Genomic and transcriptional aberrations linked to breast cancer pathophysiologies.

This study explores the roles of genome copy number abnormalities (CNAs) in breast cancer pathophysiology by identifying associations between recurrent CNAs, gene expression, and clinical outcome in a set of aggressively treated early-stage breast tumors. It shows that the recurrent CNAs differ between tumor subtypes defined by expression pattern and that stratification of patients according to outcome can be improved by measuring both expression and copy number, especially high-level amplification. Sixty-six genes deregulated by the high-level amplifications are potential therapeutic targets. Nine of these (FGFR1, IKBKB, ERBB2, PROCC, ADAM9, FNTA, ACACA, PNMT, and NR1D1) are considered druggable. Low-level CNAs appear to contribute to cancer progression by altering RNA and cellular metabolism.

Quantum dot-related genotoxicity perturbation can be attenuated by PEG encapsulation.

Nanomaterial-biosystem interaction is emerging as a major concern hindering wide adoption of nanomaterials. Using quantum dots (Qdots) of different sizes (Qdot-440nm and Qdot-680nm) as a model system, we studied the effects of polyethylene glycol (PEG) thin-layer surface modification in attenuating Qdot-related cytotoxicity, genotoxicity perturbation and oxidative stress in a cellular system. We found that uncoated Qdots (U-Qdots) made of core/shell CdSe/ZnS could indeed induce cytotoxic effects, including the inhibition of cell growth. Also, both the neutral comet assay and γH2AX foci formation showed that U-Qdots caused significant DNA damage in a time- and dose-dependent manner. In contrast, results from cytotoxicity analysis and γH2AX generation indicate minimal impact on cells after exposure to PEG-coated Qdots. This lack of observed toxic effects from PEG-coated Qdots may be due to the fact that PEG-coating can inhibit ROS generation induced by U-Qdots. Based on these observations, we conclude that the genotoxicity of Qdots could be significantly decreased following proper surface modification, such as PEG encapsulation. In addition, PEG encapsulation may also serve as a general method to attenuate nanotoxicity for other nanoparticles.

Picomolar sensitivity MRI and photoacoustic imaging of cobalt nanoparticles.

Multimodality imaging based on complementary detection principles has broad clinical applications and promises to improve the accuracy of medical diagnosis. This means that a tracer particle advantageously incorporates multiple functionalities into a single delivery vehicle. In the present work, we explore a unique combination of MRI and photoacoustic tomography (PAT) to detect picomolar concentrations of nanoparticles. The nanoconstruct consists of ferromagnetic (Co) particles coated with gold (Au) for biocompatibility and a unique shape that enables optical absorption over a broad range of frequencies. The end result is a dual-modality probe useful for the detection of trace amounts of nanoparticles in biological tissues, in which MRI provides volume detection, whereas PAT performs edge detection.

Facile functionalization of multilayer fullerenes (carbon nano-onions) by nitrene chemistry and "grafting from" strategy.

Facile functionalization of multilayer fullerenes (carbon nano-onions, CNOs) was carried out by [2+1] cycloaddition of nitrenes. The products were further derivatized by using the "grafting from" strategy of in situ ring-opening polymerization (ROP) and atom transfer radical polymerization (ATRP). Using one-step nitrene chemistry with high-energy reagents, such as azidoethanol and azidoethyl 2-bromo-2-methyl propanoate, in N-methyl-2-pyrrolidone at 160 degrees C for 16 h, hydroxyl and bromide functionalities were introduced onto the surfaces of CNOs. These hydroxyl CNOs (CNO-OH) and bromic CNOs (CNO-Br) were extensively characterized by various techniques such as thermal gravimetric analysis (TGA), transmission electron microscopy (TEM), Raman spectroscopy and X-ray photo electron spectroscopy (XPS). TGA measurements indicated that the surface hydroxyl and bromide group density reached 1.49 and 0.49 mmol g(-1), respectively. The as-functionalized CNOs showed much better solubility in solvents than pristine CNOs. The CNO-OH were also observed to fluoresce at lambda = 453 nm in water. The CNO-OH and CNO-Br can be conveniently utilized as macroinitiators to conduct surface-initiated in-situ polymerizations. Poly(epsilon-caprolactone) (PCL, 45 wt%) and polystyrene (PS, 60 wt%) were then grafted from surfaces of CNOs through the ROP of epsilon-caprolactone with the macroinitiator CNO-OH and the ATRP of styrene with the macroinitiator CNO-Br, respectively. The structures and morphology of the resulting products were characterized by (1)H NMR, scanning electron microscopy (SEM), TEM, and atomic force microscopy (AFM). The polymer functionalized CNOs have good solubility/dispersibility in common organic solvents. The facile and scalable functionalization approaches can pave the way for the comprehensive investigation of chemistry of CNOs and fabrication of novel CNO-based nanomaterials and nanodevices.

Peptide-nanoparticle hybrid SERS probes for optical detection of protease activity.

Real-time in situ detection of active proteases is crucial for early-stage cancer screening and cell signaling pathway study; however, it is difficult to achieve using fluorescence or radioactive probes at volumes below 1 nL. Here we demonstrated a hybrid optical probe by incorporating nanocrescent particle and peptides with artificial tag molecules. We performed a proof-of-concept study using prostate specific antigen (PSA), one of the most prominent prostate cancer markers, and a serine protease present in patients' seminal fluid and serum. The Raman spectral signal from the tag molecules is enhanced by the nanocrescent and the signal is monitored as the indicator for peptide cleavage in a femtoliter reaction volume, at levels close to a single proteolytically active PSA molecule. The high reaction specificity of the peptides on individual nanoparticles minimizes the false detection of other serine proteases and background Raman signal, which results in a high-fidelity and high-signal-to-noise-ratio cancer nanoprobe that can be easily incorporated into nano/microfluidic devices.

Lithographic techniques and surface chemistries for the fabrication of PEG-passivated protein microarrays.

This article presents a new technique to fabricate patterns of functional molecules surrounded by a coating of the inert poly(ethylene glycol) (PEG) on glass slides for applications in protein microarray technology. The chief advantages of this technique are that it is based entirely on standard lithography processes, makes use of glass slides employing surface chemistries that are standard in the microarray community, and has the potential to massively scale up the density of microarray spots. It is shown that proteins and antibodies can be made to self-assemble on the functional patterns in a microarray format, with the PEG coating acting as an effective passivating agent to prevent non-specific protein adsorption. Various standard surface chemistries such as aldehyde, epoxy and amine are explored for the functional layer, and it is conclusively demonstrated that only an amine-terminated surface satisfies all the process constraints imposed by the lithography process sequence. The effectiveness of this microarray technology is demonstrated by patterning fluorescent streptavidin and a fluorescent secondary antibody using the well-known and highly specific interaction between biotin and streptavidin.

DNA damage evaluated by gammaH2AX foci formation by a selective group of chemical/physical stressors.

It has been reported that the phosphorylated form of histone variant H2AX (gammaH2AX) plays an important role in the recruitment of DNA repair and checkpoint proteins to sites of DNA damage, particularly at double strand breaks (DSBs). Using gammaH2AX foci formation as an indicator for DNA damage, several chemicals/stress factors were chosen to assess their ability to induce gammaH2AX foci in a 24h time frame in a human amnion FL cell line. Two direct-acting genotoxins, methyl methanesulfonate (MMS) and N-ethyl-N-nitrosourea (ENU), can induce gammaH2AX foci formation in a time- and dose-dependent manner. Similarly, an indirect-acting genotoxin, benzo[a]pyrene (BP), also induced the formation of gammaH2AX foci in a time- and dose-dependent manner. Another indirect genotoxin, 2-acetyl-aminofluorene (AAF), did not induce gammaH2AX foci formation in FL cells; however, AAF can induce gammaH2AX foci formation in Chinese hamster CHL cells. Neutral comet assays also revealed the induction of DNA strand breaks by these agents. In contrast, epigenetic carcinogens azathioprine and cyclosporine A, as well as non-carcinogen dimethyl sulfoxide, did not induce gammaH2AX foci formation in FL cells. In addition, heat shock and hypertonic saline did not induce gammaH2AX foci. Cell survival analyses indicated that the induction of gammaH2AX is not correlated with the cytotoxic effects of these agents/factors. Taken together, these results suggest that gammaH2AX foci formation could be used for evaluating DNA damage; however, the different cell types used may play an important role in determining gammaH2AX foci formation induced by a specific agent.

A comparative study of using comet assay and gammaH2AX foci formation in the detection of N-methyl-N'-nitro-N-nitrosoguanidine-induced DNA damage.

Comet assay is a useful technique in the detection of DNA damages, particularly DNA strand breaks; and it has been utilized to show that a potent carcinogen N-methyl-N'-nitro-N-nitrosoguanidine (MNNG), can induce such damages. Recently, gammaH2AX foci formation has been suggested as another sensitive way to detect DNA double strand breaks (DSBs). However, there is no systematic comparison being conducted to evaluate the consistency of these two methods. Using MNNG as a model chemical, the sensitivity of neutral comet assay and gammaH2AX foci formation in detecting MNNG-induced damage was studied. It was found that at concentrations of 0.1 and 1 microg/ml, both methods can detect MNNG-induced damage in human amnion FL cells. However, at 0.1 microg/ml, comet assay revealed more percentage of cells with DNA damage than gammaH2AX fluorescence revealed. On the other hand, while gammaH2AX foci were readily formed at very early times by 10 microg/ml MNNG treatment, neutral comet assay did not detect any significant DNA damage at the same time points. In addition, 10 microg/ml MNNG induced a distinct whole nuclei staining pattern of gammaH2AX, a type of DNA damage which was not detected by neutral comet assay but could be detected by alkaline comet assay. Therefore, gammaH2AX may be used as a sensitive indicator for DNA damage.

Suppression of a DNA double-strand break repair gene, Ku70, increases radio- and chemosensitivity in a human lung carcinoma cell line.

Ku70 protein, cooperating with Ku80 and DNA-dependent protein kinase (DNA-PK) catalytic subunit (DNA-PKcs), is involved in DNA double-strand break (DNA DSB) repair and V(D)J recombination. Recent studies have revealed increased ionizing radiosensitivity in Ku70-deficient cells. The presented study, using a human squamous cell lung carcinoma cell line, demonstrated that introduction of an antisense Ku70 nucleic acid made the cells more radio- and chemosensitive than the parental cells. Ku70 protein expression was suppressed in the cells with antisense Ku70 construct when compared to the wild-type cells. A relatively small but statistically significant increase in radiosensitivity of the cells was achieved by the introduction of the antisense Ku70. The increased radiosensitivity in vitro was accompanied by an approximately two-fold increase in alpha and alpha/beta values in a linear-quadratic model. The antisense Ku70 increased the chemosensitivity of the cells to some DNA-damaging agents such as bleomycin and methyl methanesulfonate, but not to cisplatin, mitomycin C, and paclitaxel. This system provides us with partial suppression of Ku70, and will be a useful experimental model for investigating the physiological roles of the DNA DSB repair gene.

Gene expression changes in normal human skin fibroblasts induced by HZE-particle radiation.

Studies have shown that radiation exposure affects global gene expression in mammalian cells. However, little is known about the effects of HZE particles on gene expression. To study these effects, human skin fibroblasts were irradiated with HZE particles of different energies and LETs. The data obtained from these experiments indicate that changes in gene expression are dependent on the energy of the radiation source. Particles with the highest energy, i.e. iron, induced the biggest expression changes in terms of numbers of genes and magnitudes of changes. Many genes were found to undergo significant expression changes after HZE-particle irradiation, including CDKN1A/p21, MDM2, TNFRSF6/fas, PCNA and RAD52. Unlike X rays, HZE particles expose cells to two types of radiation: primary ions and delta rays. We hypothesized that the biological effects of delta rays, which are secondary electron emissions, should resemble the effects of X rays. To explore this idea, gene expression changes between cells that had been irradiated with HZE particles and X rays were compared. The results support our hypothesis since the number of genes that commonly changed after exposure to both radiations increased as a function of particle energy.

Gene expression profiles of normal human fibroblasts after exposure to ionizing radiation: a comparative study of low and high doses.

Several types of cellular responses to ionizing radiation, such as the adaptive response or the bystander effect, suggest that low-dose radiation may possess characteristics that distinguish it from its high-dose counterpart. Accumulated evidence also implies that the biological effects of low-dose and high-dose ionizing radiation are not linearly distributed. We have investigated, for the first time, global gene expression changes induced by ionizing radiation at doses as low as 2 cGy and have compared this to expression changes at 4 Gy. We applied cDNA microarray analyses to G1-arrested normal human skin fibroblasts subjected to X irradiation. Our data suggest that both qualitative and quantitative differences exist between gene expression profiles induced by 2 cGy and 4 Gy. The predominant functional groups responding to low-dose radiation are those involved in cell-cell signaling, signal transduction, development and DNA damage responses. At high dose, the responding genes are involved in apoptosis and cell proliferation. Interestingly, several genes, such as cytoskeleton components ANLN and KRT15 and cell-cell signaling genes GRAP2 and GPR51, were found to respond to low-dose radiation but not to high-dose radiation. Pathways that are specifically activated by low-dose radiation were also evident. These quantitative and qualitative differences in gene expression changes may help explain the non-linear correlation of biological effects of ionizing radiation from low dose to high dose.

Nanoparticle-mediated systemic delivery of siRNA for treatment of cancers and viral infections.

RNA interference (RNAi) is an endogenous post-transcriptional gene regulatory mechanism, where non-coding, double-stranded RNA molecules interfere with the expression of certain genes in order to silence it. Since its discovery, this phenomenon has evolved as powerful technology to diagnose and treat diseases at cellular and molecular levels. With a lot of attention, short interfering RNA (siRNA) therapeutics has brought a great hope for treatment of various undruggable diseases, including genetic diseases, cancer, and resistant viral infections. However, the challenge of their systemic delivery and on how they are integrated to exhibit the desired properties and functions remains a key bottleneck for realizing its full potential. Nanoparticles are currently well known to exhibit a number of unique properties that could be strategically tailored into new advanced siRNA delivery systems. This review summarizes the various nanoparticulate systems developed so far in the literature for systemic delivery of siRNA, which include silica and silicon-based nanoparticles, metal and metal oxides nanoparticles, carbon nanotubes, graphene, dendrimers, polymers, cyclodextrins, lipids, hydrogels, and semiconductor nanocrystals. Challenges and barriers to the delivery of siRNA and the role of different nanoparticles to surmount these challenges are also included in the review.

Proteomic analysis of cellular response induced by multi-walled carbon nanotubes exposure in A549 cells.

The wide application of multi-walled carbon nanotubes (MWCNT) has raised serious concerns about their safety on human health and the environment. However, the potential harmful effects of MWCNT remain unclear and contradictory. To clarify the potentially toxic effects of MWCNT and to elucidate the associated underlying mechanisms, the effects of MWCNT on human lung adenocarcinoma A549 cells were examined at both the cellular and the protein level. Cytotoxicity and genotoxicity were examined, followed by a proteomic analysis (2-DE coupled with LC-MS/MS) of the cellular response to MWCNT. Our results demonstrate that MWCNT induces cytotoxicity in A549 cells only at relatively high concentrations and longer exposure time. Within a relatively low dosage range (30 µg/ml) and short time period (24 h), MWCNT treatment does not induce significant cytotoxicity, cell cycle changes, apoptosis, or DNA damage. However, at these low doses and times, MWCNT treatment causes significant changes in protein expression. A total of 106 proteins show altered expression at various time points and dosages, and of these, 52 proteins were further identified by MS. Identified proteins are involved in several cellular processes including proliferation, stress, and cellular skeleton organization. In particular, MWCNT treatment causes increases in actin expression. This increase has the potential to contribute to increased migration capacity and may be mediated by reactive oxygen species (ROS).

Convection-enhanced delivery of targeted quantum dot-immunoliposome hybrid nanoparticles to intracranial brain tumor models.

AIM: The aim of this work is to evaluate combining targeting strategy and convection-enhanced delivery in brain tumor models by imaging quantum dot-immunoliposome hybrid nanoparticles. MATERIALS & METHODS: An EGF receptor-targeted, quantum dot-immunoliposome hybrid nanoparticle (QD-IL) was synthesized. In vitro uptake was measured by flow cytometry and intracellular localization was imaged by confocal microscopy. In the in vivo study, QD-ILs were delivered to intracranial xenografts via convection-enhanced delivery and fluorescence was monitored noninvasively in real-time. RESULTS: QD-ILs exhibited specific and efficient uptake in vitro and exhibited approximately 1.3- to 5.0-fold higher total fluorescence compared with nontargeted counterpart in intracranial brain tumor xenografts in vivo. CONCLUSION: QD-ILs serve as an effective imaging agent in vitro and in vivo, and the data suggest that ligand-directed liposomal nanoparticles in conjunction with convection-enhanced delivery may offer therapeutic benefits for glioblastoma treatment as a result of specific and efficient uptake by malignant cells.

Fabrication of quantum dots-encoded microbeads with a simple capillary fluidic device and their application for biomolecule detection.

Monodispersed quantum dots (QDs)-encoded polymer microbeads were generated using a simple capillary fluidic device (CFD). The polymer and QDs solution was emulsified into monodispersed microdroplets by the CFD and obtained droplets were solidified via solvent evaporation. Polymer microbeads can be fabricated in a range of different sizes through changing the flow rates of the two immiscible phases, and have a highly narrow size distribution and uniform shape. QDs-encoding capacity of the microbeads was investigated through adjusting the concentrations and ratios of QDs in the polymer solution. Mono-color encoded microbeads with five intensities and a dual-color QDs-encoded 5×5 microbeads array were obtained, and the spectral profiles of the microbeads were examined by a fluorescent microscope coupled with a spectral imaging system. QDs-tagged microbeads prepared with this method were more stable than the porous beads swollen with QDs in the buffer with various pH and crosslinking chemicals. Finally, the application of such microbeads for biomolecule detection was demonstrated by conjugation of rabbit IgG molecules on the surface of the microbeads via carboxyl groups, which were then detected by fluorophores-labeled goat-anti-rabbit IgG antibodies.

Hybrid nanocluster plasmonic resonator for immunological detection of hepatitis B virus.

Approximately 88% of the world population lives in regions with intermediate to high incidence of Hepatitis B virus (HBV), yet current serological and DNA-based detection methods have limited sensitivity and convenience. Here, we describe a preassembled plasmonic resonance nanocluster for HBV detection. The gold nanoparticle acceptors (AuNPs), with HBV surface antigen (HBsAg) epitope, and quantum dot (QD) donors with Fab antibody, are assembled into an immuno-mediated 3D-oriented complex with enhanced energy transfer and fluorescence quenching. The coherent plasmonic resonance between Au and QD nanoparticles is exploited to achieve improved donor-acceptor resonance within the nanocluster, which in the presence of HBV viral particles is disassembled in a highly specific manner. The nanocluster provides high detection specificity and sensitivity of HBV, with a sensitivity limit down to 1-100 viral particles per microliter and to attomolar levels of HBsAg. This general platform could be used to establish multiplex diagnostic assays for a variety of other microbial pathogens.

Effects of Fluid Shear Stress on a Distinct Population of Vascular Smooth Muscle Cells.

Vascular smooth muscle cells (SMCs) are a major cell type involved in vascular remodeling. The various developmental origins of SMCs such as neural crest and mesoderm result in heterogeneity of SMCs, which plays an important role in the development of vascular remodeling and diseases. Upon vascular injury, SMCs are exposed to blood flow and subjected to fluid shear stress. Previous studies have shown that fluid shear stress inhibits SMC proliferation. However, the effect of shear stress on the subpopulation of SMCs from specific developmental origin and vascular bed is not well understood. Here we investigated how shear stress regulates human aortic SMCs positive for neural crest markers. DNA microarray analysis showed that shear stress modulates the expression of genes involved in cell proliferation, matrix synthesis, cell signaling, transcription and cytoskeleton organization. Further studies demonstrated that shear stress induced SMC proliferation and cyclin D1, downregulated cell cycle inhibitor p21, and activated Akt pathway. Inhibition of PI-3 kinase blocked these shear stress-induced changes. These results suggest that SMCs with neural crest characteristics may respond to shear stress in a different manner. This finding has significant implications in the remodeling and diseases of blood vessels.

Radiosensitivity profiles from a panel of ovarian cancer cell lines exhibiting genetic alterations in p53 and disparate DNA-dependent protein kinase activities.

The variability of radiation responses in ovarian tumors and tumor-derived cell lines is poorly understood. Since both DNA repair capacity and p53 status can significantly alter radiation sensitivity, we evaluated these factors along with radiation sensitivity in a panel of sporadic human ovarian carcinoma cell lines. We observed a gradation of radiation sensitivity among these sixteen lines, with a five-fold difference in the LD50 between the most radiosensitive and the most radioresistant cells. The DNA-dependent protein kinase (DNA-PK) is essential for the repair of radiation induced DNA double-strand breaks in human somatic cells. Therefore, we measured gene copy number, expression levels, protein abundance, genomic copy and kinase activity for DNA-PK in all of our cell lines. While there were detectable differences in DNA-PK between the cell lines, there was no clear correlation with any of these differences and radiation sensitivity. In contrast, p53 function as determined by two independent methods, correlated well with radiation sensitivity, indicating p53 mutant ovarian cancer cells are typically radioresistant relative to p53 wild-type lines. These data suggest that the activity of regulatory molecules such as p53 may be better indicators of radiation sensitivity than DNA repair enzymes such as DNA-PK in ovarian cancer.

Time-resolved single-step protease activity quantification using nanoplasmonic resonator sensors.

Protease activity measurement has broad application in drug screening, diagnosis and disease staging, and molecular profiling. However, conventional immunopeptidemetric assays (IMPA) exhibit low fluorescence signal-to-noise ratios, preventing reliable measurements at lower concentrations in the clinically important picomolar to nanomolar range. Here, we demonstrated a highly sensitive measurement of protease activity using a nanoplasmonic resonator (NPR). NPRs enhance Raman signals by 6.1 x 10(10) times in a highly reproducible manner, enabling fast detection of proteolytically active prostate-specific antigen (paPSA) activities in real-time, at a sensitivity level of 6 pM (0.2 ng/mL) with a dynamic range of 3 orders of magnitude. Experiments on extracellular fluid (ECF) from the paPSA-positive cells demonstrate specific detection in a complex biofluid background. This method offers a fast, sensitive, accurate, and one-step approach to detect the proteases' activities in very small sample volumes.

Quantitative and label-free technique for measuring protease activity and inhibition using a microfluidic cantilever array.

We report the use of a SiN x based gold coated microcantilever array to quantitatively measure the activity and inhibition of a model protease immobilized on its surface. Trypsin was covalently bound to the gold surface of the microcantilever using a synthetic spacer, and the remaining exposed silicon nitride surface was passivated with silanated polyethylene glycol. The nanoscale cantilever motions induced by trypsin during substrate turnover were quantitatively measured using an optical laser-deflection technique. These microcantilever deflections directly correlated with the degree of protease turnover of excess synthetic fibronectin substrate ( K M = 0.58 x 10 (-6) M). Inhibition of surface-immobilized trypsin by soybean trypsin inhibitor (SBTI) was also observed using this system.