Investigation of the endemic Madagascan plant Uvaria sp. for antiproliferative activity against the A2780 ovarian cancer cell line led to the isolation of two new acetogenins. The structures of these two compounds were elucidated based on analysis of their 1D and 2D NMR spectra, circular dichroism and mass spectrometric data, together with chemical modification. The two acetogenins display weak antiproliferative activity against the A2780 ovarian cancer, the A2058 melanoma, and the H522 lung cancer cell lines.
Genome-wide association studies (GWAS) have identified approximately three dozen single nucleotide polymorphisms (SNPs) consistently associated with prostate cancer (PCa) risk. Despite the reproducibility of these associations, the molecular mechanism for most of these SNPs has not been well elaborated as most lie within non-coding regions of the genome. Androgens play a key role in prostate carcinogenesis. Recently, using ChIP-on-chip technology, 22,447 androgen receptor (AR) binding sites have been mapped throughout the genome, greatly expanding the genomic regions potentially involved in androgen-mediated activity.
To test the hypothesis that sequence variants in AR binding sites are associated with PCa risk, we performed a systematic evaluation among two existing PCa GWAS cohorts; the Johns Hopkins Hospital and the Cancer Genetic Markers of Susceptibility (CGEMS) study population. We demonstrate that regions containing AR binding sites are significantly enriched for PCa risk-associated SNPs, i.e. more than expected by chance alone. In addition, compared with the entire genome, these newly observed risk-associated SNPs in these regions are significantly more likely to overlap with established PCa risk-associated SNPs from previous GWAS. These results are consistent with our previous finding from a bioinformatics analysis that one-third of the 33 known PCa risk-associated SNPs discovered by GWAS are located in regions of the genome containing AR binding sites.
The results to date provide novel statistical evidence suggesting an androgen-mediated mechanism by which some PCa associated SNPs act to influence PCa risk. However, these results are hypothesis generating and ultimately warrant testing through in-depth molecular analyses.
AR; prostate cancer; GWAS; pathway association study
Investigation of the Madagascan endemic plant Ambavia gerrardii (Baill.) Le Thomas (Annonaceae) for antiproliferative activity against the A2780 ovarian cancer cell line led to the isolation of the three new alkaloids 8-hydroxyeupolauridine (1), 9-methoxyeupolauridine 1-oxide (2) and 11-methoxysampangine (3), and the three known alkaloids 4–6. The structures of 1 and 2 were confirmed by synthesis. Compounds 3, 4, and 6 showed moderate to good antiproliferative activities, with IC50 values of 10.3, 3.5, and 0.60 µM, respectively, against the A2780 human ovarian cancer cell line, and with IC50 values of 0.57, 1.77, and 0.58 µM, respectively, against the H460 human lung cancer cell line.
Investigation of the endemic Madagascar plant Leptadenia madagascariensis Decne. (Apocynaceae) for antiproliferative activity against the A2780 ovarian cancer cell line led to the isolation of the four new cardenolides 1–4. The structure elucidations of these compounds were based on analyses of their 1D and 2D NMR spectra and mass spectrometric data. The cardenolides were strongly antiproliferative to the A2780 ovarian cancer cell line, with IC50 values of 0.18, 0.21, 0.17 and 0.29 μM line, and to the H460 human lung cancer cell line, with IC50 values of 0.16, 0.68, 0.37 and 0.48 μM respectively.
Antiproliferative activity; cardenolide; biodiversity; NMR
Bioassay-guided fractionation of an ethanol extract of the roots of the endemic Malagasy plant Pongamiopsis pervilleana (Baill.) R. Vig. led to the isolation of the three new compounds 2′R,4′-hydroxyemoroidocarpan (1), pongavilleanine (3), and epipervilline (4) together with two known compounds identified as emoroidocarpan (2) and rotenolone (5). The structures of all compounds were determined by physical, chemical and spectroscopic evidence. The stereochemistry at C-2′ of the previously reported compound emoroidocarpan was determined to be R by the observation of a negative Cotton effect at 474 nm in the CD spectrum of its osmate ester derivative. Compounds 2–5 displayed moderate antiproliferative activity against the A2780 human ovarian cancer cell line, and rotenolone also showed micromolar antiproliferative activity towards the breast cancer BT-549, prostate cancer DU 145, NSCLC NCI-H460, and colon cancer HCC-2998 cell lines.
Fractionation of an ethanol extract of a Madagascar collection of the leaves and fruit of Cassipourea lanceolata Tul. led to the isolation of three euphane triterpenoids 1–3. The 1H and 13C NMR spectra of all compounds were fully assigned using a combination of 2D NMR experiments, including COSY, TOCSY, HSQC (HMQC), HMBC and ROESY sequences. The three compounds showed weak antiproliferative activities against the A2780 human ovarian cancer cell line, with IC50 values of 25, 25 and 32 μM, respectively.
Cassipourea lanceolata; Rhizophoraceae; Euphanes; Triterpenoids; NMR; Antiproliferative activity
Glycan arrays have enabled detailed studies of the specificities of glycan-binding proteins. A challenge in the interpretation of glycan array data is to determine the specific features of glycan structures that are critical for binding. To address this challenge, we have developed a systematic method to interpret glycan array data using a motif-based analysis. Each glycan on a glycan array is classified according to its component sub-structures, or motifs. We analyze the binding of a given lectin to each glycan in terms of the motifs in order to identify the motifs that are selectively present in the glycans that are bound by the lectin. We compared two different methods to calculate the identification, termed intensity segregation and motif segregation, for the analysis of three well-characterized lectins with highly divergent behaviors. Both methods accurately identified the primary specificities as well as the weaker, secondary specificities of all three lectins. The complex binding behavior of wheat germ agglutinin was reduced to its simplified, independent specificities. We compiled the motif specificities of a wide variety of plant lectins, human lectins, and glycan-binding antibodies to uncover the relationships among the glycan-binding proteins and to provide a means to search for lectins with particular binding specificities. This approach should be valuable for rapidly analyzing and using glycan array data, for better describing and understanding glycan-binding specificities, and as a means to systematize and compare data from glycan arrays.
glycan arrays; glycan microarrays; glycan-binding protein; lectin; motif analysis
Bioassay-guided fractionation of an EtOH extract obtained from the roots of the Madagascan plant Dodonaea viscosa led to the isolation of two new antiproliferative oleanane-type triterpenoid saponins, dodoneasides A and B (1 and 2). The structures of these two new compounds were elucidated using 1D and 2D NMR experiments and mass spectrometry. Compounds 1 and 2 showed antiproliferative activity against the A2780 human ovarian cancer cell line with IC50 values of 0.79 and 0.70 μM, respectively.
Bioassay-guided fractionation of an ethanol extract of a Malleastrum sp. afforded three new limonoids (1-3), malleastrones A-C, respectively. Each limonoid contained the rare tetranortriterpenoid skeleton. Structure elucidation of the isolates was carried out by analysis of one and two-dimensional NMR and X-ray diffraction data. The novel isolates 1 and 2 were tested for antiproliferative activity against a panel of cancer cell lines, and exhibited IC50 values ranging from 0.19 – 0.63 μM.
Bioassay-guided fractionation of an ethanol extract of a Madagascar
collection of Elaeodendron alluaudianum led to the isolation of
two new cardenolide glycosides (1 and 2). The
1H and 13C NMR spectra of both compounds were fully
assigned using a combination of 2D NMR experiments, including
1H-1H COSY, HSQC, HMBC, and ROESY sequences. Both
compounds 1 and 2 were tested against the A2780 human
ovarian cancer cell line and the U937 human histiocytic lymphoma cell line
assays, and showed significant antiproliferative activity with IC50
values of 0.12 and 0.07 μM against the A2780 human ovarian cancer cell
line, and 0.15 and 0.08 μM against the U937 human histiocytic lymphoma
cell line, respectively.
As a first step in analyzing high-throughput data in genome-wide studies, several algorithms are available to identify and prioritize candidates lists for downstream fine-mapping. The prioritized candidates could be differentially expressed genes, aberrations in comparative genomics hybridization studies, or single nucleotide polymorphisms (SNPs) in association studies. Different analysis algorithms are subject to various experimental artifacts and analytical features that lead to different candidate lists. However, little research has been carried out to theoretically quantify the consensus between different candidate lists and to compare the study specific accuracy of the analytical methods based on a known reference candidate list. Within the context of genome-wide studies, we propose a generic mathematical framework to statistically compare ranked lists of candidates from different algorithms with each other or, if available, with a reference candidate list. To cope with the growing need for intuitive visualization of high-throughput data in genome-wide studies, we describe a complementary customizable visualization tool. As a case study, we demonstrate application of our framework to the comparison and visualization of candidate lists generated in a DNA-pooling based genome-wide association study of CEPH data in the HapMap project, where prior knowledge from individual genotyping can be used to generate a true reference candidate list. The results provide a theoretical basis to compare the accuracy of various methods and to identify redundant methods, thus providing guidance for selecting the most suitable analysis method in genome-wide studies.
genome-wide association studies; candidate lists
Bioassay-guided fractionation of an ethanol extract of Artabotrys madagascariensis led to the isolation of the new compound artabotrol A (1), two butenolides (2 and 3), and the tetracyclic triterpene polycarpol (4). Structure elucidation was determined on the basis of one and two-dimensional NMR, and absolute configuration of compounds 2–4 was verified by analysis of CD and optical rotation spectra. Two of the isolates, melodorinol (2) and acetylmelodorinol (3), were found to display antiproliferative activity against five different tumor cell lines with IC50 values ranging from 2.4 to 12 µM.
butenolides; Artabotrys; Annonaceae; antiproliferative activity; NMR; HPLC
Bioassay-guided fractionation of an ethanol extract obtained from the Madagascar plant Elaeodendron sp. led to the isolation of two new cardenolides, elaeodendrosides T and U (1 and 2). The structures of the new compounds were elucidated using 1D and 2D NMR experiments, and mass spectrometry. Compounds 1, 3, 4, and 5 showed significant antiproliferative activity against A2780 human ovarian cancer cells with IC50 values of 0.085, 0.019, 0.19, and 0.10 µM, respectively, while compounds 2 and 6 were less active.
When using cDNA microarrays, normalization to correct labeling bias is a common preliminary step before further data analysis is applied, its objective being to reduce the variation between arrays. To date, assessment of the effectiveness of normalization has mainly been confined to the ability to detect differentially expressed genes. Since a major use of microarrays is the expression-based phenotype classification, it is important to evaluate microarray normalization procedures relative to classification. Using a model-based approach, we model the systemic-error process to generate synthetic gene-expression values with known ground truth. These synthetic expression values are subjected to typical normalization methods and passed through a set of classification rules, the objective being to carry out a systematic study of the effect of normalization on classification. Three normalization methods are considered: offset, linear regression, and Lowess regression. Seven classification rules are considered: 3-nearest neighbor, linear support vector machine, linear discriminant analysis, regular histogram, Gaussian kernel, perceptron, and multiple perceptron with majority voting. The results of the first three are presented in the paper, with the full results being given on a complementary website. The conclusion from the different experiment models considered in the study is that normalization can have a significant benefit for classification under difficult experimental conditions, with linear and Lowess regression slightly outperforming the offset method.
Previous studies have demonstrated that surface antigen proteins, in particular SAG-1, of Toxoplasma gondii are important to this parasite as attachment ligands for the host cell. An in vitro assay was developed to test whether these ligands and other secretory proteins are involved in the immune response of human cells to toxoplasma. Human monocytes were infected with tachyzoites in the presence of antiparasite antibodies, and their effect on mitogen-induced lymphoproliferation was examined. The presence of antibody to either parasite-excreted proteins (MIC-1 and MIC-2) or surface proteins (SAG-1 and SAG-2) during infection neutralized the marked decrease seen in mitogen-induced lymphoproliferation in the presence of infected monocytes. Conversely, antibodies to other secreted proteins (ROP-1) and cytoplasmic molecules had no effect on parasite-induced, monocyte-mediated downregulation. Fluorescence microscope analysis detected microneme and surface antigen proteins on the monocyte cell surface during infection. These results suggest that microneme and surface antigen proteins trigger monocytes to downregulate mitogen-induced lymphoproliferation.