Cloning and characterization of a novel human gene related to vascular endothelial growth factor

This paper describes the cloning and characterization of a new member of the vascular endothelial growth factor (VEGF) gene family, which we have designated VRF for VEGF-related-factor. Sequencing of cDNAs from a human fetal brain library and RT-PCR products from normal and tumor tissue cDNA pools indicate two alternatively spliced messages with open reading frames of 621 and 564 bp, respectively. The predicted proteins differ at their carboxyl ends resulting from a shift in the open reading frame. Both isoforms show strong homology to VEGF at their amino termini, but only the shorter isoform maintains homology to VEGF at its carboxyl terminus and conserves all 16 cysteine residues of VEGF165. Similarity comparisons of this isoform revealed overall protein identity of 48% and conservative substitution of 69% with VEGF189. VRF is predicted to contain a signal peptide, suggesting that it may be a secreted factor. The VRF gene maps to the D11S750 locus at chromosome band 11q13, and the protein coding region, spanning approximately 5 kb, is comprised of 8 exons that range in size from 36 to 431 bp. Exons 6 and 7 are contiguous and the two isoforms of VRF arise through alternate splicing of exon 6. VRF appears to be ubiquitously expressed as two transcripts of 2.0 and 5.5 kb; the level of expression is similar among normal and malignant tissues.

Compilation of somatic mutations of the CDKN2 gene in human cancers : non-random distribution of base substitutions

The CDKN2 gene, encoding the cyclin-dependent kinase inhibitor p16, is a tumour suppressor gene that maps to chromosome band 9p21-p22. The most common mechanism of inactivation of this gene in human cancers is through homozygous deletion; however, in a smaller proportion of tumours and tumour cell lines intragenic mutations occur. In this study we have compiled a database of over 120 published point mutations in the CDKN2 gene from a wide variety of tumour types. A further 50 deletions, insertions, and splice mutations in CDKN2 have also been compiled. Furthermore, we have standardised the numbering of all mutations according to the full-length 156 amino acid form of p16. From this study we are able to define several hot spots, some of which occur at conserved residues within the ankyrin domains of p16. While many of the hotspots are shared by a number of cancers, the relative importance of each position varies, possibly reflecting the role of different carcinogens in the development of certain tumours. As reported previously, the mutational spectrum of CDKN2 in melanomas differs from that of internal malignancies and supports the involvement of UV in melanoma tumorigenesis. Notably, 52% of all substitutions in melanoma-derived samples occurred at just six nucleotide positions. Nonsense mutations comprise a comparatively high proportion of mutations present in the CDKN2 gene, and possible explanations for this are discussed.

CDKN2A/p16 is inactivated in most melanoma cell lines

The CDKN2A gene maps to chromosome 9p21-22 and is responsible for melanoma susceptibility in some families. Its product, p16, binds specifically to CDK4 and CDK6 in vitro and in vivo, inhibiting their kinase activity. CDKN2A is homozygously deleted or mutated in a large proportion of tumor cell lines and some primary tumors, including melanomas. The aim of this study was to investigate the involvement of CDKN2A and elucidate the mechanisms of p16 inactivation in a panel of 60 cell lines derived from sporadic melanomas. Twenty-six (43%) of the melanoma lines were homozygously deleted for CDKN2A, and an additional 15 (25%) lines carried missense, nonsense, or frameshift mutations. All but one of the latter group were shown by microsatellite analysis to be hemizygous for the region of 9p surrounding CDKN2A. p16 was detected by Western blotting in only five of the cell lines carrying mutations. Immunoprecipitation of p16 in these lines, followed by Western blotting to detect the coprecipitation of CDK4 and CDK6, revealed that p16 was functionally compromised in all cell lines but the one that carried a heterozygous CDKN2A mutation. In the remaining 19 lines that carried wild-type CDKN2A alleles, Western blot analysis and immunoprecipitation indicated that 11 cell lines expressed a wild-type protein. Northern blotting was performed on the remaining eight cell lines and revealed that one cell line carried an aberrantly sized RNA transcript, and two other cell lines failed to express RNA. The promoter was found to be methylated in five cell lines that expressed CDKN2A transcript but not p16. Presumably, the message seen by Northern blotting in these cell lines is the result of cross-hybridization of the total cDNA probe with the exon 1beta transcript. Microsatellite analysis revealed that the majority of these cell lines were hemi/homozygous for the region surrounding CDKN2A, indicating that the wild-type allele had been lost. In the 11 cell lines that expressed functional p16, microsatellite analysis revealed loss of heterozygosity at the markers immediately surrounding CDKN2A in five cases, and the previously characterized R24C mutation of CDK4 was identified in one of the remaining 6 lines. These data indicate that 55 of 60 (92%) melanoma cell lines demonstrated some aberration of CDKN2A or CDK4, thus suggesting that this pathway is a primary genetic target in melanoma development.

Evidence for three tumor suppressor loci on chromosome 9p involved in melanoma development

Cytogenetic and loss of heterozygosity (LOH) studies have long indicated the presence of a tumor suppressor gene (TSG) on 9p involved in the development of melanoma. Although LOH at 9p has been reported in approximately 60% of melanoma tumors, only 5-10% of these tumors have been shown to carry CDKN2A mutations, raising the possibility that another TSG involved in melanoma maps to chromosome 9p. To investigate this possibility, a panel of 37 melanomas derived from 35 individuals was analyzed for CDKN2A mutations by single-strand conformation polymorphism analysis and sequencing. The melanoma samples were then typed for 15 markers that map to 9p13-24 to investigate LOH trends in this region. In those tumors demonstrating retention of heterozygosity at markers flanking CDKN2A and LOH on one or both sides of the gene, multiplex microsatellite PCR was performed to rule out homozygous deletion of the region encompassing CDKN2A. CDKN2A mutations were found in tumors from 5 patients [5 (14%) of 35], 4 of which demonstrated LOH across the entire region examined. The remaining tumor with no observed LOH carried two point mutations, one on each allele. Although LOH was identified at one or more markers in 22 (59%) of 37 melanoma tumors corresponding to 20 (57%) of 35 individuals, only 11 tumors from 9 individuals [9 (26%) of 35] demonstrated LOH at D9S942 and D9S1748 the markers closest to CDKN2A. Of the remaining 11 tumors with LOH 9 demonstrated LOH at two or more contiguous markers either centromeric and/or telomeric to CDKN2A while retaining heterozygosity at several markers adjacent to CDKN2A. Multiplex PCR revealed one tumor carried a homozygous deletion extending from D9S1748 to the IFN-alpha locus. In the remaining eight tumors, multiplex PCR demonstrated that the observed heterozygosity was not attributable to homozygous deletion and stromal contamination at D9S1748, D9S942, or D9S974, as measured by comparative amplification strengths, which indicates that retention of heterozygosity with flanking LOH does not always indicate a homozygous deletion. This report supports the conclusions of previous studies that a least two TSGs involved in melanoma development in addition to CDKN2A may reside on chromosome 9p.

PTEN inactivation is rare in melanoma tumours but occurs frequently in melanoma cell lines

Deletions detected in cytogenetic and loss of heterozygosity (LOH) studies indicate that at least one tumour suppressor gene maps to the long arm of chromosome 10. Previous deletion mapping studies have observed LOH on 10q in about 30% of melanomas analysed. The PTEN gene, mapping to chromosome band 10q23.3, encodes a protein with both lipid and protein phosphatase activity. Somatic mutations and deletions in have been detected in a variety of cell lines and tumours, including melanoma samples. We performed mutation analyses and extensive allelic loss studies to investigate the role this gene plays in melanoma pathogenesis. We found that a total of 34 out of 57 (60%) melanoma cell lines carried hemizygous deletions of chromosome 10q encompassing the PTEN locus. A further three cell lines carried smaller deletions excluding PTEN. Inactivation of both PTEN alleles by exon-specific homozygous deletion or mutation was observed in 13 out of 57 (23%) melanoma cell lines. The mutation spectrum observed does not indicate an important role for ultraviolet radiation in the genesis of these mutations, and evidence from three cell lines supports the acquisition of PTEN aberrations in culture. Ten out of 49 (20%) matched melanoma tumour/normal samples harboured hemizygous deletions of either the whole chromosome or most of the long arm. Mutations within were detected in only one of the 10 tumours demonstrating LOH at 10q23 that were analysed. These results suggest that PTEN inactivation may be important for the propagation of melanoma cells in culture, and that another chromosome 10 tumour suppressor gene may be important for melanoma pathogenesis.

The Drinking Expectancy Questionnaire for Men who have Sex with Men (DEQ-MSM): A measure of substance-related beliefs

Introduction and Aims. Alcohol expectancies are associated with drinking behaviour and post-drinking use thoughts, feelings and behaviours. The expectancies held by specific cultural or sub-cultural groups have rarely been investigated. This research maps expectancies specific to gay and other men who have sex with men (MSM) and their relationship with substance use. This study describes the specific development of a measure of such beliefs for alcohol, the Drinking Expectancy Questionnaire for Men who have Sex with Men (DEQ-MSM). Design and Methods. Items selected through a focus group and interviews were piloted on 220 self-identified gay or other MSM via an online questionnaire. Results. Factor analysis revealed three distinct substance reinforcement domains ('Cognitive impairment', 'Sexual activity' and 'Social and emotional facilitation'). These factors were associated with consumption patterns of alcohol, and in a crucial test of discriminant validity were not associated with the consumption of cannabis or stimulants. Similarities and differences with existing measures will also be discussed. Discussion and Conclusions. The DEQ-MSM represents a reliable and valid measure of outcome expectancies, related to alcohol use among MSM, and represents an important advance as no known existing alcohol expectancy measure, to date, has been developed and/or normed for use among this group. Future applications of the DEQ-MSM in health promotion, clinical settings and research may contribute to reducing harm associated with alcohol use among MSM, including the development of alcohol use among young gay men.

Microscale study of electrical characteristics of epoxy-multiwall carbon nanotube nanocomposites

Epoxy-multiwall carbon nanotube nanocomposite thin films were prepared by spin casting. High power air plasma was used to preferentially etch a coating of epoxy and expose the underlying carbon nanotube network. Scanning electron microscopy (SEM) examination revealed well distributed and spatially connected carbon nanotube network in both the longitudinal direction (plasma etched surface) and traverse direction (through-thickness fractured surface). Topographical examination and conductive mode imaging of the plasma etched surface using atomic force microscope (AFM) in the contact mode enabled direct imaging of topography and current maps of the embedded carbon nanotube network. Bundles consisting of at least three single carbon nanotubes form part of the percolating network observed under high resolution current maps. Predominantly non-ohmic response is obtained in this study; behaviour attributed to less than effective polymer material removal when using air plasma etching.

The evidence-based development of an intervention to address the information needs of adults newly diagnosed with primary brain tumours and their carers

Adults diagnosed with primary brain tumours often experience physical, cognitive and neuropsychiatric impairments and decline in quality of life. Although disease and treatment-related information is commonly provided to cancer patients and carers, newly diagnosed brain tumour patients and their carers report unmet information needs. Few interventions have been designed or proven to address these information needs. Accordingly, a three-study research program, that incorporated both qualitative and quantitative research methods, was designed to: 1) identify and select an intervention to improve the provision of information, and meet the needs of patients with a brain tumour; 2) use an evidence-based approach to establish the content, language and format for the intervention; and 3) assess the acceptability of the intervention, and the feasibility of evaluation, with newly diagnosed brain tumour patients. Study 1: Structured concept mapping techniques were undertaken with 30 health professionals, who identified strategies or items for improving care, and rated each of 42 items for importance, feasibility, and the extent to which such care was provided. Participants also provided data to interpret the relationship between items, which were translated into ‘maps’ of relationships between information and other aspects of health care using multidimensional scaling and hierarchical cluster analysis. Results were discussed by participants in small groups and individual interviews to understand the ratings, and facilitators and barriers to implementation. A care coordinator was rated as the most important strategy by health professionals. Two items directly related to information provision were also seen as highly important: "information to enable the patient or carer to ask questions" and "for doctors to encourage patients to ask questions". Qualitative analyses revealed that information provision was individualised, depending on patients’ information needs and preferences, demographic variables and distress, the characteristics of health professionals who provide information, the relationship between the individual patient and health professional, and influenced by the fragmented nature of the health care system. Based on quantitative and qualitative findings, a brain tumour specific question prompt list (QPL) was chosen for development and feasibility testing. A QPL consists of a list of questions that patients and carers may want to ask their doctors. It is designed to encourage the asking of questions in the medical consultation, allowing patients to control the content, and amount of information provided by health professionals. Study 2: The initial structure and content of the brain tumour specific QPL developed was based upon thematic analyses of 1) patient materials for brain tumour patients, 2) QPLs designed for other patient populations, and 3) clinical practice guidelines for the psychosocial care of glioma patients. An iterative process of review and refinement of content was undertaken via telephone interviews with a convenience sample of 18 patients and/or carers. Successive drafts of QPLs were sent to patients and carers and changes made until no new topics or suggestions arose in four successive interviews (saturation). Once QPL content was established, readability analyses and redrafting were conducted to achieve a sixth-grade reading level. The draft QPL was also reviewed by eight health professionals, and shortened and modified based on their feedback. Professional design of the QPL was conducted and sent to patients and carers for further review. The final QPL contained questions in seven colour-coded sections: 1) diagnosis; 2) prognosis; 3) symptoms and problems; 4) treatment; 5) support; 6) after treatment finishes; and 7) the health professional team. Study 3: A feasibility study was conducted to determine the acceptability of the QPL and the appropriateness of methods, to inform a potential future randomised trial to evaluate its effectiveness. A pre-test post-test design was used with a nonrandomised control group. The control group was provided with ‘standard information’, the intervention group with ‘standard information’ plus the QPL. The primary outcome measure was acceptability of the QPL to participants. Twenty patients from four hospitals were recruited a median of 1 month (range 0-46 months) after diagnosis, and 17 completed baseline and follow-up interviews. Six participants would have preferred to receive the information booklet (standard information or QPL) at a different time, most commonly at diagnosis. Seven participants reported on the acceptability of the QPL: all said that the QPL was helpful, and that it contained questions that were useful to them; six said it made it easier to ask questions. Compared with control group participants’ ratings of ‘standard information’, QPL group participants’ views of the QPL were more positive; the QPL had been read more times, was less likely to be reported as ‘overwhelming’ to read, and was more likely to prompt participants to ask questions of their health professionals. The results from the three studies of this research program add to the body of literature on information provision for brain tumour patients. Together, these studies suggest that a QPL may be appropriate for the neuro-oncology setting and acceptable to patients. The QPL aims to assist patients to express their information needs, enabling health professionals to better provide the type and amount of information that patients need to prepare for treatment and the future. This may help health professionals meet the challenge of giving patients sufficient information, without providing ‘too much’ or ‘unnecessary’ information, or taking away hope. Future studies with rigorous designs are now needed to determine the effectiveness of the QPL.