Analysis of molecular intra-patient variation and delineation of a prognostic 12-gene signature in non-muscle invasive bladder cancer; technology transfer from microarrays to PCR

Background:

Multiple clinical risk factors and genetic profiles have been demonstrated to predict progression of non-muscle invasive bladder cancer; however, no easily clinical applicable gene signature has been developed to predict disease progression independent of disease stage and grade.

Methods:

We measured the intra-patient variation of an 88-gene progression signature using 39 metachronous tumours from 17 patients. For delineation of the optimal quantitative reverse transcriptase PCR panel of markers, we used 115 tumour samples from patients in Denmark, Sweden, UK and Spain.

Results:

Analysis of intra-patient variation of the molecular markers showed 71% similar classification results. A final panel of 12 genes was selected, showing significant correlation with outcome. In multivariate Cox regression analysis, we found that the 12-gene signature was an independent prognostic factor (hazard ratio=7.4 (95% confidence interval: 3.4–15.9), P<0.001) when adjusting for stage, grade and treatment. Independent validation of the 12-gene panel and the determined cut-off values is needed and ongoing.

Conclusion:

Intra-patient marker variation in metachronous tumours is present. Therefore, to increase test sensitivity, it may be necessary to test several metachronous tumours from a patient’s disease course. A PCR-based 12-gene signature significantly predicts disease progression in patients with non-muscle invasive bladder cancer.

Multimodal communication in animals, humans and robots: an introduction to perspectives in brain-inspired informatics

Recent years have seen convergence in research on brain mechanisms and neurocomputational approaches, culminating in the creation of a new generation of robots whose artificial "brains" respect neuroscience principles and whose "cognitive" systems venture into higher cognitive domains such as planning and action sequencing, complex object and concept processing, and language. The present article gives an overview of selected projects in this general multidisciplinary field. The work reviewed centres on research funded by the EU in the context of the New and Emergent Science and Technology, NEST, funding scheme highlighting the topic "What it means to be human". Examples of such projects include learning by imitation (Edici project), examining the origin of human rule-based reasoning (Far), studying the neural origins of language (Neurocom), exploring the evolutionary origins of the human mind (Pkb140404), researching into verbal and non-verbal communication (Refcom), using and interpreting signs (Sedsu), characterising human language by structural complexity (Chlasc), and representing abstract concepts (Abstract). Each of the communication-centred research projects revealed individual insights; however, there had been little overall analysis of results and hypotheses. In the Specific Support Action Nestcom, we proposed to analyse some NEST projects focusing on the central question "What it means to communicate" and to review, understand and integrate the results of previous communication-related research, in order to develop and communicate multimodal experimental hypotheses for investigation by future projects. The present special issue includes a range of papers on the interplay between neuroinformatics, brain science and robotics in the general area of higher cognitive functions and multimodal communication. These papers extend talks given at the NESTCOM workshops, at ICANN (http://www.his.sunderland.ac.uk/nestcom/workshop/icann.html) in Porto and at the first meeting of the Federation of the European Societies of Neuropsychology in Edinburgh in 2008 (http://www.his.sunderland.ac.uk/nestcom/workshop/esn.html). We hope that the collection will give a vivid insight into current trends in the field.

History of safe use as applied to the safety assessment of novel foods and foods derived from genetically modified organisms

Very few traditional foods that are consumed have been subjected to systematic toxicological and nutritional assessment, yet because of their long history and customary preparation and use and absence of evidence of harm, they are generally regarded as safe to eat. This 'history of safe use' of traditional foods forms the benchmark for the comparative safety assessment of novel foods, and of foods derived from genetically modified organisms. However, the concept is hard to define, since it relates to an existing body of information which describes the safety profile of a food, rather than a precise checklist of criteria. The term should be regarded as a working concept used to assist the safety assessment of a food product. Important factors in establishing a history of safe use include: the period over which the traditional food has been consumed; the way in which it has been prepared and used and at what intake levels; its composition and the results of animal studies and observations from human exposure. This paper is aimed to assist food safety professionals in the safety evaluation and regulation of novel foods and foods derived from genetically modified organisms, by describing the practical application and use of the concept of 'history of safe use'.

A hotel-based outbreak of Salmonella enterica subsp. Enterica serovar Enteritidis (Salmonella Enteritidis) in the United Kingdom, 2006

An outbreak of food-borne Salmonella Enteritidis PT4 occurred in Cumbria, in north-west England, in the summer of 2006. Fifteen people, all with positive stool samples, met the case definition; three of these were admitted to hospital, including one patient who died. Preliminary investigations suggested a link to a meal served at a local hotel. A case control study was implemented, together with microbiological and environmental investigations. Fifteen microbiologically confirmed cases and 27 unmatched controls were included in the study, controls being randomly selected from people who had eaten at the hotel on the same day. The epidemiological evidence indicated a very strong association between infection and consumption of tiramisu made with raw shell eggs, although none were available for microbiological investigation. These results are in line with other salmonellosis outbreaks that have been associated with the use of raw shell eggs in food manufacturing and production.This paper highlights the continuing need for a greater awareness by those who work in the food industry of the health risks associated with the consumption of raw shell eggs.

E. coli O157 phage type 21/28 outbreak in North Cumbria associated with pasteurized milk

In March 1999, a large community outbreak of Escherichia coli O157 infection occurred in North Cumbria. A total of 114 individuals were reported to the Outbreak Control Team (OCT); 88 had laboratory confirmed E. coli O157. Twenty-eight (32%) of the confirmed cases were admitted to hospital, including three children (3.4%) with haemolytic uraemic syndrome. There were no deaths. A case-control study found that illness was strongly associated with drinking pasteurized milk from a local farm (P = <0.0001) on single variable analysis. Microbiological investigations at the farm revealed E. coli O157 phage type (PT) 21/28 VT 2 which was indistinguishable from the human isolates by pulsed field gel electrophoresis. At the time of occurrence this was the largest E. coli O157 outbreak in England and Wales and the first E. coli O157 PT 21/28 VT 2 outbreak associated with pasteurized milk. This outbreak highlights lessons to be learnt regarding on-farm pasteurization.

The contribution of epidemiology

Epidemiologic studies directly contribute data on risk (or benefit) in humans as the investigated species, and in the full food intake range normally encountered by humans. This paper starts with introducing the epidemiologic approach, followed by a discussion of perceived differences between toxicological and epidemiologic risk assessment. Areas of contribution of epidemiology to the risk assessment process are identified, and ideas for tailoring epidemiologic studies to the risk assessment procedures are suggested, dealing with data collection, analyses and reporting of both existing and new epidemiologic studies. The dietary habits and subsequent disease occurrence of over three million people are currently under observation worldwide in cohort studies, offering great potential for use in risk assessment. The use of biomarkers and data on genetic susceptibility are discussed. The paper describes a scheme to classify epidemiologic studies for use in risk assessment, and deals with combining evidence from multiple studies. Using a matrix approach, the potential contribution to each of the steps in the risk assessment process is evaluated for categories of food substances. The contribution to risk assessment of specific food substances depends on the quality of the exposure information. Strengths and weaknesses are summarized. It is concluded that epidemiology can contribute significantly to hazard identification, hazard characterisation and exposure assessment.

N-Arylsulfonylindole derivatives as serotonin 5-HT(6) receptor ligands

A series of N(1)-arylsulfonyltryptamines were found to be potent ligands of the human serotonin 5-HT(6) receptor with the 5-methoxy-1-benzenesulfonyl analogue (19) having the highest affinity. Additionally, it was discovered that a group such as 3-(3-methoxybenzyl)-1,2,4-oxadiazol-5-yl in the 2-position of the indole ring (43) can replace the arylsulfonyl substituent in the 1-position with no loss of affinity. This suggested that the binding conformation of the aminoethyl side chain at this receptor was toward the 4-position of the indole ring and was supported by the fact that the 4-(aminoethyl)indoles (45) also displayed high affinity, as did the conformationally rigid 1,3,4,5-tetrahydrobenz[c,d]indole (49). Molecular modeling showed that 19, 43, and 45 all had low-energy conformers that overlaid well onto 49. Both 19 and 49 had good selectivity over other serotonin receptors tested, with 49 also showing excellent selectivity over all dopamine receptors. In a functional adenylate cyclase stimulation assay, 19 and 49 had no agonist activity, whereas 45 behaved as a partial agonist. Finally, it was shown that 19 had good activity in the 5-HT(2A) centrally mediated mescaline-induced head twitch assay, which implies that it is brain-penetrant.

From efficacy to effectiveness: managing organisational change to improve health services for young people with deliberate self harm behaviour

Repeat Deliberate Self Harm is a recognised risk factor for completed suicide and therefore reduction by effective health service response represents a valid contribution to suicide prevention. However, only a small fraction of people with deliberate self harm presentations to general health settings actually reach specialist mental health follow-up appointments. Therefore, even if responses at that point are known to be effective they do not make a significant contribution to reducing repeat self-harm overall. We describe health system organisational change strategies to improve health service engagement for the target group, and present data demonstrating the effectiveness of these strategies.

Micromachining of a piezocomposite transducer using a copper vapor laser

A 1-3 piezocomposite transducer with front face dimensions of 2 x 2 mm has been micromachined using a copper vapor laser. The device consists of PZT5A piezoceramic pillars with a 65-micron pitch suspended in a low viscosity thermosetting polymer. The kerf width is 13 microns, and the transducer thickness is 170 microns, making the device suitable for ultrasonic reception at frequencies close to 10 MHz.

A germline deletion of p14(ARF) but not CDKN2A in a melanoma-neural system tumour syndrome family

The melanoma-astrocytoma syndrome is characterized by a dual predisposition to melanoma and neural system tumours, commonly astrocytoma. Germline deletions of the region on 9p21 containing the CDKN2A and CDKN2B genes and CDKN2A exon 1beta have been reported in kindreds, implicating contiguous tumour suppressor gene deletion as a cause of this syndrome. We describe a family characterized by multiple melanoma and neural cell tumours segregating with a germline deletion of the p14(ARF)-specific exon 1beta of the CDKN2A gene. This deletion does not affect the coding or minimal promoter sequences of either the CDKN2A or CDKN2B genes. Our results are consistent with either: (i) loss of p14(ARF) function being the critical abnormality associated with this syndrome, rather than contiguous loss of both the CDKN2A and CDKN2B genes as suggested previously; or (ii) disruption of expression of p16 by mechanisms as yet unknown.

Correlation between human immunodeficiency virus genotypic resistance and virologic response in patients receiving nelfinavir monotherapy or nelfinavir with lamivudine and zidovudine

The relationship between detectable human immunodeficiency virus (HIV) genotypic resistance and virologic response was compared in patients receiving nelfinavir as monotherapy (16 weeks) or in combination with lamuvidine and zidovudine (48 weeks). Two patient groups were defined on the basis of the presence or absence of substitutions associated with nelfinavir, a protease (PR) inhibitor, and/or a reverse transcriptase (RT) inhibitor. HIV RNA levels <50 copies/mL were achieved in 17 (85%) of 20 combination-therapy patients without genotypic resistance (PR-RT(-)) versus only 1 (17%) of 6 patients with genotypic resistance (PR-RT(+)). PR-RT(-) patients exhibited greater and more durable virus suppression compared with PR-RT(+) patients. All 6 PR-RT(+) patients had virus with M184V (lamuvidine resistance); 3 isolates also contained D30N (nelfinavir resistance). M184V preceded D30N in all determinable instances. In this study, suppression of HIV replication to <50 copies/mL was associated with durable response and reduced incidence of resistance. Results also indicate that combination regimens can fail despite the absence of detectable genotypic PR resistance.

Micro-ablation with high power pulsed copper vapor lasers

Visible and UV lasers with nanosecond pulse durations, diffraction-limited beam quality and high pulse repetition rates have demonstrated micro-ablation in a wide variety of materials with sub-micron precision and sub-micron-sized heat-affected zones. The copper vapour laser (CVL) is one of the important industrial lasers for micro-ablation applications. Manufacturing applications for the CVL include orifice drilling in fuel injection components and inkjet printers, micro-milling of micromoulds, via hole drilling in printed circuit boards and silicon machining. Recent advances in higher power (100W visible, 5W UV), diffraction-limited, compact CVLs are opening new possibilities for manufacturing with this class of nanosecond laser.

Genes for human arylamine N-acetyltransferases in relation to loss of the short arm of chromosome 8 in bladder cancer

Polymorphisms of N-acetyltransferase type 2 (NAT2) conferring the slow acetylator phenotype have been linked to increased susceptibility to arylamine-induced bladder cancer in Caucasians. Genes for NAT2, the other NAT isozyme, NAT1, and a NAT pseudogene (NATP) are found on 8p22, a region displaying loss of heterozygosity, particularly in invasive bladder tumours. A restriction enzyme digestion map has defined the relative positions of the NAT genes to each other and to adjacent CpG islands. NAT2, as a polymorphic gene of known function, is a potentially valuable marker for the detection of loss of heterozygosity in 8p22. Two approaches to investigate loss of heterozygosity at the NAT2 locus in bladder tumours have been used. (1) A cosmid containing NAT2 has been used in fluorescence in-situ hybridization on human exfoliated bladder cells collected from unselected bladder cancer outpatients. Loss of signal from the NAT2 cosmid was found in nine of the 20 patients. (2) A panel of 13 human bladder tumours was investigated for loss of heterozygosity using the polymorphism in the NAT2 gene as a marker. Loss of heterozygosity at the NAT2 locus has been compared with loss of heterozygosity at adjacent microsatellite marker sites known to be located on 8p. There is agreement between loss of heterozygosity at the NAT2 locus and adjacent microsatellite marker loci in 11 of the tumours but two of the tumours appear to show retention at the NAT2 locus. More extensive mapping of the region around the NAT loci, particularly on the centromeric side, is important to pinpoint possible tumour suppressor genes or their modifiers in the region. There are no other expressed sequences known in this region and therefore NAT genes are important genetic landmarks.

Genotypic and phenotypic characterization of human immunodeficiency virus type 1 variants isolated from patients treated with the protease inhibitor nelfinavir

Nelfinavir mesylate (formerly AG1343) is a potent and selective inhibitor of human immunodeficiency virus (HIV) protease approved for the treatment of individuals infected with HIV. Nucleotide sequence analysis of protease genes from plasma HIV type 1 (HIV-1) RNA revealed a unique aspartic acid (D)-to-asparagine (N) substitution at residue 30 (D30N) in 25 of 55 patients treated with nelfinavir for a median of 13 weeks. Although the appearance of D30N was occasionally associated with concurrent or sequential emergence of other changes (e.g., at residues 35, 36, 46, 71, 77, and 88), genotypic changes associated with phenotypic resistance to other protease inhibitors were not observed (e.g., at residues 48, 50, 82, and 84) or were only rarely observed (e.g., at residue 90). In phenotypic assays, viral isolates with high-level resistance to nelfinavir remained susceptible to indinavir, saquinavir, ritonavir, and amprenavir (formerly VX-478/141W94). Similar results were observed in phenotypic assays utilizing HIV-1 NL4-3, which contained the D30N substitution alone or in combination with substitutions at other residues (e.g., residues 46, 71, and 88). These data indicate that the initial pathway of resistance to nelfinavir is unique and suggest that individuals failing short courses of nelfinavir-containing regimens may respond to regimens containing other protease inhibitors.

Longitudinal analysis of pulmonary function decline in patients with cystic fibrosis

BACKGROUND

Chronic progressive lung disease is the most prominent cause of morbidity and death in patients with cystic fibrosis (CF), but severity of lung disease and rate of lung function decline are widely variable. Accurate estimates of decline have been difficult to define and compare because the timing of measurements and duration of follow-up differ in various patient groups.

PATIENTS

Three hundred sixty-six patients with CF, born from 1960 to 1974, were selected from a CF database birth cohort if they had two or more measurements of pulmonary function, at least one of which was performed before the age of 10 years.

METHODS

Mixed model regression analysis provided estimates of the average rate of decline of spirometry measurements in subgroups on the basis of survival age, sex, pancreatic status, and genotype.

RESULTS

Patients who died before the age of 15 years had significantly poorer pulmonary function when first tested and a more rapid decline in pulmonary function thereafter than patients who survived beyond the age of 15 years. In the latter, functional levels at the age of 5 years were normal, but average rates of decline were significantly related to survival age. Female patients had significantly steeper decline than male patients, and those with pancreatic insufficiency had much steeper decline than those with pancreatic sufficiency. In the subset of 197 who survived to 1990 and were subsequently genotyped, rate of decline was greater in those homozygous for the delta F508 mutation, compared with those who were heterozygous for delta F508 or those, who had two other mutations.

DISCUSSION

All but the most severely affected patients, who died before age 15, appear to have had normal pulmonary function when first tested in early childhood. Pancreatic sufficiency, male gender, and some non-delta F508 mutations are associated with a slower rate of pulmonary function decline. Mixed model analysis is a valuable tool for describing and comparing pulmonary function decline in groups of patients with CF.

Biological profile of L-745,870, a selective antagonist with high affinity for the dopamine D4 receptor

L-745,870,(3-([4-(4-chlorophenyl)piperazin-1-yl]methyl)-1H- pyrollo[2,3-b] pyridine, was identified as a selective dopamine D4 receptor antagonist with excellent oral bioavailability and brain penetration. L-745,870 displaced specific binding of 0.2 nM [3H] spiperone to cloned human dopamine D4 receptors with a binding affinity (Ki) of 0. 43 nM which was 5- and 20-fold higher than that of the standard antipsychotics haloperidol and clozapine, respectively. L-745,870 exhibited high selectivity for the dopamine D4 receptor (>2000 fold) compared to other dopamine receptor subtypes and had moderate affinity for 5HT2, sigma and alpha adrenergic receptors(IC50 < 300 nM). In vitro, L-745,870 (0.1-1 microM) exhibited D4 receptor antagonist activity, reversing dopamine (1 microM) mediated 1) inhibition of adenylate cyclase in hD4HEK and hD4CHO cells; 2) stimulation of [35S] GTPgammaS binding and 3) stimulation of extracellular acidification rate, but did not exhibit any significant intrinsic activity in these assays. Although standard antipsychotics increase dopamine metabolism or plasma prolactin levels in rodents, L-745,870 (</=30 mg/kg p.o.) had no effect in these assays. The lack of a suitable in vivo assay for D4 receptor activation prompted the use of in vivo surrogate marker assays which confirmed that doses of 5-60 microg/kg L-745,870 would be sufficient to occupy 50% D4 receptors in the brain. These results show that dopamine D4 receptor antagonism in the brain does not result in the same neurochemical consequences (increased dopamine metabolism or hyperprolactinemia) observed with typical neuroleptics.

Proficiency testing of clinical microbiology laboratories using modified decontamination procedures for detection of nontuberculous mycobacteria in sputum samples from cystic fibrosis patients. The Nontuberculous Mycobacteria in Cystic Fibrosis Study Group

An improved decontamination method has been demonstrated to reduce overgrowth of mycobacterial media by Pseudomonas aeruginosa and allow the successful recovery of nontuberculous mycobacteria (NTM) from cystic fibrosis (CF) patients. Twenty microbiology laboratories participating in a multicenter investigation designed to determine the significance of NTM in CF patients were required to demonstrate proficiency in the incorporation of this improved method; this was accomplished by successful decontamination and culture workup of a panel of simulated sputum samples seeded with P. aeruginosa and various NTM. All laboratories successfully recovered NTM from samples with acid-fast bacillus (AFB) smear scores of 3+/4+ (i.e., 2 to 18 or > 18 organisms/field). Low-inoculum samples (1+/2+ AFB smears [2 to 18 organisms in 100 or 10 fields]) were problematic in that processed specimens were often smear and/or culture negative.

Report on the Fifth International Workshop on Chromosome 9 held at Eynsham, Oxfordshire, UK, September 4-6, 1996

The Fifth International workshop on chromosome 9 comprised a gathering of 36 scientists from seven countries and included a fairly even distribution of interests along chromosome 9 as well as a strong input from more global activities and from comparative mapping. At least eight groups had participated in the goal set at the previous workshop which was to improve the fine genetic mapping in different regions of chromosome 9 by meiotic breakpoint mapping in allocated regions and this has resulted in some greatly improved order information. Excellent computing facilities were available and all contributed maps were entered not only into SIGMA (and thence submitted to GDB) but also into a dedicated version of ACEDB which can be accessed on the Web in the form of one of 28 slices into which the chromosome has been arbitrarily divided. It was generally agreed that the amount of data is now overwhelming and that the integration and validation of all data is not only unrealistic in a short meeting but probably impossible until the whole chromosome has been sequenced and fully annotated. Sequence-ready contigs presented at the meeting totalled about 3 MB which is about one fiftieth of the estimated length. The single biggest barrier to integration of maps is the problem of non-standard nomenclature of loci. In the past 2 workshops efforts have been made to compare traditional 'consensus' maps made by human insight (still probably best for small specific regions) with those generated with some computer assistance (such as SIGMA) and those generated objectively by defined computer algorithms such as ldb. Since no single form of map or representation is entirely satisfactory for all purposes the maps reproduced in the published version of the report are confined to one of the genetic maps, in which Genethon and older markers have been incorporated, a Sigma map of the genes as symbols together with a listing of known 'disease' genes on chromosome 9, and a revised assessment of the mouse map together with a list of mouse loci predicted to be on human chromosome 9. One of the 28 ACEDB slices is also shown to illustrate strengths and weaknesses of this approach. Workshop files include not only all maps available at the time but also details of loci and details of the meiotic breakpoints in the CEPH families (http:/(/)www.gene.ucl.ac.uk/scw9db.shtml) .

Allelic loss on chromosomes 8p, 22q and 18q (DCC) in human prostate cancer

Previous studies have suggested the involvement of tumour-suppressor genes on chromosomes 8p, 22q and 18q (DCC) in prostate cancer. The aim of this study was to further characterize these regions. We investigated 20 polymorphic regions on the 3 chromosome arms in 43 cancers and 10 cases of benign prostatic hyperplasia (BPH). Allelic loss was observed in 72% of cancers on 8p, 16% on 22q and 24% at DCC. For BPH, loss was observed in 20% on 8p and in 12% at DCC. The low incidence of LOH on 22q implies that this locus has no significant role in prostate carcinogenesis. At DCC, although the overall incidence was low, tumours with LOH were mostly of high grade or had metastases, suggesting a role for this gene in prostate cancer progression. On chromosome 8p, 29% of cancers had deletions at the LPL locus on 8p22 and 60% had deletions within a region flanked by the markers D8S339 and ANKI on 8p 11.1-p21.1. Within this region, 2 distinct areas of allelic loss were observed, at one or both ANKI and D8S255, and in the region defined by the markers D8S259-D8S505. For the regions 8p22 and ANKI-D8S255, tumours with metastases had a greater frequency of LOH compared to non-metastasizing tumours, suggesting the presence of putative metastasis-suppressor genes in these regions.