Characterization of proteins in human pancreatic cancer serum using differential gel electrophoresis and tandem mass spectrometry

The purpose of this study was to develop techniques for identifying cancer biomarkers in human serum using differential in-gel electrophoresis (DIGE), and characterizing the protein biomarkers using tandem mass spectrometry (MS/MS). A major problem in profiling protein expression by DIGE comes from the presence of high concentrations of a small number of proteins. Therefore, serum samples were first chromatographed using an immunoaffinity HPLC column (Agilent Technologies), to selectively remove albumin, immunoglobulins, transferrin, haptoglobin, and antitrypsin. Serum samples from three individuals with pancreatic cancer and three individuals without cancer were compared. Serum samples were processed using the immunoaffinity column. Differential protein analysis was performed using DIGE. A total of 56 protein spot-features were found to be significantly increased and 43 significantly decreased in cancer serum samples. These spot features were excised, trypsin digested, and analyzed by MALDI/TOF/TOF (4700 Proteomics Analyzer, Applied Biosystems). We identified 24 unique proteins that were increased and 17 unique proteins that were decreased in cancer serum samples. Western blot analysis confirmed increased levels of several of these proteins in the pancreatic cancer serum samples. In an independent series of serum samples from 20 patients with pancreatic cancer and 14 controls, increased levels of apolipoprotein E, alpha-1-antichymotrypsin, and inter-alpha-trypsin inhibitor were found to be associated with pancreatic cancer. These results suggest that affinity column enrichment and 2-D DIGE can be used to identify numerous proteins differentially expressed in serum from individuals with pancreatic cancer.     

Comparison of normal and breast cancer cell lines using proteome, genome, and interactome data

Normal and cancer cell line proteomes were profiled using high throughput mass spectrometry techniques. Application of protein-level and peptide-level sample fractionation combined with LC-MS/MS analysis enabled identification of 2235 unmodified proteins representing a broad range of functional and compartmental classes. An iterative multistep search strategy was used to identify post-translational modifications, revealing several proteins that are preferentially modified in cancer cells. Information regarding both unmodified and modified protein forms was combined with publicly available gene expression and protein-protein interaction data. The resulting integrated dataset revealed several functionally related proteins that are differentially regulated between normal and cancer cell lines.     

Phosphotyrosine profiling of human cerebrospinal fluid

Background

Cerebrospinal fluid (CSF) is an important source of potential biomarkers that affect the brain. Biomarkers for neurodegenerative disorders are needed to assist in diagnosis, monitoring disease progression and evaluating efficacy of therapies. Recent studies have demonstrated the involvement of tyrosine kinases in neuronal cell death. Thus, neurodegeneration in the brain is related to altered tyrosine phosphorylation of proteins in the brain and identification of abnormally phosphorylated tyrosine peptides in CSF has the potential to ascertain candidate biomarkers for neurodegenerative disorders.

Methods

In this study, we used an antibody-based tyrosine phosphopeptide enrichment method coupled with high resolution Orbitrap Fusion Tribrid Lumos Fourier transform mass spectrometer to catalog tyrosine phosphorylated peptides from cerebrospinal fluid. The subset of identified tyrosine phosphorylated peptides was also validated using parallel reaction monitoring (PRM)-based targeted approach.

Results

To date, there are no published studies on global profiling of phosphotyrosine modifications of CSF proteins. We carried out phosphotyrosine profiling of CSF using an anti-phosphotyrosine antibody-based enrichment and analysis using high resolution Orbitrap Fusion Lumos mass spectrometer. We identified 111 phosphotyrosine peptides mapping to 66 proteins, which included 24 proteins which have not been identified in CSF previously. We then validated a set of 5 tyrosine phosphorylated peptides in an independent set of CSF samples from cognitively normal subjects, using a PRM-based targeted approach.

Conclusions

The findings from this deep phosphotyrosine profiling of CSF samples have the potential to identify novel disease-related phosphotyrosine-containing peptides in CSF.

     

Species distribution and antifungal susceptibility among clinical isolates of Candida parapsilosis complex from India

Background

Candida parapsilosis is recognized as a species complex: Candida parapsilosis sensu stricto, Candida orthopsilosis and Candida metapsilosis are three distinct but closely related species.

Structure-Function Relationship of the Bik1-Bim1 Complex

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Heme metabolism in promastigotes of Leishmania donovani

Promastigotes of Leishmania donovani (Dd-8 strain) showed presence of important key enzymes of heme synthesizing (d-aminolevulinic acid synthase and ferrochelatase) and degrading (heme oxygenase and biliverdin reductase) systems, classical leishmanicidal drugs viz allopurinol, amphotericin B, pentamidine and CDRI compound 93/202 inhibited the heme oxygenase activity of the parasite, whereas, -aminolevulinic acid synthase activity practically remained unaffected. The Km, Vmax ad pH values of heme oxygenase of promastigotes were found to be 1666 M hemin, 625 nmol of bilirubin formed h-1 mg protein-1 and 7.5 respectively. The findings suggest the presence and importance of heme metabolism in the de novo synthesis of different hemoproteins of the Leishmania parasite as well as the detoxification and its defence against biological insults.     

Oxidized low density lipoproteins stimulate galactosyltransferase activity, ras activation, p44 mitogen activated protein kinase and c-fos expression in aortic smooth muscle cells

Previously, our laboratory has shown that oxidized low densitylipoproteins (Ox-LDL) can exert a concentration-dependent stimulationin the proliferation of aortic smooth muscle cells, "a hallmarkin the pathogenesis of atherosclerosis" (Chatterjeey,S. (1992)Mol Cell Biochem., 111, 143–147). Here we report a novelaspect of Ox-LDL-mediated signal transduction. We demonstratethat in aortic smooth muscle cells, Ox-LDL stimulates the activityof a UDP-galactose:glucosylceramide ß1     

Thermoluminescence investigations on the site of action of o-phthalaldehyde in photosynthetic electron transport

Glow curves from spinach leaf discs infiltrated with o-phthalaldehyde (OPA) show significant similarity to those obtained by DCMU treatment which is known to block the electron flow from Q_A, the stable acceptor of Photosystem II (PS II). In both the cases, the thermoluminescence (TL) peak II (Q band) was intensified significantly, whereas peaks III and IV (B band) were suppressed. Total TL yield of the glow curve remained constant even when the leaf discs were infiltrated with high concentrations of OPA (4 mM) or with DCMU (100 M), indicating that even at these high concentrations no significant change in the number of species undergoing charge recombination in PS II occurred. However, studies with thylakoids revealed significant differences in the action of OPA and DCMU on PS II. Although OPA, at a certain concentration and time of incubation, reduced the B band intensity by about 50–70%, and completely abolished the detectable oxygen evolution, it still retained the TL flash yield pattern, and, thus, S state turnover. OPA is known to inhibit the oxidoreductase activity of in vitro Cyt b₆/f (Bhagwat et al. (1993) Arch Biochem Biophys 304: 38–44). However, in the OPA treated thylakoids the extent of inhibition of O₂ evolution was not reduced even in the presence of oxidized tetramethyl-p-phenylenediamine which accepts electrons from plastoquinol and feeds then directly to Photosystem I. This suggests that OPA inhibition is at a site prior to plastoquinone pool in the electron transport chain, in agreement with it being between Q_A and Q_B. However, an unusual feature of OPA inhibition is that even though all oxygen evolution was completely suppressed, a significant fraction of PS II centers were functional and turned over with the same periodicity of four in the absence of any added electron donor, an observation which appears to be similar to that reported by Wydrzynski (Wydrzynski et al. (1985) Biochim Biophys Acta 809: 125–136) with lauroylcholine chloride, a lipid analogue compound. The detailed chemistry of OPA inhibition remains to be studied. Since we dedicate this paper to William A. Arnold, discoverer of delayed light and TL in photosynthesis, we have also included in the Introduction, a brief history of how TL work was initiated at BARC (Bombay, India).Abbreviations Chl chlorophyll - Cyt b₆/f Cytochrome b₆/f - DBMIB 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone - DCIP 2,6-dichloropenolindophenol - DCMU 3-(3,4-dichlorophenyl-) 1,1-dimethyl urea - HEPES (N-[2-hydroxyethyl]piperazine-N-[2-ethanesulfonic acid]) - LCC lauroylcholine chloride - OPA o-phthalaldehyde - PS I Photosystem I - PS II Photosystem II - TL thermoluminescence - TMPD 2,3,5,6-tetramethyl-p-phenylenediamine