cyanine-dye-3 and Breast-Neoplasms

Discriminative identification of homologous miRNAs in miRNA family with high specificity and sensitivity is crucial for accurate classification, diagnosis and prognosis of breast cancer. Herein, we report a reliable, sensitive, and selective assay by coupling fluorescence resonance energy transfer (FRET) with cascade signal amplification. The strategy is developed by designing two programmable DNA probes that can be triggered to shift from "off" to "on" state in a cascade hybridization reaction in the presence of target miRNA let-7a, leading to the generation of an amplified signal. The assay can detect concentrations as low as ∼3.0 pM let-7a and discriminate let-7a from other highly homologous members in the let-7 miRNA family. Moreover, it can also be used to determine let-7a levels at single-cell resolution and evaluate the drug efficacy of let-7a expression among various molecular types of breast cancer cell lines. The advantage of this assay is a combined result of signal generation and amplification triggered by target miRNA, which can satisfy an assay of analogous miRNA in a downregulated manner with high specificity. It has promising potential as a selective assay for homologous miRNAs in precision medicine.

Topics: Antineoplastic Agents; Breast Neoplasms; Carbocyanines; Cell Line, Tumor; DNA Probes; Fluorescence Resonance Energy Transfer; Fluorescent Dyes; Humans; Inverted Repeat Sequences; MicroRNAs; Microscopy, Confocal; Microscopy, Fluorescence; Nucleic Acid Hybridization; Paclitaxel; Proof of Concept Study

Silver nanoparticles (AgNPs) have a high affinity for sulfhydryl (thiol) groups, which can be exploited for functionalization with various tracking and targeting moieties. Here, we describe how to reliably and reproducibly functionalize AgNPs with the fluorescent moiety cyanine3-polyethelyne glycol (5000 molecular weight)-thiol (Cy3-PEG

Topics: Breast Neoplasms; Carbocyanines; Cell Culture Techniques; Female; Fluorescent Dyes; Humans; Metal Nanoparticles; Molecular Imaging; Silver; Spectrophotometry, Ultraviolet; Tumor Cells, Cultured

Nanoparticle delivery is becoming an increasingly more valuable technique in cancer drug treatments. The use of fluorescent probes, in particular, can provide noninvasive strategies to interrogate the internalization mechanisms of cancer cells and aid in drug design. Here we describe the delivery of fluorescently labeled polysaccharide-based nanoparticles to breast cancer cells in vitro and their subsequent immunofluorescence microscopy examination. The description of the synthesis, preparation, and delivery of the nanoparticles can be widely applicable to other in vitro drug delivery studies.

Topics: Animals; Biological Transport; Breast Neoplasms; Carbocyanines; Cell Line, Tumor; Cryopreservation; Fluorescent Dyes; Intracellular Space; Mice; Microscopy, Fluorescence; Nanoparticles; Particle Size; Polysaccharides; Sterilization

We present label-free, in situ monitoring of individual DNA hybridization in microfluidics. By immobilizing molecular sentinel probes on nanoporous gold disks, we demonstrate sensitivity approaching the single-molecule limit via surface-enhanced Raman scattering which provides robust signals without photobleaching for more than an hour. We further demonstrate that a target concentration as low as 20 pM can be detected within 10 min under diffusion-limited transport.

Topics: Breast Neoplasms; Carbocyanines; Diffusion; DNA; DNA, Single-Stranded; Female; Gold; Humans; Light; Metal Nanoparticles; Microfluidic Analytical Techniques; Microfluidics; Nanostructures; Nanotechnology; Nucleic Acid Hybridization; Porosity; Receptor, ErbB-2; Spectrum Analysis, Raman; Surface Plasmon Resonance

DNA damage responses (DDR) occur during oncogenesis and therapeutic responses to DNA damaging cytotoxic drugs. Thus, a real-time method to image DNA damage in vivo would be useful to diagnose cancer and monitor its treatment. Toward this end, we have developed fluorophore- and radioisotope-labeled immunoconjugates to target a DDR signaling protein, phosphorylated histone H2A variant H2AX (γH2AX), which forms foci at sites of DNA double-strand breaks. Anti-γH2AX antibodies were modified by the addition of diethylenetriaminepentaacetic acid (DTPA) to allow (111)In labeling or the fluorophore Cy3. The cell-penetrating peptide Tat (GRKKRRQRRRPPQGYG) was also added to the immunoconjugate to aid nuclear translocation. In irradiated breast cancer cells, confocal microscopy confirmed the expected colocalization of anti-γH2AX-Tat with γH2AX foci. In comparison with nonspecific antibody conjugates, (111)In-anti-γH2AX-Tat was retained longer in cells. Anti-γH2AX-Tat probes were also used to track in vivo DNA damage, using a mouse xenograft model of human breast cancer. After local X-ray irradiation or bleomycin treatment, the anti-γH2AX-Tat probes produced fluorescent and single photon emission computed tomography signals in the tumors that were proportionate to the delivered radiation dose and the amount of γH2AX present. Taken together, our findings establish the use of radioimmunoconjugates that target γH2AX as a noninvasive imaging method to monitor DNA damage, with many potential applications in preclinical and clinical settings.

Topics: Amino Acid Sequence; Animals; Antibodies; Breast Neoplasms; Carbocyanines; Cell Line, Tumor; DNA Damage; DNA, Neoplasm; Female; Gene Products, tat; Histones; Humans; Immunoconjugates; Indium Radioisotopes; Mice; Mice, Inbred BALB C; Mice, Nude; Molecular Sequence Data; Pentetic Acid; Transplantation, Heterologous

Breast cancer presents greatest challenge in health care in today's world. The key to ultimately successful treatment of breast cancer disease is an early and accurate diagnosis. Current breast cancer treatments are often associated with severe side effects. Driven by the need, we report the design of novel hybrid nanomaterial using gold nano popcorn-attached single wall carbon nanotube for targeted diagnosis and selective photothermal treatment. Targeted SK-BR-3 human breast cancer cell sensing have been performed in 10 cancer cells/mL level, using surface enhanced Raman scattering of single walls carbon nanotube's D and G bands. Our data show that S6 aptamer attached hybrid nanomaterial based SERS assay is highly sensitive to targeted human breast cancer SK-BR-3 cell line and it will be able to distinguish it from other non targeted MDA-MB breast cancer cell line and HaCaT normal skin cell line. Our results also show that 10 min of photothermal therapy treatment by 1.5 W/cm(2) power, 785 nm laser is enough to kill cancer cells very effectively using S6 aptamer attached hybrid nanomaterials. Possible mechanisms for targeted sensing and operating principle for highly efficient photothermal therapy have been discussed. Our experimental results reported here open up a new possibility for using aptamers modified hybrid nanomaterial for reliable diagnosis and targeted therapy of cancer cell lines quickly.

Topics: Aptamers, Nucleotide; Breast Neoplasms; Carbocyanines; Cell Line, Tumor; Female; Gold; Humans; Metal Nanoparticles; Nanostructures; Nanotubes, Carbon; Phototherapy; Spectrum Analysis, Raman

We present a new application of multispectral analysis for subcellular measurement of multiple proteins in formalin-fixed paraffin embedded tissue and cells. Typically, the targets of interest are present in the same or spatially overlapping cellular compartments. Such co-localization can complicate analysis and interpretation of the images obtained using traditional fluorescence, especially when spectrally overlapping labels are present. The spectral properties of currently available fluorescent dyes set an upper limit to the number of molecules that can be detected simultaneously with traditional fluorescence. By exciting a set of fluorophores at the same wavelength and unmixing their emission signals from background autofluorescence, we were able to image three targets in a single channel. This parallel imaging approach provides significant advantages for multiplexed analysis of tissues and cells.

Topics: Algorithms; Animals; Biomarkers; Breast; Breast Neoplasms; Carbocyanines; Cyclic AMP Response Element-Binding Protein; Female; Humans; Image Processing, Computer-Assisted; Lung; Male; Mice; Microscopy, Fluorescence; Microscopy, Fluorescence, Multiphoton; Prostate; Proteins; Signal Processing, Computer-Assisted; Tissue Array Analysis

Non-biological signal (or noise) has been the bane of microarray analysis. Hybridization effects related to probe-sequence composition and DNA dye-probe interactions have been observed in differential methylation hybridization (DMH) microarray experiments as well as other effects inherent to the DMH protocol.. We suggest two models to correct for non-biologically relevant probe signal with an overarching focus on probe-sequence composition. The estimated effects are evaluated and the strengths of the models are considered in the context of DMH analyses.. The majority of estimated parameters were statistically significant in all considered models. Model selection for signal correction is based on interpretation of the estimated values and their biological significance.

Topics: Base Sequence; Breast Neoplasms; Carbocyanines; Cell Line, Tumor; DNA Methylation; DNA Probes; Female; Fluorescent Dyes; Gene Expression Profiling; Humans; Methylation; Models, Genetic; Models, Statistical; Nucleic Acid Hybridization; Oligonucleotide Array Sequence Analysis; Sequence Analysis, DNA; Signal Transduction

Differential in-gel electrophoresis (DIGE) experiments allow three protein samples to be run per gel. The three samples are labeled with the spectrally resolvable fluorescent dyes, Cy2, Cy3, and Cy5, respectively. Here, we show that protein-specific dye effects exist, and we present a linear mixed model for analysis of DIGE data which takes dye effects into account. A Java implementation of the model, called DIGEanalyzer, is freely available at http://bioinfo.thep.lu.se/digeanalyzer.html. Three DIGE experiments from our laboratory, with 173, 64, and 24 gels, respectively, were used to quantify and verify the dye effects. DeCyder 5.0 and 6.5 were used for spot detection and matching. The fractions of proteins with a statistically significant (0.001 level) dye effect were 19, 34, and 23%, respectively. The fractions of proteins with a dye effect above 1.4-fold change were 1, 4, and 6%, respectively. The median magnitude of the dye effect was 1.07-fold change for Cy5 versus Cy3 and 1.16-fold change for Cy3 versus Cy2. The maximal dye effect was a seven-fold change. The dye effects of spots corresponding to the same protein tend to be similar within each of the three experiments, and to a smaller degree across experiments.

Topics: Algorithms; Animals; Brain Chemistry; Breast Neoplasms; Carbocyanines; Computational Biology; Electrophoresis, Gel, Two-Dimensional; Female; Fluorescent Dyes; Humans; Image Processing, Computer-Assisted; Internet; Linear Models; Ovarian Neoplasms; Proteins; Proteomics; Rats; Software; Tandem Mass Spectrometry

Spotted cDNA microarrays generally employ co-hybridization of fluorescently-labeled RNA targets to produce gene expression ratios for subsequent analysis. Direct comparison of two RNA samples in the same microarray provides the highest level of accuracy; however, due to the number of combinatorial pair-wise comparisons, the direct method is impractical for studies including large number of individual samples (e.g., tumor classification studies). For such studies, indirect comparisons using a common reference standard have been the preferred method. Here we evaluated the precision and accuracy of reconstructed ratios from three indirect methods relative to ratios obtained from direct hybridizations, herein considered as the gold-standard.. We performed hybridizations using a fixed amount of Cy3-labeled reference oligonucleotide (RefOligo) against distinct Cy5-labeled targets from prostate, breast and kidney tumor samples. Reconstructed ratios between all tissue pairs were derived from ratios between each tissue sample and RefOligo. Reconstructed ratios were compared to (i) ratios obtained in parallel from direct pair-wise hybridizations of tissue samples, and to (ii) reconstructed ratios derived from hybridization of each tissue against a reference RNA pool (RefPool). To evaluate the effect of the external references, reconstructed ratios were also calculated directly from intensity values of single-channel (One-Color) measurements derived from tissue sample data collected in the RefOligo experiments. We show that the average coefficient of variation of ratios between intra- and inter-slide replicates derived from RefOligo, RefPool and One-Color were similar and 2 to 4-fold higher than ratios obtained in direct hybridizations. Correlation coefficients calculated for all three tissue comparisons were also similar. In addition, the performance of all indirect methods in terms of their robustness to identify genes deemed as differentially expressed based on direct hybridizations, as well as false-positive and false-negative rates, were found to be comparable.. RefOligo produces ratios as precise and accurate as ratios reconstructed from a RNA pool, thus representing a reliable alternative in reference-based hybridization experiments. In addition, One-Color measurements alone can reconstruct expression ratios without loss in precision or accuracy. We conclude that both methods are adequate options in large-scale projects where the amount of a common reference RNA pool is usually restrictive.

Topics: Adenocarcinoma; Breast Neoplasms; Carbocyanines; Carcinoma, Renal Cell; DNA, Complementary; DNA, Neoplasm; Female; Fluorescent Dyes; Gene Expression Regulation, Neoplastic; Humans; Kidney Neoplasms; Male; Nucleic Acid Hybridization; Oligonucleotide Array Sequence Analysis; Prostatic Neoplasms