Application of laser capture microdissection combined with two-dimensional electrophoresis for the discovery of differentially regulated proteins in pancreatic ductal adenocarcinoma

Molecular changes in pancreatic cancer

As with many human malignancies, pancreatic cancer is a complex genetic disorder. Several thousand disease-associated alterations on the DNA, mRNA, miRNA and protein levels have been reported to date. Some of these alterations, including a number of gatekeeper mutations, which are of pre-eminent importance for the onset and progression of the disease, have been extensively studied in primary tissues, in vitro experiments and transgenic mouse models. For the vast majority of alterations, however, data about the functional significance are lacking. The situation is complicated by the fact that no certainty exists concerning the identity of the cells that originally undergo malignant transformation nor about the precise nature and fate of premalignant lesions that are observed in pancreatic tissues.

Identification of distinctive protein expression patterns in colorectal adenoma

PURPOSE

As a pre-malignant precursor, adenoma provides an ideal tissue for proteome profiling to investigate early colorectal cancer development and provide possible targets for preventive interventions. The aim of this study was to identify patterns of differential protein expression that distinguish colorectal adenoma from normal tissue.

EXPERIMENTAL DESIGN

Twenty paired samples of adenoma and normal mucosa were analysed by 2-DE and MALDI-TOF/TOF MS to detect proteins with ≥2-fold differential expression.

RESULTS

Four proteins were up-regulated in adenoma (Annexin A3, S100A11, S100P and eIF5A-1) and three were down-regulated (Galectin-1, S100A9 and FABPL). S100P, galectin-1, S100A9 and FABPL expression was localised by immunohistochemistry.

CONCLUSIONS AND CLINICAL RELEVANCE

Distinctive patterns of in vivo protein expression in colorectal adenoma were identified for the first time. These proteins have important functions in cell differentiation, proliferation and metabolism, and may play a crucial role in early colorectal carcinogenesis. The ability to recognise premalignant lesions may have important applications in cancer prevention.

Analysis of the pancreatic tumor progression by a quantitative proteomic approach and immunhistochemical validation

To increase the knowledge about the development of pancreatic ductal adenocarcinoma, (PDAC) detailed analysis of the tumor progression is required. To identify proteins differentially expressed in the pancreatic intraepithelial neoplasia (PanIN), the precursor lesions of PDAC, we conducted a quantitative proteome study on microdissected PanIN cells. Proteins from 1000 microdissected cells were subjected to a procedure combining fluorescence dye saturation labeling with high resolution two-dimensional gel electrophoresis (2-DE). Differentially regulated protein spots were identified using protein lysates from PDAC tissues as a reference proteome followed by nanoLC-ESI-MS/MS. Thirty-seven single lesions of different PanIN grade (PanIN 1A/B, PanIN 2, PanIN 3) from nine patients were analyzed. Their protein expression was compared with each other, with PDAC cells and with normal ductal cells. The differential expression of differentially regulated protein spots was validated by means of immunohistochemistry using tissue microarrays. Of 2500 protein spots, 86 were found to be significantly regulated (p < 0.05, ratio > 1.6) during PanIN progression. Thirty-one nonredundant proteins were identified by mass spectrometry. Immunohistochemistry revealed that the differential expression of the selected candidate proteins major vault protein (MVP), anterior gradient 2 (AGR 2) and 14-3-3 sigma, annexin A4, and S100A10 could be successfully validated in PanIN lesions. The highly sensitive and robust proteome analysis revealed differentially regulated proteins involved in pancreatic tumor progression. The analysis of normal preneoplastic and neoplastic pancreatic tissue establishes a basis for identification of candidate biomarkers in PanIN progression that can be detected in pancreatic juice and in serum or are candidates for in vivo imaging approaches.

S100A6 binds to annexin 2 in pancreatic cancer cells and promotes pancreatic cancer cell motility

Background:

High levels of S100A6 have been associated with poor outcome in pancreatic cancer patients. The functional role of S100A6 is, however, poorly understood.

Methods:

Immunoprecipitation followed by two-dimensional gel electrophoresis and mass spectrometry were undertaken to identify S100A6 interacting proteins in pancreatic cancer cells. Immunohistochemistry and coimmunofluorescence were performed to examine expression or colocalisation of proteins. siRNA was used to deplete specific proteins and effects on motility were measured using Boyden Chamber and wound healing assays.

Results:

Our proteomic screen to identify S100A6 interacting proteins revealed annexin 11, annexin 2, tropomyosin β and a candidate novel interactor lamin B1. Of these, annexin 2 was considered particularly interesting, as, like S100A6, it is expressed early in the development of pancreatic cancer and overexpression occurs with high frequency in invasive cancer. Reciprocal immunoprecipitation confirmed the interaction between annexin 2 and S100A6 and the proteins colocalised, particularly in the plasma membrane of cultured pancreatic cancer cells and primary pancreatic tumour tissue. Analysis of primary pancreatic cancer specimens (n=55) revealed a strong association between high levels of cytoplasmic S100A6 and the presence of annexin 2 in the plasma membrane of cancer cells (P=0.009). Depletion of S100A6 was accompanied by diminished levels of membrane annexin 2 and caused a pronounced reduction in the motility of pancreatic cancer cells.

Conclusion:

These findings point towards a functional role for S100A6 that may help explain the link between S100A6 expression in pancreatic cancer and aggressive disease.

Proteomic and tissue array profiling identifies elevated hypoxia-regulated proteins in pancreatic ductal adenocarcinoma

We identified a group of hypoxia-regulated proteins upregulated in microdissected pancreatic cancer nests compared with normal pancreatic ducts. Immunohistochemical study further validated that pancreatic cancers had significantly higher expression levels of glucose-regulated protein 78, macrophage migration inhibitory factor and annexin A5 than normal pancreas tissues, these protein biomarkers also demonstrated high receiver operating characteristic curves in discriminating pancreatic cancers from normal pancreas. In conclusion, our study indicated a link between pancreatic cancer and hypoxia-regulated proteins. Glucose-regulated protein 78, macrophage migration inhibitory factor and annexin A5 might be promising targets for pancreatic cancer diagnosis and therapy.

Application of proteomics in the study of digestive system tumors

Proteomics is the study of all proteins present in a given organism, tissue, cell, and even organelle. Two-dimensional gel electrophoresis and mass spectrography are two core technologies in proteomics. Proteomic studies can help us understand the life as a whole. As a new platform for tumor research, proteomics is of important significance for early diagnosis, biomarker discovery, therapy and discovery of novel drug targets for esophageal carcinoma, gastric cancer, liver cancer, pancreatic cancer and colorectal cancer. Thus, it has potential broad application prospects.

Pancreatic cancer: proteomic approaches to a challenging disease

PURPOSE OF REVIEW

To describe progress in the application of proteomic approaches to advance our understanding of the biology of pancreatic cancer as well as contribute potential protein biomarkers for this disease.

RECENT FINDINGS

Here we review proteomic studies relating to pancreatic cancer that have been published in the past 12 months. We describe novel techniques for the simplification of complex protein samples, focusing particularly on emerging methods for reducing the complexity of blood. We provide examples, where possible, of the application of these novel technologies to pancreatic cancer research.

SUMMARY

Both the range of proteomic-based approaches and their sensitivities for the detection of low-abundance proteins has increased. This provides promise that further research will yield insight into pancreatic cancer, including valuable information on proteins that may ultimately serve as biomarkers for pancreatic cancer.

Cell-based proteome analysis: the first stage in the pipeline for biomarker discovery

The early detection of a distinct disease is crucial for a successful treatment and depends on a sensitive as well as specific diagnosis. In last years tremendous attempts were undertaken to identify new biomarker applying proteomics, but no relevant candidate has been identified for clinical application. Although proteomics is enabling quantitative and qualitative analysis of proteins within complex mixtures it could not significantly contribute to this field. Therefore, different proteomics approaches have been established focusing on the direct analysis of cell populations involved in pathogenic processes to identify candidate biomarkers even for in vitro diagnosis. Here, we will outline approaches applying cell- and tissue based proteome analysis as the first decisive step in the pipeline for the discovery of new diagnostic biomarkers. We will show examples for analysing precursor lesions of the pancreatic ductal adenocarcinoma (PDAC), nephron glomeruli and fibrotic and non-fibrotic liver tissue. This article provides also an overview about currently available techniques in the field of cell enrichment and quantitative proteome analysis of lowest amounts of sample.

Use of combination proteomic analysis to demonstrate molecular similarity of head and neck squamous cell carcinoma arising from different subsites

OBJECTIVE

To evaluate head and neck squamous cell carcinomas (HNSCCs) for differences in protein expression between oral cavity, oropharynx, larynx, and hypopharynx subsites.

DESIGN

Retrospective proteomic analysis using tissue microarray (TMA) and 2-dimensional difference gel electrophoresis (2D-DIGE). For the TMA, automated quantitative protein expression analysis was used to interrogate levels of 4 cell-cycle regulatory proteins chosen for their known roles in cancer (cyclin D1, p53, Rb, and p14). For the 2D-DIGE, lesional and normal adjacent tissues were enriched by laser capture microdissection. Total protein was extracted, analyzed by 2D-DIGE with saturation dye labeling, and evaluated for relative abundance levels of individual protein spots.

SETTING

Two tertiary-care academic medical centers.

PATIENTS

Seventy-one patients with HNSCC for TMA, and 14 patients with HNSCC with frozen tumor and normal tissue for 2D-DIGE.

RESULTS

The automated quantitative analysis of protein expression analysis revealed no difference between subsite for cyclin D1, p53, Rb, or p14 expression. The 2D-DIGE study was based on 28 gels (14 cancer gels and 14 adjacent normal gels), and 732 spots were identified as matching across more than 90% of gels. Significance was evaluated based on false discovery rate (FDR) estimated from permuted data sets. There were no significant differences in protein expression between subsites (FDR greater than or equal to 30% in all instances).

CONCLUSIONS

Observed differences in outcomes between HNSCCs from different subsites may not reflect differences in tumor biologic characteristics between subsites. Rather, it is possible that observed clinical heterogeneity among HNSCCs may be based on other factors, such as viral vs chemical carcinogenesis.

A tumor sorting protocol that enables enrichment of pancreatic adenocarcinoma cells and facilitation of genetic analyses

Molecular profiling of human cancer is complicated by both stromal contamination and cellular heterogeneity within samples from tumor biopsies. In this study, we developed a tissue-processing protocol using mechanical dissociation and flow cytometric sorting that resulted in the respective enrichment of stromal and tumor fractions from frozen pancreatic adenocarcinoma samples. Molecular profiling of DNA from the sorted populations using high-density single nucleotide polymorphism arrays revealed widespread chromosomal loss of heterozygosity in tumor fractions but not in either the stromal fraction or unsorted tissue specimens from the same sample. Similarly, a combination of KRAS mutations and chromosomal copy number changes at key pancreatic cancer loci, such as CDK2NA and TP53, was detected in a substantial proportion of the tumor fractions but not in matched stromal fractions from the same sample. This approach to tissue processing could greatly expand the amount of archived tissue that is available for molecular profiling of human cancer and enable a more accurate diagnosis of genetic alterations in patient samples.

Characterization of Molecular Markers Indicative of Cervical Cancer Progression

Cervical cancer originates with human papillomavirus (HPV) infection and progresses via histologically-defined premalignant stages. Here we compare normal cervical epithelium and patient-matched high grade squamous intraepithelial lesions (HSIL) with cervical carcinoma tissue from the same patient population (n=10 per group). Specimens were analyzed by combined laser capture microdissection and 2D-DIGE. Significant expression changes were seen with 53 spots resulting in identification of 23 unique proteins at the molecular level. These include eight that uniquely distinguish normal epithelium and HSIL and four that uniquely distinguish HSIL and carcinoma. In addition, one protein, cornulin, distinguishes all three states. Other identified proteins included differentiation markers, oncogene DJ-1, serpins, stress and interferon-responsive proteins, detoxifying enzymes, and serum transporters. A literature review, performed for all identified proteins, allowed most changes to be assigned to one of three causes: direct or indirect HPV oncoprotein interactions, growth selection during latency, or interactions in the lesion microenvironment. Selected findings were confirmed by immunohistochemistry using either frozen sections from the same cohort or formalin fixed paraffin embedded samples from a tissue microarray. Novel markers described here have potential applications for increasing the predictive value of current screening methods.

Proteomic profiling in pancreatic cancer with and without lymph node metastasis

The aim of the study was to observe different protein profiles in pancreatic cancer with and without lymph node metastasis (LNM), and search for novel LNM-associated proteins, which would help to understand the metastatic mechanisms and provide targets for therapeutic interventions. Cancer nests were manually miscrodissected from 8 LNM and 7 non-LNM pancreatic cancer tissues, and the protein extracts were then separated by difference gel electrophoresis (DIGE) and identified by MALDI-TOF-TOF. Four differently regulated proteins, ezrin, radixin, moesin, and c14orf166, were selected for further validation by Western blot and immunohistochemistry. In DIGE analysis, we identified 18 up-regulated proteins and 15 down-regulated proteins in LNM pancreatic cancer nests compared with non-LNM ones. Western blot and immunohistochemical analyses confirmed that radixin, moesin and c14orf166, but not ezrin, had significantly higher expression levels in LNM pancreatic cancers than in non-LNM controls. In conclusion, the specific protein profiles found in this study might provide new insights into the mechanism of lymph node metastasis. For the first time, c14orf166 was identified asa novel metastasis-associated protein, and the roles of radixin, moesin and c14orf166 in cancer metastasis deserve further investigations.

The current state of proteomics in GI oncology

Proteomics refers to the study of the entire set of proteins in a given cell or tissue. With the extensive development of protein separation, mass spectrometry, and bioinformatics technologies, clinical proteomics has shown its potential as a powerful approach for biomarker discovery, particularly in the area of oncology. More than 130 exploratory studies have defined candidate markers in serum, gastrointestinal (GI) fluids, or cancer tissue. In this article, we introduce the commonly adopted proteomic technologies and describe results of a comprehensive review of studies that have applied these technologies to GI oncology, with a particular emphasis on developments in the last 3 years. We discuss reasons why the more than 130 studies to date have had little discernible clinical impact, and we outline steps that may allow proteomics to realize its promise for early detection of disease, monitoring of disease recurrence, and identification of targets for individualized therapy.

Proteomic analyses of pancreatic cyst fluids

OBJECTIVES

There are currently no diagnostic indicators that are consistently reliable, obtainable, and conclusive for diagnosing and risk-stratifying pancreatic cysts. Proteomic analyses were performed to explore pancreatic cyst fluids to yield effective diagnostic biomarkers.

METHODS

We have prospectively recruited 20 research participants and prepared their pancreatic cyst fluids specifically for proteomic analyses. Proteomic approaches applied were as follows: (1) matrix-assisted laser-desorption-ionization time-of-flight mass spectrometry peptidomics with LC/MS/MS (HPLC-tandem mass spectrometry) protein identification; (2) 2-dimensional gel electrophoresis; (3) GeLC/MS/MS (tryptic digestion of proteins fractionated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and identified by LC/MS/MS).

RESULTS

Sequencing of more than 350 free peptides showed that exopeptidase activities rendered peptidomics of cyst fluids unreliable; protein nicking by proteases in the cyst fluids produced hundreds of protein spots from the major proteins, making 2-dimensional gel proteomics unmanageable; GeLC/MS/MS revealed a panel of potential biomarker proteins that correlated with carcinoembryonic antigen (CEA).

CONCLUSIONS

Two homologs of amylase, solubilized molecules of 4 mucins, 4 solubilized CEA-related cell adhesion molecules (CEACAMs), and 4 S100 homologs may be candidate biomarkers to facilitate future pancreatic cyst diagnosis and risk-stratification. This approach required less than 40 microL of cyst fluid per sample, offering the possibility to analyze cysts smaller than 1 cm in diameter.

Proteomic analysis of the stroma-related proteins in nasopharyngeal carcinoma and normal nasopharyngeal epithelial tissues

The stroma surrounding cancer cell population is increasingly recognized as playing an important role in cancer proliferation, invasion, and metastasis. To identify the stromal proteins involved in nasopharyngeal carcinoma (NPC) carcinogenesis, differences in protein expression of the stroma from NPC and normal nasopharyngeal epithelium tissues (NNET) were assessed using a comparative proteomic approach combined with laser capture microdissection (LCM). LCM was performed to purify stromal cells from NPC and NNET, respectively. Proteins between the pooled microdissected tumor and normal stroma were separated by two-dimensional electrophoresis (2-DE) and differential proteins were identified by mass spectrometry (MS). Sixty differential proteins between normal stroma (NS) and tumor stroma (TS) were identified, and the expression of CapG protein was further confirmed by western blotting and immunohistochemical analysis. Our results will be helpful to study the role of stroma in the NPC carcinogenesis and may provide helpful clues for pathogenesis, early diagnosis, and progression of NPC.

Confounding effect of obstructive jaundice in the interpretation of proteomic plasma profiling data for pancreatic cancer

It is well established that variation in sampling, processing and storage protocols can alter the levels of potential biomarkers in serum and plasma. Here, using pancreatic cancer as an example, we demonstrate that consideration of clinical parameters related to the patient's illness is equally important when seeking cancer-specific biomarkers. Bile duct-obstruction is a feature of pancreatic disease that can cause jaundice. Comparing patients with pancreatic cancer, chronic pancreatitis or biliary duct obstruction, we observed that the plasma levels of apolipoprotein A1, transthyretin, and apolipoprotein E, when examined in isolation, were each associated with pancreatic cancer. However, when the effect of bile duct obstruction was considered, only transthyretin levels were independently associated with cancer likelihood. Our results demonstrate the importance of accounting for disease-related confounding factors when analyzing data for the detection of cancer biomarkers.

Proteomic analysis of pancreatic ductal adenocarcinoma compared with normal adjacent pancreatic tissue and pancreatic benign cystadenoma

BACKGROUND

Dual expression of potential biomarkers in both benign and malignant pancreatic tumors was a major obstacle in the development of diagnostic biomarkers of early pancreatic cancer.

METHODS

To better understand the limitations of potential protein biomarkers in pancreatic cancer, we employed two-dimensional difference gel electrophoresis technology and tandem mass spectrometry to study protein expression profiles in pancreatic cancer tissues, benign pancreatic adenoma and normal adjacent pancreas. Seven differently expressed proteins were selected for validation by Western blot and/or immunohistochemistry.

RESULTS

21 spots were overexpressed and 24 spots were downexpressed in pancreatic cancer compared with benign and normal adjacent tissues. Our study demonstrated that three candidate pancreatic ductal adenocarcinoma biomarkers identified in previous studies, fructose-bisphosphate aldolase A, alpha-smooth muscle actin and vimentin, were also overexpressed in pancreatic cystadenoma, which might lower their further utility as biomarkers for pancreatic cancer. Aflatoxin B(1) aldehyde reductase (AKR7A2) was confirmed to be only highly expressed in pancreatic cancer, not in normal adjacent pancreas and benign tumors.

CONCLUSIONS

The protein profile pattern of pancreatic cystadenoma was more similar to normal adjacent pancreas than pancreatic cancer. We identified panels of the upregulated proteins in pancreatic cancer, which have not been reported in prior proteomic studies. AKR7A2 may be a novel potential biomarker for pancreatic cancer.

Tissue proteomics for cancer biomarker development: laser microdissection and 2D-DIGE

Novel cancer biomarkers are required to achieve early diagnosis and optimized therapy for individual patients. Cancer is a disease of the genome, and tumor tissues are a rich source of cancer biomarkers as they contain the functional translation of the genome, namely the proteome. Investigation of the tumor tissue proteome allows the identification of proteomic signatures corresponding to clinico-pathological parameters, and individual proteins in such signatures will be good biomarker candidates. Tumor tissues are also a rich source for plasma biomarkers, because proteins released from tumor tissues may be more cancer specific than those from non-tumor cells. Two-dimensional difference gel electrophoresis (2D-DIGE) with novel ultra high sensitive fluorescent dyes (CyDye DIGE Fluor satulation dye) enables the efficient protein expression profiling of laser-microdissected tissue samples. The combined use of laser microdissection allows accurate proteomic profiling of specific cells in tumor tissues. To develop clinical applications using the identified biomarkers, collaboration between research scientists, clinicians and diagnostic companies is essential, particularly in the early phases of the biomarker development projects. The proteomics modalities currently available have the potential to lead to the development of clinical applications, and channeling the wealth of produced information towards concrete and specific clinical purposes is urgent.

Differential diagnosis of pancreatic tumors by molecular analysis of clinical specimens

OBJECTIVE

To describe the capabilities and limitations of the current state of the art in pancreatic cancer diagnostics and to discuss recent progress in the development of novel, highly accurate molecular diagnostic approaches.

RESULTS

Molecular analyses currently under evaluation as novel diagnostic tests include detection of point mutations, genomic imbalances, aberrant methylation patterns and gene expression changes on the mRNA and protein levels in pancreatic juice, fine needle aspiration biopsies and brush cytologies.

CONCLUSIONS

In exploratory studies, several candidate molecular markers show great potential to serve as general indicators of malignancy, but need to be validated in large, controlled, prospective studies. Multiplexing of diagnostic tests, e.g. in the form of specialized DNA microarrays, may provide more differentiated diagnoses such as the distinction of various tumor types or prognostic information for individual patients. The MolDiag-Paca consortium is strongly engaged in advancing these developments on a European level.

High histone deacetylase 7 (HDAC7) expression is significantly associated with adenocarcinomas of the pancreas

BACKGROUND

Alterations in HDACs gene expression have been reported in a number of human cancers. No information is available concerning the status of HDACs in pancreatic cancer tumors. The aim of the present study was to evaluate the expression levels of members of class I (HDAC1, 2,, 3), class II (HDAC4, 5, 6, and 7), and class III (SIRT1, 2, 3, 4, 5, and 6) in a set of surgically resected pancreatic tissues.

METHODS

Total RNA was isolated from 11 pancreatic adenocarcinomas (PA): stage 0 (n = 1), IB (n = 1), IIB (n = 6), III (n = 1), IV (n = 2), one serous cystadenoma (SC), one intraductal papillary mucinous tumor of the pancreas (IMPN), one complicating chronic pancreatitis (CP), and normal pancreas (NP) obtained during donor liver transplantation. Moreover, six other control pancreatic were included. HDACs gene expression was conducted using quantitative real-time polymerase chain reaction (qPCR). Protein expression levels were analyzed by Western blot and their localization by immunohistochemistry analyses of cancer tissues sections.

RESULTS

Remarkably, 9 of the 11 PA (approximately 81%) showed significant increase of HDAC7 mRNA levels. In contrast to PA samples, message for HDAC7 was reduced in CP, SC, and IMPN specimens. The Western blot analysis showed increased expression of HDAC7 protein in 9 out of 11 PA samples, in agreement with the qPCR data. Most of the PA tissue sections examined showed intense labeling in the cytoplasm when reacted against antibodies to HDAC7.

CONCLUSION

The data showed alteration of HDACs gene expression in pancreatic cancer. Increased expression of HDAC7 discriminates PA from other pancreatic tumors.

Proteomics of pancreatic cancer

Pancreatic cancer is a devastating disease, with a mortality rate almost identical with its incidence. Late diagnosis and limited therapeutic options make early detection of pancreatic cancer a pressing clinical problem. In this context, the investigation of the pancreatic cancer proteome has recently gained considerable attention because profiles of proteins may be able to more accurately identify disease states, such as cancer. Recent pancreatic cancer proteome studies may be categorized into basic studies cataloguing the pancreatic proteome, studies investigating differential protein expression patterns, and studies searching for proteome-based biomarkers for early cancer detection and differentiation. Although these studies clearly demonstrate that a range of biological samples are suitable for proteomic analyses, comparison of different studies is problematic due to the diversity of methodologies, sample sources, and characterization of patient populations. Reproducibility between studies has rarely been investigated, and no investigation has compared the different methods of proteomic research. The results of this review have shown that more stringent requirements concerning the design and the analysis of future studies should be implemented. These include an adequate patient number, obligatory histological examination of tissues, appropriate control groups, identification of proteins and peaks, validation of differential expression using independent cohorts and/or a second methodology, and, finally, demonstration of result reproducibility. This will hopefully lead to the discovery of prognostic and predictive biomarkers that help to improve prognosis of pancreatic cancer patients.

Identification of novel nasopharyngeal carcinoma biomarkers by laser capture microdissection and proteomic analysis

PURPOSE

To identify novel nasopharyngeal carcinoma (NPC) biomarkers by laser capture microdissection and a proteomic approach.

EXPERIMENTAL DESIGN

Proteins from pooled microdissected NPC and normal nasopharyngeal epithelial tissues (NNET) were separated by two-dimensional gel electrophoresis, and differential proteins were identified by mass spectrometry. Expression of three differential proteins (stathmin, 14-3-3sigma, and annexin I) in the above two tissues as well as four NPC cell lines was determined by Western blotting. Immunohistochemistry was also done to detect the expression of three differential proteins in 98 cases of primary NPC, 30 cases of NNET, and 20 cases of cervical lymph node metastases, and the correlation of their expression levels with clinicopathologic features and clinical outcomes were evaluated.

RESULTS

Thirty-six differential proteins between the NPC and NNET were identified. The expression levels of stathmin, 14-3-3sigma, and annexin I in the two types of tissues were confirmed and related to differentiation degree and/or metastatic potential of the NPC cell lines. Significant stathmin up-regulation and down-regulation of 14-3-3sigma and annexin I were observed in NPC versus NNET, and significant down-regulation of 14-3-3sigma and annexin I was also observed in lymph node metastasis versus primary NPC. In addition, stathmin up-regulation and down-regulation of 14-3-3sigma and annexin I were significantly correlated with poor histologic differentiation, advanced clinical stage, and recurrence, whereas down-regulation of 14-3-3sigma and annexin I was also significantly correlated with lymph node and distant metastasis. Furthermore, survival curves showed that patients with stathmin up-regulation and down-regulation of 14-3-3sigma and annexin I had a poor prognosis. Multivariate analysis revealed that the expression status of stathmin, 14-3-3sigma, and annexin I was an independent prognostic indicator.

CONCLUSION

The data suggest that stathmin, 14-3-3sigma, and annexin I are potential biomarkers for the differentiation and prognosis of NPC, and their dysregulation might play an important role in the pathogenesis of NPC.

Combining laser capture microdissection and proteomics techniques

Laser microdissection is an effective technique to harvest pure cell populations from complex tissue sections. In addition to using the microdissected cells in several DNA and RNA studies, it has been shown that the small number of cells obtained by this technique can also be used for proteomics analysis. Combining laser capture microdissection and different types of mass spectrometers opened ways to find and identify proteins that are specific for various cell types, tissues, and their morbid alterations. Although the combination of microdissection followed by the currently available techniques of proteomics has not yet reached the stage of genome wide representation of all proteins present in a tissue, it is a feasible way to find significant differentially expressed proteins in target tissues. Recent developments in mass spectrometric detection followed by proper statistics and bioinformatics enable to analyze the proteome of not more than 100-200 cells. Obviously, validation of result is essential. The present review describes and discusses the various methods developed to target cell populations of interest by laser microdissection, followed by analysis of their proteome.

Proteome analysis of human pancreatic ductal adenocarcinoma tissue using two-dimensional gel electrophoresis and tandem mass spectrometry for identification of disease-related proteins

A comparative proteomic approach has been used to identify and analyze proteins related to pancreatic cancer. Proteomes of eight pairs of clinical pancreatic ductal adenocarcinoma (PDAC) tissue samples and samples of normal adjacent tissue were obtained by two-dimensional gel electrophoresis (2DE). Comprehensive analysis of proteins was focused on total protein spots for which there were statistical differences between the two groups. Proteins were identified by peptide mass fingerprinting with tandem mass spectrometry (MS-MS). Western blotting and immunohistochemistry (IHC) were also performed to verify the expression of some candidate proteins. Thirty protein spots were identified, including proteases, antioxidant proteins, signal-transduction proteins, calcium-binding proteins, structural proteins, chaperones, and others. Western blotting and IHC confirmed up-regulated expression of two candidate proteins, nucleotide diphosphatase kinase (NDPK) and annexin II, in tumorous tissues. These results suggest that combination of 2DE with MS is an effective strategy for discovery of differently expressed proteins in PDAC which may be molecular markers for diagnosis or therapeutic targets.

The role of S100P in the invasion of pancreatic cancer cells is mediated through cytoskeletal changes and regulation of cathepsin D

Up-regulation of S100P, a member of the S100 calcium-binding protein family, is an early molecular event in the development of pancreatic cancer and it is expressed at high levels in both precursor lesions and invasive cancer. To gain more insight into the molecular mechanisms underlying the functional roles of this protein, we stably overexpressed S100P in the Panc1 pancreatic cancer cell line and identified the consequent changes in global protein expression by two-dimensional difference in-gel electrophoresis. The observed changes in target proteins were confirmed by Western blot analysis and immunofluorescence, whereas their functional effect was investigated using motility and invasion assays. In this study, we have shown that overexpression of S100P led to changes in the expression levels of several cytoskeletal proteins, including cytokeratins 8, 18, and 19. We have also shown disorganization of the actin cytoskeleton network and changes in the phosphorylation status of the actin regulatory protein cofilin. Additionally, we have shown that overexpression of S100P leads to increased expression of another early pancreatic cancer marker, S100A6, as well as the aspartic protease cathepsin D, both of which are involved in cellular invasion. Functional studies showed that the increased invasive potential of S100P-overexpressing cells was at least partially due to the increase in cathepsin D expression. In summary, our data suggest that these changes could contribute to the metastatic spread of pancreatic cancer and may explain the devastating prognosis of this disease.

Microdissecting the proteome

The complexity of the proteome is extremely high, because every organ or even a part of it can differ considerably in its protein composition. Performing proteomic studies therefore means to separate these functional different tissue areas before analysis. Otherwise all gained results will be depending on the question whether they are incorrect or at least dubious and do they reflect the different functions of tissues at all. The separation of functional tissue areas can be achieved by laser-based microdissection. In this review we will discuss the compatibly of microdissected formalin or cryofixed tissue with different proteomic techniques like 2-DE, MS and protein arrays.

Upregulated expression of S100A6 in human gastric cancer

OBJECTIVE

The expression of S100A6 (calcyclin), a member of the S100 calcium binding protein family, is elevated in a number of malignant tumors, but there have been few reports about its expression in gastric cancer. The aim of this study was to investigate its expression regulations in human gastric cancer and noncancerous mucosa, and the response to chemotherapeutic drugs in the gastric cancer cell line.

MATERIALS AND METHODS

In one matched gastric cancer sample pair, the serial analysis of gene expression (SAGE) experiment was conducted to compare the gene expression profiles between cancerous and adjacent tissues. To detect the expression regulations among more cancerous tissues, microarrays were carried out and real-time RT-PCR was conducted to validate the results. At the protein level, Western blot and tissue microarray (TMA) examination were further used to verify S100A6 expression. The regulation detection of S100A6 with flurouracil and doxorubicin at the mRNA and protein level was performed in the SGC7901 cell line.

RESULTS

With the SAGE strategy, five times more S100A6 tags were identified in cancer tissues than in normal tissues. With the cDNA microarray, S100A6 was found to be significantly upregulated in 21 of 42 (50%) nonselective gastric cancers. In 10 other paired samples, the upregulation of S100A6 was consolidated with RT-PCR and Western blot analysis as well. A total of 14 endoscopy-sectioned gastric noncancerous lesions and corresponding normal gastric mucosa were also applied to profile the gene expression; both cDNA microarray and RT-PCR demonstrated no significant alterations of S100A6 at the mRNA level. TMA examination showed that 34 of 52 (65.4%) cancer samples were positively stained, while only 17 of 80 (21.3%) noncancerous lesions were positively detected and all nine normal mucosae were detected to be negative. An in vitro experiment showed that in the gastric cell line SGC-7901, S100A6 mRNA was detected to be upregulated from 24 to 72 h after treatment with 5 mg/L 5-flurouracil or 0.3 mg/L doxorubicin, and there were two wave upregulations of the S100A6 protein.

CONCLUSION

The observed regulated expression of S100A6 suggests that it is associated with gastric cancer tumorigenesis and quantitation of S100A6 is a promising tool for diagnosis of gastric cancer.

Proteome analysis of human gastric cardia adenocarcinoma by laser capture microdissection

Background

The incidence of gastric cardiac adenocarcinoma (GCA) has been increasing in the past two decades in China, but the molecular changes relating to carcinogenesis have not been well characterised.

Methods

In this study, we used a comparative proteomic approach to analyse the malignant and nonmalignant gastric cardia epithelial cells isolated by navigated laser capture microdissection (LCM) from paired surgical specimens of human GCA.

Results

Twenty-seven spots corresponding to 23 proteins were consistently differentially regulated. Fifteen proteins were shown to be up-regulated, while eight proteins were shown to be down-regulated in malignant cells compared with nonmalignant columnar epithelial cells. The identified proteins appeared to be involved in metabolism, chaperone, antioxidation, signal transduction, apoptosis, cell proliferation, and differentiation. In addition, expressions of HSP27, 60, and Prx-2 in GCA specimens were further confirmed by immunohistochemical and western blot analyses.

Conclusion

These data indicate that the combination of navigated LCM with 2-DE provides an effective strategy for discovering proteins that are differentially expressed in GCA. Such proteins may contribute in elucidating the molecular mechanisms of GCA carcinogenesis. Furthermore, the combination provides potential clinical biomarkers that aid in early detection and provide potential therapeutic targets.

Genetics and prevention of pancreatic cancer

BACKGROUND

Pancreatic cancer is an aggressive disease with a poor prognosis. Hereditary factors have been reported in up to 10% of cases of pancreatic cancer. The clinical characteristics and genetic abnormalities have been identified for a proportion of this high-risk group, and the development of preventive strategies for these individuals is now a primary goal of cancer clinicians.

METHODS

A review of the current literature regarding the genetics, screening, and prevention of pancreatic cancer and its precursor lesions was undertaken.

RESULTS

Risk factors for pancreatic cancer include smoking, chronic pancreatitis, and a genetic predisposition. The role of diabetes or a diet high in fat or meat remains unclear. The genetic mutations that accompany pancreatic cancer appear to occur in a temporal sequence, beginning in the earliest of precursor lesions. These mutations are detectable in pancreatic juice and, in conjunction with imaging, form the basis of screening programs for high-risk individuals. Not all precursor lesions will undergo malignant transformation, and testing is currently limited in its ability to determine which lesions will undergo transformation.

CONCLUSIONS

Avoiding tobacco smoking and minimizing risk factors associated with chronic pancreatitis are recommended to reduce the risk of pancreatic cancer. Individuals with a high-risk genetic background require counseling, genetic testing if appropriate (BRCA2 mutation or p16INK4A inactivity) and secondary screening for pancreatic cancer in specialist centers. Risk stratification will improve as more genetic abnormalities causing pancreatic cancer are defined.

Proteomics in cancer

Proteomic studies have generated numerous datasets of potential diagnostic, prognostic, and therapeutic significance in human cancer. Two key technologies underpinning these studies in cancer tissue are two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and mass spectrometry (MS). Although surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF)-MS is the mainstay for serum or plasma analysis, other methods including isotope-coded affinity tag technology, reverse-phase protein arrays, and antibody microarrays are emerging as alternative proteomic technologies. Because there is little overlap between studies conducted with these approaches, confirmation of these advanced technologies remains an elusive goal. This problem is further exacerbated by lack of uniform patient inclusion and exclusion criteria, low patient numbers, poor supporting clinical data, absence of standardized sample preparation, and limited analytical reproducibility (in particular of 2D-PAGE). Despite these problems, there is little doubt that the proteomic approach has the potential to identify novel diagnostic biomarkers in cancer. In therapeutic proteomics, the challenge is significant due to the complexity systems under investigation (i.e., cells generate over 10(5) different polypeptides). However, the most significant contribution of therapeutic proteomics research is expected to derive not from single experiments, but from the synthesis and comparison of large datasets obtained under different conditions (e.g., normal, inflammation, cancer) and in different tissues and organs. Thus, standardized processes for storing and retrieving data obtained with different technologies by different research groups will have to be developed. Shifting the emphasis of cancer proteomics from technology development and data generation to careful study design, data organization, formatting, and mining is crucial to answer clinical questions in cancer research.

Identifying molecular markers for the early detection of pancreatic neoplasia

Pancreatic cancer is the fourth most common cause of cancer death in the United States. There is a great need for better diagnostic markers of pancreatic neoplasia. Better markers would improve the early diagnosis of pancreatic cancer and allow more patients to undergo curative surgical resection. Identifying individuals at high risk of developing pancreatic cancer and applying markers that could identify precancerous lesions of the pancreas in these individuals could allow such lesions to be resected before the development of pancreatic cancer. As we continue to characterize the genetic, epigenetic, and proteomics alterations that occur in pancreatic cancers and their percursors, better diagnostic markers of pancreatic cancer are expected to follow.

Technology insight: the application of proteomics in gastrointestinal disease

Analysis of the human genome has increased our knowledge of the genes that are associated with disease. At the same time, however, it has become clear that having complete DNA sequences alone is not sufficient to elucidate the biological functions of the proteins that they encode. For this reason, proteomics-the analysis of proteins-has become increasingly attractive, because the proteome reflects both the intrinsic genetic programming of a cell and the impact of its immediate environment. The principal goals of clinical proteomics are to identify biomarkers for the early diagnosis of disease and potential targets for therapeutic intervention. Other goals include the identification of biomarkers for the early detection of disease recurrence (relapse) and how they might be combined with diagnostic imaging techniques to improve the sensitivity for detecting disease. This Review describes conventional proteomic technologies, their strengths and limitations, and demonstrates their application to clinical practice, with specific reference to their use in the gastroenterology field.

Comparative proteomic analysis of human pancreatic juice: methodological study

Pancreatic cancer is the most lethal of all the common malignancies. Markers for early detection of this disease are urgently needed. Here, we optimized and applied a proteome analysis of human pancreatic juice to identify biomarkers for pancreatic cancer. Pancreatic juice samples, devoid of blood or bile contamination, were collected from patients with pancreatic cancer (n = 5), benign pancreatic diseases (n = 6), or cholelithiasis (n = 3) during endoscopic retrograde cholangiopancreatography (ERCP). After ultramembrane centrifugation sample preparation, pancreatic juice proteins were separated by 2-DE and identified by MALDI-TOF-MS. A 2-DE dataset of pancreatic juice from patients with cholelithiasis was established, consisting of 76 protein spots representing 22 different proteins. Disease-associated obstruction of the pancreatic duct strongly effected the protein composition of pancreatic juice. Concurrently, pancreatic juice from patients with pancreatic cancer was compared to nonmalignant controls with comparable obstruction of pancreatic ducts. Seven protein spots were identified that consistently appeared at changed levels in pancreatic juice from patients with pancreatic cancer. In conclusion, comparative proteomic analysis of human pancreatic juice can be used to identify biomarkers of pancreatic cancer.

The expression of S100A8 in pancreatic cancer-associated monocytes is associated with the Smad4 status of pancreatic cancer cells

The cross-talk between tumour cells and the surrounding supporting host cells (stroma) is a key regulator of cancer growth and progression. By undertaking 2-DE analysis of laser capture microdissected malignant and stromal components of pancreatic tumours and benign ductal elements, we have identified high levels of S100A8 and S100A9 in tumour-associated stroma but not in benign or malignant epithelia. Immunohistochemical analysis (n = 71 patients) revealed strong expression of both proteins in stromal myeloid cells, subsequently identified as CD14(+)/CD68(- )monocytes/macrophages. Co-immunofluorescence revealed that S100A8 was expressed in a subset of S100A9-positive cells. Correlation of the expression of S100A8 and S100A9 to patient parameters revealed that the microenvironments of tumours which lacked expression of the tumour suppressor protein, Smad4, had significantly reduced numbers of S100A8-immunoreactive (p = 0.023) but not S100A9-immunoreactive (p = 0.21) cells. The ratio of S100A8- to S100A9-positive cells within individual tumours was significantly lower in Smad4-negative tumours than in Smad4-positive tumours (p<0.003). Pancreatitic specimens also contained S100A8- and S100A9-expressing cells, although this was not observed in regions displaying extensive fibrosis. In conclusion, our study provides an extensive analysis of S100A8 and S100A9 in pancreatic disease and highlights a potentially important relationship between pancreatic cancer cells and their surrounding microenvironment.

Research progress in screening biomarkers of pancreatic cancer by proteomic techniques

Pancreatic cancer is one kind of devastating diseases. Those patients without nonspecific symptoms at early stage had mostly lost the opporunity of surgical therapy when pancreatic cancer was detected at advanced stage. Rapid growth of proteomic technologies provides possibilities to study etiopathogenesis, and screen early diagnostic and prognosis biomarkers of pancreatic cancer. In this paper, the application of proteomic techniques in cell lines, tissues, serum and pancreatic juice from patients with pancreatic cancer is reviewed briefly.

Involvement of deterioration in S100C/A11-mediated pathway in resistance of human squamous cancer cell lines to TGFβ-induced growth suppression

Recently, we demonstrated that S100C/A11 comprises an essential pathway for growth suppression by TGFbeta in normal human keratinocytes. Nuclear transfer of S100C/A11 was a hallmark of the activation of the process. In the present study, we examined the possible deterioration in the pathway in human squamous cancer cell lines, focusing on intracellular localization of S100C/A11 and its functional partners Smad3 and Smad4. All four human squamous cancer cell lines examined (A431, BSCC-93, DJM-1, and HSC-5) were resistant to growth suppression by TGFbeta. In BSCC-93, DJM-1, and HSC-5 cells exposed to TGFbeta, S100C/A11 was not transferred to the nuclei, and p21(WAF1) was not induced. Overexpression of nucleus-targeted S100C/A11 partially recovered induction of p21(WAF1) and p15(INK4B) and growth suppression by TGFbeta1 in these cells. These results indicate that the deterioration in the S100C/A11-mediated pathway conferred upon the cancer cell lines resistance to TGFbeta. In A431 cells, S100C/A11, Smad3, and Smad4 were simultaneously transferred to the nuclei, and p21(WAF1) was induced upon exposure to TGFbeta. We provide evidence to indicate that refractoriness of A431 cells to TGFbeta was probably because the amount of p21(WAF1) induced by TGFbeta was insufficient to counteract cyclin A, which is highly overexpressed in A431 cells. Thus, the newly found S100C/A11-mediated pathway is at least partly involved in conferring upon human squamous cell cancers resistant to TGFbeta-induced growth suppression, which is considered to play a critical role for the initiation and progression of many human cancers.

Protein profiling of microdissected pancreas carcinoma and identification of HSP27 as a potential serum marker

BACKGROUND

Patients with pancreatic adenocarcinomas have a poor prognosis because of late clinical manifestation and the tumor's aggressive nature. We used proteomic techniques to search for markers of pancreatic carcinoma.

METHODS

We performed protein profiling of microdissected cryostat sections of 9 pancreatic adenocarcinomas and 10 healthy pancreatic tissue samples using ProteinChip technology (surface-enhanced laser desorption/ionization). We identified proteins by use of 2-dimensional gel electrophoresis, peptide fingerprint mapping, and immunodepletion and used immunohistochemistry for in situ localization of the proteins found. We used ELISA to quantify these proteins in preoperative serum samples from 35 patients with pancreatic cancer and 37 healthy individuals.

RESULTS

From among the differentially expressed signals that were detected by ProteinChip technology, we identified 2 proteins, DJ-1 and heat shock protein 27 (HSP27). We then detected HSP27 in sera of patients by use of ELISA, indicating a sensitivity of 100% and a specificity of 84% for the recognition of pancreatic cancer.

CONCLUSIONS

The detection of DJ-1 and HSP27 in pure defined tissue and the retrieval of HSP27 in serum by antibody-based methods identifies a potential marker for pancreatic cancer.

SLURP1 Is a Late Marker of Epidermal Differentiation and Is Absent in Mal de Meleda

SLURP1 is a secreted member of the LY6/PLAUR protein family. Mutations in the SLURP1 gene are the cause of Mal de Meleda (MDM), a rare autosomal recessive genetic disease, characterized by inflammatory palmoplantar keratoderma. In this study, we have analyzed the expression of SLURP1 in normal and MDM skin. SLURP1 was found to be a marker of late differentiation, predominantly expressed in the granular layer of skin, notably the acrosyringium. Moreover, SLURP1 was also identified in several biological fluids such as sweat, saliva, tears, and urine from normal volunteers. In palmoplantar sections from MDM patients, as well as in their sweat, mutant SLURP1, including the new variant R71H-SLURP1, was either absent or barely detectable. Transfected human embryonic kidney 293T cells expressed the MDM mutant SLURP1 containing the single amino-acid substitution G86R but did not tolerate the MDM mutation W15R located in the signal peptide. Thus, most MDM mutations in SLURP1 affect either the expression, integrity, or stability of the protein, suggesting that a simple immunologic test could be used as a rapid screening procedure.

Proteomics studies of pancreatic cancer

Pancreatic cancer is the fourth leading cause of cancer death in the United States, with 4% survival 5 years after diagnosis. Biomarkers are desperately needed to improve earlier, more curable cancer diagnosis and to develop new effective therapeutic targets. The development of quantitative proteomics technologies in recent years offers great promise for understanding the complex molecular events of tumorigenesis at the protein level, and has stimulated great interest in applying the technology for pancreatic cancer studies. Proteomic studies of pancreatic tissues, juice, serum/plasma, and cell lines have recently attempted to identify differentially expressed proteins in pancreatic cancer to dissect the abnormal signaling pathways underlying oncogenesis, and to detect new biomarkers. It can be expected that the continuing evolution of proteomics technology with better resolution and sensitivity will greatly enhance our capability in combating pancreatic cancer.

Proteomics in human cancer research

Proteomics is now widely employed in the study of cancer. Many laboratories are applying the rapidly emerging technologies to elucidate the underlying mechanisms associated with cancer development, progression, and severity in addition to developing drugs and identifying patients who will benefit most from molecular targeted compounds. Various proteomic approaches are now available for protein separation and identification, and for characterization of the function and structure of candidate proteins. In spite of significant challenges that still exist, proteomics has rapidly expanded to include the discovery of novel biomarkers for early detection, diagnosis and prognostication (clinical application), and for the identification of novel drug targets (pharmaceutical application). To achieve these goals, several innovative technologies including 2-D-difference gel electrophoresis, SELDI, multidimensional protein identification technology, isotope-coded affinity tag, solid-state and suspension protein array technologies, X-ray crystallography, NMR spectroscopy, and computational methods such as comparative and de novo structure prediction and molecular dynamics simulation have evolved, and are being used in different combinations. This review provides an overview of the field of proteomics and discusses the key proteomic technologies available to researchers. It also describes some of the important challenges and highlights the current pharmaceutical and clinical applications of proteomics in human cancer research.

Application of proteomic strategies to the identification of urinary biomarkers for prostate cancer: a review

In the post-genomic era, genes and proteins are now studied on a more comprehensive scale. Studying disease processes at only the genetic or transcriptomic level will give an incomplete amount of information. A proteomic approach potentially allows for a more global overview of how disease processes affect the proteins present in cells, tissues and organisms. The challenge arises in determining which proteins are affected in specific diseases and establishing which of these changes are unique to a particular disease. Existing and emerging proteomic technologies allow for high throughput analysis of proteins in a variety of sample types. Prostate cancer is a significant male health problem in the Western world. It is widely accepted that more specific prognostic and diagnostic markers of prostate cancer are urgently required. The present paper suggests that urine may be an attractive biofluid in which to pursue the identification of novel biomarkers of prostate cancer. This review introduces some proteomic techniques including mass spectrometry and the newer, quantitative proteomic strategies. It focuses on the potential application of these platforms to novel urinary biomarker identification in prostate malignancy. It also includes a synopsis of the current literature on urinary proteomics.