Proteome analysis of gastric cancer metastasis by two-dimensional gel electrophoresis and matrix assisted laser desorption/ionization-mass spectrometry for identification of metastasis-related proteins

Modulatory effect of Tagetes erecta flowers essential oils via Nrf2/HO-1/NF-κB/p65 axis mediated suppression of N-methyl-N'nitro-N-nitroguanidine (MNNG) induced gastric cancer in rats

Protective effect of Tagetes erecta flowers essential oils was investigated on oxidative stress, immune response, inflammation, and apoptosis against N-methyl-N'nitro-N-nitroguanidine (MNNG) induced gastric cancer in rats. Essential oil were extracted from Tagetes erecta flowers and analyzed using gas chromatography-mass spectrometry (GC-MS). For observing a protective effect against MNNG induced gastric cancer, we divided rats into 4 groups (group A to D) having 10 rats in each group. Performed various experiments and measured a different parameters to investigate antioxidant activity, immune response, anti-inflammatory and anti-apoptotic activity. The levels of malondialdehyde were markedly increased in the presence of N-methyl-N'nitro-N-nitroguanidine, whereas, the antioxidant activities of superoxide dismutase, and catalase were lowered in the treated rats in contrast with the control. Intervention with TEEO to gastric cancer-induced rats upregulated the redox status and the activity of the immune system to decrease cancer risk. The proinflammatory cytokines (IL-6 and TNF-α) secretions that were induced by MNNG were markedly inhibited by TEEO. Administration of TEEO also significantly reduced terminal deoxynucleotidyl transferase dUTP nick end labeling positive gastric cancer cells, expression of mRNA of caspase-3, and Bax. Whereas, the expression of Bcl-2 was increased. Additionally, downregulation of nuclear factor E2-related factor 2 (Nrf2) and heme oxygenase-1 (HO-1) and IκBα degradation and the nuclear factor-κB (NF-κB) p65 expression in tissues of the stomach of MNNG-induced-rats were markedly elevated due to TEEO. This suggested possession of TEEO with a protective shield against MNNG induced gastric cancer by the exertion of antioxidative stress, anti-apoptotic response, the anti-inflammatory response through Nrf2/HO-1, and NF-κB signaling pathways.

Protein disulphide isomerase can predict the clinical prognostic value and contribute to malignant progression in gliomas

Increasing evidence from structural and functional studies has indicated that protein disulphide isomerase (PDI) has a critical role in the proliferation, survival and metastasis of several types of cancer. However, the molecular mechanisms through which PDI contributes to glioma remain unclear. Here, we aimed to investigate whether the differential expression of 17 PDI family members was closely related to the different clinicopathological features in gliomas from The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas data sets. Additionally, four subgroups of gliomas (cluster 1/2/3/4) were identified based on consensus clustering of the PDI gene family. These findings not only demonstrated that a poorer prognosis, higher WHO grade, lower frequency of isocitrate dehydrogenase mutation and higher 1p/19q non‐codeletion status were significantly correlated with cluster 4 compared with the other clusters, but also indicated that the malignant progression of glioma was closely correlated with the expression of PDI family members. Moreover, we also constructed an independent prognostic marker that can predict the clinicopathological features of gliomas. Overall, the results indicated that PDI family members may serve as possible diagnostic markers in gliomas.

Proteomic characterization of early lung response to breast cancer metastasis in mice

INTRODUCTION

The tumor-promoting rearrangement of the lungs facilitates the process of cancer cell survival in a foreign microenvironment and enables their protection against immune defense. The study aimed to define the fingerprint of the early rearrangement of the lungs via the proteomic profiling of the lung tissue in the experimental model of tumor metastasis in a murine 4T1 mammary adenocarcinoma.

MATERIALS AND METHODS

The studies were performed on 7-8-week-old BALB/c female mice. Viable 4T1 cancer cells were orthotopically inoculated into the right mammary fat pad. The experiment was performed in the early phase of the tumor metastasis one and two weeks after cancer cell inoculation. The comparative analysis of protein profiles was carried out with the aid of the two-dimensional difference in gel electrophoresis (2D-DIGE). Proteins, of which expression differed significantly, were identified using nano-liquid chromatography coupled to a high-resolution mass spectrometry (nanoLC/hybrid ion trap- Orbitrap XL Discovery).

RESULTS

Palpable primary tumors were noted in the 2^nd week after cancer cell inoculation. The investigated period preceded the formation of numerous macrometastases in the lungs, however the metastasis-promoting changes were visible very early. Primary tumor-induced inflammation developed in the lungs as early as after the 1^st week and progressed during the 2^nd week, accompanied by increased concentration of 2-OH-E⁺, an oxidative stress marker, and imbalance in nitric oxide metabolites, pointing to endothelium dysfunction. The early proteomic changes in the lungs in the 1^st week after 4T1 cell inoculation resulted in the reorganization of lung tissue structure [actin, cytoplasmic 1 (Actb), tubulin beta chain (Tubb5), lamin-B1 (Lmnb1), serine protease inhibitor A3K (Serpina3k)] and activation of defense mechanisms [selenium-binding protein 1 (Selenbp1), endoplasmin (Hsp90b1), stress 70 protein, mitochondrial (Hspa9), heat shock protein HSP 90-beta (Hsp90ab1)], but also modifications in metabolic pathways [glucose-6-phosphate 1-dehydrogenase X (G6pdx), ATP synthase subunit beta, mitochondrial (Atp5b), L-lactate dehydrogenase B chain (Ldhb)]. Further development of the solid tumor after the 2^nd week following cancer cell inoculation, secretion of prolific tumor-derived factors as well as the presence of the increasing number of circulating cancer cells and extravasation processes further impose reorganization of the lung tissue [Actb, vimentin (Vim), clathrin light chain A (Clta)], altering additional metabolic pathways [annexin A5 (Anxa5), Rho GDP-dissociation inhibitor 2 (Arhgdib), complement 1 Q subcomponent-binding protein, mitochondrial (C1qbp), 14-3-3 protein zeta/delta (Ywhaz), peroxiredoxin-6 (Prdx6), chitinase-like protein 4 (Chi3l4), reticulocalbin-1 (Rcn1), EF-hand domain-containing protein D2 (Efhd2), calumenin (Calu)]. Interestingly, many of differentially expressed proteins were involved in calcium homeostasis (Rcn1, Efhd2, Calu, Actb, Vim, Lmnb1, Clta, Tubb5, Serpina3k, Hsp90b1, Hsp90ab1, Hspa9. G6pdx, Atp5b, Anxa5, Arhgdib, Ywhaz).

CONCLUSION

The analysis enabled revealing the importance of calcium signaling during the early phase of metastasis development, early cytoskeleton and extracellular matrix reorganization, activation of defense mechanisms and metabolic adaptations. It seems that the tissue response is an interplay between pro- and anti-metastatic mechanisms accompanied by inflammation, oxidative stress and dysfunction of the barrier endothelial cells.

Potential involvement of heat shock proteins in pancreatic-duodenal homeobox-1-mediated effects on the genesis of gastric cancer: A 2D gel-based proteomic study

AIM

To identify functional proteins involved in pancreatic-duodenal homeobox-1 (PDX1)-mediated effects on gastric carcinogenesis.

METHODS

A PDX1-overexpressed model was established by transfecting gastric cancer cell line SGC7901 with pcDNA3.1(+)-PDX1 vector (SGC-PDX1). Transfection with empty pcDNA3.1 vector (SGC-pcDNA) served as control. Comparative protein profiles of the two groups were analyzed by two-dimensional electrophoresis based-proteomics (2DE gel-based proteomics). The differential proteins identified by 2DE were further validated by qRT-PCR and immunoblotting. Finally, co-immunoprecipitation was used to determine any direct interactions between PDX1 and the differential proteins.

RESULTS

2DE gel proteomics identified seven differential proteins in SGC-PDX1 when compared with those in SGC-pcDNA. These included four heat shock proteins (HSPs; HSP70p1B, HSP70p8, HSP60, HSP27) and three other proteins (ER60, laminin receptor 1, similar to epsilon isoform of 14-3-3 protein). Immunoblotting validated the expression of the HSPs (HSP70, HSP60, HSP27). Furthermore, their expressions were lowered to 80%, 20% and 24%, respectively, in SGC-PDX1, while PDX1 exhibited a 9-fold increase, compared to SGC-pcDNA. However, qRT-PCR analysis revealed that mRNA levels of the HSPs were increased in SGC-PDX1, suggesting that the expression of the HSPs was post-translationally regulated by the PDX1 protein. Finally, co-immunoprecipitation failed to identify any direct interaction between PDX1 and HSP70 proteins.

CONCLUSION

This study demonstrates the potential involvement of HSPs in PDX1-mediated effects on the genesis of gastric cancer.

Progress and prospects for the discovery of biomarkers for gastric cancer: a focus on proteomics

INTRODUCTION

Patient outcomes from gastric cancer vary due to the complexity of stomach carcinogenesis. Recent research using proteomic technologies has targeted components of all of these systems in order to develop biomarkers to aid the early diagnosis of gastric cancer and to assist in prognostic stratification. Areas covered: This review is comprised of evidence obtained from literature searches from PubMed. It covers the evidence of diagnostic, prognostic, and predictive biomarkers for gastric cancer using proteomic technologies, and provides up-to-date references. Expert commentary: The proteomic technologies have not only enabled the screening of a large number of samples, but also enabled the identification of diagnostic, prognostic and predictive biomarkers for gastric cancer. While major challenges still remain, to date, proteomic studies in gastric cancer have provided a wealth of information in revealing proteome alterations associated with the disease.

What gastric cancer proteomic studies show about gastric carcinogenesis?

Gastric cancer is a complex, heterogeneous, and multistep disease. Over the past decades, several studies have aimed to determine the molecular factors that lead to gastric cancer development and progression. After completing the human genome sequencing, proteomic technologies have presented rapid progress. Differently from the relative static state of genome, the cell proteome is dynamic and changes in pathologic conditions. Proteomic approaches have been used to determine proteome profiles and identify differentially expressed proteins between groups of samples, such as neoplastic and nonneoplastic samples or between samples of different cancer subtypes or stages. Therefore, proteomic technologies are a useful tool toward improving the knowledge of gastric cancer molecular pathogenesis and the understanding of tumor heterogeneity. This review aimed to summarize the proteins or protein families that are frequently identified by using high-throughput screening methods and which thus may have a key role in gastric carcinogenesis. The increased knowledge of gastric carcinogenesis will clearly help in the development of new anticancer treatments. Although the studies are still in their infancy, the reviewed proteins may be useful for gastric cancer diagnosis, prognosis, and patient management.

Filamin C, a dysregulated protein in cancer revealed by label-free quantitative proteomic analyses of human gastric cancer cells

Gastric cancer (GC) is the fourth and fifth most common cancer in men and women, respectively. We identified 2,750 proteins at false discovery rates of 1.3% (protein) and 0.03% (spectrum) by comparing the proteomic profiles of three GC and a normal gastric cell lines. Nine proteins were significantly dysregulated in all three GC cell lines, including filamin C, a muscle-specific filamin and a large actin-cross-linking protein. Downregulation of filamin C in GC cell lines and tissues were verified using quantitative PCR and immunohistochemistry. Data-mining using public microarray datasets shown that filamin C was significantly reduced in many human primary and metastasis cancers. Transient expression or silencing of filamin C affected the proliferation and colony formation of cancer cells. Silencing of endogenous filamin C enhanced cancer cell migration and invasion, whereas ectopic expression of filamin C had opposing effects. Silencing of filamin C increased the expression of matrix metallopeptidase 2 and improved the metastasis of prostate cancer in a zebrafish model. High filamin C associated with better prognosis of prostate cancer, leukemia and breast cancer patients. These findings establish a functional role of filamin C in human cancers and these data will be valuable for further study of its mechanisms.

"Omics" in pharmaceutical research: overview, applications, challenges, and future perspectives

In the post-genomic era, biological studies are characterized by the rapid development and wide application of a series of "omics" technologies, including genomics, proteomics, metabolomics, transcriptomics, lipidomics, cytomics, metallomics, ionomics, interactomics, and phenomics. These "omics" are often based on global analyses of biological samples using high through-put analytical approaches and bioinformatics and may provide new insights into biological phenomena. In this paper, the development and advances in these omics made in the past decades are reviewed, especially genomics, transcriptomics, proteomics and metabolomics; the applications of omics technologies in pharmaceutical research are then summarized in the fields of drug target discovery, toxicity evaluation, personalized medicine, and traditional Chinese medicine; and finally, the limitations of omics are discussed, along with the future challenges associated with the multi-omics data processing, dynamics omics analysis, and analytical approaches, as well as amenable solutions and future prospects.

Comparative two-dimensional polyacrylamide gel electrophoresis of the salivary proteome of children with autism spectrum disorder

In the last decades, prevalence of autism spectrum disorder (ASD) has been on the rise. However, clear aetiology is still elusive and improvements in early diagnosis are needed. To uncover possible biomarkers present in ASD, we used two-dimensional polyacrylamide gel electrophoresis and nanoliquid chromatography-tandem mass spectrometry (nanoLC-MS/MS), to compare salivary proteome profiling of children with ASD and controls. A total of 889 spots were compared and only those spots with a fold change ≥1.7 and a P-value <0.05 or a fold change of ≥3.0 between ASD cases and controls were analysed by nanoLC-MS/MS. Alpha-amylase, CREB-binding protein, p532, Transferrin, Zn alpha2 glycoprotein, Zymogen granule protein 16, cystatin D and plasminogen were down-regulated in ASD. Increased expression of proto-oncogene Frequently rearranged in advanced T-cell lymphomas 1 (FRAT1), Kinesin family member 14, Integrin alpha6 subunit, growth hormone regulated TBC protein 1, parotid secretory protein, Prolactin-inducible protein precursor, Mucin-16, Ca binding protein migration inhibitory factor-related protein 14 (MRP14) was observed in individuals with ASD. Many of the identified proteins have previously been linked to ASD or were proposed as risk factors of ASD at the genetic level. Some others are involved in pathological pathways implicated in ASD causality such as oxidative stress, lipid and cholesterol metabolism, immune system disturbances and inflammation. These data could contribute to protein signatures for ASD presence, risk and subtypes, and advance understanding of ASD cause as well as provide novel treatment targets for ASD.

Proteomics in gastric cancer research: Benefits and challenges

Among various cancers, gastric cancer (GC) exhibits relatively high morbidity and mortality rate worldwide. The lack of effective methods in early detection and diagnosis, and immediate therapies makes treating such disease a challenge for both clinicians and oncologists. Proteomics has emerged as a promising technology platform for rationally identifying biomarkers and novel therapeutic targets for GC, as well as discovering underlying mechanisms of carcinogenesis. Its application has greatly benefited mechanistic studies of this disease. This review will demonstrate the applications of proteomic technology in GC research. The advantages and shortcomings of this technology, as reflected by current studies, will also be discussed to improve and expand its application in the field of cancer research.

Short-term exposure of nontumorigenic human bronchial epithelial cells to carcinogenic chromium(VI) compromises their respiratory capacity and alters their bioenergetic signature

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Chromium(VI) impaired respiration and increased glycolytic flux in BEAS-2B cells.

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Cr(VI)-exposed cells shifted to a more fermentative metabolism.

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This metabolic shift was in line with a decreased β-F1-ATPase/GAPDH protein ratio.

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Increased oxidative stress levels suggest impairment of antioxidant defenses.

Previous studies on the impact of hexavalent chromium [Cr(VI)] on mammalian cell energetics revealed alterations suggestive of a shift to a more fermentative metabolism. Aiming at a more defined understanding of the metabolic effects of Cr(VI) and of their molecular basis, we assessed the impact of a mild Cr(VI) exposure on critical bioenergetic parameters (lactate production, oxygen consumption and intracellular ATP levels). Cells derived from normal human bronchial epithelium (BEAS-2B cell line), the main in vivo target of Cr(VI) carcinogenicity, were subjected for 48 h to 1 μM Cr(VI). We could confirm a shift to a more fermentative metabolism, resulting from the simultaneous inhibition of respiration and stimulation of glycolysis. This shift was accompanied by a decrease in the protein levels of the catalytic subunit (subunit β) of the mitochondrial H⁺-ATP synthase (β-F₁-ATPase) and a concomitant marked increase in those of glyceraldehyde-3-phosphate dehydrogenase (GAPDH). The corresponding alteration in the β-F₁-ATPase/GAPDH protein ratio (viewed as a bioenergetic signature) upon Cr(VI) exposure was in agreement with the observed attenuation of cellular respiration and enhancement of glycolytic flux. Altogether, these results constitute a novel finding in terms of the molecular mechanisms of Cr(VI) effects.

Functional genomic analysis of cancer metastasis: biologic insights and clinical implications

Metastasis, the spread of cancer from primary tumors to distant vital organs, has devastating consequences. Lack of effective tools to study this complex problem has hindered the development of accurate prognostic methods and effective treatments for metastatic cancer. In the postgenomic era, the application of genomic profiling methods to the analysis of clinical metastasis samples and animal metastasis models has revolutionized the field of metastasis research. This article reviews recent breakthroughs in the functional genomic analysis of metastasis. In addition, its impacts on our understanding of the molecular basis of metastasis and on clinical practice are discussed.

Proteomic analysis profile of engineered articular cartilage with chondrogenic differentiated adipose tissue-derived stem cells loaded polyglycolic acid mesh for weight-bearing area defect repair

The present study was designed to investigate the possibility of full-thickness defects repair in porcine articular cartilage (AC) weight-bearing area using chondrogenic differentiated autologous adipose-derived stem cells (ASCs) with a follow-up of 3 and 6 months, which is successive to our previous study on nonweight-bearing area. The isolated ASCs were seeded onto the phosphoglycerate/polylactic acid (PGA/PLA) with chondrogenic induction in vitro for 2 weeks as the experimental group prior to implantation in porcine AC defects (8 mm in diameter, deep to subchondral bone), with PGA/PLA only as control. With follow-up time being 3 and 6 months, both neo-cartilages of postimplantation integrated well with the neighboring normal cartilage and subchondral bone histologically in experimental group, whereas only fibrous tissue in control group. Immunohistochemical and toluidine blue staining confirmed similar distribution of COL II and glycosaminoglycan in the regenerated cartilage to the native one. A vivid remolding process with repair time was also witnessed in the neo-cartilage as the compressive modulus significantly increased from 70% of the normal cartilage at 3 months to nearly 90% at 6 months, which is similar to our former research. Nevertheless, differences of the regenerated cartilages still could be detected from the native one. Meanwhile, the exact mechanism involved in chondrogenic differentiation from ASCs seeded on PGA/PLA is still unknown. Therefore, proteome is resorted leading to 43 proteins differentially identified from 20 chosen two-dimensional spots, which do help us further our research on some committed factors. In conclusion, the comparison via proteome provided a thorough understanding of mechanisms implicating ASC differentiation toward chondrocytes, which is further substantiated by the present study as a perfect supplement to the former one in nonweight-bearing area.

Discovery of diagnostic serum biomarkers of gastric cancer using proteomics

Gastric cancer has significant morbidity and mortality worldwide and locally. Good prognosis relies on an early diagnosis. However, this remains a challenge due to the lack of specific and sensitive serum biomarkers for early detection. Hence, there is a constant search for these biomarkers for screening purposes. Proteomic profiling enables a new approach to the discovery of biomarkers in disease. This review presents recent attempts in search of gastric cancer serum biomarker using proteomics. Different methodologies and different types of samples were employed by different groups of researchers. Major difficulties were encountered in the discovery processes, including interference from abundant proteins and continuous changing serum proteomes from different individuals.

S100A9, GIF and AAT as potential combinatorial biomarkers in gastric cancer diagnosis and prognosis

PURPOSE

We have mined the gastric fluid proteome for potential gastric cancer (GC) biomarkers that may enhance disease detection and facilitate prognostic monitoring.

EXPERIMENTAL DESIGN

In biomarker discovery, a total of 12 patient gastric fluid samples (stages I, III, IV and gastritis) were analysed by 2DE for expression changes that correlated with GC status or disease progression. Gastric fluid proteins showing differential expression with GC were identified by MALDI-TOF/TOF MS as putative biomarkers. Levels of these potential biomarker candidates were independently validated by Western blotting in further 60 gastritis and GC patients. A targeted approach that recruits biomarker candidates for panel consideration was adopted to test if two or more biomarkers in combination improved diagnostic power.

RESULTS

From the 15 differentially regulated proteins identified, expression levels of S100A9, GIF and AAT in the gastric fluid clearly correlated with GC status. S100A9/AAT (AUC = 0.81) and S100A9/GIF (AUC = 0.92) were revealed as promising biomarker pairs for early GC diagnosis and disease monitoring, respectively.

CONCLUSION AND CLINICAL RELEVANCE

Early diagnosis, accurate staging and constant disease monitoring remain the prerequisites for effective treatment against GC. As current biomarkers like CA19-9 and carcinoembryonic antigen (CEA) lack sensitivity and specificity, there is a pressing need for novel GC detection and monitoring methods. To this end, S100A9, GIF and AAT from the gastric fluid may significantly augment existing methods of GC detection and monitoring, and eliminate the need for invasive tissue biopsies.

Carcinoma of the stomach: A review of epidemiology, pathogenesis, molecular genetics and chemoprevention

Carcinoma of the stomach is still the second most common cause of cancer death worldwide, although the incidence and mortality have fallen dramatically over the last 50 years in many regions. The incidence of gastric cancer varies in different parts of the world and among various ethnic groups. Despite advances in diagnosis and treatment, the 5-year survival rate of stomach cancer is only 20 per cent. Stomach cancer can be classified into intestinal and diffuse types based on epidemiological and clinicopathological features. The etiology of gastric cancer is multifactorial and includes both dietary and nondietary factors. The major diet-related risk factors implicated in stomach cancer development include high content of nitrates and high salt intake. Accumulating evidence has implicated the role of Helicobacter pylori (H. pylori) infection in the pathogenesis of gastric cancer. The development of gastric cancer is a complex, multistep process involving multiple genetic and epigenetic alterations of oncogenes, tumor suppressor genes, DNA repair genes, cell cycle regulators, and signaling molecules. A plausible program for gastric cancer prevention involves intake of a balanced diet containing fruits and vegetables, improved sanitation and hygiene, screening and treatment of H. pylori infection, and follow-up of precancerous lesions. The fact that diet plays an important role in the etiology of gastric cancer offers scope for nutritional chemoprevention. Animal models have been extensively used to analyze the stepwise evolution of gastric carcinogenesis and to test dietary chemopreventive agents. Development of multitargeted preventive and therapeutic strategies for gastric cancer is a major challenge for the future.

Discovery of biomarkers for gastric cancer: a proteomics approach

Gastric cancer is the second leading cause of cancer-related deaths worldwide. Although many treatment options exist for patients with gastric tumors, the incidence and mortality rate of gastric cancer are on the rise. The early stages of gastric cancer are non-symptomatic, and the treatment response is unpredictable. This situation is further aggravated by a lack of diagnostic biomarkers that can aid in the early detection and prognosis of gastric cancer and in the prediction of chemoresistance. Moreover, clinical surgical specimens are rarely obtained, and traditional biomarkers of gastric cancer are not very effective. Many studies in the field of proteomics have contributed to the discovery and establishment of powerful diagnostic tools (e.g., ProteinChip array) in the management of cancer. The evolution in proteomic technologies has not only enabled the screening of a large number of samples but also enabled the identification of pathologically significant proteins, such as phosphoproteins, and the quantitation of difference in protein expression under different conditions. Multiplexed assays are used widely to accurately fractionate various complex samples such as blood, tissue, cells, and Helicobacter pylori-infected specimens to identify differentially expressed proteins. Biomarker detection studies have substantially contributed to the areas of secretome, metabolome, and phosphoproteome. Here, we review the development of potential biomarkers in the natural history of gastric cancer, with specific emphasis on the characteristics of target protein convergence.

Overexpression of ADP-ribosylation factor 1 in human gastric carcinoma and its clinicopathological significance

Gastric cancer is the sixth leading cause of cancer-related death in Taiwan, and the identification of related factors is essential to increase patient survival. ADP-ribosylation factor 1 (ARF1) was initially identified using 2-D electrophoresis combined with MALDI-time-of-flight mass spectrometry. ADP-ribosylation factor 1 belongs to the Ras superfamily or GTP-binding protein family and has been shown to enhance cell proliferation. In the current study, we evaluated the potential of ARF1 as a biomarker for gastric cancer detection. ADP-ribosylation factor 1 mRNA was upregulated in tumor tissues (compared with adjacent non-tumor tissues, n = 55) in approximately 67.2% of gastric cancer patients. Expression of ARF1 protein was additionally observed using Western blot and immunohistochemistry (IHC) analyses. The clinicopathological correlations of ARF1 were further evaluated. Elevated ARF1 expression was strongly correlated with lymph node metastasis (P = 0.008), serosal invasion (P = 0.046), lymphatic invasion (P = 0.035), and pathological staging (P = 0.010). Moreover, the 5-year survival rate for the lower ARF1 expression group (n = 50; IHC score < 90) was higher than that of the higher expression group (n = 60; IHC score ≥ 90) (P = 0.0228, log-rank test). To establish the specific function of ARF1 in human gastric cancer, isogenic ARF1-overexpressing cell lines were prepared. Our results showed that ARF1-overexpressing clones display enhanced cell proliferation, migration, and invasion. Furthermore, ARF1-overexpression might contribute to poor prognosis of patients. These findings collectively support the utility of ARF1 as a novel prognostic marker for gastric cancer and its role in cell invasion.

Proteomic analysis of gastric cancer and immunoblot validation of potential biomarkers

AIM: To search for and validate differentially expressed proteins in patients with gastric adenocarcinoma.

METHODS: We used two-dimensional gel electrophoresis and mass spectrometry to search for differentially expressed proteins in patients with gastric adenocarcinoma. A set of proteins was validated with immunoblotting.

RESULTS: We identified 30 different proteins involved in various biological processes: metabolism, development, death, response to stress, cell cycle, cell communication, transport, and cell motility. Eight proteins were chosen for further validation by immunoblotting. Our results show that gastrokine-1, 39S ribosomal protein L12 (mitochondrial precursor), plasma cell-induced resident endoplasmic reticulum protein, and glutathione S-transferase mu 3 were significantly underexpressed in gastric adenocarcinoma relative to adjacent non-tumor tissue samples. On the other hand, septin-2, ubiquitin-conjugating enzyme E2 N, and transaldolase were significantly overexpressed. Translationally controlled tumor protein was shown to be differentially expressed only in patients with cancer of the gastric cardia/esophageal border.

CONCLUSION: This work presents a set of possible diagnostic biomarkers, validated for the first time. It might contribute to the efforts of understanding gastric cancer carcinogenesis.

Identification of proteins differentially expressed in gastric cancer cells with high metastatic potential for invasion to lymph nodes

In a search for proteins involved in cancer metastasis, we analyzed proteomes of the human gastric cancer cell OCUM-2M and its metastatic subline OCUM-2MLN. We observed that aspartate aminotransferase (AAT), D-site binding protein (DBP), and anterior gradient protein 2 (AGR2) are differentially expressed in metastatic OCUM-2MLN cells. Measurement of protein expression in clinical samples indicated that DBP and AAT are also down-regulated in metastatic adenocarcinoma. Additionally, urokinase-type tissue plasminogen activator is up-regulated in OCUM-2MLN cells and also in metastatic gastric cancer samples. Collectively, these results raise a possibility that AAT, DBP and AGR2 are functionally implicated in the invasiveness of gastric cancer cells.

Cancer: a proteomic disease

The development of cancer is a pathological process involving multiple environmental carcinogenic factors and genetic alterations. For decades, cancer researchers have focused on genomic and transcriptomic analyses. The completion of the Human Genome Project has opened the door to the post-genome era and oncoproteomics. Proteins play a critical role in tumorigenesis and influence the differences between normal cells and malignant cells. This report proposes the concept that cancer is a proteomic disease. This concept is based on examining protein expression profiles, post-translational modifications, and protein-protein interactions in carcinogenesis using recent advances in comparative, functional and structural proteomics. This approach provides a new way of viewing carcinogenesis, presents new clues in biomarker discovery for cancer diagnosis and therapy, and reveals important scientific findings and their significance to clinical applications.

The bioenergetic signature of isogenic colon cancer cells predicts the cell death response to treatment with 3-bromopyruvate, iodoacetate or 5-fluorouracil

Background

Metabolic reprogramming resulting in enhanced glycolysis is a phenotypic trait of cancer cells, which is imposed by the tumor microenvironment and is linked to the down-regulation of the catalytic subunit of the mitochondrial H⁺-ATPase (β-F1-ATPase). The bioenergetic signature is a protein ratio (β-F1-ATPase/GAPDH), which provides an estimate of glucose metabolism in tumors and serves as a prognostic indicator for cancer patients. Targeting energetic metabolism could be a viable alternative to conventional anticancer chemotherapies. Herein, we document that the bioenergetic signature of isogenic colon cancer cells provides a gauge to predict the cell-death response to the metabolic inhibitors, 3-bromopyruvate (3BrP) and iodoacetate (IA), and the anti-metabolite, 5-fluorouracil (5-FU).

Methods

The bioenergetic signature of the cells was determined by western blotting. Aerobic glycolysis was determined from lactate production rates. The cell death was analyzed by fluorescence microscopy and flow cytometry. Cellular ATP concentrations were determined using bioluminiscence. Pearson's correlation coefficient was applied to assess the relationship between the bioenergetic signature and the cell death response. In vivo tumor regression activities of the compounds were assessed using a xenograft mouse model injected with the highly glycolytic HCT116 colocarcinoma cells.

Results

We demonstrate that the bioenergetic signature of isogenic HCT116 cancer cells inversely correlates with the potential to execute necrosis in response to 3BrP or IA treatment. Conversely, the bioenergetic signature directly correlates with the potential to execute apoptosis in response to 5-FU treatment in the same cells. However, despite the large differences observed in the in vitro cell-death responses associated with 3BrP, IA and 5-FU, the in vivo tumor regression activities of these agents were comparable.

Conclusions

Overall, we suggest that the determination of the bioenergetic signature of colon carcinomas could provide a tool for predicting the therapeutic response to various chemotherapeutic strategies aimed at combating tumor progression.

Glycomic and glycoproteomic analysis of serum from patients with stomach cancer reveals potential markers arising from host defense response mechanisms

Despite the reduced incidence of gastric cancer in the developed world, a diagnosis of stomach carcinoma still carries a poor prognosis due to the asymptomatic nature of the disease in the early stages, subsequent advanced stage diagnosis, and a low 5 year survival rate. Endoscopy remains the primary standard for diagnosis of stomach carcinoma and the current marker, carbohydrate antigen 19-9 (CA19-9) lacks the levels of sensitivity and specificity required in order to make it clinically useful for diagnostic monitoring. Therefore, there is a current need for additional markers to improve the diagnostic accuracy for the early stages of stomach cancer. Together, glycomic, proteomic, and glycoproteomic analyses of serum have the potential to identify such probable markers. A discovery study is reported here using preoperative serum from 80 stomach cancer patients, 10 patients bearing benign stomach disease, and 20 matched controls. Glycomic analysis of the total and immunoaffinity depleted serum revealed statistically significant increases in the levels of sialyl Lewis X epitopes (SLe(X)) present on triantennary glycans accompanied by increased levels of core fucosylated agalactosyl biantennary glycans present on IgG (referred to as the IgG G0 glycoform) which are associated with increasing disease pathogenesis. Protein expression analysis using 2D-DiGE returned a number of differentially expressed protein candidates in the depleted serum, many of which were shown to carry triantennary SLe(X) during subsequent glycomic investigations. Biological pathway analysis of the experimental data returned complement activation and acute phase response signaling as the most significantly altered pathways in the stomach cancer patient serum. Upon the basis of these findings, it is suggested that increased expression of IgG G0 and complement activation are a host response to the presence of the stomach tumor while the increased expression of SLe(X) and acute phase response proteins is a result of pro-inflammatory cytokine signaling, including IL-6, during carcinogenesis. The approach presented herein provides an insight into the underlying mechanisms of disease and the resulting changes in the glycome and glycoproteome offer promise as potential markers for diagnosis and prognostic monitoring in stomach cancer.

Metabolomics of gastric cancer metastasis detected by gas chromatography and mass spectrometry

AIM: To elucidate the underlying mechanisms of metastasis and to identify the metabolomic markers of gastric cancer metastasis.

METHODS: Gastric tumors from metastatic and non-metastatic groups were used in this study. Metabolites and different metabolic patterns were analyzed by gas chromatography, mass spectrometry and principal components analysis (PCA), respectively. Differentiation performance was validated by the area under the curve (AUC) of receiver operating characteristic curves.

RESULTS: Twenty-nine metabolites were differentially expressed in animal models of human gastric cancer. Of the 29 metabolites, 20 were up-regulated and 9 were down-regulated in metastasis group compared to non-metastasis group. PCA models from the metabolite profiles could differentiate the metastatic from the non-metastatic specimens with an AUC value of 1.0. These metabolites were mainly involved in several metabolic pathways, including glycolysis (lactic acid, alaline), serine metabolism (serine, phosphoserine), proline metabolism (proline), glutamic acid metabolism, tricarboxylic acid cycle (succinate, malic acid), nucleotide metabolism (pyrimidine), fatty acid metabolism (docosanoic acid, and octadecanoic acid), and methylation(glycine). The serine and proline metabolisms were highlighted during the progression of metastasis.

CONCLUSION: Proline and serine metabolisms play an important role in metastasis. The metabolic profiling of tumor tissue can provide new biomarkers for the treatment of gastric cancer metastasis.

Heat shock protein 27 is over-expressed in tumor tissues and increased in sera of patients with gastric adenocarcinoma

BACKGROUND

In a previous study, we found that heat shock protein 27 (HSP27) was over-expressed in gastric adenocarcinoma (GA) tissue. In this study, our goal was to further verify the expression profile of HSP27 in patients with GA.

METHODS

Western blot and immunohistochemistry were employed to determine HSP27 expression in 50 paired tumor and adjacent normal tissue. ELISA was used to quantify serum HSP27 concentrations in the same 50 GA patients and 50 healthy individuals.

RESULTS

Compared to adjacent normal tissues, HSP27 was over-expressed in 25 (50%, p=0.000) and 24 (48%, p=0.000) cases of GA tissue by Western blot and immunohistochemistry, respectively. ELISA revealed significantly higher serum concentrations of HSP27 in patients with GA patients (mean=986 pg/mL) compared to healthy individuals (mean=573 pg/mL) (p=0.003). In addition, infection with Helicobacter pylori (HP) in healthy individuals was associated with increased expression of HSP27 in both gastric mucosa and serum.

CONCLUSIONS

These data suggest that HSP27 is over-expressed in GA tissue and serum concentrations of HSP27 are increased in patients with GA. Over-expression of HSP27 may indicate a gastric malignant/infectious process. The detection of serum HSP27 concentrations by ELISA may be useful for screening for GA.

Selective inhibition of β-F1-ATPase mRNA translation in human tumours

Down-regulation of β-F1-ATPase (the catalytic subunit of the mitochondrial H+-ATP synthase) is a hallmark of many human tumours. The expression level of β-F1-ATPase provides a marker of the prognosis of cancer patients, as well as of the tumour response to chemotherapy. However, the mechanisms that participate in down-regulating its expression in human tumours remain unknown. In the present study, we have investigated the expression of β-F1-ATPase mRNA (termed β-mRNA) in breast, colon and lung adenocarcinomas and squamous carcinomas of the lung. Despite the down-regulation of the protein, tumour β-mRNA levels remained either unchanged (breast and lung adenocarcinomas) or significantly increased (colon and squamous lung carcinomas) when compared with paired normal tissues, suggesting a specific translation-masking event for β-mRNA in human cancer. Consistently, we show using cell-free translation assays that a large fraction (~70%) of protein extracts derived from breast and lung adenocarcinomas specifically repress the translation of β-mRNA. We show that the 3′UTR (3′ untranslated region) of human β-mRNA is a relevant cis-acting element required for efficient translation of the transcript. However, an RNA chimaera bearing the 3′UTR of human β-mRNA does not recapitulate the inhibitory effect of tumour extracts on β-mRNA translation. Overall, the findings of the present study support the hypothesis that down-regulation of the bioenergetic activity of mitochondria in human tumours is exerted by translation silencing of β-mRNA.

In silico analysis of protein neoplastic biomarkers for cervix and uterine cancer

Worldwide, cervical and uterine cancers are the most deadly cancers in women, with high prevalences, especially in developing countries. The Human Protein Atlas (HPA) portal was explored for proteins expressed in a tissue- or cervix and uterine cancer-specific manner. The group of proteins differentially expressed and with enhanced expression in the glandular and surface epithelial (squamous) cells retrieved from HPA were further explored using the Protein Information and Knowledge Extractor (PIKE) portal to compile biological information that is found in different databases, and repositories on the Internet. Thus, the lists of candidate proteins found in HPA, and PIKE portals may be used as a starting point for the discovery and validation of biomarkers for cervix and uterine cancer employing proteomics approaches as described in the present article.

Conventional and Proteomic Technologies for the Detection of Early Stage Malignancies: Markers for Ovarian Cancer

Our understanding of the tumor microenvironment continues to evolve and allows for the identification of biomarkers that should detect the presence of early stage malignancies. Recent advances in computational analysis and biomedical technologies have come together to elucidate signatures associated with cancer and that are capable of identifying unique tumor-specific proteins. Within the tumor microenvironment, we continue to characterize the proteophysiology of the different steps associated with tumor progression. The urgent need for biomarkers accurately detecting early-stage epithelial ovarian cancer has prompted us, and others, to engage in a search for specific peptide signatures that may discriminate transformed cells from those of the normal ovarian microenvironment. This endeavor also provides new insights into the biology of the disease, which may not only be applicable to detection but may also help to initiate new therapies and optimize patient care.

Glucose avidity of carcinomas

The cancer cell phenotype has been summarized in six hallmarks [D. Hanahan, R.A. Weinberg, The hallmarks of cancer, Cell 100 (1) (2000) 57-70]. Following the conceptual trait established in that review towards the comprehension of cancer, herein we summarize the basis of an underlying principle that is fulfilled by cancer cells and tumors: its avidity for glucose. Our purpose is to push forward that the metabolic reprogramming that operates in the cancer cell represents a seventh hallmark of the phenotype that offers a vast array of possibilities for the future treatment of the disease. We summarize the metabolic pathways that extract matter and energy from glucose, paying special attention to the concerted regulation of these pathways by the ATP mass-action ratio. The molecular and functional evidences that support the high glucose uptake and the "abnormal" aerobic glycolysis of the carcinomas are detailed discussing also the role that some oncogenes and tumor suppressors have in these pathways. We overview past and present evidences that sustain that mitochondria of the cancer cell are impaired, supporting the original Warburg's formulation that ascribed the high glucose uptake of cancer cells to a defective mitochondria. A simple proteomic approach designed to assess the metabolic phenotype of cancer, i.e., its bioenergetic signature, molecularly and functionally supports Warburg's hypothesis. Furthermore, we discuss the clinical utility that the bioenergetic signature might provide. Glycolysis is presented as the "selfish" pathway used for cellular proliferation, providing both the metabolic precursors and the energy required for biosynthetic purposes, in the context of a plethora of substrates. The glucose avidity of carcinomas is thus presented as the result of both the installment of glycolysis for cellular proliferation and of the impairment of mitochondrial activity in the cancer cell. At the end, the repression of mitochondrial activity affords the cancer cell with a cell-death resistant phenotype making them prone to malignant growth.

Overexpression of heat shock protein 27 in squamous cell carcinoma of the uterine cervix: a proteomic analysis using archival formalin-fixed, paraffin-embedded tissues

Proteomic analysis of squamous cell carcinoma of the uterine cervix was performed using total protein from archival formalin-fixed, paraffin-embedded tissues. A wide range of proteins with molecular weights of 10 to greater than 200 kd was extracted from formalin-fixed, paraffin-embedded tissues using a recently developed protocol based on the heat-induced antigen retrieval technique. The extracted proteins from normal squamous epithelium (n = 53) and squamous cell carcinoma (n = 21) were fluorescently labeled and separated using 2-dimensional gel electrophoresis. We identified 728 differentially expressed proteins, with 144 up-regulated and 584 down-regulated as compared with normal squamous epithelial tissue samples. Nine proteins showing pronounced up-regulation in squamous cell carcinoma were analyzed on liquid chromatography-tandem mass spectrometry. Among the candidate proteins identified, minichromosome maintenance 8, a disintegrin and metalloproteinase domain 18, and heat shock protein 27 were analyzed in Western blotting, resulting in significant overexpression of heat shock protein 27 in squamous cell carcinoma over normal mucosa (P < .05). Furthermore, immunostaining revealed heat shock protein 27 overexpression not only in squamous cell carcinoma but in various stages of cervical intraepithelial neoplasia (grades 1-3, n = 90), including dysplasia and carcinoma in situ. The expression levels of heat shock protein 27 in cervical intraepithelial neoplasia grades 1 to 3 and squamous cell carcinoma were significantly higher than that in normal mucosa (P < .05). In the neoplastic lesions, heat shock protein 27 expression levels in cervical intraepithelial neoplasia grade 3 and squamous cell carcinoma were significantly higher than that in cervical intraepithelial neoplasia grade 1 (P < .05). These results may suggest a role of heat shock protein 27 in tumor development and progression in the cervical intraepithelial neoplasia-squamous cell carcinoma sequence. Future experiments using formalin-fixed, paraffin-embedded tissue-based proteomic analysis will be a powerful tool for various pathologic studies.

PKD, PKD2, and p38 MAPK mediate Hsp27 serine-82 phosphorylation induced by neurotensin in pancreatic cancer PANC-1 cells

It is widely recognized that Hsp27 is a downstream substrate of the p38 MAPK cascade whereas the role of PKD family members in mediating receptor-stimulated Hsp27 Ser-82 phosphorylation has not been evaluated. Here, we show that neurotensin induced a rapid and striking increase in Hsp27 Ser-82 phosphorylation in PANC-1 cells, which was closely correlated with stimulation of activation loop phosphorylation of PKDs and p38 MAPK Thr180/Tyr182 phosphorylation. Treatment of PANC-1 cells with either the selective PKC inhibitor GF-I or the p38 MAPK inhibitor SB202190 partially reduced neurotensin-induced Hsp27 Ser-82 phosphorylation. However, treatment of the cells with a combination of GF-I and SB202190 virtually abolished neurotensin-induced Hsp27 Ser-82 phosphorylation. Overexpression of PKD in stably transfected PANC-1 cells increased the magnitude and prolonged the duration of Hsp27 Ser-82 phosphorylation in response to neurotensin. Either PKD or PKD2 gene silencing utilizing siRNAs targeting distinct PKD or PKD2 sequences reduced neurotensin-stimulated Hsp27 Ser-82 phosphorylation, but cotransfection of siRNAs targeting both, PKD and PKD2, markedly decreased neurotensin-induced Hsp27 Ser-82 phosphorylation. Knockdown of PKD and PKD2 abolished Hsp27 phosphorylation in cells treated with SB202190. Thus, neurotensin induces Hsp27 Ser-82 phosphorylation through p38 MAPK- and PKC/PKD-dependent pathways in PANC-1 cells. Our results demonstrate, for the first time, that neurotensin induces a striking increase in Hsp27 phosphorylation on Ser-82 in PANC-1 cells through convergent p38 MAPK, PKD, and PKD2 signaling.

Phosphorylation of Ser78 of Hsp27 correlated with HER-2/neu status and lymph node positivity in breast cancer

Background

Abnormal amplification/expression of HER-2/neu oncogene has been causally linked with tumorigenesis and metastasis in breast cancer and associated with shortened overall survival of patients. Recently, heat shock protein 27 (Hsp27) was reported to be highly expressed in HER-2/neu positive tumors and cell lines. However, putative functional links between phosphorylation of Hsp27 with HER-2/neu status and other clinicopathological features remain to be elucidated.

Results

Comparative phosphoproteomic studies of HER-2/neu positive and -negative breast tumors revealed that Hsp27, one of the identified phosphoproteins, was highly phosphorylated in HER-2/neu positive tumors. The extent of Hsp27 phosphorylation at its Ser¹⁵, Ser⁷⁸ and Ser⁸² residues were further evaluated with site-specific antibodies in tumor samples by tissue lysate array- and tissue microarray-based analyses, and in the BT474 breast cancer cell line treated with heregulin α1 (HRG α1) or the p38 MAPK inhibitor, SB203580. The tissue lysate array study indicated that only the level of pSer⁷⁸ in HER-2/neu positive tumors was more than 2-fold that in HER-2/neu negative tumors. Treatment of BT474 cells with HRG α1 and SB203580 indicated that Ser⁷⁸ phosphorylation was mainly regulated by the HER-2/neu-p38 MAPK pathway. Immunohistochemical staining of sections from a tissue microarray with 97 breast tumors showed that positive staining of pSer⁷⁸ significantly correlated with HER-2/neu (p = 0.004) and lymph node positivity (p = 0.026).

Conclusion

This investigation demonstrated the significant correlation of enhanced phosphorylation of the Ser⁷⁸ residue of Hsp27 with HER-2/neu and lymph node positivity in breast cancer.

Gastrointestinal fluids proteomics

Seventy million people suffer from diseases of the gastrointestinal tract annually in US, translating to US$85.5 billion in direct healthcare costs. The debilitating effects of these gastrointestinal (GI) diseases can be circumvented with good biomarkers for early detection of these disorders, which will greatly increase the success of curative treatments. GI fluids represent a potential reservoir of biomarkers for early diagnosis of various GI and systemic diseases since these fluids are the most proximal fluid bathing diseased cells. They are anticipated to have proteomes that closely reflect the ensemble of proteins secreted from the respective GI tissues. Most importantly, the disease markers present in GI fluids should be present in higher concentrations than in sera, thus offering greater sensitivity in their detection. However, proteome analysis of GI fluids can be complex mainly due to the dynamic range of protein content and the numerous PTMs of proteins in each specialized GI compartment. This review attempts to discuss the physiology of the various GI fluids, the special technical considerations required for proteome analysis of each fluid, as well as to summarize the current state of knowledge of biomarker discoveries and clinical utility of GI fluids such as salivary, gastric, pancreatic, and biliary secretions.

Peptidomic analysis of rat urine using capillary electrophoresis coupled to mass spectrometry

We have established and validated a protocol for the peptidomic analysis of rat urine using CE coupled to MS (CE-MS). In the first experiments, the reproducibility of the CE-MS set-up and of the established preparation procedure were assessed. To establish a first rat urinary peptidome map, samples were also analyzed using CE-FT-ICR. The subsequent analysis of independent samples from two different strains (WISTAR and CD) indicated strain-specific differences, which were validated in a blinded assessment. MS/MS revealed the presence of specific fragments from well-known urinary rat peptides, such as collagens, alpha-1-antitrypsin, and serum albumin. The CE-MS-based peptidomics platform may provide novel insights into body fluids of animal models, such as rat or mice. Together with peptide identification, the technology appears to be an excellent, complimentary, and non-invasive tool to analyze toxicological or other (patho)physiological effects of pharmaceutical compounds in animal models.

Early advances of α1-antitrypsin precursor using the proteomic approach in gastric juice

Evaluation of: Hsu PI, Chen CH, Hsieh CS et al.: α1-antitrypsin precursor in gastric juice is a novel biomarker for gastric cancer and ulcer. Clin. Cancer Res. 13(3), 876–883 (2007) [1] . The authors have identified the α1-antitrypsin precursor as a new protein marker of gastric cancer in gastric juice by 2D electrophoresis gel and mass spectrometric analyses. Three different pathologic classes of patients were considered with duodenal ulcer, gastric ulcer and gastric cancer and compared with healthy cases. α1-antitrypsin precursor was present, like the main peptide, in the specific band pattern, and seemed to be more expressed not only in advanced gastric cancer, but also in early forms of tumor. The study provides a fine contribution to this field of medicine, significantly correlating the α1-antrypsin precursor with gastric hypoacidity, gastric ulcer and gastric cancer. In addition, the utilization of gastric juice for biomarker recognition avoids the invasive resection of tissues. In conclusion, the research underlines, with an innovative and thorough approach, the role of the α1-antitrypsin precursor as a valid biomarker in gastric cancer and ulcers. However, it does not contribute to the advancement of research aimed at discovering the possible origin of the protein, and this could be the aim of future investigations.

Mitochondrial alterations in human gastric carcinoma cell line

We compared mitochondrial function, morphology, and proteome in the rat normal gastric cell line RGM-1 and the human gastric cancer cell line AGS. Total numbers and cross-sectional sizes of mitochondria were smaller in AGS cells. Mitochondria in AGS cells were deformed and consumed less oxygen. Confocal microscopy indicated that the mitochondrial inner membrane potential was hyperpolarized and the mitochondrial Ca(2+) concentration was elevated in AGS cells. Interestingly, two-dimensional electrophoresis proteomics on the mitochondria-enriched fraction revealed high expression of four mitochondrial proteins in AGS cells: ubiquinol-cytochrome c reductase, mitochondrial short-chain enoyl-coenzyme A hydratase-1, heat shock protein 60, and mitochondria elongation factor Tu. The results provide clues as to the mechanism of the mitochondrial changes in cancer at the protein level and may serve as potential cancer biomarkers in mitochondria.

Comprehensive analysis of proteins of pH fractionated samples using monolithic LC/MS/MS, intact MW measurement and MALDI-QIT-TOF MS

A comprehensive platform that integrates information from the protein and peptide levels by combining various MS techniques has been employed for the analysis of proteins in fully malignant human breast cancer cells. The cell lysates were subjected to chromatofocusing fractionation, followed by tryptic digestion of pH fractions for on-line monolithic RP-HPLC interfaced with linear ion trap MS analysis for rapid protein identification. This unique approach of direct analysis of pH fractions resulted in the identification of large numbers of proteins from several selected pH fractions, in which approximately 1.5 microg of each of the pH fraction digests was consumed for an analysis time of ca 50 min. In order to combine valuable information retained at the protein level with the protein identifications obtained from the peptide level information, the same pH fraction was analyzed using nonporous (NPS)-RP-HPLC/ESI-TOF MS to obtain intact protein MW measurements. In order to further validate the protein identification procedures from the fraction digest analysis, NPS-RP-HPLC separation was performed for off-line protein collection to closely examine each protein using MALDI-TOF MS and MALDI-quadrupole ion trap (QIT)-TOF MS, and excellent agreement of protein identifications was consistently observed. It was also observed that the comparison to intact MW and other MS information was particularly useful for analyzing proteins whose identifications were suggested by one sequenced peptide from fraction digest analysis.

Overexpression of CLIC1 in human gastric carcinoma and its clinicopathological significance

Gastric cancer is the second most common cancer worldwide and the fifth leading cause of cancer-related death in Taiwan. Identification of biomarkers is essential to improve patient survival. Fifty aberrantly expressed proteins were identified using 2-DE combined with MALDI TOF MS and were grouped based on their function. The overexpression of proteins was confirmed using real-time quantitative RT-PCR, Western blot, and immunohistochemical analysis. The clinicopathological correlations and prognostic significance of these aberrantly expressed proteins were evaluated to determine the novel gastric cancer biomarkers. In this study, expression of chloride intracellular channel 1 (CLIC1) is significantly up-regulated in 67.9% of gastric patients and was selected for further study. The CLIC1 expression in tumor tissues was increased by 1.95-fold (range, 0.01-6.19-fold) compared with that expressed by adjacent noncancerous mucosa. Elevated CLIC1 expression was strongly correlated with lymph node metastasis, lymphatic invasion, perineural invasion, and pathological staging. Additionally, the 5-year survival rate for the low CLIC1 expression group (n = 28; <1.72-fold) was higher than that for the high CLIC1 expression group (n = 28; >or=1.72-fold) (log rank, p = 0.0300). Experimental results indicate that overexpression of CLIC1 is a potential prognostic marker for gastric cancer.

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.

Development of efficient protein extraction methods for shotgun proteome analysis of formalin-fixed tissues

There are vast archives of formalin-fixed tissues spanning many conceivable conditions such as different diseases, time courses, and different treatment and allowing acquisition of the necessary numbers of samples to carry out biomarker discovery study. However, the conventional protein analysis approach is not applicable for the analysis of proteins in the formalin-fixed tissue because the formalin fixation process resulted in the cross-linking of proteins, and thus, intact proteins cannot be efficiently extracted. In this study, several protocols were investigated to extract proteins from formalin-fixed mouse liver tissue for shotgun proteome analysis. It was found that incubation of tissue in a lysis buffer containing 6 M guanidine hydrochloride at high temperature led to the highest protein yield and the largest number of proteins identified. The peptides and proteins identified from formalin-fixed tissue were first comprehensively compared with those identified from frozen-fresh tissue. It was found that a majority of peptides identified from fixed tissue were unmodified and proteome coverage for the analysis of fixed tissue was not obviously compromised by the formalin fixation process. Valuable proteome information could be obtained by shotgun proteome analysis of formalin-fixed tissue, which presents a new approach for disease biomarker discovery.

Quantitative proteomic and genomic profiling reveals metastasis-related protein expression patterns in gastric cancer cells

Gastric cancer is a leading cause of death worldwide, and patients have an overall 5-year survival rate of less than 10%. Using quantitative proteomic techniques together with microarray chips, we have established comprehensive proteome and transcriptome profiles of the metastatic gastric cancer TMC-1 cells and the noninvasive gastric cancer SC-M1 cell. Our qualitative protein profiling strategy offers the first comprehensive analysis of the gastric cancer cell proteome, identifying 926 and 909 proteins from SC-M1 and TMC-1 cells, respectively. Cleavable isotope-coded affinity tagging analysis allows quantitation of a total of 559 proteins (with a protein false-positive rate of <0.005), and 240 proteins were differentially expressed (>1.3-fold) between the SC-M1 and TMC-1 cells. We identified numerous proteins not previously associated with gastric cancer. Notably, a large subset of differentially expressed proteins was associated with tumor metastasis, including proteins functioning in cell-cell and cell-extracellular matrix (cell-ECM) adhesion, cell motility, proliferation, and tumor immunity. Gene expression profiling by DNA microarray revealed differential expression (of >2-fold) of about 1000 genes. The weak correlation observed between protein and mRNA profiles highlights the important complementarities of DNA microarray and proteomics approaches. These comparative data enabled us to map the disease-perturbed cell-cell and cell-ECM adhesion and Rho GTPase-mediated cytoskeletal pathways. Further validation of a subset of genes suggests the potential use of vimentin and galectin 1 as markers for metastasis. We demonstrate that combining proteomic and genomic approaches not only provides a rapid, robust, and sensitive platform to elucidate the molecular mechanisms underlying gastric cancer metastasis but also may identify candidate diagnostic markers and therapeutic targets.

Down-regulated expression of complement factor I: a potential suppressive protein for gastric cancer identified by serum proteome analysis

BACKGROUND

Screening tests are needed for gastric cancer. In order to find serologic biomarkers for gastric cancer screening, we used proteomics to search for protein biomarkers that may be detected in serum of gastric cancer patients.

METHODS

Four groups of serum samples (from 20 gastric cancer patients) included pTNM stages I to IV were compared with two control groups of serum samples. The serum samples were first chromatographed using an immunoaffinity column to selectively remove albumin and IgG. Then serum proteins separated by 2-DE and identified by MALDI-TOF/TOF-MS.

RESULTS

There were 3 proteins including complement C4-B precursor, complement factor I (CFI) precursor and haptoglobin precursor were found significantly different between the healthy and gastric cancer patients. Further validation study by Western blot showed that the detection of CFI precursor was under-expressed in gastric cancer sera compared to normal sera (p<0.05), in addition to a declining expression with the advanced pTNM stage from stage I to IV of gastric cancer patients. Area under the receiver operating characteristic (ROC) curve was 0.78 for the expression of CFI precursor (p<0.01).

CONCLUSIONS

2-DE-based serum proteome analysis may be useful in the screening of serum biomarkers for gastric cancer. CFI precursor could aid in the diagnosis and indicate the advancement of gastric cancer.

Identification of over-expressed proteins in oral squamous cell carcinoma (OSCC) patients by clinical proteomic analysis

BACKGROUND

Oral cancer is a worldwide problem. It is a universal aggressive disease in the population of smoking and drinking. The oral cancer mortality has been ranked 5th place in Taiwan in male cancer patients. A number of protein markers for oral cancer are still not applicable in large populations. Proteomic technologies provide excellent tools for rapid screening of a large number of potential biomarkers in malignant cells.

METHOD

Proteomics and real-time quantitative RT-PCR were used to analyze over-expressed proteins in 10 OSCC patients.

RESULT

Forty-one proteins were identified as commonly over-expressed in OSCC tissues. In OSCC tissues, alphaB-crystallin, tropomyosin 2, myosin light chain 1, heat shock protein 27 (HSP27), stratifin, thioredoxin-dependent peroxide reductase, flavin reductase, vimentin, rho GDP-dissociation inhibitor 2 (rho GDI-2), glutathione S-transferase Pi (GST-pi) and superoxide dismutase [Mn] (MnSOD) were significantly over-expressed (an average of 7.2, 6.0, 5.7, 4.3, 3.6, 3.4, 3.0, 3.0, 2.6, 2.5, 2.1-fold, respectively). In real-time quantitative RT-PCR analysis, the gene expressions of alphaB-crystallin, HSP27 and MnSOD were also increased in the cancer tissues, consistent with proteomic results.

CONCLUSION

The identified proteins in this experiment may be used in future studies of carcinogenesis or as diagnostic markers and therapeutic targets for OSCC.

Identification of breast cancer metastasis-associated proteins in an isogenic tumor metastasis model using two-dimensional gel electrophoresis and liquid chromatography-ion trap-mass spectrometry

To better understand the molecular mechanisms underlying breast cancer metastasis and search for potential markers for metastatic progression, we have developed a highly metastatic variant of human MDA-MB-435 breast cancer cell line through in vivo stepwise selection of pulmonary metastatic cells caused by parental MDA-MB-435 cells in the athymic mice. Comparative proteomic analysis using 2-DE and LC-IT-MS revealed that 102 protein spots were reproducibly altered more than three-fold between the selected variant and its parental counterpart. Eleven differentially expressed protein spots were identified with high confidence using SEQUEST with uninterpreted tandem mass raw data. Cathepsin D precursor, peroxiredoxin 6 (PDX6), heat shock protein 27 (HSP27), HSP60, tropomyosin 1 (TPM1), TPM2, TPM3, TPM4, 14-3-3 protein epsilon, and tumor protein D54 were up-regulated in the highly metastatic variant, whereas alpha B-crystalline (CRAB) was only detected in its parental counterpart. Differential expression was confirmed for four proteins including PDX6, CRAB, TPM4, and HSP60 by real-time quantitative PCR and Western blotting analysis in our model. Immunohistochemical analysis in 80 breast cancer donors demonstrated a significant association of TPM4 (p = 0.002), HSP60 (p = 0.001), PDX6 (p = 0.002) but not CRAB (p = 0.113) staining with the presence of lymph node metastasis. In addition, TPM4 staining was also associated with clinical stage (p = 0.000), but no significant association was found between TPM4, PDX6, CRAB, and HSP60 expression and tumor size, hormone receptor, and HER-2 status (p > 0.05). The functional implication of these identified proteins was also discussed. These proteomic data are valuable and informative for understanding breast cancer metastasis and searching for potential markers for metastatic progression.

Proteomic Profiling for Cellular Responses to Different Concentrations of N-Methyl-N‘-nitro-N-nitrosoguanidine

Alkylating agent MNNG (N-methyl-N'-nitro-N-nitrosoguanidine) can induce DNA damages which can lead to chromosomal aberrations, mutations, and cell death. Previous reports from our laboratory have found that low concentration of MNNG can induce nontargeted mutations (NTM) at undamaged bases in DNA, clustering of epidermal growth factor receptor (EGFR) and interference of EGFR mediated signaling, as well as activation of endoplasmic reticulum stress. Thus, the cellular responses to MNNG exposure are very complex, and can be triggered by signals originated from different compartments of the exposed cells. To further probe the molecular mechanisms involved in cellular responses to MNNG treatment, and to find potential biomarkers for MNNG induced stress condition, we performed proteomic analysis of whole cellular proteins from human amnion epithelial cells after exposing to MNNG at 3 different doses. More than 80 proteins were affected by MNNG treatment, and 71 proteins among them were identified using matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry. These proteins take part in a wide variety of cellular processes including regulation of transcription, metabolism, cytoskeleton organization, cell cycle, cell proliferation, signal transduction, transportation, etc. The significance of these proteins in the genesis of MNNG induced cellular defensive response and hazardous effect remains to be elucidated, the results may also give a clue for biomarker search for monitoring the exposure risk of MNNG.