Abstract 5326: COSMIC: Enhancing the world's knowledge of somatic mutations in human cancer

COSMIC, the Catalogue Of Somatic Mutations In Cancer (http://cancer.sanger.ac.uk) is the world's largest and most comprehensive online resource for exploring the impact of somatic mutations in human cancer. Now running for over 10 years, the 67th release (Oct 2013) describes 1592109 mutations in 947213 tumour samples across 25606 genes. This information is curated manually from the scientific literature, and automatically from genome resequencing consortium data portals. Full curation of the scientific literature provides in-depth understanding of the impact that each gene has in human cancer, and this has been achieved for 127 point-mutated cancer genes, and 185 fusion gene pairs. Curated genes are selected from the Cancer Gene Census (http://cancer.sanger.ac.uk/census), a listing of all genes with substantial evidence implicating them in cancer promotion, currently numbering 513 and updated frequently.

The mutations discovered in the re-sequencing of over 8000 tumour genomes are now present in COSMIC (viewable in isolation from the genic curations, http://cancer.sanger.ac.uk/wgs). In addition, the Sanger has now fully exome sequenced 1015 common cancer cell lines, identifying 1146874 coding mutations annotated for functional significance, and this is available exclusively in COSMIC at (http://cancer.sanger.ac.uk/cell_lines). While COSMIC has focused on point mutations and gene fusions, many other mutation mechanisms cause oncogenesis and these are now being integrated. The 67th COSMIC release includes copy number mutations integrated into the database and major web page views. To allow easy graphical examination of this data, copy number information was reduced to ‘gain’ and ‘loss’ annotations for inclusion in histograms and tables, with much more precise detail available with a further click. Copy number data is available in detail for every gene in COSMIC, and also for every tissue. Exploring cancer via COSMIC’s Cancer Browser (http://cancer.sanger.ac.uk/cosmic/browse/tissue), results not just in a plot of the most mutated genes, but now also a circular genome plot summarizing the copy number gains and losses across all the samples from that tumour type, all explorable in more detail via clicks on the pictures.

As the genomic data increases in COSMIC, it is becoming more important to qualitatively annotate the information, indicating which is more important or significant to oncogenesis. We are now building systems to better highlight known or putative functional mutations, improving the signal-to-noise ratio of cancer genome resequencing.

Citation Format: C Boutselakis, S A. Forbes, P Gunasekaran, M Jia, D Beare, N Bindal, C Y. Kok, K Leung, D Minjie, R Shepherd, S Bamford, S Ward, C Cole, J W. Teague, M Stratton, P Campbell, U McDermott. COSMIC: Enhancing the world's knowledge of somatic mutations in human cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5326. doi:10.1158/1538-7445.AM2014-5326

Wide-scale pollen banking of ornamental plants through cryopreservation

BACKGROUND

Cryopreservation has been proved to be an efficient method for the long-term storage of pollen, based on our previous studies establishing cryo pollen banks for Camellia, Paeonia, and Prunus mume.

OBJECTIVE

In the present study, we aimed to extend and verify the applicability of the cryopreservation protocol for ornamental plants.

MATERIALS AND METHODS

71 species or cultivars from 19 families were cryopreserved using the established protocol.

RESULTS

Pollen from 60 species or cultivars (85% of those experimented on) retained viability after 1 year's cryopreservation; of these, 36 (51% of the total investigated) retained a sufficiently high germination capability compared with fresh pollen to enable longer term cryopreservation.

CONCLUSION

This study confirms that wide-scale pollen banking of ornamental plants is feasible.

Expression, purification, crystallization and preliminary X-ray diffraction analysis of EtFPOX from Eupenicillium terrenum sp

The flavoenzyme fructosyl peptide oxidase (FPOX) catalyses the oxidative deglycation of fructosyl amino acids or fructosyl dipeptides to produce amino acids, glucosone and hydrogen peroxide. In this study, FPOX protein from Eupenicillium terrenum sp. (EtFPOX) was expressed in Escherichia coli and purified by Ni-affinity and gel-filtration chromatography. EtFPOX crystals were obtained using the sitting-drop vapour-diffusion method with polyethylene glycol 3350 as precipitant. X-ray diffraction data were collected to 1.90 Å resolution using a synchrotron-radiation source. The crystals belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 65.6, b = 80.0, c = 83.4 Å, and contained one molecule in the asymmetric unit. The calculated Matthews coefficient and solvent content were 2.22 Å(3) Da(-1) and 44.62%, respectively.

Impaired natural killer cell-induced antibody-dependent cell-mediated cytotoxicity is associated with human immunodeficiency virus-1 disease progression

This study evaluates the correlation between natural killer (NK) cell function and human immunodeficiency virus (HIV)-1 disease progression in 133 untreated HIV-1 positive Chinese subjects, including 41 former plasma donors (FPDs) and 92 men who have sex with men, and 35 HIV-negative controls. Flow cytometry was used to determine the abundance of NK cell subsets, the expression levels of receptor species, human leucocyte antigen (HLA) genotyping and the antibody-dependent cell-mediated cytotoxicity (ADCC) responses of NK cells. We observed a decreased expression of CD56(dim) CD16(+) NK cell subsets and an increased expression of CD56(-) CD16(+) with HIV-1 infection. As well, the expression of activating and inhibitory receptors increased significantly in NK cells, but CD16 receptor levels and the NKG2A/NKG2C ratio were down-regulated with HIV-1 infection. ADCC responses were higher in elite controllers than in all other groups, and were correlated inversely with HIV-1 viral load but correlated positively with CD4 count only in FPDs. Furthermore, individuals infected for < 1 year have lower ADCC responses than those infected for > 1 year. We also observed a negative association between ADCC responses and viral load in those who carry the HLA-A*30/B*13/Cw*06 haplotype. The positive correlation between CD16 expression and ADCC responses and a negative correlation trend between CD158a and ADCC responses were also observed (P = 0·058). Our results showed that the ADCC response is associated with patients' disease status, receptor expression levels, infection time and specific HLA alleles, which indicates that ADCC may offer protective effects against HIV-1 infection.

Expression, purification, crystallization and preliminary X-ray diffraction analysis of Arabidopsis thaliana Deg8

Arabidopsis thaliana Deg8, an ATP-independent serine endopeptidase, is involved in the repair of photosystem II (PSII), specifically the degradation of the photo-damaged PSII reaction centre D1 protein. To understand the molecular mechanism underlying the participation of Deg8 in the degradation of the photo-damaged D1 protein, the structure of Deg8 is needed. Until recently, however, no structure of Deg8 had been solved. In this study, Deg8 from A. thaliana was cloned, overexpressed and purified in Escherichia coli. Crystallization was performed at 277 K using tribasic sodium citrate as the precipitant and the crystals diffracted to 2.0 Å resolution, belonging to space group C2 with unit-cell parameters a = 129.5, b = 124.2, c = 93.3 Å, α = γ = 90, β = 132.4°. Assuming one trimer in the asymmetric unit, the Matthews coefficient and the solvent content were calculated to be 2.35 Å(3) Da(-1) and 47.6%, respectively.

Molecular cloning, expression, purification and crystallographic analysis of zebrafish THEM2

Thioesterase superfamily member 2 (THEM2) is essential for cell proliferation of mammalian cells. It belongs to the hotdog-fold thioesterase superfamily and catalyzes the hydrolysis of the thioester bonds of acyl-CoA in vitro. In this study, THEM2 protein from zebrafish (fTHEM2) was expressed in Escherichia coli and purified by Ni-affinity and gel-filtration chromatography. fTHEM2 crystals were obtained using the sitting-drop vapour-diffusion method with PEG 10 000 as precipitant. X-ray diffraction data were collected to 1.80 Å resolution using a synchrotron-radiation source. The crystals belonged to the monoclinic space group C2, with unit-cell parameters a=77.1, b=74.4, c=96.6 Å, β=93.7°.

FUS-NLS/Transportin 1 complex structure provides insights into the nuclear targeting mechanism of FUS and the implications in ALS

The C-terminal nuclear localization sequence of FUsed in Sarcoma (FUS-NLS) is critical for its nuclear import mediated by transportin (Trn1). Familial amyotrophic lateral sclerosis (ALS) related mutations are clustered in FUS-NLS. We report here the structural, biochemical and cell biological characterization of the FUS-NLS and its clinical implications. The crystal structure of the FUS-NLS/Trn1 complex shows extensive contacts between the two proteins and a unique α-helical structure in the FUS-NLS. The binding affinity between Trn1 and FUS-NLS (wide-type and 12 ALS-associated mutants) was determined. As compared to the wide-type FUS-NLS (K(D) = 1.7 nM), each ALS-associated mutation caused a decreased affinity and the range of this reduction varied widely from 1.4-fold over 700-fold. The affinity of the mutants correlated with the extent of impaired nuclear localization, and more importantly, with the duration of disease progression in ALS patients. This study provides a comprehensive understanding of the nuclear targeting mechanism of FUS and illustrates the significance of FUS-NLS in ALS.

The progress of selective fluorescent chemosensors by boronic acid

As a cutting-edge scientific research field, the detection of biological active substance is very important for the prevention, diagnosis and treatment of diseases. Boronic acid interacts with cis-1,2-or 1,3-diol to form five- or six-membered ring which could be used as the reporter of fluorescent sensors to probe carbohydrates and bioactive substance. This review summarizes the recent progress of boronic acid sensors for carbohydrates, L-dopamine, fluoride, copper ion, mercury ion and hydrogen peroxide. In this article, we will briefly introduce the chemistry of boronic acid, and then give a description of the fluorescence properties of each boronic acid sensor, such as fluorescence intensity change, excitation and emission wavelengths, quantum yields and water solubility. In addition, we summarize the mechanisms of fluorescent signal output for some representative sensors and discuss the strategies for developing new fluorescent probes.

Potential autophagy enhancers attenuate rotenone-induced toxicity in SH-SY5Y

Recent studies have shown that autophagy upregulation may be a tractable therapeutic intervention for clearing the disease-causing proteins, including α-synuclein, ubiquitin, and other misfolded or aggregated proteins in Parkinson's disease (PD). In this study, we explored a novel pharmacotherapeutic approach to treating PD by utilizing potential autophagy enhancers valproic acid (VPA) and carbamazepine (CBZ). Pretreatment with VPA (3 mM) and CBZ (50 μM) along with positive control rapamycin (Rap, 0.2 μM) or lithium (LiCl, 10 mM) significantly enhanced cell viability, decreased rotenone-induced nuclear fragmentation and apoptosis, ameliorated the decrease in mitochondrial membrane potential, reduced reactive oxygen species generation in the human neuroblastoma SH-SY5Y cells. Specifically, the numbers of lysosomes and autophagic vacuolar organelles were increased and the microtubule-associated protein 1 light chain 3-II (LC3-II) expression was up-regulated by VPA, CBZ, Rap, and LiCl (53%, 31%, 72%, and 63%), suggesting that these agents activated autophagic pathways. Moreover, pretreatment with the autophagy inhibitor chloroquine (Chl, 10 μM) remarkably strengthened rotenone toxicity in these cells. Our results suggest that VPA and CBZ, the most commonly used anti-epilepsy and mood-stabilizing medications with low-risk and easy administration might be potential therapeutics for PD.

Loss of balance between T helper type 17 and regulatory T cells in chronic human immunodeficiency virus infection

The aim of this study is to characterize the changes of CD4(+) CD25(high) forkhead box P3 (FoxP3(+) ) regulatory T cells (T(reg) ), interleukin (IL)-17 secreting T helper type 17 (Th17) cell frequencies and the balance of these two subsets in a cohort of chronic human immunodeficiency virus type 1 (HIV-1)-infected patients in China. A total of 115 untreated chronic HIV-infected individuals and 32 healthy donors were recruited in this study. Peripheral blood mononuclear cells were isolated from ethylenediamine tetracetic acid (EDTA) anti-coagulated fresh whole blood and stained to characterize the frequencies of T(reg) and Th17. Of a total 115 patients, 42 individuals including 10 elite controllers were followed-up for more than 1 year, and changes of T(reg) and Th17 frequencies were analysed over time. The continuous loss of Th17 cells was accompanied by a concomitant rise in the frequency of T(reg) cells, resulting in a loss of Th17/T(reg) balance during the progressive HIV infection. Meanwhile, the T(reg) levels, Th17 levels and Th17/T(reg) ratios of the elite controller group were comparable to those of the HIV-1 negative controls in the follow-up study. Additionally, we demonstrated that loss of balance between Th17 and T(reg) is associated with an earlier CD4 T cell decline during the course of HIV infection. Our results indicate that a loss of immune-balance of Th17 to T(reg) during HIV-1 disease progression and the persistence of such an immune-balance in the elite controllers may have a critical role in HIV-1 infection and further shed new light into understanding the pathogenesis of HIV-1.

Glyceraldehyde-3-phosphate dehydrogenase: activity inhibition and protein overexpression in rotenone models for Parkinson's disease

Rotenone, a widely used pesticide and an environmental risk factor for Parkinson's disease (PD), induces nigrostriatal injury, Lewy body-like inclusions, and Parkinsonian symptoms in rat models for PD. Our previous data indicated that glyceraldehyde-3-phosphate dehydrogenase (GAPDH) overexpression and glycolytic inhibition were co-current in rotenone-induced PC12 (rat adrenal pheochromocytoma cells) cell death. However, whether GAPDH overexpression plays any role in dopaminergic neurodegeneration in vivo remains unknown. In this study, we have found that GAPDH overexpression and GAPDH-positive Lewy body-like aggregates in nigral dopaminergic neurons while nigral GAPDH glycolytic activity decreases in rotenone-based PD animal models. Furthermore, GAPDH knockdown reduces rotenone toxicity significantly in PC12. These in vitro and in vivo data suggest that GAPDH contributes to the pathogenesis of Parkinson's disease, possibly representing a new molecular target for neuroprotective strategies and alternative therapies for PD.

Kinase suppressor of Ras 2 is involved in regulation of cell proliferation and is up-regulated in human invasive ductal carcinomas of breast

AIM

To study the expression of Kinase Suppressor of Ras 2 (KSR2) in human breast tumors and its effect on proliferation of breast epithelial cells. We reported previously that KSR2 was up-regulated in immortalized human breast epithelial cells.

METHODS

Proteomics technologies, systems biology tool for a KSR2 network analysis, immunoblotting, siRNA technology, overexpression of KSR2, cell proliferation assays and immunohistochemistry of tissue microarray of human breast tumors and normal breast tissue were used.

RESULTS

In conditionally immortalized primary epithelial cells KSR2 expression was shown to be up-regulated. The involvement of KSR2 in regulation of cell proliferation was predicted by a KSR2-centered network analysis. We observed that KSR2 down-regulation with specific siRNA inhibited cell proliferation. By immunohistochemistry of tissue microarray it was demonstrated that KSR2 expression was enhanced in human invasive breast carcinomas.

CONCLUSION

Our findings propose KSR2 as a new marker of immortalization, which has an impact on cell proliferation.

Crystal structure of the C-terminal domain of the ɛ subunit of human translation initiation factor eIF2B

Eukaryotic translation initiation factor eIF2B, the guanine nucleotide exchange factor (GEF) for eIF2, catalyzes conversion of eIF2·GDP to eIF2·GTP. The eIF2B is composed of five subunits, α, β, γ, δ and ɛ, within which the ɛ subunit is responsible for catalyzing the guanine exchange reaction. Here we present the crystal structure of the C-terminal domain of human eIF2Bɛ (eIF2Bɛ-CTD) at 2.0-Å resolution. The structure resembles a HEAT motif and three charge-rich areas on its surface can be identified. When compared to yeast eIF2Bɛ-CTD, one area involves highly conserved AA boxes while the other two are only partially conserved. In addition, the previously reported mutations in human eIF2Bɛ-CTD, which are related to the loss of the GEF activity and human VWM disease, have been discussed. Based on the structure, most of such mutations tend to destabilize the HEAT motif.

Application of cumulative odds logistic model on risk factors analysis for sexually transmitted infections among female sex workers in Kaiyuan city, Yunnan province, China

OBJECTIVES

To investigate the epidemiology of sexually transmitted infections (STI) among female sex workers (FSW) in Kaiyuan city, Yunnan province, China, and to identify risk factors associated with STI.

METHODS

A cross-sectional study of 737 FSW was carried out from March to May 2006, with confidential interviews and laboratory tests for STI. A cumulative logit model was used to evaluate the risk factors for STI.

RESULTS

The overall prevalence of HIV is 10.3%. The prevalence of syphilis, herpes simplex virus type 2, gonorrhoea, chlamydia and trichomonas was 7.5%, 68.1%, 8.3%, 25.9% and 10.6%, respectively. In multivariate cumulative odds logistic analysis, the factors associated with STI were education level, living in the entertainment location, injection drug use, non-injection drug use, over five clients in the previous week and inconsistent use of condoms with clients.

CONCLUSION

The findings highlight the gravity of the STI epidemic among FSW in China, where sexual transmission has now overtaken unsafe injection practices as the dominant mode of HIV transmission. Targeted intervention programmes for FSW should focus on increasing condom use, strengthening knowledge and awareness of STI/HIV and encouraging routine screening and treatment-seeking behaviours. Reducing the spread of STI also has profound implications for the prevention of HIV.

Stigmatization and shame: consequences of caring for HIV/AIDS patients in China

Using a representative sample of 478 doctors, nurses, and lab technicians working with people living with HIV/AIDS (PLWHA), a cross-sectional study was conducted to assess the impact of the AIDS epidemic on medical care systems and service providers in China. Correlation analyses showed significant association between internalized shame reported by service providers and their perception of being stigmatized due to working with PLWHA. Multivariate analyses revealed that the perceived level of institutional support for AIDS care was significantly related to the stigmatization and shame reported by the service providers. The study findings suggest that improved institutional support for AIDS care at the facility level and HIV-related stigma reduction intervention are crucial to maintain a high quality performance by the workforce in the health care system.

Vortices, circumfluence, symmetry groups, and Darboux transformations of the (2+1) -dimensional Euler equation

The Euler equation (EE) is one of the basic equations in many physical fields such as fluids, plasmas, condensed matter, astrophysics, and oceanic and atmospheric dynamics. A symmetry group theorem of the (2+1) -dimensional EE is obtained via a simple direct method which is thus utilized to find exact analytical vortex and circumfluence solutions. A weak Darboux transformation theorem of the (2+1) -dimensional EE can be obtained for an arbitrary spectral parameter from the general symmetry group theorem. Possible applications of the vortex and circumfluence solutions to tropical cyclones, especially Hurricane Katrina 2005, are demonstrated.