Retrospective Proteomic Analysis of a Novel, Cancer Metastasis-Promoting RGD-Containing Peptide.

Patients who undergo surgical extirpation of a primary liver carcinoma followed by radiotherapy and chemotherapy leading to complete remission are nevertheless known to develop cancerous metastases 3-10 years later. We retrospectively examined the blood sera collected over 8 years from 30 patients who developed bone metastases after the complete remission of liver cancer to identify serum proteins showing differential expression compared to patients without remission. We detected a novel RGD (Arg-Gly-Asp)-containing peptide derived from the C-terminal portion of fibrinogen in the sera of metastatic patients that appeared to control the EMT (epithelial-mesenchymal transition) of cancer cells, in a process associated with miR-199a-3p. The RGD peptide enhanced new blood vessel growth and increased vascular endothelial growth factor levels when introduced into fertilized chicken eggs. The purpose of this study was to enable early detection of metastatic cancer cells using the novel RGD peptide as a biomarker, and thereby develop new drugs for the treatment of metastatic cancer.

Identification of potential serum markers for endometrial cancer using protein expression profiling.

OBJECTIVES: Screening method of endometrial cancer (EC) has not been established yet. Our study was to explore serum biomarkers of EC patients using surface-enhanced laser desorption and ionization-time-of-flight mass spectrometry (SELDI-TOF MS). METHODS: Serum samples from 65 EC patients and 40 controls were analyzed by SELDI-TOF MS (training set). Single- and multi-variant analyses were performed to compare protein profiles in serum of EC patients and healthy controls. Subsequently, blind test set including 40 EC patients and 40 controls were analyzed for validation. RESULTS: A panel of four biomarker candidates were selected in training set analysis. These markers could also distinguish stage I patients from controls. Among them, two biomarkers were purified and identified as apolipoprotein A1 and a modified form of apolipoprotein C1. Screening for blind test set using dual-biomarker analysis yielded a sensitivity of 82% and a specificity of 86%. CONCLUSIONS: Involvement of apolipoproteins with EC is first suggested in this study. In addition to possibility of screening method for EC, findings of these new biomarkers might be related with carcinogenesis or predisposition to EC.

Targeted serum glycoproteomics for the discovery of lung cancer-associated glycosylation disorders using lectin-coupled ProteinChip arrays.

To screen for glycoproteins showing aberrant sialylation patterns in sera of cancer patients and apply such information for biomarker identification, we performed SELDI-TOF MS analysis coupled with lectin-coupled ProteinChip arrays (Jacalin or SNA) using sera obtained from lung cancer patients and control individuals. Our approach consisted of three processes (i) removal of 14 abundant proteins in serum, (ii) enrichment of glycoproteins with lectin-coupled ProteinChip arrays, and (iii) SELDI-TOF MS analysis with acidic glycoprotein-compatible matrix. We identified 41 protein peaks showing significant differences (p<0.05) in the peak levels between the cancer and control groups using the Jacalin- and SNA-ProteinChips. Among them, we identified loss of Neu5Ac (alpha2,6) Gal/GalNAc structure in apolipoprotein C-III (apoC-III) in cancer patients through subsequent MALDI-QIT-TOF MS/MS. Furthermore, subsequent validation experiments using an additional set of 60 lung adenocarcinoma patients and 30 normal controls demonstrated that there is a higher frequency of serum apoC-III with loss of alpha2,6-linkage Neu5Ac residues in lung cancer patients compared to controls. Our results have demonstrated that lectin-coupled ProteinChip technology allows the high-throughput and specific recognition of cancer-associated aberrant glycosylations, and implied a possibility of its applicability to studies on other diseases.

Proteomics-based identification of biomarkers for predicting sensitivity to a PI3-kinase inhibitor in cancer.

To identify biomarkers for predicting sensitivity to phosphatidylinositol 3-kinase (PI3K) inhibitors, we have developed a proteomics-based approach. Using surface-enhanced laser desorption-ionization time-of-flight mass spectrometry (SELDI-TOF MS), we measured the expression of 393 proteins in 39 human cancer cell lines (JFCR-39), and combined it with our previously established chemosensitivity database to select for proteins whose expressions show significant correlations to drug sensitivities. This integrated approach allowed us to identify peaks from two proteins, 11.6 and 11.8 kDa, that showed significant correlations with the sensitivity to a PI3K inhibitor, LY294002. We found that the 11.8 kDa protein was a phosphorylated form of the 11.6 kDa protein. While the 11.8 kDa protein showed a positive correlation with the sensitivity to LY294002, the 11.6 kDa protein showed a negative correlation with that of the LY294002. The 11.6 kDa protein was purified chromatographically, and was identified by SELDI-TOF MS as the ribosomal P2 protein, which possesses two prospective phosphorylation sites. These results suggested that the phosphorylation status of the ribosomal P2 was responsible for determining the sensitivity to LY294002, and that the ribosomal P2 could be a potential biomarker for predicting chemosensitivity.

A carbohydrate-binding protein, Galectin-1, promotes proliferation of adult neural stem cells.

In the subventricular zone of the adult mammalian forebrain, neural stem cells (NSCs) reside and proliferate to generate young neurons. We screened factors that promoted the proliferation of NSCs in vitro by a recently developed proteomics technique, the ProteinChip system. In this screen, we identified a soluble carbohydrate-binding protein, Galectin-1, as a candidate. We show herein that Galectin-1 is expressed in a subset of slowly dividing subventricular zone astrocytes, which includes the NSCs. Based on results from intraventricular infusion experiments and phenotypic analyses of knockout mice, we demonstrate that Galectin-1 is an endogenous factor that promotes the proliferation of NSCs in the adult brain.

Detection, epitope-mapping and function of anti-Fas autoantibody in patients with silicosis.

Dysregulation of apoptosis through the Fas-Fas ligand pathway is associated with the onset of autoimmune disease. Since autoantibodies directed against unknown antigens are present in the sera of these patients, sera samples were examined for the presence of autoantibodies directed against the Fas molecule. Using Western blotting and a ProteinChip analysis, autoantibodies against Fas were detected in patients with silicosis, systemic lupus erythematosus (SLE) and systemic sclerosis (SSc), and weakly detected in healthy individuals. Using epitope mapping employing 12-amino-acid polypeptides with the SPOTs system, a minimum of four epitopes and a maximum of 10 epitopes were found. Several amino acid residues involved in binding FasL, such as C66, R87, L90, E93 and H126, were presented within the epitopes. Serum containing a large amount of anti-Fas autoantibody from silicosis patients inhibited the growth of a Fas-expressing human cell line, but did not inhibit the growth of a low Fas-expresser nor a Fas-expresser in which the Fas gene had been silenced by small interference RNA. All epitopes in the intracellular region of Fas were located in the death domain. The possible roles of anti-Fas autoantibody detected in healthy volunteers and patients with silicosis or autoimmune diseases are discussed here.

Identification of serum proteins related to adverse effects induced by docetaxel infusion from protein expression profiles of serum using SELDI ProteinChip system.

BACKGROUND: For the development of quick and easy methods for screening and identifying treatment-responsive proteins, we determined the protein expression profile of the serum after docetaxel infusion using a surface-enhanced laser desorption/ionization time-of-flight mass spectroscopy (SELDI TOF-MS) system. MATERIALS AND METHODS: Blood from breast cancer patients was collected before and 4, 8, 24 and 48 hours after docetaxel infusion. The protein expression profile was determined by a SELDI TOF-MS system. The relative expression levels of target proteins were compared during the time-course after docetaxel injection. RESULTS: We identified two representative proteins with molecular weights of 7790 Da and 9285 Da. The 7790 Da protein was high molecular weight kininogen, and the 9285 Da protein was apolipoprotein A-II. These two proteins had similar expression patterns in 5 patients, except one patient who experienced severe, acute, adverse effects. CONCLUSION: These results suggest that protein expression profiles determined by SELDI TOF-MS represent useful data for the identification of treatment-responsive proteins.

Identification of pleiotrophin in conditioned medium secreted from neural stem cells by SELDI-TOF and SELDI-tandem mass spectrometry.

Neural stem cells (NSCs) are multipotential progenitor cells that have self-renewal activity. Since the fates of the NSCs in situ depend on their niche containing growth factors and cytokines, we performed surface enhanced laser desorption/ionization time-of flight mass spectrometry (SELDI-TOF-MS) to screen for differentially secreted proteins in conditioned medium of neural stem cells and compared with that of NIH3T3 cells. A 15.3-kDa protein detected only in the conditioned medium of neural stem cells was determined as pleiotrophin (PTN) by SELDI-TOF-MS and ProteinChip-tandem MS systems. Identification of pleiotrophin was further confirmed by one-dimensional SDS gel electrophoresis and Edman degradation analysis. The mRNA transcripts of PTN and its receptors [receptor protein tyrosine phosphatase (RPTP) beta/zeta, N-syndecan and anaplastic lymphoma kinase (ALK)] were detected in neurosphere, suggesting that pleiotrophin signaling systems are present in the neural stem cells and are involved in the modulation of fate of neural stem cells.

Rapid discovery and identification of a tissue-specific tumor biomarker from 39 human cancer cell lines using the SELDI ProteinChip platform.

Useful biomarkers are needed for early detection of cancers. To demonstrate the potential diagnostic usefulness of a new proteomic technology, we performed Expression Difference Mapping analysis on 39 cancer cell lines from 9 different tissues using ProteinChip technology. A protein biomarker candidate of 12kDa was found in colon cancer cells. We then optimized the purification conditions for this biomarker by utilizing Retentate Chromatography mass spectrometry (RC-MS). The optimized purification conditions developed "on-chip" were directly transferred to conventional chromatography to purify the biomarker, which was identified as prothymosin-alpha by ProteinChip time-of-flight mass spectrometry (TOF MS) and ProteinChip-Tandem MS systems. The relative expression level of prothymosin-alpha between colon cancer cells and normal colon mucosal cells was evaluated on the same ProteinChip platform. Prothymosin-alpha expression in colon cancer cells was clearly higher than in normal colon cells. These results indicate that prothymosin-alpha could be a potential biomarker for colon cancer, and that the ProteinChip platform could perform the whole process of biomarker discovery from screening to evaluation of the identified marker.

Molecular cloning and characterization of ryanodine receptor from unfertilized sea urchin eggs.

Unfertilized eggs of sea urchins (Hemicentrotus pulcherrimus) demonstrated cyclic ADP-ribose (cADPR)-induced Ca(2+) release and caffeine-induced Ca(2+) release, both of which were considered to be mediated through the ryanodine receptor (RyR). We cloned cDNAs for sea urchin egg RyR (suRyR), which encode a 597-kDa protein of 5,317 amino acids. suRyR shares common structural features with known RyRs: the well-conserved COOH-terminal domain, which forms a functional Ca(2+) channel, and a large hydrophilic NH2-terminal domain. suRyR shows amino acid sequence identity (43-45%) similar to the three mammalian RyR isoforms. Phylogenetic analysis indicates that suRyR branched from three isoforms of vertebrates before they diverged, suggesting that suRyR may be the only RyR isoform in the sea urchin. Four in-frame insertions were found in suRyR cDNAs, one of which was novel and unique, in that it had a cluster of serine residues. The transcripts with and without these insertions were found in the egg RNA. These results suggest that suRyR may be expressed as a functional Ca(2+)-induced Ca(2+) release channel, which might also be involved in cADPR-induced Ca(2+) release.