Construction of a chromosome 17 transcriptome in serous ovarian cancer identifies differentially expressed genes.

Cytogenetic, molecular genetic, and functional analyses have implicated chromosome 17 genes in epithelial ovarian cancer (EOC). To further characterize the contribution of chromosome 17 genes in EOC, the Affymetrix U133A GeneChip was used to perform transcriptome analyses of 15 primary cultures of normal ovarian surface epithelial (NOSE) cells and 17 malignant ovarian tumor (TOV) samples of the serous histopathologic subtype. A two-way comparative analysis of 776 known genes and expressed sequences identified 253 genes that exhibited at least a threefold difference in expression in at least one TOV sample compared to the mean of NOSE samples. Within this data set, 99 of the 253 (39.1%) genes exhibited similar patterns of expression across all tested samples, suggesting a high degree of concordance in the chromosome 17 transcriptome. This observation was supported by hierarchical clustering analysis that segregated the TOV and NOSE samples into two separate groups. There were 77 genes that were differentially expressed in at least 50% of the TOV samples. Five genes (AdoRA(2B)at 17p12, CCL2 at 17q12, ACLY at 17q21.2, WIPI1 at 17q24.2, and SLC16A3 at 17q25.3) were significantly (P < 5.13E-11) differentially expressed at least threefold in all serous TOV samples, and all five genes were underexpressed in these TOV samples as compared to the NOSE samples. Interestingly, several of these differentially expressed genes have been previously associated with response to hypoxia.

Transfer of chromosome 3 fragments suppresses tumorigenicity of an ovarian cancer cell line monoallelic for chromosome 3p.

Multiple chromosome 3p tumor suppressor genes (TSG) have been proposed in the pathogenesis of ovarian cancer based on complex patterns of 3p loss. To attain functional evidence in support of TSGs and identify candidate regions, we applied a chromosome transfer method involving cell fusions of the tumorigenic OV90 human ovarian cancer cell line, monoallelic for 3p and an irradiated mouse cell line containing a human chromosome 3 in order to derive OV90 hybrids containing normal 3p fragments. The resulting hybrids showed complete or incomplete suppression of tumorigenicity in nude mouse xenograft assays, and varied in their ability to form colonies in soft agarose and three-dimensional spheroids in a manner consistent with alteration of their in vivo tumorigenic phenotypes. Expression microarray analysis identified a set of common differentially expressed genes, such as SPARC, DAB2 and VEGF, some of which have been shown implicated in ovarian cancer. Genotyping assays revealed that they harbored normal 3p fragments, some of which overlapped candidate TSG regions (3p25-p26, 3p24 and 3p14-pcen) identified previously in loss of heterozygosity analyses of ovarian cancers. However, only the 3p12-pcen region was acquired in common by all hybrids where expression microarray analysis identified differentially expressed genes. The correlation of 3p12-pcen transfer and tumor suppression with a concerted re-programming of the cellular transcriptome suggest that the putative TSG may have affected key underlying events in ovarian cancer.

[Electronic coupling and charge transfer of DNA: energy control]. / Couplage électronique et transferts de charges dans l'ADN: étude du contrôle énergétique.

The influence of the energetic gap on the effective distance-decay rate of electronic coupling (beta(eff)) in DNA is investigated in the context of the superexchange mechanism. The DNA double helix is described by a tight-binding electronic Hamiltonian model, in which all orbitals have the same energy and interact with one another through an exponentially decaying function of distance. Our numerical results concerning the beta(eff) values obtained for two different DNA molecules are analyzed within the theoretical framework of the "continuous-medium approximation," previously developed by Lopez-Castillo et al. (J.-M. Lopez-Castillo, A. Filali-Mouhim, I.L. Plante, and J.-P. Jay-Gerin. J. Phys. Chem. 99 : 6864-6875, 1995). We find that the intervening DNA bridge between the donor and acceptor sites is defined by a unique dimensionless control parameter gamma/E, where E is the energy of the orbitals of this medium with respect to those of the redox site orbitals (energetic gap) and gamma is the electronic band width of the bridge considered as a continuous medium. In the narrow-band regime, our "through-space" coupling model predicts beta(eff) values that are in good order of magnitude agreement with those calculated by other theoretical approaches as well as with those obtained from experiment. Moreover, under equivalent energetic conditions, the DNA-mediated transfers of holes and electrons differ considerably. This difference depends upon the sign of the parameter gamma/E.

Monte Carlo calculation of the primary radical and molecular yields of liquid water radiolysis in the linear energy transfer range 0.3-6.5 keV/micrometer: application to 137Cs gamma rays.

Monte Carlo simulations of the radiolysis of neutral liquid water and 0.4 M H(2)SO(4) aqueous solutions at ambient temperature are used to calculate the variations of the primary radical and molecular yields (at 10(-6)s) as a function of linear energy transfer (LET) in the range approximately 0.3 to 6.5 keV/micrometer. The early energy deposition is approximated by considering short (approximately 20-100 micrometer) high-energy (approximately 300-6.6 MeV) proton track segments, over which the LET remains essentially constant. The subsequent nonhomogeneous chemical evolution of the reactive species formed in these tracks is simulated by using the independent reaction times approximation, which has previously been used successfully to model the radiolysis of water under various conditions. The results obtained are in good general agreement with available experimental data over the whole LET range studied. After normalization of our computed yields relative to the standard radical and molecular yields for (60)Co gamma radiation (average LET approximately 0.3 keV/micrometer), we obtain empirical relationships of the primary radiolytic yields as a function of LET over the LET range studied. Such relationships are of practical interest since they allow us to predict a priori values of the radical and molecular yields for any radiation from the knowledge of the average LET of this radiation only. As an application, we determine the corresponding yields for the case of (137)Cs gamma radiation. For this purpose, we use the value of approximately 0.91 keV/micrometer for the average LET of (137)Cs gamma rays, chosen so that our calculated yield G(Fe(3+)) for ferrous-ion oxidation in air-saturated 0.4 M sulfuric acid reproduces the value of 15.3 molecules/100 eV for this radiation recommended by the International Commission on Radiation Units and Measurements. The uncertainty range on those primary radical and molecular yields are also determined knowing the experimental error (approximately 2%) for the measured G(Fe(3+)) value. The following values (expressed in molecules/100 eV) are obtained: (1) for neutral water: G(e(-)(aq)) = 2.50 +/- 0.16, G(H(.)) = 0.621 +/- 0.019, G(H(2)) = 0.474 +/- 0.025, G((.)OH) = 2.67 +/- 0.14, G(H(2)O(2)) = 0.713 +/- 0.031, and G(-H(2)O) = 4.08 +/- 0.22; and (2) for 0.4 M H(2)SO(4) aqueous solutions: G(H(.)) = 3.61 +/- 0.09, G(H(2)) = 0.420 +/- 0.019, G((.)OH) = 2.78 +/- 0.12, G(H(2)O(2)) = 0.839 +/- 0.037, and G(-H(2)O) = 4.46 +/- 0.16. These computed values are found to differ from the standard yields for (60)Co gamma rays by up to approximately 6%.

Lysozyme fragmentation induced by gamma-radiolysis.

Irradiation of lysozyme in frozen states in the absence of oxygen induces specific fragmentation at defined sites along the backbone chain. This paper localizes radio-fragmentation sites by two methods. First, N-terminal sequencing of radiolysis fragments after separation by SDS-polyacrylamide gel electrophoresis and estimation of their molecular masses. Secondly, after purification of radiolysis fragments by reverse phase-HPLC and determination of their molecular mass by electro-spray-ionization mass-spectrometric analysis, combined to N-terminal sequencing and total amino acid analysis. Evidence for the breakage of the peptide bond itself (CO-NH) is given, with radio-fragmentation sites mostly found at the surface of irradiated lysozyme in solvent exposed loops and turns.