PubMed Health⌕ Search

Biomedical subjects

Helen Davies

Publications and source records attributed to Helen Davies.

At least 19 recordsLinked to original sources
PubMed2006

Mutation analysis of 24 known cancer genes in the NCI-60 cell line set.

The panel of 60 human cancer cell lines (the NCI-60) assembled by the National Cancer Institute for anticancer drug discovery is a widely used resource. The NCI-60 has been characterized pharmacologically and at the molecular level more extensively than any other set of cell lines. However, no systematic mutation analysis of genes causally implicated in oncogenesis has been reported. This study reports the sequence analysis of 24 known cancer genes in the NCI-60 and an assessment of 4 of the 24 genes for homozygous deletions. One hundred thirty-seven oncogenic mutations were identified in 14 (APC, BRAF, CDKN2, CTNNB1, HRAS, KRAS, NRAS, SMAD4, PIK3CA, PTEN, RB1, STK11, TP53, and VHL) of the 24 genes. All lines have at least one mutation among the cancer genes examined, with most lines (73%) having more than one. Identification of those cancer genes mutated in the NCI-60, in combination with pharmacologic and molecular profiles of the cells, will allow for more informed interpretation of anticancer agent screening and will enhance the use of the NCI-60 cell lines for molecularly targeted screens.

Cell Line, Tumor↗
PubMed2006

Recurrent KRAS codon 146 mutations in human colorectal cancer.

An activating point mutation in codon 12 of the HRAS gene was the first somatic point mutation identified in a human cancer and established the role of somatic mutations as the common driver of oncogenesis. Since then, there have been over 11,000 mutations in the three RAS (HRAS, KRAS and NRAS) genes in codons 12, 13 and 61 reported in the literature. We report here the identification of recurrent somatic missense mutations at alanine 146, a highly conserved residue in the guanine nucleotide binding domain. In two independent series of colorectal cancers from Hong Kong and the United States we detected KRAS A146 mutations in 7/126 and 2/94 cases, respectively, giving a combined frequency of 4%. We also detected KRAS A146 mutations in 2/40 (5%) colorectal cell lines, including the NCI-60 colorectal cancer line HCC2998. Codon 146 mutations thus are likely to make an equal or greater contribution to colorectal cancer than codon 61 mutations (4.2% in our combined series, 1% in the literature). Lung adenocarcinomas and large cell carcinomas did not show codon 146 mutations. We did, however, identify a KRAS A146 mutation in the ML-2 acute myeloid leukemia cell line and an NRAS A146 mutation in the NALM-6 B-cell acute lymphoblastic leukemia line, suggesting that the contribution of codon 146 mutations is not entirely restricted to colorectal cancers or to KRAS.

Adenocarcinoma↗
PubMed2006

A hypermutation phenotype and somatic MSH6 mutations in recurrent human malignant gliomas after alkylator chemotherapy.

Malignant gliomas have a very poor prognosis. The current standard of care for these cancers consists of extended adjuvant treatment with the alkylating agent temozolomide after surgical resection and radiotherapy. Although a statistically significant increase in survival has been reported with this regimen, nearly all gliomas recur and become insensitive to further treatment with this class of agents. We sequenced 500 kb of genomic DNA corresponding to the kinase domains of 518 protein kinases in each of nine gliomas. Large numbers of somatic mutations were observed in two gliomas recurrent after alkylating agent treatment. The pattern of mutations in these cases showed strong similarity to that induced by alkylating agents in experimental systems. Further investigation revealed inactivating somatic mutations of the mismatch repair gene MSH6 in each case. We propose that inactivating somatic mutations of MSH6 confer resistance to alkylating agents in gliomas in vivo and concurrently unleash accelerated mutagenesis in resistant clones as a consequence of continued exposure to alkylating agents in the presence of defective mismatch repair. The evidence therefore suggests that when MSH6 is inactivated in gliomas, alkylating agents convert from induction of tumor cell death to promotion of neoplastic progression. These observations highlight the potential of large scale sequencing for revealing and elucidating mutagenic processes operative in individual human cancers.

Aged↗
PubMed2006

High throughput DNA sequence variant detection by conformation sensitive capillary electrophoresis and automated peak comparison.

We report the development of a heteroduplex-based mutation detection method using multicapillary automated sequencers, known as conformation-sensitive capillary electrophoresis (CSCE). Our optimized CSCE protocol detected 93 of 95 known base substitution sequence variants. Since the optimization of the method, we have analyzed 215 Mb of DNA and identified 3397 unique variants. An analysis of this data set indicates that the sensitivity of CSCE is above 95% in the central 56% of the average PCR product. To fully exploit the mutation detection capacity of this method, we have developed software, canplot, which automatically compares normal and test results to prioritize samples that are most likely to contain variants. Using multiple fluorescent dyes, CSCE has the capacity to screen over 2.2 Mb on one ABI3730 each day. Therefore this technique is suitable for projects where a rapid and sensitive DNA mutation detection system is required.

Algorithms↗
PubMed2006

Sequence analysis of the protein kinase gene family in human testicular germ-cell tumors of adolescents and adults.

The protein kinase gene family is the most frequently mutated in human cancer. Previous work has documented activating mutations in the KIT receptor tyrosine kinase in testicular germ-cell tumors (TGCT). To investigate further the potential role of mutated protein kinases in the development of TGCT and to characterize the prevalence and patterns of point mutations in these tumors, we have sequenced the coding exons and splice junctions of the annotated protein kinase family of 518 genes in a series of seven seminomas and six nonseminomas. Our results show a remarkably low mutation frequency, with only a single somatic point mutation, a K277E mutation in the STK10 gene, being identified in a total of more than 15 megabases of sequence analyzed. Sequencing of STK10 in an additional 40 TGCTs revealed no further mutations. Comparative genomic hybridization and LOH analysis using SNP arrays demonstrated that the 13 TGCTs mutationally screened through the 518 protein kinase genes were uniformly aneuploid with consistent chromosomal gains on 12p, 8q, 7, and X and losses on 13q, 18q, 11q, and 4q. Our results do not provide evidence for a mutated protein kinase implicated in the development of TGCT other than KIT. Moreover, they demonstrate that the general prevalence of point mutations in TGCT is low, in contrast to the high frequency of copy number changes.

Adolescent↗
PubMed2006

Development of an information source for patients and the public about general practice services: an action research study.

OBJECTIVE: The publication of information about the performance of health-care providers is regarded as central to promoting greater accountability and empowering patients to exercise choice. The evidence suggests that the public is not very interested in accessing or using current sources of information. This study aimed to explore the information needs of patients in the context of UK primary care and to develop an information source about general practice services, designed to be usable by and useful to patients. DESIGN: An action research study making use of data from formal and informal interviews, focus groups, participant observation and document review. SETTING: The geographical areas covered by two Primary Care Trusts in the north of England and two Local Health Boards in south Wales. PARTICIPANTS: A partnership between 103 members of the public, general practice staff from 19 practices, NHS managers from four Primary Care Organizations and the research team. RESULTS: The public would like to know more about the quality and range of general practice services but current sources of information do not meet their needs. The public do not like league tables comparing the performance of practices and only a small number of people want to use comparative information to choose between practices. They seem to be more interested in the context and availability of services and the willingness of practices to improve, than in the practice's absolute or relative performance. They want to be clear about the source of the information so that they can make personal judgements about its veracity. Information is most likely to be useful if it adheres to the basic principles of cognitive science in terms of its structure, content and presentation format. Using these findings, paper and electronic prototype versions of a guide to general practice services have been developed. CONCLUSIONS: In order to maximize the potential use of performance information by the public it is necessary to move beyond provider-led and professionally constructed approaches to information provision and ensure that the public is actively involved in the development of information sources. Such involvement produces a different kind of information to that currently available to the public. The findings of this study have important implications for policy. Most importantly, it seems that the traditional consumerist model underlying a policy of making comparative performance information available to the public to enable them to exercise choice between primary care providers may not be appropriate. An alternative model of information provision, which recognizes the public's commitment to their practice and is integrated with 'soft' sources of knowledge is more likely to engage and be of use to the public.

England↗
PubMed2005

Somatic mutations of the protein kinase gene family in human lung cancer.

Protein kinases are frequently mutated in human cancer and inhibitors of mutant protein kinases have proven to be effective anticancer drugs. We screened the coding sequences of 518 protein kinases (approximately 1.3 Mb of DNA per sample) for somatic mutations in 26 primary lung neoplasms and seven lung cancer cell lines. One hundred eighty-eight somatic mutations were detected in 141 genes. Of these, 35 were synonymous (silent) changes. This result indicates that most of the 188 mutations were "passenger" mutations that are not causally implicated in oncogenesis. However, an excess of approximately 40 nonsynonymous substitutions compared with that expected by chance (P = 0.07) suggests that some nonsynonymous mutations have been selected and are contributing to oncogenesis. There was considerable variation between individual lung cancers in the number of mutations observed and no mutations were found in lung carcinoids. The mutational spectra of most lung cancers were characterized by a high proportion of C:G > A:T transversions, compatible with the mutagenic effects of tobacco carcinogens. However, one neuroendocrine cancer cell line had a distinctive mutational spectrum reminiscent of UV-induced DNA damage. The results suggest that several mutated protein kinases may be contributing to lung cancer development, but that mutations in each one are infrequent.

Adenocarcinoma↗
PubMed2005

A survey of homozygous deletions in human cancer genomes.

Homozygous deletions of recessive cancer genes and fragile sites are known to occur in human cancers. We identified 281 homozygous deletions in 636 cancer cell lines. Of these deletions, 86 were homozygous deletions of known recessive cancer genes, 17 were of sequenced common fragile sites, and 178 were in genomic regions that do not overlap known recessive oncogenes or fragile sites ("unexplained" homozygous deletions). Some cancer cell lines have multiple homozygous deletions whereas others have none, suggesting intrinsic variation in the tendency to develop this type of genetic abnormality (P < 0.001). The 178 unexplained homozygous deletions clustered into 131 genomic regions, 27 of which exhibit homozygous deletions in more than one cancer cell line. This degree of clustering indicates that the genomic positions of the unexplained homozygous deletions are not randomly determined (P < 0.001). Many homozygous deletions, including those that are in multiple clusters, do not overlap known genes and appear to be in intergenic DNA. Therefore, to elucidate further the pathogenesis of homozygous deletions in cancer, we investigated the genome landscape within unexplained homozygous deletions. The gene count within homozygous deletions is low compared with the rest of the genome. There are also fewer short interspersed nuclear elements (SINEs), long interspersed nuclear elements (LINEs), and low-copy-number repeats (LCRs). However, DNA within homozygous deletions has higher flexibility. These features may signal the presence of currently unrecognized zones of susceptibility to DNA rearrangement. They may also reflect a tendency to reduce the adverse effects of homozygous deletions by minimizing the number of genes removed.

Cell Line, Tumor↗
PubMed2004

Lung cancer: intragenic ERBB2 kinase mutations in tumours.

The protein-kinase family is the most frequently mutated gene family found in human cancer and faulty kinase enzymes are being investigated as promising targets for the design of antitumour therapies. We have sequenced the gene encoding the transmembrane protein tyrosine kinase ERBB2 (also known as HER2 or Neu) from 120 primary lung tumours and identified 4% that have mutations within the kinase domain; in the adenocarcinoma subtype of lung cancer, 10% of cases had mutations. ERBB2 inhibitors, which have so far proved to be ineffective in treating lung cancer, should now be clinically re-evaluated in the specific subset of patients with lung cancer whose tumours carry ERBB2 mutations.

Carcinoma, Non-Small-Cell Lung↗
PubMed2004

Mutations in the DLG3 gene cause nonsyndromic X-linked mental retardation.

We have identified truncating mutations in the human DLG3 (neuroendocrine dlg) gene in 4 of 329 families with moderate to severe X-linked mental retardation. DLG3 encodes synapse-associated protein 102 (SAP102), a member of the membrane-associated guanylate kinase protein family. Neuronal SAP102 is expressed during early brain development and is localized to the postsynaptic density of excitatory synapses. It is composed of three amino-terminal PDZ domains, an src homology domain, and a carboxyl-terminal guanylate kinase domain. The PDZ domains interact directly with the NR2 subunits of the NMDA glutamate receptor and with other proteins responsible for NMDA receptor localization, immobilization, and signaling. The mutations identified in this study all introduce premature stop codons within or before the third PDZ domain, and it is likely that this impairs the ability of SAP102 to interact with the NMDA receptor and/or other proteins involved in downstream NMDA receptor signaling pathways. NMDA receptors have been implicated in the induction of certain forms of synaptic plasticity, such as long-term potentiation and long-term depression, and these changes in synaptic efficacy have been proposed as neural mechanisms underlying memory and learning. The disruption of NMDA receptor targeting or signaling, as a result of the loss of SAP102, may lead to altered synaptic plasticity and may explain the intellectual impairment observed in individuals with DLG3 mutations.

Base Sequence↗
PubMed2004

Estimation of septic tank setback distances based on transport of E. coli and F-RNA phages.

Setback distances between septic tank systems and the shorelines of Lake Okareka, New Zealand were determined from model simulations for a worst-case scenario, using the highest hydraulic conductivity and gradient measured in the field, removal rates of the microbial indicators (Escherichia coli and F-RNA phages) determined from a column experiment, and maximum values of the design criteria for the disposal system, and assuming an absence of an unsaturated zone, a continuous discharge of the raw effluent from a failed or non-complying treatment system (both indicators at concentrations of 1x10(7) counts/100 ml) into the groundwater and no sorption of pathogens in the aquifer. Modelling results suggest that the minimal setback distances were 16 m to satisfy the New Zealand Recreational Water Quality Guidelines for E. coli <126 per 100 ml (Ministry for the Environment, 1999) and 48 m to meet the Drinking-Water Standards for New Zealand 2000 for enteric virus <1 per 100 l (Ministry of Health, 2000). These distances may be applicable for other lakeshores in pumice sand aquifers with groundwater velocities <7 m/day. Findings of laboratory column and batch experiments provided an insight into the microbial attenuation and transport processes in pumice sand aquifers. Bacterial removal was predominately through filtration (87-88%) and partially by die-off (12-13%), while viral removal was by both die-off (45%) and filtration (55%). In addition, microbial die-off in groundwater without aquifer material (i.e., free microbes) was much lower than die-off in groundwater with aquifer material (i.e., sorbed microbes) and contributed only 2-6% to the total removal. This implies that the setback distances estimated from die-off rates for the free microbes, determined in the laboratory without considering aquifer media and other removal processes, which are often reported in the literature, could be larger than necessary.

Escherichia coli↗
PubMed2003

Water quality fluxes for eastern UK rivers entering the North Sea: a summary of information from the Land Ocean Interaction Study (LOIS).

Over the past decade a major initiative examined the chemical flux transfers from eastern UK Rivers to the North Sea as part of an ambitious community research programme, the Land Ocean Interaction Study (LOIS). In this paper, a compilation of data on flux and flux per unit area for five major river basins, the Tweed, the Wear, the Humber, the Great Ouse and the Thames is presented based on an extensive riverine monitoring programme within the LOIS. The compilation includes details on the fluxes of major, minor and trace elements as well as the nutrients and sediments. In the process, the flux inputs are related to the major tributary sources for these basins and compared with earlier studies based on complementary information for eastern UK Rivers entering the North Sea collected within the Harmonized Monitoring Scheme. The significance of the southern Humber Rivers to pollution fluxes to the North Sea is highlighted in relation to the predominance of urban and industrial sources.

Journal Article↗
PubMed2003

Fluoride in UK rivers.

Fluoride concentrations in eastern UK rivers (the Humber, Tweed, Wear, Great Ouse and Thames) are described based on information collected within the Land-Ocean Interaction Study (LOIS) and by the Environment Agency (EA) of England and Wales. The results show varied fluoride concentrations across the region, with a range from <0.01 to >10 mg l(-1); and mean, median and range in mean concentrations of 0.30, 0.21 and 0.05-3.38 mg l(-1) (excluding one outlier point), respectively. Within the main rivers and tributaries, the mean fluoride concentration varied from approximately 0.5 to over 2 mg l(-1) and the highest values occurred within the Don basin (Don, Dearne and Rother) and parts of the Trent basin (upper Tame and mid-upper Derbyshire Derwent) in highly industrialised and urbanised areas (Sheffield and Rotherham in the Don basin; Birmingham and Derby on the Trent). For localised inputs to the rivers, fluoride concentrations were slightly higher, and considerably higher in one outlier case. Correspondingly, the other rivers examined typically had mean fluoride concentrations between approximately 0.2 and 0.5 mg l(-1), but fluoride concentrations were lower in the headwater areas. As there is much less information on fluoride levels in upland areas, extensive data collected as part of an acid waters survey are used to show that fluoride concentrations are generally less than 0.1 mg l(-1) for the upland UK. The data are summarised in terms of both fluoride concentrations and flux, and the values are cross-referenced to other determinands collected within LOIS. The high positive correlation with boron and negative correlation with flow show the importance of point source (sewage) inputs of fluoride, while strong positive correlations between fluoride and barium indicate the relative importance of vein mineralisation in the bedrock in supplying fluoride to the waters of the Yorkshire Ouse and its tributaries. There seems to be some process that limits the fluoride concentrations within the more contaminated rivers, and this is indicated by a negative upper bound between fluoride and calcium. The waters are undersaturated with respect to fluorite and oversaturated with respect to calcium fluoro-phosphates. This upper bound may reflect either physical controls, such as the availability and size of point and diffuse sources for fluoride coupled to mixing of these sources with rain and soil runoff of low concentration, or solubility controls for a pure or mixed-phase mineral that cannot be specified here.

Journal Article↗
PubMed2002

BRAF and RAS mutations in human lung cancer and melanoma.

BRAF encodes a RAS-regulated kinase that mediates cell growth and malignant transformation kinase pathway activation. Recently, we have identified activating BRAF mutations in 66% of melanomas and a smaller percentage of many other human cancers. To determine whether BRAF mutations account for the MAP kinase pathway activation common in non-small cell lung carcinomas (NSCLCs) and to extend the initial findings in melanoma, we screened DNA from 179 NSCLCs and 35 melanomas for BRAF mutations (exons 11 and 15). We identified BRAF mutations in 5 NSCLCs (3%; one V599 and four non-V599) and 22 melanomas (63%; 21 V599 and 1 non-V599). Three BRAF mutations identified in this study are novel, altering residues important in AKT-mediated BRAF phosphorylation and suggesting that disruption of AKT-induced BRAF inhibition can play a role in malignant transformation. To our knowledge, this is the first report of mutations documenting this interaction in human cancers. Although >90% of BRAF mutations in melanoma involve codon 599 (57 of 60), 8 of 9 BRAF mutations reported to date in NSCLC are non-V599 (89%; P < 10(-7)), strongly suggesting that BRAF mutations in NSCLC are qualitatively different from those in melanoma; thus, there may be therapeutic differences between lung cancer and melanoma in response to RAF inhibitors. Although uncommon, BRAF mutations in human lung cancers may identify a subset of tumors sensitive to targeted therapy.

Carcinoma, Non-Small-Cell Lung↗
PubMed2002

Similarity of the phenotypic patterns associated with BRAF and KRAS mutations in colorectal neoplasia.

Activation of the RAS/RAF/extracellular signal-regulated kinase-mitogen-activated protein kinase/extracellular signal-regulated kinase/mitogen-activated protein kinase pathway by RAS mutations is commonly found in human cancers. Recently, we reported that mutation of BRAF provides an alternative route for activation of this signaling pathway and can be found in melanomas, colorectal cancers, and ovarian tumors. Here we perform an extensive characterization of BRAF mutations in a large series of colorectal tumors in various stages of neoplastic transformation. BRAF mutations were found in 11 of 215 (5.1%) colorectal adenocarcinomas, 3 of 108 (2.8%) sporadic adenomas, 1 of 63 (1.6%) adenomas from familial adenomatous polyposis (FAP) patients, and 1 of 3 (33%) hyperplastic polyps. KRAS mutations were detected in 34% of carcinomas, 31% of sporadic adenomas, 9% of FAP adenomas, and no hyperplastic polyps. Eight of 16 BRAF mutations were V599E, the previously described hotspot, and none of these was associated with a KRAS mutation in the same lesion. The remaining eight mutations involve other conserved amino acids in the kinase domain, and 62.5% have a KRAS mutation in the same tumor. Our data suggest that BRAF mutations are, to some extent, biologically similar to RAS mutations in colorectal cancer because both occur at approximately the same stage of the adenoma-carcinoma sequence, both are associated with villous morphology, and both are less common in adenomas from FAP cases. By contrast, colorectal adenocarcinomas with BRAF mutations are associated with early Dukes' tumor stages (P = 0.006) and no such relationship was observed for KRAS mutations. The presence in some colorectal neoplasms of mutations in both BRAF and KRAS suggests that modulation of the RAS-RAF-extracellular signal-regulated kinase-mitogen-activated protein kinase/extracellular signal-regulated kinase/mitogen-activated protein kinase signaling pathway may occur by mutation of multiple components.

Adenocarcinoma↗
PubMed2002

Cognitive status and behavioral problems in older hospitalized patients.

OBJECTIVES: (a) To determine the quantity and quality of behavioral problems in older hospitalized patients on acute care units; (b) to determine the burden of these behaviors on staff; and (c) to identify predictors of behavioral problems. METHODS: Upon admission, patients performed the Mini-Mental State Exam (MMSE), the Geriatric Depression Scale (GDS), and information was obtained on age, ethnicity, level of education, living arrangement, and psychiatric history. Two days post-admission, a clinical staff member caring for each patient, performed the Neuropsychiatric Inventory-Questionnaire (NPI-Q) to assess patients' behavioral problems and staff distress. PARTICIPANTS AND SETTING : Forty-two patients, over 60 years of age, admitted to medical and surgical units of the Veterans Affairs Hospitals in Palo Alto and San Francisco, participated. RESULTS: Twenty-three of 42 (55%) patients exhibited behavioral problems. Anxiety, depression, irritability, and agitation/aggression were the most frequently observed behaviors. The severity of the behavioral problems was significantly correlated with staff distress. Lower performance on the MMSE at admission was significantly associated with higher NPI-Q ratings. Specifically, of those cases with scores less than or equal to 27 on the MMSE, 66% had behavioral problems during hospitalization, compared to only 31% of those with scores greater than 27. CONCLUSION: Behavioral problems in older hospitalized patients appear to occur frequently, are a significant source of distress to staff, and can result in the need for psychiatric consultation. Assessment of the mental status of older adults at admission to hospital may be valuable in identifying individuals at increased risk for behavioral problems during hospitalization.

Journal Article↗
PubMed2002

Mutations of the BRAF gene in human cancer.

Cancers arise owing to the accumulation of mutations in critical genes that alter normal programmes of cell proliferation, differentiation and death. As the first stage of a systematic genome-wide screen for these genes, we have prioritized for analysis signalling pathways in which at least one gene is mutated in human cancer. The RAS RAF MEK ERK MAP kinase pathway mediates cellular responses to growth signals. RAS is mutated to an oncogenic form in about 15% of human cancer. The three RAF genes code for cytoplasmic serine/threonine kinases that are regulated by binding RAS. Here we report BRAF somatic missense mutations in 66% of malignant melanomas and at lower frequency in a wide range of human cancers. All mutations are within the kinase domain, with a single substitution (V599E) accounting for 80%. Mutated BRAF proteins have elevated kinase activity and are transforming in NIH3T3 cells. Furthermore, RAS function is not required for the growth of cancer cell lines with the V599E mutation. As BRAF is a serine/threonine kinase that is commonly activated by somatic point mutation in human cancer, it may provide new therapeutic opportunities in malignant melanoma.

3T3 Cells↗