This effort focuses on three types of biomarker discovery: protein biomarkers in tissues and cells, bodily fluid (blood, urine, and other fluids) protein biomarkers, and transcriptome (RNA) biomarkers. These approaches together facilitate translational cancer research by providing new tools to the clinician for the enhanced diagnosis, follow-up and screening of cancer patients.
Tissue Proteins: Cell and tissue analysis of cancer specimens allows researchers to assess the exact site and expression level of protein cancer biomarkers in architecturally preserved or homogenized tissues. Analysis can include histomorphological examination in collaboration with a pathologist, use of immunohistochemical staining with specific antibodies on cell and whole mount tissue specimens, and Western blot analysis of cell or tissue homogenates.
Fluid Proteins: The emerging field of proteomics provides new tools for the early detection of cancer from human serum, cerebral spinal fluid, urine and other complex samples. Proteomic research provides information regarding the proteome’s dynamic and rapid changes which result from exogenous exposure or endogenous factors. The CTCR Core offers a fee-per-service proteomic analysis based on the patented Surface Enhanced Laser Desorption/Ionization (SELDI) technology, Ciphergen’s ProteinChip® System. Assays using SELDI time-of-flight mass spectrometry (TOF-MS) to provide a means to identify new candidate biomarker proteins because of their ability to detect and quantify multiple post-translationally modified and processed protein forms in a single assay. The ability to interface ProteinChip® Arrays with tandem mass spectrometry allows for direct amino acid sequencing from ProteinChip experiments. ProteinChip arrays require only microliter volumes of sera, cell extracts, or tissue lysates for analysis.
RNA Molecules: New methods to analyze gene expression or the “transcriptome” of cancer cells for comparison to the patterns of normal cells provides a powerful new means of identifying RNA biomarkers for specific cancers. Several research projects are underway using the core facilities available to CTCR researchers. These projects seek to analyze total expressed RNA using microarrays, microRNAs that function as regulators of protein expression, quantitative analysis of single genes using Q-PCR, and to develop new methods to analyze RNA expression in archived cancer tissue specimens.