 years. Given that only 23 other persons with SGS have been reported to date worldwide, we suggest that SGS may be more common than previously assumed.

Oculo-auriculo-vertebral spectrum (OAVS): clinical evaluation and severity scoring of 53 patients and proposal for a new classification

Oculo-auriculo-vertebral spectrum (OMIM164210) is a phenotypically and probably also a genetically heterogeneous disorder, characterized by anomalies of the ear (mostly microtia), hemifacial microsomia, and defects of the vertebral column. Associated clinical findings include anomalies of the eye and brain, and developmental delay. We have evaluated the clinical data and photographs of 53 unrelated patients with OAVS, all presenting with either isolated microtia or preauricular tags in association with hemifacial microsomia as minimal diagnostic criteria; five had a positive family history for OAVS. Based on the main clinical findings and unilateral or bilateral involvement, we have developed a new classification system for OAVS, consisting of six subgroups. There is a statistically significant correlation between the subgroup and number of associated clinical findings, and a statistically significant difference regarding prognosis in uni- and bilaterally affected patients, suggesting that this classification is clinically relevant to the categorization of patients with OAVS. The newly developed scoring system (two points for each main clinical finding and one for each associated clinical finding) presented here, also aids prognosis, especially for delay of motor development and brain anomalies, and statistical analysis revealed significant clustering between different clinical findings of OAVS confirming the clinical impression previously published by several authors.

Prader–Willi syndrome with a karyotype 47,XY,+min(15)(pter->q11.1:) and maternal UPD 15—case report plus review of similar cases

Prader-Willi (PWS) and Angelman (AS) are syndromes of developmental impairment that can result either from a 15q11-q13 deletion, paternal uniparental disomy (UPD), imprinting, or UBE3A mutations. A small cytogenetic subset of PWS and AS patients are carriers of a so-called small supernumerary marker chromosome (sSMC). Here, we report on an previously unreported PWS case with a karyotype 47,XY,+min(15)(pter->q11.1:) plus maternal heterodisomic UPD 15. A review of the literature revealed, that for both, PWS and AS patients, cases with (1) a sSMC plus microdeletion of the PWS/AS critical region, (2) inv dup(15) plus uniparental disomy (UPD) 15 and (3) cases without exclusion of a microdeletion an UBE3A mutation or UPD are described. The present case as well as the review of similar cases provides further evidence for the necessity to test UPD in prenatal cases with a de novo sSMC and in postnatal cases with otherwise unexplainable clinical phenotype.

MRI brain volumetry in Rasmussen encephalitis: The fate of affected and “unaffected” hemispheres

Rasmussen encephalitis (RE) is regarded as a unihemispheric disease. Serial three-dimensional MRIs of 18 patients under immunotherapy were analyzed volumetrically and planimetrically. Median volume loss was significantly higher in the affected than in the unaffected hemispheres (29.9 cm3/y vs 6.8 cm3/y). Correlation of the planimetrically and volumetrically assessed hemispheric ratios (HRs) was significant. The results support the concept of RE as a basically unilateral disease. Planimetric HR assessment is valid and time efficient.

Global gene expression profiling and cluster analysis in Xenopus laevis

We have undertaken a large-scale microarray gene expression analysis using cDNAs corresponding to 21,000 Xenopus laevis ESTs. mRNAs from 37 samples, including embryos and adult organs, were profiled. Cluster analysis of embryos of different stages was carried out and revealed expected affinities between gastrulae and neurulae, as well as between advanced neurulae and tadpoles, while egg and feeding larvae were clearly separated. Cluster analysis of adult organs showed some unexpected tissue-relatedness, e.g. kidney is more related to endodermal than to mesodermal tissues and the brain is separated from other neuroectodermal derivatives. Cluster analysis of genes revealed major phases of co-ordinate gene expression between egg and adult stages. During the maternal-early embryonic phase, genes maintaining a rapidly dividing cell state are predominantly expressed (cell cycle regulators, chromatin proteins). Genes involved in protein biosynthesis are progressively induced from mid-embryogenesis onwards. The larval-adult phase is characterised by expression of genes involved in metabolism and terminal differentiation. Thirteen potential synexpression groups were identified, which encompass components of diverse molecular processes or supra-molecular structures, including chromatin, RNA processing and nucleolar function, cell cycle, respiratory chain/Krebs cycle, protein biosynthesis, endoplasmic reticulum, vesicle transport, synaptic vesicle, microtubule, intermediate filament, epithelial proteins and collagen. Data filtering identified genes with potential stage-, region- and organ-specific expression. The dataset was assembled in the iChip microarray database, , which allows user-defined queries. The study provides insights into the higher order of vertebrate gene expression, identifies synexpression groups and marker genes, and makes predictions for the biological role of numerous uncharacterized genes.

Twenty-six novelEFNB1 mutations in familial and sporadic craniofrontonasal syndrome (CFNS)

Craniofrontonasal syndrome (CFNS) is an X-linked disorder characterized by a more severe manifestation in heterozygous females than in hemizygous males. Heterozygous females have craniofrontonasal dysplasia (CFND) and occasionally extracranial manifestations including midline defects and skeletal abnormalities, whereas hemizygous males show no or only mild features such as hypertelorism and rarely show cleft lip or palate. Mutations in the EFNB1 gene in Xq12 are responsible for familial and sporadic CFNS. The EFNB1 gene encodes ephrin-B1, a transmembrane ligand that also exhibits receptor-like effects. We performed mutation analysis in nine unrelated families and 29 sporadic patients with CFNS. DNA sequencing revealed mutations in 33 (86.8%) cases including 26 distinct novel mutations. A recurrent nonsense mutation, c.196C>T/R66X, was detected in one family and four sporadic patients. The majority of mutations (26/33) were located in exons 2 and 3 of the EFNB1 gene encoding the extracellular ephrin domain. The mutation spectrum includes frameshift, nonsense, missense, and splice site mutations, with a predominance of frameshift and nonsense mutations resulting in premature truncation codons. For the first time we describe mutations in exons 4 and 5 of EFNB1. Of particular interest are the frameshift mutations located in the last 25 codons of EFNB1 encoding the carboxyterminal end of ephrin-B1. They result in an extension by 44 residues. These mutations disrupt the intracellular binding sites for Grb4 and PDZ-effector proteins involved in reverse signaling. We conclude that the major causes of familial as well as sporadic CFNS are loss of function mutations in the EFNB1 gene that comprise premature termination or abrogate receptor-ligand interaction, oligomerization, and ephrin-B1 reverse signaling.

Genotyping in 46 patients with tentative diagnosis of Treacher Collins syndrome revealed unexpected phenotypic variation

To define the range of phenotypic expression in Treacher Collins syndrome (TCS; Franceschetti-Klein syndrome), we performed mutation analysis in the TCOF1 gene in 46 patients with tentative diagnosis of TCS and evaluated the clinical data, including a scoring system. A total of 27 coding exons of TCOF1 and adjacent splice junctions were analysed by direct sequencing. In 36 patients with a clinically unequivocal diagnosis of TCS, we detected 28 pathogenic mutations, including 25 novel alterations. No mutation was identified in the remaining eight patients with unequivocal diagnosis of TCS and 10 further patients, in whom the referring diagnosis of TCS was clinically doubtful. There is no overt genotype-phenotype correlation except that conductive deafness is significantly less frequent in patients with mutations in the 3' part of the open reading frame. Inter- and intrafamilial variation is wide. Some mutation carriers, parents of typically affected patients, are so mildly affected that the diagnosis might be overlooked clinically. This suggests that modifying factors are important for phenotypic expression. Based on these findings, minimal diagnostic criteria were defined: downward slanting palpebral fissures and hypoplasia of the zygomatic arch. The difficulties in genetic counselling, especially diagnosis of family members with a mild phenotype, are described.

Applying Support Vector Machines for Gene Ontology based gene function prediction

Background

The current progress in sequencing projects calls for rapid, reliable and accurate function assignments of gene products. A variety of methods has been designed to annotate sequences on a large scale. However, these methods can either only be applied for specific subsets, or their results are not formalised, or they do not provide precise confidence estimates for their predictions.

Results

We have developed a large-scale annotation system that tackles all of these shortcomings. In our approach, annotation was provided through Gene Ontology terms by applying multiple Support Vector Machines (SVM) for the classification of correct and false predictions. The general performance of the system was benchmarked with a large dataset. An organism-wise cross-validation was performed to define confidence estimates, resulting in an average precision of 80% for 74% of all test sequences. The validation results show that the prediction performance was organism-independent and could reproduce the annotation of other automated systems as well as high-quality manual annotations. We applied our trained classification system to Xenopus laevis sequences, yielding functional annotation for more than half of the known expressed genome. Compared to the currently available annotation, we provided more than twice the number of contigs with good quality annotation, and additionally we assigned a confidence value to each predicted GO term.

Conclusions

We present a complete automated annotation system that overcomes many of the usual problems by applying a controlled vocabulary of Gene Ontology and an established classification method on large and well-described sequence data sets. In a case study, the function for Xenopus laevis contig sequences was predicted and the results are publicly available at .

Gene expression analysis on biochemical networks using the Potts spin model

MOTIVATION

Microarray technology allows us to profile the expression of a large subset or all genes of a cell. Biochemical research over the last three decades has elucidated an increasingly complete image of the metabolic architecture. For less complex organisms, such as Escherichia coli, the biochemical network has been described in much detail. Here, we investigate the clustering of such networks by applying gene expression data that define edge lengths in the network.

RESULTS

The Potts spin model is used as a nearest neighbour based clustering algorithm to discover fragmentation of the network in mutants or in biological samples when treated with drugs. As an example, we tested our method with gene expression data from E.coli treated with tryptophan excess, starvation and trpyptophan repressor mutants. We observed fragmentation of the tryptophan biosynthesis pathway, which corresponds well to the commonly known regulatory response of the cells.

Reliability of gene expression ratios for cDNA microarrays in multiconditional experiments with a reference design

In a typical gene expression profiling experiment with multiple conditions, a common reference sample is used for co-hybridization with the samples to yield expression ratios. Differential expression for any other sample pair can then be calculated by assembling the ratios from their hybridizations with the reference. In this study we test the validity of this approach. Differential expression of a sample pair (i, j) was obtained in two ways: directly, by hybridizations of sample i versus j, and indirectly, by multiplying the expression ratios for hybridizations of sample i versus pool and pool versus sample j. We performed gene expression profiling using amphibian embryos (Xenopus laevis). Every sample combination of four different stages and a pool was profiled. Direct and indirect values were compared and used as the quality criterion for the data. Based on this criterion, 82% of all ratios were found to be sufficiently accurate. To increase the reliability of the signals, several widely used filtering techniques were tested. Filtering by differences of repeated hybridizations was found to be the optimal filter. Finally, we compared microarray-based gene expression profiles with the corresponding expression patterns obtained by whole-mount in situ hybridizations, resulting in a 90% correspondence.

Holoprosencephaly, bilateral cleft lip and palate and ectrodactyly: another case and follow up

We describe a male patient with lobar holoprosencephaly, ectrodactyly, and cleft lip/palate, a syndrome which has been seen previously in only six patients. In addition, our patient developed hypernatraemia, which has been described in three patients before.

Alport syndrome with diffuse leiomyomatosis

Alport syndrome (AS) is a hereditary nephropathy with hematuria progressing to end-stage renal failure (ESRF), sensorineural deafness, and specific eye signs (lenticonus, macular flecks, and congenital cataracts). Inheritance is X-linked in about 85% of the cases, caused by different mutations in the COL4A5 gene. Rarely AS is seen in combination with diffuse leiomyomatosis (DL). DL is a tumorous process involving smooth muscle cells, mostly of the esophagus, but also of the tracheobronchial tree and the female genital tract. Characteristically, the patients have deletions of the 5'-end of both the COL4A5 and the COL4A6 genes, respectively. We here present a 9-year-old boy who was admitted because of a newly diagnosed sensorineural deafness. He was born with cataracts and presented symptoms of dysphagia and bronchial irritation in the first year of life. Macroscopic hematuria was first noticed at 2 years during a febrile infection. Since early childhood the boy suffered from severe constipation. Taking together these symptoms, the diagnosis of Alport syndrome with diffuse leiomyomatosis (AS-DL) has to be considered. Genetic analysis demonstrated the predicted deletion of the COL4A5/COL4A6 genes.

Tuberous sclerosis complex with disseminated telencephalic distribution of atypical cells and their relation to corticogenesis

In 2 cases of tuberous sclerosis complex (TSC), a disseminated distribution of atypical cells throughout the white matter and cortex of the telencephalon has been found. No cortical tubera were observed. In 1 of the cases, ventricular wall tumors (giant astrocytomas) were present. Stripes and candle guttering excrescences of groups of atypical cells perpendicular to the ventricular wall and to the cortical surface indicate erroneous genetic information in sets of neuroepithelial germ cells. This is compatible with the somatic second hit hypothesis effective in addition to the basic defect of TSC1 and TSC2 genes. The normal age-correspondend corticogenesis with regular layering and regular differentiation of neurons and glia without any cortical malformation or dysplasia and the sparing of allocortical parts of the telencephalon (hippocampus) as well as of basal ganglia, cerebellum, brain stem and spinal cord point to the rather late appearance of atypical cells which manifest in loco and do not interfere with corticogenesis. The bidirectional potential of atypical cells is obvious by their strong GFAP and APP surface staining. This coexpression indicates glial as well as neuronal features and emphasizes the relatively low level of differentiation of these cells. In their disseminated localization in our cases, these cells do not form tumors in the telencephalic white matter or cortex thus escaping sonographic detection before birth.

New advanced operational regime on the W7-AS stellarator

A promising new plasma operational regime on the Wendelstein stellarator W7-AS has been discovered. It is extant above a threshold density and characterized by flat density profiles, high energy and low impurity confinement times, and edge-localized radiation. Impurity accumulation is avoided. Quasistationary discharges with line-averaged densities n(e) to 4 x 10(20) m(-3), radiation levels to 90%, and partial plasma detachment at the divertor target plates can be simultaneously realized. Energy confinement is up to twice that of a standard scaling. At B(t) = 0.9 T, an average beta value of 3.1% is achieved. The high n(e) values allow demonstration of electron Bernstein wave heating using linear mode conversion.

A novel lentivirus vector derived from apathogenic simian immunodeficiency virus

The improvement of gene transfer efficiency in growth-arrested cells using human immunodeficiency virus type 1 (HIV-1)-derived vectors led to the development of vectors derived from other members of the lentivirus family. Here we report the generation of a lentiviral vector derived from the apathogenic molecular virus clone SIVagm3mc of the simian immunodeficiency virus from African green monkeys (Cercocebus pygerythrus). Upon pseudotyping with the G-protein of vesicular stomatitis virus (VSV-G), the SIVagm-derived vector was shown to transduce proliferating and growth-arrested mammalian cell lines, including human cells. After in vivo inoculation into the striatum of the adult rat brain, the vector was shown to transduce terminally differentiated neurons and oligodendrocytes as well as quiescent and reactive astrocytes. Moreover, SIVagm transfer vector mRNA was efficiently packaged by HIV-1 vector particles. Homologous [SIV(SIV)] vectors generated by using the SIVagm-derived envelope glycoproteins allowed selective gene transfer into human CD4(+)/CCR5(+) cells. Thus, the SIVagm3mc-derived vector is a useful alternative to HIV-1-derived lentiviral vectors in somatic gene therapy.

Effects of heavy metal ions on resting and antigen-activated CD4(+) T cells

Heavy metal environmental pollutants increase susceptibility of affected individuals to bacterial and viral infections, but the mechanisms responsible for this effect are not known. We established cellular in vitro systems to identify molecular targets for the action of heavy metal ions. We used two model systems to determine the effects of heavy metal ions on antigen-induced T lymphocyte responses. The first system was representative of primary antigen responses and utilized CD4(+) primary T lymphocytes derived from DO.11.10 T cell receptor transgenic mice. The second system represented a memory T cell phenotype and utilized the CD4(+) T helper 1 clone, pGL2. We measured the effects of the four heavy metals cadmium, lead, mercury, and vanadium on cytokine and proliferation responses by purified CD4(+) T cell to antigenic stimulation. Cytokine responses were differentially affected by lead and vanadium at concentrations that did not affect T cell proliferation in response to antigen. We also determined whether the metal ions induced apoptotic cell death. Mercury induced apoptosis at concentrations as low as 0.5 microM, whereas cadmium required a concentration of 100 microM. Lead (maximal concentration tested was 200 microM) and vanadium (100 microM) did not induce apoptosis. The results suggested that the different heavy metal ions differentially affected antigen-stimulated responses in T helper cells. These in vitro systems can now be applied to test whether heavy metal ions alter antigen-induced T cell signal transduction pathways in CD4(+) T helper cells.

Effects of cadmium and vanadium ions on antigen-induced signaling in CD4(+) T cells

Heavy metal environmental pollutants modulate antigen-directed responses by T lymphocytes, but the molecular mechanisms by which certain metal ions exert their effects are only poorly understood. We tested the hypothesis that cadmium and vanadium ions alter antigen-induced T cell signal transduction pathways in CD4(+) T helper cells. We used CD4(+) primary T lymphocytes and splenic T cells from DO.11.10 T cell receptor transgenic mice. We determined the effects of cadmium chloride and sodium orthovanadate at concentrations that did not induce apoptotic cell death, but affected cytokine or proliferation responses to antigenic stimulation. We used electrophoretic mobility shift assays to measure effects of cadmium and vanadium ions on antigen-induced activation of the nuclear transcriptional regulator proteins, nuclear factor-kappaB, cyclic AMP response element binding protein, nuclear factor of activated T cells, and activator protein-1. Different signaling pathways lead to activation of these transcription factors. Our results suggest that the two heavy metal ions differentially affect signaling pathways. This knowledge will help in the development of molecular epidemiological assays.

Solvent entropy-driven searching for protein modeling examined and tested in simplified models

Solvent entropy is a force to consider in protein folding and protein design but is difficult to model. It is investigated here in the context of the hp model: Two types of residues, hydrophobic and hydrophilic, are modeled on a lattice. Nine chains and two- and three-dimensional simulations are compared. We show that considering solvent entropy alone, efficient folding of lattice chains (identification of the native fold) can be achieved by an entropy-driven simulation on its own. Moreover, in a detailed comparison over a wide range of parameters, entropy-guided searching outperforms an energy-driven search in the model. The combination of energy- and entropy-driven search yields the most efficient searching. It is compared in detail with the above results, indicating also how this solvent shell model may advantageously be implemented in more complex protein modeling simulations.

[Obstruction of surgical portosystemic shunts in the early postoperative phase: interventional treatment by angioplasty with stent implantation]

PURPOSE

Recurrent variceal bleeding in patients treated with surgical porto-systemic shunting is most often due to shunt stenoses or occlusion. Radiological interventional procedures are a possible method of therapy and our experience herein is described in this report.

PATIENTS AND METHODS

From 1997 to 1999 54 patients with recurrent variceal bleeding were treated with a surgical porto-systemic shunt procedure. Of these early shunt occlusion occurred in 5 patients, which was treated with percutaneous transcatheter techniques.

RESULTS

In only one patient was PTA alone sufficient to reestablish shunt patency, in four patient stent placement was necessary in addition. In the follow-up period 1 patient died 26 month after intervention with (autopsy-proven) patent shunt, in one patient shunt reocclusion occurred after 11 months and in 3 patients the shunt is still patent.

CONCLUSIONS

PTA, if necessary in combination with stent placement, is an attractive alternative method of therapy in case of an early surgical porto-systemic shunt occlusion.

Post-thymic selection of peripheral CD4+ T-lymphocytes on class II major histocompatibility antigen-bearing cells

Following positive and negative selection in the thymus, mature CD4+ T-cells emigrate into peripheral lymphoid organs. Whether resting T-cells require periodic stimulation to remain viable in the absence of antigen is important for understanding peripheral T-cell homeostasis. A prerequisite for T-cell receptor (TCR)-mediated signals in maintaining peripheral CD4+ T-cell longevity has been demonstrated. Here, we show in mice expressing a mutant I-Abeta transgene on an I-Abeta knockout background that naïve CD4+ T-cells also require engagement of their CD4 coreceptors by peripheral, class II MHC-bearing cells for their survival. The transgene's product combines with endogenous Aalpha, but this mutant AalphaAbeta heterodimer cannot interact with CD4 molecules, although it efficiently presents antigens to TCRs. Resting CD4+ T-lymphocytes from mutant Abeta transgenic mice die by apoptosis at a much higher rate than do CD4+ T-cells from normal mice. Apoptosis of CD4+ T-cells in mutant Abeta transgenic mice is partially mediated by Fas. Adoptive transfer experiments revealed that the increase in apoptosis is due to a lack of interactions with mutant MHC class II rather than to an intrinsic defect in the CD4+ T-cells selected on mutant Abeta-expressing thymic epithelial cells. Thus, interactions between CD4 and MHC class II molecules contribute to the regulation of homeostasis in the peripheral immune system. Our results further suggest that thymic emigrant cells are continuously retested in the periphery for appropriate coreceptor interactions. Peripheral selection may be important in eliminating potentially autoreactive T-cells.

[Hypomelanosis Ito in translocation trisomy 9/mosaicism (46,XX/46,XX,t(9;9)(p24;p24)). Spontaneous remission in childhood]

A 4 5/12 years old girl with hypomelanosis of Ito (HI) presented on the 3rd day of life with hypopigmented streaks and whorls following the lines of Blaschko on the back, the arms and the legs. In addition, patchy depigmented areas were present on the trunk. Extracutaneous manifestations included dystopia of the right kidney, atrial septal defect, persistent ductus arteriosus, hearing impairment, EEG abnormalities, and asymmetric dilatation of the ventricle system and a vermal atrophy as documented in the MRT of the brain. Cytogenetic analysis showed a mosaic 46,XX/46,XX,t(9;9)(p24;p24) present in the lymphocytes and skin fibroblasts. The mother's karyotype in her lymphocytes was normal. At reexamination at the age of 4 5/12 years the girl was retarded. In particular, the speech development was severely delayed. Interestingly we found only very small areas of hypopigmentation, which, unless one knew the previous findings, would not have been diagnostic.