Using whole-genome sequencing to implicate the androgen receptor as the predominant driver of DNA breakpoints and fusion events in prostate cancer

67

Background: Structural rearrangements in cancers genomes have the potential to disrupt normal gene function and result in a selective growth advantage, either by inactivating tumour suppressors or creating novel gene fusions with oncogenic gain-of-function. Specific fusion genes identified to date are found in particular tumor types rather than being present in all cancers suggesting there are tissue-specific mechanisms underlying these events. The most well-known fusion event in prostate cancer is TMPRSS2-ERG. Recent studies have suggested that androgen receptor may play a role in the formation of TMPRSS2-ERG fusions, bringing the two loci in close proximity in the nucleus and facilitating DNA strand break and repair along with AR associated enzymes. Methods: To explore this mechanism more comprehensively, we performed whole-genome sequencing of 14 prostate cancers from seven patients as well as paired whole blood controls. Results: Across the cancer genomes we identified approximately 4,500 high confidence DNA breakpoints and found that a large proportion of these breakpoints were in close proximity to curated androgen receptor binding sites. Furthermore, when we examined breakpoints in 11 other cancers from the TCGA and ICGC projects, we identified a similar association with androgen (and estrogen) receptor binding sites specifically in hormone-dependent tumour types, suggesting a role for steroid hormone receptors in the formation of cancer driving structural rearrangements. In addition, in at least one patient, the formation of a novel gene fusion contributed directly to the lethal evolution of his tumour. Conclusions: These data suggest that the androgen receptor drives genome wide breakpoints and novel fusion events in prostate cancer.

Identified differently expressed genes in renal cell carcinoma by using multiple microarray datasets running head: differently expressed genes in renal cell carcinoma

OBJECTIVE

The purpose of this study was to identify differentially expressed genes and analysis biological processes related to renal cell carcinoma.

METHODS

A meta-analysis was performed using the Rank Product package of Gene Expression Omnibus datasets of renal cell carcinoma. Then Gene Ontology enrichment analyses and pathway analysis were performed based on Gene Ontology website and Kyoto Encyclopedia of Genes and Genomes. Protein-protein interaction network was constructed used Cytoscape software.

RESULTS

We identified a total of 1992 differentially expressed genes Rank Product package of renal cell carcinoma, 840 of them were not involved in individual DEGs. Gene Ontology enrichment analyses showed that those 840 genes enriched in terms such as response to hormone stimulus, endogenous stimulus, biological adhesion, and cell proliferation. Pathway analysis showed that significant pathways included pyruvate metabolism, glycerolipid metabolism, complement and coagulation cascades and so on. Protein-protein interaction network indicated that MT2A, MYC, CENPF and NEK2 has high degree which participated many interactions.

CONCLUSIONS

Our study displayed genes that were consistently differentially expressed in renal cell carcinoma, and the biological pathways, protein-protein interaction network associated with those genes.

Determining the depth of insertion of dynamically invisible membrane peptides by gel-phase ¹H spin diffusion heteronuclear correlation NMR

Solid-state NMR determination of the depth of insertion of membrane peptides and proteins has so far utilized (1)H spin diffusion and paramagnetic relaxation enhancement experiments, which are typically conducted in the liquid-crystalline phase of the lipid bilayer. For membrane proteins or peptide assemblies that undergo intermediate-timescale motion in the liquid-crystalline membrane, these approaches are no longer applicable because the protein signals are broadened beyond detection. Here we show that the rigid-solid HETCOR experiment, with an additional spin diffusion period, can be used to determine the depth of proteins in gel-phase lipid membranes, where the proteins are immobilized to give high-intensity solid-state NMR spectra. Demonstration on two membrane peptides with known insertion depths shows that well-inserted peptides give rise to high lipid cross peak intensities and low water cross peaks within a modest spin diffusion mixing time, while surface-bound peptides have higher water than lipid cross peaks. Furthermore, well-inserted membrane peptides have nearly identical (1)H cross sections as the lipid chains, indicating equilibration of the peptide and lipid magnetization. Using this approach, we measured the membrane topology of the α-helical fusion peptide of the paramyxovirus, PIV5, in the anionic POPC/POPG membrane, in which the peptide undergoes intermediate-timescale motion at physiological temperature. The gel-phase HETCOR spectra indicate that the α-helical fusion peptide is well inserted into the POPC/POPG bilayer, spanning both leaflets. This insertion motif gives insight into the functional role of the α-helical PIV5 fusion peptide in virus-cell membrane fusion.

Vertical-cavity and randomly scattered lasing from different thicknesses of epitaxial ZnO films grown on Y₂O₃-buffered Si (111)

Two different types of lasing modes, vertical Fabry-Perot cavity and random lasing, were observed in ZnO epi-films of different thicknesses grown on Si (111) substrates. Under optical excitation at room temperature by a frequency tripled Nd:YVO₄ laser with wavelength of 355 nm, the lasing thresholds are low due to high crystalline quality of the ZnO epitaxial films, which act as microresonators. For the thick ZnO layer (1,200 nm), its lasing action is originated from the random scattering due to the high density of crack networks developed in the thick ZnO film. However, the low crack density of the thin film (555 nm) fails to provide feedback loops essential for random scattering. Nevertheless, even the lower threshold lasing is achieved by the Fabry-Perot cavity formed by two interfaces of the thin ZnO film. The associated lasing modes of the thin ZnO film can be characterized as the transverse Gaussian modes attributed to the smooth curved surfaces.

IGFBP-3 binds GRP78, stimulates autophagy and promotes the survival of breast cancer cells exposed to adverse microenvironments

Despite the established role of insulin-like growth factor binding protein-3 (IGFBP-3) as a growth inhibitor in vitro, a high level of IGFBP-3 in breast tumor tissue is associated with the stimulation of xenograft growth in mice and poor prognosis in patients. To understand the contribution of IGFBP-3 to breast cancer progression, tandem affinity purification was used to identify novel interacting proteins. The endoplasmic reticulum protein, glucose-regulated protein 78 (GRP78), was shown to bind to IGFBP-3, confirmed by colocalization, coimmunoprecipitations, glutathione S-transferase (GST) pulldowns and a nanomolar binding affinity. GST pulldowns also indicated that the GRP78 ATPase domain mediated the interaction with IGFBP-3. The critical roles of GRP78 in the unfolded protein response and macroautophagy led to an investigation of possible links between IGFBP-3, GRP78 and cellular stress responses. IGFBP-3 was found to stimulate the survival of breast cancer cells subjected to glucose starvation and hypoxia. Pharmacological inhibitors and small interfering RNA knockdown established that the increased survival of IGFBP-3-expressing cells was dependent on an intact autophagy response, as well as GRP78. The contribution of autophagy was confirmed by the demonstration that IGFBP-3 expression increases both the formation of autophagic puncta and flux through the system. In conclusion, we have shown that IGFBP-3 stimulates autophagy and thereby promotes the survival of breast cancer cells exposed to conditions that represent the adverse microenvironments encountered by solid tumor cells in vivo.

Characteristics of diet patterns in metabolically obese, normal weight adults (Korean National Health and Nutrition Examination Survey III, 2005)

BACKGROUND AND AIMS

Metabolically obese normal weight (MONW) subjects are a subgroup of individuals who have a normal weight and body mass index (BMI), but exhibit obesity-related abnormalities. The objective of this study was to analyze the prevalence of metabolic syndrome (MetS) and characteristics of diet patterns in MONW Koreans.

METHODS AND RESULTS

We analyzed the data of 3050 adults > 20 years of age with a normal BMI (18.5~24.9 kg/m(2)) obtained from the Korea National Health and Nutrition Examination Survey III. Anthropometric measurements and information on health behaviors were obtained. The diagnostic criteria for MetS were defined by the International Diabetes Federation consensus. Dietary intake was assessed by the 24-h recall method. The weighted prevalence of MONW was 14.3%. The risk of MONW correlated inversely with the frequency of snacking and positively with the type of snack, particularly those with high carbohydrates. A high carbohydrate diet (≥73.9% of energy intake) compared to a low carbohydrate diet (<59.9% of energy intake) was positively associated with the risk of MONW (OR = 2.54; 95% CI: 1.41, 4.56), whereas a high protein diet (≥17.1% of energy intake) compared to a low protein diet (<12.2% of energy intake) reduced the risk of MONW (OR = 0.60; 95% CI: 0.39, 0.92) in females, but not in males.

CONCLUSIONS

This study suggests that a reduced intake of carbohydrates and carbohydrate snacks were associated with a lower prevalence of MONW in females.

An oncogenic role of miR-142-3p in human T-cell acute lymphoblastic leukemia (T-ALL) by targeting glucocorticoid receptor-α and cAMP/PKA pathways

MicroRNAs (miRNAs) are a family of 19-24 nucleotide non-coding RNAs with posttranscriptional regulatory functions. The involvement of miRNAs in normal hematopoiesis implies that deregulated miRNAs might contribute to leukemogenesis. To date, although certain miRNAs have been established a clear oncogenic role in hematological malignancies, other individual miRNAs potentially involved in human leukemogenesis still remain elusive. In this report, we showed that miR-142-3p was upregulated in human T-leukemic cell lines and primary T-leukemic cells isolated from T-cell acute lymphoblastic leukemia (T-ALL) patients and its expressive levels were correlated with patients' prognosis. Such an oncogenic role of miR-142-3p could be explained by its targeting cyclic adenosine monophosphate (cAMP)/protein kinase A (PKA) and glucocorticoid receptor alpha (GRα). High levels of miR-142-3p resulted in low levels of cAMP and weak activity of PKA, thus relieving the inhibitory effect of PKA on T-leukemic cell proliferation. Meanwhile, miR-142-3p decreased GRα protein expression by directly targeting the 3'-untranslational region of GRα mRNA, leading to glucocorticoid resistance. Transfection of the miR-142-3p inhibitor effectively converted glucocorticoid resistance, because of the resultant increase of GRα expression and PKA activity. These findings suggest that miR-142-3p is critical in T-cell leukemogenesis and may serve as a potential therapeutic target in T-ALL patients.

STRUCTURAL AND MAGNETIC PROPERTIES OF SINGLE CRYSTAL RARE EARTH Gd-Y SUPERLATTICES

High quality single crystal rare earth Gd-Y superlattices with wavelength varying from 8to 42 atomic layers were grown by the recently developed metal molecular beam epitaxy technique. The crystallinity and coherence of the superlattices were examined by X-ray diffraction, and the profiles of composition modulation and strain modulation were determined from a quantitative analysis based on a simple diffusion model for the Gd-Y interfaces. The sharp boundaries achieved in these metallic superlattices are approaching those in semiconductor superlattices. The various in-plane magnetization behavior at low fieldsamong superlattices of different wavelengths suggests the possible presence of new magnetic ordering structures as caused by the artificial modulation.

Direct Observation of Intermixing in GAAS/AIAS Multilayers After Very Low-Dose Ion-Implantation

We combine chemical lattice imaging and digital vector pattern recognition to study quantitatively, kinetic intermixing in GaAs/AlAs multilayers. We thus obtain, with atomic plane resolution and near-atomic sensitivity, composition profiles across each interface of a multilayer stack before and after ion-implantation. Our results show significant intermixing even when only one 320 keV Ga+ ion is implanted at 77 K into each 2000 A2 area of the interface. This corresponds to an incident ion dose of 5×l012/cm2.

The intermixing is not uniform along the interface. At each interface, we observe more intensely intermixed regions, whose widths correspond to those created by the damage track of a single implanted ion, as expected from Monte-Carlo simulations. It thus appears that we can directly image intermixing due to single energetic ions implanted into the multilayered GaAs/AlAs structure.

Advances in GaAs Mosfet's Using Ga2O3(Gd2O3) as Gate Oxide

In this article, we review the recent progress on GaAs MOSFET's using in-situ MBE-grown Ga2O3(Gd2O3) as the gate dielectric. Both depletion-mode (D-mode) and inversion-mode (I-mode) GaAs MOSFET's with negligible drain current drift and hysteresis are demostrated. The absence of drain current drift and hysteresis indicates that the excellent stability of the oxide and low oxide/GaAs interface state density have been achieved. The drain current density and transconductance are about one order of magnitude higher than the best previous reported data in the literature for an inversion-mode GaAs MOSFET. Excellent high frequency and power performances were also measured from the depletion-mode devices. These improvements are attributed to the excellent Ga2O3(Ga2O3) oxide properties and novel processing techniques.

Dielectrics for GaN Based MIS-Diodes

GaN MIS diodes were demonstrated utilizing AIN and Ga2O3(Gd2O3) as insulators. A 345 Åof AIN was grown on the MOCVD grown n-GaN in a MOMBE system using trimethylamine alane as Al precursor and nitrogen generated from a wavemat ECR N2 plasma. For the Ga2O3(Gd2O3) growth, a multi-MBE chamber was used and a 195 Å oxide is E-beam evaporated from a single crystal source of Ga5Gd3O12. The forward breakdown voltage of AlN and Ga2O3( Gd2O3) diodes are 5V and 6V, respectively, which are significantly improved from ˜1.2 V of schottky contact. From the C-V measurements, both kinds of diodes showed good charge modulation from ccumulation to depletion at different frequencies. The insulator/GaN interface roughness and the thickness of the insulator were measured with x-ray reflectivity.