Proteomics for Cancer Biomarker Discovery - Pt. 2
Surface-enhanced Laser Desorption/Ionization
Affinity-based MS techniques present a novel proteomic approach for the identification and measurement of cancer-associated biomarkers. On the basis of the work of Hutchens and Yip, Ciphergen Biosystems, Inc. has developed the surface-enhanced laser desorption/ionization (SELDI) ProteinChip® MS technology platform, which brings to the field of proteomics a user-friendly methodology. SELDI has several advantages over other existing technologies, such as LC-MS, two-dimensional gel electrophoresis-coupled MS, ELISA, and fluorescent-based binding assays, for high-throughput screening because of its versatility, ease of use, speed, and low cost. It is rapid, reproducible, highly sensitive (detection limit in the femtomolar range), and readily adaptable to a diagnostic format. Additionally, molecules that have been traditionally difficult to identify have been detected with ease by use of the SELDI platform. Through the use of addressable protein binding sites, the SELDI platform provides a layer of specificity when one is probing for biomarkers along defined signaling pathways or specific posttranslationally modified protein species.
Xiao et al used SELDI successfully to quantify prostate-specific membrane antigen (PSMA) from serum for differential diagnosis of prostate cancer. PSMA has been suggested as a biomarker for malignant prostate disease and was observed to be differentially expressed in benign prostatic hyperplasia (BPH) and prostate cancer. This holds great promise for identifying patients with BPH and reducing unnecessary biopsies, and also in more sensitive identification of prostate cancer patients whose prostate-specific antigen concentrations fall in the gray zone. Using samples from a serum bank and utilizing SELDI as an immunoassay platform, Wright’s group demonstrated that PSMA in combination with prostate-specific antigen could discriminate BPH patient from prostate cancer patients. In addition, these researchers have undertaken a comprehensive approach for biomarker discovery in prostate cancer from cells and body fluids through use of the SELDI platform.
Specificity
Protein markers can be used in detection, diagnosis, monitoring of therapy, and ultimately, prevention and risk assessment. Given the complex nature of neoplasia, the best approach to prevention may be to screen for a cluster of markers from blood and tissue to give a more accurate assessment. Both mRNA and protein expression profiles are necessary to infer cell behavior, suggesting that more than one marker is needed for risk assessment or early detection. Because the progression to cancer is a complex process, multiple alterations have to be targeted to achieve efficient detection. A major concern in screening is the issue of false positives when a single biomarker is considered. Ideally, high specificity is favored to avoid unnecessary diagnostic tests on healthy individuals. As novel technologies unravel the mysteries of cellular mechanisms, multiple tools will become available to detect, target, and manipulate the process of neoplasia. The use of a panel of biomarkers would enhance the positive predictive value of a test and minimize false positives or false negatives. In an epidemiologic perspective, cancer progresses through two distinct phases after the point of biological onset. The preclinical phase spans the interval from the point of onset to the time when symptoms appear. The more visible clinical phase encompasses the time from when symptoms appear through the time of therapy. Early detection lies in the preclinical phase of this continuum, and biomarkers predictive of this phase hold the greatest promise in helping to design effective interventions to stop or reverse progression.
Many issues have to be addressed in parallel concerning the specificity of the protein biomarkers that are discovered. Studies would have to be directed at their efficacy between genders and among races and ethnic groups. The ability of biomarkers to identify interindividual differences in susceptibility for monitoring high-risk groups should be assessed. In addition, the new biomarkers should be able to increase our understanding of the neoplastic process and help identify harmful exposures. Specificity should be also measured through preliminary work on model systems to infer whether a marker is a part of disease pathogenesis and not merely part of an adaptive response. The effect of other comorbid conditions on the specificity of a particular biomarker should also be assessed. To be of public health value, the assay should adaptable to a high-throughput format with minimal misclassification.
Source: Pother R. Srinivas, Mukesh Verma, Yinming Zhao, Sudhir Srivastava
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