Protein Biomarkers for Cancer Diagnostics
Al Luderer, CEO of Integrated Diagnostics (Indi®), describes the power of proteomics as the ability to deliver noninvasive, molecular diagnostic tests that can be used early in the process of a patient work-up—in cancer that means before and perhaps instead of a biopsy. According to Luderer, the main limitation in developing proteomic diagnostics based on validated protein biomarkers at present is the availability of well-annotated clinical repositories of plasma samples for the clinical indication being targeted.
“You need the clinical material to support discovery through validation," notes Luderer. “You need to demonstrate the patient work-up path and to show medical utilization, as that is a key element for reimbursement.”
Indi’s first commercial proteomic test, Xpresys Lung, a blood-based diagnostic test, came on the market in October 2013. Designed to help clinicians assess lung nodules 8–30 mm in size identified on lung CT, the Xpresys Lung test determines the probability that a lung nodule is benign. A test result indicative of a high probability of being benign allows patients to enter a period of watchful waiting without the need for more invasive diagnostic studies or biopsy. Of the approximately 3 million people in the United States who present with a lung nodule on CT each year, about 200,000 will have lung cancer; the rest will have benign lung nodules.
Xpresys Lung is a multiplexed protein assay designed with a high negative predictive value to rule out cancer. To develop the test, Indi measured hundreds of proteins in blood samples from individuals with benign or cancerous lung nodules in prospective studies, looking for significant changes associated with malignant transformation. From these proteins, the company developed an assay consisting of a panel of 11 validated proteins (Science Translational Medicine 2013; 5: 207ra142). Indi developed the test on a multiple reaction monitoring (MRM)-MS platform, which is capable of detection in the sub-nanogram/milliliter range.
In addition to Indi, several companies are applying high-throughput analytical technology to translate protein biomarkers to commercial products. Gus Salem, president and CEO of SISCAPA Assay Technologies (SAT), predicts that “in the next 12 months, we will see another five or six companies have good clinically validated panels on the market in venture-backed CLIA models.”
“There has been no lack of success in proteomic discovery and the identification of protein biomarkers,” continues Salem. “But until now, proteomic discovery wasn’t followed up by the validation needed to translate those biomarkers to the clinic.” That required the analytical technology to do targeted protein quantitation and to compare measurements in large numbers of clinical samples.
Founded in 2011 by proteomics pioneer Leigh Anderson, chairman and CSO of SAT, the company uses Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA) technology to develop tools and methods for performing targeted, highly multiplexed protein measurements on a MRM-MS workflow. SAT’s goal is to validate protein biomarkers identified in the research arena and bring them forward into clinical applications.
The company offers an alternative to the traditional workflow of LC-MS, eliminating the need for chromatography through digestion of an entire protein sample up front, followed by the addition of an antibody that can specifically identify and fish out a peptide that serves as a surrogate for the target protein of interest in a disease indication. The result is higher throughput protein detection and quantification that allows for thousands of patient samples to be run in highly multiplexed assays in a day on a single mass spectrometer.
This approach, notes Salem, also overcomes the protein-protein interactions and antibody interference problems that have limited the ability to multiplex on and validate the individual components of traditional immunoassay platforms used to measure protein biomarkers. “In clinical proteomics there will most likely not be a single analyte that will be predictive of disease,” Salem adds. “We believe the high-value clinical answers will come from a panel of proteins.”
The MRM-MS technology and SISCAPA workflow used by the company for protein panel development is already validated and being used in the clinical setting. Earlier this year, Mayo Medical Laboratories began using SISCAPA technology combined with LC and tandem MS to measure serum thyroglobulin for monitoring patients treated for thyroid cancer to detect persistent or recurrent disease. In 20–30% of these patients, the presence of anti-thyroglobulin autoantibodies interferes with the standard immunoassay used in disease monitoring. SISCAPA-MS avoids the autoantibody problem by eliminating the interferences through digestion of the entire sample.