Outcome of array CGH analysis for 255 subjects with intellectual disability and search for candidate genes using bioinformatics

Array CGH enables the detection of pathogenic copy number variants (CNVs) in 5-15% of individuals with intellectual disability (ID), making it a promising tool for uncovering ID candidate genes. However, most CNVs encompass multiple genes, making it difficult to identify key disease gene(s) underlying ID etiology. Using array CGH we identified 47 previously unreported unique CNVs in 45/255 probands. We prioritized ID candidate genes using five bioinformatic gene prioritization web tools. Gene priority lists were created by comparing integral genes from each CNV from our ID cohort with sets of training genes specific either to ID or randomly selected. Our findings suggest that different training sets alter gene prioritization only moderately; however, only the ID gene training set resulted in significant enrichment of genes with nervous system function (19%) in prioritized versus non-prioritized genes from the same de novo CNVs (7%, p < 0.05). This enrichment further increased to 31% when the five web tools were used in concert and included genes within mitogen-activated protein kinase (MAPK) and neuroactive ligand-receptor interaction pathways. Gene prioritization web tools enrich for genes with relevant function in ID and more readily facilitate the selection of ID candidate genes for functional studies, particularly for large CNVs.

A cross-laboratory comparison of expression profiling data from normal human postmortem brain

Expression profiling of post-mortem human brain tissue has been widely used to study molecular changes associated with neuropsychiatric diseases as well as normal processes such as aging. Changes in expression associated with factors such as age, gender or postmortem interval are often more pronounced than changes associated with disease. Therefore in addition to being of interest in their own right, careful consideration of these effects are important in the interpretation of disease studies. We performed a large meta-analysis of genome-wide expression studies of normal human cortex to more fully catalogue the effects of age, gender, postmortem interval and brain pH, yielding a "meta-signature" of gene expression changes for each factor. We validated our results by showing a significant overlap with independent gene lists extracted from the literature. Importantly, meta-analysis identifies genes which are not significant in any individual study. Finally, we show that many schizophrenia candidate genes appear in the meta-signatures, reinforcing the idea that studies must be carefully controlled for interactions between these factors and disease. In addition to the inherent value of the meta-signatures, our results provide critical information for future studies of disease effects in the human brain.

Giant abdominal aortic aneurysms: clinical and technical considerations

The rupture risk of abdominal aortic aneurysms (AAA) depends primarily on their diameter and increases substantially in large aneurysms. Only a few cases of giant AAAs, with a maximum diameter > 13 cm have been reported in the English literature. This case series report describes 3 cases of giant AAAs presented with rupture. All cases were managed with open surgical repair, since anatomic factors prevented us from choosing an endovascular approach. The huge size of the aneurysm, the short length of the neck and the dislodgement of abdominal organs, that may be densely adhered to its surface with fistula formation, make surgery of this entity very challenging. Open repair of giant AAAs is often the only available treatment, though not always with good results.

A population genomic approach to map recent positive selection in model species

Based on nearly complete genome sequences from a variety of organisms data on naturally occurring genetic variation on the scale of hundreds of loci to entire genomes have been collected in recent years. In parallel, new statistical tests have been developed to infer evidence of recent positive selection from these data and to localize the target regions of selection in the genome. These methods have now been successfully applied to Drosophila melanogaster, humans, mice and a few plant species. In genomic regions of normal recombination rates, the targets of positive selection have been mapped down to the level of individual genes.

Granulocyte chemotactic protein 2 (gcp-2/cxcl6) complements interleukin-8 in periodontal disease

BACKGROUND AND OBJECTIVE

Mucosal inflammatory responses are orchestrated largely by pro-inflammatory chemokines. The chemokine granulocyte chemotactic protein 2 (CXCL6) is involved in neutrophil recruitment and migration. Previous studies have shown that granulocyte chemotactic protein 2 is up-regulated during mucosal inflammation (e.g. in inflammatory bowel disease), similarly to the functionally and structurally related chemokine interleukin-8. Nevertheless, unlike interleukin-8, a role of granulocyte chemotactic protein 2 in gingival inflammation has not been yet demonstrated. In this study we aimed to evaluate the expression of the chemokine granulocyte chemotactic protein 2 in clinically healthy vs. diseased gingival tissues and to explore possible correlations with clinical and microbiological markers of periodontitis.

MATERIAL AND METHODS

Gene expression in 184 'diseased' and 63 'healthy' gingival tissue specimens from 90 patients with periodontitis was analyzed using Affymetrix U133Plus2.0 arrays. The expression of granulocyte chemotactic protein 2 was further confirmed by real-time reverse transcription-polymerase chain reaction, western blotting and enzyme-linked immunosorbent assay, while the localization of granulocyte chemotactic protein 2 in gingival tissues was analyzed by immunohistochemistry. Plaque samples from the adjacent periodontal pockets were collected and evaluated for 11 species of periodontal bacteria using checkerboard DNA-DNA hybridizations.

RESULTS

Among all known chemokines, GCP-2 expression was the most up-regulated (3.8-fold, p < 1.1 x 10(-16)), in 'diseased' vs. 'healthy' tissue as compared to a 2.6-fold increased expression of interleukin-8 mRNA (p < 1.2 x 10(-15)). Increased expression of granulocyte chemotactic protein 2 correlated with higher levels of 'red' and 'orange' complex pathogens and with increased probing depth, but not with attachment loss. Immunohistochemistry showed that granulocyte chemotactic protein 2 was expressed in gingival vascular endothelium.

CONCLUSION

The level of expression of granulocyte chemotactic protein 2 correlates with the severity of periodontitis and appears to act as a hitherto unrecognized functional adjunct to interleukin-8 in diseased gingival tissues.

Misleading findings of subclavian artery and vein transection

Trauma involving the subclavian and axillary arteries is relatively infrequent. However, it can result in devastating functional disability of the upper limb due to significant and permanent associated neurologic deficits. Uncertainty exists in relation to certain aspects of therapeutical management of patients with trauma of the upper limb. Although decision pathway and algorithms have been proposed by several authors, the indications for surgery remain uncertain and not established. Two main points seem to be the most important determinants of the therapeutical strategy; first the viability of the limb and second the accurate determination of the vascular and nerve damage. We present a patient with a traumatic disruption of the subclavian artery and vein and concomitant brachial plexus injury following a road traffic accident. We highlight the role of accurate diagnosis to avoid life and limb-threatening complications from missed diagnosis. Also we review the recent literature emphasizing the therapeutical strategy and the role of conventional surgical repair and endovascular treatment.

IDENTIFICATION OF TASTE QUALITY WITH THE USE OF MEG

We investigated the localization of current sources for spontaneous magnetoencephalographic (MEG) data in the frequency domain. MEGs were evaluated in three different states: (i) physiological condition; (ii) sweet taste, and (iii) salt taste. Low frequencies can be seen in the maps obtained with the sweet taste, whereas in the physiological and salt taste, the maps show higher frequencies in the majority of channels. A differentiation in the spatial distribution of the frequencies provides novel insights into the identification of taste quality with the MEG systems.

Anastomotic Pseudoaneurysms: Our Experience with 49 Cases

We investigated the factors implicated in the pathogenesis of anastomotic aneurysm formation and the postoperative course of patients with such a complication. Forty-five patients with 49 anastomotic aneurysms were diagnosed and treated in two vascular surgery departments in Athens, Greece, during an 8-year period. Emergent complications occurred in 15 cases, rupture in 11, and thromboembolic episodes in another four. Preoperative diagnostic workup in the remaining elective cases (n = 34) included color duplex scan, computed tomographic scan, and angiography. All patients underwent operation, and cultures were obtained during the surgical procedures. Histological examination of the host artery wall adjacent to the aneurysm was also performed. Aortobifemoral bypass was the original operation performed in the majority of cases (71%), and the femoral anastomosis was the most frequent site involved (85.7%). Emergent procedures were associated with increased mortality (46.6%), whereas elective operation resulted in high patency rates and no mortality. In an attempt to isolate predisposing factors that contributed to aneurysm formation, we concluded that the etiology was multifactorial in approximately one-third of the cases and degenerative host artery disease was the main cause (40%). Arterial degeneration is the leading cause of anastomotic aneurysm formation, and emergency arterial reconstruction in cases of aneurysm complication is associated with a poor prognosis.

Gene expression in juvenile arthritis and spondyloarthropathy: pro-angiogenic ELR+ chemokine genes relate to course of arthritis

OBJECTIVE

To evaluate the ability of microarray-based methods to identify genes with disease-specific expression patterns in peripheral blood mononuclear cells (PBMC) and synovial fluid mononuclear cells (SFMC) of juvenile arthritis patients and healthy controls.

METHODS

Microarray data (Affymetrix U95Av2) from 26 PBMC and 20 SFMC samples collected from patients with active disease (classified by course according to ACR criteria) were analysed for expression patterns that correlated with disease characteristics. For comparison, PBMC gene expression profiles were obtained from 15 healthy controls. Real-time PCR was used for confirmation of gene expression differences.

RESULTS

Statistical analysis of gene expression patterns in PBMC identified 378 probe sets corresponding to 342 unique genes with differing expression levels between polyarticular course patients and controls (t test, P<0.0001). The genes represented by these probe sets were enriched for functions related to regulation of immune cell functions, receptor signalling as well as protein metabolism and degradation. Included in these probe sets were a group of CXCL chemokines with functions related to angiogenesis. Further analysis showed that, whereas angiogenic CXCL (ELR+) gene expression was elevated in polyarticular PBMC, expression of angiostatic CXCL (ELR-) chemokines was lower in polyarticular SFMC compared with corresponding pauciarticular samples (t test, P<0.05).

CONCLUSIONS

This pilot study demonstrates that juvenile arthritis patients exhibit complex patterns of gene expression in PBMC and SFMC. The presence of disease-correlated biologically relevant gene expression patterns suggests that the power of this approach will allow better understanding of disease mechanisms, identify distinct clinical phenotypes in disease subtypes, and suggest new therapeutic approaches.

Bioinformatic analysis of autism positional candidate genes using biological databases and computational gene network prediction

Common genetic disorders are believed to arise from the combined effects of multiple inherited genetic variants acting in concert with environmental factors, such that any given DNA sequence variant may have only a marginal effect on disease outcome. As a consequence, the correlation between disease status and any given DNA marker allele in a genomewide linkage study tends to be relatively weak and the implicated regions typically encompass hundreds of positional candidate genes. Therefore, new strategies are needed to parse relatively large sets of 'positional' candidate genes in search of actual disease-related gene variants. Here we use biological databases to identify 383 positional candidate genes predicted by genomewide genetic linkage analysis of a large set of families, each with two or more members diagnosed with autism, or autism spectrum disorder (ASD). Next, we seek to identify a subset of biologically meaningful, high priority candidates. The strategy is to select autism candidate genes based on prior genetic evidence from the allelic association literature to query the known transcripts within the 1-LOD (logarithm of the odds) support interval for each region. We use recently developed bioinformatic programs that automatically search the biological literature to predict pathways of interacting genes (PATHWAYASSIST and GENEWAYS). To identify gene regulatory networks, we search for coexpression between candidate genes and positional candidates. The studies are intended both to inform studies of autism, and to illustrate and explore the increasing potential of bioinformatic approaches as a compliment to linkage analysis.

A high-throughput study of gene expression in preterm labor with a subtractive microarray approach

OBJECTIVE

We propose that elucidation of the pathophysiology of preterm labor can be achieved with genome-scale analyses of differential gene expression.

STUDY DESIGN

CD-1 mice on day 14.5 of a 19- to 20-day gestation were assigned to one of 4 treatment groups modeling different clinical conditions (n = 5 per group): group A, infection with labor (intrauterine injection of 10(10) heat-killed Escherichia coli, which causes delivery within an average of 20 hours); group B, infection without labor (intrauterine injection of 10(7) heat-killed E coli, which leads to normal delivery at term); group C, labor without infection (ovariectomy, which causes delivery within an average of 27 hours); and group D, no infection and no labor (intrauterine injection of vehicle). Total pooled myometrial RNA was prepared 3.5 hours after surgery for groups A, B, and D and 5 hours after surgery for group C. The relative expression of 4963 genes was assayed in these pools by using DNA microarrays. Transcripts specifically involved in infection-induced labor were identified by subtracting from the list of differentially regulated genes in group A those with common expression in groups B and C.

RESULTS

In group A 68 differentially expressed transcripts (>or=2-fold upregulation or downregulation) were identified. Among these are 39 characterized genes. Fourteen (45%) are involved in inflammatory responses, 7 (18%) are involved in growth-differentiation-oncogenesis, and 3 (8%) are involved in apoptosis. Subtraction identified 13 gene products most likely to be important for bacterially induced labor, as opposed to labor without infection or bacterial exposure without labor.

CONCLUSION

This study demonstrates the potential of the subtractive DNA microarray technique to identify transcripts important specifically for bacterially induced preterm labor.

Promoter region-based classification of genes

In this paper we consider the problem of extracting information from the upstream untranslated regions of genes to make predictions about their transcriptional regulation. We present a method for classifying genes based on motif-based hidden Markov models (HMMs) of their promoter regions. Sequence motifs discovered in yeast promoters are used to construct HMMs that include parameters describing the number and relative locations of motifs within each sequence. Each model provides a Fisher kernel for a support vector machine, which can be used to predict the classifications of unannotated promoters. We demonstrate this method on two classes of genes from the budding yeast, S. cerevisiae. Our results suggest that the additional sequence features captured by the HMM assist in correctly classifying promoters.

Pair recordings reveal all-silent synaptic connections and the postsynaptic expression of long-term potentiation

The activation of silent synapses is a proposed mechanism to account for rapid increases in synaptic efficacy such as long-term potentiation (LTP). Using simultaneous recordings from individual pre- and postsynaptic neurons in organotypic hippocampal slices, we show that two CA3 neurons can be connected entirely by silent synapses. Increasing release probability or application of cyclothiazide does not produce responses from these silent synapses. Direct measurement of NMDAR-mediated postsynaptic responses in all-silent synaptic connections before and after LTP induction show no change in failure rate, amplitude, or area. These data do not support hypotheses that synapse silent results from presynaptic factors or that LTP results from increases in presynaptic glutamate release. LTP is also associated with an increase in postsynaptic responsiveness to exogenous AMPA. We conclude that synapse silence, activation, and expression of LTP are postsynaptic.

Analysis of strain and regional variation in gene expression in mouse brain

BACKGROUND

We performed a statistical analysis of a previously published set of gene expression microarray data from six different brain regions in two mouse strains. In the previous analysis, 24 genes showing expression differences between the strains and about 240 genes with regional differences in expression were identified. Like many gene expression studies, that analysis relied primarily on ad hoc 'fold change' and 'absent/present' criteria to select genes. To determine whether statistically motivated methods would give a more sensitive and selective analysis of gene expression patterns in the brain, we decided to use analysis of variance (ANOVA) and feature selection methods designed to select genes showing strain- or region-dependent patterns of expression.

RESULTS

Our analysis revealed many additional genes that might be involved in behavioral differences between the two mouse strains and functional differences between the six brain regions. Using conservative statistical criteria, we identified at least 63 genes showing strain variation and approximately 600 genes showing regional variation. Unlike ad hoc methods, ours have the additional benefit of ranking the genes by statistical score, permitting further analysis to focus on the most significant. Comparison of our results to the previous studies and to published reports on individual genes show that we achieved high sensitivity while preserving selectivity.

CONCLUSIONS

Our results indicate that molecular differences between the strains and regions studied are larger than indicated previously. We conclude that for large complex datasets, ANOVA and feature selection, alone or in combination, are more powerful than methods based on fold-change thresholds and other ad hoc selection criteria.

Molecular and functional heterogeneity of hyperpolarization-activated pacemaker channels in the mouse CNS

The hyperpolarization-activated cation current (termed I(h), I(q), or I(f)) was recently shown to be encoded by a new family of genes, named HCN for hyperpolarization-activated cyclic nucleotide-sensitive cation nonselective. When expressed in heterologous cells, each HCN isoform generates channels with distinct activation kinetics, mirroring the range of biophysical properties of native I(h) currents recorded in different classes of neurons. To determine whether the functional diversity of I(h) currents is attributable to different patterns of HCN gene expression, we determined the mRNA distribution across different regions of the mouse CNS of the three mouse HCN genes that are prominently expressed there (mHCN1, 2 and 4). We observe distinct patterns of distribution for each of the three genes. Whereas mHCN2 shows a widespread expression throughout the CNS, the expression of mHCN1 and mHCN4 is more limited, and generally complementary. mHCN1 is primarily expressed within neurons of the neocortex, hippocampus, and cerebellar cortex, but also in selected nuclei of the brainstem. mHCN4 is most highly expressed within neurons of the medial habenula, thalamus, and olfactory bulb, but also in distinct neuronal populations of the basal ganglia. Based on a comparison of mRNA expression with an electrophysiological characterization of native I(h) currents in hippocampal and thalamic neurons, our data support the idea that the functional heterogeneity of I(h) channels is attributable, in part, to differential isoform expression. Moreover, in some neurons, specific functional roles can be proposed for I(h) channels with defined subunit composition.

Presynaptic protein kinase activity supports long-term potentiation at synapses between individual hippocampal neurons

Simultaneous microelectrode recording from two individual synaptically connected neurons enables the direct analysis of synaptic transmission and plasticity at a minimal synaptic connection. We have recorded from pairs of CA3 pyramidal neurons in organotypic hippocampal slices to examine the properties of long-term potentiation (LTP) at such minimal connections. LTP in minimal connections was found to be identical to the NMDA-dependent LTP expressed by CA3-CA1 synapses, demonstrating this system provides a good model for the study of the mechanisms of LTP expression. The LTP at minimal synaptic connections does not behave as a simple increase in transmitter release probability, because the amplitude of unitary EPSCs can increase several-fold, unlike what is observed when release probability is increased by raising extracellular calcium. Taking advantage of the relatively short axon connecting neighboring CA3 neurons, we found it feasible to introduce pharmacological agents to the interior of presynaptic terminals by injection into the presynaptic soma and have used this technique to investigate presynaptic effects on basal transmission and LTP. Presynaptic injection of nicotinamide reduced basal transmission, but LTP in these pairs was essentially normal. In contrast, presynaptic injection of H-7 significantly depressed LTP but not basal transmission, indicating a specific role of presynaptic protein kinases in LTP. These results demonstrate that pharmacological agents can be directly introduced into the presynaptic cell and that a purely presynaptic perturbation can alter this plasticity.

Synaptic transmission in pair recordings from CA3 pyramidal cells in organotypic culture

We performed simultaneous whole cell recordings from pairs of monosynaptically coupled hippocampal CA3 pyramidal neurons in organotypic slices. Stimulation of an action potential in a presynaptic cell resulted in an AMPA-receptor-mediated excitatory postsynaptic current (EPSC) in the postsynaptic cell that averaged approximately 34 pA. The average size of EPSCs varied in amplitude over a 20-fold range across different pairs. Both paired-pulse facilitation and depression were observed in the synaptic current in response to two presynaptic action potentials delivered 50 ms apart, but the average usually was dominated by depression. In addition, the amplitude of the second EPSC depended on the amplitude of the first EPSC, indicating competition between successive events for a common resource that is not restored within the 50-ms interpulse interval. Variation in the synaptic strength among pairs could arise from a variety of sources. Our data from anatomic reconstruction, 1/CV2 analysis, paired-pulse analysis, and manipulations of calcium/magnesium ratio suggest that differences in quantal size and release probability do not appear to vary sufficiently to fully account for the observed differences in amplitude. Thus it seems most likely that the variability in EPSC amplitude between pairs arises primarily from differences in the number of functional synapses. Injections of the calcium chelator bis-(o-aminophenoxy)-N, N,N',N'-tetraacetic acid into the presynaptic neuron resulted in a rapid and nearly complete block of transmission, whereas injection of the slower-acting chelator EGTA resulted in a variable and partial block. In addition to demonstrating the feasibility of manipulating the intracellular presynaptic environment by injection into the presynaptic soma, these data, and the EGTA results in particular may suggest variability in the linkage between calcium entry sites an release sites in these synapses.

[Transluminal treatment in aneurysm of the abdominal aorta. Role of diagnostic imaging]

PURPOSE

To emphasize the importance of diagnostic imaging: a) in the selection of patients to be treated with the transluminal approach b) during stent-graft positioning c) in the follow-up of treated patients.

MATERIAL AND METHODS

From January 1997 to May 1998, twenty-five patients with abdominal aortic aneurysms (AAA) were treated with transfemoral stent-grafts (AneuRx Medtronic). All patients were submitted to a preoperative study including digital angiography (DSA) and Spiral CT. Intraoperatively they underwent DSA and intravascular ultrasound (IVUS). Follow-up was performed with Spiral CT.

RESULTS

Twenty-four bifurcated and one straight device were inserted in twenty-five patients with AAA. In two cases it was impossible to position the endoprosthesis due to narrow or tortuous artery access. Following the intention to treat criteria, the technical success rate was 92.5%. All the stents were patent and no dislodgement was observed at follow-up. Partial thrombosis of the stent was observed in three patients. Owing to incomplete distal covering, early endoleak occurred in one patient with an aortoiliac aneurysm; the positioning of two cuffs allowed a successful outcome. CT examination performed 6 months after positioning revealed the presence of endoleaks in three patients, due to persistence of lumbar and inferior mesenteric artery patency. The AAA was no more appreciable in five of the ten patients submitted to CT follow-up one year after the procedure. In three of ten cases it was reduced in size and in two patients there was no change.

DISCUSSION

Spiral CT plays a basic role in the selection of patients because it helps assess the length and diameter of the proximal neck, thus permitting to choose the device to be inserted. Preoperative DSA is mandatory in the evaluation of size and tortuosity of the iliac arteries. IVUS allows to monitor the site of delivery during the maneuver and to make the final measurements while DSA plays a role in checking the correct positioning of the device and excluding the presence of endoleaks at the end of the procedure. Late follow-up with Spiral CT aims at demonstrating possible malfunctioning of the endoprosthesis and confirms the definitive exclusion of AAA.

CONCLUSIONS

Diagnostic imaging plays a basic role in the endovascular treatment of AAA, much more than that required for traditional surgical treatment. In particular, pretreatment planning is critical and requires sophisticated imaging including Spiral CT with 3D reconstruction and angiographic evaluation using catheters with calibrated markers.

Basal and apical synapses of CA1 pyramidal cells employ different LTP induction mechanisms

Nitric oxide (NO) production has been widely reported to be required for the induction of long-term potentiation (LTP) in hippocampal CA1 cells. Of the two constitutive isoforms of NO synthase, the endothelial form (eNOS) has been implicated in the induction of LTP in these cells. The distribution of eNOS within CA1 cells is not uniform, however, being present in the cell bodies and apical dendrites but absent from the basal dendrites. Using extracellular and intracellular recording techniques, we demonstrate that LTP induction in stratum radiatum synapses (onto apical dendrites) is dependent on NO production, being attenuated by pretreatment with a NOS inhibitor. LTP induced in stratum oriens synapses (onto basal dendrites) is, however, resistant to NOS inhibitors. Both forms of LTP require the activation of N-methyl-D-aspartate (NMDA) receptors because induction of LTP in both stratum radiatum and stratum oriens is blocked by AP5. Thus, it appears that synapses onto apical and basal dendrites of CA1 cells use different cellular mechanisms of LTP induction.

Seizures and failures in the giant fiber pathway of Drosophila bang-sensitive paralytic mutants

Drosophila bang-sensitive paralytic mutants suffer from hyperactivity and paralysis following a mechanical shock; after recovery from paralysis, they cannot be paralyzed for a refractory period lasting up to 1 hr. Previously, we have shown that in easily shocked (eas), a typical bang-sensitive mutant, electrical shocks delivered to the brain cause seizure-like activity in the dorsal longitudinal flight motor neurons (DLMmns), and failure of giant fiber (GF) stimulation to evoke DLM potentials via the escape response pathway (Pavlidis et al., 1994). Here, we show that seizure and failure in the GF pathway with a refractory period is common to all six members of the bang-sensitive class. This syndrome was not found in any of eight other excitability mutants, including those affecting voltage-gated sodium or potassium-channel function. We show that failure occurs at the synapse between a peripherally synapsing interneuron (PSI) and the DLMmns, while the DLMmn-DLM neuromuscular junctions remain functional. Additionally, failure occurs in all other GF pathway-activated muscles. Failures occurred without seizures in the tergotrochanteral jump muscle (TTM), as was also found in approximately 10% of DLM tests, suggesting that seizures and failures may be independent events. This hypothesis is supported by the finding that, in double mutant combination with mlenapts, which suppresses behavioral bang sensitivity, DLM failures, but not seizures, were reduced.