Proteomics in biomarker discovery and drug development

A concentration-dependent analysis method for high density protein microarrays

Protein microarray technology is rapidly growing and has the potential to accelerate the discovery of targets of serum antibody responses in cancer, autoimmunity and infectious disease. Analytical tools for interpreting this high-throughput array data, however, are not well-established. We developed a concentration-dependent analysis (CDA) method which normalizes protein microarray data based on the concentration of spotted probes. We show that this analysis samples a data space that is complementary to other commonly employed analyses, and demonstrate experimental validation of 92% of hits identified by the intersection of CDA with other tools. These data support the use of CDA either as a preprocessing step for a more complete proteomic microarray data analysis or as a stand-alone analysis method.

Identification of alpha-actinin 4 and 67 kDa laminin receptor as stage-specific markers in esophageal cancer via proteomic approaches

BACKGROUND

Esophageal squamous cell carcinoma (ESCC) is one of the most common malignancies in the world with a very poor prognosis. The majority of ESCC patients present with advanced metastatic disease upon diagnosis. Therefore, it is important to understand the molecular mechanism in the tumor invasion process and to find new biomarkers for early diagnosis and prognostic evaluation.

METHODS

Differentially expressed proteins among different stages of primary ESCCs and their matched surrounding normal tissues were compared by proteomics-based technology. The correlations between interesting proteins and clinical features of ESCC were further investigated by using ESCC tissue microarray (TMA) by immunohistochemical staining.

RESULTS

Compared with normal tissues, a total of 18 differentially expressed proteins were identified in ESCC in this study. Among them, expression levels of alpha-actinin 4 (ACTN4) and 67 kDa laminin receptor (67LR) were progressively increased from stage I to III. Clinicopathological correlation using TMA revealed that overexpression of ACTN4 was significantly associated with advanced tumor stage (P = .026) and lymph node metastasis (P = .049), whereas overexpression of 67LR was significantly correlated with advanced tumor stage (P = .019) but not lymph node metastasis.

CONCLUSIONS

These findings suggested that overexpression of ACTN4 and 67 LR is associated with ESCC progression and that these biomarkers may potentially be useful to prognostic evaluation, molecular biological classification, and therapeutic targeting.

Isolation of cytoplasmatic proteins from cultured cells for two-dimensional gel electrophoresis

Cytoplasma is the cell interior place between the cellular membrane and the nucleus, where various intracellular activities take place, including energy production, reactive oxygen species (ROS) detoxification, heme synthesis, nitrogen and lipid metabolism, phosphorylation in signal transduction, and cytoskeletal meshwork construction. The rich cytoplasmatic proteins carrying out these intracellular functions are interesting targets for biochemical and molecular biological studies. The relatively recent discipline of proteomics offers a chance to globally analyze the changes in cytoplasmic proteins corresponding to drug treatments or disease conditions, and thus provide target candidates for further biological validation in drug development and biomarker discovery. Isolation of cytoplasmic proteins from cells is a necessary step for high resolution protein separation by two-dimensional gel electrophoresis (2DE) and specific proteomic analysis.

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.

Proteomic expression profiling of breast cancer

Breast cancer is one of the most common cancers observed in women in industrialized Western countries. The development of novel diagnostic methods and the application of modern systemic therapies have significantly optimized early detection and therapy of breast cancer. However, many patients are currently overtreated. Traditionally, tumours have been categorized on the basis of histopathological criteria. However, staining pattern and intensity of cancer cells are not sufficient to reflect the molecular events driving tumour development and progression. Therefore, new genomic, transcriptomic and proteomic techniques are applied to clinical samples aiming to identify new targets for a therapy tailored for an individual patient. After an introduction to common genomic and transcriptomic profiling technologies and their relevance for clinical use, we will focus on analytical and preanalytical applications for the identification of new therapeutic targets by protein profiling, with a special emphasis on two-dimensional gel-technologies (2D-PAGE), particularly as they apply to the study of breast cancer.

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.

Magneto immuno-PCR: a novel immunoassay based on biogenic magnetosome nanoparticles

We describe an innovative modification of the Immuno-PCR technology for automatable high sensitive antigen detection. The Magneto Immuno-PCR (M-IPCR) is based on antibody-functionalized biogenic magnetosome nanoparticles revealing major advantages over synthetic magnetic particles. The general principle of the M-IPCR is similar to that of a two-sided (sandwich) immunoassay. However, antibody-functionalized magnetosome conjugates were employed for the immobilization and magnetic enrichment of the signal generating detection complex enabling the establishment of a surface independent immunoassay. To this end, the M-IPCR was carried out by simultaneously tagging the antigen with the reagent for read-out, i.e., a conjugate comprising the specific antibody and DNA fragments, in the presence of the antibody-functionalized magnetosomes. To demonstrate the general functionality of the M-IPCR, the detection of recombinant Hepatitis B surface Antigen (HBsAg) in human serum was established. We observed a detection limit of 320pg/ml of HBsAg using the M-IPCR, which was about 100-fold more sensitive than the analogous Magneto-ELISA, established in parallel for comparison purposes.

Proteomic alteration in gastic adenocarcinomas from Japanese patients

Background

Gastric adenocarcinomas comprise one of the common types of cancers in Asian countries including Japan. Comprehensive protein profiling of paired surgical specimens of primary gastric adenocarcinomas and nontumor mucosae derived from Japanese patients was carried out by means of two-dimensional gel electrophoresis (2D-EP) and liquid chromatography-electrospray ionic tandem mass spectrometry (LC-ESI-MS) to establish gastric cancer-specific proteins as putative clinical biomarkers and molecular targets for chemotherapy.

Results

Relatively common alterations in protein expression were revealed in the tumor tissues. Increases in manganese dismutase and nonhistone chromosomal protein HMG-1 (HMG-1) were observed, while decreases in carbonic anhydrases I and II, glutatione-S-transferase and foveolin precursor (gastrokine-1) (FOV), an 18-kDa stomach-specific protein with putative tumor suppressor activity, were detected. RT-PCR analysis also revealed significant down-regulation of FOV mRNA expression in tumor tissues.

Conclusion

A possible pathological role for down-regulation of FOV in gastric carcinogenesis was demonstrated. Evaluation of the specific decreases in gene and protein expression of FOV in patients may be utilized as clinical biomarkers for effective diagnosis and assessment of gastric cancer.

Casting light on molecular events underlying anti-cancer drug treatment: What can be seen from the proteomics point of view?

Regardless of continuous advances in technology and expansion of the knowledge in the field of genomic information, cancer still remains one of the leading causes of death in developed countries for many reasons, including non-selectiveness of commonly used anti-cancer drugs that often influence non-specific rather than tumour-specific targets. As cancer cells are characterized by the ability to divide and multiply in an uncontrolled manner whereby a set of specific proteins modulate cell division processes, proteomics seems to be a suitable tool for seeking out molecular mediators of anti-cancer drugs action and resistance, thus improving chemotherapy outcome. This review will focus on the recent knowledge of the molecular mechanisms involved in the anti-cancer drugs response revealed by the proteomics tools. In addition, we will touch upon the effects of "gene drugs" with p53 and p21(waf1/cip1) genes on the protein complement of tumour cells assessed by the two-dimensional gel electrophoresis combined with mass spectrometry. Such studies could substantially contribute to further drug optimization prior to its clinical use and represent an important but still small step in the long way of drug discovery. However, fluctuations in protein expression, distribution, posttranslational modifications, interactions, functions and compartmentalization make it difficult to use exclusively expression proteomics data without putting it in broader biological context. Thus, the challenge today is to shift from the identification of drug response and disease biomarkers to more time-consuming process of revealing the biochemical mechanism that connects a specific protein with a disease or cellular response to a drug.

Proteome analysis of bronchoalveolar lavage in lung diseases

The proteomic approach is complementary to genomics and enables protein composition to be investigated under various clinical conditions. Its application to the study of bronchoalveolar lavage (BAL) is extremely promising. BAL proteomic studies were initially based on two-dimensional electrophoretic separation of complex protein samples and subsequent identification of proteins by different methods. With the techniques available today it is possible to attain many different research objectives. BAL proteomics can contribute to the identification of proteins in alveolar spaces with possible insights into pathogenesis and clinical application for diagnosis, prognosis and therapy. Many proteins with different functions have already been identified in BAL. Some could be biomarkers that need to be individually confirmed by correlation with clinical parameters and validation by other methods on larger cohorts of patients. The standardization of BAL sample preparation and processing for proteomic studies is an important goal that would promote and facilitate clinical applications. Here, we review the principal literature on BAL proteomic analysis applied to the study of lung diseases.

Toward the application of proteomics to human thyroid tissue

CONTEXT

In this paper we describe for the first time a systematic approach to proteome analysis of human thyroid tissue.

OBJECTIVE AND DESIGN

We report different methods to decrease the complexity of the human thyroid tissue proteome by applying different solubilization strategies and correcting for thyroglobulin protein abundance; to increase the protein resolution by prefractionation and by the use of narrow-range pH gradients; to detect proteins using sensitive and quantitative stains; and to identify soluble and membrane-bound thyroid tissue proteins by mass spectrometry analysis. MAIN OUTCOME/RESULTS: We found that buffers containing high contents of urea and detergents allow the best solubilization of human thyroid tissue proteins; highly variable abundance of thyroglobulin is a major pitfall of human thyroid proteome analysis, which in contrast to centrifugal ultrafiltration, size-exclusion chromatography and microdissection, can be countered best by adapting the protein amount to the thyroglobulin content per sample; prefractionation leads to a significant enrichment of proteins and allows subcellar localization of thyroid proteins; application of narrow-range immobilized pH gradient (IPG) strips allows further improvement of spot detection and separation; and protein detection with the fluorescent stain ruthenium II Tris bathophenanthroline disulfonate (RuBPs) is a highly sensitive and reliable tool for quantitative proteome analysis. Finally, in a pilot study of four patients with benign nodular thyroid disease we found that the described procedures allow a highly reproducible detection and identification of alterations in protein expression between nodular and corresponding normal thyroid tissues.

CONCLUSIONS

Application of the described methods provides the basis for a highly sensitive and reproducible proteome analysis of the human thyroid, providing an additional novel tool to elucidate complex proteins changes in human thyroid biology as well as pathophysiology of human thyroid disease.

Analysis of differential protein expression by cisplatin treatment in cervical carcinoma cells

Cisplatin (cis-diaminedichloroplatinum), a DNA-damaging agent, which readily induces apoptosis in vitro, is one of the widely used anticancer drug in the treatment of human malignancies. Cisplatin has played an important role in cervical cancer management for effective chemotherapeutic regimen, but the underlying mechanisms inducing cell death at protein level are unknown. Using proteome analysis, an investigation aimed at a better understanding of the antiproliferative mechanisms by cisplatin was carried out in HeLa cervical carcinoma cells. In total, 21 protein spots were found to be differentially expressed following cisplatin treatment, of which 12 were upregulated (eg, regulator of G-protein signaling, TRAF:TNF (tumor necrosis factor) receptor-associated factor-interacting protein [I-TRAF], and cyclin-dependent kinase inhibitor p27 [p27(kip1)]) and 9 were downregulated (eg, myc proto-oncoprotein [c-myc] and proliferating cell nuclear antigen). Interestingly, we found the upregulation of proliferating cell nuclear antigen, which used molecular marker in cervical cancer screening. On the basis of proteomic data, we showed that cisplatin induced TRAF2-mediated NF-kappaB downregulation. In addition, our study demonstrated that cisplatin induced membrane death receptor-mediated and mitochondria-mediated apoptosis pathway. Our findings may offer new insights into the antiproliferative mechanism by cisplatin and its mode of action in cervical carcinoma cells.

Detection of redox-based modification in two-dimensional electrophoresis proteomic separations

Oxidative stress arises when cellular defenses against molecular oxygen and its by-products (reactive oxygen species; ROS) are overcome leading to covalent modification of lipids, DNA, and protein. Redox-based modification of proteins can be conveniently studied by proteomic analysis using two-dimensional electrophoresis (2D SDS-PAGE). Despite some technical shortcomings, this technique allows rapid and quantitative analysis of paired samples, the visualization of discrete protein spots, and provides a robust platform for subsequent analysis and identification of specific proteins. Exposure to oxidative stress introduces a wide range of reversible or irreversible alterations to amino acid side chains. These include carbonylation, glutathionylation, formation of mixed disulphides, effects on disulphide bridge patterns, ubiquitinylation, and racemization. Identification of proteins targeted for specific modification adds a deeper dimension to the dissection of effects of oxidative stress on the proteome with potentially far-reaching implications. This article describes key methodologies now available for identification of redox-based modifications in proteins separated by 2D SDS-PAGE.

AUF1-like protein binds specifically to DAS cis-acting element that regulates mouse alpha-fetoprotein gene expression

Alpha-fetoprotein (AFP) is one of the major serum proteins in the early life of mammals. We have previously identified a novel cis-acting element designated as DAS at the 5'-flanking region of the AFP gene and demonstrated that the DAS sequence can be specifically recognized by nuclear protein DAP-II in AFP-producing hepatoma cells and retinoic acid (RA)-induced AFP-producing F9 cells. In this study, we used DNA affinity chromatography to purify the DAP-II proteins from the nuclear extracts (NE) of RA-treated F9 cells. The purified DAP-II complex mainly contained five proteins, with molecular weights of 45, 42, 32, 30, and 20 kDa, respectively. The identification of these proteins was determined by MALDI-TOF mass spectrometric analysis and a database search. These proteins were found to belong to the AUF1 RNA-binding protein family. Protein (30 kDa), one of five proteins in an isolated DAP-II complex, was matched with amino acid sequence highly similar to muAUF1-3. The expression of this protein is inducible by RA, and the pattern of the protein expression is the same as DAP-II proteins in F9 cells after treatment with RA during differentiation. Our results suggest that the 30-kDa protein is a novel isoform of AUF1 family and is the main component of the DAP-II complex that binds to the DAS sequence.

Proteomic approach to study the cytotoxicity of dioscin (saponin)

Dioscin, extracted from the root of Polygonatum zanlanscianense pamp, exhibits cytotoxicity towards human myeloblast leukemia HL-60 cells. Proteomic analysis revealed that the expression of mitochondrial associated proteins was substantially altered in HL-60 cells corresponding to the dioscin treatment, suggesting that mitochondria are the major cellular target of dioscin. Mitochondrial functional studies validated that mitochondrial apoptotic pathway was initiated by dioscin treatment. Changes in proteome other than mitochondrial related proteins implicate that other mechanisms were also involved in dioscin-induced apoptosis in HL-60 cells, including the activity impairment in protein synthesis, alterations of phosphatases in cell signaling, and deregulation of oxidative stress and cell proliferation. Current study of protein alterations in dioscin-treated HL-60 cells suggested that dioscin exerts cytotoxicity through multiple apoptosis-inducing pathways.

Characterization of the secreted proteome of rat hepatocytes cultured in collagen sandwiches

Analysis of proteins in biological samples opens up the possibility of discovering new markers of toxicity. The liver is one of the primary targets of drug-induced toxicity, and it also secretes many plasma proteins, which can be measured clinically. Most of the plasma proteins produced by the liver are secreted by hepatocytes, but there is little information regarding the protein profile secreted by these cells. The purpose of this study was to analyze the secreted proteome of primary rat hepatocytes in a collagen gel sandwich configuration by a gel-LC-MS/MS procedure. We identified over 600 peptides corresponding to more than 200 proteins. The protein profile included over 50 plasma proteins, suggesting that the cultured hepatocytes secrete many of the proteins that they produce in vivo. Our data also suggests that the hepatocytes are actively remodeling their environment, since we identified several structural extracellular matrix proteins as well as some proteins known to be secreted specifically during liver regeneration. We also identified two proteins, alpha1-antitrypsin and alpha2-macroglobulin, whose secretions appear to be down-regulated in cells exposed to aflatoxin B1. It was noted that a 15 nM dose of aflatoxin B1 led to substantially diminished levels of these proteins and that day 6 of incubation was the ideal time point for medium collection. These data suggest that proteins in the conditioned medium of hepatocyte sandwich culture might lead to the discovery of biomarkers for drug-induced chemical toxicity.

PROTEOMICS TECHNOLOGY AND THERAPEUTICS

1. Proteins are the workhorses of biological systems and, thus, it is not surprising that the field of proteomics has flourished in recent years. The present review briefly surveys the general proteomic approaches taken to identify drug targets and to evaluate drug efficacy and toxicity in the preclinical and clinical settings. These generally fall into three basic categories: a profiling approach, a functional approach and a structural approach. 2. The current 'tools' used and applied to the drug-discovery process will be highlighted. These include the two-dimensional gel electrophoresis, liquid chromatography, mass spectrometry, isotope-coded affinity tag and protein biochips. 3. Clearly, proteomics has begun to set a foothold in every stage of the drug-discovery process. Future developments in this area will likely make a significant impact in our quest for better, safer and cost-effective drugs.

Proteomic analysis of prodigiosin-induced apoptosis in a breast cancer mitoxantrone-resistant (MCF-7 MR) cell line

Prodigiosin (PG) is a bacterial, red-pigmented antibiotic with immunosuppressive and apoptotic activities. To better understand its mechanisms of action, we tried to identify proteins associated with apoptosis induced by PG. For this purpose, the variation of protein expression on exposure to apoptotic concentrations of PG was examined, by high-resolution two-dimensional gel electrophoresis (2D-E), in the MCF-7 cancer cell line resistant to mitoxantrone (MCF-7-MR). Six PG apoptosis-associated protein spots were further characterized by complementary peptide mass fingerprinting and tandem mass spectrometry data obtained on a matrix-assisted laser desorption ionization-time-of-flight/time-of-flight (MALDI-TOF/TOF) mass spectrometer. The proteins identified were involved in various cellular functions, including cell defence, DNA repair and cellular organization. Our data provide novel information on cell response to PG, a new apoptotic drug with interesting anticancer activity.

Proteomic characterization of the cytotoxic mechanism of gold (III) porphyrin 1a, a potential anticancer drug

There has been increasing interest in the potential applications of gold (III) complexes as anticancer drugs with higher cytotoxicity and fewer side effects than existing metal anticancer drugs. Our previous findings demonstrated that gold (III) porphyrin 1a preferentially induced apoptosis in a cancer cell line (SUNE1). In this study, we identified differentially expressed proteins related to the drug's cytotoxic action by comparing the protein alterations induced by gold (III) porphyrin 1a and cisplatin treatments. Several clusters of altered proteins were identified, including cellular structure and stress-related chaperone proteins, proteins involved in reactive oxygen species and enzyme proteins, translation factors, proteins that mediate cell proliferation or differentiation, and proteins participating in the internal degradation systems. Our results indicated that multiple factors leading to apoptosis were involved in drug cytotoxicity in SUNE1 cells. The balance between pro-apoptotic and anti-apoptotic signals determined the final fate of cancer cells.

Comparative proteomic analysis of esophageal squamous cell carcinoma

Ranking as the fourth commonest cancer, esophageal squamous cell carcinoma (ESCC) represents one of the leading causes of cancer death in China. One of the main reasons for the low survival rate is that neoplasms in esophagus are not detected until they have invaded into surrounding tissues or spread throughout the body at advanced stages. A better understanding of the malignant mechanism and early diagnosis are important for fighting ESCC. In this study, we used proteomics to analyze ESCC tissues, aiming at defining the proteomic features implicated in the multistage progression of esophageal carcinogenesis. Proteins that exhibited significantly different expressions were identified by peptide mass fingerprinting and validated by Western blotting and reverse transcriptase-polymerase chain reaction. The protein changes were then correlated to the different grades of disease differentiation. Compared to those in adjacent normal epitheliums, the expression of 15 proteins including enolase, elongation factor Tu, isocitrate dehydrogenase, tubulin alpha-1 chain, tubulin beta-5 chain, actin (cytoplasmic 1), glyceraldehyde-3 phosphate dehydrogenase, tropomyosin isoform 4 (TPM4), prohibitin, peroxiredoxin 1 (PRX1), manganese-containing superoxide dismutase (MnSOD), neuronal protein, and transgelin was up-regulated; and the expression of five proteins including TPM1, squamous cell carcinoma antigen 1 (SCCA1), stratifin, peroxiredoxin 2 isoform a, and alpha B crystalline was down-regulated in cancer tissues with a statistical significance (p < 0.05). In addition, the differential expression of SCCA1, PRX1, MnSOD, TPM4, and prohibitin can be observed in precancerous lesions of ESCC. The expression of stratifin, prohibitin, and SCCA1 dropped with increasing dedifferentiation of ESCC. These data may suggest that these proteins contribute to the multistage process of carcinogenesis, tumor progression, and invasiveness of ESCC.

BIOMARKERS IN PSYCHOTROPIC DRUG DEVELOPMENT: Integration of Data across Multiple Domains

This review focuses on the current status of biomarkers and/or approaches critical to assessing novel neuroscience targets with an emphasis on new paradigms and challenges in this field of research. The importance of biomarker data integration for psychotropic drug development is illustrated with examples for clinically used medications and investigational drugs. The question remains how to verify access to the brain. Early imaging studies including micro-PET can help to overcome this. However, in case of delayed tracer development or because of no feasible application of brain imaging effects of the molecule, using CSF as a matrix could fill this gap. Proteomic research using CSF will hopefully have a major impact on the development of treatments for psychiatric disorders.

Serological protein profiling of neuroblastoma by ProteinChip SELDI-TOF technology

Serological proteins of neuroblastoma were profiled and analyzed by ProteinChip-SELDI-TOF MS technology with five types of protein chips. By comparing with normal control, a number of protein or polypeptide signals were found significantly and consistently different in their intensities (expression levels) in tumor sera. Interestingly, nine polypeptide peaks in these proteomic features can be simultaneously detected with consistent variations by more than one type of protein chips. None of the expression differences of these nine polypeptides was found in similar comparisons between healthy controls and hepatomas. Preliminary protein identification showed hints for that some of these proteomic alterations may be closely related to the tumorigenesis of neuroblastoma. These results demonstrated the potential of serological biomarker identification for neuroblastoma by ProteinChip-SELDI technology.

Application of proteomics in the study of tumor metastasis

Tumor metastasis is the dominant cause of death in cancer patients. However, the molecular and cellular mechanisms underlying tumor metastasis are still elusive. The identification of protein molecules with their expressions correlated to the metastatic process would help to understand the metastatic mechanisms and thus facilitate the development of strategies for the therapeutic interventions and clinical management of cancer. Proteomics is a systematic research approach aiming to provide the global characterization of protein expression and function under given conditions. Proteomic technology has been widely used in biomarker discovery and pathogenetic studies including tumor metastasis. This article provides a brief review of the application of proteomics in identifying molecular factors in tumor metastasis process. The combination of proteomics with other experimental approaches in biochemistry, cell biology, molecular genetics and chemistry, together with the development of new technologies and improvements in existing methodologies will continue to extend its application in studying cancer metastasis.

The use of proteomics in the discovery of serum biomarkers from patients with severe acute respiratory syndrome

Severe acute respiratory syndrome (SARS) is a new infectious disease with a global impact. Understanding its pathogenesis and developing specific diagnostic methods for its early diagnosis are crucial for the effective management and control of this disease. By using proteomic technology, truncated forms of α₁‐antitrypsin (TF‐α₁‐AT) were found to increase significantly and consistently in sera of SARS patients compared to control subjects. The result showed a sensitivity of 100% for SARS patients and a specificity of 92.8% for controls. Furthermore, the levels of these proteins significantly correlated with certain clinico‐pathological parameters. The dramatic increase in TF‐α₁‐AT may be the result of degradation of α₁‐AT. As α₁‐AT plays an important role in the protection of lung function, its degradation may be an important factor in the pathogenesis of SARS. These findings indicate that increased TF‐α₁‐AT may be therapeutically relevant, and may also be a useful biological marker for the diagnosis of SARS.

Molecular biomarkers in drug development

Arguably, the most immediately promising reverberation of the genomics era has been the application of biomarkers to drug development. The promise of applying biomarkers to early drug development is that they might aid in preclinical and early clinical decisions such as dose ranging, definition of treatment regimen, or even a preview of efficacy. Later in the clinic, biomarkers could be used to facilitate patient stratification, selection and the description of surrogate endpoints. Information derived from biomarkers should result in a better understanding of preclinical and clinical data, which ultimately benefits patients and drug developers. If the promise of biomarkers is realized, they will become a routine component of drug development and companions to newly discovered therapies.

Identification of tumor-associated proteins in oral tongue squamous cell carcinoma by proteomics

Oral tongue carcinoma is an aggressive tumor that particularly affects chronic smokers, drinkers and betel squid chewers. Patients often present symptoms at a late stage, and there is a high recurrence rate after treatment. In this article, we report the first proteomic analysis of oral tongue carcinoma to globally search for tumor related proteins. Apart from helping us to understand the molecular pathogenesis of the carcinoma, these proteins may also have potential clinical applications as biomarkers, enabling the tumor to be identified at an early stage in high risk individuals, treatment response to be predicted, and residual or recurrent carcinoma to be detected sooner after treatment. The protein expression profiles of ten oral tongue squamous cell carcinomas and their matched normal mucosal resection margins were examined by two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization-time of flight mass spectroscopy. A number of tumor-associated proteins including heat shock protein (HSP)60, HSP27, alpha B-crystalline, ATP synthase beta, calgranulin B, myosin, tropomyosin and galectin 1 were consistently found to be significantly altered in their expression levels in tongue carcinoma tissues, compared with their paired normal mucosae. The expression profile portrays a global protein alteration that appears specific to oral tongue cancer. The potential of utilizing these tumor related proteins for screening cancer and monitoring recurrence warrants further investigation.

Development of a bioreactor based on trypsin immobilized on monolithic support for the on-line digestion and identification of proteins

The preparation and characterization of a new trypsin-based bioreactor is here described for on-line protein digestion and peptide analysis. Trypsin was immobilized on an epoxy-modified silica monolithic support with a single reaction step and the amount of immobilized enzyme was found to be 66.07 mg (+/-11.75 S.D.)/column (n = 6). The bioreactor was coupled through a switching valve to an analytical column for the on-line digestion, peptide separation and identification of test proteins by ESI-MS-MS. The influence of various parameters (flow rate, temperature, buffer pH and molarity, etc.) on enzymatic activity was investigated by an experimental design and the mostly significant factor was found to be the flow rate. The efficacy of the reported on-line bioreactor for tryptic mapping is reported for somatostatin and myoglobin, selected as model compounds. Tryptic peptide maps obtained by on-line digestion of myoglobin were compared to those obtained by traditional off-line digestion. Sequence coverage obtained with the on-line protocol (21 peptides, 75.16% coverage of myoglobin sequence) was found to be comparable to the one obtained with the off-line protocol (18 peptides, 76.47% coverage). Sensitivity for myoglobin digestion and identification was 0.1 mg/ml. The reproducibily of the peptide maps in terms of retention time was from 1.53 to 4.31%, R.S.D.

The Embryotrophic Activity of Oviductal Cell-derived Complement C3b and iC3b, a Novel Function of Complement Protein in Reproduction

The oviduct-derived embryotrophic factor, ETF-3, enhances the development of trophectoderm and the hatching process of treated embryos. Monoclonal anti-ETF-3 antibody that abolishes the embryotrophic activity of ETF-3 recognized a 115-kDa protein from the conditioned medium of immortalized human oviductal cells. Mass spectrometry analysis showed that the protein was complement C3. Western blot analysis using an antibody against C3 confirmed the cross-reactivities between anti-C3 antibody with ETF-3 and anti-ETF-3 antibody with C3 and its derivatives, C3b and iC3b. Both derivatives, but not C3, were embryotrophic. iC3b was most efficient in enhancing the development of blastocysts with larger size and higher hatching rate, consistent with the previous reported embryotrophic activity of ETF-3. Embryos treated with iC3b contained iC3b immunoreactivity. The oviductal epithelium produced C3 as evidenced by the presence of C3 immunoreactivity and mRNA in the human oviduct and cultured oviductal cells. Cyclical changes in the expression of C3 immunoreactivity and mRNA were also found in the mouse oviduct with the highest expression at the estrus stage. Molecules involving in the conversion of C3b to iC3b and binding of iC3b were present in the human oviduct (factor I) and mouse preimplantation embryo (Crry and CR3), respectively. In conclusion, the present data showed that the oviduct produced C3/C3b, which was converted to iC3b to stimulate embryo development.