Application of SELDI-TOF mass spectrometry for the identification of differentially expressed proteins in transformed follicular lymphoma

Abstract

Completion of the human genome project has focused scientific attention on the development of methods that permit rapid characterization of proteins that are encoded by the genome. Recent improvements in twodimensional separation techniques in combination with protein identification software/databases and mass spectrometry (MS) now permit rapid comprehensive large-scale analysis of individual proteins within complex protein mixtures. We have performed pairwise comparisons of low-grade and transformed follicular lymphomas (FLs) in order to identify proteins that may be involved in FL progression using surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) mass spectrometer (ProteinChipt, Ciphergen Biosystems). This system utilizes preactivated differential binding surfaces to achieve multidimensional chromatography. The protein-bound chips were then analyzed by a SELDI-TOF mass spectrometer to generate protein profiles. In preliminary experiments, we established that the MS data obtained from SELDI-TOF MS were reproducible, and that reduction in sample complexity improved the ability to detect lower abundance proteins. With specific regard to FL transformation, we rapidly identified a number of potential candidate proteins involved in this process. These included an upregulated 32 kDa protein and a down-regulated 11.8 kDa protein. Protein database searches revealed several candidates, among them cyclin D3 (32.5 kDa) and caspase 3 (11.8 kDa) whose differential expression were confirmed by immunoblotting and/or immunohistochemical analysis on the primary tissue specimens. Our studies demonstrate the utility of SELDI-TOF-MS for the rapid discovery of differentially expressed proteins using femtomolar quantities of crude protein derived from biopsy material. The versatility of this methodology supports its application to the rapid discovery of potential biomarkers in a variety of cellular systems.

Application of MALDI imaging for the diagnosis of classical Hodgkin lymphoma

“…Another proteomic based study identified proteins of different cellular fractions from Hodgkin lymphoma-derived cell lines as well as secreted proteins extracted from serum-free culture media (Wallentine et al 2007). Apart from HL there are few proteomic studies on different Non-Hodgkin lymphomas such as anaplastic large cell lymphoma (Crockett et al 2005), mantle-cell lymphoma (Ghobrial et al 2005), follicular lymphoma as well as cell lines from different lymphoid neoplasms (Fujii et al 2005;Lin et al 2004).…”

Analysis of Mass Spectrometry Profiles of the Serum Proteome

“…It is now clear that SELDI profiling of the proteome can successfully detect anonymous proteins that are produced at higher (or lower) concentrations in the tissues or fluids of cancer patients than in healthy individuals (1)(2)(3). There is also preliminary evidence that we may be able to discover patterns that can reliably distinguish cancer patients from healthy individuals (4 -7 ).…”

Mass Spectrometry, Proteomics, Data Mining Strategies and Their Applications in Infectious Disease Research.

“…These mass spectral patterns can be used to differentiate patient samples from one another, such as from normal versus diseased. Although, this technology was initially used specifically to determine the mass-to-charge ratio of proteins within a sample, more recently SELDI-TOF instruments coupled to tandem mass spectrometers have been developed to enable protein identification and quantitation [58][59][60].…”