ProteinChip array profiling for identification of disease- and chemotherapy-associated biomarkers of nasopharyngeal carcinoma

Validity of serum amyloid A and HMGB1 as biomarkers for early diagnosis of gastric cancer

Background and aim

Gastric carcinomais a frequent neoplasm with poor outcome, and its early detection would improve prognosis. This study was designed to evaluate the possible use of new biomarkers, namely SAA and HMGB1, for early diagnosis of gastric cancer.

Methods

A total of 100 patients presenting with gastric symptoms were included. All patients underwent upper endoscopic evaluation, histopathological diagnosis and serum CEA, SAA, and HMGB1 measurements.

Results

Patients were classed endoscopically with neoplastic, inflammatory, and normal-appearing gastric mucosa: 50, 25, and 25 patients, respectively. Histologically, half the patients had chronic gastritis and the remaining cases gastric carcinoma of diffuse (n=28) or intestinal (n=22) type. SAA at cutoff of 18.5 mg/L had the best validity to differentiate gastritis from gastric carcinoma, with AUC, sensitivity, specificity, negative predictive value (NPV), and positive predictive value (PPV) of 0.99, 98%, 100%, 100%, and 98%, respectively, followed by HMGB1 at cutoff of 14.5 pg/μL, with AUC, sensitivity, specificity, PPV, and NPV of 0.91, 70%, 96%, 94.6%, and 76.2%, respectively. Sensitivity, specificity, PPV, and NPV of serum CEA at cutoff of 2.9 ng/mL to differentiate gastritis from gastric carcinoma were 42%, 72%, 60%, and 55.4%, respectively, with AUC of 0.53. Nonetheless, higher serum levels of both SAA and HMGB1 reflected higher tumor grade (P=0.027 and P=0.016, respectively) and advanced tumor stage (P-OBrk-0.001 for both).

Conclusion

Serum levels of both SAA and HMGB1 could be of great value for early diagnosis of gastric carcinoma, comparable to the diagnostic role of serum CEA, which is not valid for early diagnosis of gastric cancer.

Proteomic Profiling of Invasive Ductal Carcinoma (IDC) using Magnetic Beads-based Serum Fractionation and MALDI-TOF MS

AIM

To reveal the serum proteomic profiling of intraductal carcinoma (IDC) patients in China, establish a serum proteome fractionation technique for choosing magnetic beads for proteomic analysis in breast cancer research; and identify differentially expressed peptides (m/z; P < 0.0001) as potential biomarkers of early IDCs.

METHODS

We used two different kinds of magnetic beads (magnetic bead-based weak cation exchange chromatography (MB-WCX) and immobilized metal ion affinity chromatography (MB-IMAC-Cu)) to analyze 32 patients with early stage (stages I-II) IDC and 32 healthy control serum samples for proteomic profiling by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis. The mass spectra, analyzed using ClinProTools software, distinguished between IDC patients and healthy individuals based on k-nearest neighbor genetic algorithm.

RESULTS

The serum samples purified in the MB-WCX group provided better proteomic patterns than the MB-IMAC-Cu group. The samples purified by MB-WCX had better average peak numbers, higher peak intensities, and better capturing ability of low abundance proteins or peptides in serum samples. In addition, the MB-WCX and MB-IMAC-Cu purification methods, followed MALDI-TOF MS identification and use of ClinProTools software accurately distinguished patients with early stage IDC from healthy individuals.

CONCLUSION

Serum proteomic profiling by MALDI-TOF MS is a novel potential tool for the clinical diagnosis of patients with IDC in China.

Biomarker discovery of nasopharyngeal carcinoma by proteomics

Nasopharyngeal carcinoma (NPC) is one of the most common malignant tumors in southern China and southern Asia, and poses one of the most serious public health problems in these areas. Early diagnosis, predicting metastasis, recurrence, prognosis and therapeutic response of NPC remain a challenge. Discovery of diagnostic and predictive biomarkers is an ideal way to achieve these objectives. Proteomics has great potential in identifying cancer biomarkers. Comparative proteomics has identified a large number of potential biomarkers associated with NPC, although the clinical performance of such biomarkers needs to be further validated. In this article, we review the latest discovery and progress of biomarkers for early diagnosis, predicting metastasis, recurrence, prognosis and therapeutic response of NPC, inform the readers of the current status of proteomics-based NPC biomarker findings and suggest avenues for future work.

Analysis of serum proteome profiles in nasopharyngeal carcinoma with different radiosensitivity

PURPOSE

The research is endeavored to establish a serum protein fingerprint model for predicting radiosensitivity of nasopharyngeal carcinoma through the analysis of the serum expressed proteins of the pre- and post-treatment nasopharyngeal carcinoma patients treated with radiotherapy.

METHODS

Surface-enhanced laser desorption ionization-time of flight-mass spectrometry and CM-10 protein chip were used to detect the serum proteomic patterns of 50 nasopharyngeal carcinoma patients with different radiosensitivity. Thirty-eight of the 50 patients after the treatment were also studied. Biomarker Wizard 3.01 and Biomarker Pattern 5.01 were used in combination to analyze the data and to develop predicting models.

RESULTS

At the molecular weight range of 2,000-20,000, the software identified an average of 83 mass peaks between radiation sensitive group and radiation resistant group. 11 protein peaks were significantly different. Of the 83 mass peaks, 4 mass peaks (mass/charge ratio [m/z] 2,575, 3,942, 6,117 and 6,778) were chosen automatically to construct a classification tree. The diagnostic accuracy was 78.0 %. M/z 6,117 and 6,778 of the radiation sensitive group after the treatment trended to those of the radiation resistant group.

CONCLUSIONS

The technology of surface-enhanced laser desorption ionization-time of flight-mass spectrometry can be used to screen and identify differentially expressed proteins associated with different radiosensitivity in nasopharyngeal cancer. It should be a very useful tool for predicting radiosensitivity of nasopharyngeal carcinoma.

Peptidomic profiles of post myocardial infarction rats affinity depleted plasma using matrix-assisted laser desorption/ionization time of flight (MALDI-ToF) mass spectrometry

Background

Despite major advances in drug development, effective cardiovascular therapies and suitable cardiovascular biomarkers remain limited. The aim of this study was to leverage mass spectrometry (MS) based peptide profiling strategies to identify changes that occur in peptidomic profiles of rat plasma following coronary artery ligation generated myocardial infarction (MI).

Methods

One week after MI, rats were randomized to receive either an ACE inhibitor (ramipril, Ram-1 mg/kg/day), or vehicle (Veh) for 12 weeks. Echocardiography and hemodynamic measurements were made before sacrifice and plasma collection. High abundance proteins were depleted with affinity capture before MS profiling. Differentially expressed peptide ions were identified using proprietary software (ClinProtTools).

Results

MI increased heart/body weight (18%), lung/body weight (56%), and left ventricular (LV) end diastolic pressure (LVEDP, 247%); and significantly reduced percentage fractional shortening (FS, 75%) and rate of pressure rise in the LV (dP/dtmax, 20%). Ram treatment significantly attenuated the changes in LVEDP (61%) and FS (27%). Analysis of MALDI-ToF generated mass spectra demonstrated that peptide ions 1271, 1878, 1955, 2041 and 2254 m/z were consistently decreased by Ram treatment (p < 0.001) and thus may be associated with the agent’s therapeutic effects. Among peptides that were significantly changed, synapsin-2, adenomatous polyposis coli protein and transcription factor jun-D were identified as significantly reduced by Ram treatment.

Conclusions

This approach allows us to screen for potential biomarkers in a window of the blood proteome that previously has been difficult to access. The data obtained from such an approach may potentially useful in prognosis, diagnosis, and monitoring of treatment response.

Identification of serum amyloid A in the serum of gastric cancer patients by protein expression profiling

The purpose of this study was to screen serum samples from gastric carcinoma patients and to determine whether serum amyloid A protein (SAA) served as a biomarker. SELDI technology was used to screen for changes in SAA levels in the serum samples. A mass cluster with a mass/charge (m/z) value between 11.1 and 11.9 kDa was identified in the serum samples from gastric carcinoma patients which was much higher than that of the control group. Furthermore, the increase in this m/z peak correlated with the severity of the cancer. High-performance liquid chromatography (HPLC) analysis confirmed that the peak was SAA1. In conclusion, this increase in SAA may be used as a potential biomarker for gastric cancer.

Diagnosis of gallbladder cancer using matrix-assisted laser desorption/ionization time-of-flight profiling

Proteomic fingerprint technology combining magnetic beads with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry was used to profile and compare the serum proteins from 45 patients with gallbladder cancer and 50 healthy blood donors. The proteomic patterns were identified; the tree model of biomarkers was constructed and evaluated using the Biomarker Patterns Software. The model tree was constructed based on the 3 biomarkers (5913 Da, 6181 Da and 13,752 Da), which generated excellent separation between the gallbladder cancer and control groups. The sensitivity was 86.7% and the specificity was 93.3%. The blind test data showed a sensitivity of 80% and a specificity of 90%. Taken together, our studies suggested that biomarkers for gallbladder cancer could be discovered in serum by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry combined with the use of magnetic beads. The pattern of combined markers would provide a powerful and reliable diagnostic method for gallbladder cancer with high sensitivity and specificity.

New serum biomarkers for detection of endometriosis using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

This study used proteomic fingerprint technology, combining nano-sized magnetic beads with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS), to screen for potential protein biomarkers for the diagnosis of endometriosis. Serum proteins from 126 patients with endometriosis and 120 healthy controls were profiled and compared. Biomarker pattern software identified 46 discriminating mass-to-charge m/z ratio peaks that were related to endometriosis. The model constructed by the software, based on three of these peaks (m/z 5988.7, 7185.3 and 8929.8), generated excellent separation between the endometriosis and control groups. The sensitivity was 91.4% and the specificity 95.0%. Blind testing on a second series of serum samples from patients with endometriosis and healthy controls indicated a sensitivity of 89.3% and a specificity of 90.0%. Biomarkers for endometriosis can be discovered in serum by MALDI-TOF-MS in combination with nano-sized magnetic beads. The pattern of combined markers provides a powerful and reliable diagnostic method for endometriosis, with high sensitivity and specificity.

New serum biomarkers for detection of tuberculosis using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry

BACKGROUND

New technologies for the early detection of tuberculosis (TB) are urgently needed. Pathological changes within an organ might be reflected in proteomic patterns in serum. The aim of the present study was to screen for the potential protein biomarkers in serum for the diagnosis of TB using proteomic fingerprint technology.

METHODS

Proteomic fingerprint technology combining protein chips with surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) was used to profile the serum proteins from 50 patients with TB, 25 patients with lung disease other than TB, and 25 healthy volunteers. The protein fingerprint expression of all the serum samples and the resulting profiles between TB and control groups were analyzed with the Biomarker Wizard system.

RESULTS

A total of 30 discriminating m/z peaks were detected that were related to TB (p<0.01). The model of biomarkers constructed by the Biomarker Patterns Software based on the three biomarkers (2024, 8007, and 8598 Da) generated excellent separation between the TB and control groups. The sensitivity was 84.0% and the specificity was 86.0%. Blind test data indicated a sensitivity of 80.0% and a specificity of 84.2%.

CONCLUSIONS

The data suggested a potential application of SELDI-TOF MS as an effective technology to profile serum proteome, and with pattern analysis, a diagnostic model comprising three potential biomarkers was indicated to differentiate people with TB and healthy controls rapidly and precisely.

MALDI-TOF MS combined with magnetic beads for detecting serum protein biomarkers and establishment of boosting decision tree model for diagnosis of colorectal cancer

The aim of present study is to study the serum protein fingerprint of patients with colorectal cancer (CRC) and to screen protein molecules that are closely related to colorectal cancer during the onset and progression of the disease with Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Serum samples from 144 patients with CRC and 120 healthy volunteers were adopted in present study. Weak cation exchange (WCX) magnetic beads and PBSII-C protein chips reader (Ciphergen Biosystems Ins.) were used. The protein fingerprint expression of all the Serum samples and the resulted profiles between cancer and normal groups were analyzed with Biomarker Wizard system. Several proteomic peaks were detected and four potential biomarkers with different expression profiles were identified with their relative molecular weights of 2870.7 Da, 3084 Da, 9180.5 Da, and 13748.8 Da, respectively. Among the four proteins, two proteins with m/z 2870.7 and 3084 were down-regulated, and the other two with m/z 9180.5 and 13748.8 were up-regulated in serum samples from CRC patients. The present diagnostic model could distinguish CRC from healthy controls with the sensitivity of 92.85% and the specificity of 91.25%. Blind test data indicated a sensitivity of 86.95% and a specificity of 85%. The result suggested that MALDI technology could be used to screen critical proteins with differential expression in the serum of CRC patients. These differentially regulated proteins were considered as potential biomarkers for the patients with CRC in the serum and of the potential value for further investigation.

Identification of disease- and therapy-associated proteome changes in the sera of patients with myelodysplastic syndromes and del(5q)

Using ProteinChip array technology, which is based on the surface-enhanced laser desorption/ionization time-of-flight mass spectrometry, we performed proteomic analyses on sera from myelodysplastic syndromes (MDSs) patients with an interstitial deletion of the long arm of chromosome 5 (del(5q)) and those from control individuals. One analysis with 80 samples from 29 patients and 51 control subjects resulted in the detection of 61 peak differences. Another analysis with 36 paired-samples from 18 patients collected before and after the treatment with lenalidomide (Revlimid) identified 19 differential peak features. We also observed differential profiles between the pre-treatment samples from the responders and those from the non-responders reflected by eight peak differences. On the basis of these data we developed two classification models that could distinguish between the diseased and the control subjects or between the responders and the non-responders. Efforts were made to purify and identify a range of differential peak proteins. We conclude that inter-α trypsin inhibitor, heavy chain H4 (fragments), serum transferrin, transthyretin (variants), haemoglobin and a protein peak at m/z 2791 could be potential disease-associated markers for del(5q) MDS. Platelet factor 4 (PF-4) and a peak at m/z 8559 may serve as therapy-associated markers and be potentially useful for monitoring and predicting the response to therapy.

Serum amyloid A is elevated in the serum of lung cancer patients with poor prognosis

Background:

Lung cancer is known as the top cancer killer in most developed countries. However, there is currently no promising diagnostic or prognostic biomarker for lung cancer. This study aims to discover non-invasive differential markers in the serum of lung cancer patients, to determine the protein identity of the candidate biomarker(s), and to investigate any clinical implication of the biomarker(s) concerned.

Methods:

Blood specimens were collected from 154 pre-operative patients with lung cancer and 35 healthy blood donors with no evidence of lung cancer. Fractionated serum samples were processed by surface-enhanced laser desorption/ionisation time-of-flight mass spectrometry (MS). Candidate biomarker was identified using sodium dodecyl sulphate polyacrylamide gel electrophoresis and tryptic digestion followed by tandem MS fragmentation analysis, which was subsequently validated with immunoassay.

Results:

A differential protein with m/z 11.6 kDa was detected and identified as an isoform of human serum amyloid A (SAA). It was significantly increased by 1822% in lung cancer patients when compared with the healthy controls, which gave an area under the receiver operator characteristic curve of 0.88. In addition, the protein was also significantly elevated by 77% in lung cancer patients with survival <5 years when compared with patients with survival ⩾5 years.

Conclusion:

There are several functions of the SAA protein, described in the context of inflammation, that are compatible with the mechanism of tumour invasion and metastasis. Our study not only detected increased SAA level in the serum of lung cancer patients but also identified that elevated SAA level may be a non-invasive biomarker useful for the prediction of lung cancer prognosis.

New serum biomarkers for detection of esophageal carcinoma using Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

PURPOSE

To screen for the potential protein biomarkers in serum for the diagnosis of esophageal carcinoma (EC) using proteomic fingerprint technology.

METHODS

Proteomic fingerprint technology combining magnetic beads with MALDI-TOF-MS was used to profile and compare the serum proteins from 78 patients with EC and 95 healthy blood donors. Proteomic patterns associated with EC were identified by Biomarker Patterns Software. Model of biomarkers was constructed and evaluated using the Biomarker Patterns Software.

RESULTS

A total of 60 discriminating m/z peaks were identified that were related to EC (P < 0.01). The model of biomarkers constructed by the Biomarker Patterns Software based on the four biomarkers (2049.6, 3936.5, 5339.9, and 13748.8 Da) generated excellent separation between the EC and control groups. The sensitivity was 92.5% and the specificity was 88%. Blind test data indicated a sensitivity of 89.5% and a specificity of 84.4%.

CONCLUSIONS

Biomarkers for EC can be discovered in serum by MALDI-TOF-MS combining the use of magnetic beads. The pattern of combined markers provides a powerful and reliable diagnostic method for EC with a high sensitivity and specificity.

[Research progress in SELDI-TOF MS and its clinical applications]

Proteinchip profiling is a powerful and innovative proteomic technology for the discovery of biomarkers and the development of diagnostic/prognostic assays. On the basis of surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS), Ciphergen’s proteinchip system offers a single, unified, and high throughput platform for a multitude of proteomic research applications. Proteins are the major functional components of the cell. The study of proteomics helps to better understand the mechanism of a disease. Remarkable findings in disease biomarkers have shed light on the early diagnosis, monitoring, and prognosis of various diseases, especially for cancer. In this paper, the development and technology of SELDI-TOF MS are introduced. The research progress and encouraging research results in malignancies, infectious diseases, neurological diseases, and diabetes mellitus using SELDI-TOF MS are reviewed. This paper concludes by evaluating the pros and cons, and the future perspectives are also expounded.

SELDI-TOF MS profiling of serum for detection of nasopharyngeal carcinoma

Background

No satisfactory biomarkers are currently available to screen for nasopharyngeal carcinoma (NPC). We have developed and evaluated surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) for detection and analysis of multiple proteins for distinguishing individuals with NPC from control individuals.

Methods

A preliminary learning set and a classification tree of spectra derived from 24 patients with NPC and a group of 24 noncancer controls were used to develop a proteomic model that discriminated cancer from noncancer effectively. Then, the validity of the classification tree was challenged with a blind test set, which included another 20 patients with NPC and 12 noncancer controls.

Results

A panel of 3 biomarkers ranging m/z 3–20 k was selected to establish Decision Tree model by BPS with sensitivity of 91.66% and specificity of 95.83%. The ability to detect NPC patients was evaluated, a sensitivity of 95.0% and specificity of 83.33% were validated in blind testing set.

Conclusion

This high-flux proteomic classification system will provide a highly accurate and innovative approach for the detection/diagnosis of NPC.

Reducing agent-mediated precipitation of high-abundance plasma proteins

Depletion of high-abundance proteins is regarded as a critical sample preparation step for most plasma proteomic analyses and profiling strategies. This report describes a process that rapidly and reproducibly precipitates high-abundance disulfide-rich proteins, including albumin and transferrin, from serum and plasma. A low volume of concentrated reducing agent, viz. dithiothreitol (DTT) or tris(2-carboxyethyl)phosphine (TCEP), was added directly to plasma followed by a brief incubation at ambient temperature. Removal of the precipitate via centrifugation and identification of the protein content revealed an albumin-enriched pellet. Direct analysis of the supernatant by MALDI-TOF-MS afforded peptidome and small protein profiles with enhanced features and minimal ionization of full-length albumin. The reproducible and quantitative nature of the method has been demonstrated by monitoring the plasma levels of an antiangiogenic protein biologic, rKringle5 (rK5). The 10.5-kDa analyte was only reliably detected in plasma after treatment with reducing agent, ionizing linearly from 150 to 1200 fmol (on-target) with a mean CV of 7%. This method distinguishes itself from immunoaffinity resin-based approaches since it can be scaled to large milliliter quantities and it is compatible with plasma from all species tested.

Serum amyloid A: an acute-phase protein involved in tumour pathogenesis

The synthesis of acute-phase protein serum amyloid A (SAA) is largely regulated by inflammation- associated cytokines and a high concentration of circulating SAA may represent an ideal marker for acute and chronic inflammatory diseases. However, SAA is also synthesized in extrahepatic tissues, e.g. human carcinoma metastases and cancer cell lines. An increasing body of in vitro data supports the concept of involvement of SAA in carcinogenesis and neoplastic diseases. Accumulating evidence suggests that SAA might be included in a group of biomarkers to detect a pattern of physiological events that reflect the growth of malignancy and host response. This review is meant to provide a broad overview of the many ways that SAA could contribute to tumour development, and accelerate tumour progression and metastasis, and to gain a better understanding of this acute-phase reactant as a possible link between chronic inflammation and neoplasia.

Autoantibodies as potential biomarkers for nasopharyngeal carcinoma

Autoantibody signatures, as new biomarkers, may improve the early detection of nasopharyngeal carcinoma (NPC). We constructed a T7 phage cDNA library from mixed NPC tissues, and we isolated 31 tumor-associated proteins using biopan enrichment techniques with sera from NPC patients and from healthy population. DNA sequence analysis showed that among 31 phage-displayed proteins, 22 have sequence identity with known or putative tumor-associated proteins. The results of immunochemical reactivity of patients' sera with phage-expressed proteins showed enrichment in the number of immunogenic phage clones in the biopanning process and also confirmed that antibodies were present in the sera of patients but not in the sera of healthy donors. The autoantibody against phage-expressed protein MAGE, HSP70, Fibronectin, and CD44 measured by ELISA had greater predictive value than that against EBNA-1, respectively. The antibody levels against MAGE in sera positively correlated with the clinical stages of NPC, and the antibody levels against other three proteins partly correlated with the clinical stages of NPC. Our studies suggested that the autoantibodies against tumor-associated antigens in the sera of NPC patients could be used as a screening test for NPC. Studies of the corresponding proteins may have significances in tumor biology, novel drug development, and immunotherapy.

Proteomic approach to biomarker discovery in cancer tissue from lung adenocarcinoma among nonsmoking Chinese women in Hong Kong

Half of the female patients with adenocarcinoma in East Asia are never-smokers. Proteomic analysis of tumor tissue may throw important light on the pathogenesis of this interesting subgroup of lung cancer. The cancer and adjacent normal lung tissue were taken from 21 never-smoked adenocarcinoma and profiled using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS). Fifty-two proteins were significantly discriminatory between tumor and normal lung tissues. Ninety-three proteins were found to have high accuracy in discriminating between adenocarcinoma with or without smoking history. These proteins may yield new insights about the altered pathogenetic pathways of never-smoked lung cancers.

Structure and function of inter-alpha-trypsin inhibitor heavy chains

Inter-alpha-trypsin inhibitor family proteins are mainly detected in plasma and urine and comprise the common light chain bikunin and at least 6 closely related heavy chains. The bikunin moiety exhibits protease inhibitory activity and has been studied extensively; however, the heavy chains have been largely overlooked. Recent studies clearly indicate that the heavy chain moieties have important biological functions either in association with or independent of bikunin. Because the heavy chains comprise the main part of the protein structure of this family, it is important to understand their functions. This review summarizes the domain structural features of heavy chains, the heavy chain-interacting molecules identified thus far, and the association of heavy chains with diseases to encourage the discovery of novel heavy chains-interacting molecules and to gain a deeper insight into their functions.

Contribution of oncoproteomics to cancer biomarker discovery

Oncoproteomics is the study of proteins and their interactions in a cancer cell by proteomic technologies. Proteomic research first came to the fore with the introduction of two-dimensional gel electrophoresis. At the turn of the century, proteomics has been increasingly applied to cancer research with the wide-spread introduction of mass spectrometry and proteinchip. There is an intense interest in applying proteomics to foster an improved understanding of cancer pathogenesis, develop new tumor biomarkers for diagnosis, and early detection using proteomic portrait of samples. Oncoproteomics has the potential to revolutionize clinical practice, including cancer diagnosis and screening based on proteomic platforms as a complement to histopathology, individualized selection of therapeutic combinations that target the entire cancer-specific protein network, real-time assessment of therapeutic efficacy and toxicity, and rational modulation of therapy based on changes in the cancer protein network associated with prognosis and drug resistance. Besides, oncoproteomics is also applied to the discovery of new therapeutic targets and to the study of drug effects. In pace with the successful completion of the Human Genome Project, the wave of proteomics has raised the curtain on the postgenome era. The study of oncoproteomics provides mankind with a better understanding of neoplasia. In this article, the discovery of cancer biomarkers in recent years is reviewed. The challenges ahead and perspectives of oncoproteomics for biomarkers development are also addressed. With a wealth of information that can be applied to a broad spectrum of biomarker research projects, this review serves as a reference for biomarker researchers, scientists working in proteomics and bioinformatics, oncologists, pharmaceutical scientists, biochemists, biologists, and chemists.

Nasopharyngeal carcinoma: molecular biomarker discovery and progress

Nasopharyngeal carcinoma (NPC) is a rare malignancy in most part of the world and it is one of the most confusing, commonly misdiagnosed and poorly understood diseases. The cancer is an Epstein-Barr virus-associated malignancy with a remarkable racial and geographical distribution. It is highly prevalent in southern Asia where the disease occurs at a prevalence about a 100-fold higher compared with other populations not at risk. The etiology of NPC is thought to be associated with a complex interaction of genetic, viral, environmental and dietary factors. Thanks to the advancements in genomics, proteomics and bioinformatics in recent decades, more understanding of the disease etiology, carcinogenesis and progression has been gained. Research into these components may unravel the pathways in NPC development and potentially decipher the molecular characteristics of the malignancy. In the era of molecular medicine, specific treatment to the potential target using technologies such as immunotherapy and RNAi becomes formulating from bench to bedside application and thus makes molecular biomarker discovery more meaningful for NPC management. In this article, the latest molecular biomarker discovery and progress in NPC is reviewed with respect to the diagnosis, monitoring, treatment and prognostication of the disease.