Proteomics: a new approach to the study of disease

Identification of cancer-associated proteins by proteomics and downregulation of β-tropomyosin expression in colorectal adenoma and cancer

Elucidating the molecular mechanism underlying the development of adenoma, the major precursor lesion of colorectal cancer (CRC), would provide a basis for early detection, prevention as well as treatment of CRC. Using the highly sensitive 2-D DIGE method coupled with MS, we identified 24 differentially expressed proteins in adenoma tissues compared with matched normal colonic mucosa and CRC tissues. Fifteen proteins were downregulated and three proteins were upregulated in adenoma tissues when compared with individual-matched normal colonic mucosa. Five proteins were downregulated, while one protein was upregulated in adenoma tissues when compared with matched CRC tissues. A protein, β-tropomyosin (TM-β), recently suggested to be a biomarker of esophageal squamous carcinoma, was downregulated in both adenoma and CRC tissues. Additionally, the reduction in the level of TM-β in adenoma and CRC tissues was further validated by Western blotting (p<0.05) and RT-PCR (p<0.001). Our findings suggest that downregulation of TM-β is involved in the early development of CRC and that differentially expressed proteins might serve as potential biomarkers for detection of CRC.

LC-MS Based Detection of Differential Protein Expression

While several techniques are available in proteomics, LC-MS based analysis of complex protein/peptide mixtures has turned out to be a mainstream analytical technique for quantitative proteomics. Significant technical advances at both sample preparation/separation and mass spectrometry levels have revolutionized comprehensive proteome analysis. Moreover, automation and robotics for sample handling process permit multiple sampling with high throughput.For LC-MS based quantitative proteomics, sample preparation turns out to be critical step, as it can significantly influence sensitivity of downstream analysis. Several sample preparation strategies exist, including depletion of high abundant proteins or enrichment steps that facilitate protein quantification but with a compromise of focusing on a smaller subset of a proteome. While several experimental strategies have emerged, certain limitations such as physiochemical properties of a peptide/protein, protein turnover in a sample, analytical platform used for sample analysis and data processing, still imply challenges to quantitative proteomics. Other aspects that make analysis of a proteome a challenging task include dynamic nature of a proteome, need for efficient and fast analysis of protein due to its constant modifications inside a cell, concentration range of proteins that exceed dynamic range of a single analytical method, and absence of appropriate bioinformatics tools for analysis of large volume and high dimensional data.This paper gives an overview of various LC-MS methods currently used in quantitative proteomics and their potential for detecting differential protein expression. Fundamental steps such as sample preparation, LC separation, mass spectrometry, quantitative assessment and protein identification are discussed.For quantitative assessment of protein expression, both label and label free approaches are evaluated for their set of merits and demerits. While most of these methods edge on providing "relative abundance" information, absolute quantification is achieved with limitation as it caters to fewer proteins. Isotope labeling is extensively used for quantifying differentially expressed proteins, but is severely limited by successful incorporation of its heavy label. Lengthy labeling protocols restrict the number of samples that can be labeled and processed. Alternatively, label free approach appears promising as it can process many samples with any number of comparisons possible but entails reproducible experimental data for its application.

Could proteomic research deliver the next generation of treatments for pneumococcal meningitis?

Streptococcus pneumoniae is the most common bacterial cause of community-acquired meningitis worldwide. Despite optimal antibiotic therapy and supportive care, the mortality of this condition remains very high at 20–30% in the developed world and over 60% in under-resourced hospitals. In developed countries, approximately half of the survivors suffer intellectual impairment, hearing loss, or other neurological damage. There is an urgent need for more information about the mechanisms of brain damage and death in pneumococcal meningitis so that new treatments can be designed. Using proteomic techniques and bioinformatics, the protein content of cerebrospinal fluid can be examined in great detail. Animal models have added greatly to our knowledge of possible mechanisms and shown that hippocampal apoptosis and cortical necrosis are distinct mechanisms of neuronal death. The contribution of these pathways to human disease is unknown. Using proteomic techniques, neuronal death pathways could be described in CSF samples. This information could lead to the design of novel therapies to minimize brain damage and lower mortality. This minireview will summarize the known pathogenesis of meningitis, and current gaps in knowledge, that could be filled by proteomic analysis.

A vitronectin M381T polymorphism increases risk of hemangioblastoma in patients with VHL gene defect

Hemangioblastomas, highly vascular tumors, occur sporadically or associated with von Hippel-Lindau (VHL) disease. Diverse mutations in the VHL gene inactivate the VHL protein and constitute the molecular etiology of the disease. Changes in VHL gene were analyzed in patients with multiplex ligation-dependent probe amplification and single-strand conformation polymorphism analyses. We report here that other angiogenesis-related changes in vitronectin were identified with 2D electrophoresis of plasma samples and restriction fragment length polymorphisms. Our findings revealed that most patients (80.0%) with a familial VHL deletion carried the threonine (T) allele at vitronectin codon 381. Adults simultaneously carrying a VHL defect and the T allele were 5.0-fold more likely to be affected by VHL disease than were methionine/methionine (M/M) homozygotes carrying a VHL defect. Patients with sporadic hemangioblastoma, C-terminally truncated VHL protein or a large deletion in the VHL gene, and the T allele were 18.0-fold more likely to develop recurrent disease. Taken together, individuals with mutated VHL are more likely to be affected by familial or recurrent sporadic hemangioblastoma when carrying the M/T or T/T genotype at codon 381 of vitronectin.

Comparative serum proteome expression of osteonecrosis of the femoral head in adults

Osteonecrosis of the femoral head (ONFH) is a skeletal disorder characterized by ischemic deterioration, bone marrow edema and eventually femoral head collapse. The systemic regulation of ONFH in adult patients has not been examined. Serum proteomic is an innovative tool that potentially detects simultaneous expressions of serum proteins in pathological contexts. We compared the serum proteome profiles of 11 adult patients with ONFH (3 females and 8 males) and 11 healthy volunteers (3 females and 8 males). The proteins in the aliquots of sera were subjected to isoelectric focusing, two-dimensional gel electrophoresis and silver staining. The protein spots were matched and quantified using an imaging analysis system. The differentially expressed protein spots were subjected to in-gel trypsin digestion. The peptide mass fingerprints were identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF/TOF) and a bioinformation search. We found that ONFH patients showed significantly higher abundances of kininogen 1 variant, complement factor C3 precursor, and complement factor H and lower levels of antithrombin III chain B, apolipoprotein A--IV precursor, and gelsolin isoform alpha precursor. These proteins of interest were reported to modulate thrombotic/fibrinolytic reactions, oxidative stress, vessel injury, tissue necrosis or cell apoptosis in several tissue types under pathological contexts. Taken together, the occurrence of ONFH was associated with various serum protein expressions. Our high--throughput serum proteomic findings indicated that multiple pathological reactions presumably occurred in ONFH.

Potential artefacts in proteome analysis of plasma of Gaucher patients due to protease abnormalities

The plasma proteome of type I Gaucher disease patients was investigated by 2D gel electrophoresis (2DGE). Using the classical procedure with 8 M urea treated plasma, several high molecular weight proteins were absent from Gaucher plasma specimens, while additional low molecular weight proteins were visible. The latter were identified as proteolytic degradation products. Adding small amounts of patient plasma to control plasma gave extensive protein breakdown. The presence of 2.2 M thiourea/7.7 M urea in the rehydration solution totally prevented breakdown. In the 'urea only' solution, protease(s) uniquely present in Gaucher plasma, appear to be still active towards other denatured plasma proteins at low pH. Therapy of patients results in gradual disappearance of proteolytic capacity from plasma specimens, indicating it to be related to the presence of Gaucher storage cells. The proteolytic activity could be partly removed from Gaucher plasma samples by Concanavalin A, suggesting that glycoproteins are involved. Reduction of proteolysis by Pepstatin A and Leupeptin implies that cathepsins, proteases known to be overproduced by Gaucher storage cells, are involved. In conclusion, 2DGE Gaucher plasma proteomes should be interpreted cautiously given the abnormal high levels of proteases associated with this disorder.

Biomarker identification in human pancreatic cancer sera

OBJECTIVE

The aim of this study is to identify biomarkers in sera of pancreatic cancer patients using mass spectrometry (MS) approaches.

METHODS

Sera from patients diagnosed with pancreatic adenocarcinoma and sera from normal volunteers were subjected to gel electrophoresis to resolve and quantify differences in protein levels. Protein bands that differed quantitatively were digested with trypsin, and peptides were identified by electrospray ionization (ESI) ion-trap tandem MS. Mass spectra were also collected directly from pancreatic cancer sera as well as healthy control sera using ESI-MS.

RESULTS

Three large-mass proteins were found to be elevated in pancreatic cancer sera versus normal sera, alpha-2 macroglobulin, ceruloplasmin, and complement 3C. Complement 3C is a major regulator of inflammatory responses. The ESI-MS of human pancreatic cancer sera versus normal sera revealed greater heterogeneity in cancer sera than control sera, especially in the low-mass region. Bootstrapping statistical analysis identified 20 low-mass serum peaks that correlated with control sera and 20 different peaks that correlated with pancreatic cancer sera.

CONCLUSIONS

The fact that inflammation-sensitive proteins were identified as increased in pancreatic cancer sera supports the hypothesis that inflammatory-driven processes are involved in pancreatic carcinogenesis. Liquid ESI-MS analyses of sera hold promise for future pancreatic cancer blood tests as well as for understanding mechanisms of pancreatic carcinogenesis. The variability observed between the low-mass regions of normal versus pancreatic cancer spectra may aid in diagnosis and therapy.

Elucidation of the molecular mechanisms of preeclampsia using proteomic technologies

Preeclampsia, a disease of pregnancy, is a multisystem disorder associated with elevated maternal blood pressure, proteinurea, oedema, and fetal abnormalities. It is a major cause of mortality, morbidity, perinatal death, and premature delivery. Despite active research in the past decade, there is yet no definitive cure for preeclampsia. The disease has been treated symptomatically with antihypertensives, antieclamptics, bed rest, and a whole gamut of isolated therapies. In an attempt to understand the molecular basis of this disease and many other fatal diseases including cancer and heart disease, the scientific community has been turning to understanding the genome and more lately the "proteome". Proteomics enables researchers to identify all proteins expressed in a cell or organ and detect any PTM in the protein expression patterns. Deciphering the placental proteome and studying the differences in protein expression patterns in the normal as against the preeclamptic proteome might possibly in future lead to early detection and therapeutic targeting of preeclampsia.

Identification of mitochondrial FoF1-ATP synthase involved in liver metastasis of colorectal cancer

Liver metastasis is a major cause of poor survival of colorectal cancer patients. In order to identify the proteins associated with liver metastasis in colorectal cancer, we carried out two-dimensional gel electrophoresis-based comparative proteomic analysis of normal colon mucosa, primary colon cancer tissue and corresponding metastatic tumor tissue in liver. The proteins identified were further validated by immunohistochemical analysis of 67 quadruplet samples of normal colon primary colorectal cancer and normal liver-synchronous liver metastasis, and 251 colorectal cancers as well as in vitro invasion assay of the human colon cancer cell line, SNU-81. From proteomic assessment, the mitochondrial FoF1-ATP synthase (ATP synthase) alpha-subunit was identified as a protein that is upregulated in liver metastasis compared with the primary tumor. Immunohistochemical analyses confirmed a significant increase in the expression of ATP synthase alpha- and d-subunits in synchronous liver metastasis compared with primary tumor and normal mucosa, respectively. ATP synthase alpha- and d-subunits were overexpressed in 197 (78.5%) and 190 (75.7%), respectively, of the 251 colorectal cancers. The alpha- and d-subunits were significantly associated with liver metastasis (P < 0.05) as well as low histological grade (P < 0.0001). The d-subunit also correlated with venous invasion (P = 0.026) and distant metastasis (P = 0.032). In stage III cancers, d-subunit expression was independently associated with poor survival (P = 0.017). Furthermore, transfection of small interfering RNA targeted to ATP synthase alpha- and d-subunits resulted in decreased in vitro invasiveness of the human colon cancer cell line. Our overall findings demonstrate that increased ATP synthase is associated with liver metastasis of colorectal cancer.

Identification of differentially secreted biomarkers using LC-MS/MS in isogenic cell lines representing a progression of breast cancer

Proteins secreted (the secretome) from cancer cells are potentially useful as biomarkers of the disease. Using LC-MS/MS, the secreted proteomes from a series of isogenic breast cancer cell lines varying in aggressiveness were analyzed by mass spectrometry: nontumorigenic MCF10A, premalignant/tumorigenic MCF10AT, tumorigenic/locally invasive MCF10 DCIS.com, and tumorigenic/metastatic MCF 10CA cl. D. Proteomes were obtained from conditioned serum-free media, partially fractionated using a small reverse phase C2 column, and digested with trypsin for analysis by LC-MS/MS, using a method previously shown to give highly enriched secreted proteomes (Mbeunkui et al. J. Proteome Res. 2006, 5, 899-906). The search files produced from five analyses (three separate preparations) were combined for database searching (Mascot) which produced a list of over 250 proteins from each cell line. The aim was to discover highly secreted proteins which changed significantly in abundance corresponding with aggressiveness. The most apparent changes were observed for alpha-1-antichymotrypsin and galectin-3-binding protein which were highly secreted proteins from MCF10 DCIS.com and MCF10CA cl. D, yet undetected in the MCF10A and MCF10AT cell lines. Other proteins showing increasing abundance in the more aggressive cell lines included alpha-1-antitrypsin, cathepsin D, and lysyl oxidase. The S100 proteins, often associated with metastasis, showed variable changes in abundance. While the cytosolic proteins were low (e.g., actin and tubulin), there was significant secretion of proteins often associated with the cytoplasm. These proteins were all predicted as products of nonclassical secretion (SecretomeP, Center for Biological Sequence Analysis). The LC-MS/MS results were verified for five selected proteins by western blot analysis, and the relevance of other significant proteins is discussed. Comparisons with two other aggressive breast cancer cell lines are included. The protein with consistent association with aggressiveness in all lines, and in unrelated cancer cells, was the galectin-3-binding protein which has been associated with breast, prostate, and colon cancer earlier, supporting the approach and findings. This analysis of an isogenic series of cell lines suggests the potential usefulness of the secretome for identifying prospective markers for the early detection and aggressiveness/progression of cancer.

Identification of differentially expressed proteins in experimental autoimmune encephalomyelitis (EAE) by proteomic analysis of the spinal cord

The present study used isobaric tags for relative and absolute quantitation (iTRAQ) to identify novel targets in experimental autoimmune encephalomyelitis (EAE), an animal model of multiple sclerosis. The expression of 41 proteins was significantly altered in the inflamed spinal cord. Twenty of these are implicated in EAE for the first time and many have previously been shown to play a role in antigen processing, inflammation, neuroprotection, or neurodegeneration.

Proteomics identifies enhanced expression of stefin A in neonatal murine skin compared with adults: functional implications

BACKGROUND

Skin develops through a process of epidermal proliferation, maturation, and remodelling of the epidermis and dermis. This period also involves the maturation of the skin immune system, such that antigen applied though the skin of a neonatal mouse always results in immunosuppression, whereas in adults, immunity will occur.

OBJECTIVES

Using proteomics, to identify proteins uniquely involved in the development of the skin and skin immune system.

METHODS

Proteins were extracted from whole skin of mice aged 4 and 21 days, and separated using two-dimensional electrophoresis.

RESULTS

Of the 25 proteins that were sequenced by peptide mass fingerprinting with matrix-assisted laser desorption/ionization-time of flight-mass spectrometry, three were known markers of keratinocyte differentiation and proliferation. These were cyclophilin A, epidermal fatty acid binding protein 5 and stefin A. Of interest were the two isoforms of stefin A, an intracellular protease inhibitor, found in neonatal skin. The strong expression of stefin A in neonates was confirmed by immunohistochemical analysis, suggesting an important role in the development of the epidermis. Additionally, Western blotting identified two larger isoforms in adult skin, revealing a change in the stefin A during development.

CONCLUSIONS

We propose that stefin A is involved in development of the skin, that development of the skin and of immune function is linked, and that stefin A has an important function in neonatal skin and potentially the neonatal immune response.

Proteomics in neurosciences

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

Leveraging protein purification strategies in proteomics

The proteomic studies, although, tend to be analytical in nature, yet many strategies of preparative protein purification can be usefully employed in such studies. This review points out the importance of purification techniques which are capable of dealing with samples which are suspensions rather than clear solution, e.g. aqueous two phase partitioning, three phase partitioning, expanded bed chromatography, etc. The review also outlines the potential of non-chromatographic techniques in dealing with fractionation of proteomes. Separation protocols which can deal with post-translationally modified (PTM) proteins are also considered.

Identification of potential markers for the detection of pancreatic cancer through comparative serum protein expression profiling

OBJECTIVE

Early detection is the only promising approach to significantly improve the survival of patients with pancreatic cancer (PCa). Noninvasive tools for the diagnosis, prognosis, and monitoring of this disease are of urgent need. The purpose of this study was to identify and validate new biomarkers in PCa patient serum samples.

METHODS

Surface-enhanced laser desorption/ionization time-of-flight mass spectrometry has been applied to analyze serum protein alterations associated with PCa and to identify sets of potential biomarkers indicative for this disease. A cohort of 96 serum samples from patients undergoing PCa surgery was compared with sera from 96 healthy volunteers as controls. The sera were fractionated by anion exchange chromatography, and 3 of 6 fractions were analyzed onto 2 different chromatographic arrays.

RESULTS

Data analysis revealed 24 differentially expressed protein peaks (P < 0.001), of which 21 were downregulated in the PCa samples. The best single marker can predict 92% of the controls and 89% of the cancer samples correctly. In addition, multivariate pattern analysis was performed. The best pattern model using a set of 3 markers was obtained using fraction 6 on immobilized metal affinity capture, loaded with Cu-Cu arrays. With this pattern model, a sensitivity of 100% and a specificity of 98% for the training data set and a sensitivity of 83% and specificity of 77% for the test data set were achieved with the PCa group set as true positive. Several of protein peaks, including the best single marker at 17.27 kd and other proteins from the pattern models, were purified and identified by peptide mapping and postsource decay-matrix-assisted laser desorption ionization-time-of-flight mass spectrometry. Apolipoprotein A-II, transthyretin, and apolipoprotein A-I were identified as markers, and these identified proteins were decreased at least 2-fold in PCa serum when compared with the control group.

CONCLUSIONS

PCa is associated with a specific decrease of distinct serum proteins, which allows a reliable differentiation between pancreatic cancer and healthy controls.

Gastrokine 1 expression in patients with and without Helicobacter pylori infection

BACKGROUND

To understand the molecular changes underlying Helicobacter pylori-related gastric diseases is mandatory to prevent gastric cancer. Proteomic technology is providing a rapid expansion of the basic knowledge, particularly in the discovery of new biomarkers involved in the tumourigenesis.

AIM

To characterise changes in protein expression level of the gastric mucosa in H. pylori-infected patients.

METHODS

The population enrolled comprised 41 dyspeptic patients. Proteins extracted from gastric mucosal specimens were analysed by 2-dimensional electrophoresis, sequenced by MALDI-TOF and identified by Edman's degradation.

RESULTS

Twenty-one out of 41 patients had H. pylori infection of whom 17 had anti-CagA IgG antibodies. Several proteins were identified, of which Rho guanosine diphosphatase dissociation inhibitor alpha and heat shock protein 27 increased and glutathione transferase and antrum mucosa protein-18 decreased in H. pylori-positive in respect to H. pylori-negative patients. Interestingly, antrum mucosa protein-18, currently referred as gastrokine-1, showed two isoforms differing in the first N-terminal amino acid residue. Both gastrokine-1 isoforms were observed in the H. pylori-negative group whereas a lower expression or even absence of the gastrokine-1 basic isoform was found in a subgroup (7/21) of H. pylori-positive patients with moderate-severe gastritis.

CONCLUSION

Our study demonstrated the presence of gastrokine-1 isoforms of which the basic isoform was reduced in a subset of patients with H. pylori infection.

Proteomic analysis of cancer tissues: shedding light on carcinogenesis and possible biomarkers

Lung, gastric, colorectal, pancreatic, and esophageal cancers, as well as hepatocellular carcinoma (HCC), were the six most common and highly fatal cancers for Japanese men in Japan in 2003, while for women uterine cervical cancer could also be added to this list. To identify diagnostic or therapeutic biomarkers for these cancers, investigators are nowadays performing proteomic analyses of cancer tissues and cells, and revealing a large number of molecules which are diagnostic, prognostic and informative of carcinogenesis. From reports of proteomic analyses of cancerous tissues and noncancerous tissues sampled from HCC, and pancreatic, esophageal, gastric, colorectal, lung and uterine cervical cancers, we classified the proteins into digestive enzymes, growth factors, cell adhesion molecules, calcium-binding proteins, proteases, protease inhibitors, transporter proteins, structural molecules, apoptosis inhibitor, molecular chaperone, as well as proteins related to cell growth, cell differentiation, cell transformation, tumor invasion, carcinogen metabolism, and others. The aim of this study was to understand carcinogenesis of major cancers from a proteomics perspective using samples from cancer patients, and to elucidate their tumor biomarkers.

Comparative proteomics analysis to annexin B1 DNA and protein vaccination in mice

DNA vaccines have been widely reported to elicit both effective humoral and cellular immune responses, but the mechanisms of antigen processing and presentation in DNA immunization is still ambiguous. Aiming to molecular mechanisms involved in DNA immunization, comparative serum proteomics was introduced to discover differentially expressed proteins after different immunizations. Using two-dimensional electrophoresis and matrix-assisted laser desorption ionisation-time-of-flight mass spectrometry, 23 three-fold or greater up-regulated proteins were separated and identified, including 14 from ANXB1 DNA immunized mice and 9 from annexin B1 protein immunized mice. The histocompatibility class I molecule H2-Q10 (HA10_MOUSE) and proteasome activator PA28 alpha-subunit (PSME1_MOUSE) were found up-regulated in ANXB1 DNA immunized mice, which may contribute to the augmented activation of T lymphocytes. These proteins may serve as potential surrogate markers of successful vaccination and provide research targets for molecular mechanisms of vaccinology.

Protein disulfide isomerase expression is related to the invasive properties of malignant glioma

By serial transplantation of human glioblastoma biopsies into the brain of immunodeficient nude rats, two different tumor phenotypes were obtained. Initially, the transplanted xenografts displayed a highly invasive phenotype that showed no signs of angiogenesis. By serial transplantation in animals, the tumors changed to a less invasive, predominantly angiogenic phenotype. To identify novel proteins related to the invasive phenotype, the xenografts were analyzed using a global proteomics approach. One of the identified proteins was protein disulfide isomerase (PDI) A6 precursor. PDI is a chaperone protein that mediates integrin-dependent cell adhesion. It is both present in the cytosol and at the cell surface. We show that PDI is strongly expressed on invasive glioma cells, in both xenografts and at the invasive front of human glioblastomas. Using an in vitro migration assay, we also show that PDI is expressed on migrating glioma cells. To determine the functional significance of PDI in cell migration, we tested the effect of a PDI inhibitor, bacitracin, and a PDI monoclonal antibody on glioma cell migration and invasion in vitro. Both tumor spheroids derived from human glioblastoma xenografts in nude rat brain and cell line spheroids were used. The PDI antibody, as well as bacitracin, inhibited tumor cell migration and invasion. The anti-invasive effect of bacitracin was reversible after withdrawal of the inhibitor, indicating a specific, nontoxic effect. In conclusion, using a global proteomics approach, PDI was identified to play an important role in glioma cell invasion, and its action was effectively inhibited by bacitracin.

Biomarkers in cancer screening, research and detection: present and future: a review

Biomarkers provide a powerful and dynamic approach to understanding the spectrum of malignancies with applications in observational and analytic epidemiology, randomized clinical trials, screening, diagnosis and prognosis. Defined as alterations in the constituents of tissues or body fluids, these markers offer a means for homogeneous classification of a disease and risk factor, and they can extend one's basic information about the underlying pathogenesis of disease. The goals in cancer research include finding biomarkers that can be used for the early detection of cancers, design individual therapies, and to identify underlying processes involved in the disease. Because so many myriad processes are involved in the diseased states, the goal is similar to 'finding a needle in a haystack'. However, the development of many -omic technologies, such as genomics and proteomics, has allowed us to monitor a large number of key cellular pathways simultaneously. This has enabled the identification of biomarkers and signalling molecules associated with cell growth, cell death and cellular metabolism. These are also facilitating in monitoring the functional disturbance, molecular and cellular damage, and damage response. This brief review describes the development of biomarkers in cancer research and detection with emphasis on different proteomic tools for the identification and discovery of new biomarkers, different clinical assays to detect various biomarkers in different specimens, role of biomarkers in cancer screening and last but not the least, the challenges in this direction of cancer research.

Current status and prospects of clinical proteomics studies on detection of colorectal cancer: Hopes and fears

Colorectal adenocarcinoma (CRC) is the third most common type of cancer and the fourth most frequent cause of death due to cancer worldwide. Given the natural history of CRC, early diagnosis appears to be the most appropriate tool to reduce disease-related mortality. A field of recent interest is clinical proteomics, which was reported to lead to high sensitivity and specificities for early detection of several solid tumors. This emerging field uses mass spectrometry-based protein profiles/patterns of easy accessible body fluids to distinguish cancer from non-cancer patients. These discrepancies may be a result of: (1) proteins being abnormally produced or shed and added to the serum proteome, (2) proteins clipped or modified as a consequence of the disease process, or (3) proteins subtracted from the proteome owing to disease-related proteolytic degradation pathways. Therefore, protein pattern diagnostics would provide easy and reliable tools for detection of cancer. This paper focuses on the current status of clinical proteomics research in oncology and in colorectal cancer especially, and will reflect on pitfalls and fears in this relatively new area of clinical medicine, which are reproducibility issues and pre-analytical factors, statistical issues, and identification and nature of discriminating proteins/peptides.

Proteomics of the human brain: sub-proteomes might hold the key to handle brain complexity

Proteomics is a promising approach, which provides information about the expression of proteins and increasingly finds application in life science and disease research. Meanwhile, proteomics has proven to be applicable even on post mortem human brain tissue and has opened a new area in neuroproteomics. Thereby, neuroproteomics is usually employed to generate large protein profiles of brain tissue, which mostly reflect the expression of highly abundant proteins. As a complementary approach, the focus on sub-proteomes would enhance more specific insight into brain function. Sub-proteomes are accessible via several strategies, including affinity pull-down approaches, immunoprecipitation or subcellular fractionation. The extraordinary potential of subcellular proteomics to reveal even minute differences in the protein constitution of related cellular organelles is exemplified by a recent global description of neuromelanin granules from the human brain, which could be identified as pigmented lysosome-related organelles.

Increased expression and phosphorylation of liver glutamine synthetase in well-differentiated hepatocellular carcinoma tissues from patients infected with hepatitis C virus

Hepatocellular carcinoma (HCC) is one of the most common fatal cancers, and chronic infection with hepatitis C virus (HCV) is thought to be one of the main causes in Japan. To identify diagnostic or therapeutic biomarkers for HCC associated with HCV (HCV-HCC), we tried to elucidate the factors related to the products from cancerous tissues of HCV-infected patients. From proteomic differential display analysis of liver tissue samples from HCV-HCC cancerous tissues and corresponding non-cancerous tissues from patients, three protein spots of the same molecular mass (42 kDa), whose expression increased in well-differentiated cancerous tissues, were detected. Although their pI were different, they were identified as glutamine synthetase (GS) by PMF with MALDI-TOF MS and by Western blotting using anti-GS specific mAb. Immunohistochemical analysis showed that tumor tissue consists of two parts, GS-positive cell and GS-negative cell regions, suggesting that GS-producing cells grew in the tumor tissue as a nodule in nodules. The tryptic peptides of the most acidic GS isoform lost the signal of 899.5 Da, corresponding a peptide of SASIRIPR, and gained a signal of 1059.5 Da, which was submitted to PSD analysis. PSD analysis showed the neutral loss by elimination of two phosphate groups, supposed to be on serine residues of the 899.5-Da peptide, from serine 320 to arginine 327 in GS. PMF followed by PSD analysis is thought to be useful for the determination of phosphorylation sites of proteins showing molecular heterogeneity.

Ubiquitous mitochondrial creatine kinase downregulated in oral squamous cell carcinoma

In this study, we performed two-dimensional electrophoresis (2-DE) and matrix-assisted laser desorption/ionisation time of fly mass spectrometry to identify the protein(s) associated with the development of oral squamous cell carcinomas (OSCCs) by comparing patterns of OSCC-derived cell lines with normal oral keratinocytes (NOKs), and found that downregulation of ubiquitous mitochondrial creatine kinase (CKMT1) could be a good candidate. Decreased levels of CKMT1 mRNA and protein were detected in all OSCC-derived cell lines examined (n=9) when compared to those in primary normal oral keratinocytes. Although no sequence variation in the coding region of the CKMT1 gene with the exception of a nonsense mutation in exon 8 was identified in these cell lines, we found a frequent hypermethylation in the CpG island region. CKMT1 expression was restored by experimental demethylation. In addition, when we transfected CKMT1 into the cell lines, they showed an apoptotic phenotype but no invasiveness. In clinical samples, high frequencies of CKMT1 downregulation were detected by immunohistochemistry (19 of 52 (37%)) and quantitative real-time RT-PCR (21 of 50 (42%)). Furthermore, the CKMT1 expression status was significantly correlated with tumour differentiation (P<0.0001). These results suggest that the CKMT1 gene is frequently inactivated during oral carcinogenesis and that an epigenetic mechanism may regulate loss of expression, which may lead to block apoptosis.

A sequence alignment-independent method for protein classification

Annotation of the rapidly accumulating body of sequence data relies heavily on the detection of remote homologues and functional motifs in protein families. The most popular methods rely on sequence alignment. These include programs that use a scoring matrix to compare the probability of a potential alignment with random chance and programs that use curated multiple alignments to train profile hidden Markov models (HMMs). Related approaches depend on bootstrapping multiple alignments from a single sequence. However, alignment-based programs have limitations. They make the assumption that contiguity is conserved between homologous segments, which may not be true in genetic recombination or horizontal transfer. Alignments also become ambiguous when sequence similarity drops below 40%. This has kindled interest in classification methods that do not rely on alignment. An approach to classification without alignment based on the distribution of contiguous sequences of four amino acids (4-grams) was developed. Interest in 4-grams stemmed from the observation that almost all theoretically possible 4-grams (20(4)) occur in natural sequences and the majority of 4-grams are uniformly distributed. This implies that the probability of finding identical 4-grams by random chance in unrelated sequences is low. A Bayesian probabilistic model was developed to test this hypothesis. For each protein family in Pfam-A and PIR-PSD, a feature vector called a probe was constructed from the set of 4-grams that best characterised the family. In rigorous jackknife tests, unknown sequences from Pfam-A and PIR-PSD were compared with the probes for each family. A classification result was deemed a true positive if the probe match with the highest probability was in first place in a rank-ordered list. This was achieved in 70% of cases. Analysis of false positives suggested that the precision might approach 85% if selected families were clustered into subsets. Case studies indicated that the 4-grams in common between an unknown and the best matching probe correlated with functional motifs from PRINTS. The results showed that remote homologues and functional motifs could be identified from an analysis of 4-gram patterns.

Investigation of early protein changes in the urinary bladder following partial bladder outlet obstruction by proteomic approach

We investigated the pathophysiological mechanism by proteomic approach as a possible tool to detect the marker proteins to develop lower urinary tract symptoms following bladder outlet obstruction (BOO). Rats were randomized into 3 groups; control, sham operation and BOO groups. BOO group was divided into 1, 3, and 5 day-group. Conventional proteomics was performed with high resolution 2-D gel electrophoresis followed by computational image analysis and protein identification using mass spectrometry using rat urinary bladders. A comparison of bladder of BOO group with control bladder showed that three proteins of optineurin, thioredoxin and preprohaptoglobin were over-expressed in the bladder of BOO group. In addition, four proteins, such as peroxiredoxin 2, transgelin, hippocampal cholinergic neurostimulating peptide (HCNP) and beta-galactoside-binding lectin, were under-expressed in the bladder of BOO group. These data supported that downregulation of HCNP might make detrusor muscle be supersensitive to acetylcholine, up-regulation of optineurin means the protection of nerve injury, and down-regulation of transgelin means the decreased contractility of detrusor muscle. Beside these proteins, other proteins are related to oxidative stress or have a nonspecific function in this study. However more information is needed in human bladder tissue for clinical usage.

Preliminary study on proteomics of gastric carcinoma and its clinical significance

AIM: To explore the preliminary identification of serum protein pattern models that may be novel potential biomarkers in the detection of gastric cancer.

METHODS: A total of 130 serum samples, including 70 from patients with gastric cancer and 60 from healthy adults, were detected by surface-enhanced laser desorption and ionization time-of-flight mass spectrometry (SELDI-TOF-MS). The data of spectra were analyzed by Biomarker Patterns Software (BPS). Thirty serum samples of gastric cancer patients and 30 serum samples of healthy adults were grouped into the training group to build models, and the other 70 samples were used to test and evaluate the models. The samples of the test group were judged only with their peaks’ height and were separated into cancer group or healthy control group by BPS automatically and the judgments were checked with the histopathologic diagnosis of the samples.

RESULTS: Sixteen mass peaks were found to be potential biomarkers with a significant level of P<0.01. Among them, nine mass peaks showed increased expression in patients with gastric cancer. Analyzed by BPS, two peaks were chosen to build the model for gastric cancer detection. The sensitivity, specificity, and accuracy of the model were 90%, 36/40, 86.7%, 26/30, and 88.6%, 62/70, respectively, which were greatly higher than those of clinically used serum biomarkers CEA (carcinoembryonic antigen), CA19-9 and CA72-4. Stage I/II gastric cancer samples of the test group were all judged correctly.

CONCLUSION: The novel biomarkers in serum and the established model could be potentially used in the detection of gastric cancer. However, large-scale studies should be carried on to further explore the clinical impact on the model.

Proteomic approach to identify changes in protein expression modified by 17β-oestradiol in bovine vascular smooth muscle cells

The aim of the present study was to use proteomics to analyse modifications in the level of expression of different proteins in BVSMCs (bovine vascular smooth muscle cells) incubated in the absence and presence of 17β-oestradiol. By using two-dimensional electrophoresis with a pH range of 4–7, we identified several areas on the gels in which the level of expression of proteins were different between control BVSMCs and cells incubated for 24 h with 17β-oestradiol. Changes in several isoforms of α-enolase, HSP60 (heat-shock protein 60), vimentin and PDI (protein disulphide-isomerase) were observed in BVSMCs. The expression of α-enolase isoform 1 was enhanced after 17β-oestradiol treatment. The expression of HSP60 isoform 3, vimentin isoforms 2 and 3 and caldesmon was reduced by 17β-oestradiol. Finally, the expression of PDI isoforms was reduced by 17β-oestradiol. In summary, 17β-oestradiol modified the expression of isoforms of proteins associated with smooth muscle cell proliferation (α-enolase, vimentin and HSP-60), cell contraction (vimentin and caldesmon) and cell redox modulation (PDI). These findings confirm that 17β-oestradiol may modulate a wide range of signalling pathways in vascular smooth muscle cells.

Studies on substantially increased proteins in follicular fluid of bovine ovarian follicular cysts using 2-D PAGE and MALDI-TOF MS

BACKGROUND

The objective of this study was to identify substantially increased proteins in bovine cystic follicular fluid (FF) in order to clarify the pathology and etiology of bovine ovarian follicular cysts (BOFC).

METHODS

Proteins in normal and cystic FF samples were subjected to two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) and were compared using silver stained gel images with PDQuest image analysis software. Peptides from these increased spots were analyzed by matrix assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), and were identified based on the NCBI database by a peptide mass fingerprinting method.

RESULTS

Comparative proteomic analysis showed 8 increased protein spots present in cystic FF. MS analysis and database searching revealed that the increased proteins in cystic FF were bovine mitochondrial f1-atpase (BMFA), erythroid associated factor (EAF), methionine synthase (MeS), VEGF-receptor, glyceraldehydes 3-phosphate dehydrogenase (GAPDH), heat shock protein 70 (HSP70), beta-lactoglobulin (BLG) and succinate dehydrogenase Ip subunit (SD).

CONCLUSION

Our results suggest that these proteins are overexpressed in BOFC, and that they may play important roles in the pathogenesis of BOFC. Furthermore, these proteins in the FF could be useful biomarkers for BOFC.

Diagnosis of pancreatic cancer using serum proteomic profiling

In the United States, mortality rates from pancreatic cancer (PCa) have not changed significantly over the past 50 years. This is due, in part, to the lack of early detection methods for this particularly aggressive form of cancer. The objective of this study was to use high-throughput protein profiling technology to identify biomarkers in the serum proteome for the early detection of resectable PCa. Using surface-enhanced laser desorption/ionization mass spectrometry, protein profiles were generated from sera of 49 PCa patients and 54 unaffected individuals after fractionation on an anion exchange resin. The samples were randomly divided into a training set (69 samples) and test set (34 samples), and two multivariate analysis procedures, classification and regression tree and logistic regression, were used to develop classification models from these spectral data that could distinguish PCa from control serum samples. In the test set, both models correctly classified all of the PCa patient serum samples (100% sensitivity). Using the decision tree algorithm, a specificity of 93.5% was obtained, whereas the logistic regression model produced a specificity of 100%. These results suggest that high-throughput proteomics profiling has the capacity to provide new biomarkers for the early detection and diagnosis of PCa.

LigScore: a novel scoring function for predicting binding affinities

We present two new empirical scoring functions, LigScore1 and LigScore2, that attempt to accurately predict the binding affinity between ligand molecules and their protein receptors. The LigScore functions consist of three distinct terms that describe the van der Waals interaction, the polar attraction between the ligand and protein, and the desolvation penalty attributed to the binding of the polar ligand atoms to the protein and vice versa. Utilizing a regression approach on a data set of 118 protein-ligand complexes we have obtained a linear equation, LigScore2, using these three descriptors. LigScore2 has good predictability with regard to experimental pKi values yielding a correlation coefficient, r2), of 0.75 and a standard deviation of 1.04 over the training data set, which consists of a diverse set of proteins that span more than seven protein families.

Proteomic analysis of plasma from patients during an acute coronary syndrome

OBJECTIVES

The aim of this study was to analyze modifications in the plasma protein map during an acute coronary syndrome (ACS) using proteomics.

BACKGROUND

Proteomics is a new technology that allows the detection and identification of several proteins at a given time in a sample.

METHODS

Plasma from 19 patients, 11 with acute myocardial infarction (AMI) and 8 with unstable angina (UA), was investigated. The control group included nine age-matched volunteers.

RESULTS

In two-dimensional electrophoresis using a pH range of 4 to 7, constant differences were found in at least four different areas within the plasma protein map. In area 1, we identified the presence of seven alpha(1)-antitrypsin (AAT) isoforms in plasma from control subjects. alpha(1)-antitrypsin isoform 1 was undetectable in plasma from UA and AMI patients. The AAT isoforms 5, 6, and 7 were reduced in plasma from AMI patients when compared with UA patients. Three fibrinogen gamma chain isoforms were identified in area 2. Fibrinogen gamma chain isoforms 1 and 2 were increased in AMI patients with respect to UA patients. Five apolipoprotein A-I isoforms were identified in area 3. All of them were reduced in plasma from AMI patients with respect to UA patients. In area 4, the gamma-immunoglobulin heavy chains were detected and were found increased in plasma from ACS patients.

CONCLUSIONS

Plasma proteomic analysis makes it possible to develop a map of the protein isoforms that are expressed in plasma during an ACS.

Data mining techniques for cancer detection using serum proteomic profiling

OBJECTIVE

Pathological changes in an organ or tissue may be reflected in proteomic patterns in serum. It is possible that unique serum proteomic patterns could be used to discriminate cancer samples from non-cancer ones. Due to the complexity of proteomic profiling, a higher order analysis such as data mining is needed to uncover the differences in complex proteomic patterns. The objectives of this paper are (1) to briefly review the application of data mining techniques in proteomics for cancer detection/diagnosis; (2) to explore a novel analytic method with different feature selection methods; (3) to compare the results obtained on different datasets and that reported by Petricoin et al. in terms of detection performance and selected proteomic patterns.

METHODS AND MATERIAL

Three serum SELDI MS data sets were used in this research to identify serum proteomic patterns that distinguish the serum of ovarian cancer cases from non-cancer controls. A support vector machine-based method is applied in this study, in which statistical testing and genetic algorithm-based methods are used for feature selection respectively. Leave-one-out cross validation with receiver operating characteristic (ROC) curve is used for evaluation and comparison of cancer detection performance.

RESULTS AND CONCLUSIONS

The results showed that (1) data mining techniques can be successfully applied to ovarian cancer detection with a reasonably high performance; (2) the classification using features selected by the genetic algorithm consistently outperformed those selected by statistical testing in terms of accuracy and robustness; (3) the discriminatory features (proteomic patterns) can be very different from one selection method to another. In other words, the pattern selection and its classification efficiency are highly classifier dependent. Therefore, when using data mining techniques, the discrimination of cancer from normal does not depend solely upon the identity and origination of cancer-related proteins.

Proteomic analysis of dunning prostate cancer cell lines with variable metastatic potential using SELDI-TOF

BACKGROUND

Surface enhanced laser desorption and ionization-time-of-flight (SELDI-TOF) is an evolving proteomic technology for improving biomarker discovery that allows for rapid and sensitive analysis of complex protein mixtures generated from body fluids, cells, and/or tissues. SELDI--based profiling identifies unique, differentially expressed proteins relating to specific cancer-related disease states. We utilized SELDI-TOF following pre-processing with molecular separation and chemical fractionation of cell membrane extracts from three Dunning rat prostate cancer cell lines of varying metastatic potential to search novel proteins that are differentially expressed.

METHODS

Dunning rat cell sublines of variable (%) metastatic potential; G (0%), AT-1 (20%), and Mat-Ly-Lu (100%) were cultured in two different laboratories. Cell lysis was performed in a homogenation buffer (320 mM sucrose/50 mM Tris/0.5 mM PSMF) using Dounce homogenation. After centrifugation, the membrane pellet was washed 2x and then solublized in 2% CHAPS/8 M urea. This sample was further processed using positive pressure molecular ultrafiltration at 30 kDa or precipitation with 50% ammonium sulfate. Next, each sample was applied to an IMAC3-Ni ProteinChip (Ciphergen Biosystems, Freemont, CA) and analyzed using Ciphergen's Protein Biology System with protein peak analysis software.

RESULTS

SELDI-TOF analysis differentiated the three Dunning rat cell sublines based upon protein concentration normalized profiles between 5,000 and 20,000 Da. The preparations from the three cells lines showed clear differences when the extracts from the metastatic sublines (AT-1 and MLL) were compared to the benign subline (G) for proteins with molecular weights of 9 kDa (decrease), 12 kDa (significant decrease), 14 kDa (decrease), and 17 kDa (significant gain). After pre-processing extracts with ammonium sulfate and molecular ultrafiltration, the molecular profile changes from one subline to the next became more apparent. Our results were reproducible using multiple runs including from Dunning cells cultured in a separate laboratory, and using different lots of SELDI ProteinChips.

CONCLUSIONS

The application of SELDI-TOF to a series of Dunning rat prostate cancer cell lines illustrated apparent changes in protein profiles among the three cell lines with known differences in metastatic biologic activity. SELDI-TOF identified four reproducible changes in protein expression in the AT1 and MLL metastatic cell sublines. Three of the expression changes were manifested as decreases, but one protein (17 kDa) was over-expressed in the AT1 and MLL cell lines. Emphasis will be placed on the isolation, purification, and characterization of the 17 kDa over-expressed protein and its potential role in PCa metastasis.

Proteomics in pancreatic disease

Proteomics represents a novel methodological approach to investigate the expression of all proteins by a cell or organism in its entireness, similar to global strategies for DNA (genomics) and RNA (transcriptomics). This review focuses on the history of protein analysis, which made up the golden age of pancreatic physiology, the current methodology for proteomics (2D gel electrophoresis, mass spectrometry) and the few published experiences with proteomics in the field of pancreatology until now. Finally, potential applications of proteomics for the pancreas, in concert with other techniques, are cited.

Proteomic approaches to the diagnosis, treatment, and monitoring of cancer

The field of proteomics holds promise for the discovery of new biomarkers for the early detection and diagnosis of disease, molecular targets for therapy and markers for therapeutic efficacy and toxicity. A variety of proteomics approaches may be used to address these goals. Two-dimensional gel electrophoresis (2D-PAGE) is the cornerstone of many discovery-based proteomics studies. Technologies such as laser capture microdissection (LCM) and highly sensitive MS methods are currently being used together to identify greater numbers of lower abundance proteins that are differentially expressed between defined cell populations. Newer technologies such as reverse phase protein arrays will enable the identification and profiling of target pathways in small biopsy specimens. Surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) analysis enables the high throughput characterization of lysates from very few tumor cells or body fluids and may be best suited for diagnosis and monitoring of disease. Such technologies are expected to supplement our arsenal of mRNA-based assays, and we believe that in the future, entire cellular networks and not just a single deregulated protein will be the target of therapeutics and that we will soon be able to monitor the status of these pathways in diseased cells before, during and after therapy.

Induction of G1 cell cycle arrest and P15INK4b expression by ECRG1 through interaction with Miz-1

ECRG1 is a novel candidate of tumor suppressor gene identified from human esophagus. To study the biological role of ECRG1 gene, we performed a GAL4-based yeast two-hybrid screen of a human fetal liver cDNA library. Using the ECRG1 cDNA as bait, we identified two putative clones as associated proteins, Miz-1 and FLNA (Filamin A). The interaction of ECRG1 and Miz-1 was confirmed by glutathione-S-transferase (GST)-pull-down assays in vitro and co-immunoprecipitation experiments in vivo. ECRG1 was co-localized with Miz-1 in nucleus, as shown by confocal microscopy. Transfection of ECRG1 gene into the esophageal cancer (EC) cells inhibited cell proliferation and induced G1 phase arrest of cell cycle. In the co-transfection of ECRG1 and Miz-1 assays, we found inhibition of cell proliferation and G1/S phase in EC cells, but the levels of cell proliferation inhibition and G1/S phase arrest were more strongly compared with the transfection of ECRG1 or Miz-1 alone. In addition, the interaction of ECRG1 and Miz-1 could induce expression of P15(INK4b) gene in esophageal cancer 9706 (EC9706) cells. However, the transfection of ECRG1 or Miz-1 alone was not revealed the expressions of P15(INK4b) gene. When antisense ECRG1 interdicted expression of endogenous ECRG1 in Balb/c-3T3 cells, Transfection of Miz-1 couldn't induce P15(INK4b) expression. The results provide evidences that ECRG1 and Miz-1 in EC cells may be acting as a co-functional protein associated with regulation of cell cycle and induction of P15(INK4b) expression. It suggests that ECRG1 may inhibit tumor cell growth by affecting cell cycle, and that expression of P15(INK4b) may be likely to enhance G1 cell cycle arrest during the interaction of ECRG1 and Miz-1. The physical interaction of ECRG1 and Miz-1 may play an important role in carcinogenesis of EC.

Identification of novel proteins associated with hepatocellular carcinomas using protein microarrays

Characterization of the protein profiles expressed by hepatocellular carcinomas (HCCs) may identify the genes involved in hepatocellular carcinogenesis and offers the possibility of elucidating clinical biomarkers. In an effort to discover such proteins and pathways that are deregulated in hepatocellular carcinogenesis, cellular proteomes of matched normal liver cells and carcinoma were analysed by tissue microdissection and protein microarrays. Using protein microarrays made up of 83 different antibodies, it was possible to monitor alterations of the protein levels in HCC and non-neoplastic liver tissue. Further analysis of altered proteins was performed using western blot analysis and tissue microarrays (TMAs) containing 210 HCC specimens and corresponding liver tissue. The protein microarray approach revealed differential expression between HCC and normal liver of 32 of the 83 proteins examined: 21 of these were up-regulated and 11 down-regulated. IGF (insulin growth factor) II, ADAM (a disintegrin and metalloproteases) 9, STAT (signal transducers and activators of transcription) 3, SOCS (suppressors of cytokine signalling) 3, and cyclin D1 were significantly up-regulated and collagen I, SMAD 4, FHIT (fragile histidine triad), and SOCS1 were down-regulated. The differential expression of these proteins was confirmed using western blot analysis and TMAs. Correlation of differentially regulated proteins with clinico-pathological data showed that cyclin D1 and SOCS1 were associated with tumour prognosis in univariate analysis, but not multivariate analysis. These data indicate that the development of an array-based approach for the determination of protein profiles in HCC may facilitate the identification of new proteins associated with carcinogenesis or prognosis.

Using yeast two-hybrid system to identify ECRG2 associated proteins and their possible interactions with ECRG2 gene

AIM: To identify esophageal cancer related gene2 (ECRG2) associated proteins and their possible interactions with ECRG2 gene.

METHODS: In the yeast forward two-hybrid system, ECRG2 was fused with the DNA-binding domain (DBD) of Gal4 and human fetal liver cDNA library was fused with the transcriptional activation domain (AD) of Gal4. We performed a high-stringency scale procedure to screen ECRG2 against human fetal liver cDNA library and characterized positives by sequence analysis.

RESULTS: We found the following 9 putatively associated proteins. They were metallothionein2A, metallothionein1H, metallothionein1G, ferritin, erythrocyte membrane protein band4.2, mitochondrial ribosomal protein S12, hypothetical protein FLJ10101, and a novel gene whose cDNA was found to have no strong homology to any other previously characterized gene whose DDBJ/EMBL/GenBank accession number is AF422192 mapped to human chromosome 14q31.

CONCLUSION: MT, a potential interaction partner for ECRG2, might be involved in the regulation of cell proliferation and apoptosis, and in various physiological processes. Determination of a reliability score for each single protein-protein interaction, especially interaction of ECRG2 and MT, permits the assignment of ECRG2 and unannotated proteins to biological pathways. A further understanding of the association between ECRG2 and MT should facilitate the functions of ECRG2 gene.