Technologies
Advances in structural and functional proteomics have produced compelling data indicating that proteins will likely define the changes that constitute the cancer process. The accessibility of proteins in bodily fluids and tissues has already facilitated extensive protein-focused research. But a lack of reliable methods for protein identification and measurement has led to pervasive problems with reproducibility and comparability of research results. The lack of qualified standards, reagents, and validated technologies have made it nearly impossible to develop, manage, interpret, and compare large quantities of proteomic data, and that in turn slows the translation of discoveries to clinical application.
Described below are some of the technologies that could advance our understanding of protein biology, and the challenges — in particular the need for standardization — that will be addressed through the NCI's Clinical Proteomic Technologies Initiative for Cancer.
Biospecimens
Cancer research has come to rely on biospecimens for the measurement of genetic and protein expression and the linkage of that information with clinical status and to disease pathways such as tumor growth, migration, metastasis, angiogenesis and apoptosis (cell death). Since the process of cancer diagnosis and treatment often begins with diagnostic biopsies followed by surgical resection of the tumor, there are many opportunities to collect valuable biospecimens for research.
The NCI has recognized the critical need for research access to large numbers of high-quality biospecimens annotated with clinical data. NCI is seeking to address the need by through its Office of Biorepositories and Biospecimen Research.
Mass Spectrometry
Mass spectrometry is a powerful tool used to identify and in some cases quantify the proteins or peptides in a sample. Mass spectrometers are designed to measure two properties:
- The mass-to-charge ratio (m/z) of ions (particles with an electric charge); and
- The number of ions present at each m/z value.
On a mass spectrum, each peak represents an ionized peptide, originating from a protein in the sample, with the height of the peak proportional to the abundance of the peptide. Proteins may be identified by recording their "peptide mass fingerprint" — the pattern of peaks in the mass spectrum after fragmentation by specific enzymes — or by amino-acid sequencing after breaking down the protein fragments further into a series of peptides differing by one amino acid.
Mass spectrometry, despite its potential, is not yet capable of separating the complex protein and fragment mixtures from unprocessed human biospecimens. New technologies are required to reduce the complexity of protein isolates enriching for proteins of interest, and to enhance the range and sensitivity of the instrumentation.
Protein Microarrays
Protein microarrays are solid-state protein binding assay systems that use a variety of immobilized "capture reagents" to detect and quantify proteins and protein fragments (peptides) isolated from tissues and biological fluids. A capture reagent is a molecule, such as a monoclonal antibody or a nucleic acid aptamer, which binds tightly to a specific protein or peptide, enabling one to detect it in, and possibly isolate it from, a mixture of molecules present in biological samples. The capture reagents are typically immobilized on a solid support material, including glass, synthetic membranes, microbeads, or mass spectrometer plates.
Because protein microarray elements can be miniaturized to contain tens of thousands of capture features arranged in a grid, each specific for a given protein or peptide, they are considered a multiplexed device — that is, they can conduct multiple assays simultaneously. This density permits a very high-throughput system for measuring each protein's role in the networks of biochemical and signaling interactions within a sample.
Reagents
There is a growing need in the field of proteomics for high-quality, standardized reagents that can improve proteomic technologies’ specificity and reproducibility. One widely used reagent in proteomic research is the antibody, a naturally occurring serum protein whose biological role requires high-antigen specificity. They have been useful as detection and capture reagents in proteomics.
Aptamer reagents show promise as an adjunct to antibodies. These nucleic acid-based molecules possess protein-binding specificity, similar to antibodies that make them useful as protein capture and detection reagents. Since they are nucleic acid-based, the technology for their synthesis and chemical modification is more mature than antibody production, and various mutation and selection protocols can be used to specify their binding properties.
Standard proteomic reagents will be useful for many applications in cancer research and development, including:
- Reporter molecules that detect the presence of a target (or modifications to it) in a particular biological sample;
- Capture molecules for purifying the target from a complex biological sample prior to identification and quantification using, for example, mass spectrometry;
- Functional studies to validate the role of a potential therapeutic target prior to launching drug discovery or development efforts;
- Reference materials for calibrating instruments or comparing different proteomic platform technologies.
Nanotechnologies
Nanotechnology is a multidisciplinary approach to manufacturing devices and components that range from 1 - 100 nm in at least one dimension, roughly the size range between an antibody molecule and a virus particle. Nanotechnology devices have the potential to greatly expand the capabilities of proteomics, addressing current limitations in selectively reaching a target protein in vivo through physical and biological barriers, detecting low abundance targets, and providing a "toolbox" to translate the discovery of protein biomarkers to novel therapeutics and diagnostic tests. Typical devices include nanoparticles used for the targeted delivery of anticancer drugs, energy-based therapeutics (including heat and radiation) and imaging contrast reagents. Nanowires and nanocantilever arrays can be used in biosensors that measure minute quantities of biomarkers in biological fluids.
For more information, see the NCI Alliance for Nanotechnology in Cancer.
Bioinformatics
Major areas of focus in bioinformatics research include data modeling and database design, data interoperability and comparison, gene and protein expression analysis, structural predictions, vocabularies and ontologies, and systems biology modeling. In cancer research, the development of new tools in these areas are necessary to drive the collaborative, multidisciplinary effort required to push cancer research and discovery from the laboratory to clinical practice.
The NCI is addressing the need for an IT infrastructure to enable collection, analysis and sharing of huge amounts of data for inter-institutional studies through its cancer Biomedical Informatics Grid™, or caBIG™, a voluntary network connecting individuals and institutions to enable the sharing of data and tools, creating a World Wide Web of cancer research.
