Analysis of protein glycosylation and phosphorylation using liquid phase separation, protein microarray technology, and mass spectrometry.

Protein glycosylation and phosphorylation are very common posttranslational modifications. The alteration of these modifications in cancer cells is closely related to the onset and progression of cancer and other disease states. In this protocol, strategies for monitoring the changes in protein glycosylation and phosphorylation in serum or tissue cells on a global scale and specifically characterizing these alterations are included. The technique is based on lectin affinity enrichment for glycoproteins, all liquid-phase two-dimensional fractionation, protein microarray, and mass spectrometry technology. Proteins are separated based on pI in the first dimension using chromatofocusing (CF) or liquid isoelectric focusing (IEF) followed by the second-dimension separation using nonporous silica RP-HPLC. Five lectins with different binding specificities to glycan structures are used for screening glycosylation patterns in human serum through a biotin streptavidin system. Fluorescent phosphodyes and phosphospecific antibodies are employed to detect specific phosphorylated proteins in cell lines or human tissues. The purified proteins of interest are identified by peptide sequencing. Their modifications including glycosylation and phosphorylation could be further characterized by mass-spectrometry-based approaches. These strategies can be used in biological samples for large-scale glycoproteome/phosphoproteome screening as well as for individual protein modification analysis.

Conductive polymer as a controlled microenvironment for the potentiometric high-throughput evaluation of ionic liquid cell toxicity.

This paper presents both biological and potentiometric evaluations of the cell toxicity of a widely used ionic liquid, 1-butyl-3-methylimidazolium tetrafluoroborate ([bmim]BF(4)), to Chinese hamster lung fibroblast cells (V79 cell line). The innovative potentiometric study takes advantage of the unique properties of conductive polymer polypyrrole (PPY) for the potentiometric evaluation of cell toxicity of [bmim]BF(4) to the V79 cells in a real-time, noninvasive and high-throughput manner. The conductive polymer PPY provides a controlled microenvironment that allows the quantitative release of the anions of the ionic liquids into the cells being monitored in real time and noninvasively. Parallel biological assay results showed that V79 cells exposed to [bmim]BF(4) usually grew in clusters, and that many small vacuoles could be seen in the cytoplasm. At the 24th hour after the V79 cells had been exposed to the ionic liquid (IL), the half inhibition concentration (EC(50)) of [bmim]BF(4) was around 5 mM. From a cell cycle study performed using a FACScan flow cytometer, it was found that the V79 cells could be partially locked to the G(1) phase by [bmim]BF(4), which extended the doubling time for cell growth. Comparing with the EC(50) values of cadmium chloride and mercury chloride, [bmim]BF(4) is not very toxic, but it may have a long-term toxic effect on mammalian cells. Compared to traditional biological in vitro assays, the use of a conductive polymer substrate in combination with a potentiometric sensor array is much more sensitive, faster, and enables a simpler evaluation of chemical cell toxicity. Additionally, it simplifies the study of the reversibility of cell toxicity, i.e., cell recovery, because there is no need to refresh the culture medium since a finite amount of chemicals can be doped and released. We found that the cytotoxicity of [bmim]BF(4) at a concentration of less than 6 mM was reversible for the V79 cell line, because cell morphology and proliferation rate returned to normal after the removal of the IL from the culture medium. This finding suggests that the IL [bmim]BF(4) could be used as a tool to control mammalian cell proliferation rate.

Glycoprotein microarrays with multi-lectin detection: unique lectin binding patterns as a tool for classifying normal, chronic pancreatitis and pancreatic cancer sera.

Pancreatic cancer is the fourth leading cause of cancer-related death in the United States, with a 5-year survival rate of less than 4%. Effective early detection and screening are currently not available, and tumors are typically diagnosed at a late stage, frequently after metastasis. Existing clinical markers of pancreatic cancer lack specificity, as they are also found in inflammatory diseases of the pancreas and biliary tract. In the work described here, naturally occurring glycoproteins were enriched by using lectin affinity chromatography and then further resolved by nonporous reversed-phase chromatography. Glycoprotein microarrays were then printed and probed with a variety of lectins to screen glycosylation patterns in sera from normal, chronic pancreatitis, and pancreatic cancer patients. Ten normal, 8 chronic pancreatitis, and 6 pancreatic cancer sera were investigated. Data from the glycoprotein microarrays were analyzed using bioinformatics approaches including principal component analysis (PCA) and hierarchical clustering (HC). Both normal and chronic pancreatitis sera were found to cluster close together, although in two distinct groups, whereas pancreatic cancer sera were significantly different from the other two groups. Both sialylation and fucosylation increased as a function of cancer on several proteins including Hemopexin, Kininogen-1, Antithrombin-III, and Haptoglobin-related protein, whereas decreased sialylation was detected on plasma protease C1 inhibitor. Target alterations on glycosylations were verified by lectin blotting experiments and peptide mapping experiments using microLC-ESI-TOF. These altered glycan structures may have utility for the differential diagnosis of pancreatic cancer and chronic pancreatitis and identify critical differences between biological samples from patients with different clinical conditions.

N-linked glycosylation profiling of pancreatic cancer serum using capillary liquid phase separation coupled with mass spectrometric analysis.

Glycoproteins play important roles in various biological processes including intracellular transport, cell recognition, and cell-cell interactions. The change of the cellular glycosylation profile may have profound effects on cellular homeostasis and malignancy. Therefore, we have developed a sensitive screening approach for the comprehensive analysis of N-glycans and glycosylation sites on human serum proteins. Using this approach, N-linked glycopeptides were extracted by double lectin affinity chromatography. The glycans were enzymatically cleaved from the peptides and then profiled using capillary hydrophilic interaction liquid chromatography coupled online with ESI-TOF MS. The structures of the separated glycans were determined by MALDI quadrupole ion-trap TOF mass spectrometry in both positive and negative modes. The glycosylation sites were elucidated by sequencing of PNGase F modified glycopeptides using nanoRP-LC-ESI-MS/MS. Alterations of glycosylation were analyzed by comparing oligosaccharide expression of serum glycoproteins at different disease stages. The efficiency of this method was demonstrated by the analysis of pancreatic cancer serum compared to normal serum. Ninety-two individual glycosylation sites and 202 glycan peaks with 105 unique carbohydrate structures were identified from approximately 25 mug glycopeptides. Forty-four oligosaccharides were found to be distinct in the pancreatic cancer serum. Increased branching of N-linked oligosaccharides and increased fucosylation and sialylation were observed in samples from patients with pancreatic cancer. The methodology described in this study may elucidate novel, cancer-specific oligosaccharides and glycosylation sites, some of which may have utility as useful biomarkers of cancer.