As we transition from genomics to the challenges of the functional proteome, new tools to explore the expression of proteins within tissue are essential. We have developed a method of transferring proteins from a formalin fixed, paraffin embedded tissues section to a stack of membranes which is then probed with antibodies for detection of individual epitopes. This method converts a traditional tissue section into a multiplex platform for expression profiling. A single tissue section can be transferred to up to ten membranes, each of which is probed with different antibodies, and detected with fluorescent secondary antibodies, and quantified by a microarray scanner. Total protein can be determined on each membrane, hence each antibody has its own normalization. This method works with phospho-specific antibodies as well as antibodies that do not readily work well with paraffin embedded tissue. This novel technique enables archival paraffin embedded tissue to be molecularly profiled in a rapid and quantifiable manner, and reduces the tissue microarray to a form of protein array. This method is a new tool for exploration of the vast archive of formalin fixed, paraffin embedded tissue, as well as a tool for translational medicine.

Transfer and Multiplex Immunoblotting of a Paraffin Embedded Tissue

The presently described subject matter is directed to water-soluble conjugated polyene compounds that exhibit aggregation induced emission, as well as to water dispersible, fluorescent, polymeric microparticles and/or nanoparticles comprising the water-soluble conjugated polyene compounds. Also provided are methods of making and using the compounds and particles. The described conjugated polyene compounds are useful as bioprobes for the detection biomacromolecules, as well as in the manufacture of sensors.

/pdf/fluorescent-water-soluble-conjugated-polyene-compounds-that-4t9e1f4jma.pdf

Fluorescent water-soluble conjugated polyene compounds that exhibit aggregation induced emission and methods of making and using same

Compositions, methods and kits are described for identifying biomolecules (e.g., proteins and nucleic acids) expressed in a biological sample that are associated with the presence, development, or progression of a disease (such as cancer), or more generally determination of the etiology or risk factors associated with a disease. Sample types analyzed by the disclosed methods include but are not limited to archival tissue blocks that have been preserved in a fixative, tissue biopsy samples, tissue microarrays, and so forth. The methods disclosed herein correlate expression profiles of biomolecules with various disease types, and allow for the determination of relative survival rates; in some embodiments, the methods permit determination of survival rates for a subject with cancer. In other embodiments, the disclosure relates to methods for evaluating therapeutic regimes for the treatment, such as treatment of cancer.

Ratio based biomarkers and methods of use thereof

The present invention is directed to a device and a method for detecting biomolecules in a tissue section or other two-dimensional sample by creating “carbon copies” of the biomolecules eluted from the sample and visualizing the biomolecules on the copies using antibodies or DNA probes having specific affinity for the biomolecules of interest. Thin membranes in a stacked or layered configuration are applied to the sample, such as a tissue section, and reagents and reaction conditions are provided so that the biomolecules are eluted from the sample and transferred onto each of the stacked membranes thereby producing multiple replicas of the biomolecular content of the sample.

Methods and arrays for detecting biomolecules

The expression of Her-2/neu protein on circulating cancer cells in a blood sample is detected by isolating the cancer cells from the blood sample and then performing on the isolated cancer cells a sensitive Her-2/neu immunoassay. A positive result indicates the expression of Her-2/neu on cancer cells in the blood sample. This method can be used to identify cancer patients who are likely to benefit from treatment with an anticancer agent that targets Her-2/neu, such as trastuzumab (HERCEPTIN).

Detection of elevated levels of her-2/neu protein on circulating cancer cells and treatment

The present disclosure is directed to devices, arrays, kits and methods for detecting biomolecules in a tissue section (such as a fresh or archival sample, tissue microarray, or cells harvested by an LCM procedure) or other substantially two-dimensional sample (such as an electrophoretic gel or cDNA microarray) by creating “carbon copies” of the biomolecules eluted from the sample and visualizing the biomolecules on the copies using one or more detector molecules (e.g., antibodies or DNA probes) having specific affinity for the biomolecules of interest. Specific methods are provided for identifying the pattern of biomolecules (e.g., proteins and nucleic acids) in the samples. Other specific methods are provided for the identification and analysis of proteins and other biological molecules produced by cells and/or tissue, especially human cells and/or tissue. The disclosure also provides a plurality of differentially prepared and/or processed membranes that can be used in described methods, and which permit the identification and analysis of biomolecules.

Methods, devices, arrays and kits for detecting and analyzing biomolecules

Northern blots and immunoblots are utilized in laboratories worldwide and offer several important features for analyzing mRNA and protein expression, including accuracy, low cost, evaluation of probe specificity, and information on transcript and protein forms based on molecular size. However, standard blotting techniques are hampered by three factors. They require a significant amount of input material, are laborious, and are capable of measuring only one protein or transcript at a time. Here we describe a simple yet effective technique for the multiplex analysis of standard RNA and protein gels using the layered expression scanning platform. The method relies on a novel membrane with high-affinity low-capacity binding characteristics. Using this approach, multiple blots from an RNA or protein electrophoresis gel can be simultaneously produced. We believe this method will be widely applicable to expression studies for a broad range of biological systems.

https://www.future-science.com/doi/pdf/10.2144/03356pf01

Layered expression scanning: multiplex analysis of RNA and protein gels

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Methods, devices, arrays and kits for detecting and analyzing biomolecules

Layered expression scanning: multiplex analysis of RNA and protein gels