Cover Picture: Proteomics – Clinical Applications 1/2009

AbstractIn this issue of Proteomics – Clinical Applications you will find the following highlighted articles:Modern natural historyDegrees are no longer awarded in natural history or natural philosophy, to my knowledge (although history and philosophy are valid topics). It might be time to consider restoring one of these areas for research in the complex process of the development of cancer. The work of Kim et al. looks at the requirements for progression of breast cancer cells from non‐malignant to invasive and metastatic types using an improved purification and narrow range IPG strips (pH 5.5–6.7) for 2‐D DIGE. The pH range effectively improved depletion of serum albumin. The electrophoresis system revealed 500 spots, of which 53 were identified by MS and 38 were up‐regulated. Of particular interest were three actin‐remodeling proteins: coronin‐1A, Arp2/3 complex 34‐kDa subunit 2 (p34‐Arc), and WD repeat protein 1 (Wdr1) which is involved in creation of Y junctions in actin filaments. Coronin‐A1 and p34‐Arc look promising as biomarkers.Kim, D.‐H. et al., Proteomics Clin. Appl. 2009, 3, 30–40.Tortoise and hare replicatorsResearch using model systems requires that the researcher understand the differences between the model and actual systems. This means that some amount of time must be spent evaluating the model system. Here, Bhaskaran et al. look at the proteomes and siRNA responses of two cell lines frequently used as models for breast cancer studies. Lines 184A1 and MCF10A have been used for therapeutic work because of their responsiveness to a spectrum of treatments. MCF10A cells are rapid proliferators but not tumorigenic, 184A1 cells are slow at proliferation and non‐tumorigenic, both representative of early stage breast cancer. To see which functions changed with proliferation rate, proteomic analysis (2‐D DIGE/MALDI‐TOF and ”︁shotgun”︁ LC‐MS/MS) was performed and identified 183 and 318 proteins with altered levels for 184A1 and MCF10A, respectively. The proteins quantitatively shifted included cdk4, cyclinD3, p38 and cdc25b.Bhaskaran, N. et al., Proteomics Clin. Appl. 2009, 3, 68–77.Spit and polish: what do saliva and plasma proteomes have in common?I never did understand how my roommate in the ROTC (Reserve Officers Training Corps.) could pucker up enough spit to put an award winning shine on his shoes and belt week after week. This article by Yan et al. reports the combined results of four separate labs to define a human whole saliva (WS) and ductal saliva proteomes and compare them to the independent human plasma proteome. The combined salivary proteome had 1939 proteins. Compared by size, 20 % of combined salivas have sizes <20 kDa, plasma has only 7 % under 20 kDa. Comparisons were also done for pI and cellular function (GO). Compared to the total human proteome, both saliva and plasma are over‐represented in extracellular proteins, cytoplasmic and cytoskeleton elements. Saliva also has leakage from plasma, secretions from bronchial and nasal regions, gingival crevicular fluid, and debris from ruptured bacteria, food, and epithelial cells. Immunoglobulins display significant overlap (11 %), the polishing effect was not examined.Yan, W. et al., Proteomics Clin. Appl. 2009, 3, 116–134.