Identification of five serum protein markers for detection of ovarian cancer by antibody arrays

Primary Peritoneal Serous Cancer: A Case Report of a Tumor in the Rectovaginal Septum

Peritoneal cancer is the invasion by malignant cells of serous membrane that lines the abdominal cavity, the viscera, and the coelom of the amniotes. Histologically, it is indistinguishable from ovarian counterpart, although in the former, it commonly involves the ovary only superficially, or it may totally lack an ovarian component, but with extensive involvement of the peritoneum, calcified perihepatic peritoneal nodules, or involvement of the omentum, in most cases. The current study describes the case of a 54-year-old female patient referring a history of colitis and dairy intolerance. A transvaginal ultrasound and a computed tomography (CT) scan revealed a tumor measuring 70 × 61 × 63 mm. CA-125 serum levels were 880 U/ml. Laparotomy surgery was indicated, and tumor was found at the level of the rectovaginal septum without evidence of metastasis. Tumor dissection and protective colostomy with loop sigmoid colon were performed. A pathological study gave a diagnosis of a high-grade peritoneal serous carcinoma with a micropapillary pattern. The present study describes the case of papillary serous peritoneal cancer presented as a single tumor mass without extensive involvement of the peritoneum. Additionally, the need for routine tests for its diagnosis and documenting hormonal alterations as the cause of its origin are suggested.

Use of a Recombinant Biomarker Protein DDA Library Increases DIA Coverage of Low Abundance Plasma Proteins

Credible detection and quantification of low abundance proteins from human blood plasma is a major challenge in precision medicine biomarker discovery when using mass spectrometry (MS). In this proof-of-concept study, we employed a mixture of selected recombinant proteins in DDA libraries to subsequently identify (not quantify) cancer-associated low abundance plasma proteins using SWATH/DIA. The exemplar DDA recombinant protein spectral library (rPSL) was derived from tryptic digestion of 36 recombinant human proteins that had been previously implicated as possible cancer biomarkers from both our own and other studies. The rPSL was then used to identify proteins from nondepleted colorectal cancer (CRC) EDTA plasmas by SWATH-MS. Most (32/36) of the proteins used in the rPSL were reliably identified from CRC plasma samples, including 8 proteins (i.e., BTC, CXCL10, IL1B, IL6, ITGB6, TGFα, TNF, TP53) not previously detected using high-stringency protein inference MS according to PeptideAtlas. The rPSL SWATH-MS protocol was compared to DDA-MS using MARS-depleted and postdigestion peptide fractionated plasmas (here referred to as a human plasma DDA library). Of the 32 proteins identified using rPSL SWATH, only 12 could be identified using DDA-MS. The 20 additional proteins exclusively identified using the rPSL SWATH approach were almost exclusively lower abundance (i.e., <10 ng/mL) proteins. To mitigate justified FDR concerns, and to replicate a more typical library creation approach, the DDA rPSL library was merged with a human plasma DDA library and SWATH identification repeated using such a merged library. The majority (33/36) of the low abundance plasma proteins added from the rPSL were still able to be identified using such a merged library when high-stringency HPP Guidelines v3.0 protein inference criteria were applied to our data set. The MS data set has been deposited to ProteomeXchange Consortium via the PRIDE partner repository (PXD022361).

Convergence of Plasma Metabolomics and Proteomics Analysis to Discover Signatures of High-Grade Serous Ovarian Cancer

Simple Summary

In-time diagnosing ovarian cancer, intractable cancer that has no symptoms can increase the survival of women. The aim of this study was to discover biomarkers from liquid biopsy samples using multi-omics approach, metabolomics and proteomics for the diagnosis of ovarian cancer. To verify our biomarker candidates, we conducted comparative analysis with other previous published studies. Despite the limitations of non-invasive samples, our findings are able to discover emerging properties through the interplay between metabolites and proteins and mechanism-based biomarkers through integrated protein and metabolite analysis.

Abstract

The 5-year survival rate in the early and late stages of ovarian cancer differs by 63%. In addition, a liquid biopsy is necessary because there are no symptoms in the early stage and tissue collection is difficult without using invasive methods. Therefore, there is a need for biomarkers to achieve this goal. In this study, we found blood-based metabolite or protein biomarker candidates for the diagnosis of ovarian cancer in the 20 clinical samples (10 ovarian cancer patients and 10 healthy control subjects). Plasma metabolites and proteins were measured and quantified using mass spectrometry in ovarian cancer patients and control groups. We identified the differential abundant biomolecules (34 metabolites and 197 proteins) and statistically integrated molecules of different dimensions to better understand ovarian cancer signal transduction and to identify novel biological mechanisms. In addition, the biomarker reliability was verified through comparison with existing research results. Integrated analysis of metabolome and proteome identified emerging properties difficult to grasp with the single omics approach, more reliably interpreted the cancer signaling pathway, and explored new drug targets. Especially, through this analysis, proteins (PPCS, PMP2, and TUBB) and metabolites (L-carnitine and PC-O (30:0)) related to the carnitine system involved in cancer plasticity were identified.

Emerging Technologies and Platforms for the Immunodetection of Multiple Biochemical Markers in Osteoarthritis Research and Therapy

Biomarkers, especially biochemical markers, are important in osteoarthritis (OA) research, clinical trials, and drug development and have potential for more extensive use in therapeutic monitoring. However, they have not yet had any significant impact on disease diagnosis and follow-up in a clinical context. Nevertheless, the development of immunoassays for the detection and measurement of biochemical markers in OA research and therapy is an active area of research and development. The evaluation of biochemical markers representing low-grade inflammation or extracellular matrix turnover may permit OA prognosis and expedite the development of personalized treatment tailored to fit particular disease severities. However, currently detection methods have failed to overcome specific hurdles such as low biochemical marker concentrations, patient-specific variation, and limited utility of single biochemical markers for definitive characterization of disease status. These challenges require new and innovative approaches for development of detection and quantification systems that incorporate clinically relevant biochemical marker panels. Emerging platforms and technologies that are already on the way to implementation in routine diagnostics and monitoring of other diseases could potentially serve as good technological and strategic examples for better assessment of OA. State-of-the-art technologies such as advanced multiplex assays, enhanced immunoassays, and biosensors ensure simultaneous screening of a range of biochemical marker targets, the expansion of detection limits, low costs, and rapid analysis. This paper explores the implementation of such technologies in OA research and therapy. Application of novel immunoassay-based technologies may shed light on poorly understood mechanisms in disease pathogenesis and lead to the development of clinically relevant biochemical marker panels. More sensitive and specific biochemical marker immunodetection will complement imaging biomarkers and ensure evidence-based comparisons of intervention efficacy. We discuss the challenges hindering the development, testing, and implementation of new OA biochemical marker assays utilizing emerging multiplexing technologies and biosensors.

Investigating a novel multiplex proteomics technology for detection of changes in serum protein concentrations that may correlate to tumor burden

Background: To account for cancer heterogeneity, we previously introduced the concept of "personalized" tumor markers, which are biomarkers that are informative in subsets of patients or even a single patient. Recent developments in various multiplex protein technologies create excitement for the discovery of markers of tumor burden in individual patients, but the reliability of the technologies remains to be tested for this purpose. Here, we sought to explore the potential of a novel proteomics platform, which utilizes a multiplexed antibody microarray, to detect changes in serum protein concentration that may correlate to tumor burden in pancreatic cancer. Methods: We applied the Quantibody® Human Kiloplex Array to simultaneously measure 1,000 proteins in sera obtained pre- and post-surgically from five pancreatic cancer patients. We expected that proteins which decreased post-surgery may correlate to tumor burden. Sera from two healthy individuals, split into two aliquots each, were used as controls. To validate the multiplexed results, we used single-target ELISA assays to measure the proteins with the largest serum concentration changes after surgery in sera collected pre- and post-surgically from the previous five patients and 10 additional patients. Results: The multiplexed array revealed nine proteins with more than two-fold post-surgical decrease in at least two of five patients. However, validation using single ELISAs showed that only two proteins tested displayed more than two-fold post-surgical decrease in one of the five original patients. In the independent cohort, six of the proteins tested showed at least a two-fold decrease post-surgery in at least one patient. Conclusions: Our study found that the Quantibody® Human Kiloplex Array results could not be reliably replicated with individual ELISA assays and most hits would likely represent false positives if applied to biomarker discovery. These findings suggest that data from novel, high-throughput proteomic platforms need stringent validation to avoid false discoveries.

Investigating a novel multiplex proteomics technology for detection of changes in serum protein concentrations that may correlate to tumor burden

Background: To account for cancer heterogeneity, we previously introduced the concept of "personalized" tumor markers, which are biomarkers that are informative in subsets of patients or even a single patient. Recent developments in various multiplex protein technologies create excitement for the discovery of markers of tumor burden in individual patients, but the reliability of the technologies remains to be tested for this purpose. Here, we sought to explore the potential of a novel proteomics platform, which utilizes a multiplexed antibody microarray, to detect changes in serum protein concentration that may correlate to tumor burden in pancreatic cancer. Methods: We applied the Quantibody® Human Kiloplex Array to simultaneously measure 1,000 proteins in sera obtained pre- and post-surgically from five pancreatic cancer patients. We expected that proteins which decreased post-surgery may correlate to tumor burden. Sera from two healthy individuals, split into two aliquots each, were used as controls. To validate the multiplexed results, we used single-target ELISA assays to measure the proteins with the largest serum concentration changes after surgery in sera collected pre- and post-surgically from the previous five patients and 10 additional patients. Results: The multiplexed array revealed nine proteins with more than two-fold post-surgical decrease in at least two of five patients. However, validation using single ELISAs showed that only two proteins tested displayed more than two-fold post-surgical decrease in one of the five original patients. In the independent cohort, six of the proteins tested showed at least a two-fold decrease post-surgery in at least one patient. Conclusions: Our study found that the Quantibody® Human Kiloplex Array results could not be reliably replicated with individual ELISA assays and most hits would likely represent false positives if applied to biomarker discovery. These findings suggest that data from novel, high-throughput proteomic platforms need stringent validation to avoid false discoveries.

Changes in the Concentration of Markers Participating in the Regulation of the Apoptosis Receptor Pathway Involving Soluble Tumour Necrosis Factor Ligand inducing Apoptosis (sTRAIL) and Osteoprotegerin (OPG) in the Serum of Women with Ovarian Cancer-Participation in Pathogenesis or a Possible Clinical Use?

Due to the ability to selectively induce apoptosis in cancer cells, the most interesting target for clinical research is the tumour necrosis factor ligand inducing apoptosis (TRAIL), which binds specific receptors, including osteoprotegerin (OPG). The aim of the study was to analyse the concentration of soluble TRAIL (sTRAIL) and OPG in the serum of women with serous or mucinous ovarian cancer, taking into account different levels of cancer histological differentiation. The group included 97 women with the diagnosed Cystadenocarcinoma papillare serosum IIIc and Cystadenocarcinoma mucinosum IIIc. Concentrations of parameters were measured by ELISA. Analysis of the obtained results showed a statistically significantly higher concentration of sTRAIL and OPG in the serum of women with ovarian serous and mucinous cancer compared to the control group (p < 0.0001). Statistical significance was found between sTRAIL and OPG concentration in G1 and G3 serous cancer (p < 0.01) and in OPG mucinous cancer between G1 and G3 (p < 0.01) and G2 and G3 (p < 0.01). An important role in the pathogenesis of ovarian cancer is played by disorders of the apoptosis process involving the sTRAIL/OPG system, which are associated with the histological type and the degree of histological differentiation of the tumour. Determining the concentration of tested parameters in combination with other markers may be useful in the future in the diagnosis of ovarian cancer, but that requires further research.

Screening for Multiple Autoantibodies in Plasma of Patients with Breast Cancer

BACKGROUND/AIM

Autoantibodies have potential as circulating biomarkers for early cancer detection. This study aimed to screen for known autoantibodies in human plasma using an Autoantibody Profiling System (APS) and quantify the levels in plasma of donors with/without breast cancer.

MATERIALS AND METHODS

Plasma from nine female donors diagnosed with breast cancer (test group) and nine matched donors with no personal history of cancer (reference group) were screened with an APS containing probes for 30 autoantibodies. Autoantibody levels ≥1.5 times the mean concentration of the group were considered elevated, and test/reference ratios ≥1.3 were considered higher in the test group compared to the reference group.

RESULTS

Twenty percent of the probes detected elevated levels of autoantibodies against proteins involved in different cancer mechanisms. Amongst these, the levels of autoantibodies against interleukin 29 (IL29), osteoprotegerin (OPG), survivin (SUR), growth hormone (GRH) and resistin (RES) were significantly higher in the cancer group compared to the reference group (p<0.05), whereas the level of autoantibody against cytotoxic T-lymphocyte associated antigen-4 (CTLA4) was not significantly different between the two groups (p=0.38).

CONCLUSION

Disease-relevant autoantibodies were detected in the plasma of patients with breast cancer and donors without breast cancer. This means that identifying the type and level of autoantibodies in samples will be important in determining their significance in the disease process. A microtiter plate-based array system could be a fast and inexpensive screening method for identifying and quantifying autoantibodies in human plasma.

Cancer Antigen 125 (CA125, MUC16) Protein Expression in the Diagnosis and Progression of Pancreatic Ductal Adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive carcinoma, with most patients diagnosed at an advanced stage, with a 5-year survival rate of around 5%. An urgent need exists for identifying better diagnostic, prognostic, and therapeutic markers for this lethal disease. Recently, CA125 has been identified in PDAC, and the aim of this research is to study the changes in CA125 expression during the progression of benign pancreatic tissue (BPT) to PDAC and to assess its value as a biomarker of tumor growth. To address these questions, the cellular levels of CA125 in BPT and PDAC were measured using immunohistochemistry and compared on the basis of tumor staging, and the tissue microarray technology were constructed using resected pancreatic tissues. The staining reactions for each case were evaluated semiquantitatively using the histologic score system. Our investigation demonstrates a consistent and significant upregulation of CA125 during the transition from BPT to PDAC. We also found a direct correlation between CA125 immunohistochemistry score and tumor stage (P=0.02). In conclusion, our data indicate that CA125 plays a direct role in pancreatic carcinogenesis and suggests that it may eventually be used as a diagnostic and/or prognostic biomarker of pancreatic cancer. Prospective studies are recommended to evaluate further the diagnostic and prognostic capabilities of CA125 in PDAC, and further studies are warranted to assess the use of CA125 as a therapeutic marker.

Significance of blood and salivary IEX-1 expression in diagnosis of epithelial ovarian carcinoma

AIM

This study assesses a clinical potential of immediate early responsive gene X-1 (IEX-1), also named IER3, in the diagnosis of epithelial ovarian carcinoma using blood and salivary specimens.

METHODS

Immediate early responsive gene X-1 was quantified in blood and saliva by real-time quantitative reverse transcription polymerase chain reaction in 26 cases of epithelial ovarian carcinoma, 37 cases of benign ovarian tumor and 55 cases of healthy women. The receiver operating characteristic (ROC) curve was used to evaluate the diagnostic efficacy of IEX-1.

RESULTS

Immediate early responsive gene X-1 was expressed in blood and saliva of the benign ovarian tumor group and the healthy women group, both at a level significantly higher than that of the ovarian carcinoma group (P < 0.017). There were no significant differences in IEX-1 expression in blood and saliva (P = 0.376 or 0.621, respectively) between the benign ovarian tumor and the healthy women group. Comparison of IEX-1 expression in blood between the ovarian carcinoma group and the benign ovarian tumor group or the healthy women group demonstrated the ROC-area under curves (AUC) of 0.947 or 0.929, respectively. In discriminating the ovarian carcinoma group from the benign ovarian tumor group, IEX-1 expression in blood demonstrated a sensitivity and specificity of 84.6% and 94.6%, respectively. Similarly, blood IEX-1 expression conferred a sensitivity of 84.6% and specificity of 90.9% in distinguishing the ovarian carcinoma group from the healthy women group. Moreover, salivary IEX-1 expression had ROC-AUC of 0.851 when compared between the ovarian carcinoma group and the benign ovarian tumor group or 0.896 when compared between the ovarian cancer group and the healthy women group. IEX-1 expression was able to discriminate the ovarian carcinoma group from the benign ovarian tumor group with a sensitivity and specificity of 65.4% and 94.6%, respectively, or the ovarian carcinoma from the healthy women with 92.3% sensitivity and 72.5% specificity.

CONCLUSION

These results suggest the clinical potential of IEX-1 expression in blood and saliva as a sensitive and specific diagnosis for epithelial ovarian carcinoma.

Candidate genes and pathways downstream of PAX8 involved in ovarian high-grade serous carcinoma

Understanding the biology and molecular pathogenesis of ovarian epithelial cancer (EOC) is key to developing improved diagnostic and prognostic indicators and effective therapies. Although research has traditionally focused on the hypothesis that high-grade serous carcinoma (HGSC) arises from the ovarian surface epithelium (OSE), recent studies suggest that additional sites of origin exist and a substantial proportion of cases may arise from precursor lesions located in the Fallopian tubal epithelium (FTE). In FTE cells, the transcription factor PAX8 is a marker of the secretory cell lineage and its expression is retained in 96% of EOC. We have recently reported that PAX8 is involved in the tumorigenic phenotype of ovarian cancer cells. In this study, to uncover genes and pathways downstream of PAX8 involved in ovarian carcinoma we have determined the molecular profiles of ovarian cancer cells and in parallel of Fallopian tube epithelial cells by means of a silencing approach followed by an RNA-seq analysis. Interestingly, we highlighted the involvement of pathways like WNT signaling, epithelial-mesenchymal transition, p53 and apoptosis. We believe that our analysis has led to the identification of candidate genes and pathways regulated by PAX8 that could be additional targets for the therapy of ovarian carcinoma.

Involvement of platelet-derived growth factor ligands and receptors in tumorigenesis

Platelet-derived growth factor (PDGF) isoforms and their receptors have important roles during embryogenesis, particularly in the development of various mesenchymal cell types in different organs. In the adult, PDGF stimulates wound healing and regulates tissue homeostasis. However, overactivity of PDGF signalling is associated with malignancies and other diseases characterized by excessive cell proliferation, such as fibrotic conditions and atherosclerosis. In certain tumours, genetic or epigenetic alterations of the genes for PDGF ligands and receptors drive tumour cell proliferation and survival. Examples include the rare skin tumour dermatofibrosarcoma protuberance, which is driven by autocrine PDGF stimulation due to translocation of a PDGF gene, and certain gastrointestinal stromal tumours and leukaemias, which are driven by constitute activation of PDGF receptors due to point mutations and formation of fusion proteins of the receptors, respectively. Moreover, PDGF stimulates cells in tumour stroma and promotes angiogenesis as well as the development of cancer-associated fibroblasts, both of which promote tumour progression. Inhibitors of PDGF signalling may thus be of clinical usefulness in the treatment of certain tumours.

Osteoprotegerin: A novel biomarker for inflammatory bowel disease and gastrointestinal carcinoma

Osteoprotegerin (OPG) is a member of the tumor necrosis factor receptor superfamily of proteins. Although initial data illustrated the key role that OPG plays in bone turnover, numerous recent reports indicate that OPG is also an important factor in inflammatory pathways and tumor cell survival. OPG contributes directly to inflammatory processes and has been evaluated as a novel non-invasive biomarker of gut inflammation. Furthermore, OPG affects cell turn-over, differentiation, death, and survival via extracellular pathways, correlating with worse prognosis in inflammatory bowel diseases and several gastrointestinal carcinomas. It is now clear that OPG has multiple functions and characteristics. This review gives an overview of OPG, highlights its roles in different extracellular pathways, and outlines how OPG could be used as a novel non-invasive biological marker in inflammatory bowel diseases and gastrointestinal carcinomas.

Protein microarray-mediated detection of antienterovirus antibodies in serum

Objective

To utilize prokaryotic gene expression and protein microarray to develop and evaluate a sensitive, accurate protein microarray assay for detecting antienterovirus antibodies in serum samples from patients with hand, foot and mouth disease (HFMD). Enterovirus 71 (EV71) and coxsackievirus A16 (CA16), two common causative agents for HFMD, were used for assay development.

Methods

Serum was collected from patients with HFMD and healthy controls. EV71 and CA16 VP1 and VP3 genes were expressed in transfected Escherichia coli; the resultant VP1 and 3 proteins were used in a microarray assay for human serum EV71 and CA16 immunoglobulin (Ig) M and IgG. To validate the microarray assay, serum samples were tested for EV71 IgM using enzyme-linked immunosorbent assay (ELISA).

Results

Out of 50 patients with HFMD, EV71 IgM and CA16 IgM was detected in 80% and 44% of serum samples, respectively, using protein microarray, and EV71 IgM was detected in 78% of samples using ELISA. Protein microarray and ELISA showed 100% specificity for EV71-IgM detection.

Conclusion

The protein microarray assay developed in the present study shows potential as a sensitive technique for detecting EV71 IgM in serum samples from patients with HFMD.

MicroRNA: a new and promising potential biomarker for diagnosis and prognosis of ovarian cancer

Epithelial ovarian cancer (EOC) is the leading cause of death among all gynecological malignancies. Despite the technological and medical advances over the past four decades, such as the development of several biological markers (mRNA and proteins biomarkers), the mortality rate of ovarian cancer remains a challenge because of its late diagnosis, which is specifically attributed to low specificities and sensitivities. Under this compulsive scenario, recent advances in expression biology have shifted in identifying and developing specific and sensitive biomarkers, such as microRNAs (miRNAs) for cancer diagnosis and prognosis. MiRNAs are a novel class of small non-coding RNAs that deregulate gene expression at the posttranscriptional level, either by translational repression or by mRNA degradation. These mechanisms may be involved in a complex cascade of cellular events associated with the pathophysiology of many types of cancer. MiRNAs are easily detectable in tissue and blood samples of cancer patients. Therefore, miRNAs hold good promise as potential biomarkers in ovarian cancer. In this review, we attempted to provide a comprehensive profile of key miRNAs involved in ovarian carcinoma to establish miRNAs as more reliable non-invasive clinical biomarkers for early detection of ovarian cancer compared with protein and DNA biomarkers.

Protein microarray with horseradish peroxidase chemiluminescence for quantification of serum α-fetoprotein

Objectives

To develop and evaluate a protein microarray assay with horseradish peroxidase (HRP) chemiluminescence for quantification of α-fetoprotein (AFP) in serum from patients with hepatocellular carcinoma (HCC).

Methods

A protein microarray assay for AFP was developed. Serum was collected from patients with HCC and healthy control subjects. AFP was quantified using protein microarray and enzyme-linked immunosorbent assay (ELISA).

Results

Serum AFP concentrations determined via protein microarray were positively correlated ( r = 0.973) with those determined via ELISA in patients with HCC ( n = 60) and healthy control subjects ( n = 30). Protein microarray showed 80% sensitivity and 100% specificity for HCC diagnosis. ELISA had 83.3% sensitivity and 100% specificity. Protein microarray effectively distinguished between patients with HCC and healthy control subjects (area under ROC curve 0.974; 95% CI 0.000, 1.000).

Conclusion

Protein microarray is a rapid, simple and low-cost alternative to ELISA for detecting AFP in human serum.

Extensive serum biomarker analysis in patients with ST segment elevation myocardial infarction (STEMI)

ST segment elevation myocardial infarction (STEMI) is one of the leading causes of morbidity and mortality and some characteristics of STEMI are poorly understood. The aim of the present study is to detect protein expression profiles in the serum of STEMI patients, and to identify biomarkers for this disease. Cytokine profiles of serum from STEMI patients and healthy controls were analyzed with a semi-quantitative human antibody array for 174 proteins, and the results showed blood serum concentrations of 21 cytokines differed considerably between STEMI patients and healthy subjects. In the next phase, a sandwich ELISA kit individually validated eight biomarker results from 21 of the microarray experiments. Clinical validation demonstrated a significant increase of BNDF, PDGF-AA and MMP-9 in patients with AMI. Meanwhile, BNDF, PDGF-AA and MMP-9 distinguished AMI patients from healthy controls with a mean area under the receiver operating characteristic (ROC) curves of 0.870, 0.885, and 0.81, respectively, with diagnostic cut-off points of 0.688 ng/mL, 297.86 ng/mL and 690.066 ng/mL. Our study indicated that these three cytokines were up-regulated in STEMI samples, and may hold promise for the assessment of STEMI.