Predicting Survival of De Novo Metastatic Breast Cancer in Asian Women: Systematic Review and Validation Study

Background

In Asia, up to 25% of breast cancer patients present with distant metastases at diagnosis. Given the heterogeneous survival probabilities of de novo metastatic breast cancer, individual outcome prediction is challenging. The aim of the study is to identify existing prognostic models for patients with de novo metastatic breast cancer and validate them in Asia.

Materials and Methods

We performed a systematic review to identify prediction models for metastatic breast cancer. Models were validated in 642 women with de novo metastatic breast cancer registered between 2000 and 2010 in the Singapore Malaysia Hospital Based Breast Cancer Registry. Survival curves for low, intermediate and high-risk groups according to each prognostic score were compared by log-rank test and discrimination of the models was assessed by concordance statistic (C-statistic).

Results

We identified 16 prediction models, seven of which were for patients with brain metastases only. Performance status, estrogen receptor status, metastatic site(s) and disease-free interval were the most common predictors. We were able to validate nine prediction models. The capacity of the models to discriminate between poor and good survivors varied from poor to fair with C-statistics ranging from 0.50 (95% CI, 0.48–0.53) to 0.63 (95% CI, 0.60–0.66).

Conclusion

The discriminatory performance of existing prediction models for de novo metastatic breast cancer in Asia is modest. Development of an Asian-specific prediction model is needed to improve prognostication and guide decision making.     

Breadth of humoral response and antigenic targets of sporozoite‐inhibitory antibodies associated with sterile protection induced by controlled human malaria infection

The development of an effective malaria vaccine has remained elusive even until today. This is because of our incomplete understanding of the immune mechanisms that confer and/or correlate with protection. Human volunteers have been protected experimentally from a subsequent challenge by immunization with Plasmodium falciparum sporozoites under drug cover. Here, we demonstrate that sera from the protected individuals contain neutralizing antibodies against the pre‐erythrocytic stage. To identify the antigen(s) recognized by these antibodies, a newly developed library of P. falciparum antigens was screened with the neutralizing sera. Antibodies from protected individuals recognized a broad antigenic repertoire of which three antigens, PfMAEBL, PfTRAP and PfSEA1 were recognized by most protected individuals. As a proof of principle, we demonstrated that anti‐PfMAEBL antibodies block liver stage development in human hepatocytes. Thus, these antigens identified are promising targets for vaccine development against malaria.     

Metabolite Profiling Reveals YihU as a Novel Hydroxybutyrate Dehydrogenase for Alternative Succinic Semialdehyde Metabolism in Escherichia coli

The search for novel enzymes and enzymatic activities is important to map out all metabolic activities and reveal cellular metabolic processes in a more exhaustive manner. Here we present biochemical and physiological evidence for the function of the uncharacterized protein YihU in Escherichia coli using metabolite profiling by capillary electrophoresis time-of-flight mass spectrometry. To detect enzymatic activity and simultaneously identify possible substrates and products of the putative enzyme, we profiled a complex mixture of metabolites in the presence or absence of YihU. In this manner, succinic semialdehyde was identified as a substrate for YihU. The purified YihU protein catalyzed in vitro the NADH-dependent reduction of succinic semialdehyde to γ-hydroxybutyrate. Moreover, a yihU deletion mutant displayed reduced tolerance to the cytotoxic effects of exogenous addition of succinic semialdehyde. Profiling of intracellular metabolites following treatment of E. coli with succinic semialdehyde supports the existence of a YihU-catalyzed reduction of succinic semialdehyde to γ-hydroxybutyrate in addition to its known oxidation to succinate and through the tricarboxylic acid cycle. These findings suggest that YihU is a novel γ-hydroxybutyrate dehydrogenase involved in the metabolism of succinic semialdehyde, and other potentially toxic intermediates that may accumulate under stress conditions in E. coli.The search for novel enzymes is important to better our understanding of the metabolic systems of the cell. Although computational tools can be used to functionally annotate enzymes based on sequence homology, gene structure and expression, and prediction of enzyme-like domains, the identification of the exact physiological substrates remains difficult when sequence similarity to known enzymes is low (<60%) and requires experimental confirmation (1, 2). Consequently, many gaps remain in metabolic pathways even in the model microorganism Escherichia coli (3, 4). Moreover, the identification of dispensable enzymatic activities, such as metabolic bypass pathways or the characterization of enzymes that are expressed only under specific physiological conditions, is particularly challenging.The β-hydroxyacid dehydrogenase enzyme family is a structurally conserved group of enzymes that include β-hydroxyisobutyrate dehydrogenase, 6-phosphogluconate dehydrogenase, and numerous uncharacterized homologs (5, 6). This enzyme family contains well conserved domains in its sequence that include a N-terminal Rossmann-fold characteristic of a dinucleotide binding site, a well defined sequence at the substrate binding site, and a conserved lysine residue proposed as a critical catalytic residue. This last specific structural feature has been proposed based on site-directed mutagenesis and x-ray crystal structures (6, 7). The E. coli K12 proteome appears to contain four β-hydroxyacid dehydrogenase paralogs. The product of the glxR gene has been identified as tartronate semialdehyde reductase, catalyzing the NAD⁺-dependent oxidation of d-glycerate and the NADH-dependent reduction of tartronate semialdehyde (8). This enzyme plays a role in allantoin utilization under anaerobic conditions in E. coli (9). However, the function of the other three representatives of the family remains unknown.Under aerobic conditions in E. coli, γ-aminobutyrate (GABA)² is metabolized via GABA transaminase (EC 2.6.1.19) (10) and oxidized to succinate by at least two different succinic semialdehyde dehydrogenases (EC 1.2.1.16 and EC 1.2.1.24) (11, 12), and then further metabolized in the tricarboxylic acid cycle. In some animals (13), plants (14), and bacterial species (15, 16), γ-hydroxybutyrate (GHB) can be produced during GABA catabolism through the reduction of succinic semialdehyde (SSA) under anaerobic conditions. A γ-hydroxybutyrate dehydrogenase (GHBDH) was recently identified in Arabidopsis thaliana (14). Interestingly, the Arabidopsis enzyme does not show significant homology with known GHBDHs, however, its sequence exhibits similarity to several dehydrogenases including β-hydroxyacid dehydrogenases and 6-phosphogluconate dehydrogenases. However, the existence of an equivalent of the GHBDH reaction and an alternative reductive pathway for GABA metabolism in E. coli is still unreported.We have previously developed a screening method, based on in vitro assays in combination with metabolite profiling by capillary electrophoresis-mass spectrometry (CE-MS), to discover novel enzymatic activities (17). We hereby refer to this method as Metabolic Enzyme and Reaction discovery by Metabolite profile Analysis and reactant IDentification (MERMAID). Using this method, the enzymatic activity of any uncharacterized protein can be tested in an unbiased way by monitoring changes in a complex metabolite mixture that are induced by the test protein. This can allow to directly determine the substrate(s) and/or product(s) of the reaction without designing specific assays. Compounds whose levels specifically decrease following incubation with a protein are likely substrates, whereas metabolites whose level increase during the incubation are likely products of the reaction. In this study, we screened the E. coli YihU protein using the MERMAID approach and observed that it displays reductase activity toward short chain aldehydes, predominantly toward SSA. This activity differs from that of the known β-hydroxyacid dehydrogenases. We further demonstrate the presence of an alternative reaction for SSA catabolism leading to the production of GHB in E. coli.     

Chitosan-g-PEG/DNA complexes deliver gene to the rat liver via intrabiliary and intraportal infusions

BACKGROUND: Chitosan has been shown to be a non-toxic and efficient vector for in vitro gene transfection and in vivo gene delivery through pulmonary and oral administrations. Recently, we have shown that chitosan/DNA nanoparticles could mediate high levels of gene expression following intrabiliary infusion 1. In this study, we have examined the possibility of using polyethylene glycol (PEG)-grafted chitosan/DNA complexes to deliver genes to the liver through bile duct and portal vein infusions. METHODS: PEG (Mw: 5 kDa) was grafted onto chitosan (Mw: 47 kDa, deacetylation degree: 94%) with grafting degrees of 3.6% and 9.6% (molar percentage of chitosan monosaccharide units grafted with PEG). The stability of chitosan-g-PEG/DNA complexes was studied by measuring the change in particle size and by agarose gel electrophoresis against bile or serum challenge. The influence of PEG grafting on gene transfection efficiency was evaluated in HepG2 cells using luciferase reporter gene. Chitosan and chitosan-g-PEG/DNA complexes were delivered to the liver through bile duct and portal vein infusions with a syringe pump. Gene expression in the liver and the distribution of gene expression in other organs were evaluated. The acute liver toxicity of chitosan and chitosan-g-PEG/DNA complexes was examined by measuring serum alanine aminotranferase (ALT) and aspartate aminotransferase (AST) activities as a function of time. RESULTS: Both chitosan and chitosan-g-PEG displayed comparable gene transfection efficiency in HepG2 cells. After challenge with serum and bile, chitosan-g-PEG/DNA complexes, especially those prepared with chitosan-g-PEG (GD = 9.6%), did not form large aggregates like chitosan/DNA complexes but remained stable for up to 30 min. In addition, chitosan-g-PEG prevented the degradation of DNA in the presence of serum and bile. On day 3 after bile duct infusion, chitosan-g-PEG (GD = 9.6%)/DNA complexes mediated three times higher gene expression in the liver than chitosan/DNA complexes and yielded background levels of gene expression in other organs. On day 1 following portal vein infusion, gene expression level induced by chitosan/DNA complexes was hardly detectable but chitosan-g-PEG (GD = 9.6%) mediated significant transgene expression. Interestingly, transgene expression by chitosan-g-PEG/DNA complexes in other organs after portal vein infusion increased with increasing grafting degree of PEG. The ALT and AST assays indicated that grafting of PEG to chitosan reduced the acute liver toxicity towards the complexes. CONCLUSION: This study demonstrated the potential of chitosan-g-PEG as a safe and more stable gene carrier to the liver.     

Identification of pathogenic Helicobacter species by chaperonin-60 differentiation on plastic DNA arrays

A microarray method for bacterial species identification based on cpn60 and 16S rDNA hybridization was developed. Specific cpn60 or 16S rDNA oligonucleotides from various Helicobacter or Campylobacter species were printed and immobilized onto a proprietary plastic solid support. Using universal primers, fragments derived from either cpn60 or 16S rDNA genes from single isolates or from a complex human waste sludge DNA sample spiked with Helicobacter pylori were biotinylated and hybridized to the plastic slide. Subsequent querying with a streptavidin-horseradish peroxidase conjugate followed by color development using tetramethylbenzidine resulted in accurate Helicobacter species identification with no cross-hybridization to either the 16S rDNA or the cpn60 sequence of a closely related strain of Campylobacter jejuni. The combination of a nonfluorescence visual detection system with a polymer-based DNA microarray slide has resulted in a molecular tool that should prove useful in numerous applications requiring rapid, low-cost bacterial species identification.     

Identification and molecular characterization of an N-Acetylmuraminidase, Aml, involved in Streptococcus mutans cell separation

We previously demonstrated Streptococcus mutans produces two bacteriolytic enzymes of 100 kDa and 80 kDa (G. Yoshimura et al. Microbiol. Immunol. 48, 465-469, 2004). Here, we identified the protein sequence of these enzymes and found they come from a single gene product designated as automutanolysin (Aml). Aml has a modular design where the N-terminus contains five 13-amino-acid repeats and a C-terminal enzyme active domain. Aml selectively lyses S. mutans and S. sobrinus but no other oral streptococci. This suggests Aml possesses strong substrate specificity towards cariogenic bacteria present in the human oral cavity. Analysis of S. mutans peptidoglycan fragments released by Aml shows the enzyme is an N-acetylmuraminidase. We found Ca(2+) enhances the activity; and EGTA, EDTA and iodoacetic acid inhibit the activity. The optimum pH range for lytic activity was 6 to 7. Disruption of the aml gene in S. mutans results in the formation of a longer bacterial cell chain length that was dispersed by the addition of a low concentration of Aml. This suggests Aml is involved in S. mutans cell separation.     

Investigation of differentially expressed proteins due to the inhibitory effects of berberine in human liver cancer cell line HepG2

The investigation of differentially expressed proteins was used together with other techniques to study the inhibitory effects of two different doses of berberine in human liver cancer cell line HepG2. For HepG2 cells treated with 24.0 mg l(-1) of berberine, an increase in the sub G(0) phase that was indicative of cell death was observed in cell cycle analysis with flow cytometry. However, no significant increase in sub G(0) was observed in HepG2 cells treated with 4.0 mg l(-1) of berberine. Using flow cytometric analysis, significant activation of caspase 3 was not observed with HepG2 cells treated with 4.0 and 24.0 mg l(-1) of berberine. In this work, labeling of cells with stable isotope was not used in the proposed method developed. The whole cell lysates from the control and treated cells were digested with trypsin and the peptides were separated by two-dimensional (cation exchange and reversed phase) liquid chromatography and tandem mass spectrometry. Our preliminary data showed that the proposed platform provided a rapid approach to study the molecular mechanism due to the inhibitory effects of different doses of the berberine on HepG2 cell lines. This included a network of proteins involved in mitogen-activated protein kinase (MAPK) phosphorelay systems, metabolism, regulation of cell cycle and DNA damage response. The differentially expressed proteins identified using the current approach were consistent with the data obtained from cell cycle analysis with flow cytometry.