An aptamer targeting shared tumor-specific peptide antigen of MAGE-A3 in multiple cancers.

A DNA aptamer was identified against the shared tumor-specific MAGE-A3111-125 peptide antigen. The dissociation constant between the aptamer and the peptide was measured at 57 nM. Binding of the aptamer to seven types of cancer cells, melanoma, breast, colorectal, liver, lung, pancreas and oral cancer, was confirmed with flow cytometry and fluorescence imaging. Cy3-conjugated aptamers signals were specifically localized to the surface of those cancer cells. The results indicate that the DNA aptamer against the shared tumor-specific MAGE-A3 peptide can be used in cancer cell targeting and has the potential for developing into new modalities for the diagnosis of multiple cancers.

Tissue-specific gene expression templates for accurate molecular characterization of the normal physiological states of multiple human tissues with implication in development and cancer studies.

BACKGROUND: To elucidate the molecular complications in many complex diseases, we argue for the priority to construct a model representing the normal physiological state of a cell/tissue. RESULTS: By analyzing three independent microarray datasets on normal human tissues, we established a quantitative molecular model GET, which consists of 24 tissue-specific Gene Expression Templates constructed from a set of 56 genes, for predicting 24 distinct tissue types under disease-free condition. 99.2% correctness was reached when a large-scale validation was performed on 61 new datasets to test the tissue-prediction power of GET. Network analysis based on molecular interactions suggests a potential role of these 56 genes in tissue differentiation and carcinogenesis.Applying GET to transcriptomic datasets produced from tissue development studies the results correlated well with developmental stages. Cancerous tissues and cell lines yielded significantly lower correlation with GET than the normal tissues. GET distinguished melanoma from normal skin tissue or benign skin tumor with 96% sensitivity and 89% specificity. CONCLUSIONS: These results strongly suggest that a normal tissue or cell may uphold its normal functioning and morphology by maintaining specific chemical stoichiometry among genes. The state of stoichiometry can be depicted by a compact set of representative genes such as the 56 genes obtained here. A significant deviation from normal stoichiometry may result in malfunction or abnormal growth of the cells.

Targeted drug delivery using an aptamer against shared tumor-specific peptide antigen of MAGE-A3.

We developed a DNA aptamer, Ap52, against the shared tumor-specific MAGE-A3111-125 peptide antigen that was used to target multiple types of cancer cells. Here we report the in vivo study of mice implanted with pancreatic tumor cells AsPC-1, which demonstrates accumulation of phosphorothioate-modified Ap52 (ThioAp52) at the xenograft tumor following either intravenous or in situ injection. When complexed with antitumor drug doxorubicin (Dox), ThioAp52 achieves targeted delivery to four types of cancer cells, including breast, oral, pancreatic, and skin. Image analysis shows that ThioAp52-Dox complex selectively enters cancer cells, while free Dox is taken up by all cell lines. The cytotoxicity of ThioAp52-Dox for cancer cells is enhanced as compared to that for the corresponding normal/noncancerous cells. These results indicate that this aptamer against shared tumor-specific antigen can be a potential delivery vehicle for therapeutics to treat multiple cancers.

Phototropic leaf movements and photosynthetic performance in an amphibious fern, Marsilea quadrifolia.

Diurnal phototropism has not been reported in ferns. In this study we found that the four leaflets of the amphibious fern Marsilea quadrifolia are capable of adjusting their leaflet angle and leaflet azimuth in response to changes in the position of the sun's direct beam, exhibiting more diaphototropic movements (orienting the plane of the lamina perpendicular to incident light) in the morning and late afternoon, and more paraphototropic movements (orienting the plane of the lamina parallel to incident light) at noon. In addition, by cutting off the leaflet lamina and covering portions of leaflets with black tape, the junction between the leaflet and petiole was found to be responsible for light reception. Among the light spectrum investigated, blue light was the most effective at inducing diaphototropism. The role of diurnal phototropism in enhancing carbon return and ameliorating photoinhibition was also evaluated. It was concluded that diurnal phototropic leaf movement represents one of the plastic responses enabling this amphibious fern to grow under terrestrial conditions.

Measurement of cyclin E genomic copy number and strand length in cell-free DNA distinguish malignant versus benign effusions.

PURPOSE: Previous studies have shown that the concentration of cell-free DNA was higher and its strand length longer in body fluids obtained from patients with cancer as compared to patients with benign diseases. We hypothesized that analysis of both DNA copy number and strand length of cell-free DNA from an amplified chromosomal region could improve the diagnosis of malignant diseases in body fluids. EXPERIMENTAL DESIGN: To test this hypothesis, we used ovarian cancer effusion as an example and applied a quantitative real-time PCR to measure the relative copy number and strand length of DNA fragments from one of the most frequently amplified genes, cyclin E, in ovarian serous carcinomas. RESULTS: As compared with nonamplified chromosomal loci, including beta-actin, p53, 2p24.1, and 4p15.31, measurement of cyclin E DNA copy number (100 bp) had the best performance in distinguishing malignant (n = 88) from benign (n = 70) effusions after normalization to effusion volume or Line-1 DNA with areas under the receiver operating characteristics curve (AUC) of 0.832 and 0.847, respectively. Different DNA lengths of the cyclin E locus were further analyzed and we found that the AUC was highest by measuring the 400-bp cyclin E locus (AUC = 0.896). The AUC was improved to 0.936 when it was combined with the length integrity index as defined by the relative abundance of 400 bp cyclin E to 100 bp p53 loci. Cyclin E real-time PCR assay had a higher sensitivity (95.6%) than routine cytology examination (73.9%) and was able to diagnose false-negative cytology cases in this study. CONCLUSIONS: The above findings indicate that measurement of the DNA copy number and strand length of the cyclin E locus is a useful cancer diagnostic tool.

Thickness dependence of optical second harmonic generation in collagen fibrils.

Simultaneous backward and forward second harmonic generations from isolated type-I collagen matrix are observed. Optical interference behaviors of these nonlinear optical signals are studied with accurately determined fibril thickness by an atomic force microscope. The nonlinear emission directions are strongly dependent on the coherent interaction within and between collagen fibrils. A linear relationship is obtained to estimate collagen fibril thickness with nanometer precision noninvasively by evaluating the forward/backward second harmonic generation ratio.

Accumulated immune complexes of IgE and omalizumab trap allergens in an in vitro model.

The best understood mechanisms of omalizumab are that it neutralizes free IgE and down-regulates high-affinity IgE.Fc receptors (FcepsilonRI) on basophils and mast cells. It has been proposed that since complexes of IgE and omalizumab are accumulated to 5-10 times the basal levels of IgE, they may trap incoming allergens, contributing to omalizumab's effectiveness. In order to investigate the ability of IgE:omalizumab complexes in trapping allergens and inhibiting basophil activation in an in vitro reconstitution model, the ability of IgE:omalizumab complexes to tie up antigen and hence inhibit (a) antigen binding to IgE bound by FcepsilonRI, and (b) antigen-mediated activation of basophils, was examined. The free IgE was prepared by mixing different proportions of antigen-nonspecific IgE secreted by U266 cells and antigen-specific IgE, SE44 IgE, which recognizes a synthetic 15 a.a. peptide, R15K. The antigen was (R15K)(8)-ova, i.e. ovalbumin conjugated with an average of 8 copies of R15K per molecule. The solid-phase FcepsilonRI was a recombinant protein representing the extracellular portion of the alpha chain of the FcepsilonRI receptor complex. The model FcepsilonRI(+) basophilic cell line was RBL.SX-38, a rat basophilic leukemic line transfected with the genes for alpha, beta and gamma subunits of human FcepsilonRI. The results showed that the IgE:omalizumab complexes trapped increasing amounts of antigen with increasing (a) concentration of IgE, (b) proportion of antigen-specific IgE in total IgE, and (c) concentration of total immune complexes. Such trapping decreased the antigen-induced activation of FcepsilonRI(+) cells that had been pulsed with antigen-specific IgE, resulting in decreased mediator release. These results suggest that the rapidly accumulated IgE:omalizumab complexes in omalizumab-treated patients can capture allergens and consequently contribute to the pharmacological effects of omalizumab.

Application of doxorubicin-induced rAAV2-p53 gene delivery in combined chemotherapy and gene therapy for hepatocellular carcinoma.

p53 gene transfer has been proposed as a potential therapeutic option for treatment of hepatocellular carcinoma (HCC). Compared to other commonly used gene transfer vectors such as adenovirus and retrovirus, recombinant adeno-associated virus serotype 2 (rAAV2) has shown promising results in human clinical trials. Significant enhancement in the gene transfer efficiency is needed, however, for HCC applications. In the present study, we applied chemotherapy drug Doxorubicin (DOX) to induce rAAV2 transduction of hepatomas. Using reporter assays, we showed that the DOX-treated hepatomas became more susceptible to rAAV2 infection in comparison to untreated controls: the permissiveness increased >350-fold and >120-fold for HepG2 (p53 wild-type) and Hep3B (p53 null) hepatomas, respectively. Using the induced permissiveness, we applied rAAV2-p53 transduction to restore p53 expression in the p53-null Hep3B hepatomas. Compared to rAAV2-p53 transduction alone, rAAV2-p53 transduction with DOX resulted in a >16-fold induction of p53 expression. The transduced Hep3B expressed as much as 380% more immunoreactive p53 in comparison to the wild-type p53 expression in the HepG2 hepatomas. Significantly, when Hep3B cells were treated with 0.5 muM of DOX and rAAV2-p53 (MOI = 10) for twelve hours, the cell viability dropped to 66% four days after the administration. This decrease in cell viability was similar to that of treatment with 1 microM of DOX alone in the absence of rAAV2. The 50% reduction in DOX administration--from 1 microM to 0.5 microM--revealed the antitumor property of the rAAV2-p53 transduction as well as the joint cytotoxicity of DOX and rAAV2-p53 against the p53-null hepatomas. We conclude that DOX mediates the enhancement effect on rAAV2 transduction of human hepatomas. Combined DOX and rAAV2-p53 administration may facilitate more efficient treatment for the HCC caused by p53 mutations.

Abscisic acid regulation of heterophylly in Marsilea quadrifolia L.: effects of R-(-) and S-(+) isomers.

The plant hormone abscisic acid (ABA) induces a developmental switch in the aquatic fern Marsilea quadrifolia, causing the formation of aerial type characteristics, including the elongation of petioles and roots, a change in leaf morphology, the expansion of leaf surface area, and the shortening of the internodes. A number of ABA-responsive heterophylly (ABRH) genes are induced early during the transition. Using optically pure isomers of ABA, it was found that both the natural S-(+)-ABA and the unnatural R-(-)-ABA are capable of inducing a heterophyllous switch and regulating ABRH gene expression. When dose responses are compared, the unnatural ABA gives stronger morphogenic effects than the natural ABA at the same concentration, it is effective at lower concentrations, and its optimal concentration is also lower compared with the natural ABA. Deuterium-labelled ABA enantiomers were used to trace the fate of applied ABA and to distinguish the applied compound and its metabolites from the endogenous counterparts. In tissues, the supplied (+)-ABA was metabolized principally to dihydrophaseic acid, while the supplied (-)-ABA was converted at a slower rate to 7'-hydroxy abscisic acid. Treatment with either enantiomer resulted in increased biosynthesis of ABA, as reflected in the accumulation of endogenous dihydrophaseic acid. Taken together, these results suggest two distinct mechanisms of action for (-)-ABA: either (-)-ABA is intrinsically active, or its activity is due to the stimulation of ABA biosynthesis.

Rapid and sensitive detection of multiple genes from the SARS-coronavirus using quantitative RT-PCR with dual systems.

The outbreak of severe acute respiratory syndrome (SARS) was caused by a newly identified coronavirus (SARS-CoV) in 2003. To detect early SARS-CoV infection, a one-step, real-time quantitative reverse transcription-polymerase chain reaction (RT-PCR) assay was developed that could simultaneously detect nucleocapsid (N), membrane (M), and spike (S) genes of SARS-CoV with the same PCR condition using either Applied Biosystems (ABI) Prism 7700 Sequence Detection System or Roche LightCycler. The sensitivity of this assay was evaluated using cell culture-derived viruses, in vitro transcribed viral RNA, and clinical specimens. The SARS-S, -M, and -N primer/probe sets described in this paper could detect one to ten copies of in vitro transcribed S, M, and N RNA per test using both the ABI and Roche assay systems. The relative sensitivities for detecting cell culture-derived SARS-CoV were 0.01, 0.01, and 0.001 PFU/test, respectively. It showed that SARS-N has comparable detection efficiencies to SARS2 and SARS3 which are primers sets designed by Centers for Disease Control and Prevention. In addition, SARS-S and SARS-M also demonstrated equivalent sensitivity to the commercially available RealArt HPA-Coronavirus reagents (Artus). The relative sensitivity of these primer/probe sets was also examined using human sera spiked viruses and clinical specimens from four confirmed SARS patients. Similar results as above were obtained. Specificity tests and sequence alignment showed that these primer/probe sets annealed perfectly to 31 isolates of SARS-CoV; and there was no cross detection with other coronaviruses and human respiratory tract-associated viruses. Therefore, not only is it compatible with the ABI and Roche systems, this multiple-gene detection assay also has the merit of being a rapid, safe, sensitive, and specific tool for accurate diagnosis of SARS-CoV infection.

Multiharmonic-generation biopsy of skin.

Because it avoids the in-focus photodamage and phototoxicity problem of two-photon-fluorescence excitation, multiharmonic-generation biopsy based on a 1200-1300-nm light source could provide a truly noninvasive and highly penetrative optical sectioning of skin. We study multiharmonic-generation biopsy of fixed mouse skin. Our preliminary study suggests that this technique could provide submicrometer-resolution deep-tissue noninvasive biopsy images in skin without the use of fluorescence and exogenous markers.

Studies of chi(2)/chi(3) tensors in submicron-scaled bio-tissues by polarization harmonics optical microscopy.

Optical second- and third-harmonic generations have attracted a lot of attention in the biomedical imaging research field recently due to their intrinsic sectioning ability and noninvasiveness. Combined with near-infrared excitation sources, their deep-penetration ability makes these imaging modalities suitable for tissue characterization. In this article, we demonstrate a polarization harmonics optical microscopy, or P-HOM, to study the nonlinear optical anisotropy of the nanometer-scaled myosin and actin filaments inside myofibrils. By using tight focusing we can avoid the phase-matching condition due to micron-scaled, high-order structures in skeletal muscle fibers, and obtain the submicron-scaled polarization dependencies of second/third-harmonic generation intensities on the inclination angle between the long axes of the filaments and the polarization direction of the linear polarized fundamental excitation laser light. From these dependencies, detailed information on the tensor elements of the second/third-order nonlinear susceptibilities contributed from the myosin/actin filaments inside myofibrils can thus be analyzed and obtained, reflecting the detailed arrangements and structures of the constructing biomolecules. By acquiring a whole, nonlinearly sectioned image with a submicron spatial resolution, we can also compare the polarization dependency and calculate the nonlinear susceptibilities over a large area of the tissue at the same time-which not only provides statistical information but will be especially useful with complex specimen geometry.