Gene expression profiling identifies different sub-types of retinoblastoma.

BACKGROUND: Mutation of the RB1 gene is necessary but not sufficient for the development of retinoblastoma. The nature of events occurring subsequent to RB1 mutation is unclear, as is the retinal cell-of-origin of this tumour. METHODS: Gene expression profiling of 21 retinoblastomas was carried out to identify genetic events that contribute to tumorigenesis and to obtain information about tumour histogenesis. RESULTS: Expression analysis showed a clear separation of retinoblastomas into two groups. Group 1 retinoblastomas express genes associated with a range of different retinal cell types, suggesting derivation from a retinal progenitor cell type. Recurrent chromosomal alterations typical of retinoblastoma, for example, chromosome 1q and 6p gain and 16q loss were also a feature of this group, and clinically they were characterised by an invasive pattern of tumour growth. In contrast, group 2 retinoblastomas were found to retain many characteristics of cone photoreceptor cells and appear to exploit the high metabolic capacity of this cell type in order to promote tumour proliferation. CONCLUSION: Retinoblastoma is a heterogeneous tumour with variable biology and clinical characteristics.

Giant reduction of InN surface electron accumulation: compensation of surface donors by Mg dopants.

Extreme electron accumulation with sheet density greater than 10(13) cm(-2) is almost universally present at the surface of indium nitride (InN). Here, x-ray photoemission spectroscopy and secondary ion mass spectrometry are used to show that the surface Fermi level decreases as the Mg concentration increases, with the sheet electron density falling to below 10(8) cm(-2). Surface space-charge calculations indicate that the lowering of the surface Fermi level increases the density of unoccupied donor-type surface states and that these are largely compensated by Mg acceptors in the near-surface hole depletion region rather than by accumulated electrons. This is a significant step towards the realization of InN-based optoelectronic devices.

Surface band-gap narrowing in quantized electron accumulation layers.

An energy gap between the valence and the conduction band is the defining property of a semiconductor, and the gap size plays a crucial role in the design of semiconductor devices. We show that the presence of a two-dimensional electron gas near to the surface of a semiconductor can significantly alter the size of its band gap through many-body effects caused by its high electron density, resulting in a surface band gap that is much smaller than that in the bulk. Apart from reconciling a number of disparate previous experimental findings, the results suggest an entirely new route to spatially inhomogeneous band-gap engineering.

Accurate ultra-low-energy secondary ion mass spectrometry analysis of wide bandgap GaN/In(x)Ga(1-x)N structures using optical conductivity enhancement.

Ultra-low-energy secondary ion mass spectrometry has been used to undertake a structural analysis of GaN-In(x)Ga(1-x)N (x approximately 0.25) quantum wells used in optoelectronic devices. The high resistivity of intrinsic GaN-In(x)Ga(1-x)N restricts the necessary electrical path between the analyzed area and the instrument ground potential resulting in surface charge accumulation. Consequently, unstable and unrepresentative depth profiles tend to be produced. A technique known as optical conductivity enhancement (OCE) has been used during depth profiling to reduce the material resistivity. This creates an electrical path between the sample and holder, eliminating charge build up and resulting in accurate depth profiles.

Unintentional conductivity of indium nitride: transport modelling and microscopic origins.

A three-region model for the high n-type conductivity in InN, including contributions from the bulk, surface and buffer layer interface of the sample, is considered. In particular, a parallel conduction analysis is used to show that this model can account for the carrier concentration and mobility variation with film thickness that has previously been determined from single-field Hall effect measurements. Microscopic origins for the donors in each region are considered, and the overriding tendency towards n-type conductivity is discussed in terms of the bulk band structure of InN.

The donor nature of muonium in undoped, heavily n-type and p-type InAs.

The charge state of muonium has been investigated in p-type doped, nominally undoped (low n-type) and heavily n-type doped InAs. The donor Mu(+) state is shown to be the dominant defect in all cases. Consequently, muonium does not simply counteract the prevailing conductivity in this material. This is consistent with the charge neutrality level lying above the conduction band minimum in InAs.

Response to Therapy, Treatment Intolerance and Tyrosine Kinase Inhibitor Cessation Eligibility in a Real-World Cohort of Chronic Myeloid Leukaemia Patients.

Tyrosine kinase inhibitor (TKI) therapy has revolutionised chronic myeloid leukaemia (CML) management, it is however associated with significant side effects and economic burden. Recent studies have demonstrated that treatment free remission is possible in certain patients. The aim of this study was to characterise a real-world population in terms of response to therapy, treatment intolerance and potential eligibility for stopping treatment. Included were 105 CML patients diagnosed in Northern Ireland from March 2009-February 2018. Response to treatment was defined as per the 2009 and 2013 European Leukaemia Net guidelines. Potential for treatment cessation was assessed as per the 2017 UK Interim Expert Opinion on Discontinuing Tyrosine Kinase Inhibitor Treatment in Clinical Practice for Treatment-Free Remission in Chronic Myeloid Leukaemia. Our cytogenetic data cohort had a 12-month complete cytogenetic response rate of 66% and the molecular data cohort had a 12-month major molecular response rate of 38%. Of those commenced on 2nd line TKI therapy 81% achieved an optimal response at 12 months. Twenty-two patients developed intolerance and required a change in TKI therapy. The commonest side effects were gastro-intestinal upset (18%), transaminitis (16%) and fluid retention (16%). In our cohort, 20% were considered eligible to stop TKI therapy. The commonest reason for ineligibility was insufficient duration of therapy (25%). We observed that 1st and 2nd line TKI therapy are effective but problems with failure and intolerance persist. Additionally, this study identifies a cohort of patients who may attempt TKI cessation using the UK Interim Expert Opinion report on TKI therapy discontinuation.

Molecular analysis of single colonies reveals a diverse origin of initial clonal proliferation in B-precursor acute lymphoblastic leukemia that can precede the t(12;21) translocation.

The pathogenesis of pediatric B-precursor acute lymphoblastic leukemia is largely unknown, and even with nonrandom chromosomal translocations present, the precise order of clonal molecular events is undefined. We developed an in vitro system using cytokines interleukin (IL)-3, IL-7, IL-10, and FMS-like tyrosine kinase 3 ligand with CD40 ligand-expressing fibroblasts to obtain single blast colonies from which clonal immunoglobulin heavy chain (IgH), T-cell receptor delta gene rearrangements, and, in t(12;21)-positive cases, TEL-AML1 fusion transcripts could be simultaneously PCR amplified. The proliferation of early tumor progenitors increased subclone detection enabling us, in seven diagnostic samples, to determine the stage of differentiation at which each leukemia occurred. Four were derived from the stage before initiation of IgH rearrangement, one during recombination of variable, joining, and diversity segments of the heavy chain gene VDJ(H), and two after completion of IgH rearrangement. Furthermore, analysis of a t(12;21)-positive leukemia with unusually late onset, identified both TEL-AML1-positive and -negative colonies carrying a clonal T-cell receptor delta rearrangement, inferring the presence of clonal expansion before the occurrence of the t(12;21). In contrast, in a typical, early onset t(12;21)-positive leukemia, the t(12;21) appeared to be the first clonal event. In both leukemias, the t(12;21) occurred before recombination of variable, joining and diversity segments of the heavy chain gene VDJ.

Rearrangement of the same chromosome regions in different SV40 transformed human skin keratinocyte lines is associated with tumourigenicity.

Twelve different human keratinocyte strains were transformed with recombinant plasmid pSV6-1 which contained an origin defective SV40 genome. When injected into athymic nude mice lines produced either squamous cell carcinomas (SCC) in all animals, SCC in some animals and epidermal cysts in others, or epidermal cysts only in all the animals. The tumourigenic capacity of the lines could be correlated with the chromosomal changes present initially in the transformed cells. Lines which produced SCC in all the animals within a short period of time all showed simultaneous loss of part of chromosomes 3p, 8p and 11p in one homologue. Lines which were not tumourigenic did not show these simultaneously appearing rearrangements. These specific rearrangements are acquired in vitro and the time taken for a recognisable tumour to appear is related to the proportion of such cells in the line. The rearrangement of the same chromosome regions in different tumourigenic cell lines suggests that genes in these regions are important in the development of squamous cell carcinoma, possibly by loss of heterozygosity, at particular loci.

Positive and negative mood in the elderly: the ZENITH study.

OBJECTIVE: To assess the quality of positive and negative affect (mood) in an ageing European sample. BACKGROUND: Mood quality has important implications for both physical and mental wellbeing. Poor quality moods are associated with deficits in the diverse areas of cognitive function, health, and social relationships. The ageing process presents a number of potential challenges to successful mood regulation that could have wider implications. DESIGN AND PARTICIPANTS: The current study examines the quality of positive and negative affect in 387 healthy participants from three European countries. Moods were measured four times a day for 4-7 d with the Positive and Negative Affect Schedule (PANAS) mood scales. Measures of zinc (Zn) status were taken also. SETTING: Two centres concentrated on 55-70 yr olds (Coleraine, N.Ireland, n = 93 and Clermont-Ferrand, France, n = 95), and two centres concentrated on 70-87 yr olds (Rome, Italy, n = 108, and Grenoble, France, n = 91). RESULTS: Positive affect scores for the centre in Rome were significantly (P < 0.01) lower than for the other three centres, and the Grenoble centre had significantly (P < 0.05) higher scores on negative affect than the other three centres. Mood was not related to measures of zinc status (all Ps > 0.05). CONCLUSIONS: The two centres with the oldest participants showed deficits in mood quality that may have implications for broader well-being.

Cognitive function in healthy older European adults: the ZENITH study.

OBJECTIVE: Baseline data are reported from a study of the effects of zinc supplementation on cognitive function in older adults as assessed by the CANTAB computerised test battery. DESIGN: This is a multicentre prospective intervention study employing a randomised double-blind design. SETTING: European community-based study. PARTICIPANTS: There are 387 healthy adults aged 55-87 y from centres in France, Italy and Northern Ireland. INTERVENTIONS: Measures of visual memory, working memory and attention were obtained at baseline (prior to supplementation). RESULTS: Younger adults (<70 y) performed significantly better than older adults (>70 y) on all tests, with minimal differences between centres. In addition, men outperformed women on tests of spatial span, pattern recognition memory and reaction times, although these gender differences varied somewhat between centres. CONCLUSIONS: The results are generally consistent with previous age- and gender-related effects on cognitive functioning.

Structural, optical and vibrational properties of self-assembled Pbn+1(Ti1-x Fex)nO(3n+1)-δ Ruddlesden-Popper superstructures.

Bulk crystals and thin films of PbTi(1-x)FexO3(-δ) (PTFO) are multiferroic, exhibiting ferroelectricity and ferromagnetism at room temperature. Here we report that the Ruddlesden-Popper phase Pbn+1(Ti(1-x)Fex)nO3(n+1)-δ forms spontaneously during pulsed laser deposition of PTFO on LaAlO3 substrates. High-resolution transmission electron microscopy, x-ray diffraction and x-ray photoemission spectroscopy were utilised to perform a structural and compositional analysis, demonstrating that n ≃ 8 and x ≃ 0.5. The complex dielectric function of the films was determined from far-infrared to ultraviolet energies using a combination of terahertz time-domain spectroscopy, Fourier transform spectroscopy, and spectroscopic ellipsometry. The simultaneous Raman and infrared activity of phonon modes and the observation of second harmonic generation establishes a non-centrosymmetric point group for Pbn+1(Ti0.5Fe0.5)nO3(n+1)-δ, a prerequisite for (but not proof of) ferroelectricity. No evidence of macroscopic ferromagnetism was found in SQUID magnetometry. The ultrafast optical response exhibited coherent magnon oscillations compatible with local magnetic order, and additionally was used to study photocarrier cooling on picosecond timescales. An optical gap smaller than that of BiFeO3 and long photocarrier lifetimes may make this system interesting as a ferroelectric photovoltaic.

Solution conformation of endothelin, a potent vaso-constricting bicyclic peptide. A combined use of 1H NMR spectroscopy and distance geometry calculations.

The solution structure of endothelin-1, a newly discovered potent bicyclic peptide vaso-constrictor agent, has been investigated using 1H NMR conformational constraints and distance geometry calculations. The conformation is constrained by two disulphide bridges between Cys1-Cys15 and Cys3-Cys11 but the NMR data and computed conformers show additional helical structure between residues Leu6 and Cys11. Our results are compared with previous conflicting reports on the solution conformation of this peptide.

Molecular cytogenetic characterization of two non-MYCN amplified neuroblastoma cell lines with complex t(11;17).

The pediatric tumor neuroblastoma is characterized by a very variable, and at times unpredictable, pattern of clinical behavior, ranging from a benign localized tumor to an aggressive malignancy with poor prognosis. Standard clinical and pathological assessments do not always differentiate reliably between tumor subtypes and, therefore, genetic markers are now playing an increasingly important role in treatment decisions. MYCN oncogene amplification, for example, provides a useful marker of poor prognosis. However, less than one-half of all patients who present with, or who later develop, metastatic disease show MYCN amplification. Consequently, the identification of characteristic patterns of genetic alteration in the remaining tumors is of importance. In this report, we describe two new cell lines that we have established from metastatic, non-MYCN amplified, advanced stage neuroblastomas. These cell lines show a number of features in common, including unbalanced translocation between 11q and 17q, loss of 3p, 4p and 11q and gain of 17q. Therefore, they provide a valuable resource for the characterization of genetic pathways leading to aggressive tumor growth in non-MYCN amplified neuroblastomas.

Clonal diversity of Ig and T-cell receptor gene rearrangements in childhood B-precursor acute lymphoblastic leukaemia.

The majority of paediatric B precursor acute lymphoblastic leukaemias in children are derived from a single transformed haematopoietic cell with complete or partial VDJ recombination within the immunoglobulin heavy chain gene. A high frequency of patients also show rearrangements within TCRdelta and TCRgamma loci and in up to 40% of children there is an excess of immune system gene rearrangements compared with the number of identified alleles of immune system genes, suggesting the presence of multiple leukaemic subclones -clonal diversity. It has been observed by us and other investigators that in individual patients the pattern of immune system gene rearrangements often changes between presentation and relapse. In order to explore the possibility that clonal diversity plays a biological role during disease progression we optimised methods for subclone detection and analysed the prognostic significance of clonal diversity among 75 children with B precursor-ALL. Our results suggest that clonal diversity plays a role in disease progression as patients with oligoclonal disease showed a significantly shorter disease free survival than patients with monoclonal disease. This trend was of particular importance in the 'standard risk' group of ALL where aggressive disease could not be recognised by other means. In addition, generation of independent subclones from an early, non-rearranged tumour progenitor appears to be a common feature among leukaemias with aggressive clinical behaviour. We speculate on the type of genetic factors which may participate both in the generation of subclones and also in wider genomic instability and which are likely to be required for the aggressive clinical phenotype in children with ALL.

Direct equilibration of soil water for delta(18)O analysis and its application to tracer studies.

Current methods for stable oxygen isotopic (delta (18)O) analysis of soil water rely on separation of water from the soil matrix before analysis. These separation procedures are not only time consuming and require relatively large samples of soil, but also have been shown to introduce a large potential source of error. Current research at Queen's University Belfast is focused on using direct equilibration of CO(2) with the pore water to eliminate this extraction step using the automated Multiprep system and a Micromass Prism III isotope ratio mass spectrometer (IRMS). The findings of this research indicate the method is less time consuming, more reliable, and reproducible to within accepted limits (+/-0.1% per thousand delta (18)O). In this study the direct equilibration method is used to analyse delta (18)O tracer profiles in the unsaturated zone of field soils, concurrently with chloride tracer profiles, which can be used to assess infiltration rates and mechanisms through the unsaturated zone. Copyright 1999 John Wiley & Sons, Ltd.

Exclusion of candidate genes and chromosomal regions in familial neuroblastoma.

Two families with recurrence of neuroblastoma one Italian and one British with three and two affected children respectively were genotyped using polymorphic markers on chromosome 1 spanning the p32-p36 region frequently deleted in neuroblastoma tumor cells. Linkage to this region was excluded by haplotype inspection and negative lod scores. Furthermore, the exclusion of genes involved in neurocristopathies sometimes associated with neuroblastoma was carried out by typing the Italian family with polymorphic markers located in or near the corresponding genes. Finally, linkage analysis in the two families showed negative lod scores for markers spanning the 16p12-13 chromosomal region where a locus for familial neuroblastoma has been recently mapped. Our findings indicate that different genes are involved in the pathogenesis of familial neuroblastoma.

Increased radiosensitivity and the basic defect in ataxia telangiectasia.

Various cellular defects have been found in ataxia telangiectasia (A-T) cells including increased radiosensitivity, increased sensitivity to various chemical agents, a probable DNA repair defect and a defect in DNA synthesis. How these different features are related to each other is at present unknown. It has been suggested that there is a defect in A-T that acts in tissue differentiation as well as during growth and in the mature adult. This hypothesis is supported by the observations, for example, of an immature thymus present in patients, the production of alpha-fetoprotein, which results in a high serum level, and ovarian dysgenesis. A gene for A-T has recently been localized to chromosome region 11q22-23, a site involved in chromosomes translocations in some non-lymphoid leukaemias. At the chromosomal level the spontaneous abnormalities in A-T include, first, an increased frequency of cells showing chromosome translocations involving immune system genes that normally undergo rearrangement to form a functional product; secondly, the formation of telometric dicentrics in both lymphocytes and fibroblasts; and thirdly formation of long-lived chromosome damage following exposure to ionizing radiation and radiomimetic drugs. The gene defect underlying this disorder is unknown and distinguishing between primary and secondary effects of the mutant gene is difficult. We consider alternative models for retention of translocation T cells. First, it is possible that there is a defect in recognition of site-specific damage leading to retention of translocation cells that might otherwise be removed. Secondly, a feature common to the production of illegitimate T-cell receptor gene rearrangements and to formation of telomeric dicentric chromosomes in A-T cells is an increased period of time available for chromosome interchange, possibly due to a site-specific defect in strand break repair. It is possible that this defect may also prevent chromosome restitution following exposure of cells to ionizing radiation.

Genetic and cellular features of ataxia telangiectasia.

Ataxia telangiectasia (AT) is a developmental disorder in which many organ systems are affected. The children are recognized by a progressive cerebellar deterioration. The gene for AT has now been localized to a region of chromosome 11q22-23 of no more than 3Mb in size and its product appears to be involved directly or indirectly in some form of DNA recombination. Patients and their cells are unusually sensitive to ionizing radiation and various radiometric drugs. Observations on the progressive nature of the disorder, with loss of selected cells or failure to develop normally, might be compatible with the pathological effect of an inability to correctly regulate apoptosis in some cell lineages. While this is an intriguing speculation there is, at present, no evidence for such a defect in AT.

A haplotype common to intermediate radiosensitivity variants of ataxia-telangiectasia in the UK.

In a study of ataxia-telangiectasia (A-T) in the UK, patients in 10 out of 60 families were shown to have a much lower level of chromosomal radiosensitivity compared with the majority of patients. In some patients the level of radiosensitivity was hardly distinguishable from normal. Patients in this group, however, could be distinguished clinically from the majority either by the later onset of severe cerebellar features or the slower rate of progress of the disorder. By using highly polymorphic microsatellite repeat markers a chromosome 11q22-23 haplotype common to the majority of these patients, and not occurring in any non-A-T chromosome in 60 families, was identified on one chromosome. The haplotype probably defines the region of the A-T gene in these families and the mutation associated with this haplotype may be much less severe than the second mutation thereby producing the slightly milder phenotype.