Asymptotic distribution for epistatic tests in case-control studies

We propose a statistical model for dissecting a multilocus genotypic value into its main (additive and dominant) effects and epistatic effects between different loci in a case-control association study. The model can discern four different kinds of epistasis, additive × additive, additive × dominant, dominant × additive, and dominant × dominant interactions. To test each kind of epistasis, a χ(2) test statistic was computed for a two by two contingency table derived from combined genotypes in both case and control groups. We derived an analytical approach for estimating the asymptotic distribution of the χ(2) test statistic for epistatic tests under the null hypothesis, with the result being consistent with that from Monte Carlo simulations. The new model was used to analyze a case-control data set for candidate gene studies of stroke, leading to the identification of several significant interactions between causal SNPs on this disease.

HER2 evaluation and its impact on breast cancer treatment decisions

BACKGROUND

Eighteen to twenty percent of breast cancer tumors show abnormal amplification of the Human Epidermal growth factor Receptor 2 (HER2) gene and increased expression of the associated protein. HER2 amplification is associated with rapid tumor proliferation and shorter disease-free and overall survival. Because women with HER2 amplification are more likely to benefit from treatment with the drug trastuzumab, testing for HER2 is recommended to guide therapy. However, little is known about use of HER2 testing in real-world settings. This study examined uptake, use, appropriateness of HER2 testing, and the relationship between HER2 test results and treatment decisions.

METHODS

We assessed electronic data from 3,634 patients with invasive breast cancer diagnosed from 1998 to 2007 in a large integrated health system. We collected data on patient and tumor characteristics, HER2 testing status, test results, and trastuzumab treatment.

RESULTS

From 1998 to 2000, the percent of patients who underwent HER2 evaluation increased from 12 to 94%; <3% of women with ductal carcinoma in situ, for whom HER2 testing is not recommended, were tested. Trastuzumab use increased 5-fold after 2004, when guidelines expanded to include recommending adjuvant treatment for early-stage breast cancer in addition to metastatic treatment. Ninety-five percent of women receiving trastuzumab had a positive HER2 result. After 2004, 55% of women with invasive breast cancer and overexpression of HER2 received trastuzumab treatment; this ranged from 44% of women with localized breast cancer to 80% of women with distant metastatic disease.

CONCLUSIONS

These findings illustrate appropriate and effective implementation of a HER2 testing strategy in a managed care setting.

Macrophage LXRα gene therapy ameliorates atherosclerosis as well as hypertriglyceridemia in LDLR(-/-) mice

Liver X receptors (LXRs) are implicated in the regulation of cholesterol homeostasis, inflammatory response and atherogenesis. Administration of LXR agonists inhibits the progress of atherosclerosis, and also increases plasma triglyceride levels, representing an obstacle to their use in treating this disease. The objective of this study was to develop an alternative approach that could overcome this obstacle. Eight-week-old low-density lipoprotein receptor-deficient (LDLR(-/-)) mice were transplanted with hematopoietic stem cell (HSC)-enriched bone marrow cells transduced with lentivectors expressing either green fluorescent protein (GFP) (Lenti-SP-GFP, control) or LXRα (Lenti-SP-LXRα) driven by a synthetic macrophage promoter. At 4 weeks post-transplant, the mice were fed with a Western diet for 8 weeks and then killed. Compared with Lenti-SP-GFP mice, the Lenti-SP-LXRα mice had a 30% reduction in atherosclerotic lesions, which was accompanied by increases in levels of macrophage expression of cholesterol efflux genes apolipoprotein E and ATP-binding cassette A1, as well as decreases in plasma inflammatory cytokines interleukin-6 and tumor necrosis factor-α. Intriguingly, a 50% reduction of plasma triglyceride level was also observed. We conclude that HSC-based macrophage LXRα gene therapy ameliorates the development of atherosclerosis along with an unexpected concomitant reduction of plasma triglyceride levels in LDLR(-/-) mice. These findings highlight the potential value of macrophage LXR expression as an avenue for therapeutic intervention against atherosclerosis.

Adult endothelial progenitor cells retain hematopoiesis potential

Hematopoietic stem cells (HSCs) are derived from endothelium in the aortic-gonado-mesonephric (AGM) region during embryogenesis. But little is known about whether endothelial progenitor cells (EPCs) retain hematopoiesis potential after birth. In this study, we isolated adult EPCs from the bone marrow of C57BL/6 mice and identified them with an endothelial functional assay and by the CD31(+) CD133(+) CD45(-/dim) VEGFR2(+) phenotype. EPCs isolated from green fluorescence protein (GFP) transgenic C57BL/6 mice were cotransfused with bone marrow cells from wild-type C57BL/6 mice into lethally irradiated BABL/c mice. One month after transplantation, granulocytes (25.73 ± 5.43%) and lymphocytes (12.68 ± 3.26%) in peripheral blood showed GFP(+), referred to as donor EPC-derived blood cells. After an additional month, the percentage of GFP(+) granulocytes decreased to (3.69 ± 1.43%), whereas the percentage of GFP(+) lymphocytes showed no significant difference. Most of the GFP(+) elements showed a diffuse distribution in the spleen; but some were present as aggregates forming lymphoid nodules. GFP(+) endothelial cells were observed in the liver sinusoids, intestinal villi, and lung of recipient mice. These results indicated that adult EPCs not only took part in vasculogenesis, but also retained hematopoietic ability.

C-met as a therapeutic target using ARQ 197 in renal cell carcinoma

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Background: c-Met is a receptor tyrosine kinase involved in normal cellular growth and vascular development. It has also been identified as a proto-oncogene. Activating c-Met mutations and indirect c-Met activation via von Hippel-Lindau gene silencing have been demonstrated in renal cell carcinoma (RCC) for papillary and clear cell histologic subtypes, respectively. We studied c-Met expression in a large cohort of RCC tumors and investigated in vitro activity of the new selective c-Met inhibitor, ARQ 197.

Methods: Tissue microarrays were performed to analyze c-Met protein expression in situ in 317 RCC tumor specimens using Automated Quantitative Analysis (AQUA). Western blots were performed for c-Met, phospho-c-Met and downstream pathway markers in 6 RCC cell lines (A498, ACHN, Caki-1, Caki-2, 769P, and 786-O). In vitro activity of ARQ 197 was studied by cell viability and clonogenic assays, and by changes in c-Met and down-stream mediators.

Results: c-Met expression is higher in RCC than adjacent normal renal tissue (p < 0.0001) and is expressed in all subtypes of RCC, including clear cell carcinoma; expression is highest in papillary and sarcomatoid subtypes. Greater c-Met expression correlates with higher tumor grade (p = 0.0019) and clinical stage (p = 0.0208), and is an independent predictor of poor overall survival (Multivariate Cox LR 5.7, p = 0.017). c-Met expression correlates to decreased survival in the clear cell subset as well. c-Met protein is activated (phosphorylated) in all 6 RCC cells. ARQ 197 inhibits cell growth in RCC cell lines at nanomolar concentrations (IC50 350-680 nM) and inhibits colony formation at 500 nM. ARQ 197 decreases phosphorylation of c-Met in time- and dose-dependent patterns with dose-dependent decreases in phospho-ERK.

Conclusions: c-Met expression is an independent predictor of survival in RCC, including clear cell subtype, suggesting that it is a potential therapeutic target worthy of further investigation. ARQ 197 effectively inhibits proliferation of clear cell carcinoma cell lines. Further preclinical studies are planned to determine mechanism of cellular arrest and apoptosis and markers of drug sensitivity and resistance.

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Somatostatin receptors SSTR2 and SSTR5 are expressed in the human thoracic duct

Somatostatin and its analog octreotide have been used successfully to treat postoperative chylothorax, and it has been shown that octreotide binds with high affinity to somatostatin receptor (SSTR) subtypes 2 and 5. Therefore, we investigated expression of SSTR2 and SSTR5 in the human thoracic duct by immunohistochemistry. Normal rat pancreas was used as a positive control for antibodies against SSTR2 and SSTR5, and Factor VIII-related antigen, SMA, actin, elastin, or collagen type II, III, IV or V antibodies were used to identify cell types and structures within the human thoracic duct. The antibodies against SSTR2 and SSTR5 worked well and yielded positive staining in control rat islets. In the human thoracic duct, SSTR2 was present in smooth muscle cells and some scattered structures which were stained by antibodies against Factor VIII-related antigen, SMA, actin, elastin or collagen type II, III, IV or V. SSTR5 was also present in smooth muscle cells. The presence of SSTR2 and SSTR5 in the human thoracic duct sheds light on the mechanism of somatostatin and octreotide use in the successful treatment of chylothorax and offers new molecular pathways to explore for potential future therapies.

Antitumor effects of AR-42, a novel histone deacetylase inhibitor, in embryonal carcinoma

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Background: Histone deacetylase inhibitors (HDACIs) modulate gene expression and induce cellular differentiation, growth inhibition and apoptotic cell death by chromatin hyperacetylation. Developmental arrest of germ cell differentiation earlier in the life is responsible for the pathogenesis of germ cell tumors (GCT). With current treatment nearly 95% of patients with GCT can be cured. Yet, effective agents with less toxicity are desired. In addition, those with relapsed/refractory disease have a dismal prognosis, indicating a clear need for new, more effective agents. Here we assess the antitumor effects of AR-42, a novel HDACI in in vitro and in vivo models of embryonal carcinoma.

Methods: In vitro effects of AR-42 and suberoylanilide hydroxamic acid (SAHA) were evaluated in NTERA-2, an embryonal carcinoma (EC) cell line derived from a human testicular cancer. Cell viability (MTS assay), apoptosis (caspase 3/7 activity and PARP cleavage), cell cycle analysis (flow cytometry) and HDAC inhibition (immunoblotting) were assessed. The in vivo efficacy of AR-42 was assessed in a NTERA-2 xenograft tumor model in male athymic nude mice. Mice were fed control diet and diet containing AR-42 at an average dose of 25 mg/kg/day. Tumor volumes and weights were used as in vivo endpoints.

Results: Treatment of NTERA-2 cells with both agents at 0.1-10 μM concentrations showed a time- and dose-dependent reduction in cell viability. Both agents significantly induced apoptosis, cell cycle inhibition and hyperacetylation of histones H-3 and H-4 in a dose-dependent manner. In vitro studies showed that AR-42 was more potent than SAHA. In our rodent model, AR-42-containing diet resulted in a significant reduction in tumor volumes and weights (50% and 56%, respectively). The results for intratumoral changes of proliferation and apoptosis are pending. There were no significant toxicities associated with AR-42, except for testicular atrophy, known to be reversible.

Conclusions: AR-42 appears to be a potent inhibitor of EC through different mechanisms, orally bioavailable and well tolerated in our rodent model. Our data indicates that AR- 42 may have clinical value in the treatment of GCT and requires further investigation in clinical trials.

No significant financial relationships to disclose.

Electron-beam-induced deposition and post-treatment processes to locally generate clean titanium oxide nanostructures on Si(100)

We have investigated the lithographic generation of TiO(x) nanostructures on Si(100) via electron-beam-induced deposition (EBID) of titanium tetraisopropoxide (TTIP) in ultra-high vacuum (UHV) by scanning electron microscopy (SEM) and local Auger electron spectroscopy (AES). In addition, the fabricated nanostructures were also characterized ex situ via atomic force microscopy (AFM) under ambient conditions. In EBID, a highly focused electron beam is used to locally decompose precursor molecules and thereby to generate a deposit. A drawback of this nanofabrication technique is the unintended deposition of material in the vicinity of the impact position of the primary electron beam due to so-called proximity effects. Herein, we present a post-treatment procedure to deplete the unintended deposits by moderate sputtering after the deposition process. Moreover, we were able to observe the formation of pure titanium oxide nanocrystals (<100 nm) in situ upon heating the sample in a well-defined oxygen atmosphere. While the nanocrystal growth for the as-deposited structures also occurs in the surroundings of the irradiated area due to proximity effects, it is limited to the pre-defined regions, if the sample was sputtered before heating the sample under oxygen atmosphere. The described two-step post-treatment procedure after EBID presents a new pathway for the fabrication of clean localized nanostructures.

Shallow and Deep Level Defects in GaN

Shallow and deep electronic defects in MOCVD-grown GaN were characterized by variable temperature Hall effect measurements, deep level transient spectroscopy (DLTS) and photoemission capacitance transient spectroscopy (O-DLTS). Unintentionally and Si-doped, n-type and Mg-doped, p-type GaN films were studied. Si introduces a shallow donor level into the band gap of GaN at ∼Ec - 0.02 eV and was found to be the dominant donor impurity in our unintentionally doped material. Mg is the shallowest acceptor in GaN identified to date with an electronic level at ∼Ev + 0.2 eV. With DLTS deep levels were detected in n-type and p-type GaN and with O-DLTS we demonstrate several deep levels with optical threshold energies for electron photoemission in the range between 0.87 and 1.59 eV in n-type GaN.

Improved intraportal islet transplantation outcome by systemic IKK-beta inhibition: NF-κB activity in pancreatic islets depends on oxygen availability

Intraportal islet transplantation suffers from low efficiency caused by substantial islet mass loss after transplantation. How this process is regulated is still unclear. Here, we show that NF-κB activation was detectable in islet grafts shortly after transplantation of porcine islets to diabetic NMRI nu/nu mice, and systemic NF-κB inhibition in transplanted animals significantly prolonged islet graft survival. Proinflammatory cytokines alone did not cause evident cell death in pancreatic islet within 24 h, while the combination of cytokines with hypoxia resulted in a strong induction of cell death that could be blocked dose-dependently by a selective IKK-β inhibitor. Under hypoxia, NF-κB activity impaired expression of antiapoptotic gene BCL-xL, c-FLIP and survivin. NF-κB activation in isolated islets was reduced by hypoxia in a time-dependent manner, accordingly, NF-κB activation in transplanted islets diminished by time. Our data indicate that, while NF-κB has an antiapoptotic role under normoxia, low oxygen conditions decrease its activity and transform it to a proapoptotic transcription factor in pancreatic islets. We conclude that NF-κB inhibition represents a potential strategy to improve islet transplantation efficiency.

High-energy x-ray backlighter spectrum measurements using calibrated image plates

The x-ray spectrum between 18 and 88 keV generated by a petawatt laser driven x-ray backlighter target was measured using a 12-channel differential filter pair spectrometer. The spectrometer consists of a series of filter pairs on a Ta mask coupled with an x-ray sensitive image plate. A calibration of Fuji™ MS and SR image plates was conducted using a tungsten anode x-ray source and the resulting calibration applied to the design of the Ross pair spectrometer. Additionally, the fade rate and resolution of the image plate system were measured for quantitative radiographic applications. The conversion efficiency of laser energy into silver Kα x rays from a petawatt laser target was measured using the differential filter pair spectrometer and compared to measurements using a single photon counting charge coupled device.