Cancer proteomics: from signaling networks to tumor markers

Differential protein analysis of Heracleum moellendorffii Hance seeds during stratification

Heracleum moellendorffii Hance is a medicinal vegetable species, and the seed dormancy of this species has caused many agricultural problems. One stratification technique involves alternating layers of seeds and substrate to allow post-ripening of dormant seeds under appropriate environmental conditions and to release dormancy. Non-stratified seeds (NS), cotyledon-stage-embryo seeds (CS) and germinated seeds (GS) represent key stages of H. moellendorffii seeds during stratification. To better understand the breaking of dormancy caused by stratification, tandem mass tag (TMT) mass spectrometry (MS)/MS was used to detect proteins among NS, CS and GS. A total of 876 proteins were identified, which were subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. The results showed that carbohydrate metabolic processes, responses to stress and ribosome biogenesis were the main biological processes. The changes in protein accumulation were validated by qRT-PCR. The results showed that starch, sucrose, pyruvate and fatty acid metabolism played significant roles and that the contents of stored substances were gradually degraded during stratification. This study provides a theoretical basis in terms of proteomics for exploring the post-ripening and germination of H. moellendorffii seeds.

Stamping vital cells - a force-based ligand receptor assay

Gaining information about receptor profiles on cells, and subsequently finding the most efficient ligands for these signaling receptors, remain challenging tasks in stem cell and cancer research as well as drug development. We introduce a live-cell method with great potential in both screening for surface receptors and analysing binding forces of different ligands. The technique is based on the molecular force assay, a parallel-format, high-throughput experiment on a single-molecule level. On human red blood cells, we demonstrate the detection of the interaction of N-acetyl-α-D-galactosaminyl residues with the lectin helix pomatia agglutinine and of the CD47 receptor with its antibody. The measurements are performed under nearly physiological conditions and still provide a highly specific binding signal. Moreover, with a detailed comparative force analysis on two cell types with different morphology, we show that our method even allows the determination of a DNA force equivalent for the interaction of the CD47 receptor and its antibody.

Proteomic profiling and interactome analysis of ER-positive/HER2/neu negative invasive ductal carcinoma of the breast: towards proteomics biomarkers

Breast cancer, especially ER positive/HER2/neu negative IDC, is the predominant subtype of invasive ductal carcinoma. Although proteomic approaches have been used towards biomarker discovery in clinical breast cancer, ER positive/HER2/neu negative IDC is the least studied subtype. To discover biomarkers, as well as to understand the molecular events associated with disease progression of estrogen receptor positive/HER2/neu negative subtype of invasive ductal carcinoma, differential protein expression profiling was performed by using LC-MS(E) (MS at elevated energy). A total of 118 proteins were identified, of which 26 were differentially expressed. These identified proteins were functionally classified and their interactions and coexpression were analyzed by using bioinformatic tools PANTHER (Protein Analysis THrough Evolutionary Relationships) and STRING (Search Tool for the Retrieval of Interacting Genes). These proteins were found to be upregulated and were involved in cytoskeletal organization, calcium binding, and stress response. Interactions of annexin A5, actin, S100 A10, glyceraldehyde 3 phosphate dehydrogenase, superoxide dismutase 1, apolipoprotein, fibrinogen, and heat shock proteins were prominent. Differential expression of these proteins was validated by two-dimensional gel electrophoresis and Western blot analysis. The cluster of these proteins may serve as a signature profile for estrogen receptor positive/ HER2/neu negative subtype.

Different expression of S100A8 in malignant and benign gallbladder diseases

BACKGROUND

Proteomic analysis is a powerful tool for complete establishment of protein expression. Comparative proteomic analysis of human bile from malignant and benign gallbladder diseases may be helpful in research into gallbladder cancer.

AIMS

Our objective was to establish biliary protein content for gallbladder cancer, gallbladder adenoma, and chronic calculous cholecystitis for comparative proteomic analysis.

METHODS

Bile samples were collected from patients with gallbladder cancer, gallbladder adenoma, and chronic calculous cholecystitis. Peptides of biliary proteins were separated by two-dimensional liquid chromatography then identified by tandem mass spectrometry.

RESULTS

Up to 544, 221, and 495 unique proteins were identified in bile samples from gallbladder cancer, gallbladder adenoma, and chronic calculous cholecystitis. Forty-three, 16, and 28 proteins with more than one unique peptide, respectively, were identified in the three groups. Among these, 30 proteins including S100A8 were overexpressed in gallbladder cancer, compared with benign gallbladder diseases. We also confirmed, by immunohistochemical analysis, that S100A8 is more abundant in tumor-infiltrating immune cells in cancerous tissue.

CONCLUSIONS

Compared with benign gallbladder diseases, consistently elevated S100A8 levels in malignant gallbladder bile and tissue indicate that gallbladder cancer is an inflammation-associated cancer. S100A8 may be a biomarker for gallbladder cancer.

Comparative analyses of differentially induced T-cell receptor-mediated phosphorylation pathways in T lymphoma cells

Activation of T lymphoma cells expressing Syk, but not ZAP-70 tyrosine kinase, has been shown to negatively regulate cell activation and activation-induced cell death (AICD), perhaps due to differential induction of tyrosine phosphorylation modified proteins. To better understand the role of these proteins and their associated molecules/pathways, we studied a previously described model of T lymphoma cells expressing either a kinase-activated chimeric Syk or ZAP-70 genetically linked to T-cell receptor (TCR) ζ chain (Z/Syk or Z/ZAP cells, respectively). To help identify molecules and pathways linked to cell activation or AICD, a comparative semi-quantitative proteomics-based approach was utilized to analyze tyrosine-phosphorylated protein immunoprecipitates from two-minute short-term activated Z/Syk or Z/ZAP cells. Using the resulting bioinformatics data-sets, we identified several differentially immunoprecipitated proteins that could be validated biochemically. More tyrosine-phosphorylated and phosphotyrosine-associated proteins were found in Z/Syk than in Z/ZAP cells. Proteins involved in different unique functional pathways were induced in these cells and showed altered intermolecular interactions in varied pathways. Remarkably, 41% of differentially identified proteins in Z/Syk cells belonged to cell cycle or vesicle/trafficking pathways. In contrast, 21% of such proteins in Z/ZAP cells belonged to metabolism pathways. Therefore, molecular pathways involved in post-translational modifications linked to distinct cellular/physiological functions are differentially activated, which may contribute to varied activation and AICD responses of these cells. In summary, we identified proteins belonging to novel differentially activated pathways involved in TCR-mediated signaling, which may be targets for regulating activation and AICD of T lymphoma cells and for potential cancer therapy.

Identification of metastasis-associated proteins involved in gallbladder carcinoma metastasis by proteomic analysis and functional exploration of chloride intracellular channel 1

Advanced gallbladder cancer has an extremely poor prognosis because of metastasis. Identification of metastasis-related biomarkers is essential to improve patient survival. In the present study, metastasis-associated proteins were identified by comparative proteomic analysis and the metastasis-related function of the candidate protein, chloride intracellular channel 1 (CLIC1), was further elucidated. Two cell lines with high or low metastatic potential (termed GBC-SD18H and GBC-SD18L, respectively), originating from the same parental gallbladder carcinoma GBC-SD cell line, were identified by spontaneous metastasis in vivo and characterized by metastatic phenotypes analysis in vitro. Subsequently, a proteomic approach comprised of two-dimensional gel electrophoresis analysis and mass spectroscopy was used to identify and compare the protein expression patterns between GBC-SD18L and GBC-SD18H. Twenty-six proteins were identified and further verified by one-dimensional Western blotting and semiquantitative reverse transcriptase polymerase chain reaction analysis. It was determined that CLIC1, ezrin, vimentin, annexin A3, WD repeat domain 1, triosephosphate isomerase, C1-tetrahydrofolate synthase, Rho GDP-dissociation inhibitor 1, T-complex protein 1, heterogeneous nuclear ribonucleoprotein K, glutamate dehydrogenase 1, proteasome activator complex subunit 3 and Rab GDP-dissociation inhibitor beta were significantly up-regulated in the highly metastatic GBC-SD18H cell line compared to the poorly metastatic GBC-SD18L cell line. However, phosphoglycerate kinase 1 and programmed cell death protein 8 were significantly down-regulated in the highly metastatic GBC-SD18H cell line compared to GBC-SD18L. Considering that CLIC1 was profuse in highly metastatic GBC-SD18H but scarce in poorly metastatic GBC-SD18L, the association of CLIC1 with metastasis was further elucidated by the overexpression and RNA interference of CLIC1 in GBC-SD18L cells and GBC-SD18H cells, respectively. The results demonstrated that the overexpression of CLIC1 promoted cell motility and invasion of GBC-SD18L in vitro, while RNA interference of CLIC1 remarkably decreased cell motility and invasive potency of GBC-SD18H in vitro, indicating that CLIC1 might play an important role in metastasis of gallbladder carcinoma.

Proteomics in neurosciences

This review provides an outline of the most important proteomic applications in the study of neurodegenerative disorders including Alzheimer's (AD), Parkinson's (PD), Huntington's (HD), and prion diseases, and also discusses advances in cancer and addiction. One of the scopes is to illustrate the potential of proteomics in the biomarkers discovery of these diseases. Finally, this article comments the advantages and drawbacks of the most commonly used techniques and methods for samples preparation.

Cytokeratin-20 and seminal vesicle secretory protein VI as possible marker proteins in urinary bladder preneoplastic lesions induced by N-butyl-N-(4-hydroxybutyl) nitrosamine

BACKGROUND

A simple and non-invasive methods for the diagnosis of transitional cell carcinoma of the bladder are needed for the prevention of invasive tumor. A proteomic technology has recently been developed to facilitate protein profiling of biological mixtures. We tried to detect the marker proteins by proteomic approach during the initiation stages on N-butyl-N-(4-hydroxybutyl) nitrosamine (BBN)-induced bladder carcinogenesis in rats.

METHODS

Ten rats in group A were given 0.05% BBN in drinking water for 12 weeks. Other 10 rats in group B with 10 rats were designated as a control group and were not given BBN. Whole urinary bladders of all rats were excised at 12 weeks from the beginning of the experiment. Conventional proteomics was performed with high resolution 2-dimension gel electrophoresis followed by computational image analysis and protein identification using mass spectrometry.

RESULTS

A comparison of urinary bladder hyperplasia tissue with control tissue showed that five proteins; actin gamma2 propeptide, cytokeratin-20 (CK-20), proapolipoprotein, alpha2 actin (alpha-cardiac actin) and heat shock 27 kDa protein-1 were over-expressed in hyperplastic tissues. Three proteins; transcription factor myocardin, seminal vesicle secretory protein VI (SVS-VI) precursor and hypothetical protein RMT-7 were under-expressed in hyperplastic tissues.

CONCLUSION

In our animal mode, BBN-induced urinary bladder mucosal hyperplasia resulted in an increase in the expression of five proteins and a decrease in the expression of three proteins. Of these, CK-20 and SVS-VI seem to be of particular interest. However other method such as Western blotting seems to be needed for confirmation of these proteins and more information on human bladder tissue is needed for clinical application.

Identification of growth factor-regulated proteins using 2D electrophoresis and mass spectrometry

Proteomic technology has recently emerged as a powerful tool for detecting both qualitative and quantitative changes of proteins that occur upon activation of complex signaling pathways. In the present study, comparison of the protein profile of platelet-derived growth factor (PDGF), epidermal growth factor (EGF) and nerve growth factor (NGF)-stimulated and unstimulated cells with two-dimensional electrophoresis followed by mass spectrometric analysis led to the identification of a number of proteins, several of which had not been previously shown to be regulated by receptor-tyrosine kinases. Using subcellular fractionation, our approach was able to identify not only changes due to altered gene transcription, but also due to intracellular protein translocation or modification. One of the proteins that was identified among other PDGF-regulated molecules was prohibitin, a potential tumour suppressor previously implicated in cell cycle regulation and protection of mitochondrial proteins from degradation. Further analysis confirmed that mitochondria-associated prohibitin translocates to an insoluble perinuclear compartment. This study demonstrates the utility of proteomic strategies in identifying potential growth factor-regulated effectors.

From proteomic analysis to clinical significance: overexpression of cytokeratin 19 correlates with hepatocellular carcinoma metastasis

To better understand the mechanism underlying the hepatocellular carcinoma (HCC) metastasis and to search potential markers for HCC prognosis, differential proteomic analysis on two well-established HCC cell strains with high and low metastatic potentials, MHCC97-H and MHCC97-L, was conducted using two-dimensional gel electrophoresis followed by matrix-assisted laser desorption/time-of-flight mass spectrometry. Cytokeratin 19 (CK19) was identified and found to be overexpressed in MHCC97-H as compared with MHCC97-L. This result was further confirmed by two-dimensional Western blot analysis and immunofluorescence assay. Furthermore, one-dimensional Western blot analysis showed consistently increased CK19 expression in progressively more metastatic cells. Immunohistochemical study on 102 human HCC specimens revealed that more patients in the CK19-positive group had overt intrahepatic metastases (satellite nodules, p < 0.05; vascular tumor emboli, p < 0.001; tumor node metastatis staging, p < 0.001). CK19 fragment CYFRA 21-1 levels measured in sera from nude mice model of human HCC metastasis with radioimmunoassay increased in parallel with tumor progression and rose remarkably when pulmonary metastases occurred. The results demonstrated that overexpression of CK19 in HCC cells is related to metastatic behavior. Serum CK19 level might reflect the pathological progression in some HCC and may be a useful marker for predicting tumor metastasis and a therapeutic target for the treatment of HCC patients with metastases.

Identification of metabolic enzymes in renal cell carcinoma utilizing PROTEOMEX analyses

PROTEOMEX, an approach which combines conventional proteome analysis with serological screening, is a powerful tool to separate proteins and identify immunogenic components in malignant diseases. By applying this approach, we characterized nine metabolic enzymes which were differentially expressed in renal cell carcinoma (RCC) cell lines and compared their expression profiles to that of normal kidney epithelium cells. Four of these proteins, superoxide dismutase (SODC), triosephosphatase isomerase (TPIS), thioredoxin (THIO) and ubiquitin carboxyl-terminal hydrolase (UBL1) were further analysed for both their constitutive and interferon (IFN)-gamma inducible protein expression pattern in cell lines or tissue specimens derived from RCC or normal kidney epithelium using Western blot analysis and immunohistochemistry, respectively. With the exception of the RCC cell line MZ1940RC, which completely lacks the expression of UBL1, a heterogeneous and variable expression pattern of the different metabolic enzymes was detected in RCC and normal renal epithelium. The highest differences in the expression levels were found for THIO in the RCC cell lines, which was 2-fold upregulated when compared to autologous normal kidney epithelium. Moreover, IFN-gamma treatment did not influence the constitutive expression of these metabolic enzymes. Thus, PROTEOMEX represents a valuable approach for the identification of metabolic enzymes which might be used as markers for the diagnosis of RCC.

A protein molecular weight map of ES2 clear cell ovarian carcinoma cells using a two-dimensional liquid separations/mass mapping technique

A molecular weight map of the protein content of ES2 human clear cell ovarian carcinoma cells has been produced using a two-dimensional (2-D) liquid separations/mass mapping technique. This method uses a 2-D liquid separation of proteins from whole cell lysates coupled on-line to an electrospray ionization-time of flight (ESI-TOF) mass spectrometer to map the accurate intact molecular weight (M(r)) of the protein content of the cells. The two separation dimensions involve the use of liquid isoelectric focusing as the first phase and nonporous silica reversed-phase high-performance liquid chromatography (HPLC) as the second phase of separation. The detection by ESI-TOF-MS provides an image of pI versus M(r) analogous to 2-D gel electrophoresis. Each protein is then identified based upon matrix-assisted laser desorption/ionization (MALDI)-TOF-MS peptide mapping and intact M(r) so that a standard map is produced against which other ovarian carcinoma cell lines can be compared. The accurate intact M(r) together with the pI fraction, and peptide map serve to tag the protein for future interlysate comparisons. An internal standard is also used to provide a means for quantitation for future interlysate studies. In the ES2 cell line under study it is shown that nearly 900 M(r) bands are detected over 17 pI fractions from pH 4 to 12 and a M(r) range up to 85 kDa and that around 290 of these bands can be identified using mass spectrometric based techniques. The protein M(r) is detected within an accuracy of 150 ppm and it is shown that many of the proteins in this human cancer sample are modified compared to the database. The protein M(r) map may serve as a highly reproducible standard Web-based method for comparing proteins from related human cell lines.

Role of proteomics in diagnosis of cancer

Proteomic technologies have emerged as an important addition to the genomic and antibody-based technologies for the diagnosis of cancer. Important technologies include 2-D gel electrophoresis, mass spectrometry, laser capture microdissection, detection of molecular markers of cancer and protein patterns. For clinical applications, the most likely technologies to be used widely are protein biochips. Application of these technologies to various cancers are described. Proteomic technologies have a potential in developing molecular diagnostics and markers for the early detection of cancer. However, information from various diagnostic technologies should be integrated to obtain the optimal information required for clinical management of a patient.

Nuclear matrix proteins as biomarkers for breast cancer

Breast cancer remains a leading cause of cancer death in women despite widespread screening, in part because screening mammography has high rates of false-negative results and because many women decline to have routine mammograms. The development of sensitive and specific assays for breast tumor markers would improve detection and facilitate screening, diagnosis, therapeutic monitoring and surveillance for recurrence. Nuclear matrix proteins (NMPs) are promising candidates for tumor markers because they are involved in malignant transformation. Therefore, they may be useful for screening and early diagnosis of small tumors. Proteomic analysis was used to demonstrate that a 28.3 kD serum protein, designated NMP66, can distinguish malignant disease from benign conditions and normal controls. NMP66 is now being evaluated as a potential biomarker for early breast cancer detection in large-scale clinical trials.