Protein studies of human non-Hodgkin's B-lymphoma: appraisal by two-dimensional gel electrophoresis

2-D PAGE-based comparison of proteasome inhibitor bortezomib in sensitive and resistant mantle cell lymphoma

Although gene expression following bortezomib treatment has been previously explored, direct effects of bortezomib-induced proteasome inhibition on protein level has not been analyzed so far. Using 2-D PAGE in five mantle cell lymphoma cell lines, we screened for cellular protein level alterations following treatment with 25 nM bortezomib for up to 4 h. Using MS, we identified 38 of the 41 most prominent reliably detected protein spots. Twenty-one were affected in all cell lines, whereas the remaining 20 protein spots were exclusively altered in sensitive cell lines. Western blot analysis was performed for 17 of the 38 identified proteins and 70.6% of the observed protein level alterations in 2-D gels was verified. All cell lines exhibited alterations of the cellular protein levels of heat shock-induced protein species (HSPA9, HSP7C, HSPA5, HSPD1), whereas sensitive cell lines also displayed altered cellular protein levels of energy metabolism (ATP5B, AK5, TPI1, ENO-1, ALDOC, GAPDH), RNA and transcriptional regulation (HNRPL, SFRS12) and cell division (NEBL, ACTB, SMC1A, C20orf23) as well as tumor suppressor genes (ENO-1, FH). These proteins clustered in a tight interaction network centered on the major cellular checkpoints TP53. The results were confirmed in primary mantle cell lymphoma, thus confirming the critical role of these candidate proteins of proteasome inhibition.

Proteome- and microarray-based expression analysis of lymphoma cell lines identifies a p53-centered cluster of differentially expressed proteins in mantle cell and follicular lymphoma

We used a standardized electrophoresis protocol to identify differentially expressed proteins based on a sample pooling approach comparing three follicular lymphoma and three mantle cell lymphoma-derived cell lines. One hundred and seventy-five consistently differentially expressed proteins were identified out of more than 1600 protein spots per gel. Of these 175 protein spots, 38 of the 41 most highly expressed proteins were identified by MS analysis (MALDI-TOF), involving different cellular programs such as DNA repair (Rad50), cell cycle control (Mad1L1), transcription (SAFB), and apoptosis (Luca-15 protein). Expression data were confirmed by Western blot analysis of identified proteins and 2-D gel hybridization of proteins with known overexpression (G1/S-specific cyclin-D1, apoptosis regulator Bcl-2). Comparison of proteome analysis to RNA expression array data revealed only a modest correlation of RNA and protein level emphasizing the relevance of post-translational regulation in lymphomagenesis (p = 0.36). Most interestingly, additional data bank search identified 13 out of 17 referenced proteins (76%) as members of a TP53-dependent network of cell regulation.