Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
Edited By: Michael J. Dunn
Impact Factor: 3.973
ISI Journal Citation Reports © Ranking: 2013: 14/78 (BIOCHEMICAL RESEARCH METHODS); 87/291 (Biochemistry & Molecular Biology)
Online ISSN: 1615-9861
Associated Title(s): PROTEOMICS - Clinical Applications
Cover Picture: Proteomics 23-24/2008
In this issue of Proteomics you will find the following highlighted articles:
2-DE has been around for decades but continues to find new applications. Zong et al. combined it with post-translational modification (PTM)-specific stains to study the pattern of modifications of the murine cardiac 20S proteasome. Four PTMs could be followed: phosphorylation and glycosylation by site-specific stains; oxidation and nitrosylaltion using modification-specific monoclonal antibody fragments. The basic 20S assembly includes 17 subunits that generate 25 spots by 2-DE, indicating some degree of multiple labeling under “normal” conditions. These patterns varied depending on species, tissue, organ, and age. All of these PTMs could be validated by immunoblotting and mass spectrometry. The most consistent patterns were achieved by pre-labeling samples and following the 2-D DIGE protocol. The most sensitive detection required SYPRO Ruby incubation overnight.
Zong, C. et al., Proteomics 2008, 8, 5025–5037.
The extent and degree of lymph node involvement are critical prospective indicators of outcomes of breast cancer surgery. Li et al. applied genomics, proteomics and immunohistochemistry (IHC) to track the origins of axillary lymph node metastasis. They were able to compare 29 primary tumors to metastatic lymph nodes, both near and distant, by use of array comparative genome hybridization (CGH) and 13 pairs using freshly frozen tissue for 2-D PAGE with MALDI-TOF and formalin-fixed, paraffin-embedded tissue for IHC. CGH experiments were calibrated with cells carrying trisomy 47,XX+13 and 47,XX+18. Some 135 proteins were identified by 2-DE and MALDI-TOF from functional groups such as: cell communication/signal transduction, protein metabolism, energy pathways, cell growth/maintenance, nucleic acid metabolism and transport. The data do not conclusively answer the question of how near and far metastases get their starts.
Li, J. et al., Proteomics 2008, 8, 5038–5052.
It seems to be a theme this month: 2-DE is not dead. It is no longer the only game in town but it is still a powerful contender when paired with human eyes. In this case, Zubaidah et al. were looking for markers associated with two forms of hepatocellular carcinoma (HCC). They found 78 that met the p<0.05 criteria. Two of particular interest, FUBP1 and FUBP2 (Far Upstream Binding Proteins 1 and 2), had a distinct role in regulation of c-myc, a known player in development of HCC. Just to confuse matters more, both FUBPs and c-myc regulate, and are regulated by, other factors as well. A horizontal line of FUBP spots indicates multiple, probably phosphorylated, forms that could have different targets.
Zubaidah, R. M. et al., Proteomics 2008, 8, 5086–5096.