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Discovery of Novel Ovarian Cancer Biomarkers Via Proteomics and Mass Spectrometry

Discovery of Novel Ovarian Cancer Biomarkers Via Proteomics and Mass Spectrometry
Author: Chinthaka Geeth Gunawardana
Publisher:
Total Pages:
Release: 2010
Genre:
ISBN:
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Proteins secreted or shed by tumors can be found in serum. Detecting these proteins by mass spectrometry (MS) is difficult, due to the wide dynamic range of protein concentrations in serum. To circumvent this issue, we mined the conditioned media of epithelial ovarian cancer (EOC) cell lines which is a less complex fluid to work with. We hypothesize that some of the proteins shed or secreted by EOC cell lines are similar to those secreted or shed by EOC tumors and that some of these proteins can be used as biomarkers. We mined the conditioned medium of four ovarian cancer cell lines (HTB75, TOV-112D, TOV-21G and RMUG-S) by two-dimensional liquid chromatography-mass spectrometry. Our study identified 1208, 1252, 885, and 463 proteins from the HTB-75, TOV-112D, TOV-21G, and RMUG-S cell lines respectively. In all, we identified 2039 proteins from which we focused on 420 extracellular and plasma membrane proteins. High abundance proteins such as albumin and immunoglobulins, which are problematic for serum proteomics, did not interfere with our study. Several known markers of EOC including CA-125, HE4, Mesothelin, and KLK6, were identified in this study. The list of 420 extracellular and membrane proteins was cross-referenced with the proteome of ascites fluid to generate a final list of 51 potential candidates. According to Ingenuity Pathway Analysis, two of the top 10 diseases associated with our list of 51 proteins were cancer and reproductive diseases. Of the 51 candidates, 10 proteins were selected for verification in sera from ovarian cancer patients and healthy individuals. Clusterin showed a significant difference between cancer patients and normal, with sera from cancer patients showing higher levels. Another protein, NPC2, did not show a difference in sera between cancer and normals. Protein expression studies using immunohistochemistry showed that NPC2 is highly expressed in ovarian cancer tissue and absent in normal ovarian surface epithelium. In summary, clusterin and NPC2 appear to play a role in ovarian cancer pathobiology and their role in EOC need to be studied further.

Discovery of Novel Ovarian Cancer Biomarkers Via Proteomics and Mass Spectrometry

Discovery of Novel Ovarian Cancer Biomarkers Via Proteomics and Mass Spectrometry
Author:
Publisher:
Total Pages:
Release: 2006
Genre:
ISBN:
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Proteins secreted or shed by tumors can be found in serum. Detecting these proteins by mass spectrometry (MS) is difficult, due to the wide dynamic range of protein concentrations in serum. To circumvent this issue, we mined the conditioned media of epithelial ovarian cancer (EOC) cell lines which is a less complex fluid to work with. We hypothesize that some of the proteins shed or secreted by EOC cell lines are similar to those secreted or shed by EOC tumors and that some of these proteins can be used as biomarkers. We mined the conditioned medium of four ovarian cancer cell lines (HTB75, TOV-112D, TOV-21G and RMUG-S) by two-dimensional liquid chromatography-mass spectrometry. Our study identified 1208, 1252, 885, and 463 proteins from the HTB-75, TOV-112D, TOV-21G, and RMUG-S cell lines respectively. In all, we identified 2039 proteins from which we focused on 420 extracellular and plasma membrane proteins. High abundance proteins such as albumin and immunoglobulins, which are problematic for serum proteomics, did not interfere with our study. Several known markers of EOC including CA-125, HE4, Mesothelin, and KLK6, were identified in this study. The list of 420 extracellular and membrane proteins was cross-referenced with the proteome of ascites fluid to generate a final list of 51 potential candidates. According to Ingenuity Pathway Analysis, two of the top 10 diseases associated with our list of 51 proteins were cancer and reproductive diseases. Of the 51 candidates, 10 proteins were selected for verification in sera from ovarian cancer patients and healthy individuals. Clusterin showed a significant difference between cancer patients and normal, with sera from cancer patients showing higher levels. Another protein, NPC2, did not show a difference in sera between cancer and normals. Protein expression studies using immunohistochemistry showed that NPC2 is highly expressed in ovarian cancer tissue and absent in normal ovarian surface epithelium. In summary, clu.

The Handbook of Biomarkers

The Handbook of Biomarkers
Author: Kewal K. Jain
Publisher: Springer Science & Business Media
Total Pages: 509
Release: 2010-02-06
Genre: Medical
ISBN: 1607616858
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Of the thousands of biomarkers that are currently being discovered, relatively few are being validated for further applications, and the potential of a biomarker can be quite difficult to evaluate. To aid in this imperative research, Dr. Kewal K. Jain’s Handbook of Biomarkers thoroughly describes many different types of biomarkers and their discovery using various "-omics" technologies, such as proteomics and metabolomics, along with the background information needed for the evaluation of biomarkers as well as the essential procedures for their validation and use in clinical trials. With biomarkers described first according to technologies and then according to various diseases, this detailed book features the key correlations between diseases and classifications of biomarkers, which provides the reader with a guide to sort out current and future biomarkers. Comprehensive and cutting-edge, The Handbook of Biomarkers serves as a vital guide to furthering our understanding of biomarkers, which, by facilitating the combination of therapeutics with diagnostics, promise to play an important role in the development of personalized medicine, one of the most important emerging trends in healthcare today.

Proteomic Applications in Cancer Detection and Discovery

Proteomic Applications in Cancer Detection and Discovery
Author: Timothy D. Veenstra
Publisher: John Wiley & Sons
Total Pages: 375
Release: 2013-05-30
Genre: Science
ISBN: 1118634411
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Helps researchers in proteomics and oncology work together to understand, prevent, and cure cancer Proteomic data is increasingly important to understanding the origin and progression of cancer; however, most oncologic researchers who depend on proteomics for their studies do not collect the data themselves. As a result, there is a knowledge gap between scientists, who devise proteomic techniques and collect the data, and the oncologic researchers, who are expected to interpret and apply proteomic data. Bridging the gap between proteomics and oncology research, this book explains how proteomic technology can be used to address some of the most important questions in cancer research. Proteomic Applications in Cancer Detection and Discovery enables readers to understand how proteomic data is acquired and analyzed and how it is interpreted. Author Timothy Veenstra has filled the book with examples many based on his own firsthand research experience that clearly demonstrate the application of proteomic technology in oncology research, including the discovery of novel biomarkers for different types of cancers. The book begins with a brief introduction to systems biology, explaining why cancer is a systems biology disease. Next, it covers such topics as: Mass spectrometry in cancer research Application of proteomics to global phosphorylation analysis Search for biomarkers in biofluids Rise and fall of proteomic patterns for cancer diagnostics Emergence of protein arrays Role of proteomics in personalized medicine The final chapter is dedicated to the future prospects of proteomics in cancer research. By guiding readers through the latest proteomic technologies and their applications in cancer research, Proteomic Applications in Cancer Detection and Discovery enhances the ability of researchers in proteomics and researchers in oncology to collaborate in order to better understand cancer and develop strategies to prevent and treat it.

Ovarian cancer serum biomarker discovery using proteomics

Ovarian cancer serum biomarker discovery using proteomics
Author: Musarat Kabir
Publisher:
Total Pages: 530
Release: 2008
Genre:
ISBN:
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Ovarian cancer is a lethal gynaecological malignancy which is known as the silent killer. It has a poor prognosis due to the lack of major symptoms in early stage disease and hence its late detection. Cancer antigen-125, the most widely used biomarker for ovarian cancer detection, lacks appropriate sensitivity and specificity. Thus, early biomarkers of the disease are urgently required. Proteomic analysis of human serum promises to be a valuable approach for the discovery of putative biomarkers for human malignancies like ovarian cancer, which could be developed into non-invasive blood tests. In this study, serum samples from a pilot study for ovarian cancer screening which were collected prior to diagnosis were processed at Memorial Sloan Kettering Cancer Research Centre, in collaboration with Prof. Tempst's group, who had developed a novel mass spectrometry (MS)-based technology platform for the high-throughput extraction and measurement of serum peptides. Several marker peaks were identified, which when used in combination with the ovarian cancer biomarker CA-125, assisted in the discrimination of case versus healthy samples at an earlier point prior to diagnosis. Work then involved the establishment and optimisation of a similar serum profiling platform at UCL. This involved the optimisation of a liquid-handling robot to provide semi-automated high- throughput sample purification and spotting, and optimisation of spectral acquisition and processing. The reproducibility of the platform was tested and the effects of different sample handling conditions on peptide profiles examined. The method was then used to search for putative markers of ovarian cancer, using identically processed samples from women diagnosed with malignant or benign ovarian cancer and healthy controls. Finally, as a complementary approach to discover protein biomarkers, the same samples were profiled using 2D Difference Gel Electrophoresis, employing different fractionation strategies to overcome the very large dynamic range of protein expression in serum. Mass spectrometry was used to identify several previously reported and some novel putative biomarkers of ovarian cancer, which warrant further validation.

Biomarker Discovery in the Developing World: Dissecting the Pipeline for Meeting the Challenges

Biomarker Discovery in the Developing World: Dissecting the Pipeline for Meeting the Challenges
Author: Sanjeeva Srivastava
Publisher: Springer
Total Pages: 120
Release: 2016-09-30
Genre: Medical
ISBN: 8132228375
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This book is oriented towards post-graduates and researchers with interest in proteomics and its applications in clinical biomarker discovery pipeline. Biomarker discovery has long been the research focus of many life scientists globally. However, the pipeline starting from discovery to validation to regulation as a diagnostic or therapeutic molecule follows a complex trajectory. This book aims to provide an in-depth synopsis on each of these developmental phases attendant to biomarker “life cycle” with emphasis on the emerging and significant role of proteomics. The book begins with a perspective on the role of biorepositories and need for biobanking practices in the developing world. The next chapter focuses on disease heterogeneity in context to geographical bias towards susceptibility to the disease and the role of multi-omics techniques to devise disruptive innovations towards biomarker discovery. Chapter 3 focuses on various omics-based platforms that are currently being used for biomarker discovery, their principles and workflow. Mass spectrometry is emerging as a powerful technology for discovery based studies and targeted validation. Chapter 4 aims at providing a glimpse of the basic workflow and considerations in mass spectrometry based studies. Rapid and aptly targeted research funding has often been deemed as one of the decisive factors enabling excellent science and path breaking innovations. With the need for sophistication required in multi-omics research, Chapter 5 focuses on innovative funding strategies such as crowdfunding and Angel philanthropy. Chapter 6 provides the latest advances in education innovation, the premise and reality of bioeconomy especially in a specific context of the developing world, not to mention the new concept of “social innovation” to link biomarkers with socially responsible and sustainable applications. Chapter 7, in ways similar to biomarkers, discusses the biosimilars as a field that has received much focus and prominence recently due to their immense potential in clinical and pharmaceutical innovation literatures. The broader goal post-biomarker discovery is to translate their use in clinics. However, the road from bench-to-bed side is arduous and complex that is subject to oversight from various national and international regulatory bodies. Chapter 8 underscores these regulatory science considerations and provides a concise overview on intellectual property rights in biomarker discovery. Thus, this book contributed by eminent biomarker scientists, clinicians, translational researchers and social scientists holistically covers the various facets of the biomarker discovery journey from “cell to society” in developing world. The lessons learned and highlighted here are of interest to the life sciences community in a global and interdependent world.

In Search of Protein Biomarkers in Ovarian Cancer and Gaucher Disease

In Search of Protein Biomarkers in Ovarian Cancer and Gaucher Disease
Author: Wouter Wegdam
Publisher:
Total Pages: 0
Release: 2024
Genre:
ISBN: 9789464835878
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"In this thesis we used proteomic technologies to identify biomarkers for two very different types of disease, i.e., ovarian cancer and Gaucher disease. In order to obtain reliable and reproducible classification of different sample groups in large datasets, we first experimented with optimizing study protocols and data acquisition. In chapter 2 we evaluated different pre-processing and classification methods in search of methods best suited for discovering (multivariable) biomarkers from large proteomic datasets. Using these results we showed that surface-enhanced laser desorption/ionization-time-of-flight-mass spectrometry (SELDI-TOF-MS) can produce reliable classification results in serum and tissue samples of ovarian cancer patients in chapter 3. Chapter 4 gives an overview of the existing literature describing the research on biomarkers in Gaucher disease such as chitotriosidase and the search for novel markers. It also highlights research using novel techniques such as SELDI-TOF-MS for the discovery of CCL18.Label-free liquid chromatography mass spectrometry (LC-MSe) in combination with laser capture microdissection of macrophages from spleen of Gaucher disease patients resulted in the discovery of glycoprotein nonmetastatic melanoma protein B (gpNMB) as a new marker in Gaucher disease. The results of which are presented in chapter 5.A label-free LC-MS approach was also used on serum and tissue of patients with an ovarian tumor identifying proteins which were significantly differentially expressed between benign and malignant samples in chapter 6. In chapter 7 we used LC-MSe on ovarian tumor tissue of patients with a difference in disease-free survival in an attempt to find biomarkers predicting patient survival and chemoresistance."--

Integrating High-throughput Technologies for the Identification and Validation of Novel Ovarian Cancer Biomarkers

Integrating High-throughput Technologies for the Identification and Validation of Novel Ovarian Cancer Biomarkers
Author: Felix Leung
Publisher:
Total Pages:
Release: 2016
Genre:
ISBN:
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Ovarian cancer is the most lethal gynaecological malignancy in North America. Although survival rates are high when the disease is diagnosed at an early stage, this decreases significantly in late-stage diagnoses. The majority of cases are of epithelial origin, which can be classified into four major subtypes: serous, mucinous, endometrioid and clear cell carcinoma. Unfortunately, the clinically-approved markers for ovarian cancer - CA125 and HE4 alone - perform poorly for the mucinous, endometrioid and clear cell subtypes and thus, diagnosis of these subtypes remains a significant challenge. To this end, an integrated approach to ovarian cancer biomarker discovery was developed in this study through combining proteomics with other high-throughput platforms. Using proteomic analyses of ascites fluid from women with ovarian cancer and conditioned media of ovarian cancer cell lines, 15 high-priority candidates were identified as putative novel biomarkers using said integrated approach. Serum validation revealed two markers - folate receptor 1 and kallikrein 6 - to have comparable diagnostic ability to the clinically-approved markers, albeit with similar limitations in their ability to detect patients of the non-serous histotypes as well. Fortunately, the validation of the two in-house markers served as proof-of-principle of our integrated approach to biomarker discovery. As a result, the approach was employed on non-serous ovarian cancer tissues to identify novel markers specific to the mucinous, endometrioid and clear cell subtypes of ovarian cancer. Over 9000 unique proteins were identified in this exercise and with the use of an unbiased filtering algorithm based on transcriptomics and bioinformatics, a list of high-priority candidates for each subtype was generated. Several of the high-priority candidates have shown strong biological and molecular relevance to their respective subtypes, demonstrating the robustness and utility of the integrated approach. Future studies will need to investigate these candidates in independent serum cohorts to truly assess for their ability to diagnose their respective subtypes.

Ovarian Cancer Biomarkers

Ovarian Cancer Biomarkers
Author: Khalid El Bairi
Publisher: Springer Nature
Total Pages: 236
Release: 2021-10-09
Genre: Medical
ISBN: 9811618739
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This book comprehensively summarizes the biology, etiology, and pathology of ovarian cancer and explores the role of deep molecular and cellular profiling in the advancement of precision medicine. The initial chapter discusses our current understanding of the origin, development, progression and tumorigenesis of ovarian cancer. In turn, the book highlights the development of resistance, disease occurrence, and poor prognosis that are the hallmarks of ovarian cancer. The book then reviews the role of deep molecular and cellular profiling to overcome challenges that are associated with the treatment of ovarian cancer. It explores the use of genome-wide association analysis to identify genetic variants for the evaluation of ovarian carcinoma risk and prognostic prediction. Lastly, it highlights various diagnostic and prognostic ovarian cancer biomarkers for the development of molecular-targeted therapy.