Science

Proteomics

Proteomics, which is often considered the next logical step in the study of biological systems after genomics, is instrumental in the discovery of biomarkers that indicate the presence of a particular disease. Most FDA approved drugs target protein function, not genes. Most molecular diagnostic companies analyze genes, not proteins. Because gene expression analysis cannot provide a direct measurement of actual drug targets and does not correlate nor predict most protein expression levels, however, it has less of an ability to define a cell’s working machinery or decipher its communication network. The Theranostics Health assay directly measures this key missing piece of information and measures drug target activity, enabling physicians and pharmaceutical companies to more effectively prescribe and develop drugs specifically designed to hit the molecular profile of a patient’s disease.

Proteins

Proteins perform the work of the cell and provide its structure. Their functionality is context-specific, depending on their interactions within the cellular microenvironment. Genomic sequence alone does not provide comprehensive information about the end product: the process of gene activation, transcription, splicing, translation and post-translation modification coupled with environmental influences can significantly alter the activity, interaction, and location of any given protein and protein network.

Critical information about disease can be derived from proteomics. The long and convoluted path of carcinogenesis and metastasis involves an aggregation of mutations in proteins that are not predictable from sequence alone. There is an unmet need for comprehensive examination of protein expression and activity in disease. Mapping of protein signaling networks within tumors can identify functionally important protein signaling defects associated with disease treatment failure as well as identify new targets for therapy.

Signaling proteins coordinate a variety of cellular processes, including translation control, cell division and growth, differentiation, metabolism, movement, immune response, reaction to stress, apoptosis and necrosis. The elaborate repertoire of signal transduction processes are regulated by the conversion of signals and stimuli which is largely performed by kinase phosphorylation.

Protein kinases regulate cells through the attachment of phosphate groups to specific amino acids. This phosphorylation mechanism is the most common type of regulatory modification. One third to one half of all proteins in a eukaryotic cell are phosphorylated. Some proteins have only one phosphorylated residue, others have several, a few have dozens of sites. Phosphate addition or removal alters structure, catalytic activity and substrate-binding affinity of these enzymes and allows them to coordinate the activity of most cellular processes.

Cell signaling is cell communication. Information is detected by specific cell-surface receptors, converted and amplified through a sequence of ordered biochemical reactions within the cell and culminates in a response. The variety of biological signals and responses is stunning, yet there are but a few mechanisms that facilitate this signaling. Up to 30% of all proteins can be modified by kinases, shown to regulate the majority of cellular pathways. There are 518 human protein kinases in all, associated with countless interconnected pathways.

Kinases themselves are regulated by phosphorylation and dephosphorylation, binding of activator of inhibitor proteins, small molecules, or by location. The disregulation of kinase activity is a major hallmark of disease, particularly cancer. Drugs which inhibit specific kinases have been developed to treat several diseases and continue to be a focus of drug development today.

Protein kinase inhibitors: currently a major focus of drug discovery and development efforts for a variety of human diseases, including cancer. By design or otherwise, these inhibitors often act on more than one target. Moreover, many of these same targets play crucial roles in multiple cell signaling pathways. Given this complexity, a systematic and comprehensive measurement of in vivo signaling pathway activity is required to effectively determine the consequences of therapeutic intervention with kinase inhibitors in preclinical and clinical samples. Gene expression arrays are systematic and comprehensive but are not suitable for measuring posttranslational modifications. The phosphorylation state of the substrate(s) of protein kinase targets, their downstream and upstream effectors, inter- and intrapathway crosstalk and other signaling pathway phenotypes is best measured using a phosphoproteomic approach.

Theranostics Health has focused on oncology with the goal of rendering cancer a managed disease, not a fatal illness. While applicable to all major diseases, our assay is particularly well-suited for analysis of biopsy samples which typically yield limited quantities of cells. Our capacity for quantitative analysis of over 250 endpoints from less than 500 cells is ideal for needle-aspirate and core needle biopsy samples where the starting input material is only a few hundred cells. The sensitivity of RMPA is such that low abundance phosphorylated proteins can be measured from a spotted lysate representing less than 10 cell equivalents. This level of sensitivity combined with analytical robustness is critical.

Article: 2007 Cure: Predictive Markers for Cancer

For more information contact: technology@theranosticshealth.com