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Qian L, Zhu J, Xue Z, Zhou Y, Xiang N, Xu H, Sun R, Gong W, Cai X, Sun L, Ge W, Liu Y, Su Y, Lin W, Zhan Y, Wang J, Song S, Yi X, Ni M, Zhu Y, Hua Y, Zheng Z, Guo T. Proteomic landscape of epithelial ovarian cancer. Nat Commun 2024; 15:6462. [PMID: 39085232 PMCID: PMC11291745 DOI: 10.1038/s41467-024-50786-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 07/19/2024] [Indexed: 08/02/2024] Open
Abstract
Epithelial ovarian cancer (EOC) is a deadly disease with limited diagnostic biomarkers and therapeutic targets. Here we conduct a comprehensive proteomic profiling of ovarian tissue and plasma samples from 813 patients with different histotypes and therapeutic regimens, covering the expression of 10,715 proteins. We identify eight proteins associated with tumor malignancy in the tissue specimens, which are further validated as potential circulating biomarkers in plasma. Targeted proteomics assays are developed for 12 tissue proteins and 7 blood proteins, and machine learning models are constructed to predict one-year recurrence, which are validated in an independent cohort. These findings contribute to the understanding of EOC pathogenesis and provide potential biomarkers for early detection and monitoring of the disease. Additionally, by integrating mutation analysis with proteomic data, we identify multiple proteins related to DNA damage in recurrent resistant tumors, shedding light on the molecular mechanisms underlying treatment resistance. This study provides a multi-histotype proteomic landscape of EOC, advancing our knowledge for improved diagnosis and treatment strategies.
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Affiliation(s)
- Liujia Qian
- School of Medicine, Westlake University, Hangzhou, Zhejiang Province, China
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, China
| | - Jianqing Zhu
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Zhangzhi Xue
- School of Medicine, Westlake University, Hangzhou, Zhejiang Province, China
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, China
| | - Yan Zhou
- School of Medicine, Westlake University, Hangzhou, Zhejiang Province, China
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, China
| | - Nan Xiang
- School of Medicine, Westlake University, Hangzhou, Zhejiang Province, China
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, China
| | - Hong Xu
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Science, Zhejiang University, Hangzhou, China
| | - Rui Sun
- School of Medicine, Westlake University, Hangzhou, Zhejiang Province, China
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, China
| | - Wangang Gong
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Xue Cai
- School of Medicine, Westlake University, Hangzhou, Zhejiang Province, China
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, China
| | - Lu Sun
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Weigang Ge
- Westlake Omics (Hangzhou) Biotechnology Co., Ltd., Hangzhou, Zhejiang Province, China
| | - Yufeng Liu
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Science, Zhejiang University, Hangzhou, China
| | - Ying Su
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Wangmin Lin
- Westlake Omics (Hangzhou) Biotechnology Co., Ltd., Hangzhou, Zhejiang Province, China
| | - Yuecheng Zhan
- Westlake Omics (Hangzhou) Biotechnology Co., Ltd., Hangzhou, Zhejiang Province, China
| | - Junjian Wang
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Shuang Song
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Science, Zhejiang University, Hangzhou, China
| | - Xiao Yi
- School of Medicine, Westlake University, Hangzhou, Zhejiang Province, China
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, China
| | - Maowei Ni
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Yi Zhu
- School of Medicine, Westlake University, Hangzhou, Zhejiang Province, China.
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China.
- Research Center for Industries of the Future, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, China.
| | - Yuejin Hua
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Science, Zhejiang University, Hangzhou, China.
| | - Zhiguo Zheng
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China.
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China.
| | - Tiannan Guo
- School of Medicine, Westlake University, Hangzhou, Zhejiang Province, China.
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China.
- Research Center for Industries of the Future, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, China.
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2
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Adnane M, de Almeida AM, Chapwanya A. Unveiling the power of proteomics in advancing tropical animal health and production. Trop Anim Health Prod 2024; 56:182. [PMID: 38825622 DOI: 10.1007/s11250-024-04037-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 05/20/2024] [Indexed: 06/04/2024]
Abstract
Proteomics, the large-scale study of proteins in biological systems has emerged as a pivotal tool in the field of animal and veterinary sciences, mainly for investigating local and rustic breeds. Proteomics provides valuable insights into biological processes underlying animal growth, reproduction, health, and disease. In this review, we highlight the key proteomics technologies, methodologies, and their applications in domestic animals, particularly in the tropical context. We also discuss advances in proteomics research, including integration of multi-omics data, single-cell proteomics, and proteogenomics, all of which are promising for improving animal health, adaptation, welfare, and productivity. However, proteomics research in domestic animals faces challenges, such as sample preparation variation, data quality control, privacy and ethical considerations relating to animal welfare. We also provide recommendations for overcoming these challenges, emphasizing the importance of following best practices in sample preparation, data quality control, and ethical compliance. We therefore aim for this review to harness the full potential of proteomics in advancing our understanding of animal biology and ultimately improve animal health and productivity in local breeds of diverse animal species in a tropical context.
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Affiliation(s)
- Mounir Adnane
- Department of Biomedicine, Institute of Veterinary Sciences, University of Tiaret, Tiaret, 14000, Algeria.
| | - André M de Almeida
- LEAF-Linking Landscape, Environment, Agriculture and Food Research Center, Associate Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, Lisboa, 1349-017, Portugal
| | - Aspinas Chapwanya
- Department of Clinical Sciences, Ross University School of Veterinary Medicine, Basseterre, 00265, Saint Kitts and Nevis
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Artuyants A, Guo G, Flinterman M, Middleditch M, Jacob B, Lee K, Vella L, Su H, Wilson M, Eva L, Shelling AN, Blenkiron C. The tumour-derived extracellular vesicle proteome varies by endometrial cancer histology and is confounded by an obesogenic environment. Proteomics 2024; 24:e2300055. [PMID: 38644352 DOI: 10.1002/pmic.202300055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 04/23/2024]
Abstract
Endometrial cancer, the most common gynaecological cancer worldwide, is closely linked to obesity and metabolic diseases, particularly in younger women. New circulating biomarkers have the potential to improve diagnosis and treatment selections, which could significantly improve outcomes. Our approach focuses on extracellular vesicle (EV) biomarker discovery by directly profiling the proteome of EVs enriched from frozen biobanked endometrial tumours. We analysed nine tissue samples to compare three clinical subgroups-low BMI (Body Mass Index) Endometrioid, high BMI Endometrioid, and Serous (any BMI)-identifying proteins related to histological subtype, BMI, and shared secreted proteins. Using collagenase digestion and size exclusion chromatography, we successfully enriched generous quantities of EVs (range 204.8-1291.0 µg protein: 1.38 × 1011-1.10 × 1012 particles), characterised by their size (∼150 nm), expression of EV markers (CD63/81), and proposed endometrial cancer markers (L1CAM, ANXA2). Mass spectrometry-based proteomic profiling identified 2075 proteins present in at least one of the 18 samples. Compared to cell lysates, EVs were successfully depleted for mitochondrial and blood proteins and enriched for common EV markers and large secreted proteins. Further analysis highlighted significant differences in EV protein profiles between the high BMI subgroup and others, underlining the impact of comorbidities on the EV secretome. Interestingly, proteins differentially abundant in tissue subgroups were largely not also differential in matched EVs. This research identified secreted proteins known to be involved in endometrial cancer pathophysiology and proposed novel diagnostic biomarkers (EIF6, MUC16, PROM1, SLC26A2).
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Affiliation(s)
- Anastasiia Artuyants
- Department of Molecular Medicine and Pathology, The University of Auckland, Auckland, New Zealand
- Auckland Cancer Society Research Centre, The University of Auckland, Auckland, New Zealand
| | - George Guo
- Department of Physiology in the School of Medical Sciences, The University of Auckland, Auckland, New Zealand
- Mass Spectrometry Hub, The University of Auckland, Auckland, New Zealand
| | - Marcella Flinterman
- Auckland Cancer Society Research Centre, The University of Auckland, Auckland, New Zealand
| | - Martin Middleditch
- Technical Services, Faculty of Science, The University of Auckland, Auckland, New Zealand
| | - Bincy Jacob
- Centre of eResearch, Faculty of Science, The University of Auckland, Auckland, New Zealand
| | - Kate Lee
- Department of Molecular Medicine and Pathology, The University of Auckland, Auckland, New Zealand
| | - Laura Vella
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria, Australia
- Department of Surgery, The Royal Melbourne Hospital, The University of Melbourne, Parkville, Victoria, Australia
| | - Huaqi Su
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Michelle Wilson
- Cancer and Blood, Auckland City Hospital, Auckland, New Zealand
- Department of Oncology, The University of Auckland, Auckland, New Zealand
| | - Lois Eva
- Department of Gynaecological Oncology, Auckland City Hospital, Auckland, New Zealand
- Department of Obstetrics and Gynaecology, The University of Auckland, Auckland, New Zealand
| | - Andrew N Shelling
- Department of Obstetrics and Gynaecology, The University of Auckland, Auckland, New Zealand
- Centre for Cancer Research, The University of Auckland, Auckland, New Zealand
| | - Cherie Blenkiron
- Department of Molecular Medicine and Pathology, The University of Auckland, Auckland, New Zealand
- Auckland Cancer Society Research Centre, The University of Auckland, Auckland, New Zealand
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Kaur Jawanda I, Soni T, Kumari S, Prabha V. Deciphering the potential of proteomic-based biomarkers in women's reproductive diseases: empowering precision medicine in gynecology. Biomarkers 2024; 29:7-17. [PMID: 38252065 DOI: 10.1080/1354750x.2024.2308827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 01/14/2024] [Indexed: 01/23/2024]
Abstract
CONTEXT Gynecological disorders represent a complex set of malignancies that result from a diverse array of molecular changes affecting the lives of over a million women worldwide. Ovarian, Endometrial, and Cervical cancers, Endometriosis, PCOS are the most prevalent ones that pose a grave threat to women's health. Proteomics has emerged as an invaluable tool for developing novel biomarkers, screening methods, and targeted therapeutic agents for gynecological disorders. Some of these biomarkers have been approved by the FDA, but regrettably, they have a constrained diagnostic accuracy in early-stage diagnosis as all of these biomarkers lack sensitivity and specificity. Lately, high-throughput proteomics technologies have made significant strides, allowing for identification of potential biomarkers with improved sensitivity and specificity. However, limited successes have been shown with translation of these discoveries into clinical practice. OBJECTIVE This review aims to provide a comprehensive overview of the current and potential protein biomarkers for gynecological cancers, endometriosis and PCOS, discusses recent advances and challenges, and highlights future directions for the field. CONCLUSION We propose that proteomics holds great promise as a powerful tool to revolutionize the fight against female reproductive diseases and can ultimately improve personalized patient outcomes in women's biomedicine.
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Affiliation(s)
| | - Thomson Soni
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Seema Kumari
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Vijay Prabha
- Department of Microbiology, Panjab University, Chandigarh, India
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Albertí-Valls M, Megino-Luque C, Macià A, Gatius S, Matias-Guiu X, Eritja N. Metabolomic-Based Approaches for Endometrial Cancer Diagnosis and Prognosis: A Review. Cancers (Basel) 2023; 16:185. [PMID: 38201612 PMCID: PMC10778161 DOI: 10.3390/cancers16010185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/22/2023] [Accepted: 12/23/2023] [Indexed: 01/12/2024] Open
Abstract
Endometrial cancer, the most prevalent gynecological malignancy in developed countries, is experiencing a sustained rise in both its incidence and mortality rates, primarily attributed to extended life expectancy and lifestyle factors. Currently, the absence of precise diagnostic tools hampers the effective management of the expanding population of women at risk of developing this disease. Furthermore, patients diagnosed with endometrial cancer require precise risk stratification to align with optimal treatment planning. Metabolomics technology offers a unique insight into the molecular landscape of endometrial cancer, providing a promising approach to address these unmet needs. This comprehensive literature review initiates with an overview of metabolomic technologies and their intrinsic workflow components, aiming to establish a fundamental understanding for the readers. Subsequently, a detailed exploration of the existing body of research is undertaken with the objective of identifying metabolite biomarkers capable of enhancing current strategies for endometrial cancer diagnosis, prognosis, and recurrence monitoring. Metabolomics holds vast potential to revolutionize the management of endometrial cancer by providing accuracy and valuable insights into crucial aspects.
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Affiliation(s)
- Manel Albertí-Valls
- Oncologic Pathology Group, Biomedical Research Institute of Lleida (IRBLleida), University of Lleida, Av. Rovira Roure 80, 25198 Lleida, Spain; (C.M.-L.); (A.M.); (S.G.); (X.M.-G.)
| | - Cristina Megino-Luque
- Oncologic Pathology Group, Biomedical Research Institute of Lleida (IRBLleida), University of Lleida, Av. Rovira Roure 80, 25198 Lleida, Spain; (C.M.-L.); (A.M.); (S.G.); (X.M.-G.)
- Department of Medicine, Division of Hematology and Oncology, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anna Macià
- Oncologic Pathology Group, Biomedical Research Institute of Lleida (IRBLleida), University of Lleida, Av. Rovira Roure 80, 25198 Lleida, Spain; (C.M.-L.); (A.M.); (S.G.); (X.M.-G.)
| | - Sònia Gatius
- Oncologic Pathology Group, Biomedical Research Institute of Lleida (IRBLleida), University of Lleida, Av. Rovira Roure 80, 25198 Lleida, Spain; (C.M.-L.); (A.M.); (S.G.); (X.M.-G.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC)
| | - Xavier Matias-Guiu
- Oncologic Pathology Group, Biomedical Research Institute of Lleida (IRBLleida), University of Lleida, Av. Rovira Roure 80, 25198 Lleida, Spain; (C.M.-L.); (A.M.); (S.G.); (X.M.-G.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC)
- Laboratory of Precision Medicine, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), Department of Pathology, Hospital de Bellvitge, Gran via de l’Hospitalet 199, 08908 Barcelona, Spain
| | - Núria Eritja
- Oncologic Pathology Group, Biomedical Research Institute of Lleida (IRBLleida), University of Lleida, Av. Rovira Roure 80, 25198 Lleida, Spain; (C.M.-L.); (A.M.); (S.G.); (X.M.-G.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC)
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Romano A, Rižner TL, Werner HMJ, Semczuk A, Lowy C, Schröder C, Griesbeck A, Adamski J, Fishman D, Tokarz J. Endometrial cancer diagnostic and prognostic algorithms based on proteomics, metabolomics, and clinical data: a systematic review. Front Oncol 2023; 13:1120178. [PMID: 37091170 PMCID: PMC10118013 DOI: 10.3389/fonc.2023.1120178] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/06/2023] [Indexed: 04/09/2023] Open
Abstract
Endometrial cancer is the most common gynaecological malignancy in developed countries. Over 382,000 new cases were diagnosed worldwide in 2018, and its incidence and mortality are constantly rising due to longer life expectancy and life style factors including obesity. Two major improvements are needed in the management of patients with endometrial cancer, i.e., the development of non/minimally invasive tools for diagnostics and prognostics, which are currently missing. Diagnostic tools are needed to manage the increasing number of women at risk of developing the disease. Prognostic tools are necessary to stratify patients according to their risk of recurrence pre-preoperatively, to advise and plan the most appropriate treatment and avoid over/under-treatment. Biomarkers derived from proteomics and metabolomics, especially when derived from non/minimally-invasively collected body fluids, can serve to develop such prognostic and diagnostic tools, and the purpose of the present review is to explore the current research in this topic. We first provide a brief description of the technologies, the computational pipelines for data analyses and then we provide a systematic review of all published studies using proteomics and/or metabolomics for diagnostic and prognostic biomarker discovery in endometrial cancer. Finally, conclusions and recommendations for future studies are also given.
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Affiliation(s)
- Andrea Romano
- Department of Gynaecology, Maastricht University Medical Centre (MUMC), Maastricht, Netherlands
- GROW – School for Oncology and Reproduction, Maastricht University, Maastricht, Netherlands
- *Correspondence: Andrea Romano, ; Tea Lanišnik Rižner,
| | - Tea Lanišnik Rižner
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- *Correspondence: Andrea Romano, ; Tea Lanišnik Rižner,
| | - Henrica Maria Johanna Werner
- Department of Gynaecology, Maastricht University Medical Centre (MUMC), Maastricht, Netherlands
- GROW – School for Oncology and Reproduction, Maastricht University, Maastricht, Netherlands
| | - Andrzej Semczuk
- Department of Gynaecology, Lublin Medical University, Lublin, Poland
| | | | | | | | - Jerzy Adamski
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Dmytro Fishman
- Institute of Computer Science, University of Tartu, Tartu, Estonia
- Quretec Ltd., Tartu, Estonia
| | - Janina Tokarz
- Institute for Diabetes and Cancer, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
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Cervical Fluids Are a Source of Protein Biomarkers for Early, Non-Invasive Endometrial Cancer Diagnosis. Cancers (Basel) 2023; 15:cancers15030911. [PMID: 36765869 PMCID: PMC9913506 DOI: 10.3390/cancers15030911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/19/2023] [Accepted: 01/28/2023] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Abnormal uterine bleeding is the main symptom of endometrial cancer (EC), but it is highly nonspecific. This represents a huge burden for women's health since all women presenting with bleeding will undergo sequential invasive tests, which are avoidable for 90-95% of those women who do not have EC. METHODS This study aimed to evaluate the potential of cervical samples collected with five different devices as a source of protein biomarkers to diagnose EC. We evaluated the protein quantity and the proteome composition of five cervical sampling methods. RESULTS Samples collected with a Rovers Cervex Brush® and the HC2 DNA collection device, Digene, were the most suitable samples for EC proteomic studies. Most proteins found in uterine fluids were also detected in both cervical samples. We then conducted a clinical retrospective study to assess the expression of 52 EC-related proteins in 41 patients (22 EC; 19 non-EC), using targeted proteomics. We identified SERPINH1, VIM, TAGLN, PPIA, CSE1L, and CTNNB1 as potential protein biomarkers to discriminate between EC and symptomatic non-EC women with abnormal uterine bleeding in cervical fluids (AUC > 0.8). CONCLUSIONS This study opens an avenue for developing non-invasive protein-based EC diagnostic tests, which will improve the standard of care for gynecological patients.
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Sykaras AG, Christofidis K, Politi E, Theocharis S. Exosomes on Endometrial Cancer: A Biomarkers Treasure Trove? Cancers (Basel) 2022; 14:cancers14071733. [PMID: 35406505 PMCID: PMC8996953 DOI: 10.3390/cancers14071733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/24/2022] [Accepted: 03/27/2022] [Indexed: 11/16/2022] Open
Abstract
Endometrial cancer (EC) is one of the main causes of cancer-related death among women. In the last decade, the incidence of EC is on the rise, and the relative 5-year survival remains unchanged. This creates a dire need for new diagnostic and therapeutic approaches that can only result from a deeper understanding of the pathogenesis of the disease. In this direction, exosomes are under heavy research, with two main aims: to identify the potential diagnostic and prognostic markers and to develop technologies based on their use as therapeutic vectors targeting EC cells. Exosomes are widely available in all bodily fluids and are sources of ideal biomarkers for liquid biopsies. They are extracellular vesicles containing DNA, RNA, lipids, and proteins, which they transfer between cells, serving multiple functions and being implicated in both the physiological processes and the pathogenesis of diseases. Of all the biomolecules contained in exosomes, microRNAs (miRNAs) seem to have the most clinical utility in the diagnosis and treatment of EC. Exosomal miRNAs mediate the communication between EC cells, cancer-associated fibroblasts (CAFs), and tumor-associated macrophages (TAMs) and have a pivotal role in the tumor cells' proliferation, epithelial to mesenchymal transition (EMT), and the formation of a tumor microenvironment. They participate in many processes that are tied to carcinogenesis and cancer progression, and they are therefore considered as attractive therapeutic targets. Here, we review the functions of exosomes in EC, focusing on potential biomarkers of diagnostic and prognostic significance or potential therapeutic use.
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Affiliation(s)
- Alexandros G. Sykaras
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (A.G.S.); (K.C.)
- Department of Cytopathology, Aretaieion Hospital, Medical School, National and Kapodistrian University of Athens, 11528 Athens, Greece;
| | - Konstantinos Christofidis
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (A.G.S.); (K.C.)
| | - Ekaterini Politi
- Department of Cytopathology, Aretaieion Hospital, Medical School, National and Kapodistrian University of Athens, 11528 Athens, Greece;
| | - Stamatios Theocharis
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (A.G.S.); (K.C.)
- Correspondence:
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Targeted Selected Reaction Monitoring Verifies Histology Specific Peptide Signatures in Epithelial Ovarian Cancer. Cancers (Basel) 2021; 13:cancers13225713. [PMID: 34830868 PMCID: PMC8616310 DOI: 10.3390/cancers13225713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 11/05/2021] [Accepted: 11/08/2021] [Indexed: 12/05/2022] Open
Abstract
Simple Summary Ovarian cancer is a lethal disease due to its late phase discovery. Any steps towards improving early diagnostics will dramatically increase survival rates. To identify new ovarian cancer biomarker panels, we need to focus on early-stage disease and all histologic subtypes. In this study we have, based on prior discoveries, constructed a multiplexed targeted selected-reaction-monitoring assay to detect peptides from 177 proteins in only 20 µL of plasma. The assay was evaluated in patients with a focus on early-stages and all ovarian cancer histologies in separate groups. With multivariate analysis, we found the highest predictive value in the benign vs. low-grade serous (Q2 = 0.615) and mucinous (Q2 = 0.611) early stage compared to all malignant (Q2 = 0.226) or late stage (Q2 = 0.43) ovarian cancers. The results show that each ovarian cancer histology subgroup can be identified by a unique panel of proteins. Abstract Epithelial ovarian cancer (OC) is a disease with high mortality due to vague early clinical symptoms. Benign ovarian cysts are common and accurate diagnosis remains a challenge because of the molecular heterogeneity of OC. We set out to investigate whether the disease diversity seen in ovarian cyst fluids and tumor tissue could be detected in plasma. Using existing mass spectrometry (MS)-based proteomics data, we constructed a selected reaction monitoring (SRM) assay targeting peptides from 177 cancer-related and classical proteins associated with OC. Plasma from benign, borderline, and malignant ovarian tumors were used to verify expression (n = 74). Unsupervised and supervised multivariate analyses were used for comparisons. The peptide signatures revealed by the supervised multivariate analysis contained 55 to 77 peptides each. The predictive (Q2) values were higher for benign vs. low-grade serous Q2 = 0.615, mucinous Q2 = 0.611, endometrioid Q2 = 0.428 and high-grade serous Q2 = 0.375 (stage I–II Q2 = 0.515; stage III Q2 = 0.43) OC compared to benign vs. all malignant Q2 = 0.226. With targeted SRM MS we constructed a multiplexed assay for simultaneous detection and relative quantification of 185 peptides from 177 proteins in only 20 µL of plasma. With the approach of histology-specific peptide patterns, derived from pre-selected proteins, we may be able to detect not only high-grade serous OC but also the less common OC subtypes.
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Ura B, Biffi S, Monasta L, Arrigoni G, Battisti I, Di Lorenzo G, Romano F, Aloisio M, Celsi F, Addobbati R, Valle F, Rampazzo E, Brucale M, Ridolfi A, Licastro D, Ricci G. Two Dimensional-Difference in Gel Electrophoresis (2D-DIGE) Proteomic Approach for the Identification of Biomarkers in Endometrial Cancer Serum. Cancers (Basel) 2021; 13:cancers13143639. [PMID: 34298850 PMCID: PMC8305989 DOI: 10.3390/cancers13143639] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/29/2021] [Accepted: 07/16/2021] [Indexed: 12/14/2022] Open
Abstract
Endometrial cancer is the most common gynecologic malignancy arising from the endometrium. Identification of serum biomarkers could be beneficial for its early diagnosis. We have used 2D-Difference In Gel Electrophoresis (2D-DIGE) coupled with Mass Spectrometry (MS) procedures to investigate the serum proteome of 15 patients with endometrial cancer and 15 non-cancer subjects. We have identified 16 proteins with diagnostic potential, considering only spots with a fold change in %V ≥ 1.5 or ≤0.6 in intensity, which were statistically significant (p < 0.05). Western blotting data analysis confirmed the upregulation of CLU, ITIH4, SERPINC1, and C1RL in endometrial and exosome cancer sera compared to those of control subjects. The application of the logistic regression constructed based on the abundance of these four proteins separated the controls from the cancers with excellent levels of sensitivity and specificity. After a validation phase, our findings support the potential of using the proposed algorithm as a diagnostic tool in the clinical stage.
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Affiliation(s)
- Blendi Ura
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, 34137 Trieste, Italy; (S.B.); (L.M.); (G.D.L.); (F.R.); (M.A.); (F.C.); (R.A.); (G.R.)
- Correspondence:
| | - Stefania Biffi
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, 34137 Trieste, Italy; (S.B.); (L.M.); (G.D.L.); (F.R.); (M.A.); (F.C.); (R.A.); (G.R.)
| | - Lorenzo Monasta
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, 34137 Trieste, Italy; (S.B.); (L.M.); (G.D.L.); (F.R.); (M.A.); (F.C.); (R.A.); (G.R.)
| | - Giorgio Arrigoni
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy; (G.A.); (I.B.)
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, 35131 Padova, Italy
- CRIBI Biotechnology Center, University of Padova, 35131 Padova, Italy
| | - Ilaria Battisti
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy; (G.A.); (I.B.)
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, 35131 Padova, Italy
| | - Giovanni Di Lorenzo
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, 34137 Trieste, Italy; (S.B.); (L.M.); (G.D.L.); (F.R.); (M.A.); (F.C.); (R.A.); (G.R.)
| | - Federico Romano
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, 34137 Trieste, Italy; (S.B.); (L.M.); (G.D.L.); (F.R.); (M.A.); (F.C.); (R.A.); (G.R.)
| | - Michelangelo Aloisio
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, 34137 Trieste, Italy; (S.B.); (L.M.); (G.D.L.); (F.R.); (M.A.); (F.C.); (R.A.); (G.R.)
| | - Fulvio Celsi
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, 34137 Trieste, Italy; (S.B.); (L.M.); (G.D.L.); (F.R.); (M.A.); (F.C.); (R.A.); (G.R.)
| | - Riccardo Addobbati
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, 34137 Trieste, Italy; (S.B.); (L.M.); (G.D.L.); (F.R.); (M.A.); (F.C.); (R.A.); (G.R.)
| | - Francesco Valle
- Consorzio Sistemi a Grande Interfase, Department of Chemistry, University of Firenze, 50019 Firenze, Italy; (F.V.); (M.B.); (A.R.)
- Consiglio Nazionale delle Ricerche, Istituto per lo Studio dei Materiali Nanostrutturati (CNRISMN), 40129 Bologna, Italy
| | - Enrico Rampazzo
- Department of Chemistry “Giacomo Ciamician”, University of Bologna, 40126 Bologna, Italy;
| | - Marco Brucale
- Consorzio Sistemi a Grande Interfase, Department of Chemistry, University of Firenze, 50019 Firenze, Italy; (F.V.); (M.B.); (A.R.)
- Consiglio Nazionale delle Ricerche, Istituto per lo Studio dei Materiali Nanostrutturati (CNRISMN), 40129 Bologna, Italy
| | - Andrea Ridolfi
- Consorzio Sistemi a Grande Interfase, Department of Chemistry, University of Firenze, 50019 Firenze, Italy; (F.V.); (M.B.); (A.R.)
- Consiglio Nazionale delle Ricerche, Istituto per lo Studio dei Materiali Nanostrutturati (CNRISMN), 40129 Bologna, Italy
- Department of Chemistry, University of Firenze, 50019 Firenze, Italy
| | - Danilo Licastro
- ARGO Laboratorio Genomica ed Epigenomica, AREA Science Park, Basovizza, 34149 Trieste, Italy;
| | - Giuseppe Ricci
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, 34137 Trieste, Italy; (S.B.); (L.M.); (G.D.L.); (F.R.); (M.A.); (F.C.); (R.A.); (G.R.)
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34149 Trieste, Italy
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Coll-de la Rubia E, Martinez-Garcia E, Dittmar G, Gil-Moreno A, Cabrera S, Colas E. Prognostic Biomarkers in Endometrial Cancer: A Systematic Review and Meta-Analysis. J Clin Med 2020; 9:E1900. [PMID: 32560580 PMCID: PMC7356541 DOI: 10.3390/jcm9061900] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 06/12/2020] [Accepted: 06/15/2020] [Indexed: 12/23/2022] Open
Abstract
Endometrial cancer (EC) is the sixth most common cancer in women worldwide and its mortality is directly associated with the presence of poor prognostic factors driving tumor recurrence. Stratification systems are based on few molecular, and mostly clinical and pathological parameters, but these systems remain inaccurate. Therefore, identifying prognostic EC biomarkers is crucial for improving risk assessment pre- and postoperatively and to guide treatment decisions. This systematic review gathers all protein biomarkers associated with clinical prognostic factors of EC, recurrence and survival. Relevant studies were identified by searching the PubMed database from 1991 to February 2020. A total number of 398 studies matched our criteria, which compiled 255 proteins associated with the prognosis of EC. MUC16, ESR1, PGR, TP53, WFDC2, MKI67, ERBB2, L1CAM, CDH1, PTEN and MMR proteins are the most validated biomarkers. On the basis of our meta-analysis ESR1, TP53 and WFDC2 showed potential usefulness for predicting overall survival in EC. Limitations of the published studies in terms of appropriate study design, lack of high-throughput measurements, and statistical deficiencies are highlighted, and new approaches and perspectives for the identification and validation of clinically valuable EC prognostic biomarkers are discussed.
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Affiliation(s)
- Eva Coll-de la Rubia
- Biomedical Research Group in Gynecology, Vall Hebron Institute of Research, Universitat Autònoma de Barcelona, CIBERONC, 08035 Barcelona, Spain;
| | - Elena Martinez-Garcia
- Quantitative Biology Unit, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (E.M.-G.); (G.D.)
| | - Gunnar Dittmar
- Quantitative Biology Unit, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (E.M.-G.); (G.D.)
| | - Antonio Gil-Moreno
- Biomedical Research Group in Gynecology, Vall Hebron Institute of Research, Universitat Autònoma de Barcelona, CIBERONC, 08035 Barcelona, Spain;
- Gynecological Department, Vall Hebron University Hospital, CIBERONC, 08035 Barcelona, Spain
| | - Silvia Cabrera
- Biomedical Research Group in Gynecology, Vall Hebron Institute of Research, Universitat Autònoma de Barcelona, CIBERONC, 08035 Barcelona, Spain;
- Gynecological Department, Vall Hebron University Hospital, CIBERONC, 08035 Barcelona, Spain
| | - Eva Colas
- Biomedical Research Group in Gynecology, Vall Hebron Institute of Research, Universitat Autònoma de Barcelona, CIBERONC, 08035 Barcelona, Spain;
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Van Gool A, Corrales F, Čolović M, Krstić D, Oliver-Martos B, Martínez-Cáceres E, Jakasa I, Gajski G, Brun V, Kyriacou K, Burzynska-Pedziwiatr I, Wozniak LA, Nierkens S, Pascual García C, Katrlik J, Bojic-Trbojevic Z, Vacek J, Llorente A, Antohe F, Suica V, Suarez G, t'Kindt R, Martin P, Penque D, Martins IL, Bodoki E, Iacob BC, Aydindogan E, Timur S, Allinson J, Sutton C, Luider T, Wittfooth S, Sammar M. Analytical techniques for multiplex analysis of protein biomarkers. Expert Rev Proteomics 2020; 17:257-273. [PMID: 32427033 DOI: 10.1080/14789450.2020.1763174] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION The importance of biomarkers for pharmaceutical drug development and clinical diagnostics is more significant than ever in the current shift toward personalized medicine. Biomarkers have taken a central position either as companion markers to support drug development and patient selection, or as indicators aiming to detect the earliest perturbations indicative of disease, minimizing therapeutic intervention or even enabling disease reversal. Protein biomarkers are of particular interest given their central role in biochemical pathways. Hence, capabilities to analyze multiple protein biomarkers in one assay are highly interesting for biomedical research. AREAS COVERED We here review multiple methods that are suitable for robust, high throughput, standardized, and affordable analysis of protein biomarkers in a multiplex format. We describe innovative developments in immunoassays, the vanguard of methods in clinical laboratories, and mass spectrometry, increasingly implemented for protein biomarker analysis. Moreover, emerging techniques are discussed with potentially improved protein capture, separation, and detection that will further boost multiplex analyses. EXPERT COMMENTARY The development of clinically applied multiplex protein biomarker assays is essential as multi-protein signatures provide more comprehensive information about biological systems than single biomarkers, leading to improved insights in mechanisms of disease, diagnostics, and the effect of personalized medicine.
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Affiliation(s)
- Alain Van Gool
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center , Nijmegen, The Netherlands
| | - Fernado Corrales
- Functional Proteomics Laboratory, Centro Nacional De Biotecnología , Madrid, Spain
| | - Mirjana Čolović
- Department of Physical Chemistry, "Vinča" Institute of Nuclear Sciences, University of Belgrade , Belgrade, Serbia
| | - Danijela Krstić
- Institute of Medical Chemistry, Faculty of Medicine, University of Belgrade , Belgrade, Serbia
| | - Begona Oliver-Martos
- Neuroimmunology and Neuroinflammation Group. Instituto De Investigación Biomédica De Málaga-IBIMA. UGC Neurociencias, Hospital Regional Universitario De Málaga , Malaga, Spain
| | - Eva Martínez-Cáceres
- Immunology Division, LCMN, Germans Trias I Pujol University Hospital and Research Institute, Campus Can Ruti, Badalona, and Department of Cellular Biology, Physiology and Immunology, Universitat Autònoma De Barcelona , Cerdanyola Del Vallès, Spain
| | - Ivone Jakasa
- Laboratory for Analytical Chemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb , Zagreb, Croatia
| | - Goran Gajski
- Mutagenesis Unit, Institute for Medical Research and Occupational Health , Zagreb, Croatia
| | - Virginie Brun
- Université Grenoble Alpes, CEA, Inserm, IRIG, BGE , Grenoble, France
| | - Kyriacos Kyriacou
- Department of Electron Microscopy/Molecular Biology, The Cyprus School of Molecular Medicine/The Cyprus Institute of Neurology and Genetics , Nicosia, Cyprus
| | - Izabela Burzynska-Pedziwiatr
- Medical Faculty, Department of Biomedical Sciences, Chair of Medical Biology & Department of Structural Biology, Medical University of Lodz , Łódź, Poland
| | - Lucyna Alicja Wozniak
- Medical Faculty, Department of Biomedical Sciences, Chair of Medical Biology & Department of Structural Biology, Medical University of Lodz , Łódź, Poland
| | - Stephan Nierkens
- Center for Translational Immunology, University Medical Center Utrecht & Princess Máxima Center for Pediatric Oncology , Utrecht, The Netherlands
| | - César Pascual García
- Materials Research and Technology Department, Luxembourg Institute of Science and Technology (LIST) , Belvaux, Luxembourg
| | - Jaroslav Katrlik
- Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences , Bratislava, Slovakia
| | - Zanka Bojic-Trbojevic
- Laboratory for Biology of Reproduction, Institute for the Application of Nuclear Energy - INEP, University of Belgrade , Belgrade, Serbia
| | - Jan Vacek
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University , Olomouc, Czech Republic
| | - Alicia Llorente
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital , Oslo, Norway
| | - Felicia Antohe
- Proteomics Department, Institute of Cellular Biology and Pathology "N. Simionescu" of the Romanian Academy , Bucharest, Romania
| | - Viorel Suica
- Proteomics Department, Institute of Cellular Biology and Pathology "N. Simionescu" of the Romanian Academy , Bucharest, Romania
| | - Guillaume Suarez
- Center for Primary Care and Public Health (Unisanté), University of Lausanne , Lausanne, Switzerland
| | - Ruben t'Kindt
- Research Institute for Chromatography (RIC) , Kortrijk, Belgium
| | - Petra Martin
- Department of Medical Oncology, Midland Regional Hospital Tullamore/St. James's Hospital , Dublin, Ireland
| | - Deborah Penque
- Human Genetics Department, Instituto Nacional De Saúde Dr Ricardo Jorge, Lisboa, Portugal and Centre for Toxicogenomics and Human Health, Universidade Nova De Lisboa , Lisbon,Portugal
| | - Ines Lanca Martins
- Human Genetics Department, Instituto Nacional De Saúde Dr Ricardo Jorge, Lisboa, Portugal and Centre for Toxicogenomics and Human Health, Universidade Nova De Lisboa , Lisbon,Portugal
| | - Ede Bodoki
- Analytical Chemistry Department, Faculty of Pharmacy, "Iuliu Hatieganu" University of Medicine and Pharmacy , Cluj-Napoca, Romania
| | - Bogdan-Cezar Iacob
- Analytical Chemistry Department, Faculty of Pharmacy, "Iuliu Hatieganu" University of Medicine and Pharmacy , Cluj-Napoca, Romania
| | - Eda Aydindogan
- Department of Chemistry, Graduate School of Sciences and Engineering, Koç University , Istanbul, Turkey
| | - Suna Timur
- Institute of Natural Sciences, Department of Biochemistry, Ege University , Izmir, Turkey
| | | | | | - Theo Luider
- Department of Neurology, Erasmus MC , Rotterdam, The Netherlands
| | | | - Marei Sammar
- Ephraim Katzir Department of Biotechnology Engineering, ORT Braude College , Karmiel, Israel
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Njoku K, Chiasserini D, Whetton AD, Crosbie EJ. Proteomic Biomarkers for the Detection of Endometrial Cancer. Cancers (Basel) 2019; 11:cancers11101572. [PMID: 31623106 PMCID: PMC6826703 DOI: 10.3390/cancers11101572] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/07/2019] [Accepted: 10/11/2019] [Indexed: 01/01/2023] Open
Abstract
Endometrial cancer is the leading gynaecological malignancy in the western world and its incidence is rising in tandem with the global epidemic of obesity. Early diagnosis is key to improving survival, which at 5 years is less than 20% in advanced disease and over 90% in early-stage disease. As yet, there are no validated biological markers for its early detection. Advances in high-throughput technologies and machine learning techniques now offer unique and promising perspectives for biomarker discovery, especially through the integration of genomic, transcriptomic, proteomic, metabolomic and imaging data. Because the proteome closely mirrors the dynamic state of cells, tissues and organisms, proteomics has great potential to deliver clinically relevant biomarkers for cancer diagnosis. In this review, we present the current progress in endometrial cancer diagnostic biomarker discovery using proteomics. We describe the various mass spectrometry-based approaches and highlight the challenges inherent in biomarker discovery studies. We suggest novel strategies for endometrial cancer detection exploiting biologically important protein biomarkers and set the scene for future directions in endometrial cancer biomarker research.
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Affiliation(s)
- Kelechi Njoku
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 5th Floor Research, St Mary's Hospital, Oxford Road, Manchester M13 9WL, UK.
- Department of Obstetrics and Gynaecology, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester M13 9WL, UK.
- Stoller Biomarker Discovery Centre, Institute of Cancer Sciences, Faculty of Medical and Human Sciences, University of Manchester, Manchester M13 9PL, UK.
| | - Davide Chiasserini
- Stoller Biomarker Discovery Centre, Institute of Cancer Sciences, Faculty of Medical and Human Sciences, University of Manchester, Manchester M13 9PL, UK.
| | - Anthony D Whetton
- Stoller Biomarker Discovery Centre, Institute of Cancer Sciences, Faculty of Medical and Human Sciences, University of Manchester, Manchester M13 9PL, UK.
| | - Emma J Crosbie
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 5th Floor Research, St Mary's Hospital, Oxford Road, Manchester M13 9WL, UK.
- Department of Obstetrics and Gynaecology, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester M13 9WL, UK.
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Expression of TRA2B in endometrial carcinoma and its regulatory roles in endometrial carcinoma cells. Oncol Lett 2019; 18:2455-2463. [PMID: 31452736 PMCID: PMC6676653 DOI: 10.3892/ol.2019.10553] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 05/16/2019] [Indexed: 12/24/2022] Open
Abstract
Expression levels of Transformer 2 protein homolog beta (TRA2B) in patients with endometrial carcinoma were assessed to investigate the impact of TRA2B on endometrial carcinoma cells. Furthermore, we analyzed the expression of several genes in the tissue samples from patients with endometrial cancer (EC) to identify whether cancer related genes we chose are differently expressed between the endometrial carcinoma tissues and adjacent normal tissues. The results of RT-qPCR analysis, western blot technology and immunofluorescence method consistently manifested that the expression of several genes in endometrial carcinoma tissue was significantly dysregulated between the two groups. Among the dysregulated genes, the strongly upregulated TRA2B in the tissues and serum from patients with EC was selected for further analysis. Endometrial carcinoma cells were transfected with chemically synthesized TRA2B plasmid, siRNA-TRA2B and their corresponding negative control respectively to assess the effects of TRA2B on the EC cells. Overexpression of TRA2B increased both the cell viability and proliferation potency of EC cells. Whereas, the viability and the proliferation ability of EC cells were strongly decreased by siRNA-TRA2B treatment. Furthermore, the invasion of EC cells was promoted by transfection of TRA2B and overexpression of TRA2B decreased the apoptosis of EC cells. Moreover, siRNA-TRA2B transfection inhibited the invasion but accelerated apoptosis of EC cells. Our results demonstrated that TRA2B is closely related to the development of endometrial carcinoma, and inhibition of TRA2B can decrease viability, proliferation and invasion of endometrial carcinoma, suggesting TRA2B is associated with the pathogenesis of human EC. Knockdown of TRA2B may be used for treatment of endometrial carcinoma, furthermore, these findings suggest an experimental foundation to clinical prognostic role of TRA2B in patients with endometrial carcinoma.
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Ciocan-Cartita CA, Jurj A, Buse M, Gulei D, Braicu C, Raduly L, Cojocneanu R, Pruteanu LL, Iuga CA, Coza O, Berindan-Neagoe I. The Relevance of Mass Spectrometry Analysis for Personalized Medicine through Its Successful Application in Cancer "Omics". Int J Mol Sci 2019; 20:ijms20102576. [PMID: 31130665 PMCID: PMC6567119 DOI: 10.3390/ijms20102576] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/21/2019] [Accepted: 05/24/2019] [Indexed: 01/06/2023] Open
Abstract
Mass spectrometry (MS) is an essential analytical technology on which the emerging omics domains; such as genomics; transcriptomics; proteomics and metabolomics; are based. This quantifiable technique allows for the identification of thousands of proteins from cell culture; bodily fluids or tissue using either global or targeted strategies; or detection of biologically active metabolites in ultra amounts. The routine performance of MS technology in the oncological field provides a better understanding of human diseases in terms of pathophysiology; prevention; diagnosis and treatment; as well as development of new biomarkers; drugs targets and therapies. In this review; we argue that the recent; successful advances in MS technologies towards cancer omics studies provides a strong rationale for its implementation in biomedicine as a whole.
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Affiliation(s)
- Cristina Alexandra Ciocan-Cartita
- MEDFUTURE -Research Center for Advanced Medicine," Iuliu Hațieganu" University of Medicine and Pharmacy, 4-6 Louis Pasteur Street, 400349 Cluj-Napoca, Romania.
| | - Ancuța Jurj
- Research Center for Functional Genomics, Biomedicine and Translational Medicine," Iuliu Hațieganu" University of Medicine and Pharmacy.
| | - Mihail Buse
- MEDFUTURE -Research Center for Advanced Medicine," Iuliu Hațieganu" University of Medicine and Pharmacy, 4-6 Louis Pasteur Street, 400349 Cluj-Napoca, Romania.
| | - Diana Gulei
- MEDFUTURE -Research Center for Advanced Medicine," Iuliu Hațieganu" University of Medicine and Pharmacy, 4-6 Louis Pasteur Street, 400349 Cluj-Napoca, Romania.
| | - Cornelia Braicu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine," Iuliu Hațieganu" University of Medicine and Pharmacy.
| | - Lajos Raduly
- Research Center for Functional Genomics, Biomedicine and Translational Medicine," Iuliu Hațieganu" University of Medicine and Pharmacy.
| | - Roxana Cojocneanu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine," Iuliu Hațieganu" University of Medicine and Pharmacy.
| | - Lavinia Lorena Pruteanu
- MEDFUTURE -Research Center for Advanced Medicine," Iuliu Hațieganu" University of Medicine and Pharmacy, 4-6 Louis Pasteur Street, 400349 Cluj-Napoca, Romania.
| | - Cristina Adela Iuga
- MEDFUTURE -Research Center for Advanced Medicine," Iuliu Hațieganu" University of Medicine and Pharmacy, 4-6 Louis Pasteur Street, 400349 Cluj-Napoca, Romania.
- Department of Pharmaceutical Analysis, Faculty of Pharmacy, "Iuliu Hațieganu" University of Medicine and Pharmacy, 6 Louis Pasteur Street, 400349 Cluj-Napoca.
| | - Ovidiu Coza
- Department of Oncology, "Iuliu Hațieganu" University of Medicine and Pharmacy, 34-36 Republicii Street, 400015 Cluj-Napoca, Romania.
- Department of Radiotherapy with High Energies and Brachytherapy, Oncology Institute "Prof. Dr. Ion Chiricuta", 34-36 Republicii Street, 400015 Cluj-Napoca.
| | - Ioana Berindan-Neagoe
- MEDFUTURE -Research Center for Advanced Medicine," Iuliu Hațieganu" University of Medicine and Pharmacy, 4-6 Louis Pasteur Street, 400349 Cluj-Napoca, Romania.
- Research Center for Functional Genomics, Biomedicine and Translational Medicine," Iuliu Hațieganu" University of Medicine and Pharmacy.
- Department of Functional Genomics and Experimental Pathology, Ion Chiricuțǎ Oncology Institute, 34-36 Republicii Street, 400015 Cluj-Napoca.
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Dieters-Castator DZ, Rambau PF, Kelemen LE, Siegers GM, Lajoie GA, Postovit LM, Köbel M. Proteomics-Derived Biomarker Panel Improves Diagnostic Precision to Classify Endometrioid and High-grade Serous Ovarian Carcinoma. Clin Cancer Res 2019; 25:4309-4319. [PMID: 30979743 DOI: 10.1158/1078-0432.ccr-18-3818] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 02/18/2019] [Accepted: 04/08/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE Ovarian carcinomas are a group of distinct diseases classified by histotypes. As histotype-specific treatment evolves, accurate classification will become critical for optimal precision medicine approaches. EXPERIMENTAL DESIGN To uncover differences between the two most common histotypes, high-grade serous (HGSC) and endometrioid carcinoma, we performed label-free quantitative proteomics on freshly frozen tumor tissues (HGSC, n = 10; endometrioid carcinoma, n = 10). Eight candidate protein biomarkers specific to endometrioid carcinoma were validated by IHC using tissue microarrays representing 361 cases of either endometrioid carcinoma or HGSC. RESULTS More than 500 proteins were differentially expressed (P < 0.05) between endometrioid carcinoma and HGSC tumor proteomes. A ranked set of 106 proteins was sufficient to correctly discriminate 90% of samples. IHC validated KIAA1324 as the most discriminatory novel biomarker for endometrioid carcinoma. An 8-marker panel was found to exhibit superior performance for discriminating endometrioid carcinoma from HGSC compared with the current standard of WT1 plus TP53 alone, improving the classification rate for HGSC from 90.7% to 99.2%. Endometrioid carcinoma-specific diagnostic markers such as PLCB1, KIAA1324, and SCGB2A1 were also significantly associated with favorable prognosis within endometrioid carcinoma suggesting biological heterogeneity within this histotype. Pathway analysis of proteomic data revealed differences between endometrioid carcinoma and HGSC pertaining to estrogen and interferon signalling. CONCLUSIONS In summary, these findings support the use of multi-marker panels for the differential diagnosis of difficult cases resembling endometrioid carcinoma and HGSC.
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Affiliation(s)
- Dylan Z Dieters-Castator
- Department of Anatomy and Cell Biology, Western University, London, Ontario, Canada.,Department of Oncology University of Alberta, Edmonton, Alberta, Canada
| | - Peter F Rambau
- Pathology Department, Catholic University of Health and Allied Sciences-Bugando, Mwanza, Tanzania
| | - Linda E Kelemen
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, South Carolina
| | | | - Gilles A Lajoie
- Department of Biochemistry, Western University, London, Ontario, Canada.
| | - Lynne-Marie Postovit
- Department of Anatomy and Cell Biology, Western University, London, Ontario, Canada. .,Department of Oncology University of Alberta, Edmonton, Alberta, Canada.,Department of Obstetrics and Gynecology, University of Alberta, Edmonton, Alberta, Canada
| | - Martin Köbel
- Department of Pathology and Laboratory Medicine, University of Calgary, Foothills Medical Center, Calgary, Alberta, Canada.
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17
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Sinha A, Hussain A, Ignatchenko V, Ignatchenko A, Tang KH, Ho VWH, Neel BG, Clarke B, Bernardini MQ, Ailles L, Kislinger T. N-Glycoproteomics of Patient-Derived Xenografts: A Strategy to Discover Tumor-Associated Proteins in High-Grade Serous Ovarian Cancer. Cell Syst 2019; 8:345-351.e4. [PMID: 30981729 DOI: 10.1016/j.cels.2019.03.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 12/10/2018] [Accepted: 03/14/2019] [Indexed: 01/21/2023]
Abstract
High-grade serous ovarian carcinoma (HGSC) is the most common and lethal subtype of gynecologic malignancy in women. The current standard of treatment combines cytoreductive surgery and chemotherapy. Despite the efficacy of initial treatment, most patients develop cancer recurrence, and 70% of patients die within 5 years of initial diagnosis. CA125 is the current FDA-approved biomarker used in the clinic to monitor response to treatment and recurrence, but its impact on patient survival is limited. New strategies for the discovery of HGSC biomarkers are urgently needed. Here, we describe a proteomics strategy to detect tumor-associated proteins in serum of HGSC patient-derived xenograft models. We demonstrate proof-of-concept applicability using two independent, longitudinal serum cohorts from HGSC patients.
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Affiliation(s)
- Ankit Sinha
- University of Toronto, Department of Medical Biophysics, Toronto, ON M5G 1L7, Canada
| | - Ali Hussain
- University of Toronto, Department of Medical Biophysics, Toronto, ON M5G 1L7, Canada
| | - Vladimir Ignatchenko
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Alexandr Ignatchenko
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Kwan Ho Tang
- Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY 10016, USA
| | - Victor W H Ho
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Benjamin G Neel
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada; Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY 10016, USA
| | - Blaise Clarke
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada; University of Toronto, Department of Laboratory Medicine and Pathobiology, Toronto, ON M5S 1A8, Canada
| | - Marcus Q Bernardini
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada; University of Toronto, Department of Obstetrics and Gynaecology, Toronto, ON M5G 1E2, Canada
| | - Laurie Ailles
- University of Toronto, Department of Medical Biophysics, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Thomas Kislinger
- University of Toronto, Department of Medical Biophysics, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada.
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18
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Yu L, Li K, Xu Z, Cui G, Zhang X. Integrated omics and gene expression analysis identifies the loss of metabolite-metabolite correlations in small cell lung cancer. Onco Targets Ther 2018; 11:3919-3929. [PMID: 30013371 PMCID: PMC6039056 DOI: 10.2147/ott.s166149] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND AND OBJECTIVE Small cell lung cancer (SCLC) is the most aggressive type of lung carcinoma with high metastatic potential and chemoresistance upon relapse. Cancer cells remodel the existing metabolic pathways for their benefits and the perturbations in cellular metabolism are the hallmark of cancer. However, the extent of these changes remains largely unknown for SCLC. MATERIALS AND METHODS We characterized the metabolic perturbations in SCLC cells (SCLCC) by metabolomics. Large-scale correlation analysis was performed between metabolites. Targeted proteomics and gene expression analysis were employed to investigate the changes of key enzymes and genes in the disturbed pathways. RESULTS We found dramatic decrease of metabolite-metabolite correlations in SCLCC compared with normal control cells and non-small cell lung cancer cells. Pathway analysis revealed that the loss of correlations was associated with the alternations of fatty acid oxidation, urea cycle, and purine salvage pathway in SCLCC. Targeted proteomics and gene expression analysis confirmed significant changes of the expression for the key enzymes and genes in the pathways in SCLCC including the upregulation of carbamoyl phosphate synthase 1 (urea cycle) and carnitine palmitoyltransferase 1A (fatty acid oxidation), and the downregulation of hypoxanthine-guanine phosphoribosyltransferase and adenine phosphoribosyltransferase in purine salvage pathway. CONCLUSION We demonstrated the loss of metabolite-metabolite correlations in SCLCC associated with the upregulation of fatty acid oxidation and urea cycle and the downregulation of purine salvage pathways. Our findings provide insights into the metabolic reprogramming in SCLCC and highlight the potential therapeutic targets for the treatment of SCLC.
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Affiliation(s)
- Li Yu
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China,
| | - Kefeng Li
- School of Medicine, University of California-San Diego, San Diego, CA, USA
| | - Zhaoguo Xu
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China,
| | - Guoyuan Cui
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China,
| | - Xiaoye Zhang
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China,
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19
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Quantitative proteomic analysis of pancreatic cyst fluid proteins associated with malignancy in intraductal papillary mucinous neoplasms. Clin Proteomics 2018; 15:17. [PMID: 29713252 PMCID: PMC5907296 DOI: 10.1186/s12014-018-9193-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 04/04/2018] [Indexed: 12/13/2022] Open
Abstract
Background
The application of advanced imaging technologies for identifying pancreatic cysts has become widespread. However, accurately differentiating between low-grade dysplasia (LGD), high-grade dysplasia (HGD), and invasive intraductal papillary mucinous neoplasms (IPMNs) remains a diagnostic challenge with current biomarkers, necessitating the development of novel biomarkers that can distinguish IPMN malignancy.
Methods Cyst fluid samples were collected from nine IPMN patients (3 LGD, 3 HGD, and 3 invasive IPMN) during their pancreatectomies. An integrated proteomics approach that combines filter-aided sample preparation, stage tip-based high-pH fractionation, and high-resolution MS was applied to acquire in-depth proteomic data of pancreatic cyst fluid and discover marker candidates for IPMN malignancy. Biological processes of differentially expressed proteins that are related to pancreatic cysts and aggressive malignancy were analyzed using bioinformatics tools such as gene ontology analysis and Ingenuity pathway analysis. In order to confirm the validity of the marker candidates, 19 cyst fluid samples were analyzed by western blot.
Results A dataset of 2992 proteins was constructed from pancreatic cyst fluid samples. A subsequent analysis found 2963 identified proteins in individual samples, 2837 of which were quantifiable. Differentially expressed proteins between histological grades of IPMN were associated with pancreatic diseases and malignancy according to ingenuity pathway analysis. Eighteen biomarker candidates that were differentially expressed across IPMN histological grades were discovered—7 DEPs that were upregulated and 11 that were downregulated in more malignant grades. HOOK1 and PTPN6 were validated by western blot in an independent cohort, the results of which were consistent with our proteomic data. Conclusions This study demonstrates that novel biomarker candidates for IPMN malignancy can be discovered through proteomic analysis of pancreatic cyst fluid. Electronic supplementary material The online version of this article (10.1186/s12014-018-9193-1) contains supplementary material, which is available to authorized users.
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20
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ALCAM shedding at the invasive front of the tumor is a marker of myometrial infiltration and promotes invasion in endometrioid endometrial cancer. Oncotarget 2018; 9:16648-16664. [PMID: 29682175 PMCID: PMC5908276 DOI: 10.18632/oncotarget.24625] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 02/20/2018] [Indexed: 11/25/2022] Open
Abstract
Endometrial cancer (EC) is the sixth deadliest cancer in women. The depth of myometrial invasion is one of the most important prognostic factors, being directly associated with tumor recurrence and mortality. In this study, ALCAM, a previously described marker of EC recurrence, was studied by immunohistochemistry at the superficial and the invasive tumor areas from 116 EC patients with different degree of myometrial invasion and related to a set of relevant epithelial and mesenchymal markers. ALCAM expression presented a heterogeneous functionality depending on its localization, it correlated with epithelial markers (E-cadherin/β-catenin) at the superficial area, and with mesenchymal markers at the invasive front (COX-2, SNAIL, ETV5, and MMP-9). At the invasive front, ALCAM-negativity was an independent marker of myometrial invasion. This negativity, together with an increase of soluble ALCAM in uterine aspirates from patients with an invasive EC, and its positive correlation with MMP-9 levels, suggested that ALCAM shedding by MMP-9 occurs at the invasive front. In vivo and in vitro models of invasive EC were generated by ETV5-overexpression. In those, we demonstrated that ALCAM shedding was related to a more invasive pattern and that full-ALCAM recovery reverted most of the ETV5-cells mesenchymal abilities, partially through a p-ERK dependent-manner.
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21
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Rödiger A, Baginsky S. Tailored Use of Targeted Proteomics in Plant-Specific Applications. FRONTIERS IN PLANT SCIENCE 2018; 9:1204. [PMID: 30174680 PMCID: PMC6107752 DOI: 10.3389/fpls.2018.01204] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 07/26/2018] [Indexed: 05/03/2023]
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22
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Borràs E, Sabidó E. What is targeted proteomics? A concise revision of targeted acquisition and targeted data analysis in mass spectrometry. Proteomics 2017; 17. [PMID: 28719092 DOI: 10.1002/pmic.201700180] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 07/06/2017] [Accepted: 07/11/2017] [Indexed: 12/14/2022]
Abstract
Targeted proteomics has gained significant popularity in mass spectrometry-based protein quantification as a method to detect proteins of interest with high sensitivity, quantitative accuracy and reproducibility. However, with the emergence of a wide variety of targeted proteomics methods, some of them with high-throughput capabilities, it is easy to overlook the essence of each method and to determine what makes each of them a targeted proteomics method. In this viewpoint, we revisit the main targeted proteomics methods and classify them in four categories differentiating those methods that perform targeted data acquisition from targeted data analysis, and those methods that are based on peptide ion data (MS1 targeted methods) from those that rely on the peptide fragments (MS2 targeted methods).
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Affiliation(s)
- Eva Borràs
- Proteomics Unit, Centre de Regulació Genòmica, Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Eduard Sabidó
- Proteomics Unit, Centre de Regulació Genòmica, Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
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23
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Martinez-Garcia E, Lopez-Gil C, Campoy I, Vallve J, Coll E, Cabrera S, Ramon Y Cajal S, Matias-Guiu X, Van Oostrum J, Reventos J, Gil-Moreno A, Colas E. Advances in endometrial cancer protein biomarkers for use in the clinic. Expert Rev Proteomics 2017; 15:81-99. [PMID: 29183259 DOI: 10.1080/14789450.2018.1410061] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
INTRODUCTION Endometrial cancer (EC) is the fourth most common cancer in women in developed countries. The identification of sensitive and specific biomarkers to improve early detection of EC is crucial for an appropriate management of this disease, in which 30% of patients are diagnosed only at advanced stages, which is associated with high levels of morbidity and mortality. Despite major efforts and investments made to identify EC biomarkers, no protein has yet reached the stage of clinical application. Areas covered: This review gathers the numerous candidate biomarkers for EC diagnosis proposed in proteomic studies published from 1978 to 2017. Additionally, we summarize limitations associated with the proteomic technologies and study designs employed in those articles. Finally, we address new perspectives in EC biomarker research, including the comprehensive knowledge of previously suggested candidate biomarkers in conjunction with novel mass spectrometry-based proteomic technologies with enhanced sensitivity and specificity not yet applied to EC studies and a directed clinical perspective in the study design. Expert commentary: These ingredients could be the recipe to accelerate the application of protein biomarkers in the clinic.
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Affiliation(s)
- Elena Martinez-Garcia
- a Biomedical Research Group in Gynecology, Vall Hebron Research Institute (VHIR) , Universitat Autonoma de Barcelona, CIBERONC , Barcelona , Spain
| | - Carlos Lopez-Gil
- a Biomedical Research Group in Gynecology, Vall Hebron Research Institute (VHIR) , Universitat Autonoma de Barcelona, CIBERONC , Barcelona , Spain
| | - Irene Campoy
- a Biomedical Research Group in Gynecology, Vall Hebron Research Institute (VHIR) , Universitat Autonoma de Barcelona, CIBERONC , Barcelona , Spain
| | - Julia Vallve
- a Biomedical Research Group in Gynecology, Vall Hebron Research Institute (VHIR) , Universitat Autonoma de Barcelona, CIBERONC , Barcelona , Spain
| | - Eva Coll
- a Biomedical Research Group in Gynecology, Vall Hebron Research Institute (VHIR) , Universitat Autonoma de Barcelona, CIBERONC , Barcelona , Spain
| | - Silvia Cabrera
- b Gynecology Department , Vall Hebron University Hospital , Barcelona , Spain
| | | | - Xavier Matias-Guiu
- d Pathological Oncology Group and Pathology Department , University Hospital Arnau de Vilanova, IRBLLEIDA, University of Lleida, CIBERONC , Barcelona , Spain.,e Gynecology Cancer Group , University Hospital Bellvitge, Idibell, CIBERONC , Barcelona , Spain
| | - Jan Van Oostrum
- f Luxembourg Clinical Proteomics Center (LCP) , Luxembourg Institute of Health (LIH) , Strassen , Luxembourg
| | - Jaume Reventos
- e Gynecology Cancer Group , University Hospital Bellvitge, Idibell, CIBERONC , Barcelona , Spain.,g Basic Sciences Department , International University of Catalonia , Barcelona , Spain
| | - Antonio Gil-Moreno
- a Biomedical Research Group in Gynecology, Vall Hebron Research Institute (VHIR) , Universitat Autonoma de Barcelona, CIBERONC , Barcelona , Spain.,c Pathology Department , Vall Hebron University Hospital, CIBERONC , Barcelona , Spain
| | - Eva Colas
- a Biomedical Research Group in Gynecology, Vall Hebron Research Institute (VHIR) , Universitat Autonoma de Barcelona, CIBERONC , Barcelona , Spain
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24
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Ura B, Monasta L, Arrigoni G, Franchin C, Radillo O, Peterlunger I, Ricci G, Scrimin F. A proteomic approach for the identification of biomarkers in endometrial cancer uterine aspirate. Oncotarget 2017; 8:109536-109545. [PMID: 29312627 PMCID: PMC5752540 DOI: 10.18632/oncotarget.22725] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 11/01/2017] [Indexed: 12/31/2022] Open
Abstract
Endometrial cancer arises from the endometrium. It has a slow progression and a reported survival rate of 75%. The identification of soluble biomarkers in the uterine aspirate may be very useful for its early diagnosis. Uterine aspirates from 10 patients with endometrial cancer and 6 non-endometrial cancer controls were analyzed by two-dimensional gel electrophoresis coupled with mass spectrometry and western blotting for data verification. A total of 25 proteins with fold change in %V ≥2 or ≤0.5 in intensity were observed to change significantly (P<0.05). From the discovery phase, four proteins (costars family protein ABRACL, phosphoglycerate mutase 2, fibrinogen beta chain, annexin A3) were found to be present in the uterine aspirate of endometrial cancers and not in healthy aspirates. Western blotting verification data demonstrated that costars family protein ABRACL, phosphoglycerate mutase 2 were present only in endometrial cancer uterine aspirate while fibrinogen beta chain, annexin A3 were also present in healthy aspirates. To our knowledge, phosphoglycerate mutase 2 has not been previously associated with endometrial cancer. In this study we demonstrate that uterine aspirates are a promising biological fluid in which to identify endometrial cancer biomarkers. In our opinion proteins like costars family protein ABRACL and phosphoglycerate mutase 2 have a great potential to reach the clinical phase after a validation phase.
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Affiliation(s)
- Blendi Ura
- Institute for Maternal and Child Health-IRCCS "Burlo Garofolo", Trieste, Italy
| | - Lorenzo Monasta
- Institute for Maternal and Child Health-IRCCS "Burlo Garofolo", Trieste, Italy
| | - Giorgio Arrigoni
- Department of Biomedical Sciences, University of Padova, Padova, Italy.,Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, Padova, Italy
| | - Cinzia Franchin
- Department of Biomedical Sciences, University of Padova, Padova, Italy.,Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, Padova, Italy
| | - Oriano Radillo
- Institute for Maternal and Child Health-IRCCS "Burlo Garofolo", Trieste, Italy
| | - Isabel Peterlunger
- Institute for Maternal and Child Health-IRCCS "Burlo Garofolo", Trieste, Italy
| | - Giuseppe Ricci
- Institute for Maternal and Child Health-IRCCS "Burlo Garofolo", Trieste, Italy.,Department of Medical, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Federica Scrimin
- Institute for Maternal and Child Health-IRCCS "Burlo Garofolo", Trieste, Italy
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25
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Gianazza E, Miller I, Guerrini U, Palazzolo L, Parravicini C, Eberini I. Gender proteomics II. Which proteins in sexual organs. J Proteomics 2017; 178:18-30. [PMID: 28988880 DOI: 10.1016/j.jprot.2017.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 09/26/2017] [Accepted: 10/04/2017] [Indexed: 02/08/2023]
Abstract
In continuity with the review dealing with differences by gender in non-sexual organs [1], this review collects data on the proteomes of the sexual organs as involved in human reproduction, under both physiological and pathological conditions. It also collects data on the tissue structures and biological fluids typical of pregnancy, such as placenta and amniotic fluid, as well as what may be tested on preimplantation embryos during medically assisted reproduction. The review includes as well mention to all fluids and secretions connected with sex organs and/or reproduction, including sperm and milk, to exemplify two distinctive items in male and female physiology. SIGNIFICANCE The causes of infertility are only incompletely understood; the same holds for the causes, and even the early markers, of the most frequent complications of pregnancy. To these established medical challenges, present day practice adds new issues connected with medically assisted reproduction. Omics approaches, including proteomics, are building the database for basic knowledge to possibly translate into clinical testing and eventually into medical routine in this critical branch of health care.
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Affiliation(s)
- Elisabetta Gianazza
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, I-20133 Milano, Italy.
| | - Ingrid Miller
- Institut für Medizinische Biochemie, Veterinärmedizinische Universität Wien, Veterinärplatz 1, A-1210 Wien, Austria
| | - Uliano Guerrini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, I-20133 Milano, Italy
| | - Luca Palazzolo
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, I-20133 Milano, Italy
| | - Chiara Parravicini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, I-20133 Milano, Italy
| | - Ivano Eberini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, I-20133 Milano, Italy
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26
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Martinez-Garcia E, Lesur A, Devis L, Cabrera S, Matias-Guiu X, Hirschfeld M, Asberger J, van Oostrum J, Casares de Cal MDLÁ, Gómez-Tato A, Reventos J, Domon B, Colas E, Gil-Moreno A. Targeted Proteomics Identifies Proteomic Signatures in Liquid Biopsies of the Endometrium to Diagnose Endometrial Cancer and Assist in the Prediction of the Optimal Surgical Treatment. Clin Cancer Res 2017; 23:6458-6467. [PMID: 28790116 DOI: 10.1158/1078-0432.ccr-17-0474] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 04/05/2017] [Accepted: 08/03/2017] [Indexed: 11/16/2022]
Abstract
Purpose: Endometrial cancer (EC) diagnosis relies on the observation of tumor cells in endometrial biopsies obtained by aspiration (i.e., uterine aspirates), but it is associated with 22% undiagnosed patients and up to 50% of incorrectly assigned EC histotype and grade. We aimed to identify biomarker signatures in the fluid fraction of these biopsies to overcome these limitations.Experimental Design: The levels of 52 proteins were measured in the fluid fraction of uterine aspirates from 116 patients by LC-PRM, the latest generation of targeted mass-spectrometry acquisition. A logistic regression model was used to assess the power of protein panels to differentiate between EC and non-EC patients and between EC histologic subtypes. The robustness of the panels was assessed by the "leave-one-out" cross-validation procedure performed within the same cohort of patients and an independent cohort of 38 patients.Results: The levels of 28 proteins were significantly higher in patients with EC (n = 69) compared with controls (n = 47). The combination of MMP9 and KPYM exhibited 94% sensitivity and 87% specificity for detecting EC cases. This panel perfectly complemented the standard diagnosis, achieving 100% of correct diagnosis in this dataset. Nine proteins were significantly increased in endometrioid EC (n = 49) compared with serous EC (n = 20). The combination of CTNB1, XPO2, and CAPG achieved 95% sensitivity and 96% specificity for the discrimination of these subtypes.Conclusions: We developed two uterine aspirate-based signatures to diagnose EC and classify tumors in the most prevalent histologic subtypes. This will improve diagnosis and assist in the prediction of the optimal surgical treatment. Clin Cancer Res; 23(21); 6458-67. ©2017 AACR.
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Affiliation(s)
- Elena Martinez-Garcia
- Biomedical Research Group in Gynecology, Vall Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, CIBERONC, Barcelona, Spain
| | - Antoine Lesur
- Luxembourg Clinical Proteomics Center (LCP), Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | - Laura Devis
- Biomedical Research Group in Gynecology, Vall Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, CIBERONC, Barcelona, Spain
| | - Silvia Cabrera
- Gynecology Department, Vall Hebron University Hospital, Barcelona, Spain
| | - Xavier Matias-Guiu
- Pathological Oncology Group and Pathology Department, University Hospital Arnau de Vilanova, and University Hospital Bellvitge, IRBLLEIDA and Idibell, University of Lleida, CIBERONC, Barcelona, Spain
| | - Marc Hirschfeld
- Department of Obstetrics and Gynecology, University Medical Center, Albert-Ludwigs-University, Freiburg, Germany
- Institute of Veterinary Medicine, Georg-August-University Goettingen, Germany
| | - Jasmin Asberger
- Department of Obstetrics and Gynecology, University Medical Center, Albert-Ludwigs-University, Freiburg, Germany
| | - Jan van Oostrum
- Luxembourg Clinical Proteomics Center (LCP), Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | | | - Antonio Gómez-Tato
- Faculty of Mathematics, University of Santiago de Compostela (USC), Santiago de Compostela, Spain
| | - Jaume Reventos
- Biomedical Research Group in Gynecology, Vall Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, CIBERONC, Barcelona, Spain
- Basic Sciences Department, International University of Catalonia, CIBERONC, Barcelona, Spain
| | - Bruno Domon
- Luxembourg Clinical Proteomics Center (LCP), Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | - Eva Colas
- Biomedical Research Group in Gynecology, Vall Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, CIBERONC, Barcelona, Spain.
| | - Antonio Gil-Moreno
- Biomedical Research Group in Gynecology, Vall Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, CIBERONC, Barcelona, Spain.
- Gynecology Department, Vall Hebron University Hospital, Barcelona, Spain
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