Summary
The low molecular weight fraction of the human blood serum proteome ('serum peptidome') is greatly expanded ('boosted') in the course of serum preparation; i.e., after blood samples have been taken. This is the result of proteolytic activities that target endogenous substrates, such as abundant blood proteins and fragments thereof. The process is subject to variations in time, temperature, pH, enzyme cofactors and inhibitors. Together, activities, substrates and other controlling factors and conditions make for a virtually unlimited combinatorial variability to generate peptides of different size and composition. The potential pool could in theory equal or exceed the number of gene transcripts and proteins, and may therefore provide a robust functional correlate of biological events and disorders. Serum peptide profiling can therefore be considered a form of 'functional (i.e., activity-based) proteomics', with a 'peptide metabolomic' read-out, whereby virtually all signal is produced by post-sampling, in vitro catalytic activities.
The present technology is based on 'boosted peptidome' profiling of patient sera, using a direct mass spectrometric (MS) read-out, identified qualitative and relative-quantitative patterns, consisting of a few dozen peptides each, that clearly indicated the presence or absence of solid tumors. It also appeared that at least three different cancer types could be readily distinguished based on the resultant test (Villanueva et al., 2006).
This approach can be generalized for many diagnostic and predictive purposes, as an in vitro phenotypic read-out of endogenous catalytic and metabolic activities in body fluids or tissues, utilizing either endogenous or exogenous substrates, followed by qualitative and quantitative product analysis. Various analytical read-outs, product selection schemes, and activity attenuation procedures can be envisioned to provide more, or different, data points and to tailor the process to each specific case of pattern discovery.
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Area of Application
Diagnostics.
Direct MALDI-TOF MS-based serum peptide profiling is in fact a form of activity-based proteomics, monitoring surrogate biomarkers in the form of proteome 'metabolomic' products. This can be exploited for diagnostic and predictive purposes as a phenotypic read-out of catalytic and other metabolic activities in body fluids or tissues, utilizing endogenous (or exogenous) substrates and quantitative product analysis. It also makes this approach particularly well suited for detection of cancer as proteases are well-established components of cancer progression and invasiveness.
Proteolytic degradative patterns in the serum peptidome hold important information that may have direct clinical utility as a surrogate marker for detection and classification of cancer.
The patterns may also
- have diagnostic value for identifying cancer subtype and stage,
- mark a given clinical outcome of interest, or
- may reliably distinguish clinically insignificant from significant cancer.
Lead Inventor:
Dr. P. Tempst
Patent Information:
PCT patent application PCT/US06/31957 filed 8/16/2006, published 02/22/2007, WO 2007-022248.
Publications:
Contact Information:
Yashodhara Dash, MBBS, PhD, MBA
Tel. 212-639-6181; Fax212-717-3439
E-mail: dashy@mskcc.org
