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PDF file, 86K, Clinico-pathological characteristics, mutation status and FGA in 160 UC.

PDF file, 114K.

PDF file, 123K, Copy number (CN), mutation status (MS), loss of heterozygosity analysis (LOH) and immunohistochemistry (IHC) data for all tumors (n=160).

Purpose: The phosphatidylinositol 3-kinase (PI3K) pathway can be activated by alterations affecting several pathway components. For rational application of targeted therapies, detailed understanding of tumor biology and approaches to predict efficacy in individual tumors are required. Our aim was to assess the frequency and distribution of pathway alterations in bladder cancer.Experimental Design: We examined the pathway components (PIK3CA, PTEN, TSC1, RHEB, and LKB1) and putative upstream regulators (FGFR3 and RAS genes) for mutation, allelic loss, copy number alteration, and expression in bladder tumors and cell lines.Results: No mutations were found in RHEB and only a single mutation in LKB1. PIK3CA mutations were detected in 25% of tumors and 26% of cell lines with a significant excess of helical domain mutations (E542K and E545K). There was over-representation but not amplification of the gene. Loss of heterozygosity of the PTEN region and homozygous deletion were found in 12% and 1.4% of tumors, and reduced expression in 49%. Forty-six percent of cell lines showed alterations that implicated PTEN. Sixteen percent of tumors and 11% of cell lines showed TSC1 mutation, and 9q loss of heterozygosity was common (57%). Pathway alterations were independently distributed, suggesting that the mutation of two pathway members may have additive or synergistic effects through noncanonical functions.Conclusions: PI3K pathway alterations are common in bladder cancer. The lack of redundancy of alterations suggests that single-agent PI3K-targeted therapy may not be successful in these cancers. This study provides a well-characterized series of cell lines for use in preclinical studies of targeted agents. (Clin Cancer Res 2009;15(19):6008–17)

PDF file, 59K, Relationship between copy number gains and losses and individual Ta, T1G3 and ≥T2 clusters.

Purpose: There is a need for improved subclassification of urothelial carcinoma (UC) at diagnosis. A major aim of this study was to search for novel genomic subgroups.Experimental design: We assessed 160 tumors for genome-wide copy number alterations and mutation in genes implicated in UC. These comprised all tumor grades and stages and included 49 high-grade stage T1 (T1G3) tumors.Results: Our findings point to the existence of genomic subclasses of the “gold-standard” grade/stage groups. The T1G3 tumors separated into 3 major subgroups that differed with respect to the type and number of copy number events and to FGFR3 and TP53 mutation status. We also identified novel regions of copy number alteration, uncovered relationships between molecular events, and elucidated relationships between molecular events and clinico-pathologic features. FGFR3 mutant tumors were more chromosomally stable than their wild-type counterparts and a mutually exclusive relationship between FGFR3 mutation and overrepresentation of 8q was observed in non-muscle-invasive tumors. In muscle-invasive (MI) tumors, metastasis was positively associated with losses of regions on 10q (including PTEN), 16q and 22q, and gains on 10p, 11q, 12p, 19p, and 19q. Concomitant copy number alterations positively associated with TP53 mutation in MI tumors were losses on 16p, 2q, 4q, 11p, 10q, 13q, 14q, 16q, and 19p, and gains on 1p, 8q, 10q, and 12q. Significant complexity was revealed in events affecting chromosome 9.Conclusions: These findings may lead to improved biologic understanding and the development of prognostic biomarkers. Novel regions of copy number alteration may reveal potential therapeutic targets. Clin Cancer Res; 18(21); 5865–77. ©2012 AACR.

PDF file, 507K, Relationship between PTEN loss, RB1 loss and TP53 mutation status and time to metastasis.

PDF file, 3635K, Unsupervised hierarchical cluster analysis of aCGH data from all tumor samples and genome-wide frequency plots of copy number alterations in individual ≥T2 clusters.

PDF file, 902K, Loss and gain in tumors from individual Ta, T1 and ≥T2 clusters.

PDF file, 44K, TP53 and FGFR3 mutation in all Ta tumors, and tumors from individual T1G3 and ≥T2 clusters.

PDF file, 1713K, Fraction of genome altered (FGA%).

Supplementary Data from Spectrum of Phosphatidylinositol 3-Kinase Pathway Gene Alterations in Bladder Cancer

Supplementary Figures 1-2 from MRE11 Expression Is Predictive of Cause-Specific Survival following Radical Radiotherapy for Muscle-Invasive Bladder Cancer

Radical radiotherapy and surgery achieve similar cure rates in muscle-invasive bladder cancer, but the choice of which treatment would be most beneficial cannot currently be predicted for individual patients. The primary aim of this study was to assess whether expression of any of a panel of DNA damage signaling proteins in tumor samples taken before irradiation could be used as a predictive marker of radiotherapy response, or rather was prognostic. Protein expression of MRE11, RAD50, NBS1, ATM, and H2AX was studied by immunohistochemistry in pretreatment tumor specimens from two cohorts of bladder cancer patients (validation cohort prospectively acquired) treated with radical radiotherapy and one cohort of cystectomy patients. In the radiotherapy test cohort (n = 86), low tumor MRE11 expression was associated with worse cancer-specific survival compared with high expression [43.1% versus 68.7% 3-year cause-specific survival (CSS), P = 0.012] by Kaplan-Meier analysis. This was confirmed in the radiotherapy validation cohort (n = 93; 43.0% versus 71.2%, P = 0.020). However, in the cystectomy cohort (n = 88), MRE11 expression was not associated with cancer-specific survival, commensurate with MRE11 being a predictive marker. High MRE11 expression in the combined radiotherapy cohort had a significantly better cancer-specific survival compared with the high-expression cystectomy cohort (69.9% versus 53.8% 3-year CSS, P = 0.021). In this validated immunohistochemistry study, MRE11 protein expression was shown and confirmed as a predictive factor associated with survival following bladder cancer radiotherapy, justifying its inclusion in subsequent trial designs. MRE11 expression may ultimately allow patient selection for radiotherapy or cystectomy, thus improving overall cure rates. Cancer Res; 70(18); 7017–26. ©2010 AACR.

Multiple myeloma (MM) shows constitutive activation of canonical and non-canonical nuclear factor-ĸB (NF-ĸB) signaling through genetic mutations or stimuli from the tumour microenvironment (TME). A subset of MM cell lines showed dependency for cell growth and survival on the canonical NF-ĸB transcription factor RELA alone, suggesting a critical role for a RELA-mediated biological program in MM pathogenesis. Here, we determined the RELA-dependent transcriptional program in MM cell lines and found the expression of the cell surface molecules IL-27 receptor-α (IL-27Rα) and the adhesion molecule JAM2 to be responsive to RELA at the mRNA and protein levels. IL-27Rα and JAM2 were expressed on primary MM cells at higher levels than on normal long-lived plasma cells (PCs) in the bone marrow. IL-27 activated STAT1, and to a lesser extent STAT3, in MM cell lines and in PCs generated from memory B-cells in an IL-21-dependent in vitro PC-differentiation assay. Concomitant activity of IL-21 and IL-27 enhanced differentiation into PCs and increased cell-surface expression of the known STAT target gene CD38. In accordance, a subset of MM cell lines and primary MM cells cultured with IL-27 upregulated CD38 cell-surface expression, a finding with potential implications for enhancing the efficacy of CD38-directed monoclonal antibody (mAb) therapies by increasing CD38-expression on tumour cells. The elevated expression of IL-27Rα and JAM2 on MM cells compared to normal PCs may be exploited for the development of targeted therapeutic strategies that modulate the interaction of MM cells with the TME.

In the petrochemical industry, control room operators must address safety-critical alarms and other tasks using complex interfaces. This study developed a guide for assessing human performance using standard human factors measurement tools, and tested the sensitivity of those tools with two interface designs (i.e., gray and black) at three levels of workload (i.e., easy, medium, and difficult). The guide measures human performance through speed and accuracy, perceived workload using two standard instruments (i.e., NASA Task Load Index (NASA-TLX) and Subjective Workload Assessment Technique (SWAT)), situation awareness through the Situation Awareness Global Assessment Technique (SAGAT), and gaze through eye tracking coordinates. Twelve engineering student participants completed one simulation session at each of the three workload levels using one of two interface designs. Workload was manipulated through the number of simulated events (failures) in each session. Overall, the speed and accuracy measures, workload ratings, and eye tracking showed sensitivity to differences in workload level, and situation awareness showed sensitivity to the interaction between workload level and interface type. None of the tools were sensitive to interface type alone. Accuracy was highest under easy workload. Time per failure decreased at higher workload levels. Perceived workload ratings from the SWAT increased as workload increased, but workload ratings from the NASA-TLX were not different across workload levels. When workload increased, situation awareness remained steady for the gray interface but decreased sharply for the black interface, illustrating an interaction effect. Finally, the percentage of time spent looking at different areas of the screen during steady-state periods differed among workload levels. The tools in this guide can be used in the petrochemical industry to make design decisions for control room interfaces when workload levels are a concern.

Within the work–family literature little is known about the work–family challenges and opportunities faced by families that have one or more children with autism spectrum disorder. However, it has been consistently demonstrated that parents of children with autism spectrum disorder are at a higher risk of experiencing a host of negative outcomes. Using a qualitative design, within grounded theory, the present study sheds light on the needs, experiences, and challenges that parents of children with autism spectrum disorder face and also offers insight into ways to expand the scope of work–family research in this area. The present research provides evidence of how the family domain can greatly impact experiences and decisions made in the work domain for families with special needs. The present research adds to the small but growing literature examining the interplay between home and work life for families with special needs and demonstrates that this is an important research domain in need of additional conceptual and empirical consideration.

Submitted by Vitor Silverio Rodrigues (vitorsrodrigues@reitoria.unesp.br) on 2014-05-27T11:22:37Z No. of bitstreams: 0Bitstream added on 2014-05-27T14:33:38Z : No. of bitstreams: 1 2-s2.0-35349019691.pdf: 4144234 bytes, checksum: 9b86846640bd2e66375c65e289357bd0 (MD5) Made available in DSpace on 2014-05-27T11:22:37Z (GMT). No. of bitstreams: 0 Previous issue date: 2007-10-24 Aicardi-Goutières syndrome (AGS) is a genetic encephalopathy whose clinical features mimic those of acquired in utero viral infection. AGS exhibits locus heterogeneity, with mutations identified in genes encoding the 3′→5′ exonuclease TREX1 and the three subunits of the RNASEH2 endonuclease complex. To define the molecular spectrum of AGS, we performed mutation screening in patients, from 127 pedigrees, with a clinical diagnosis of the disease. Biallelic mutations in TREX1, RNASEH2A, RNASEH2B, and RNASEH2C were observed in 31, 3, 47, and 18 families, respectively. In five families, we identified an RNASEH2A or RNASEH2B mutation on one allele only. In one child, the disease occurred because of a de novo heterozygous TREX1 mutation. In 22 families, no mutations were found. Null mutations were common in TREX1, although a specific missense mutation was observed frequently in patients from northern Europe. Almost all mutations in RNASEH2A, RNASEH2B, and RNASEH2C were missense. We identified an RNASEH2C founder mutation in 13 Pakistani families. We also collected clinical data from 123 mutation-positive patients. Two clinical presentations could be delineated: an early-onset neonatal form, highly reminiscent of congenital infection seen particularly with TREX1 mutations, and a later-onset presentation, sometimes occurring after several months of normal development and occasionally associated with remarkably preserved neurological function, most frequently due to RNASEH2B mutations. Mortality was correlated with genotype; 34.3% of patients with TREX1, RNASEH2A, and RNASEH2C mutations versus 8.0% RNASEH2B mutation-positive patients were known to have died (P = .001). Our analysis defines the phenotypic spectrum of AGS and suggests a coherent mutation-screening strategy in this heterogeneous disorder. Additionally, our data indicate that at least one further AGS-causing gene remains to be identified. © 2007 by The American Society of Human Genetics. All rights reserved. Leeds Institute of Molecular Medicine, Leeds DNA Laboratory Department of Clinical Genetics St. James's University Hospital, Leeds Cancer Research UK Mutation Detection Facility, Leeds Department of Paediatric Neurology Leeds General Infirmary, Leeds Department of Paediatric Neurology Erasme Hospital, Brussels Children's Hospital Queen Fabiola, Brussels Service de Neuropédiatrie Hôpital Trousseau Department of Paediatric Neurology Hôpital Trousseau Pediatric Neurology Department Hôpital Bicêtre Institut de Myologie Groupe Hospitalier Pitié-Salpêtrière Service de Virologie Hôpital Cochin-St. Vincent de Paul, Paris Department of Clinical Biochemistry Hospital Sant Joan de Déu-Ciberer, Barcelona Department of Barcelona Pediatric Neurology Hospital Sant Joan de Déu-Ciberer, Barcelona Department of Paediatrics St. Luke's Hospital, Guardamangia Department of Molecular and Human Genetics Baylor College of Medicine, Houston Serive de Neurologie Centre Hospitalier, Pau Department of Paediatrics Children's Hospital, Sheffield Developmental and Metabolic Neurology Branch National Institute of Neurological Disorders and Stroke National Institutes of Health, Bethesda Department of Human Genetics Rheinisch-Westfälische Technische Hochschule Aachen University, Aachen Unit of Molecular Medicine Bambino Gesù Children's Research Hospital, Rome Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS) Casa Sollievo Della Sofferenza Mendel Institute, Rome Muscular and Neurodegenerative Disease Unit G. Gaslini Institute, Genova Department of Clinical Genetics Churchill Hospital, Oxford Division of Clinical Chemistry and Biochemistry University Children's Hospital, Zurich Clinical Genetics Unit Birmingham Women's Hospital, Birmingham Department of Paediatrics Sandwell and West Birmingham NHS Trust, Birmingham Neurology Department Birmingham Children's Hospital, Birmingham Department of Human Genetics Radboud University, Nijmegen Department of Pediatric Neurology Radboud University, Nijmegen Department of Paediatric Neurology Royal Children's Hospital, Brisbane, QLD Genetic Health Queensland Royal Children's Hospital, Brisbane, QLD Serviço de Aconselhamento Genético Universidade Estadual de São Paulo, Botucatu Academic Unit of Medical Genetics St. Mary's Hospital, Manchester Kinderkrankenhaus Auf der Bult, Hannover Department of Paediatrics Bradford National Health Service (NHS) Trust, Bradford Developmental Neurology Department Fondazione Istituto Neurologico C. Besta, Milan Grampian Clinical Genetics Centre, Aberdeen Department of Neonatology University Hospital, Ghent Department of Pediatrics University Hospital, Ghent Department of Clinical Genetics Maastricht University Hospital, Maastricht Department of Neurology Maastricht University Hospital, Maastricht Department of Paediatrics and Imaging Sciences Imperial College Great Ormond Street Hospital, London St. Mary's NHS Trust Great Ormond Street Hospital, London Department of Ophthalmology Great Ormond Street Hospital, London North East Thames Regional Genetics Service Great Ormond Street Hospital, London Evelina Children's Hospital Guy's and St. Thomas' NHS Trust, London Department of Paediatrics Université Laval Medical School, Québec Clinical Genetics Unit Hospital de Cruces, Baracaldo Service de Génétique Médicale Centre Hospitalier Universitaire Pellegrin Enfants, Bordeaux Unité de Neurologie de l'Enfant et de l'Adolescent Centre Hospitalier Universitaire Pellegrin Enfants, Bordeaux National Centre for Medical Genetics Our Lady's Hospital, Dublin Department of Paediatric Neurology Children's University Hospital, Dublin Department of Medical Genetics Rikshospitalet-Radiumhospitalet, Oslo Department of Paediatrics Rikshospitalet-Radiumhospitalet, Oslo Rikshospitalet-Radiumhospitalet, Oslo Department of Pediatrics Academic Medical Center, Amsterdam Department of Child Neurology Vrije Universiteit Medical Center, Amsterdam Medical Research Council Human Genetics Unit Western General Hospital, Edinburgh Department of Clinical Genetics Leiden University Medical Center, Leiden Division of Pediatric Neurology Oregon Health and Science University, Portland, OR Pediatric Neurology Klinikum Aschaffenburg, Aschaffenburg Department of Neurology Royal Children's Hospital, Parkville, Vic. Division of Clinical Genetics Department for Medical Genetics Medical University Innsbruck, Innsbruck Department of Pediatrics Division of Pediatric Neurology and Inborn Errors of Metabolism Children's Hospital Innsbruck, Innsbruck Klinik für Kinder und Jugendliche, Konstanz Paediatric Neurology University Hospitals of Gasthuisberg, Leuven Department of Child Neurology and Psychiatry IRCCS Casimiro Mondino Institute of Neurology, Pavia Department of Neurogenetics School of Medicine of Ribeirao Preto, Ribeirao Preto Greenwood Genetic Center, Greenwood, SC Raphael Recanati Genetic Institute Rabin Medical Center, Petach-Tikva Department of Paediatrics Crosshouse Hospital, Ayr Fraser of Allander Neurosciences Unit Royal Hospital for Sick Children, Glasgow Duncan Guthrie Institute of Medical Genetics Royal Hospital for Sick Children, Glasgow Division of Medical Genetics Montreal Children's Hospital, Montreal Department of Paediatric Neurology University Hospitals of Leicester NHS Trust, Leicester University Hospital of Aarhus, Aarhus Division of Pediatric Dermatology British Columbia's Children's Hospital, Vancouver, BC Institut de Pathologie et de Génétique, Gosselies Pediatric Neurology Department Guide Chauliac Hospital, Montpellier Servicio de Pediatría Hospital Universitario Doctor Peset, Valencia Genetic Institute Ha'Emek Medical Center, Afula Rappaport Faculty of Medicine Technion, Haifa Neuropediatrics Unit Complejo Hospitalario de Jean, Jean Department of Paediatrics Manor Hospital, Walsall Division of Neuropediatrics University Hospital, Freiburg Genetic Health Services Victoria Royal Children's Hospital, Vic. Service de Génétique Hôpital Debrousse, Lyon Lancashire Teaching Hospitals Trust, Preston Neonatal Intensive Care Unit Arcispedale Santa Maria Nuova, Reggio Emilia Center for Medical Genetics, Antwerp Department of Neurology Children's National Medical Center, Washington, DC Department of Neuropediatrics Humboldt University, Berlin Leeds Institute of Molecular Medicine St. James's University Hospital Wellcome Trust Brenner Building, Leeds LS9 7TF Serviço de Aconselhamento Genético Universidade Estadual de São Paulo, Botucatu

Detection of DNA sequence variation is fundamental to the identification of the genomic basis of phenotypic variability. Denaturing high-performance liquid chromatography (DHPLC) is a novel technique that has been used to detect mutations in human DNA. We report on the first study to use this technique as a tool to detect mutations in genes encoding antibiotic resistance in bacteria. Three methicillin-sensitive and three methicillin-resistant clinical Staphylococcus aureus isolates, susceptible to ciprofloxacin (MICor= 0.4 mg/L), were used to derive mutants resistant to ciprofloxacin, levofloxacin, sparfloxacin, trovafloxacin and moxifloxacin. Genomic DNA from each strain was subjected to PCR amplification of 225-500 bp regions spanning the quinolone resistance determining regions of the gyrA, gyrB, grlA and grlB genes. Following DNA sequencing of these amplicons and identification of resistance mutations, DHPLC was undertaken to correlate the distinctive chromatogram with DNA sequence. The mutations detected by DHPLC resulted in the following amino acid substitutions: Ser-84--Leu, Ser-112--Pro, Glu-88--Lys in GyrA, Glu-84--Val, Ser-80--Phe in GrlA, Pro-456--Ser in GyrB and Glu-422--Asp, Pro-451--Ser, Asp-432--Gly in GrlB. Mutations could be rapidly and reproducibly identified from the PCR products using DHPLC, producing specific peak patterns that correlate with genotypes. This system facilitates the detection of resistance alleles, providing a rapid (5 min per sample), economic (96 sample per run) and reliable technique for characterizing antibiotic resistance in bacteria.

Gallstone spillage is recognised as a possible complication of laparoscopic cholecystectomy and there are countless examples of untoward short and long term sequelae resulting from their non-retrieval. We present the case of a 65-year-old gentleman with sterile pyuria and lower midline abdominal mass which proved to be a complex gallstone inflammatory mass related to the dome of the bladder. This patient’s investigative course was exhaustive and the definitive diagnosis not achieved until histopathological assessment of the intraoperative specimen. The diagnosis of these lower abdominal wall masses can be difficult, particularly with complex lesions.

Loss of heterozygosity (LOH) of chromosome arm 4p is a common event in bladder and other malignancies. At least three distinct regions of deletion have been identified, but the deletion targets have so far remained elusive. In this study, we have identified a novel region of deletion mapping to 4p16.3 spanning 0-2.1 Mb, in 15% of bladder tumors and 24% of bladder cancer cell lines. FGFRL1, which maps within this region, was investigated as putative deletion target. The retained FGFRL1 allele was not mutated in cell lines and tumors with LOH, although in patients heterozygous for the rs4647930 functional polymorphism, the common allele was preferentially lost in tumor tissue. Epigenetic silencing of the retained allele was also excluded as levels of FGFRL1 mRNA and protein were similar in cell lines and tumors with and without 4p16.3 loss. However, while FGFRL1 protein was moderately expressed in all layers of the normal bladder epithelium, the majority of tumors showed areas of downregulation. Overall, average FGFRL1 protein expression was significantly lower in bladder tumors compared to normal tissue, but downregulation was independent from 4p16.3 LOH status, FGFR3 mutation, and tumor grade and stage. In conclusion, although we found no evidence supporting a "two-hit" inactivation of FGFRL1 in bladder carcinogenesis, the effect of heterozygous deletion coupled with functional polymorphisms, and the role of post-transcriptional downregulation deserves further investigation.

A rapid, highly-specific ELISA for tyrosine kinases readily detects such activity in crude extracts prepared from rat mammary epithelial and fibroblastic cells that have been stimulated with epidermal growth factor or basic fibroblast growth factor. Tyrosine kinase activity is also found in extracts of pupae of the cotton leafworm, Spodoptera littoralis. Both the mammalian and the insect tyrosine kinases are ATP-dependent. Both cytosol and membrane-associated (Triton-X-100-soluble) fractions of Spodoptera littoralis pupae contain tyrosine kinase activity. The growth factor-stimulated tyrosine kinase activities in extracts of growth factor-stimulated rat mammary cells are inhibited by genistein and an analogue of erbstatin: methyl 2,5-dihydroxycinnamate. However, the tyrosine kinase activities present in pupae of Spodoptera littoralis are not sensitive to these inhibitors, suggesting that the major tyrosine kinases of Spodoptera littoralis pupae may be distinct from the growth factor-stimulated mammalian tyrosine kinases.

The ability of anti-T cell monoclonal antibody G4.18 and polyclonal anti-lymphocyte serum (ALS) to induce long-term graft survival was examined in a high-responder rat heart transplant model. Heterotopic heart allografts were performed from PVG rat strain donors to high-responder Lewis recipients. Immunosuppressive properties of G4.18 and ALS were investigated by immunohistochemistry and PCR analysis. Untreated graft rejection was 8.5 days while treatment with 1 ml ALS prolonged survival to 11.5 days (p = 0.01). Treatment with 7 mg/kg G4.18 on days 1 and 3 prolonged survival to > 100 days (p = 0.002 vs. control and p = 0.002 vs. ALS) but did not induce tolerance. Acceptance was associated with marked inhibition of cellular infiltration and inflammatory cytokine expression and only a brief, slight increase in Foxp3:T cell ratio in the graft and no increase in the spleen. In conclusion, G4.18 treatment led to long-term heart transplant survival associated with marked inhibition of early inflammation. Failure to develop tolerance was associated with a lack of early accumulation of Foxp3 cells in the graft or spleen.