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.

Effect of influenza on cardiorespiratory and all-cause mortality in Hong Kong, Singapore and Guangzhou

1. Using a common modelling approach, mortality attributable to influenza was higher in the two subtropical cities Guangzhou and Hong Kong than in the tropical city Singapore. 2. The virus activity appeared more synchronised in subtropical cities, whereas seasonality of influenza tended to be less marked in the tropical city. 3. High temperature was associated with increased mortality after influenza infection in Hong Kong, whereas relative humidity was an effect modifier for influenza in Guangzhou. No effect modification was found for Singapore. 4. Seasonal and environmental factors probably play a more important role than socioeconomic factors in regulating seasonality and disease burden of influenza. Further studies are needed in identifying the mechanism behind the regulatory role of environmental factors.

A New Approach to the Detection of Lesions in Mammography Using Fuzzy Clustering

Breast cancer is a leading cause of female mortality and its early detection is an important means of reducing this. The present study investigated an approach, based on fuzzy clustering, to detect small lesions, such as microcalcifications and other masses, that are hard to recognize in breast cancer screening. A total of 180 mammograms were analysed and classified by radiologists into three groups ( n = 60 per group): those with microcalcifications; those with tumours; and those with no lesions. Twenty mammograms were taken as training data sets from each of the groups. The algorithm was then applied to the data not taken for training. Analysis by fuzzy clustering achieved a mean accuracy of 99.7% compared with the radiologists' findings. It was concluded that the fuzzy clustering algorithm allowed for more efficient and accurate detection of breast lesions and may improve the early detection of breast tumours.

Synthesis, characterization and biocompatibility of poly(2-ethyl-2-oxazoline)-poly(D,L-lactide)-poly(2-ethyl-2-oxazoline) hydrogels

A novel thermoreversible hydrogel based on poly(2-ethyl-2-oxazoline)-derived amphiphilic triblock copolymer, poly(2-ethyl-2-oxazoline)-poly(D,L-lactide)-poly(2-ethyl-2-oxazoline) (PEOz-PLA-PEOz), was developed. The synthesis of PEOz-PLA-PEOz was carried out by coupling monohydroxylated PEOz-PLA diblocks with adipoyl chloride as coupling agent and dimethylamino pyridine as catalyst. The tube inverting and rheological tests showed that triblock copolymers had sol-gel-sol transition behavior with increasing temperature, and the gelation was found to be thermoreversible. The critical gelation concentration, the sol-gel transition temperature at a given concentration depended on the EOz/LA ratio and the molecular weight of PEOz. Scanning electron microscopy observation revealed that the resultant bulky gel exhibited an interconnected porous three-dimensional (3D) microstructure after freeze-drying. In addition, the hydrogels showed good cytocompatibility in vitro. MTT assays revealed that the human skin fibroblast cells encapsulated within the hydrogels were viable and proliferated inside the 3D scaffold. This newly described thermoreversible hydrogel demonstrated attractive properties to serve as cell matrix for a variety of tissue engineering applications or pharmaceutical delivery vehicles.

Liposome impaired the adhesion and spreading of HEK293 cells: an AFM study

Gene transfer has been proven to be a promising approach for treatment of several diseases. The cytotoxicity of transfection reagents is one of the key factors for clinical applications. The cytotoxicity of liposome has been extensively studied. However, its effects on the adhesion and spreading of transformed cells are still unclear. In this study, the cytotoxic effects of liposome on cell viability and mitochondrial membrane potential of HEK293 cells were first evaluated. Then, an atomic force microscope (AFM) was recruited to investigate the effects of liposome on the adhesion and spreading of HEK293 cells. AFM data indicated that liposome induced a significant decrease in number of cellular pseudopodia and cell-surface particles, in cell-surface roughness, and in average adhesion force of cell membranes. The AFM data implied that liposome impaired the adhesion and spreading of HEK293 cells.

Bax dimerizes via a symmetric BH3:groove interface during apoptosis

During apoptotic cell death, Bax and Bak change conformation and homo-oligomerize to permeabilize mitochondria. We recently reported that Bak homodimerizes via an interaction between the BH3 domain and hydrophobic surface groove, that this BH3:groove interaction is symmetric, and that symmetric dimers can be linked via the α6-helices to form the high order oligomers thought responsible for pore formation. We now show that Bax also dimerizes via a BH3:groove interaction after apoptotic signaling in cells and in mitochondrial fractions. BH3:groove dimers of Bax were symmetric as dimers but not higher order oligomers could be linked by cysteine residues placed in both the BH3 and groove. The BH3:groove interaction was evident in the majority of mitochondrial Bax after apoptotic signaling, and correlated strongly with cytochrome c release, supporting its central role in Bax function. A second interface between the Bax α6-helices was implicated by cysteine linkage studies, and could link dimers to higher order oligomers. We also found that a population of Bax:Bak heterodimers generated during apoptosis formed via a BH3:groove interaction, further demonstrating that Bax and Bak oligomerize via similar mechanisms. These findings highlight the importance of BH3:groove interactions in apoptosis regulation by the Bcl-2 protein family.

A prospective, multicenter trial of complementary and alternative medicine (CAM) utilization by patients undergoing definitive breast radiotherapy

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Background: A substantial number of breast cancer (BC) pts use complementary and alternative medicines (CAM), but there is a paucity of data on CAM specifically during radiation therapy (RT). The purpose of this study was to prospectively assess the utilization of CAM during RT for BC pts.

Methods: 456 pts w/stage 0-III BC were accrued from 5 RT centers from 9/07-2/09. Participating MDs were advised not to discuss CAM. A validated survey instrument was administered during the last week of RT under guidance of a study nurse, which included demographics, details regarding types/doses/frequency of CAM and skin assessments by pt and nurse.

Results: 360 pts were eligible for analysis (79%); median age 57 yrs; stage 0-II, 91%; white race 89%; chemotherapy 39%; hormone therapy (HT) w/ RT, 26%; > college education, 59%. CAM was reported in 54% (n = 195), of which 72% reported programs/activities (i.e., Reiki, healing touch, visualization, etc.), and 66% oral/topical CAM. Only 16% reported counseling prior to starting CAM. CAM use did not differ by ethnicity, chemotherapy or stage (all p > 0.05), but correlated significantly with higher education level (p = 0.0001) and inversely correlated w/ HT/RT (p = 0.015). There was a trend towards CAM use in younger pts (p = 0.069). On MVA, education (RC: 1.859; OR: 6.417, 95% CI: 2.023, 20.357, p = 0.002) and HT/RT (RC: -0.530, OR: 0.589, 95% CI: 0.357, 0.970, p = 0.038) independently predicted for CAM use. Rationale for oral/topical: 32% “improve their chance of cure”; 24% “provide treatment-related symptom relief”. For programs/activities: 31% “relaxation/stress reduction”; 11% “reduces treatment-related symptoms”. Despite these beliefs, there were no significant differences between the perception of the pts to nursing skin assessment score as a function of CAM use (p = 0.497).

Conclusions: To our knowledge, this is the first and largest prospective study of CAM during RT for BC pts. Given the high prevalence of undocumented CAM use during RT, questions regarding CAM should be considered during consultation and weekly tx visits. A better understanding of CAM practices during RT will facilitate evaluation of potential interactions of CAM and RT for BC.

Ginseng derivative ocotillol enhances neuronal activity through increased glutamate release: a possible mechanism underlying increased spontaneous locomotor activity of mice

Ginsenosides are the main active ingredients in ginseng and have recently been reported to have beneficial effects on the CNS. Ocotillol is a derivate of pseudoginsenoside-F11, which is an ocotillol-type ginsenoside found in American ginseng. We examined the effects of ocotillol (a) on neuronal activity of projection neurons, mitral cells (MC), in a mouse olfactory bulb brain slice preparation using whole-cell patch-clamp recording, and (b) on animal behavior by measuring locomotor activity of mice in vivo. Ocotillol displayed an excitatory effect on spontaneous action potential firing and depolarized the membrane potential of MCs. The effect was concentration-dependent, with an EC(50) of 4 μM. In the presence of blockers of ionotropic glutamatergic and GABAergic synaptic transmission (6-cyano-7-nitroquinoxaline-2,3-dione [CNQX], 10 μM; D-AP5, 50 μM; gabazine, 5 μM), the excitatory effect of ocotillol on firing was abolished. Further experiments showed that the ocotillol-induced neuronal excitation persisted in the presence of GABA(A) receptor antagonist gabazine but was eliminated by applying AMPA/kainate receptor antagonist CNQX and N-methyl-d-aspartate (NMDA) receptor antagonist D-AP5, suggesting that ionotropic glutamate transmission was involved in mediating the effects of ocotillol. Bath application of ocotillol evoked an inward current as well as an increased frequency of spontaneous glutamatergic excitatory postsynaptic currents (EPSCs). Both the inward current and sEPSCs could be blocked by ionotropic glutamate receptor antagonists CNQX and D-AP5. These results indicate that the excitatory action of ocotillol on MCs was mediated by enhanced glutamate release. Behavioral experiments demonstrated that ocotillol increased locomotor activities of mice. Our results suggest that ocotillol-evoked neuronal excitability was mediated by increased release of glutamate, which may be responsible for the increased spontaneous locomotor activities in vivo.

Sonodynamic effects of hematoporphyrin monomethyl ether on CNE-2 cells detected by atomic force microscopy

Hematoporphyrin monomethyl ether (HMME) has been effectively used to treat solid tumors of some types. However, its application in nasopharyngeal carcinoma has not been studied yet. In this paper, the detailed sonodynamic effects of HMME-SDT (sonodynamic therapy) on CNE-2 cells including cell growth inhibition, apoptosis induction, and membrane toxicity were investigated. It was found that HMME alone had less cytotoxicity whereas HMME-SDT could suppress the cell proliferation in a dose-dependent manner as detected by MTT assay. The annexin V-based flow cytometric data indicated that upon SDT, different concentrations of HMME induce distinct types of cell death, apoptosis by low concentration (60 µg/ml) of HMME and necrosis by higher concentration (120 µg/ml). The immunofluorescence of cytoskeleton and nuclei morphology showed that upon HMME-SDT, the cells became rounding and the cytoskeletal network disappeared, and, the nuclei represented a total fragmented morphology of nuclear bodies. These alternations showed the apoptosis induction by HMME-SDT. Further AFM study showed that the cell membrane structure and cytoskeleton networks were destroyed, and, the Young's modulus, tip-cell-surface adhesion force decreased to 0.22 ± 0.11 Mpa, 35.4 ± 12.8 pN of cells with 120 µg/ml HMME-SDT from 0.48 ± 0.21 Mpa, 69.6 ± 22.3 pN of native cells, respectively. These membrane changes caused the collapse of mitochondrial transmembrane potential and disturbance of intracellular calcium homeostasis, which was consistent with the results detected by flow cytometry. Therefore, membrane toxicity and cytoskeleton disrupture induced by HMME-SDT maybe important factors to induce cell apoptosis, and, the disturbance of mitochondrial transmembrane potential and calcium channels might be the apoptosis mechanisms.

Enhanced antitumor effects of tumor antigen-pulsed dendritic cells by their transfection with GM-CSF gene

To investigate the biological characterization and antitumor activities of GM-CSF gene-transfected dendritic cells, the splenic dendritic cells were infected with GM-CSF recombinant replication-deficient adenovirusesin vitro. Their enhanced expression of B7 was demonstrated by FACS analysis, and more potent stimulatory activity was confirmed by allogeneic MLR. Immunization of dendritic cells pulsed with irradiated B16 melanoma cells induced significant CTL and enabled host to resist the challenge of wild-type B16 cells. When they were transfected with GM-CSF gene subsequently, the induced CTL activity was higher, and the produced protection against B16 cell challenge and therapeutic effect on the mice with preestablished pulmonary metastases more effective. These data suggest that the dendritic cells pulsed with tumor antigen then transfected with GM-CSF gene can be used as an effective vaccine in tumor immunotherapy.

Interleukin-21 is upregulated in hepatitis B-related acute-on-chronic liver failure and associated with severity of liver disease

The immune mechanism(s) that lead to hepatitis B-related acute-on-chronic liver failure (HB-ACLF) are poorly understood. Interleukin-21 is a newly discovered cytokine that is involved in autoimmune and inflammatory diseases. Its potential role in HB-ACLF remains unknown. The serum levels of 12 immune cytokines measured by cytometric bead arrays and the frequency of IL-21-secreting CD4+ T cells in peripheral blood mononuclear cells (PBMC) measured by intracellular cytokine staining were compared in moderate chronic hepatitis B (M-CHB, n = 20), severe chronic hepatitis B (S-CHB, n = 20), HB-ACLF (n = 39) and healthy controls (n = 10). PBMC from M-CHB patients or healthy subjects were stimulated with rhIL-21 in vitro, and cytokines in supernatants were measured by FlowCytomix. The frequencies of IL-21-secreting CD4+ T cells were higher in HB-ACLF (both P < 0.001) and S-CHB (P = 0.002 and 0.001) as compared to M-CHB patients and controls. Serum IL-21 levels were highest (P < 0.001) in HB-ACLF and positively associated with high MELD score (P = 0.001) and mortality (P = 0.038). Recovery from HB-ACLF was associated with reduced serum IL-21 levels (P = 0.003) and lower CD4+ IL-21(+) T-cell frequency (P = 0.006). The secretions of IL-1β (P < 0.001), IL-6 (P < 0.001), IL-10 (P < 0.001), IFN-γ (P = 0.001) and TNF-α (P = 0.042) from PBMC were significantly increased with rhIL-21 stimulation. In summary, IL-21 has a causal role in the development of severe liver inflammation, which is upregulated in HB-ACLF and associated with severity of liver disease.

Effect of O2 on the adsorption of SO2 on carbon-supported Pt electrocatalysts

Adsorption of SO(2) in the presence of O(2) on Pt/C catalysts often used as electrocatalysts has been investigated by temperature programmed desorption (TPD) and X-ray photoelectron spectroscopy (XPS). The amounts of SO(2) adsorption on Pt/C in the presence of O(2) were much higher than those in the absence of O(2) (SO(2)-N(2)) and from the carbon support (Vulcan XC-72) alone. Adsorption is dependent on oxygen concentration over the range 0-20% but reaches saturation at 20% O(2). The spillover of SO(2) from Pt to the carbon support has been proposed for 10, 20, and 40% Pt loadings, characterized by desorption temperatures of approximately 150 and 260 °C for SO(2) adsorbed on Pt and carbon, respectively. Adsorbed Pt-S, C-S, C-SO(x), and Pt-SO(4) species were identified by XPS as S-containing species on both Pt and carbon. Both TPD and XPS indicate that the carbon support plays a major role in SO(2) adsorption, primarily as SO(x) (x = 3, 4). The bonding of S and SO(x) on the carbon support was strong enough that back diffusion to the Pt surface did not occur.

Various novel erythromycin derivatives obtained by different modifications: recent advance in macrolide antibiotics

The rapid emergence of drug resistance intensified the search for new antimicrobial agents, leading to lots of novel derivatives obtained from 14- and 15-membered macrolides by chemical modifications. Many of them exhibited enhanced antibacterial activity and expanded antibacterial spectrum. Especially some of them were found to be potent for the treatment of multi-drug-resistant bacterial infections. Besides, the other biological effects of macrolide derivatives were also found. In this article, we reviewed the recent advance in the novel macrolide derivatives designed by different structural modifications on erythronolide skeleton, cladinose and desosamine in the structures.