• Abnormal gene expression can be linked to chromosomal gains and losses in paediatric astrocytoma

      Potter, N.; Poh, R.; Ward, Samantha; Phipps, Kim; Hayward, Richard; Harkness, William; Thompson, Dominic; Thomas, David G.; Rees, J.; Darling, John L.; Warr, Tracy (Society for Neuro-Oncology and Duke University Press, 2006)
      Brain tumors are the most frequently found solid tumor in children, 40% of which are astrocytomas. These are graded according to the WHO classification into the more common low-grade (I and II) and high-grade (III and IV) tumors. Little is known about the genetic basis underlying the development of pediatric astrocytomas. In this study, we have studied the correlation between abnormal gene expression in pediatric astrocytoma with genomic copy number changes. We used the Affymetrix HGU133A array to identify differentially expressed genes in a group of pediatric astrocytoma short-term cell cultures comprising 9 grade I, 11 grade II and 12 grade IV tumors. Data analysis was carried out using Genespring version 6.0 software. In addition, we used the Spectral Chip 2600 to generate array-comparative genomic hybridization (aCGH) profiles of each short-term cell culture. Chromosome regions of gain and loss were then compared with differential gene expression using Formatter software. Hierarchical clustering of the short-term cultures according to expression profile similarity showed that the tumors clustered into 3 clear groups that were independent of grade. Two groups were predominantly low-grade tumors, comprised of a mixture of grade I and II tumors with 3 grade IV tumors, and the third group contained predominantly high-grade tumors with 2 low-grade tumors. Genes involved in the phosphatidylinositol signaling system, the cell cycle pathway, and the regulation of the actin cytoskeleton, were significantly differentially expressed between the 3 groups. Differential disruption of these cell pathways may be associated with subtypes of pediatric astrocytoma. Most tumors in the third group (including the low-grade tumors) showed copy number changes that can be correlated with changes in gene expression. In specific tumors, the downregulation of TSB1 (thrombospondin-1) correlated with loss at 15q15. This gene has previously been found to be downregulated in astrocytoma and is involved in cell adhesion. This finding suggests that gene expression in a subset of pediatric astrocytomas is influenced by gene dosage.
    • Adenovirus vector-mediated delivery of the prodrug-converting enzyme carboxypeptidase G2 in a secreted or GPI-anchored form: High-level expression of this active conditional cytotoxic enzyme at the plasma membrane.

      Cowen, Rachel L.; Williams, Judith C.; Emery, Steve; Blakey, David; Darling, John L.; Lowenstein, Pedro R.; Castro, Maria G. (nature.com, 2002)
      Carboxypeptidase G2 (CPG2) is a powerful prodrug-converting enzyme. Without a requirement for endogenous enzymes or cofactors, it can directly activate mustard alkylating prodrugs to cytotoxic species, killing both quiescent and dividing cells. This paper provides the first report of its use in the context of a clinically relevant delivery vehicle using adenovirus vectors. To strengthen the efficacy of the prodrug-activating system, the enzyme has been engineered to be secreted or glycosylphosphatidylinositol (GPI) anchored to the extracellular membrane of tumor cells, resulting in an enhanced bystander effect by facilitating diffusion of the active drug through extracellular, rather than intracellular, activation. Using the vectors, we have achieved expression of functional secreted or GPI-anchored CPG2 in a panel of tumor cell lines demonstrating no loss in efficacy as a result of GPI anchor retention. Despite variable transduction efficiencies inherent to these vectors, greater than 50% cell kill was achievable in all of the cell lines tested following only a single exposure to the prodrug ZD2767P. Even in cell lines refractive to infection with the vectors, substantial cell death was recorded, indicative of the enhanced bystander effect generated following extracellular prodrug activation. A direct evaluation of the efficacy of our system has been made against adenoviral delivery of herpes simples virus thymidine kinase plus ganciclovir (GCV), a suicide gene therapy approach already in the clinic. In a short-term human glioma culture (IN1760) resistant to the clinical chemotherapeutic drug CCNU (1-(2-chloroethyl)-3-cyclohexyl-1-nitrosourea), thymidine kinase/GCV effected no cell killing compared to 70% cell killing with our system.
    • Adenovirus-mediated expression of HSV1-TK or Fas ligand induces cell death in primary human glioma-derived cell cultures that are resistant to the chemotherapeutic agent CCNU.

      Maleniak, Tricia C.; Darling, John L.; Lowenstein, Pedro R.; Castro, Maria G. (Nature Publishing Group, 2001)
      Due to minimal treatment success with surgery, radiotherapy, and chemotherapy, the aim of this study was to test the therapeutic potential of gene therapy for the treatment of glioblastoma multiforme (GBM). We have quantitatively analyzed two gene therapy approaches using short-term human glioma cell cultures derived from surgical biopsies (designated IN859, IN1612, IN2045, IN1760, and IN1265) and compared the results of gene therapy with the chemosensitivity of the same cells. All of the glioma cell cultures tested were susceptible to recombinant adenovirus (RAd)-mediated infection. Expression of herpes simplex virus type 1-thymidine kinase (RAd128), followed by ganciclovir treatment, induced apoptosis in all of the glioma cell cultures studied, including three that are resistant to the chemotherapeutic drug 1-(2-chloroethyl)-3-cyclohexyl-1-nitrosourea (CCNU). Expression of murine Fas ligand (RAdhCMV-mFasL) also induced cell death in four of the five cell cultures studied. One cell culture that was resistant to CCNU was also resistant to apoptosis induced by mFasL expression. These results suggest that sensitivity to chemotherapeutic agents does not necessarily correlate with the sensitivity to gene therapy treatments. RAds expressing therapeutic gene products in human glioma cell cultures are able to induce apoptosis even in some cells that are resistant to a commonly used chemotherapeutic agent. Therefore, RAd-mediated gene transfer could be a good candidate to further develop gene therapy for the treatment of GBM.
    • Apoptosis of malignant cells in Hodgkin's disease is related to expression of the cdk inhibitor p27KIP1.

      Kolar, Zdenek; Flavell, Joanne R.; Ehrmann, Jiri; Rihakova, Petra; Macak, Jirka; Lowe, Derek; Crocker, John; Vojtesek, Borivoj; Young, Lawrence S.; Murray, Paul G. (John Wiley And Sons, 2000)
      Previous results from B-cell chronic lymphocytic leukaemia suggest that expression of p27KIP1 might be important in protection from apoptosis. Given the relevance of apoptosis to the pathogenesis of Hodgkin's disease (HD), it was decided to examine the expression of p27KIP1 in relation to apoptosis in these lesions. Paraffin-wax sections from a total of 65 histologically confirmed HD tumours were used to derive apoptotic index (AI) and DNA fragmentation index (DFI) scores, which were compared with the expression of various cell-cycle-regulating proteins, including p27KIP1 (p27), p21WAF1/CIP1 (p21) and cyclin D1, and with Epstein-Barr virus (EBV) status. The DFI was measured by TdT-mediated dUTP-FITC nick end-labelling (TUNEL), and the AI by conventional morphology. Cells showing the typical morphology of apoptosis, together with those resembling so-called 'mummified' Hodgkin/Reed-Sternberg (HRS) cells, were included in AI measurements. Increasing numbers of p27-positive HRS cells were associated with lower levels of apoptosis in these cells, as indicated by significantly lower AI and DFI scores. There was a trend towards poorer survival in those patients with the highest numbers of p27-positive HRS cells and with lower AI and DFI scores, but these differences were not statistically significant. p21-positive HRS cells were significantly more frequent in those cases with lower AI scores. A similar trend was observed for p21 and DFI, although this relationship was not statistically significant. There was also a trend towards higher levels of cyclin D1 protein in HD cases with high AI and DFI values. A tendency for increasing numbers of p27-positive and p21-positive HRS cells in EBV-positive cases was noted, but this relationship was not statistically significant. EBV status did not correlate with either AI or DFI scores. The results of this study suggest that p27, and possibly also p21, may be involved in protection from apoptosis in HD.
    • The Aspergillus nidulans stress response transcription factor StzA is ascomycete-specific and shows species-specific polymorphisms in the C-terminal region.

      Chilton, Ian J.; Delaney, C. E,; Barham-Morris, J.; Fincham, Daron A.; Hooley, Paul; Whitehead, Michael P. (Elsevier, 2008)
      Orthologues of the Aspergillus nidulans gene stzA were identified and characterised in an additional 19 fungi. These orthologues were restricted to, and found within all the Pezizomycotina subphyla of the Ascomycota, for which data are available, but not the Saccharomycotina or Taphrinomycotina subphyla. Intron analysis indicated that both intron loss and gain have occurred in this gene. The orthologous proteins demonstrate considerable size variation (between 663 and 897 amino acids); with almost all this variability accounted for by a hyper-variable region that is carboxy terminal to the zinc finger region. The Hypocrea jecorina orthologue (ACE1) has the binding site 5'AGGCA. There is evidence of competition, or interaction, between the ACE1/StzA and AreA binding sites in promoters of stzA and its orthologues, as well as genes involved in the metabolism of amino acids. The A. nidulans and A. fumigatus cpcA promoters have seven potential ACE1/StzA binding sites, six of which are highly conserved in position. Two very closely positioned sites are conserved across 14 of the 19 fungi analysed. Potential CpcA binding sites (5'TGAC/GTCA) have been identified between -50 and -170bp of the ATG start in the promoters of 16 of the stzA orthologues.
    • Aspirin and alterations in DNA repair proteins in the SW480 colorectal cancer cell line.

      Dibra, H. K.; Brown, J. E.; Hooley, Paul; Nicholl, I. D. (Spandios Publications, 2010)
      Regular aspirin intake is associated with a reduction in the incidence of colorectal cancer. Aspirin has been shown to be cytotoxic to colorectal cancer cells in vitro. The molecular basis for this cytotoxicity is controversial, with a number of competing hypotheses in circulation. One suggestion is that the protective effect is related to the induction of expression of the DNA mismatch repair (MMR) proteins hMLH1, hMSH2, hMSH6 and hPMS2 in DNA MMR proficient cells. We report that treatment of the DNA MMR competent/p53 mutant colorectal cancer cell line SW480 with 1 mM aspirin for 48 h caused changes in mRNA expression of several key genes involved in DNA damage signalling pathways, including a significant down-regulation in transcription of the genes ATR, BRCA1 and MAPK12. Increases in the transcription of XRCC3 and GADD45alpha genes are also reported. Regulation of these genes could potentially have profound effects on colorectal cancer cells and may play a role in the observed chemo-protective effect of aspirin in vivo. Although a correlation was not seen between transcript and protein levels of ATR, BRCA1 and GADD45alpha, an increase in XRCC3 encoded protein expression upon aspirin treatment in SW480 cells was observed by immunoblotting, immunofluorescence and immunohistochemical analysis. This is the first report of XRCC3 gene transcription and encoded protein expression being susceptible to exposure to the non-steroidal anti-inflammatory drug, aspirin. Furthermore, this study indicates that alterations in gene transcription seen in microarray studies must be verified at the protein level.
    • Assigning Level in Data-mining Exercises

      Hooley, Paul; Chilton, Ian J.; Fincham, Daron A.; Burns, Alan T. H.; Whitehead, Michael P. (Centre for Bioscience, the Higher Education Academy, 2007)
      There is currently much interest in ascribing outcomes to Masters (M) level programmes. It is particularly difficult to define M level outcomes in bioinformatics for students on non-specialist programmes. An approach is described that attempts to discriminate undergraduate from M level in a data-mining exercise. Differentiation of level is based upon the taxonomic origin of a DNA sequence, the relative increase in gene complexity from lower to higher eukaryote and the initiative required to use a wider range of databases and analytical tools.
    • Bovine enterovirus as an oncolytic virus: foetal calf serum facilitates its infection of human cells.

      Smyth, M.S.; Symonds, A.; Brazinova, S.; Martin, Jan H. (University of Crete, 2002)
      Many viruses have been investigated for their oncolytic properties and potential use as therapeutic agents for cancer treatment. Most of these replication-competent viruses are human pathogens. We investigated the oncolytic properties of an animal virus which is non pathogenic for both its natural host and humans. Bovine enterovirus has previously been shown to exhibit a very wide tissue tropism for cell types in vitro. We compare the ability of bovine enterovirus to replicate in and to cause cytopathic effect in freshly isolated human monocytes and monocyte derived macrophages with the monocyte-like U937 tumour cell line. We also include the adherent ZR-75-1 human breast cancer cell line. We have also carried out infections of bovine enterovirus in the presence and in the absence of serum of bovine origin. Our study shows that the virus will replicate in and produce cytopathic effect in the U937 and ZR-75-1 cell types to the same extent as the cells (BHK-21) in which the virus is routinely propagated. We believe bovine enterovirus to be a worthwhile candidate for further study as an anti-tumour agent.
    • Changes in growth and gene expression induced by sulphur deficiency in garlic

      Wei, Wenxue; Bilsborrow, Paul E.; Hooley, Paul; Bibi, H. (Taylor & Francis, 2002)
      Sulfur deficiency in garlic Allium sativum L. caused a reduction in growth together with chlorosis and necrosis of leaves. Large differences in shoot sulfur and sulphate concentrations between deficient and high sulfur treatments were only observed after 54 days growth. Using the mRNA differential display technique, a novel cDNA was isolated from shoots grown in sulfur depleted nutrient solution for 24 days. This novel cDNA was constitutively expressed in the shoots during further growth in sulfur depleted solution, but it was undetectable following 30 days recovery with sulfur supplementation. The cDNA sequence demonstrated a high degree of identity with a coat protein gene of a garlic latent carlavirus. The results suggest a possible relationship between low plant sulfur status and the induction of a latent carlavirus in garlic.
    • Cloning of a novel gene encoding a C2H2 zinc finger protein that alleviates sensitivity to abiotic stresses in Aspergillus nidulans

      O'Neil, John D.; Bugno, Marcin; Stanley, Michele S.; Barham-Morris, Julia B.; Woodcock, Nicola A.; Clement, Darren J.; Clipson, Nicholas J. W.; Whitehead, Michael P.; Fincham, Daron A.; Hooley, Paul (Elsevier Science Direct, 2002)
      We report the cloning and sequencing of a DNA fragment encoding a putative C2H2 zinc finger protein from Aspergillus nidulans. The gene was isolated by complementation cloning of a salt sensitive phenotype of the A. nidulans sltAl mutant. A 3.8 kb Pst I fragment that restored wild type salt tolerance contained one large open reading frame of 2202 bp. The predicted protein (StzA) from this reading frame comprises 698 amino acids and has three Zinc fingers along with a putative transcriptional activation domain rich in acidic amino acids. The corresponding sequence from a sltAl mutant contains a premature STOP codon resulting in loss of the putative transcriptional activator in the C-terminal region. The Zinc fingers show conserved motifs with a number of transcription factors including CreA from A. nidulans and the human Wilm's tumour susceptibility protein WT-1.
    • Correlation of copy number aberrations with clinico-pathological criteria in paediatric glial tumours

      Ward, Samantha; Hayward, Richard; Harkness, William; Phipps, Kim; Thompson, Dominic; Harding, Brian; Wilkins, Peter; Darling, John L.; Thomas, David G.; Warr, Tracy (Society for Neuro-Oncology and Duke University Press, 2003)
      Glial cell tumours represent the largest group of brain tumours in childhood and include astrocytoma (WHO grades I-IV) and ependymoma (WHO grade II-III). However, little is known about the pathogenesis of these tumours. We have used comparative genomic hybridisation (CGH) to investigate the genetic alterations in 128 tumours from children and young adults (< 30 years of age) comprising 52 ependymoma, including 40 samples that have previously been reported (44 grade II and 8 grade III) and 76 astrocytoma (consisting of 34 grade I, 17 grade II, 7 grade III, and 18 grade IV). Genetic alterations were compared to clinicopathological data such as histology, tumour recurrence, and survival in order to identify potential prognostic markers. In ependymoma, 39% of the tumours had no detectable copy number aberrations (CNAs). In the remaining tumours, the most common regions of gain were 4q (29%), 6q (21%), 1q (17%), and 2q (15%). The most common regions of loss were 22 (29%), 16p (17%), 17p (13%), and 20q (13%). Three regions of high copy number amplification were observed in 3 tumours at 1q24-31 (3 cases), 8q21-23 (3 cases), and 9p (1 case). There was no association between any CNA and histology, tumour recurrence, or length of survival. In contrast, in the astrocytoma group there was a clear association between histology and the presence of CNAs. The pattern of genetic alterations became increasingly complex with tumour grade, and grade IV tumours were more likely to have CNAs than lower grade tumours (p = 0.0502). Overall, the most frequent alterations observed in astrocytoma were gain of 4q (11%), loss 16p (10.5%), and loss 17p (10.5%). However, several CNAs were seen predominantly in grade IV tumours (gain 1q, 2q, 4q, and 5q). Fourteen amplicons were observed in 8 tumours of all grades, of which the most common were localised to 7q31 (4 cases), 8q21-22 (3 cases), 19p (2 cases), 2q (2 cases), and 12q15-21 (2 cases). From this study, it appears that paediatric glial tumours are much more genetically heterogeneous than their adult counterparts, and further molecular investigations are needed to define clinically useful subgroups.
    • Demystified. Human endogenous retroviruses.

      Nelson, Paul N.; Carnegie, P.R.; Martin, Jan H.; Ejtehadi, H. Davari; Hooley, Paul; Roden, Denise A.; Rowland-Jones, S.; Warren, Phil; Astley, S.J.; Murray, Paul G. (BMJ Publishing, 2003)
      Human endogenous retroviruses (HERVs) are a family of viruses within our genome with similarities to present day exogenous retroviruses. HERVs have been inherited by successive generations and it is possible that some have conferred biological benefits. However, several HERVs have been implicated in certain cancers and autoimmune diseases. This article demystifies these retroviruses by providing an insight into HERVs, their means of classification, and a synopsis of HERVs implicated in cancer and autoimmunity. Furthermore, the biological roles of HERVs are explored.
    • Development and application of RT-PCR systems to determine HERV expression in astrocytoma cell lines

      Nelson, Paul N.; Smith, R.; Conde, Gillian; Roden, Denise A.; Darling, John L. (Society for Neuro-Oncology and Duke University Press, 2005)
      Human endogenous retroviruses (HERVs) belong to the family of transposable elements that make up 8% of the human genome. Unlike exogenous retrovirus (e.g., HIV and HTLV), HERVs are inherited in a Mendelian manner. More than 22 families of HERVs have been identified over the past two decades. Importantly, some HERVs have been found to possess large open reading frames and produce viral like particles. More latterly, these viruses have been linked with certain autoimmune diseases and cancers. Indeed, HERVs may contribute toward carcinogenesis through retrotransposition, promoter insertion, immunomodulation, disruption of normal HERV-related functions, recombination, or by the production of fusion proteins. Of importance, HERV-K, HERV-W, and HERV-H have the potential to be transcriptionally active in the brain. We have developed robust RT-PCR systems using primers/probes specific to HERV-K and HERV-W to assess mRNA expression in conjunction with the house keeping gene, histidyl tRNA synthetase. In employing a gel-documentation system, we are able to provide semiquantitative levels of HERV expression in cell lines. Pilot data shows markedly enhanced expression of HERV-K in the cell line U251-MG (derived from a glioblastoma multiforme; WHO grade IV astrocytoma) as compared to a control cell line SW480 (colon adenocarcinoma): RT-PCR values; 1.0 and 0.42, respectively. This observation raises an intriguing possibility that HERV-K expression may be elevated in malignant brain tumors. In addition, this approach provides a useful approach to optimize primers and probes prior to using real-time quantitative PCR.
    • Disulfiram-mediated inhibition of NF-kappaB activity enhances cytotoxicity of 5-fluorouracil in human colorectal cancer cell lines.

      Wang, Weiguang; McLeod, Howard; Cassidy, James (Wiley InterScience, 2003)
      5-Fluorouracil (5-FU) is the major chemotherapeutic component for colorectal cancer (CRC) and other types of solid tumours. Resistance of cancer cells to 5-FU is considered the major obstacle for successful chemotherapy. NF-kappaB is a transcription factor. Cancer cells with high NF-kappaB nuclear activity demonstrate robust chemo- and radio-resistance. We demonstrated that nuclear NF-kappaB activity in CRC cell lines, DLD-1 and RKO(WT), was significantly induced by 5-FU in a concentration- and time-dependent manner. 5-FU induced IkappaBalpha degradation and promoted both NF-kappaB nuclear translocation and its DNA binding activity. 5-FU treatment did not influence the activities of AP-1, AP-2, Oct-1, SP-1, CRE-B and TFIID. Disulfiram (DS), a clinically used anti-alcoholism drug, strongly inhibited constitutive and 5-FU-induced NF-kappaB activity in a dose-dependent manner. DS inhibited both NF-kappaB nuclear translocation and DNA binding activity but had no effect on 5-FU-induced IkappaBalpha degradation. Used in combination, DS significantly enhanced the apoptotic effect of 5-FU on DLD-1 and RKO(WT) cell lines and synergistically potentiated the cytotoxicity of 5-FU to both cell lines. DS also effectively abolished 5-FU chemoresistance in a 5-FU resistant cell line H630(5-FU) in vitro. As DS has extensive preclinical and clinical experience, translating its anticancer usage from in vitro study to clinical trials is relatively straightforward.
    • Does an apple a day keep the doctor away because a phytoestrogen a day keeps the virus at bay? A review of the anti-viral properties of phytoestrogens.

      Martin, Jan H.; Crotty, Stephen; Warren, Phil; Nelson, Paul N. (Elsevier, 2007)
      From dengue to herpes and influenza to AIDS, the phytoestrogens that are present in many fruits and vegetables have been shown to exert anti-viral properties. Here we review the various different anti-viral mechanisms employed by phytoestrogens.
    • Down-regulation of nitric oxide production by droloxifene and toremifene in human breast cancer cells.

      Martin, Jan H.; Symonds, A.; Chohan, S. (Spandidos Publications Ltd, 2003)
      We investigated the effect of tamoxifen, 4-OH tamoxifen, toremifene droloxifene, interferon-alpha2a, interferon-alpha2b and interferon-alpha2c, singly and in combination, for their effect on nitric oxide production by MCF-7 and ZR-75-1 human breast cancer cells. Tamoxifen and 4-OH tamoxifen singly had no effect on nitric oxide production by either cell line. However, treatment with droloxifene or toremifene significantly reduced nitric oxide production by both MCF-7 and ZR-75-1 human breast cancer cell lines. Combination treatment with anti-estrogens and interferon-alpha2a interferon-alpha2b or interferon-alpha2c had no synergistic or additive effect compared to each drug singly.
    • Drug resistance in malignant brain tumours

      Darling, John L. (Trivandrum, India: Research Signpost, 2006)
      THIS BOOK: Major advances have been made in recent years towards understanding the genetic basis of cancer. The molecular events occurring in cancer growth, invasion and its secondary spread are being continually elucidated. This book focuses on these events, the genetics of the disease, the nature and temporal changes of gene expression, and the deregulation of genetic programmes that lie at the root of cancer progression. The authors, experts in their respective fields, have attempted to link the genetic alterations with the biological behaviour of cancers. The discussions, reasoning and inferences are based on the behaviour of a fairly wide spectrum of human cancer, thus greatly augment the potential applicability and value of the postulates to the study and treatment of the disease. The construction of molecular profiles of progression might lead to the identification of reliable markers and chemotherapeutic targets and in this way aid in the treatment and management of patients. This book presents comprehensive accounts that would be useful to research workers in the fields of cancer biology, genetics and molecular biology, clinical and medical oncologists, and will be of interest also to graduate and post-graduate students.
    • Epidermal growth factor receptor kinase domain mutations in esophageal and pancreatic adenocarcinomas.

      Kwak, Eunice L.; Jankowski, Janusz; Thayer, Sarah P.; Lauwers, Gregory Y.; Brannigan, Brian W.; Harris, Patricia L.; Okimoto, Ross A.; Haserlat, Sara M.; Driscoll, David R.; Ferry, David R.; Muir, Beth; Settleman, Jeff; Fuchs, Charles S.; Kulke, Matthew H.; Ryan, David P.; Clark, Jeff W.; Sgroi, Dennis C.; Haber, Daniel A.; Bell, Daphne W. (American Association for Cancer Research, 2006)
      PURPOSE: Specific activating mutations within the epidermal growth factor receptor (EGFR) identify a subset of non-small cell lung cancers with dramatic sensitivity to the specific tyrosine kinase inhibitors (TKI), gefitinib and erlotinib. Despite the abundant expression of EGFR protein in a broad range of epithelial cancers, EGFR mutations have not been reported in a substantial fraction of other cancers. Given recent reports of TKI-responsive cases of esophageal and pancreatic cancer, this study was designed to determine the prevalence of EGFR mutations in these gastrointestinal cancers. EXPERIMENTAL DESIGN: We sequenced exons 18 to 21 of EGFR from 21 cases of Barrett's esophagus, 5 cases of high-grade esophageal dysplasia, 17 cases of esophageal adenocarcinoma, and 55 cases of pancreatic adenocarcinoma. Subsets of esophageal (n = 7) and pancreatic cancer cases (n = 5) were obtained from patients who were subsequently treated with gefitinib or erlotinib-capecitabine, respectively. RESULTS: Mutations of EGFR were identified in two esophageal cancers (11.7%), three cases of Barrett's esophagus (14.2%), and two pancreatic cancers (3.6%). The mutations consisted of the recurrent missense L858R and in-frame deletion delE746-A750, previously characterized as activating EGFR mutations in non-small cell lung cancer. We also identified the TKI drug resistance-associated EGFR T790M mutation in an untreated case of Barrett's esophagus and the corresponding adenocarcinoma. CONCLUSION: The presence of activating mutations within EGFR in both esophageal and pancreatic adenocarcinomas defines a previously unrecognized subset of gastrointestinal tumors in which EGFR signaling may play an important biological role. EGFR mutations in premalignant lesions of Barrett's esophagus also point to these as an early event in transformation of the esophageal epithelium. The role of genotype-directed TKI therapy should be tested in prospective clinical trials.
    • Eukaryote polyphosphate kinases: is the 'Kornberg' complex ubiquitous?

      Hooley, Paul; Whitehead, Michael P.; Brown, Michael R. W. (Elsevier, 2008)
      Polyphosphate (poly P) is a polymer of up to several hundred phosphate residues and is important to a variety of cell processes. The main poly P synthetic enzyme in many bacteria is poly P kinase 1 (PPK1), which until recently had been detected among eukaryotes in some protists only. There is now evidence for the presence in several other eukaryotes of PPK1 homologues and also a second bacteria-type enzyme, PPK2. The latest genome databases reveal that the 'Kornberg' enzyme complex of three actin-related proteins, termed DdPPK2 in Dictyostelium discoideum, might also be ubiquitous in eukaryotes. Owing to the intimate association of poly P synthesis with the formation of structural fibres, this ubiquity indicates a central role for this molecule in the evolution of eukaryotic cells.
    • Expression profiling in ependymoma reveals differences between benign and anaplastic ependymoma

      Suarez-Merino, Blanca; Hubank, Mike; Hayward, Richard; Harkness, William; Thompson, Dominic; Phipps, Kim; Revesz, Tamas; Darling, John L.; Thomas, David G.; Warr, Tracy (Society for Neuro-Oncology and Duke University Press, 2003)
      Ependymomas arise from the ependymal cells lining the ventricular system of the CNS and account for approximately 10% of paediatric brain tumours. Approximately 70% of ependymomas are histologically benign and correspond to WHO grade II, whilst the remainder are anaplastic (WHO grade III). The 5-year survival rates in children are 34–45%, with local recurrence being the major source of therapeutic failure. Anaplasia does not appear to be associated with worse prognosis, and at present there are no molecular or genetic markers which can be used as predictors of outcome. Indeed, the genetic events that contribute to the pathogenesis of ependymoma are essentially unknown. We have used human oligonucleotide arrays to generate gene expression profiles in 10 ependymoma samples from patients with different histopathological/clinical parameters in order to identify new prognostic markers. Our sample group is composed of 7 ependymoma (WHO grade II) and 3 anaplastic ependymoma (WHO grade III). Three patients were <3 years of age at first presentation. Five tumours have chromosomal aberrations identified by comparative genomic hybridisation (CGH). Our preliminary data show that overexpression of specific functional categories of genes is dependant on histology when compared to normal controls. Cell cycle and adhesion related genes, oncogenes, and genes involved in apoptosis were mainly overexpressed in anaplastic tumours. Benign tumours, however, overexpressed mainly growth factor related genes. Some common candidates emerged for all tumours; Wee1+, a cell cycle related gene that regulates entry into mitosis, was up to six fold overexpressed in tumours. The oncogene c-myc, which maps to an amplicon at 8q24 detected by CGH in a subset of ependymomas, was also overexpressed in some tumours and may be an interesting candidate in their development. To our knowledge, none of these genes have been associated previously with this class of brain tumours. Further analysis of differential gene expression profiles using large series of tumours will help in the identification of molecular markers. This information, when linked to clinical and pathology data, could also help in the classification of these tumours and the choice of therapy.