Protein based microarrays: A tool for probing the proteome of cancer cells and tissues

A novel proteomic approach for probing cell and tissue proteome, which combines liquid phase protein separations with microarray technology has been developed. Proteins in cell and tissue lysates or in cellular subfractions are separated using any one of a number of separation modes which may consist of ion exchange liquid chromatography (LC), reverse phase LC, carrier ampholyte based separations, e.g. the use of Rotofor, affinity based separations, or gel based separations. Each first-dimension fraction obtained using one separation mode can be further resolved using one or more of the other separation modes to yield either purified protein in solution or liquid fractions with substantially reduced protein complexity. The advantage of a liquid based separation system is that proteins in hundreds of individual fractions can be arrayed directly and used as targets for a variety of probes. Constituent proteins in reactive fractions are identified by mass spectrometry and may be further resolved to determine the nature of the reactive protein(s). We present in this report initial data based on microarray analysis of individual Rotofor fractions obtained from lung adenocarcinoma cell line A549 lysates which have been probed with antibodies against specific proteins.     

Heterogeneity of the complex N-linked oligosaccharides at specific glycosylation sites of two secreted carrot glycoproteins

The N-linked glycans from the 52/54-kDa medium protein and cell wall beta-fructosidase, two glycoproteins secreted by carrot suspension culture cells, were characterized. Carrot cells were labelled with [3H]glucosamine or [3H]fucose. The 52/54-kDa medium protein was isolated from the culture medium and beta-fructosidase from cell walls. The purified proteins were digested with trypsin and glycopeptides were isolated and sequenced. Glycans obtained from individual glycopeptides were separated by gel filtration chromatography and characterized by concanavalin A chromatography, by treatments with exoglycosidases and by sugar composition analysis. The 52/54-kDa medium protein and cell wall beta-fructosidase have one high-mannose-type glycan similar to those from yeast and animal glycoproteins. In addition, the 52/54-kDa medium protein has three complex-type and cell wall beta-fructosidase two complex-type glycans per polypeptide. The complex-type glycans isolated from individual glycosylation sites are fairly large and very heterogeneous. The smallest of these glycans has the structure [Xyl](Man)3[Fuc](GlcNAc]2Asn (square brackets indicating branching) whereas the larger ones carry additional sugars like terminal N-acetylglucosamine and possibly rhamnose and arabinose in the case of the 52/54-kDa medium protein and only arabinose in the case of cell wall beta-fructosidase. These terminal sugars are linked to the alpha-mannose residues of the glycan cores. The 52/54-kDa medium protein is secreted with large and homogeneous complex glycans, their heterogeneity originates from slow processing after secretion. The complex glycans from cell wall beta-fructosidase are processed before the enzyme is integrated into the cell wall.     

Isolation and identification of mannose‐binding proteins and estimation of their abundance in sera from hepatocellular carcinoma patients

The interaction of glycan‐binding proteins (GBPs) and glycans plays a significant biological role that ranges from cell–cell recognition to cell trafficking, and glycoprotein targeting. The anomalies of GBPs related to the types and/or quantities were not clearly known in cancer incidence. It is imperative to identify and annotate the GBPs related with the canceration. Here the mannose‐binding proteins (MBPs) from the clinical sera were isolated and identified by the mannose‐magnetic particle conjugates and the high‐accuracy MS analysis. Seventy‐five MBPs from normal donors’ sera and 79 MBPs from hepatocellular carcinoma patients’ sera were identified and annotated. By using the stringent criteria of exponentially modified protein abundance index (emPAI) quantification, 12 MBPs were estimated to be significantly upregulated (emPAI ratio > 4) and nine MBPs were estimated to be significantly downregulated (emPAI ratio < 0.25) in the hepatocellular carcinoma sera. Real‐time quantitative PCR, Western blotting, and protein microarrays were also used to confirm the altered MBPs expression level and the specific binding between the isolated MBPs and mannose. The sequence recognition motifs and structure preference of the isolated MBPs were characterized. The functional enrichment analysis revealed that over 57% of the isolated MBPs were binding protein and the upregulated MBPs were involved in cell death, tumor progression, and macromolecular complex remodeling.     

Identification and characterization of a tumor cell receptor for CSVTCG, a thrombospondin adhesive domain

We have previously shown that peptides derived from the thrombospondin sequence, CSVTCG, promoted tumor cell adhesion. To further investigate this observation, the CSVTCG-tumor cell adhesion receptor from A549 human lung adenocarcinoma cells was isolated and characterized. A single protein peak was isolated by CSVTCG affinity chromatography which also analyzed as a single peak by anion exchange chromatography. The purified protein had a pI of 4.7 and analyzed on SDS-gels as a single band of M(r) = 50,000 under nonreducing conditions and as two protein bands of M(r) = 50,000, and 60,000 under reducing conditions. Purified CSVTCG binding protein (CBP) bound either CSVTCG- or TSP- Sepharose but showed little interaction with either VCTGSC- or BSA- Sepharose. CBP was cell surface exposed. CSVTCG derivatized with [125I] Bolton-Hunter reagent was taken up by cells in a dose-dependent manner and the cell association was inhibited with a monospecific polyclonal anti-CBP antibody. Examination of the cell proteins crosslinked to labeled CSVTCG by SDS-gel electrophoresis revealed one band that comigrated with purified CPB. Using an in vitro binding assay, purified CBP bound mannose, galactose, and glucosamine-specific lectins. CBP bound TSP saturably and reversibly. The binding was Ca+2/Mg+2 ion dependent and inhibited with fluid phase TSP and anti-CBP. Little or no binding was observed on BSA, fibronectin, GRGES, and GRGDS. Heparin, but not lactose, inhibited binding. Anti-CBP IgG and anti-CSVTCG peptide IgG inhibited A549 cell spreading and adhesion on TSP but not on fibronectin and laminin. These results indicate that CBP and the CSVTCG peptide domain of TSP can mediate TSP-promoted tumor cell adhesion.     

Surface glycoproteomic analysis of hepatocellular carcinoma cells by affinity enrichment and mass spectrometric identification

Cell surface glycoproteins are one of the most frequently observed phenomena correlated with malignant growth. Hepatocellular carcinoma (HCC) is one of the most malignant tumors in the world. The majority of hepatocellular carcinoma cell surface proteins are modified by glycosylation in the process of tumor invasion and metastasis. Therefore, characterization of cell surface glycoproteins can provide important information for diagnosis and treatment of liver cancer, and also represent a promising source of potential diagnostic biomarkers and therapeutic targets for hepatocellular carcinoma. However, cell surface glycoproteins of HCC have been seldom identified by proteomics approaches because of their hydrophobic nature, poor solubility, and low abundance. The recently developed cell surface-capturing (CSC) technique was an approach specifically targeted at membrane glycoproteins involving the affinity capture of membrane glycoproteins using glycan biotinylation labeling on intact cell surfaces. To characterize the cell surface glycoproteome and probe the mechanism of tumor invasion and metastasis of HCC, we have modified and evaluated the cell surface-capturing strategy, and applied it for surface glycoproteomic analysis of hepatocellular carcinoma cells. In total, 119 glycosylation sites on 116 unique glycopeptides were identified, corresponding to 79 different protein species. Of these, 65 (54.6?%) new predicted glycosylation sites were identified that had not previously been determined experimentally. Among the identified glycoproteins, 82?% were classified as membrane proteins by a database search, 68?% had transmembrane domains (TMDs), and 24?% were predicted to contain 2-13 TMDs. Moreover, a total of 26 CD antigens with 50 glycopeptides were detected in the membrane glycoproteins of hepatocellular carcinoma cells, comprising 43?% of the total glycopeptides identified. Many of these identified glycoproteins are associated with cancer such as CD44, CD147 and EGFR. This is a systematic characterization of cell surface glycoproteins of HCC. The membrane glycoproteins identified in this study provide very useful information for probing the mechanism of liver cancer invasion and metastasis.     

Cloning and characterization of angiocidin, a tumor cell binding protein for thrombospondin-1

Thrombospondin-1 (TSP-1) is a matrix protein that has been implicated in mechanisms of tumor progression. Our laboratory previously showed that the CSVTCG (cys-ser-val-thr-cys-gly) sequence of TSP-1 functioned as a tumor cell adhesion domain and CSVTCG peptides as well as an anti-peptide antibody possessed anti-metastatic activity in a murine model of lung metastasis. In a subsequent study, a putative TSP-1 binding protein from lung carcinoma was isolated by CSVTCG-peptide affinity chromatography. In this study, we present the full-length cDNA of this binding protein isolated from a prostate cancer cell (PC3-NI) cDNA library. The purified recombinant protein, termed angiocidin, is a potent inhibitor of tumor growth of Lewis Lung carcinoma in vivo and tumor invasion and angiogenesis in vitro. In addition, the recombinant protein inhibits tumor and endothelial cell proliferation and induces apoptosis. The activity of angiocidin both in vivo and in vitro is partially dependent on its TSP-1 binding activity, since an angiocidin deletion mutant missing a high affinity-binding site for TSP-1 failed to inhibit tumor growth in vivo and was less active in its anti-tumor and anti-angiogenic activities in vitro. These results suggest that the anti-tumor activity of TSP-1 reported in many studies may be mediated in part by binding proteins such as angiocidin. Such proteins may function as tumor-suppressor proteins, which limit the growth of tumors by inhibiting angiogenesis and cell matrix interaction.     

新型抗肿瘤转移多肽-三聚β肽(β３)在大肠杆菌中的表达及其抗粘附作用

自行设计了抗肿瘤转移多肽－三聚β肽（β3）,人工合成了β3的基因片段,构建了β3的表达质粒pET-His-β3,在大肠杆菌BL21(DE3)plysS中表达。在用IPTG诱导15h后可见明显的His-β3融合蛋白的表达,表达产物约占细胞总蛋白的4％,占细胞总不溶性蛋白的10％。每升pET-His-β3/BL21(DE3)plysS细菌培养液用金属螯合琼脂糖凝胶6B FF分离后可回收纯度为92.2%的β3产物约20mg。所表达出的β3肽对人肝癌细胞株SMMC-7721细胞及人肝癌高转移细胞株HCCLM6细胞与纤连蛋白（fibronectin, FN）粘附具有特异的抑制作用,呈现剂量效应相关关系和时间效应相关关系,抑制作用强于β肽（β1）、3倍浓度的β1（3×β1）和GRGDS。研究结果表明：pET-His-β3/BL21(DE3)plysS是β3适合的表达系统;表达的β3肽具有特异的抗肿瘤细胞粘附作用。     

Purification and patch clamp analysis of a 40-pS channel from rat liver mitochondria.

Patch clamp analysis of membranes reconstituted with a fraction isolated from detergent-solubilized mitochondrial membranes by affinity chromatography on immobilized quinine earlier indicated the presence of two classes of ion channels, of about 40- and 140-pS conductance in medium including 150 mM KCl. Now a 57-kDa constituent of the quinine-affinity column eluate has been identified as the 40-pS channel. Protein fractions derived from the quinine-affinity column eluate by preparative isoelectric focusing with a Rotofor cell have been reconstituted into phospholipid vesicle membranes by detergent dialysis, and vesicles have been enlarged for patch clamping by dehydration and rehydration. Voltage clamp analysis has been carried out on excised patches bathed symmetrically in buffered medium containing 150 mM KCl and 100 microM CaCl2. Patches of membrane incorporating the 57-kDa protein exhibit 40-pS conductance transitions. The magnitude of conductance transitions is similar when Na+ replaces K+ in the bathing medium, indicating little selectivity of the 40-pS channel for K+ relative to Na+. Another fraction derived from the quinine-affinity column eluate is found to contain the larger channel, now estimated to have an average conductance of about 130 pS. Patches of control membrane prepared in the same way but without protein exhibit no channel activity.     

Alkaline phosphatase retained in HepG2 hepatocarcinoma cells vs. alkaline phosphatase released to culture medium: difference of aberrant glycosylation

Liver tissue is the source of 90% of serum alkaline phosphatase (AP). The serum levels and structures of tumor marker proteins change under many disease conditions as well as cancer. The study was aimed at determining the type of alkaline phosphatase (AP) present in HepG2 hepatocellular carcinoma cell line. Alkaline phosphatase rich extracts of healthy human liver, HepG2 hepatocarcinoma cells, as well as the condition medium of HepG2 cells were prepared by extraction with 40% n-butanol and 30-50% acetone precipitation, and subjected to various chromatographic procedures. Lectin affinity chromatography of the samples with concanavalin A-Sepharose 4B showed considerable differences in the elution patterns. Non-denaturing polyacrylamide gel electrophoresis of the culture medium yielded a relatively slow migrating band of activity that coincided with none of the three bands of activity produced by the normal liver extract, nor with the bands of the cell pellet extract. Inhibition patterns were established by measuring the enzyme activities in the presence of varying concentrations of L-phenylalanine, L-leucine, L-homoarginine, and levamisole. The APs from the cell line were neuraminidase sensitive. According to the results the main AP produced and released to the medium by HepG2 cell line is an aberrantly glycosylated tissue non-specific AP. In addition, the differences between the cell-pellet AP and the culture medium AP seemed to stem from different sugar moieties in their structures.     

Lysozyme: a major secretory product of a human colon carcinoma cell line

One of the major proteins secreted by an established human colon adenocarcinoma cell line has been isolated in 25% yield from the serum-free medium in which the cells were grown and identified as lysozyme. Its purification was achieved by sequential steps of acidification, cation-exchange chromatography, and reversed-phase high-performance liquid chromatography. It was recognized to be a human lysozyme on the basis of its molecular weight (14 000), isoelectric point (10.5), amino acid composition, and enzymatic activity. Its identity with previously characterized human lysozymes was established by amino-terminal sequence, peptide composition, immunological properties, NMR, and crystallography. A 4-day, 7-L collection of conditioned medium contained 20.3 mg of secreted protein of which 4.9 mg or approximately 24% of the total was tumor-derived lysozyme. The intracellular level of lysozyme was approximately 18 ng per 10(6) carcinoma cells. The possible significance of these findings in regard to the malignant process and tumor maintenance is discussed.     

Peptide mapping of proteins in cerebrospinal fluid utilizing a rapid preparative two-dimensional electrophoretic procedure and matrix-assisted laser desorption/ionization mass spectrometry

A quick two-step procedure involving liquid phase isoelectric focusing in the Rotofor cell in combination with electroelution in the Mini whole cell gel eluter has been used for purification of proteins from human cerebrospinal fluid (CSF). Fractions, each highly enriched in a single protein band and virtually free of other proteins, were selected for characterization by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOFMS). Six CSF proteins, transferrin, alpha1-acid-glycoprotein, Zn-alpha2-glycoprotein, apolipoprotein A1, apolipoprotein E and beta-trace were identified by MALDI-TOFMS analysis of the tryptic digests. These results demonstrate that the combination of liquid phase IEF and electroelution is a rapid preparative two-dimensional separation which can provide single proteins of high purity, in yields sufficient for characterization by MALDI-TOFMS. Characterization of such brain-specific proteins in CSF will be useful in the investigation of the pathophysiology of different brain disorders.     

Isolation, characterization and immunocytochemical localization of bovine trophoblast protein-1

Bovine trophoblast protein-1 (bTP-1) was isolated to 90% purity from culture medium of Day 18-20 conceptuses incubated in vitro (in the presence of L-[3H]leucine) by a combination of Sephacryl S-200 gel filtration chromatography and O-(diethylaminoethyl) (DEAE) anion-exchange high-performance liquid chromatography (DEAE-HPLC). The radiolabeled protein had an Mr of 21,200 +/- 800 by one-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and had three isoelectric variants (pI 5.7-6.5) by two-dimensional SDS-PAGE. DEAE-HPLC-enriched bTP-1 cross-reacted with anti-o TP-1 serum on Western blots. A monospecific antiserum against bTP-1 was produced by excising the bTP-1 polypeptide band from preparative SDS-PAGE gels. Antiserum reacted with a single polypeptide with an Mr of 21,200 as determined by Western blotting of SDS-PAGE-separated conceptus medium proteins and by immunoprecipitation from L-[35S]methionine-labeled medium proteins followed by SDS-PAGE and autoradiography. Bovine trophoblast protein-1 was localized by immunocytochemistry in the cytoplasm of both mono- and binuclear trophectoderm cells of Day 20 bovine conceptuses, indicating that it is a product of the trophoblast.     

The molecular characteristics of a human pancreatic acidic phosphoprotein that inhibits calcium carbonate crystal growth.

A CaCO3-crystal-growth inhibitor was isolated from human pancreatic stones by using EDTA demineralization, followed by DEAE-Trisacryl chromatography. The isolated inhibitor was found to be a phosphoglycoprotein with Mr 14017 and having an unusual chemical composition. It is characterized by a high (42%) acidic amino acid content, but lacks methionine and gamma-carboxyglutamic acid. The protein contains 2.65 mol of P/mol of protein, as phosphoserine (2 mol) and phosphothreonine (0.5 mol). Isoelectric focusing of the protein yields one major band corresponding to an isoelectric point of 4.2. Immunochemical quantification of the crystal-growth inhibitor in pure pancreatic juice reveals that it constitutes 14% of the normal exocrine secretion. Our findings demonstrate that this is a novel secretory protein, which has no enzymic activity and which maintains pancreatic juice in a supersaturated state with respect to CaCO3.     

Novel tumor-associated antigen of hepatocellular carcinoma defined by monoclonal antibody E4-65

A monoclonal antibody, E4-65, produced by immunizing mice with SMMC-7721 cells, a human hepatocellular carcinoma (HCC) cell line, was used to identify and characterize an unreported HCC-associated antigen. Indirect immunofluorescence studies showed that E4-65 antibody reacted with five out of eight HCC cell lines, but not with 10 non-HCC tumor cell lines or a normal liver cell line. Using immunohistochemical examination, E4-65 antigen was detected on the cell membranes and in the cytoplasm of human liver tumor tissues, but was not found in most other tumors, or normal adult or fetal tissues, except for a weakly positive reaction in tissues of the digestive system. Western blot analysis showed that E4-65 antibody bound to a 45 kDa protein in the human HCC cell line and tissue lysates. Enzyme treatment and lectin blotting did not detect the carbohydrate chain in E4-65 antigen. This HCC-associated protein represents a potentially useful target for diagnoses and immunotherapy of human HCC.     

Purification and characterization of a novel cytotoxic substance from cell-free extract of Streptococcus pyogenes

A cytotoxic substance designated as streptococcal cytotoxic protein (SCP) was isolated from a cell-free extract of the Su strain of Streptococcus pyogenes possessing cytotoxic and antitumor activity. SCP was purified with a series of column chromatography and preparative PAGE to give a homogeneous single band as revealed by PAGE analysis. The purified SCP has a molecular mass of 165 kDa, composed of four 43 kDa subunits, and its pI is 4.3. SCP was sensitive to proteinases and was labile to heat and at acidic or alkaline pH. SCP showed inhibitory effects on the [3H]thymidine, [3H]uridine and [3H]leucine uptakes and on the growth of cells, and released 51Cr from cells when the protein was added to the cultures of Ehrlich ascites carcinoma (EAC), mouse mammary tumor (MM-2), leukemia (L-1210) and NIH-3T3 mammalian cells in vitro. SCP also showed an antitumor effect on EAC or MM-2 tumor-bearing mice but not on L-1210 tumor-bearing mice in vivo.     

Cell transformation and proteome alteration in QSG7701 cells transfected with hepatitis C virus non-structural protein 3

Persistent hepatitis C virus （HCV） infection can cause liver cirrhosis and hepatocellular carcinoma. Non-structural protein 3 （NS3）, an important part of HCV, has been implicated in the life cycle of the virus and interacts with host cellular proteins. In this study, we investigated the effect of NS3 protein on cell tranformation and related protein alteration in human hepatocyte QSG7701 cells. The results indicated that stable expression of the NS3 protein in QSG7701 cells induced transformed characters with reduced population doubling time, anchorage-independent growth and tumor development. Fifteen differentially- expressed proteins were separated and identified using 2-D electrophoresis and matrix-assisted laser desorption ionization-time of flight mass spectrometry. Western blot analysis confirmed that the increase of phospho-p44/42 and phospho-p38 proteins was associated with transformed cells. These results supported the view that HCV NS3 protein plays a transforming role and provided some clues to elucidate the carcinogenesis mechanism of HCV-related hepatocellular carcinoma.     

Isolation and characterization of epinectin, a novel adhesion protein for epithelial cells

A 70,000-mol-wt protein was isolated from A431 carcinoma cell extracellular matrix that promotes cell substratum adhesion of these epidermoid tumor cells. Extracellular matrix was isolated by a modification of a procedure described by Hedman et al. (Hedman, K., M. Kurkinen, K. Alitalo, A. Vaheri, S. Johansson, and M. Hook, 1979 J. Cell Biol., 81:83-91) and Yamada and Weston (Yamada, K., and J. A. Weston, 1974, Proc. Natl. Acad. Sci. USA, 71:3492-3496). Cells were solubilized with 0.5% deoxycholate, 10 mM Tris, 0.9% NaCl, and 1 mM phenylmethylsulfonyl fluoride, pH 8.0. The residual matrix was then removed from the plates with 6 M urea and 1 mM phenylmethylsulfonyl fluoride and phosphate-buffered saline. SDS PAGE gels of the 6 M urea extract showed one major band at 70,000-mol-wt by Coomassie Blue staining. A 70,000-mol-wt isotopically-labeled band could also be extracted from the matrix of cells incubated with [35S]methionine. Because of the presence of this protein on squamous-derived epithelial cells we have called the 70,000-mol-wt molecule epinectin. Indirect immunofluorescence with polyclonal rabbit antibodies against epinectin stained A431 cells pericellularly in dense punctate accumulations and along the plasma membrane. Enzyme-linked immunoassays and gel-transfer immunolocalization studies showed that the extract did not cross-react with antibodies to fibronectin, laminin, serum-spreading factor, epibolin, or keratin. Additionally, antibodies to epinectin did not cross-react with these proteins. Further studies showed that epinectin does not bind to gelatin. Cell-adhesion assay, using radiolabeled A431 carcinoma cells on various adhesion-promoting substrates, showed that epinectin has similar adhesion-promoting capacity as serum-spreading factor, was somewhat less active than fibronectin, but more effective than laminin or epibolin. Epinectin appears to be a unique protein isolated from epidermoid tumor cells that is distinct from other known adhesion proteins.     

Expression and purification of a putative tumor suppressor gene PP5715 in E. coli with growth inhibition of hepatocellular carcinoma cells

PP5715 is a putative tumor suppressor gene that encodes a protein of 199 amino acids. Expression of PP5715 in E. coli was mainly as inclusion bodies. The recombinant protein was purified by a NTA-Ni2+ affinity column, refolded by dialysis, and shown to suppress growth of two human hepatocellular carcinoma cell lines using the MTT assay or the clonogenic assays. Computer analysis and fusion expression of PP5175 and GFP showed that PP5715 may be a secretory protein. It may bind to receptors on the membrane surface and thus induce regulation of cell growth. These preliminary results suggest that protein PP5715 may be a new tumor suppressor with growth inhibition effects on hepatocellular carcinoma cells.     

Differing expression of genes involved in non-transferrin iron transport across plasma membrane in various cell types under iron deficiency and excess

We studied the effect of iron deficiency, i.e., 24-h preincubation in iron-free medium, and the effect of high level of non-transferrin iron, i.e., the preincubation in ferric citrate medium containing 500 muM ferric citrate, on the expression of DMT1, Dcytb, ferroportin, hephaestin, and ceruloplasmin in various functional types of human cells. The expression of these proteins potentially involved in non-transferrin iron transport across cell membranes was tested on mRNA level by quantitative real-time PCR as well as on protein level by western blot analysis in Caco-2 (colorectal carcinoma), K562 (erythroleukemia), and HEP-G2 (hepatocellular carcinoma) cells. We found that changes in non-transferrin iron availability, i.e., iron deficiency and high level of non-transferrin iron, affect the expression of tested proteins in a cell type-specific manner. We also demonstrated that changes in the expression on mRNA level do not often correlate with relevant changes on protein level.