2D-DIGE analysis of sera from transgenic mouse models reveals novel candidate protein biomarkers for human gastric cancer

Prognostic and clinicopathological significance of Hapto and Gremlin1 expression in extrahepatic cholangiocarcinoma

Background: Some studies have demonstrated that Hapto and Gremlin1 play an important biological role in many neoplasms. However, the role of Hapto and Gremlin1 in extrahepatic cholangiocarcinoma (ECC) remains to be revealed. Thus, this study investigated the prognostic and clinicopathological significance of Hapto and Gremlin1 expression in ECC.

Methods: We examined Hapto and Gremlin1 expression in 100 ECC, 30 peritumoral tissues, 10 adenoma and 15 normal biliary tract tissues using EnVision immunohistochemistry. The relationship between Hapto and Gremlin 1 expression and clinicopathological parameters was evaluated using the χ² test or Fisher's exact test. The overall survival of patients was analyzed using Kaplan-Meier univariate survival analysis and log-rank tests.

Results: Hapto and Gremlin1 proteins were overexpressed in ECC compared to peritumoral tissues, adenoma, and normal biliary tract (P<0.05 or P<0.01). The positive rate of Hapto and Gremlin1 expression was significantly higher in cases with poor differentiation, lymph node metastasis, invasion of surrounding tissues and organs, a tumor-node-metastasis (TNM) stage of III or IV and no resection. Kaplan-Meier survival analysis showed that ECC patients with positive Hapto and/or Gremlin1 expression survived significantly shorter than patients with negative Hapto and/or Gremlin1 expression. Cox multivariate analysis revealed that positive Hapto and Gremlin1 expression were independent poor prognostic factors in ECC patients.

Conclusion: The present study indicated that positive Hapto and/or Gremlin1 expression are closely associated with the pathogenesis, clinical, pathological and biological behaviors, and poor prognosis in ECC.

Exploration of vascular adhesion protein-1 expression in patients with conjunctivitis associated systemic lupus erythematosus using 2D-DIGE

Conjunctivitis associated systemic lupus erythematosus (caSLE) is a connective tissue autoimmune disease with a large spectrum of clinical manifestations. The disease may lead to ocular complications and in severe cases may be sight-threatening. This study investigated the expression of vascular adhesion protein-1 (VAP-1) in SLE patients with conjunctivitis and the relationship between VAP-1 and other proteins in the onset of the disease. Ten patients with caSLE (caSLE group) and 10 healthy volunteers (control group) were enrolled in the study, in order to evaluate the VAP-1 expression levels in blood. Protein expression profiling was performed with two-dimensional fluorescence difference gel electrophoresis (2D-DIGE) and analyzed with matrix-assisted laser desorption/deionization time-of-flight (MALDI-TOF) used in tandem with mass spectrometry. In the caSLE group, 8 proteins were expressed differenty compared with the control group: C-reactive protein, hemoglobin subunit β, VAP-1, A-albumin (AFAM), enolase and immunoglobulin heavy constant mu were upregulated; interferon regulatory factor-1 and serum amyloid A2 protein were downregulated. Western blotting results are consistent with the proteomics results, showing that in caSLE group VAP-1 expression is increased in comparison to the control group. VAP-1 protein participates in the inflammatory reaction in the form of amine oxidase, copper containing 3. Bioinformatics analysis suggested that VAP-1 protein could be used as a candidate protein for further study regarding its role as a potential protein marker for screening and effectively monitoring caSLE.

Urine afamin and afamin-creatinine ratio as biomarkers for kidney injury

AIM

The aim of this study was to evaluate the urine afamin (uAFM) and afamin-creatinine ratio (AfCR) levels in patients with glomerulonephritis.

PATIENTS & METHODS

We determined uAFM and AfCR of 247 healthy volunteers and 129 biopsy-proven glomerulonephritis patients.

RESULTS

Analytical evaluation study revealed the assay is a reliable and robust test for measuring uAFM. For reference intervals, uAFM and AfCR values were different significantly between males and females. uAFM and AfCR levels were significantly increased in patients with primary membranous nephropathy, IgA nephropathy and minimal change disease compared with healthy volunteers. uAFM and AfCR were positively correlated with urine albumin and albumin-creatinine ratio, respectively.

CONCLUSION

Our study suggested that uAFM and AfCR may be attractive biomarkers for kidney injury.

Sex hormone-binding globulin (SHBG) is a potential early diagnostic biomarker for gastric cancer

The use of blood plasma biomarkers in gastric cancer (GC) management is limited due to a lack of reliable biomarkers. An LC-MS/MS assay and a bioinformatic analysis were performed to identify blood plasma biomarkers in a GC discovery cohort. The data obtained were verified and validated by western blotting and an ELISA in an independent study cohort. A label-free quantification analysis of the MS data using PEAKS7 software found that four plasma proteins of apolipoprotein C-1, gelsolin, sex hormone-binding globulin (SHBG), and complement component C4-A were significantly overexpressed in GC patients. A western blot assay of these plasma proteins showed that only SHBG was consistently overexpressed in the patient group. ELISA measurement of SHBG blood plasma levels confirmed that the patient group had significantly higher SHBG levels than the control group. SHBG levels in the patient group remained significantly higher after being stratified by gender, age, and disease stage. These findings show that LC-MS/MS is powerful and highly sensitive for plasma biomarker discovery, and SHBG could be a potential plasma biomarker for GC management.

The cytoprotective protein clusterin is overexpressed in hypergastrinemic rodent models of oxyntic preneoplasia and promotes gastric cancer cell survival

The cytoprotective protein clusterin is often dysregulated during tumorigenesis, and in the stomach, upregulation of clusterin marks emergence of the oxyntic atrophy (loss of acid-producing parietal cells)-associated spasmolytic polypeptide-expressing metaplasia (SPEM). The hormone gastrin is important for normal function and maturation of the gastric oxyntic mucosa and hypergastrinemia might be involved in gastric carcinogenesis. Gastrin induces expression of clusterin in adenocarcinoma cells. In the present study, we examined the expression patterns and gastrin-mediated regulation of clusterin in gastric tissue from: humans; rats treated with proton pump (H+/K+-ATPase) inhibitors and/or a gastrin receptor (CCK2R) antagonist; H+/K+-ATPase β-subunit knockout (H/K-β KO) mice; and Mongolian gerbils infected with Helicobacter pylori and given a CCK2R antagonist. Biological function of secretory clusterin was studied in human gastric cancer cells. Clusterin was highly expressed in neuroendocrine cells in normal oxyntic mucosa of humans and rodents. In response to hypergastrinemia, expression of clusterin increased significantly and its localization shifted to basal groups of proliferative cells in the mucous neck cell-chief cell lineage in all animal models. That shift was partially inhibited by antagonizing the CCK2R in rats and gerbils. The oxyntic mucosa of H/K-β KO mice contained areas with clusterin-positive mucous cells resembling SPEM. In gastric adenocarcinomas, clusterin mRNA expression was higher in diffuse tumors containing signet ring cells compared with diffuse tumors without signet ring cells, and clusterin seemed to be secreted by tumor cells. In gastric cancer cell lines, gastrin increased secretion of clusterin, and both gastrin and secretory clusterin promoted survival after starvation- and chemotherapy-induced stress. Overall, our results indicate that clusterin is overexpressed in hypergastrinemic rodent models of oxyntic preneoplasia and stimulates gastric cancer cell survival.

Proteome Analysis of Drosophila Mutants Identifies a Regulatory Role for 14-3-3ε in Metabolic Pathways

The evolutionary conserved family of 14-3-3 proteins appears to have a role in integrating numerous intracellular pathways, including signal transduction, intracellular trafficking, and metabolism. However, little is known about how this interactive network might be affected by the direct abrogation of 14-3-3 function. The loss of Drosophila 14-3-3ε resulted in reduced survival of mutants during larval-to-adult transition, which is known to depend on an energy supply coming from the histolysis of fat body tissue. Here we report a differential proteomic analysis of larval fat body tissue at the onset of larval-to-adult transition, with the loss of 14-3-3ε resulting in the altered abundance of 16 proteins. These included proteins linked to protein biosynthesis, glycolysis, tricarboxylic acid cycle, and lipid metabolic pathways. The ecdysone receptor (EcR), which is responsible for initiating the larval-to-adult transition, colocalized with 14-3-3ε in wild-type fat body tissues. The altered protein abundance in 14-3-3ε mutant fat body tissue was associated with transcriptional deregulation of alcohol dehydrogenase, fat body protein 1, and lamin genes, which are known targets of the EcR. This study indicates that 14-3-3ε has a critical role in cellular metabolism involving either molecular crosstalk with the EcR or direct interaction with metabolic proteins.

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

INTRODUCTION

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

Progress in the development of protein biomarkers of oesophageal and gastric cancers

Upper gastrointestinal cancers originating in the oesophagus and stomach often present late and have a very poor prognosis. Treatment options include surgery for localised disease but, increasingly, neoadjuvant chemotherapy and radiotherapy are being employed to improve outcome. There is often a variable response to neoadjuvant treatment between individual patients and side effects are relatively common. There is an urgent need for novel biomarkers of upper gastrointestinal cancer, not only to improve screening and early diagnosis of the oesophageal and gastric cancers when treatment options are potentially more effective, but also to accurately guide therapy in more advanced disease. The development of predictive biomarkers will also help to more effectively identify those patients that will benefit from targeted therapies. Although many promising results have been derived from these studies there remains a lack of validated clinically applicable biomarkers available for translation into routine clinical use. This review will provide an overview of the recent proteomic research on upper gastrointestinal cancer protein biomarker identification and validation. The challenges faced in the development of validated, clinically acceptable and accurate protein biomarkers will also be discussed, along with possible areas of future progress.

Significance of Serum Pepsinogens as a Biomarker for Gastric Cancer and Atrophic Gastritis Screening: A Systematic Review and Meta-Analysis

BACKGROUND

Human pepsinogens are considered promising serological biomarkers for the screening of atrophic gastritis (AG) and gastric cancer (GC). However, there has been controversy in the literature with respect to the validity of serum pepsinogen (SPG) for the detection of GC and AG. Consequently, we conducted a systematic review and meta-analysis to assess the diagnostic accuracy of SPG in GC and AG detection.

METHODS

We searched PubMed, Embase, and the Chinese National Knowledge Infrastructure (CNKI) for correlative original studies published up to September 30, 2014. The summary sensitivity, specificity, positive diagnostic likelihood ratio (DLR+), negative diagnostic likelihood ratio (DLR-), area under the summary receiver operating characteristic curve (AUC) and diagnostic odds ratio (DOR) were used to evaluate SPG in GC and AG screening based on bivariate random effects models. The inter-study heterogeneity was evaluated by the I2 statistics and publication bias was assessed using Begg and Mazumdar's test. Meta-regression and subgroup analyses were performed to explore study heterogeneity.

RESULTS

In total, 31 studies involving 1,520 GC patients and 2,265 AG patients were included in the meta-analysis. The summary sensitivity, specificity, DLR+, DLR-, AUC and DOR for GC screening using SPG were 0.69 (95% CI: 0.60-0.76), 0.73 (95% CI: 0.62-0.82), 2.57 (95% CI: 1.82-3.62), and 0.43 (95% CI: 0.34-0.54), 0.76 (95% CI: 0.72-0.80) and 6.01 (95% CI: 3.69-9.79), respectively. For AG screening, the summary sensitivity, specificity, DLR+, DLR-, AUC and DOR were 0.69 (95% CI: 0.55-0.80), 0.88 (95% CI: 0.77-0.94), 5.80 (95% CI: 3.06-10.99), and 0.35 (95% CI: 0.24-0.51), 0.85 (95% CI: 0.82-0.88) and 16.50 (95% CI: 8.18-33.28), respectively. In subgroup analysis, the use of combination of concentration of PGI and the ratio of PGI:PGII as measurement of SPG for GC screening yielded sensitivity of 0.70 (95% CI: 0.66-0.75), specificity of 0.79 (95% CI: 0.79-0.80), DOR of 6.92 (95% CI: 4.36-11.00), and AUC of 0.78 (95% CI: 0.72-0.81), while the use of concentration of PGI yielded sensitivity of 0.55 (95% CI: 0.51-0.60), specificity of 0.79 (95% CI: 0.76-0.82), DOR of 6.88 (95% CI: 2.30-20.60), and AUC of 0.77 (95% CI: 0.73-0.92). For AG screening, the use of ratio of PGI:PGII as measurement of SPG yielded sensitivity of 0.69 (95% CI: 0.52-0.83), specificity of 0.84 (95% CI: 0.68-0.93), DOR of 11.51 (95% CI: 6.14-21.56), and AUC of 0.83 (95% CI: 0.80-0.86), the use of combination of concentration of PGI and the ratio of PGI:PGII yield sensitivity of 0.79 (95% CI: 0.72-0.85), specificity of 0.89 (95% CI: 0.85-0.93), DOR of 24.64 (95% CI: 6.95-87.37), and AUC of 0.87 (95% CI: 0.81-0.92), concurrently, the use of concentration of PGI yield sensitivity of 0.46 (95% CI: 0.38-0.54), specificity of 0.93 (95% CI: 0.91-0.95), DOR of 19.86 (95% CI: 0.86-456.91), and AUC of 0.86 (95% CI: 0.52-1.00).

CONCLUSION

SPG has great potential as a noninvasive, population-based screening tool in GC and AG screening. In addition, given the potential publication bias and high heterogeneity of the included studies, further high quality studies are required in the future.

Afamin--A pleiotropic glycoprotein involved in various disease states

The human glycoprotein afamin was discovered as the fourth member of the albumin gene family. Despite intense research over the last 20 years, our knowledge of afamin's physiological or pathophysiological functions is still very limited. Circulating afamin is primarily of hepatic origin and abundant concentrations are found in plasma, cerebrospinal, ovarian follicular and seminal fluids. In vitro binding studies revealed specific binding properties for vitamin E. A previously performed analytical characterization and clinical evaluation study of an enzyme-linked immunosorbent assay for quantitative measurement of afamin in human plasma demonstrated that the afamin assay meets the quality specifications for laboratory medicine. Comparative proteomics has identified afamin as a potential biomarker for ovarian cancer and these findings were confirmed by quantitative immunoassay of afamin and validated in independent cohorts of patients with ovarian cancer. Afamin has also been investigated in other types of carcinoma. Most of these studies await further evaluation with validated quantitative afamin assays and require validation in larger patient cohorts. Transgenic mice overexpressing the human afamin gene revealed increased body weight and increased blood concentrations of lipids and glucose. These transgenic mouse data were in line with three large human population-based studies showing that afamin is strongly associated with the prevalence and development of the metabolic syndrome. This review summarizes and discusses the molecular, biochemical and analytical characterization of afamin as well as possible clinical applications of afamin measurement.

Divide and conquer: subproteomic approaches toward gastric cancer biomarker and drug target discovery

The discovery of biomarkers for early detection and treatment for gastric cancer are two important gaps that proteomics have the potential to fill. Advancements in mass spectrometry, sample preparation and separation strategies are crucial to proteomics-based discoveries and subsequent translations from bench to bedside. A great number of studies exploiting various subproteomic approaches have emerged for higher-resolution analysis (compared with shotgun proteomics) that permit interrogation of different post-translational and subcellular compartmentalized forms of the same proteins as determinants of disease phenotypes. This is a unique and key strength of proteomics over genomics. In this review, the salient features, competitive edges and pitfalls of various subproteomic approaches are discussed. We also highlight valuable insights from several subproteomic studies that have increased our understanding of the molecular etiology of gastric cancer and the findings that led to the discovery of potential biomarkers/drug targets that were otherwise not revealed by conventional shotgun expression proteomics.

Identification and validation of novel candidate protein biomarkers for the detection of human gastric cancer

The timely detection of gastric cancer will contribute significantly towards effective treatment and is aided by the availability and reliability of appropriate biomarkers. A combination of several biomarkers can improve the sensitivity and specificity of cancer detection and this work reports results from a panel of 4 proteins. By combining a validated preclinical mouse model with a proteomic approach we have recently discovered novel biomarkers for the detection of gastric cancer. Here, we investigate the specificity of four of those biomarkers (afamin, clusterin, VDBP and haptoglobin) for the detection of gastric cancer using two independent methods of validation: ELISA, and a non antibody based method: Multiple Reaction Monitoring with High Resolution Mass Spectrometry (MRM-HR). All four biomarkers reliably differentiated GC from benign patient serum, and also in a small cohort of 11 early stage cases. We also present a novel isoform specific biomarker alpha-1-antitrypsin (A1AT) that was identified using a mouse model for gastric cancer. This isoform is distinct in charge and mobility in a pH gradient and was validated using human samples by isoelectric focussing and Western-blot (IEF-WB). This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge.

Protein profiling using two-dimensional difference gel electrophoresis (2-D DIGE)

2-D DIGE relies on pre-electrophoretic labeling of samples with one of three spectrally distinct fluorescent dyes, followed by electrophoresis of all samples in one 2-D gel. The dye-labeled samples are then viewed individually by scanning the gel at different wavelengths, which circumvents problems with gel-to-gel variation and spot matching between gels. Image analysis programs are used to generate volume ratios for each spot, which essentially describe the intensity of a particular spot in each test sample, and thus enable protein abundance level changes to be identified and quantified. This unit describes the 2-D DIGE procedure including sample preparation from various cell types, labeling of proteins, and points to consider in the downstream processing of fluorescently labeled samples.

Dip biosensor based on localized surface plasmon resonance at the tip of an optical fiber

A dip biosensor is realized by depositing metallic nanoparticles onto the tip of a cleaved optical fiber. Light coupled into the fiber interacts with the localized surface plasmons within the nanoparticles at the tip; a portion of the scattered light recouples into the optical fiber and is analyzed by a spectrometer. Characterization of the sensor demonstrates an inverse relationship between the sensitivity and the number of particles deposited onto the surface, with smaller quantities leading to greater sensitivity. The results obtained showed also that by depositing nanoparticles with distinct localized surface plasmon resonance signatures with limited overlap, as for the case of gold and silver nanospheres, a multiplexed dip biosensor can be realized by simply functionalizing the different nanoparticles with different antibodies after the fashion of an immunoassay. In this way different localized surface plasmons resonance bands responsive to different target analytes can be separately monitored, as further presented below, requiring a minimal quantity of reagents both for the functionalization process and for the sample analysis.

Expression of prolyl 4-hydroxylase beta-polypeptide in non-small cell lung cancer treated with Chinese medicines

OBJECTIVES

To investigate the role of prolyl 4-hydroxylase beta polypeptide (P4HB) expressed in lung carcinoma and the intervention effect of Yiqi Chutan Formula (, YQCTF).

METHODS

Lung carcinoma model was established by subcutaneously inoculating LEWIS lung carcinoma cells in C57BL/6J mice. The differential expression of P4HB protein between the YQCTF (3.0 g/kg, gavage, once daily, 21 days) group and the control group was acquired by a 2 fluorescence difference gel electrophoresis (2D-DIGE), verified by Western blotting and identified by matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF/TOF-MS). The expression of P4HB and P4HB mRNA in cultured A549 cells from cisplatin (DDP) 1.5 µg/mL group and 15% serum combined with DDP 1.5 µg/mL group were detected by cellular immunohistochemistry and reverse transcription-polymerase chain reaction, respectively.

RESULTS

The proteomics research discovered that one-third of differential proteins including P4HB were decreased in the YQCTF group (P<0.01). Clinical pathology and tissue microarray studies showed that P4HB expression in lung cancer tissue was stronger than adjacent tissues and normal lung epithelial (P<0.01). In the YQCTF and DDP combined groups, the expression of P4HB and P4HB mRNA in A549 cell were decreased significantly (P<0.01).

CONCLUSION

YQCTF could inhibit the LEWIS lung carcinoma's growth, decrease the expression of P4HB in LEWIS lung carcinoma and A549 cells. YQCTF might take effect through regulating P4HB in endoplasmic reticulum to inhibit the incidence and growth process of lung carcinoma.

Identification of N-glycosylation in hepatocellular carcinoma patients' serum with a comparative proteomic approach

AIM

This study is to explore the different expressions of serum N-glycoproteins and glycosylation sites between hepatocellular carcinoma (HCC) patients and healthy controls.

METHOD

We combined high abundant proteins depletion and hydrophilic affinity method to enrich the glycoproteins. Through liquid chromatography-tandem mass spectrometry (LC-MS/MS), we extensively surveyed different expressions of glycosylation sites and glycoproteins between the two groups.

RESULT

This approach identified 152 glycosylation sites and 54 glycoproteins expressed differently between HCC patients and healthy controls. With the absolute values of Pearson coefficients of at least 0.8, eight proteins were identified significantly up or down regulated in HCC serum. Those proteins are supposed to be involved in several biological processes, cellular components and molecular functions of hepatocarcinogenesis. Several of them had been reported abnormally regulated in several kinds of malignant tumors, and may be promising biomarkers of HCC.

CONCLUSION

Our work provides a systematic and quantitative method of glycoproteomics and demonstrates some key changes in clinical HCC serum. These proteomic signatures may help to unveil the underlying mechanisms of hepatocarcinogenesis and may be useful for the exploration of candidate biomarkers.

N-glycoprotein SRMAtlas: a resource of mass spectrometric assays for N-glycosites enabling consistent and multiplexed protein quantification for clinical applications

Protein biomarkers have the potential to transform medicine as they are clinically used to diagnose diseases, stratify patients, and follow disease states. Even though a large number of potential biomarkers have been proposed over the past few years, almost none of them have been implemented so far in the clinic. One of the reasons for this limited success is the lack of technologies to validate proposed biomarker candidates in larger patient cohorts. This limitation could be alleviated by the use of antibody-independent validation methods such as selected reaction monitoring (SRM). Similar to measurements based on affinity reagents, SRM-based targeted mass spectrometry also requires the generation of definitive assays for each targeted analyte. Here, we present a library of SRM assays for 5568 N-glycosites enabling the multiplexed evaluation of clinically relevant N-glycoproteins as biomarker candidates. We demonstrate that this resource can be utilized to select SRM assay sets for cancer-associated N-glycoproteins for their subsequent multiplexed and consistent quantification in 120 human plasma samples. We show that N-glycoproteins spanning 5 orders of magnitude in abundance can be quantified and that previously reported abundance differences in various cancer types can be recapitulated. Together, the established N-glycoprotein SRMAtlas resource facilitates parallel, efficient, consistent, and sensitive evaluation of proposed biomarker candidates in large clinical sample cohorts.