Identification of breast cancer prognosis markers using integrative sparse boosting

OBJECTIVES

In breast cancer research, it is important to identify genomic markers associated with prognosis. Multiple microarray gene expression profiling studies have been conducted, searching for prognosis markers. Genomic markers identified from the analysis of single datasets often suffer a lack of reproducibility because of small sample sizes. Integrative analysis of data from multiple independent studies has a larger sample size and may provide a cost-effective solution.

METHODS

We collect four breast cancer prognosis studies with gene expression measurements. An accelerated failure time (AFT) model with an unknown error distribution is adopted to describe survival. An integrative sparse boosting approach is employed for marker selection. The proposed model and boosting approach can effectively accommodate heterogeneity across multiple studies and identify genes with consistent effects.

RESULTS

Simulation study shows that the proposed approach outperforms alternatives including meta-analysis and intensity approaches by identifying the majority or all of the true positives, while having a low false positive rate. In the analysis of breast cancer data, 44 genes are identified as associated with prognosis. Many of the identified genes have been previously suggested as associated with tumorigenesis and cancer prognosis. The identified genes and corresponding predicted risk scores differ from those using alternative approaches. Monte Carlo-based prediction evaluation suggests that the proposed approach has the best prediction performance.

CONCLUSIONS

Integrative analysis may provide an effective way of identifying breast cancer prognosis markers. Markers identified using the integrative sparse boosting analysis have sound biological implications and satisfactory prediction performance.

Bioequivalence of two misoprostol tablets in healthy Chinese female volunteers: a single-dose, two-period, double crossover study

OBJECTIVE

To assess the bioequivalence of a new generic formulation of misoprostol (CAS 59122-46-2) 0.2 mg tablets (test) and the available branded tablet (reference) for the requirement of state regulatory criteria and the marketing of the test product in China.

METHODS

A randomized-sequence, 2-period crossover study was conducted in 20 healthy Chinese female volunteers in the fasted state. Blood samples were collected at baseline and 0.083, 0.17, 0.25, 0.33, 0.5, 0.75, 1, 1.25, 1.5, 2, 3, 4 and 6 h after a single oral dose of 0.6 mg misoprostol test or reference, followed by a 7-day washout period. Misoprostol acid, the active metabolite of misoprostol, was determined by an HPLC-MS/MS method. Drug And Statistics 2.0 was used to calculate the pharmacokinetics parameters and assess bioequivalence of the 2 formulations. It was considered bioequivalent if the 90% CIs of the mean ratios (test: reference) for Tmax, Cmax and AUC0-t were all within the range from 80% to 125%. Adverse events were monitored throughout the study based on clinical parameters and patient reports.

RESULTS

The main pharmacokinetics parameters for the test and reference were as follows: t1/2 was (0.680 ± 0.371) h and (0.650 ± 0.264) h; Tmax was (0.415 ± 0.087) h and (0.399 ± 0.097) h; Cmax was (1.941 ± 0.417) ng/mL and (2.047 ± 0.397) ng/mL; AUC0-t was (1.535 ± 0.419) ng·h/mL and (1.652 ± 0.400)ng·h/mL, and the AUC0-∞ was (1.576 ± 0.465) ng·h/mL and (1.686 ± 0.396) ng·h/mL. The mean ratios (test: reference) for Cmax, AUC0-t, and AUC0-∞ were 95.3% ±13.2%, 92.65% ± 17.31%, and 93.61%±18.97%, respectively. No significant (p>0.05) differences in pharmacokinetic parameters were found between preparations, treatments and periods.

CONCLUSIONS

This single-dose study in healthy Chinese fasted volunteers was shown that the misoprostol test and reference met the requirement of US and China regulatory criterion, and the test and reference were bioequivalent.

Beam-target double-spin asymmetry A{LT} in charged pion production from deep inelastic scattering on a transversely polarized {3}He target at 1.4<Q{2}<2.7 GeV{2}

We report the first measurement of the double-spin asymmetry A{LT} for charged pion electroproduction in semi-inclusive deep-inelastic electron scattering on a transversely polarized {3}He target. The kinematics focused on the valence quark region, 0.16<x<0.35 with 1.4<Q{2}<2.7  GeV{2}. The corresponding neutron A{LT} asymmetries were extracted from the measured {3}He asymmetries and proton over {3}He cross section ratios using the effective polarization approximation. These new data probe the transverse momentum dependent parton distribution function g{1T}{q} and therefore provide access to quark spin-orbit correlations. Our results indicate a positive azimuthal asymmetry for π{-} production on {3}He and the neutron, while our π{+} asymmetries are consistent with zero.

Assessment of modeled mercury dry deposition over the Great Lakes region

Three sets of model predicted values for speciated mercury concentrations and dry deposition fluxes over the Great Lakes region were assessed using field measurements and model intercomparisons. The model predicted values were produced by the Community Multiscale Air Quality Modeling System for the year 2002 (CMAQ2002) and for the year 2005 (CMAQ2005) and by the Global/Regional Atmospheric Heavy Metals Model for the year 2005 (GRAHM2005). Median values of the surface layer ambient concentration of gaseous elemental mercury (GEM) from all three models were generally within 30% of measurements. However, all three models overpredicted surface-layer concentrations of gaseous oxidized mercury (GOM) and particulate bound mercury (PBM) by a factor of 2-10 at the majority of the 15 monitoring locations. For dry deposition of GOM plus PBM, CMAQ2005 showed a clear gradient with the highest deposition in Pennsylvania and its surrounding areas while GRAHM2005 showed no such gradient in this region; however, GRAHM2005 had more hot spots than those of CMAQ2005. Predicted dry deposition of GOM plus PBM from these models should be treated as upper-end estimates over some land surfaces in this region based on the tendencies of all the models to overpredict GOM and PBM concentrations when compared to field measurements. Model predicted GEM dry deposition was found to be as important as GOM plus PBM dry deposition as a contributor to total dry deposition. Predicted total annual mercury dry deposition were mostly lower than 5 μg m(-2) to the surface of the Great lakes, between 5 and 15 μg m(-2) to the land surface north of the US/Canada border, and between 5 and 40 μg m(-2) to the land surface south of the US/Canada border. Predicted dry deposition from different models differed from each other by as much as a factor of 2 at regional scales and by a greater extent at local scales.

IL-7Rα deficiency in p53null mice exacerbates thymocyte telomere erosion and lymphomagenesis

Interleukin-7 (IL-7) is an essential T-cell survival cytokine. IL-7 receptor (IL-7Rα) deficiency severely impairs T-cell development due to substantial apoptosis. We hypothesized that IL-7Rα(null)-induced apoptosis is partially contributed by an elevated p53 activity. To investigate the genetic association of IL-7/IL-7Rα signaling with the p53 pathway, we generated IL-7Rα(null)p53(null) (DKO) mice. DKO mice exhibited a marked reduction of apoptosis in developing T cells and an augmented thymic lymphomagenesis with telomere erosions and exacerbated chromosomal anomalies, including chromosome duplications, breaks, and translocations. In particular, Robertsonian translocations, in which telocentric chromosomes fuse at the centromeric region, and a complete loss of telomeres at the fusion site occurred frequently in DKO thymic lymphomas. Cellular and molecular investigations revealed that IL-7/IL-7Rα signaling withdrawal diminished the protein synthesis of protection of telomere 1 (POT1), a subunit of telomere protective complex shelterin, leading to telomere erosion and the activation of the p53 pathway. Blockade of IL-7/IL-7Rα signaling in IL-7-dependent p53(null) cells reduced POT1 expression and caused telomere and chromosome abnormalities similar to those observed in DKO lymphomas. This study underscores a novel function of IL-7/IL-7Rα during T-cell development in regulating telomere integrity via POT1 expression and provides new insights into cytokine-mediated survival signals and T-cell lymphomagenesis.

Sodium valproate inhibits MDA-MB-231 breast cancer cell migration by upregulating NM23H1 expression

Breast cancer is a common cancer in women, with a highly variable course, from inoffensive to lethal. To find a more effective strategy for its treatment, sodium valproate has been tested as an anti-cancer drug; it is the only clinically available histone deacetylase inhibitor. However, data about the effects of sodium valproate on breast cancer are insufficient in both animals and humans; studies have yielded conflicting conclusions. In particular, little is known about the association between expression of the metastasis suppressor Nm23H1 gene and breast cancer. We hypothesized that sodium valproate regulates NM23H1 expression, and affects migration and/or invasion. We found that sodium valproate at concentrations of 0.8-3.2 mM inhibits migration and modulates Nm23H1 gene expression in a concentration-dependent manner. Confluent MDA-MB-231 cells were scratched by a micropipette tip after VPA treatment for 24 h; 24 h later, the scratch was almostly closed in the 0 mM VPA-treated cells, while the 3.2 mM VPA-treated cells migrated the slowest. The cell migration ratio exposed to 0.8, 1.6 and 3.2 mM VPA was about 66.67, 30.67 and 26.67% (P < 0.05). We also found evidence that sodium valproate upregulates NM23H1 expression, which is a clue to its anti-cancer mode of action. The NM23H1 gene expression was relative fold increased determined by Western blotting at 3.2 mM VPA. Collectively, these observations indicate that sodium valproate has potential for use in breast cancer treatment.

Intracranial dural arteriovenous fistulas: classification, imaging findings, and treatment

Intracranial DAVFs are pathologic dural-based shunts and account for 10%-15% of all intracranial arteriovenous malformations. These malformations derive their arterial supply primarily from meningeal vessels, and the venous drainage is either via dural venous sinuses or through the cortical veins. DAVFs have a reported association with dural sinus thrombosis, venous hypertension, previous craniotomy, and trauma, though many lesions are idiopathic. The diagnosis is dependent on a high level of clinical suspicion and high-resolution imaging. Cross-sectional imaging techniques by using CT and MR imaging aid in the diagnosis, but conventional angiography remains the most accurate method for complete characterization and classification of DAVFs. The pattern of venous drainage observed on dynamic vascular imaging determines the type of DAVF and correlates with the severity of symptoms and the risk of hemorrhage.

Microbial response to limited nutrients in shallow water immediately after the end-Permian mass extinction

Previous work indicates that a variety of microbes bloomed in the oceans after the end-Permian faunal mass extinction, but evidence is sporadically documented. Thus, the nature and geographic distribution of such microbes and their associations are unclear, addressed in this study using a series of biomarker groups. On the basis of microbial biomarker records of the 2-methylhopane index, evidence is presented for cyanobacterial blooms in both the western and eastern Tethys Sea and in both shallow and deep waters, after the mass extinction. The enhanced relative abundance of C(28) (expressed by the C(28) /C(29) ratio of) regular steranes suggests a bloom of prasinophyte algae occurred immediately after the end-Permian faunal extinction, comparable with those observed in some other mass extinctions in Phanerozoic. Significantly, cyanobacteria and prasinophyte algae show a synchronized onset of bloom in the shallow water Bulla section, north Italy, inferring for the first time their coupled response to the biotic crisis and the associated environmental conditions. However, in Meishan of Zhejiang Province in south China, the bloom declined earlier than in Bulla. The association of increased 2-methylhopane index with a negative shift in the nitrogen isotope composition infers a scenario of enhanced nitrogen fixation by cyanobacteria immediately after the faunal mass extinction. N(2) fixation by cyanobacteria is here interpreted to have provided prasinophyte algae with ammonium in nutrient-limited shallow waters, and thus caused their associated blooms.

A case report: successful treatment of meningeal metastasis with concurrent whole brain radiotherapy and erlotinib in a patient with non-small cell lung cancer

We report a case of successful treatment with erlotinib of a patient with non-small cell lung cancer (stage IV) and meningeal metastasis. Combined treatment with whole brain radiotherapy (WBRT) and erlotinib mitigated neurologic symptoms of the patient. Magnetic resonance imaging showed reduction of the brain metastasis. Partial remission was observed by chest computed tomography (CT) scan after six months of erlotinib therapy.

MeQA: a pipeline for MeDIP-seq data quality assessment and analysis

MOTIVATION

We present a pipeline for the pre-processing, quality assessment, read distribution and methylation estimation for methylated DNA immunoprecipitation (MeDIP)-sequence datasets. This is the first MeDIP-seq-specific analytic pipeline that starts at the output of the sequencers. This pipeline will reduce the data analysis load on staff and allows the easy and straightforward analysis of sequencing data for DNA methylation. The pipeline integrates customized scripting and several existing tools, which can deal with both paired and single end data.

AVAILABILITY

The package and extensive documentation, and comparison to public data is available at http://life.tongji.edu.cn/meqa/.

P5-21-01: A Renewable Tissue Resource of Phenotypically Stable Human Breast Cancer Xenografts for Preclinical Studies

Introduction Translational breast cancer research is hampered severely by difficulties in obtaining and studying primary human breast tissue, and by the lack of in vivo preclinical models that accurately reflect patient tumor biology. These limitations are due, in part, to the fact that traditional immunocompromised mouse models are not generally permissive for growth. We sought to circumvent some of these limitations by transplanting and growing human mammary tumors in the mammary fat pad of SCID/Beige immunocompromised mice in the absence of exogenous human fibroblasts.

Aims and Methods To establish a set of stable human breast cancer xenografts for preclinical studies. Human breast cancer biopsies were received, minced into small fragments and then transplanted directly into “cleared” fat pads of recipient SCID/Beige immunocompromised mice. Transplanted fat pads were checked weekly. After initial tumor was palpated and harvested, tumor fragments were transplanted into new SCID/Beige hosts for subsequent transplant generations. Serial immunohistochemical evaluations were performed to confirm human origin and biomarker status. Analytical flow cytometry for evaluating expression of proposed “cancer stem cell” markers, and gene and protein expression analysis were carried out on all stable lines.

Results and Conclusions Xenograft lines were established directly from breast cancer patient samples, without intervening culture in vitro, using the epithelium-free mammary fat pad as the transplantation site. Of the conditions tested, xenograft take rate was highest in the presence of a low-dose estradiol pellet without exogenous human fibroblasts. Thirty six stably transplantable xenograft lines representing 27 patients were established, using pre-treatment, mid-treatment, and/or post-treatment samples. Most patients yielding xenografts were “triple-negative” (ER-PR-HER2−) (n=21), we were able to establish lines from three ER-PR-HER2+ patients, one ER+PR+HER2−, one ER+PR-HER2−and one “triple-positive” (ER+PR+HER2+) patients. Serially passaged xenografts show phenotypic consistency with the tumor of origin at the histopathology level, and remarkable stability across multiple transplant generations at both the genomic, transcriptomic, and proteomic levels. Of 27 lines evaluated fully, thirteen xenografts showed metastasis to the mouse lung. These models thus serve as a renewable, quality-controlled tissue resource, and should prove useful for preclinical evaluation of experimental therapeutics.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P5-21-01.

Search for a new gauge boson in electron-nucleus fixed-target scattering by the APEX experiment

We present a search at the Jefferson Laboratory for new forces mediated by sub-GeV vector bosons with weak coupling α' to electrons. Such a particle A' can be produced in electron-nucleus fixed-target scattering and then decay to an e + e- pair, producing a narrow resonance in the QED trident spectrum. Using APEX test run data, we searched in the mass range 175-250 MeV, found no evidence for an A'→ e+ e- reaction, and set an upper limit of α'/α ~/= 10(-6). Our findings demonstrate that fixed-target searches can explore a new, wide, and important range of masses and couplings for sub-GeV forces.

Molecular Identification and Characterization of Tomato zonate spot virus in Tobacco in Guangxi, China

In Guangxi Province of southwest China, diseases caused by Tospoviruses (family Bunyaviridae) pose a serious threat to tobacco (Nicotiana tobacum) production. During surveys conducted annually at Xinrong Village in Jingxi County from 2008 to 2010, more than 130 ha of fields were found to have 10 to 50% of plants exhibiting symptoms similar to spotted wilt caused by Tomato spotted wilt virus (TSWV). During this period, disease symptoms at similar prevalence and incidence were also found at Fushan, Debao County in most of the cultivars produced in these areas, including Yunyan 85, 87, 92, 97, and K326. Symptoms on tobacco varied but commonly included dwarfing, midrib browning, distorted apical buds, and concentric ringspots that coalesced to form large areas of dead leaf tissue. Mechanical inoculation from diseased tobacco leaves with concentric ringspots back to tobacco cv. Yunyan 85 or 87, resulted in 12 of 16 plants with symptoms similar to those observed in the field. No symptoms on plants developed following inoculation with buffer only. Symptoms found in the field resembled those caused by TSWV. However, testing using TSWV-specific antiserum was shown to be negative by double-antibody sandwich-ELISA (Agdia, Elkhart, IN). Total RNA was extracted from 27 diseased tobacco plants collected from different regions in Guangxi using Trizol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer's instructions. RNA extracts were amplified by reverse transcription (RT)-PCR using the degenerate primers T2740 (ATGGGDATNTTTGATTTCATG) and T3920c (TCATGCTCATSAGRTAAATYTCTCT) designed to target the partial RNA-dependent RNA polymerase (RdRp) sequence of members in the genus Tospovirus (3). Amplification was performed at 42°C for 60 min, followed by 35 cycles of PCR (30 s denaturation at 94°C, 45 s annealing at 55°C, and 30 s extension at 72°C) and a 7-min final extension at 72°C. A PCR product of approximately 1.2 kb was amplified from 21 diseased plants. RT-PCR amplicons were cloned into the pUC19-T Simple Vector (TaKaRa, Dalian, China) and sequenced in both directions. Sequences were assembled and analyzed by DNAStar 5.01 (DNASTAR, Madison, WI). Sequences of representative isolates were deposited in GenBank (Accession Nos. JN020022 to JN020027). The 1.2-kb partial RdRp sequences of these isolates were shown to have 94.4 to 95.3% nucleotide identity and 96.5 to 97.5% amino acids identity to Tomato zonate spot virus (TZSV) (GenBank Accession No. NC_010491) (1). Among these TZSV isolates from Guangxi, the partial RdRp sequences have 98.0 to 99.4% nucleotide identity and 98.8 to 100% amino acids identity with each other. The presence of TZSV was further confirmed in diseased tobacco plants by indirect ELISA using antiserum of TZSV (provided by Prof. Zhongkai Zhang, Agricultural Academy of Yunnan, China). TZSV has been characterized as a novel tospovirus on various hosts including tobacco in Yunnan province (1,2). To our knowledge, this is the first report of TZSV-associated disease on tobacco in Guangxi Province, southwest China. Further work is necessary to study the epidemiology and management of the disease. References: (1) J. Dong et al. Arch. Virol. 153:855, 2008. (2) J. Dong et al. J. Insect Sci. 10:166, 2010. (3) Y. Lin. Master Thesis. National Chung Hsing University, Taichung, Taiwan, Republic of China, 2007.

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.

Topiramate as an adjunctive treatment for refractory partial epilepsy in the elderly

This double-blind, placebo-controlled study investigated the efficacy and tolerability of adjunctive topiramate in 86 elderly Chinese patients with refractory partial epilepsy. Patients who had at least four seizures per 4 weeks during an 8-week baseline period, despite medication with up to three standard antiepileptic drugs (AEDs), were randomly assigned to receive topiramate (n = 46) or placebo (n = 40). Topiramate dosages were titrated (target dose 200 mg/day orally) for 8 weeks and maintained at stable levels for another 12 weeks; concomitant AEDs continued at original dosages. All patients completed the study: 47.8% in the topiramate group and 7.5% on placebo reached ≥ 50% reduction in complex partial seizures. In the topiramate group, the most common adverse events were dizziness, somnolence, fatigue, headache and difficulty with memory; most events were transient and mild or moderate in severity. It was concluded that 200 mg/day topiramate was effective and well-tolerated in elderly patients with refractory partial epilepsy.