Proteomics and Bioinformatics Approaches for Identification of Serum Biomarkers to Detect Breast Cancer

Abstract

Background: Surface-enhanced laser desorption/ionization (SELDI) is an affinity-based mass spectrometric method in which proteins of interest are selectively adsorbed to a chemically modified surface on a biochip, whereas impurities are removed by washing with buffer. This technology allows sensitive and high-throughput protein profiling of complex biological specimens. Methods: We screened for potential tumor biomarkers in 169 serum samples, including samples from a cancer group of 103 breast cancer patients at different clinical stages [stage 0 (n = 4), stage I (n = 38), stage II (n = 37), and stage III (n = 24)], from a control group of 41 healthy women, and from 25 patients with benign breast diseases. Diluted serum samples were applied to immobilized metal affinity capture Ciphergen ProteinChip® Arrays previously activated with Ni2+. Proteins bound to the chelated metal were analyzed on a ProteinChip Reader Model PBS II. Complex protein profiles of different diagnostic groups were compared and analyzed using the ProPeak software package. Results: A panel of three biomarkers was selected based on their collective contribution to the optimal separation between stage 0–I breast cancer patients and noncancer controls. The same separation was observed using independent test data from stage II–III breast cancer patients. Bootstrap cross-validation demonstrated that a sensitivity of 93% for all cancer patients and a specificity of 91% for all controls were achieved by a composite index derived by multivariate logistic regression using the three selected biomarkers. Conclusions: Proteomics approaches such as SELDI mass spectrometry, in conjunction with bioinformatics tools, could greatly facilitate the discovery of new and better biomarkers. The high sensitivity and specificity achieved by the combined use of the selected biomarkers show great potential for the early detection of breast cancer.

Advances in MALDI Mass Spectrometry in Clinical Diagnostic Applications

“…After normalizing the MS signals by either total ion current and/or total peak intensity, the intensity values of the protein/ peptide peaks is highly reproducible. The intra-assay and inter-assay CVs for the normalized intensities of majority of the SELDI peaks are between 5% and 25% [103,104]. With the use of standardized experimental protocol and quality control strategy, the inter-laboratory CVs of the normalized peak intensities are between 15% and 36% [105].…”

“…As of today, there are at least 850 publications on applications of SELDI-TOF MS to protein biomarker discovery. It has been used to analyze a wide range of biological samples, for example, serum [100,[103][104][105][106], plasma [110,113,115], urine [101,113,116], tears [117][118][119], cerebrospinal fluid [120][121][122], amniotic fluid [123][124][125], tissue/cell lysate [107,[126][127][128], etc. It has been applied to the discovery of potential biomarkers for various types of diseases, for example, cancers [103-106, 112, 129], infectious diseases [99,100,115,130], autoimmune diseases [118,131], eye diseases [117,119], neurological diseases [120][121][122], perinatal and neonatal diseases [123][124][125][126], etc.…”

Development of an enhanced proteomic method to detect prognostic and diagnostic markers of healing in chronic wound fluid

“…In recent years proteomic characterization of biological samples has been successfully applied to identify potential diagnostic or prognostic markers to detect and monitor the onset, prognosis and progress of a disease state. [14][15][16] This led us to hypothesize that wound fluid produced during venous ulceration could provide a means of acquiring information regarding failed or prolonged healing of chronic ulcers. 17 Furthermore, collection of CWF is relatively easy and noninvasive, and CWF contains a heterogeneous mixture of proteins or peptides that might be indicative of the healing status of the wound environment.…”

Research progress in SELDI-TOF MS and its clinical applications

“…Besides, the SELDI technology discovered a panel of three biomarkers to separate stage 0-I breast cancer patients from noncancer controls. Bootstrap cross-validation demonstrated that a sensitivity of 93 % for cancer patients and a specificity of 91 % for controls were achieved [6] . The SELDI-TOF MS was also adopted to discover differential biomarkers for lung cancer serum, and the results have been filed in the Patent Corporation Treaty by our group.…”