New approaches to proteomic analysis of breast cancer

Abstract

Proteomic based approaches are beginning to be utilized to study the natural history and treatment of breast cancer. A variety of proteomics approaches are under study, and are summarized herein. Two-dimensional gel electrophoresis (2D-PAGE) is still the foundation of most proteomics studies. We present an analysis of 2D-PAGE studies reported to date in breast cancer, including those examining normal/tumor differences and selected populations of breast cells. Newer technologies such as laser capture microdissection and highly sensitive mass spectrometry methods are currently being used together to identify greater numbers of lower abundance proteins that are differentially expressed between defined cell populations. Novel technologies still in developmental phases will enable identification of validated targets in small biopsy specimens, including high density protein arrays, antibody arrays and lysate arrays. Surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) analysis enables the high throughput characterization of lysates from very few tumor cells and may be best suited for clinical biomarker studies. We present SELDI-TOF data herein to show the accuracy of the method in a small cohort of breast tumors, as well as its potential discriminatory capability. Such technologies are expected to supplement our armamentarium of mRNA-based assays, and provide critical information on protein levels and post-translational modifications.

Proteomic analysis of cerebrospinal fluid discriminates malignant and nonmalignant disease of the central nervous system and identifies specific protein markers

“…By contrast, we found that cystatin C was present in the large majority of nondiagnostic and reactive/inflammatory samples, with the highest-intensity bands noted in inflammatory disease. Others have demonstrated increased expression of cystatin C in inflammatory, infectious, and degenerative CNS diseases, raising the possibility of it use as a marker of non-neoplastic CSF [18,27,28], while two independent studies have yielded conflicting results regarding cystatin C as a diagnostic marker in pain syndromes [31].…”

“…Nevertheless, the technical complexity and large sample requirements for 2-DE analysis often make it impractical for clinical investigation, and therefore, direct comparisons of CSF protein patterns across different disease states by these methods have been limited in scale [17]. In contrast, SELDI-TOF-MS is a reliable, high-throughput technique for identifying protein expression patterns in small samples of complex biological fluids with high sensitivity and specificity [18]. SELDI-TOF-MS has already been utilized to detect protein biomarkers differentially shed into biologic fluids from bladder, prostate, and breast tumors [11].…”

Proteomics in human cancer research

“…2). The combination of 2-D PAGE and MS has been used to study protein expression in many cancers, including breast biopsies from metastatic and invasive breast cancer patients [21,22]. Although the standard 2-D PAGE method is the most widely used, it still has some limitations, such as gel-to-gel variations, difficulties in automating this process and in displaying hydrophobic, basic, and less-abundant proteins.…”

“…It suggests that overexpression of fibrinogen b is correlated with tumorassociated fibrin deposition [100]. Wulfkuhle et al [22] have used 2-D PAGE technology to identify a number of differentially expressed proteins in ductal carcinoma in situ (DCIS) of human breast. Interestingly, it has been shown that proteins differentially expressed in DCIS and IDCA overlap [13,22].…”

Peer Reviewed: SELDI-TOF MS for Diagnostic Proteomics

“…helped researchers discover potential diagnostic markers for prostate (3)(4)(5)(6)(7)23), bladder (8), breast (9), and ovarian (5,6,21) cancers; Alzheimer's disease (10); and interstitial cystitis (23). The technique has also been used to characterize phosphorylated and glycosylated proteins (14,15), transcription factors (16), and peptides and proteins shed or secreted by various cancer cell lines (17,20).…”