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Abstract
Biomarkers factor into the diagnosis and treatment of almost every patient with cancer. The innovation in proteomics follows improvement of mass spectrometry techniques and data processing strategy. Recently, proteomics and typical biological studies have been the answer for clinical applications. The clinical proteomics techniques are now actively adapted to protein identification in large patient cohort, biomarker development for more sensitive and specific screening based on quantitative data. And, it is important for clinical, translational researchers to be acutely aware of the issues surrounding appropriate biomarker development, in order to facilitate entry of clinically useful biomarkers into the clinic. Here, we discuss in detail include the case research for clinical proteomics. Furthermore, we give an overview on the current developments and novel findings in proteomics-based cancer biomarker research.
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Stevenson J, Barrow-McGee R, Yu L, Paul A, Mansfield D, Owen J, Woodman N, Natrajan R, Haider S, Gillett C, Tutt A, Pinder SE, Choudary J, Naidoo K. Proteomics of REPLICANT perfusate detects changes in the metastatic lymph node microenvironment. NPJ Breast Cancer 2021; 7:24. [PMID: 33674617 PMCID: PMC7935848 DOI: 10.1038/s41523-021-00227-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 01/20/2021] [Indexed: 02/08/2023] Open
Abstract
In breast cancer (BC), detecting low volumes of axillary lymph node (ALN) metastasis pre-operatively is difficult and novel biomarkers are needed. We recently showed that patient-derived ALNs can be sustained ex-vivo using normothermic perfusion. We now compare reactive (tumour-free; n = 5) and macrometastatic (containing tumour deposits >2 mm; n = 4) ALNs by combining whole section multiplex immunofluorescence with TMT-labelled LC-MS/MS of the circulating perfusate. Macrometastases contained significantly fewer B cells and T cells (CD4+/CD8+/regulatory) than reactive nodes (p = 0.02). Similarly, pathway analysis of the perfusate proteome (119/1453 proteins significantly differentially expressed) showed that immune function was diminished in macrometastases in favour of ‘extracellular matrix degradation’; only ‘neutrophil degranulation’ was preserved. Qualitative comparison of the perfusate proteome to that of node-positive pancreatic and prostatic adenocarcinoma also highlighted ‘neutrophil degranulation’ as a contributing factor to nodal metastasis. Thus, metastasis-induced changes in the REPLICANT perfusate proteome are detectable, and could facilitate biomarker discovery.
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Affiliation(s)
- Julia Stevenson
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Rachel Barrow-McGee
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Lu Yu
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Angela Paul
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - David Mansfield
- Division of Radiotherapy and Imaging, The Institute of Cancer Research, London, UK
| | - Julie Owen
- King's Health Partners Cancer Biobank, Guy's Comprehensive Cancer Centre, London, UK
| | - Natalie Woodman
- King's Health Partners Cancer Biobank, Guy's Comprehensive Cancer Centre, London, UK
| | - Rachael Natrajan
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Syed Haider
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Cheryl Gillett
- King's Health Partners Cancer Biobank, Guy's Comprehensive Cancer Centre, London, UK
| | - Andrew Tutt
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Sarah E Pinder
- School of Cancer and Pharmaceutical Sciences, King's College London, Guy's Comprehensive Cancer Centre, London, UK
| | - Jyoti Choudary
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Kalnisha Naidoo
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK. .,Department of Cellular Pathology, Imperial College Healthcare NHS Trust, Charing Cross Hospital, London, UK.
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Kaur G, Poljak A, Ali SA, Zhong L, Raftery MJ, Sachdev P. Extending the Depth of Human Plasma Proteome Coverage Using Simple Fractionation Techniques. J Proteome Res 2021; 20:1261-1279. [PMID: 33471535 DOI: 10.1021/acs.jproteome.0c00670] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Human plasma is one of the most widely used tissues in clinical analysis, and plasma-based biomarkers are used for monitoring patient health status and/or response to medical treatment to avoid unnecessary invasive biopsy. Data-driven plasma proteomics has suffered from a lack of throughput and detection sensitivity, largely due to the complexity of the plasma proteome and in particular the enormous quantitative dynamic range, estimated to be between 9 and 13 orders of magnitude between the lowest and the highest abundance protein. A major challenge is to identify workflows that can achieve depth of plasma proteome coverage while minimizing the complexity of the sample workup and maximizing the sample throughput. In this study, we have performed intensive depletion of high-abundant plasma proteins or enrichment of low-abundant proteins using the Agilent multiple affinity removal liquid chromatography (LC) column-Human 6 (Hu6), the Agilent multiple affinity removal LC column-Human 14 (Hu14), and ProteoMiner followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS PAGE) and C18 prefractionation techniques. We compared the performance of each of these fractionation approaches to identify the method that satisfies requirements for analysis of clinical samples and to include good plasma proteome coverage in combination with reasonable sample output. In this study, we report that one-dimensional (1D) gel-based prefractionation allows parallel sample processing and no loss of proteome coverage, compared with serial chromatographic separation, and significantly accelerates analysis time, particularly important for large clinical projects. Furthermore, we show that a variety of methodologies can achieve similarly high plasma proteome coverage, allowing flexibility in method selection based on project-specific needs. These considerations are important in the effort to accelerate plasma proteomics research so as to provide efficient, reliable, and accurate diagnoses, population-based health screening, clinical research studies, and other clinical work.
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Affiliation(s)
- Gurjeet Kaur
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW 2052, Australia.,Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, University of New South Wales, Wallace Wurth Building (C27), Sydney, NSW 2052, Australia
| | - Anne Poljak
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW 2052, Australia.,Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, University of New South Wales, Wallace Wurth Building (C27), Sydney, NSW 2052, Australia
| | - Syed Azmal Ali
- Cell Biology and Proteomics Lab, National Dairy Research Institute, Karnal, Haryana 132001, India
| | - Ling Zhong
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, University of New South Wales, Wallace Wurth Building (C27), Sydney, NSW 2052, Australia
| | - Mark J Raftery
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, University of New South Wales, Wallace Wurth Building (C27), Sydney, NSW 2052, Australia
| | - Perminder Sachdev
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW 2052, Australia.,Neuropsychiatric Institute, Euroa Centre, Prince of Wales Hospital, Sydney, NSW 2052, Australia
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Abstract
Multidrug resistance (MDR) is a vital issue in cancer treatment. Drug resistance can be developed through a variety of mechanisms, including increased drug efflux, activation of detoxifying systems and DNA repair mechanisms, and escape of drug-induced apoptosis. Identifying the exact mechanism related in a particular case is a difficult task. Proteomics is the large-scale study of proteins, particularly their expression, structures and functions. In recent years, comparative proteomic methods have been performed to analyze MDR mechanisms in drug-selected model cancer cell lines. In this paper, we review the recent developments and progresses by comparative proteomic approaches to identify potential MDR mechanisms in drug-selected model cancer cell lines, which may help understand and design chemical sensitizers.
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Quantitative Proteomic Analysis of Human Seminal Plasma from Normozoospermic and Asthenozoospermic Individuals. BIOMED RESEARCH INTERNATIONAL 2019; 2019:2735038. [PMID: 30984777 PMCID: PMC6431472 DOI: 10.1155/2019/2735038] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 12/02/2018] [Accepted: 02/19/2019] [Indexed: 12/11/2022]
Abstract
Seminal plasma is a complex mixture of secretions from various glands in the male genital tract. Compared to sperm cells, it contains important proteins that are both directly and indirectly associated with sperm motility. Here, we constructed quantitative proteomes of human seminal plasma from three normozoospermic and asthenozoospermic individuals. A total of 524 proteins were identified, and 366 of them were found to be quantified in all six samples. We first investigated the absolute expression features of these proteins and found that the variations of protein identification among different samples and other published datasets were mainly due to some lowly expressed proteins. By integration of various proteomic datasets and bioinformatics databases, we comprehensively annotated the biological functions, physiological originations, and disease associations of these proteins. We found that our dataset could benefit the studies of both male infertility and other male diseases. Finally, based on the relative expression values determined by chemical labeling, we identified a total of 29 differentially expressed proteins, which could be used as candidate targets for studying the molecular bases of sperm motility or developing precise diagnostic biomarkers of asthenozoospermia. We further successfully verified the expression trends of four representative proteins by Western blotting. Compared to a previous dataset based on label-free quantification, our results showed that most of the important proteins could be identified in the sample collected only once for each individual, providing the bases for personalized examination of seminal plasma proteins in clinic.
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Núñez C. Blood-based protein biomarkers in breast cancer. Clin Chim Acta 2018; 490:113-127. [PMID: 30597138 DOI: 10.1016/j.cca.2018.12.028] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/26/2018] [Accepted: 12/27/2018] [Indexed: 02/07/2023]
Abstract
Breast cancer (BCa) is a significant healthcare problem on women worldwide. Thus, early detection is very important to reduce mortality. Furthermore, better BCa prognosis could improve selection of patients eligible for adjuvant therapy. New markers for early diagnosis, accurate prognosis and prediction of response to treatment are necessary to improve BCa care. The present review summarizes important aspects of the potential usefulness of modern technologies, strategies, and scientific findings in proteomic research for discovery of breast cancer-associated blood-based protein biomarkers in the clinic.
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Affiliation(s)
- Cristina Núñez
- Research Unit, Hospital Universitario Lucus Augusti (HULA), Servizo Galego de Saúde (SERGAS), 27002 Lugo, Spain.
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