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Doulidis PG, Kuropka B, Frizzo Ramos C, Rodríguez-Rojas A, Burgener IA. Characterization of the plasma proteome from healthy adult dogs. Front Vet Sci 2024; 11:1356318. [PMID: 38638644 PMCID: PMC11024428 DOI: 10.3389/fvets.2024.1356318] [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: 12/15/2023] [Accepted: 03/04/2024] [Indexed: 04/20/2024] Open
Abstract
Introduction Bloodwork is a widely used diagnostic tool in veterinary medicine, as diagnosis and therapeutic interventions often rely on blood biomarkers. However, biomarkers available in veterinary medicine often lack sensitivity or specificity. Mass spectrometry-based proteomics technology has been extensively used in the analysis of biological fluids. It offers excellent potential for a more comprehensive characterization of the plasma proteome in veterinary medicine. Methods In this study, we aimed to identify and quantify plasma proteins in a cohort of healthy dogs and compare two techniques for depleting high-abundance plasma proteins to enable the detection of lower-abundance proteins via label-free quantification liquid chromatography-mass spectrometry. We utilized surplus lithium-heparin plasma from 30 healthy dogs, subdivided into five groups of pooled plasma from 6 randomly selected individuals each. Firstly, we used a commercial kit to deplete high-abundance plasma proteins. Secondly, we employed an in-house method to remove albumin using Blue-Sepharose. Results and discussion Among all the samples, some of the most abundant proteins identified were apolipoprotein A and B, albumin, alpha-2-macroglobulin, fibrinogen beta chain, fibronectin, complement C3, serotransferrin, and coagulation factor V. However, neither of the depletion techniques achieved significant depletion of highly abundant proteins. Despite this limitation, we could detect and quantify many clinically relevant proteins. Determining the healthy canine proteome is a crucial first step in establishing a reference proteome for canine plasma. After enrichment, this reference proteome can later be utilized to identify protein markers associated with different diseases, thereby contributing to the diagnosis and prognosis of various pathologies.
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Affiliation(s)
- Pavlos G. Doulidis
- Division for Small Animal Internal Medicine, Department for Small Animals and Horses, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Benno Kuropka
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Carolina Frizzo Ramos
- The Interuniversity Messerli Research Institute, Medical University Vienna, Vienna, Austria
- Clinical Center for Small Animals, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Alexandro Rodríguez-Rojas
- Division for Small Animal Internal Medicine, Department for Small Animals and Horses, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Iwan A. Burgener
- Division for Small Animal Internal Medicine, Department for Small Animals and Horses, University of Veterinary Medicine Vienna, Vienna, Austria
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2
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Hamza GM, Raghunathan R, Ashenden S, Zhang B, Miele E, Jarnuczak AF. Proteomics of prostate cancer serum and plasma using low and high throughput approaches. Clin Proteomics 2024; 21:21. [PMID: 38475692 DOI: 10.1186/s12014-024-09461-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 02/12/2024] [Indexed: 03/14/2024] Open
Abstract
Despite progress, MS-based proteomics in biofluids, especially blood, faces challenges such as dynamic range and throughput limitations in biomarker and disease studies. In this work, we used cutting-edge proteomics technologies to construct label-based and label-free workflows, capable of quantifying approximately 2,000 proteins in biofluids. With 70µL of blood and a single depletion strategy, we conducted an analysis of a homogenous cohort (n = 32), comparing medium-grade prostate cancer patients (Gleason score: 7(3 + 4); TNM stage: T2cN0M0, stage IIB) to healthy donors. The results revealed dozens of differentially expressed proteins in both plasma and serum. We identified the upregulation of Prostate Specific Antigen (PSA), a well-known biomarker for prostate cancer, in the serum of cancer cohort. Further bioinformatics analysis highlighted noteworthy proteins which appear to be differentially secreted into the bloodstream, making them good candidates for further exploration.
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Affiliation(s)
| | - Rekha Raghunathan
- Bioanalytical and Biomarker, Prevail Therapeutics, Wholly Owned Subsidiary of Eli Lilly and Company, New York, NY, 10016, USA
| | | | - Bairu Zhang
- Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Eric Miele
- Discovery Sciences, R&D, AstraZeneca, Cambridge, UK.
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3
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Zhu Y. Plasma/Serum Proteomics based on Mass Spectrometry. Protein Pept Lett 2024; 31:192-208. [PMID: 38869039 PMCID: PMC11165715 DOI: 10.2174/0109298665286952240212053723] [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: 11/22/2023] [Revised: 01/22/2024] [Accepted: 01/31/2024] [Indexed: 06/14/2024]
Abstract
Human blood is a window of physiology and disease. Examination of biomarkers in blood is a common clinical procedure, which can be informative in diagnosis and prognosis of diseases, and in evaluating treatment effectiveness. There is still a huge demand on new blood biomarkers and assays for precision medicine nowadays, therefore plasma/serum proteomics has attracted increasing attention in recent years. How to effectively proceed with the biomarker discovery and clinical diagnostic assay development is a question raised to researchers who are interested in this area. In this review, we comprehensively introduce the background and advancement of technologies for blood proteomics, with a focus on mass spectrometry (MS). Analyzing existing blood biomarkers and newly-built diagnostic assays based on MS can shed light on developing new biomarkers and analytical methods. We summarize various protein analytes in plasma/serum which include total proteome, protein post-translational modifications, and extracellular vesicles, focusing on their corresponding sample preparation methods for MS analysis. We propose screening multiple protein analytes in the same set of blood samples in order to increase success rate for biomarker discovery. We also review the trends of MS techniques for blood tests including sample preparation automation, and further provide our perspectives on their future directions.
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Affiliation(s)
- Yiying Zhu
- Department of Chemistry, Tsinghua University, Beijing, China
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4
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Bader JM, Albrecht V, Mann M. MS-based proteomics of body fluids: The end of the beginning. Mol Cell Proteomics 2023:100577. [PMID: 37209816 PMCID: PMC10388585 DOI: 10.1016/j.mcpro.2023.100577] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/07/2023] [Accepted: 05/11/2023] [Indexed: 05/22/2023] Open
Abstract
Accurate biomarkers are a crucial and necessary precondition for precision medicine, yet existing ones are often unspecific and new ones have been very slow to enter the clinic. Mass spectrometry (MS)-based proteomics excels by its untargeted nature, specificity of identification and quantification making it an ideal technology for biomarker discovery and routine measurement. It has unique attributes compared to affinity binder technologies, such as OLINK Proximity Extension Assay and SOMAscan. In a previous review we described technological and conceptual limitations that had held back success (Geyer et al., 2017). We proposed a 'rectangular strategy' to better separate true biomarkers by minimizing cohort-specific effects. Today, this has converged with advances in MS-based proteomics technology, such as increased sample throughput, depth of identification and quantification. As a result, biomarker discovery studies have become more successful, producing biomarker candidates that withstand independent verification and, in some cases, already outperform state-of-the-art clinical assays. We summarize developments over the last years, including the benefits of large and independent cohorts, which are necessary for clinical acceptance. They are also required for machine learning or deep learning. Shorter gradients, new scan modes and multiplexing are about to drastically increase throughput, cross-study integration, and quantification, including proxies for absolute levels. We have found that multi-protein panels are inherently more robust than current single analyte tests and better capture the complexity of human phenotypes. Routine MS measurement in the clinic is fast becoming a viable option. The full set of proteins in a body fluid (global proteome) is the most important reference and the best process control. Additionally, it increasingly has all the information that could be obtained from targeted analysis although the latter may be the most straightforward way to enter into regular use. Many challenges remain, not least of a regulatory and ethical nature, but the outlook for MS-based clinical applications has never been brighter.
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Affiliation(s)
- Jakob M Bader
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Vincent Albrecht
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
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5
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Ma C, Li Y, Li J, Song L, Chen L, Zhao N, Li X, Chen N, Long L, Zhao J, Hou X, Ren L, Yuan X. Comprehensive and deep profiling of the plasma proteome with protein corona on zeolite NaY. J Pharm Anal 2023; 13:503-513. [PMID: 37305782 PMCID: PMC10257194 DOI: 10.1016/j.jpha.2023.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/27/2023] [Accepted: 04/06/2023] [Indexed: 06/13/2023] Open
Abstract
Proteomic characterization of plasma is critical for the development of novel pharmacodynamic biomarkers. However, the vast dynamic range renders the profiling of proteomes extremely challenging. Here, we synthesized zeolite NaY and developed a simple and rapid method to achieve comprehensive and deep profiling of the plasma proteome using the plasma protein corona formed on zeolite NaY. Specifically, zeolite NaY and plasma were co-incubated to form plasma protein corona on zeolite NaY (NaY-PPC), followed by conventional protein identification using liquid chromatography-tandem mass spectrometry. NaY was able to significantly enhance the detection of low-abundance plasma proteins, minimizing the "masking" effect caused by high-abundance proteins. The relative abundance of middle- and low-abundance proteins increased substantially from 2.54% to 54.41%, and the top 20 high-abundance proteins decreased from 83.63% to 25.77%. Notably, our method can quantify approximately 4000 plasma proteins with sensitivity up to pg/mL, compared to only about 600 proteins identified from untreated plasma samples. A pilot study based on plasma samples from 30 lung adenocarcinoma patients and 15 healthy subjects demonstrated that our method could successfully distinguish between healthy and disease states. In summary, this work provides an advantageous tool for the exploration of plasma proteomics and its translational applications.
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Affiliation(s)
- Congcong Ma
- Tianjin Key Laboratory of Composite and Functional Materials, School of Materials Science and Engineering, Tianjin University, Tianjin, 300350, China
| | - Yanwei Li
- Department of Integrative Oncology, Tianjin Medical University Cancer Institute and Hospital and Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China
| | - Jie Li
- Department of Proteomics, Tianjin Key Laboratory of Clinical Multi-omics, Tianjin, 300308, China
| | - Lei Song
- Department of Proteomics, Tianjin Key Laboratory of Clinical Multi-omics, Tianjin, 300308, China
| | - Liangyu Chen
- Department of Proteomics, Tianjin Key Laboratory of Clinical Multi-omics, Tianjin, 300308, China
| | - Na Zhao
- Department of Proteomics, Tianjin Key Laboratory of Clinical Multi-omics, Tianjin, 300308, China
| | - Xueping Li
- Tianjin Key Laboratory of Composite and Functional Materials, School of Materials Science and Engineering, Tianjin University, Tianjin, 300350, China
| | - Ning Chen
- Tianjin Key Laboratory of Composite and Functional Materials, School of Materials Science and Engineering, Tianjin University, Tianjin, 300350, China
| | - Lixia Long
- Tianjin Key Laboratory of Composite and Functional Materials, School of Materials Science and Engineering, Tianjin University, Tianjin, 300350, China
| | - Jin Zhao
- Tianjin Key Laboratory of Composite and Functional Materials, School of Materials Science and Engineering, Tianjin University, Tianjin, 300350, China
| | - Xin Hou
- Tianjin Key Laboratory of Composite and Functional Materials, School of Materials Science and Engineering, Tianjin University, Tianjin, 300350, China
| | - Li Ren
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Xubo Yuan
- Tianjin Key Laboratory of Composite and Functional Materials, School of Materials Science and Engineering, Tianjin University, Tianjin, 300350, China
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Wiredu K, Aduse-Poku E, Shaefi S, Gerber SA. Proteomics for the Discovery of Clinical Delirium Biomarkers: A Systematic Review of Major Studies. Anesth Analg 2023; 136:422-432. [PMID: 36580411 DOI: 10.1213/ane.0000000000006246] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Delirium represents a significant health care burden, diagnosed in more than 2 million elderly Americans each year. In the surgical population, delirium remains the most common complication among elderly patients, and is associated with longer hospital stays, higher costs of care, increased mortality, and functional impairment. The pathomechanism of disease is poorly understood, with current diagnostic approaches somewhat subjective and arbitrary, and definitive diagnostic biomarkers are currently lacking. Despite the recent interest in delirium research, biomarker discovery for it remains new. Most attempts to discover biomarkers are targeted studies that seek to assess the involvement of one or more members of a focused panel of candidates in delirium. For a more unbiased, system-biology view, we searched literature from Medical Literature Analysis and Retrieval System Online (MEDLINE), Cochrane Central, Web of Science, SCOPUS, and Dimensions between 2016 and 2021 for untargeted proteomic discovery studies for biomarkers of delirium conducted on human geriatric subjects. Two reviewers conducted an independent review of all search results and resolved discordance by consensus. From an overall search of 1172 publications, 8 peer-reviewed studies met our defined inclusion criteria. The 370 unique perioperative biomarkers identified in these reports are enriched in pathways involving activation of the immune system, inflammatory response, and the coagulation cascade. The most frequently identified biomarker was interleukin-6 (IL-6). By reviewing the distribution of protein biomarker candidates from these studies, we conclude that a panel of proteins, rather than a single biomarker, would allow for discriminating delirium cases from noncases. The paucity of hypothesis-generating studies in the peer-reviewed literature also suggests that a system-biology view of delirium pathomechanisms has yet to fully emerge.
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Affiliation(s)
- Kwame Wiredu
- From the Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire.,Program in Quantitative Biomedical Science, Dartmouth College, Hanover, New Hampshire
| | | | - Shahzad Shaefi
- Department of Anesthesiology, Critical Care and Pain Medicine, Harvard Medical School/Critical Care and Pain Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Scott A Gerber
- From the Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire.,Program in Quantitative Biomedical Science, Dartmouth College, Hanover, New Hampshire.,Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire
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7
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Stalmach A, Boehm I, Fernandes M, Rutter A, Skipworth RJE, Husi H. Gene Ontology (GO)-Driven Inference of Candidate Proteomic Markers Associated with Muscle Atrophy Conditions. Molecules 2022; 27:molecules27175514. [PMID: 36080280 PMCID: PMC9457532 DOI: 10.3390/molecules27175514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
Skeletal muscle homeostasis is essential for the maintenance of a healthy and active lifestyle. Imbalance in muscle homeostasis has significant consequences such as atrophy, loss of muscle mass, and progressive loss of functions. Aging-related muscle wasting, sarcopenia, and atrophy as a consequence of disease, such as cachexia, reduce the quality of life, increase morbidity and result in an overall poor prognosis. Investigating the muscle proteome related to muscle atrophy diseases has a great potential for diagnostic medicine to identify (i) potential protein biomarkers, and (ii) biological processes and functions common or unique to muscle wasting, cachexia, sarcopenia, and aging alone. We conducted a meta-analysis using gene ontology (GO) analysis of 24 human proteomic studies using tissue samples (skeletal muscle and adipose biopsies) and/or biofluids (serum, plasma, urine). Whilst there were few similarities in protein directionality across studies, biological processes common to conditions were identified. Here we demonstrate that the GO analysis of published human proteomics data can identify processes not revealed by single studies. We recommend the integration of proteomics data from tissue samples and biofluids to yield a comprehensive overview of the human skeletal muscle proteome. This will facilitate the identification of biomarkers and potential pathways of muscle-wasting conditions for use in clinics.
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Affiliation(s)
- Angelique Stalmach
- Centre for Health Science, Division of Biomedical Sciences, Institute of Health Research and Innovation, School of Health, Social Care and Life Sciences, University of the Highlands and Islands, Inverness IV2 3JH, UK
| | - Ines Boehm
- Edinburgh Cancer Research UK Tissue Group, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XR, UK
- Clinical Surgery, University of Edinburgh, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Marco Fernandes
- Department of Psychiatry, University of Oxford, Oxford OX3 7JX, UK
| | - Alison Rutter
- Centre for Health Science, Division of Biomedical Sciences, Institute of Health Research and Innovation, School of Health, Social Care and Life Sciences, University of the Highlands and Islands, Inverness IV2 3JH, UK
| | - Richard J. E. Skipworth
- Clinical Surgery, University of Edinburgh, Royal Infirmary of Edinburgh, Edinburgh EH16 4SA, UK
| | - Holger Husi
- Centre for Health Science, Division of Biomedical Sciences, Institute of Health Research and Innovation, School of Health, Social Care and Life Sciences, University of the Highlands and Islands, Inverness IV2 3JH, UK
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow G12 8TA, UK
- Correspondence:
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8
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Dayon L, Cominetti O, Affolter M. Proteomics of Human Biological Fluids for Biomarker Discoveries: Technical Advances and Recent Applications. Expert Rev Proteomics 2022; 19:131-151. [PMID: 35466824 DOI: 10.1080/14789450.2022.2070477] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Biological fluids are routine samples for diagnostic testing and monitoring. Blood samples are typically measured because of their moderate collection invasiveness and high information content on health and disease. Several body fluids, such as cerebrospinal fluid (CSF), are also studied and suited to specific pathologies. Over the last two decades proteomics has quested to identify protein biomarkers but with limited success. Recent technologies and refined pipelines have accelerated the profiling of human biological fluids. AREAS COVERED We review proteomic technologies for the identification of biomarkers. Those are based on antibodies/aptamers arrays or mass spectrometry (MS), but new ones are emerging. Advances in scalability and throughput have allowed to better design studies and cope with the limited sample size that had until now prevailed due to technological constraints. With these enablers, plasma/serum, CSF, saliva, tears, urine, and milk proteomes have been further profiled; we provide a non-exhaustive picture of some recent highlights (mainly covering literature from last five years in the Scopus database) using MS-based proteomics. EXPERT OPINION While proteomics has been in the shadow of genomics for years, proteomic tools and methodologies have reached a certain maturity. They are better suited to discover innovative and robust biofluid biomarkers.
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Affiliation(s)
- Loïc Dayon
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland.,Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ornella Cominetti
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland
| | - Michael Affolter
- Proteomics, Nestlé Institute of Food Safety & Analytical Sciences, Nestlé Research, CH-1015 Lausanne, Switzerland
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9
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Brandão-Dias PFP, Deatsch AE, Tank JL, Shogren AJ, Rosi EJ, Ruggiero ST, Tanner CE, Egan SP. Novel Field-Based Protein Detection Method Using Light Transmission Spectroscopy and Antibody Functionalized Gold Nanoparticles. NANO LETTERS 2022; 22:2611-2617. [PMID: 35362986 DOI: 10.1021/acs.nanolett.1c04142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Protein detection is a universal tool critical to many applications in medicine, agriculture, and biotechnology. We developed a novel protein detection method combining light transmission spectroscopy and particle-size analysis of gold nanospheres monovalently functionalized with polyclonal antibodies and applied it to an emerging challenge for such technologies─the monitoring of environmental proteins (eProteins) present in natural aquatic systems. These are an underreported source of pollution and include the pseudopersistent Cry toxins that enter aquatic ecosystems from surrounding genetically engineered crops. The assay is capable of detecting proteins in complex matrices, such as water samples collected in the field, making it a competitive assay for eProtein detection. It is sensitive, reaching 1.25 ng mL-1, and we demonstrate its application to the detection of Cry1Ab from subsurface tile-drain and streamwater samples from agricultural waterways. The assay can also be quickly adapted for other protein detection applications in the future.
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Affiliation(s)
| | - Alison E Deatsch
- Department of Medical Physics, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Jennifer L Tank
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Arial J Shogren
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama 35401, United States
| | - Emma J Rosi
- Cary Institute of Ecosystem Studies, Millbrook, New York 12545, United States
| | - Steven T Ruggiero
- Department of Physics, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Carol E Tanner
- Department of Physics, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Scott P Egan
- Department of BioSciences, Rice University, Houston, Texas 77005, United States
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10
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Deutsch EW, Omenn GS, Sun Z, Maes M, Pernemalm M, Palaniappan KK, Letunica N, Vandenbrouck Y, Brun V, Tao SC, Yu X, Geyer PE, Ignjatovic V, Moritz RL, Schwenk JM. Advances and Utility of the Human Plasma Proteome. J Proteome Res 2021; 20:5241-5263. [PMID: 34672606 PMCID: PMC9469506 DOI: 10.1021/acs.jproteome.1c00657] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The study of proteins circulating in blood offers tremendous opportunities to diagnose, stratify, or possibly prevent diseases. With recent technological advances and the urgent need to understand the effects of COVID-19, the proteomic analysis of blood-derived serum and plasma has become even more important for studying human biology and pathophysiology. Here we provide views and perspectives about technological developments and possible clinical applications that use mass-spectrometry(MS)- or affinity-based methods. We discuss examples where plasma proteomics contributed valuable insights into SARS-CoV-2 infections, aging, and hemostasis and the opportunities offered by combining proteomics with genetic data. As a contribution to the Human Proteome Organization (HUPO) Human Plasma Proteome Project (HPPP), we present the Human Plasma PeptideAtlas build 2021-07 that comprises 4395 canonical and 1482 additional nonredundant human proteins detected in 240 MS-based experiments. In addition, we report the new Human Extracellular Vesicle PeptideAtlas 2021-06, which comprises five studies and 2757 canonical proteins detected in extracellular vesicles circulating in blood, of which 74% (2047) are in common with the plasma PeptideAtlas. Our overview summarizes the recent advances, impactful applications, and ongoing challenges for translating plasma proteomics into utility for precision medicine.
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Affiliation(s)
- Eric W Deutsch
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Gilbert S Omenn
- Institute for Systems Biology, Seattle, Washington 98109, United States.,Departments of Computational Medicine & Bioinformatics, Internal Medicine, and Human Genetics and School of Public Health, University of Michigan, Ann Arbor, Michigan 48109-2218, United States
| | - Zhi Sun
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Michal Maes
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Maria Pernemalm
- Department of Oncology and Pathology/Science for Life Laboratory, Karolinska Institutet, 171 65 Stockholm, Sweden
| | | | - Natasha Letunica
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville 3052, Victoria, Australia
| | - Yves Vandenbrouck
- Université Grenoble Alpes, CEA, Inserm U1292, Grenoble 38000, France
| | - Virginie Brun
- Université Grenoble Alpes, CEA, Inserm U1292, Grenoble 38000, France
| | - Sheng-Ce Tao
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, B207 SCSB Building, 800 Dongchuan Road, Shanghai 200240, China
| | - Xiaobo Yu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Philipp E Geyer
- OmicEra Diagnostics GmbH, Behringstr. 6, 82152 Planegg, Germany
| | - Vera Ignjatovic
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville 3052, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, 50 Flemington Road, Parkville 3052, Victoria, Australia
| | - Robert L Moritz
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Jochen M Schwenk
- Affinity Proteomics, Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Tomtebodavägen 23, SE-171 65 Solna, Sweden
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11
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Richens JL, Bramble JP, Spencer HL, Cantlay F, Butler M, O'Shea P. Towards defining the Mechanisms of Alzheimer's disease based on a contextual analysis of molecular pathways. AIMS GENETICS 2021. [DOI: 10.3934/genet.2016.1.25] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
AbstractAlzheimer's disease (AD) is posing an increasingly profound problem to society. Our genuine understanding of the pathogenesis of AD is inadequate and as a consequence, diagnostic and therapeutic strategies are currently insufficient. The understandable focus of many studies is the identification of molecules with high diagnostic utility however the opportunity to obtain a further understanding of the mechanistic origins of the disease from such putative biomarkers is often overlooked. This study examines the involvement of biomarkers in AD to shed light on potential mechanisms and pathways through which they are implicated in the pathology of this devastating neurodegenerative disorder. The computational tools required to analyse ever-growing datasets in the context of AD are also discussed.
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Affiliation(s)
- Joanna L. Richens
- Cell Biophysics Group, School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Jonathan P. Bramble
- Cell Biophysics Group, School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Hannah L. Spencer
- Cell Biophysics Group, School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Fiona Cantlay
- Cell Biophysics Group, School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Molly Butler
- Cell Biophysics Group, School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Paul O'Shea
- Cell Biophysics Group, School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
- Address as of 1st July 2016: Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
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12
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Plebani M. “Omics” translation: a challenge for laboratory medicine. PRINCIPLES OF TRANSLATIONAL SCIENCE IN MEDICINE 2021:21-32. [DOI: 10.1016/b978-0-12-820493-1.00021-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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13
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Bendes A, Dale M, Mattsson C, Dodig-Crnković T, Iglesias MJ, Schwenk JM, Fredolini C. Bead-Based Assays for Validating Proteomic Profiles in Body Fluids. Methods Mol Biol 2021; 2344:65-78. [PMID: 34115352 DOI: 10.1007/978-1-0716-1562-1_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Protein biomarkers in biological fluids represent an important resource for improving the clinical management of diseases. Current proteomics technologies are capable of performing high-throughput and multiplex profiling in different types of fluids, often leading to the shortlisting of tens of candidate biomarkers per study. However, before reaching any clinical setting, these discoveries require thorough validation and an assay that would be suitable for routine analyses. In the path from biomarker discovery to validation, the performance of the assay implemented for the intended protein quantification is extremely critical toward achieving reliable and reproducible results. Development of robust sandwich immunoassays for individual candidates is challenging and labor and resource intensive, and multiplies when evaluating a panel of interesting candidates at the same time. Here we describe a versatile pipeline that facilitates the systematic and parallel development of multiple sandwich immunoassays using a bead-based technology.
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Affiliation(s)
- Annika Bendes
- Science for Life Laboratory, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Matilda Dale
- Science for Life Laboratory, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Cecilia Mattsson
- Science for Life Laboratory, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Tea Dodig-Crnković
- Science for Life Laboratory, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Maria Jesus Iglesias
- Science for Life Laboratory, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden.,Department of Clinical Medicine, Faculty of Health Science, The Arctic University of Tromsö, Tromsö, Norway
| | - Jochen M Schwenk
- Science for Life Laboratory, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Claudia Fredolini
- Science for Life Laboratory, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden.
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14
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Rapid, deep and precise profiling of the plasma proteome with multi-nanoparticle protein corona. Nat Commun 2020; 11:3662. [PMID: 32699280 PMCID: PMC7376165 DOI: 10.1038/s41467-020-17033-7] [Citation(s) in RCA: 164] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 06/02/2020] [Indexed: 02/08/2023] Open
Abstract
Large-scale, unbiased proteomics studies are constrained by the complexity of the plasma proteome. Here we report a highly parallel protein quantitation platform integrating nanoparticle (NP) protein coronas with liquid chromatography-mass spectrometry for efficient proteomic profiling. A protein corona is a protein layer adsorbed onto NPs upon contact with biofluids. Varying the physicochemical properties of engineered NPs translates to distinct protein corona patterns enabling differential and reproducible interrogation of biological samples, including deep sampling of the plasma proteome. Spike experiments confirm a linear signal response. The median coefficient of variation was 22%. We screened 43 NPs and selected a panel of 5, which detect more than 2,000 proteins from 141 plasma samples using a 96-well automated workflow in a pilot non-small cell lung cancer classification study. Our streamlined workflow combines depth of coverage and throughput with precise quantification based on unique interactions between proteins and NPs engineered for deep and scalable quantitative proteomic studies. Large-scale, unbiased proteomics studies of biological samples like plasma are constrained by the complexity of the proteome. Herein, the authors develop a highly parallel protein quantitation platform leveraging multi nanoparticle protein coronas for deep proteome sampling and biomarker discovery.
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15
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Sun R, Hunter C, Chen C, Ge W, Morrice N, Liang S, Zhu T, Yuan C, Ruan G, Zhang Q, Cai X, Yu X, Chen L, Dai S, Luan Z, Aebersold R, Zhu Y, Guo T. Accelerated Protein Biomarker Discovery from FFPE Tissue Samples Using Single-Shot, Short Gradient Microflow SWATH MS. J Proteome Res 2020; 19:2732-2741. [PMID: 32053377 DOI: 10.1021/acs.jproteome.9b00671] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We reported and evaluated a microflow, single-shot, short gradient SWATH MS method intended to accelerate the discovery and verification of protein biomarkers in preclassified clinical specimens. The method uses a 15 min gradient microflow-LC peptide separation, an optimized SWATH MS window configuration, and OpenSWATH software for data analysis. We applied the method to a cohort containing 204 FFPE tissue samples from 58 prostate cancer patients and 10 benign prostatic hyperplasia patients. Altogether we identified 27,975 proteotypic peptides and 4037 SwissProt proteins from these 204 samples. Compared to a reference SWATH method with a 2 h gradient, we found 3800 proteins were quantified by the two methods on two different instruments with relatively high consistency (r = 0.77). The accelerated method consumed only 17% instrument time, while quantifying 80% of proteins compared to the 2 h gradient SWATH. Although the missing value rate increased by 20%, batch effects reduced by 21%. 75 deregulated proteins measured by the accelerated method were selected for further validation. A shortlist of 134 selected peptide precursors from the 75 proteins were analyzed using MRM-HR, and the results exhibited high quantitative consistency with the 15 min SWATH method (r = 0.89) in the same sample set. We further verified the applicability of these 75 proteins in separating benign and malignant tissues (AUC = 0.99) in an independent prostate cancer cohort (n = 154). Altogether, the results showed that the 15 min gradient microflow SWATH accelerated large-scale data acquisition by 6 times, reduced batch effect by 21%, introduced 20% more missing values, and exhibited comparable ability to separate disease groups.
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Affiliation(s)
- Rui Sun
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | | | | | - Weigang Ge
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | | | - Shuang Liang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | - Tiansheng Zhu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | - Chunhui Yuan
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | - Guan Ruan
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | - Qiushi Zhang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | - Xue Cai
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | - Xiaoyan Yu
- Department of Pathology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Lirong Chen
- Department of Pathology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Shaozheng Dai
- School of Computer Science and Engineering, Beihang University, Beijing 100083, China
| | - Zhongzhi Luan
- School of Computer Science and Engineering, Beihang University, Beijing 100083, China
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8049 Zurich, Switzerland.,Faculty of Science, University of Zurich, 8006 Zurich, Switzerland
| | - Yi Zhu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | - Tiannan Guo
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China.,Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
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16
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Moritz CP, Paul S, Stoevesandt O, Tholance Y, Camdessanché JP, Antoine JC. Autoantigenomics: Holistic characterization of autoantigen repertoires for a better understanding of autoimmune diseases. Autoimmun Rev 2020; 19:102450. [DOI: 10.1016/j.autrev.2019.102450] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 10/16/2019] [Indexed: 12/13/2022]
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17
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Geyer PE, Voytik E, Treit PV, Doll S, Kleinhempel A, Niu L, Müller JB, Buchholtz M, Bader JM, Teupser D, Holdt LM, Mann M. Plasma Proteome Profiling to detect and avoid sample-related biases in biomarker studies. EMBO Mol Med 2019; 11:e10427. [PMID: 31566909 PMCID: PMC6835559 DOI: 10.15252/emmm.201910427] [Citation(s) in RCA: 150] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 08/26/2019] [Accepted: 09/03/2019] [Indexed: 01/04/2023] Open
Abstract
Plasma and serum are rich sources of information regarding an individual's health state, and protein tests inform medical decision making. Despite major investments, few new biomarkers have reached the clinic. Mass spectrometry (MS)-based proteomics now allows highly specific and quantitative readout of the plasma proteome. Here, we employ Plasma Proteome Profiling to define quality marker panels to assess plasma samples and the likelihood that suggested biomarkers are instead artifacts related to sample handling and processing. We acquire deep reference proteomes of erythrocytes, platelets, plasma, and whole blood of 20 individuals (> 6,000 proteins), and compare serum and plasma proteomes. Based on spike-in experiments, we determine sample quality-associated proteins, many of which have been reported as biomarker candidates as revealed by a comprehensive literature survey. We provide sample preparation guidelines and an online resource ( www.plasmaproteomeprofiling.org) to assess overall sample-related bias in clinical studies and to prevent costly miss-assignment of biomarker candidates.
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Affiliation(s)
- Philipp E Geyer
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
- NNF Center for Protein ResearchFaculty of Health SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Eugenia Voytik
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Peter V Treit
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Sophia Doll
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
- NNF Center for Protein ResearchFaculty of Health SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Alisa Kleinhempel
- Institute of Laboratory MedicineUniversity HospitalLMU MunichMunichGermany
| | - Lili Niu
- NNF Center for Protein ResearchFaculty of Health SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Johannes B Müller
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | | | - Jakob M Bader
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Daniel Teupser
- Institute of Laboratory MedicineUniversity HospitalLMU MunichMunichGermany
| | - Lesca M Holdt
- Institute of Laboratory MedicineUniversity HospitalLMU MunichMunichGermany
| | - Matthias Mann
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
- NNF Center for Protein ResearchFaculty of Health SciencesUniversity of CopenhagenCopenhagenDenmark
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18
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Bradshaw RA, Hondermarck H, Rodriguez H. Cancer Proteomics and the Elusive Diagnostic Biomarkers. Proteomics 2019; 19:e1800445. [PMID: 31172665 DOI: 10.1002/pmic.201800445] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 06/02/2019] [Indexed: 12/11/2022]
Abstract
Despite progress in genomic and proteomic technology and applications, the validation of cancer biomarkers of use as clinical early detection diagnostics has remained elusive. As described in this brief viewpoint, there are now recognized to be many types of clinical biomarkers and proteomic analyses, particularly when combined with other 'omic analyses, have been effective in many such biomarker identifications. However, in the area of early diagnosis of cancers, the problems associated with the conversion from identification to diagnostic have largely not been overcome. Notably, the Clinical Proteomic Tumor Analysis Consortium (CPTAC) of the National Cancer Institute (NCI), has been particularly successful in refining the analytical steps needed to tackle this challenging issue and has provided positive insight into how to solve many of the underlying problems. The potential for developing clinical diagnostics for early detection of highly lethal cancers and possible new therapeutic strategies through proteomic analyses, as seen through these CPTAC successes, is more promising than ever.
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Affiliation(s)
- Ralph A Bradshaw
- Department of Physiology and Biophysics, University of California, Irvine, CA, 92697, USA.,Department of Pharmacology, University of California, San Diego, CA, 92093, USA
| | - Hubert Hondermarck
- School of Biomedical Sciences and Pharmacy, Hunter Medical Research Institute, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
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19
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Grozdanić M, Vidmar R, Vizovišek M, Fonović M. Degradomics in Biomarker Discovery. Proteomics Clin Appl 2019; 13:e1800138. [PMID: 31291060 DOI: 10.1002/prca.201800138] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 05/01/2019] [Indexed: 12/13/2022]
Abstract
The upregulation of protease expression and proteolytic activity is implicated in numerous pathological conditions such as neurodegeneration, cancer, cardiovascular and autoimmune diseases, and bone degeneration. During disease progression, various proteases form characteristic patterns of cleaved proteins and peptides, which can affect disease severity and course of progression. It has been shown that qualitative and quantitative monitoring of cleaved protease substrates can provide relevant prognostic, diagnostic, and therapeutic information. As proteolytic fragments and peptides generated in the affected tissue are commonly translocated to blood, urine, and other proximal fluids, their possible application as biomarkers is the subject of ongoing research. The field of degradomics has been established to enable the global identification of proteolytic events on the organism level, utilizing proteomic approaches and sample preparation techniques that facilitate the detection of proteolytic processing of protease substrates in complex biological samples. In this review, some of the latest developments in degradomic methodologies used for the identification and validation of biologically relevant proteolytic events and their application in the search for clinically relevant biomarker candidates are presented. The current state of degradomics in clinics is discussed and the future perspectives of the field are outlined.
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Affiliation(s)
- Marija Grozdanić
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, SI-1000, Ljubljana, Slovenia.,International Postgraduate School Jožef Stefan, SI-1000, Ljubljana, Slovenia
| | - Robert Vidmar
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, SI-1000, Ljubljana, Slovenia
| | - Matej Vizovišek
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, SI-1000, Ljubljana, Slovenia
| | - Marko Fonović
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, SI-1000, Ljubljana, Slovenia
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20
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Angel TE, Naylor BC, Price JC, Evans C, Szapacs M. Improved Sensitivity for Protein Turnover Quantification by Monitoring Immonium Ion Isotopologue Abundance. Anal Chem 2019; 91:9732-9740. [PMID: 31259532 DOI: 10.1021/acs.analchem.9b01329] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe an analytical strategy allowing for the direct quantification of stable isotope label incorporation in newly synthesized proteins following administration of the stable isotope tracer deuterium oxide. We present a demonstration of coupling high-resolution mass spectrometry, metabolic stable isotope labeling, and MS/MS-based isotopologue quantification for the measurement of protein turnover. Stable isotope labeling with deuterium oxide, followed by immonium ion isotopologue quantification, is a more sensitive strategy for determining protein fractional synthesis rates compared to peptide centric mass isotopomer distribution analysis approaches when labeling time and/or stable isotope tracer exposure is limited and, as such, offers a great advantage for human studies.
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Affiliation(s)
- Thomas E Angel
- In-vitro/In-vivo Translation Platform Group , GlaxoSmithKline , 1250 S Collegeville Road , Collegeville , Pennsylvania 19426 , United States
| | - Bradley C Naylor
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84604 , United States
| | - John C Price
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84604 , United States
| | - Christopher Evans
- In-vitro/In-vivo Translation Platform Group , GlaxoSmithKline , 1250 S Collegeville Road , Collegeville , Pennsylvania 19426 , United States
| | - Matthew Szapacs
- In-vitro/In-vivo Translation Platform Group , GlaxoSmithKline , 1250 S Collegeville Road , Collegeville , Pennsylvania 19426 , United States
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21
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Coscia F, Lengyel E, Duraiswamy J, Ashcroft B, Bassani-Sternberg M, Wierer M, Johnson A, Wroblewski K, Montag A, Yamada SD, López-Méndez B, Nilsson J, Mund A, Mann M, Curtis M. Multi-level Proteomics Identifies CT45 as a Chemosensitivity Mediator and Immunotherapy Target in Ovarian Cancer. Cell 2019; 175:159-170.e16. [PMID: 30241606 DOI: 10.1016/j.cell.2018.08.065] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 05/23/2018] [Accepted: 08/29/2018] [Indexed: 12/14/2022]
Abstract
Most high-grade serous ovarian cancer (HGSOC) patients develop resistance to platinum-based chemotherapy and recur, but 15% remain disease free over a decade. To discover drivers of long-term survival, we quantitatively analyzed the proteomes of platinum-resistant and -sensitive HGSOC patients from minute amounts of formalin-fixed, paraffin-embedded tumors. This revealed cancer/testis antigen 45 (CT45) as an independent prognostic factor associated with a doubling of disease-free survival in advanced-stage HGSOC. Phospho- and interaction proteomics tied CT45 to DNA damage pathways through direct interaction with the PP4 phosphatase complex. In vitro, CT45 regulated PP4 activity, and its high expression led to increased DNA damage and platinum sensitivity. CT45-derived HLA class I peptides, identified by immunopeptidomics, activate patient-derived cytotoxic T cells and promote tumor cell killing. This study highlights the power of clinical cancer proteomics to identify targets for chemo- and immunotherapy and illuminate their biological roles.
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Affiliation(s)
- Fabian Coscia
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; Clinical Proteomics Group, Proteomics Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Ernst Lengyel
- Department of Obstetrics and Gynecology, Section of Gynecologic Oncology, University of Chicago, Chicago, IL 60637, USA.
| | | | - Bradley Ashcroft
- Department of Obstetrics and Gynecology, Section of Gynecologic Oncology, University of Chicago, Chicago, IL 60637, USA
| | - Michal Bassani-Sternberg
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Alyssa Johnson
- Department of Obstetrics and Gynecology, Section of Gynecologic Oncology, University of Chicago, Chicago, IL 60637, USA
| | - Kristen Wroblewski
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Anthony Montag
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - S Diane Yamada
- Department of Obstetrics and Gynecology, Section of Gynecologic Oncology, University of Chicago, Chicago, IL 60637, USA
| | - Blanca López-Méndez
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Jakob Nilsson
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Andreas Mund
- Clinical Proteomics Group, Proteomics Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; Clinical Proteomics Group, Proteomics Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark.
| | - Marion Curtis
- Department of Obstetrics and Gynecology, Section of Gynecologic Oncology, University of Chicago, Chicago, IL 60637, USA
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22
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Bruderer R, Muntel J, Müller S, Bernhardt OM, Gandhi T, Cominetti O, Macron C, Carayol J, Rinner O, Astrup A, Saris WHM, Hager J, Valsesia A, Dayon L, Reiter L. Analysis of 1508 Plasma Samples by Capillary-Flow Data-Independent Acquisition Profiles Proteomics of Weight Loss and Maintenance. Mol Cell Proteomics 2019; 18:1242-1254. [PMID: 30948622 PMCID: PMC6553938 DOI: 10.1074/mcp.ra118.001288] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 03/26/2019] [Indexed: 12/14/2022] Open
Abstract
Comprehensive, high throughput analysis of the plasma proteome has the potential to enable holistic analysis of the health state of an individual. Based on our own experience and the evaluation of recent large-scale plasma mass spectrometry (MS) based proteomic studies, we identified two outstanding challenges: slow and delicate nano-flow liquid chromatography (LC) and irreproducibility of identification of data-dependent acquisition (DDA). We determined an optimal solution reducing these limitations with robust capillary-flow data-independent acquisition (DIA) MS. This platform can measure 31 plasma proteomes per day. Using this setup, we acquired a large-scale plasma study of the diet, obesity and genes dietary (DiOGenes) comprising 1508 samples. Proving the robustness, the complete acquisition was achieved on a single analytical column. Totally, 565 proteins (459 identified with two or more peptide sequences) were profiled with 74% data set completeness. On average 408 proteins (5246 peptides) were identified per acquisition (319 proteins in 90% of all acquisitions). The workflow reproducibility was assessed using 34 quality control pools acquired at regular intervals, resulting in 92% data set completeness with CVs for protein measurements of 10.9%.The profiles of 20 apolipoproteins could be profiled revealing distinct changes. The weight loss and weight maintenance resulted in sustained effects on low-grade inflammation, as well as steroid hormone and lipid metabolism, indicating beneficial effects. Comparison to other large-scale plasma weight loss studies demonstrated high robustness and quality of biomarker candidates identified. Tracking of nonenzymatic glycation indicated a delayed, slight reduction of glycation in the weight maintenance phase. Using stable-isotope-references, we could directly and absolutely quantify 60 proteins in the DIA.In conclusion, we present herein the first large-scale plasma DIA study and one of the largest clinical research proteomic studies to date. Application of this fast and robust workflow has great potential to advance biomarker discovery in plasma.
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Affiliation(s)
| | - Jan Muntel
- From the ‡Biognosys, 8952 Zurich-Schlieren, Switzerland
| | | | | | - Tejas Gandhi
- From the ‡Biognosys, 8952 Zurich-Schlieren, Switzerland
| | | | - Charlotte Macron
- §Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Jérôme Carayol
- §Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Oliver Rinner
- From the ‡Biognosys, 8952 Zurich-Schlieren, Switzerland
| | - Arne Astrup
- ¶Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Wim H M Saris
- ‖NUTRIM, School for Nutrition, Toxicology and Metabolism, Department of Human Biology, Maastricht University Medical Centre, 6200 MD Maastricht, The Netherlands
| | - Jörg Hager
- §Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Armand Valsesia
- §Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Loïc Dayon
- §Nestlé Institute of Health Sciences, 1015 Lausanne, Switzerland
| | - Lukas Reiter
- From the ‡Biognosys, 8952 Zurich-Schlieren, Switzerland;
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23
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van der Burgt YEM. Protein biomarker discovery is still relevant and has entered a new phase. EBioMedicine 2019; 43:15. [PMID: 31005515 PMCID: PMC6562059 DOI: 10.1016/j.ebiom.2019.04.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 04/12/2019] [Indexed: 12/18/2022] Open
Affiliation(s)
- Yuri E M van der Burgt
- Center for Proteomics and Metabolomics & Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, The Netherlands.
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24
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Doll S, Gnad F, Mann M. The Case for Proteomics and Phospho-Proteomics in Personalized Cancer Medicine. Proteomics Clin Appl 2019; 13:e1800113. [PMID: 30790462 PMCID: PMC6519247 DOI: 10.1002/prca.201800113] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 02/01/2019] [Indexed: 02/06/2023]
Abstract
The concept of personalized medicine is predominantly been pursued through genomic and transcriptomic technologies, leading to the identification of multiple mutations in a large variety of cancers. However, it has proven challenging to distinguish driver and passenger mutations and to deal with tumor heterogeneity and resistant clonal populations. More generally, these heterogeneous mutation patterns do not in themselves predict the tumor phenotype. Analysis of the expressed proteins in a tumor and their modification states reveals if and how these mutations are translated to the functional level. It is already known that proteomic changes including posttranslational modifications are crucial drivers of oncogenesis, but proteomics technology has only recently become comparable in depth and accuracy to RNAseq. These advances also allow the rapid and highly sensitive analysis of formalin-fixed and paraffin-embedded biobank tissues, on both the proteome and phosphoproteome levels. In this perspective, pioneering mass spectrometry-based proteomic studies are highlighted that pave the way toward clinical implementation. It is argued that proteomics and phosphoproteomics could provide the missing link to make omics analysis actionable in the clinic.
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Affiliation(s)
- Sophia Doll
- Department of Proteomics and Signal TransductionMax Planck Institute of Biochemistry82152MartinsriedGermany
- NNF Center for Protein ResearchFaculty of Health SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Florian Gnad
- Department of Bioinformatics and Computational BiologyCell Signaling Technology Inc01923DanversMAUSA
| | - Matthias Mann
- Department of Proteomics and Signal TransductionMax Planck Institute of Biochemistry82152MartinsriedGermany
- NNF Center for Protein ResearchFaculty of Health SciencesUniversity of CopenhagenCopenhagenDenmark
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25
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van den Broek I. Proteins and Clinical Mass Spectrometry: A Fairy Tale? Clin Chem 2019; 65:220-221. [DOI: 10.1373/clinchem.2018.298869] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 11/19/2018] [Indexed: 01/29/2023]
Affiliation(s)
- Irene van den Broek
- Cedars-Sinai Precision Biomarker Laboratories, Cedars-Sinai Medical Center, Los Angeles, CA
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Shapiro SJ, Dendukuri D, Doyle PS. Design of Hydrogel Particle Morphology for Rapid Bioassays. Anal Chem 2018; 90:13572-13579. [PMID: 30339359 DOI: 10.1021/acs.analchem.8b03728] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Hydrogel microparticles have been extensively used in the field of medical diagnostics for detecting targets ranging from proteins to nucleic acids. However, little is known about how the shape of hydrogel particles impacts the signal from a bioassay. In this article, we analyze the flux into porous hydrogel particles to develop scaling laws for the signal from a point-of-care bioassay. The signal can be increased by increasing the ratio of the surface area of the hydrogel particle to the two-dimensional projected imaging area used for analysis. We show that adding internal surface area to hydrogel particles increases the assay signal in a biotin-streptavidin bioassay. We also demonstrate the application of this technique to a protein-based assay for thyroid-stimulating hormone, reducing the limit of detection of the assay sixfold by changing particle shape. We anticipate that these strategies can be used broadly to optimize hydrogel-based systems for point-of-care diagnostics.
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Affiliation(s)
- Sarah J Shapiro
- Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Dhananjaya Dendukuri
- Achira Laboratories Pvt. Ltd. , 66B, 13th Cross Road, Dollar Layout, JP Nagar Phase III , Bangalore 560078 , India
| | - Patrick S Doyle
- Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
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Vizovišek M, Vidmar R, Drag M, Fonović M, Salvesen GS, Turk B. Protease Specificity: Towards In Vivo Imaging Applications and Biomarker Discovery. Trends Biochem Sci 2018; 43:829-844. [PMID: 30097385 DOI: 10.1016/j.tibs.2018.07.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 06/05/2018] [Accepted: 07/12/2018] [Indexed: 02/06/2023]
Abstract
Proteases are considered of major importance in biomedical research because of their crucial roles in health and disease. Their ability to hydrolyze their protein and peptide substrates at single or multiple sites, depending on their specificity, makes them unique among the enzymes. Understanding protease specificity is therefore crucial to understand their biology as well as to develop tools and drugs. Recent advancements in the fields of proteomics and chemical biology have improved our understanding of protease biology through extensive specificity profiling and identification of physiological protease substrates. There are growing efforts to transfer this knowledge into clinical modalities, but their success is often limited because of overlapping protease features, protease redundancy, and chemical tools lacking specificity. Herein, we discuss the current trends and challenges in protease research and how to exploit the growing information on protease specificities for understanding protease biology, as well as for development of selective substrates, cleavable linkers, and activity-based probes and for biomarker discovery.
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Affiliation(s)
- Matej Vizovišek
- Jozef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova 39, SI-1000 Ljubljana, Slovenia; These authors contributed equally to this work
| | - Robert Vidmar
- Jozef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova 39, SI-1000 Ljubljana, Slovenia; These authors contributed equally to this work
| | - Marcin Drag
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Marko Fonović
- Jozef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Guy S Salvesen
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
| | - Boris Turk
- Jozef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova 39, SI-1000 Ljubljana, Slovenia; Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna pot 113, SI-1000 Ljubljana, Slovenia.
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Abstract
One of the promises of multiomic analysis was to transform the clinical diagnostics to deliver much more exact phenotyping of disease states. However, despite enormous investments, the transformation of clinical routine has not taken place. There are many reasons for this lack of success but one is the failure to deliver quantitative and reproducible data. This failure is not only impeding progress in clinical phenotyping but also in the application of omic science in systems biology. The focus in this Viewpoint will be on lipidomics but the lessons learned are generally applicable.
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Affiliation(s)
- Kai Simons
- Max-Planck-Institute of Molecular Cell Biology and Genetics and Lipotype GmbH,, Dresden, Germany
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29
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Savickas S, Auf dem Keller U. Targeted degradomics in protein terminomics and protease substrate discovery. Biol Chem 2017; 399:47-54. [PMID: 28850541 DOI: 10.1515/hsz-2017-0187] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 08/21/2017] [Indexed: 02/06/2023]
Abstract
Targeted degradomics integrates positional information into mass spectrometry (MS)-based targeted proteomics workflows and thereby enables analysis of proteolytic cleavage events with unprecedented specificity and sensitivity. Rapid progress in the establishment of protease-substrate relations provides extensive degradomics target lists that now can be tested with help of selected and parallel reaction monitoring (S/PRM) in complex biological systems, where proteases act in physiological environments. In this minireview, we describe the general principles of targeted degradomics, outline the generic experimental workflow of the methodology and highlight recent and future applications in protease research.
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Affiliation(s)
- Simonas Savickas
- Institute of Molecular Health Sciences, ETH Zurich, Otto-Stern-Weg 7, CH-8093 Zurich, Switzerland
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Anker Engelunds Vej, Building 301, DK-2800 Kgs. Lyngby, Denmark
| | - Ulrich Auf dem Keller
- Institute of Molecular Health Sciences, ETH Zurich, Otto-Stern-Weg 7, CH-8093 Zurich, Switzerland
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Anker Engelunds Vej, Building 301, DK-2800 Kgs. Lyngby, Denmark
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Geyer PE, Holdt LM, Teupser D, Mann M. Revisiting biomarker discovery by plasma proteomics. Mol Syst Biol 2017; 13:942. [PMID: 28951502 PMCID: PMC5615924 DOI: 10.15252/msb.20156297] [Citation(s) in RCA: 479] [Impact Index Per Article: 68.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 08/04/2017] [Accepted: 08/15/2017] [Indexed: 01/13/2023] Open
Abstract
Clinical analysis of blood is the most widespread diagnostic procedure in medicine, and blood biomarkers are used to categorize patients and to support treatment decisions. However, existing biomarkers are far from comprehensive and often lack specificity and new ones are being developed at a very slow rate. As described in this review, mass spectrometry (MS)-based proteomics has become a powerful technology in biological research and it is now poised to allow the characterization of the plasma proteome in great depth. Previous "triangular strategies" aimed at discovering single biomarker candidates in small cohorts, followed by classical immunoassays in much larger validation cohorts. We propose a "rectangular" plasma proteome profiling strategy, in which the proteome patterns of large cohorts are correlated with their phenotypes in health and disease. Translating such concepts into clinical practice will require restructuring several aspects of diagnostic decision-making, and we discuss some first steps in this direction.
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Affiliation(s)
- Philipp E Geyer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
- Faculty of Health Sciences, NNF Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Lesca M Holdt
- Institute of Laboratory Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Daniel Teupser
- Institute of Laboratory Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
- Faculty of Health Sciences, NNF Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
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31
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Ganesan V, Ascherman DP, Minden JS. Immunoproteomics technologies in the discovery of autoantigens in autoimmune diseases. Biomol Concepts 2017; 7:133-43. [PMID: 27115324 DOI: 10.1515/bmc-2016-0007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 03/21/2016] [Indexed: 12/16/2022] Open
Abstract
Proteomics technologies are often used for the identification of protein targets of the immune system. Here, we discuss the immunoproteomics technologies used for the discovery of autoantigens in autoimmune diseases where immune system dysregulation plays a central role in disease onset and progression. These autoantigens and associated autoantibodies can be used as potential biomarkers for disease diagnostics, prognostics and predicting/monitoring drug responsiveness (theranostics). Here, we compare a variety of methods such as mass spectrometry (MS)-based [serological proteome analysis (SERPA), antibody mediated identification of antigens (AMIDA), circulating immune complexome (CIC) analysis, surface enhanced laser desorption/ionization-time of flight (SELDI-TOF)], nucleic acid based serological analysis of antigens by recombinant cDNA expression cloning (SEREX), phage immunoprecipitation sequencing (PhIP-seq) and array-based immunoscreening (proteomic microarrays), luciferase immunoprecipitation systems (LIPS), nucleic acid programmable protein array (NAPPA) methods. We also review the relevance of immunoproteomic data generated in the last 10 years, with a focus on the aforementioned MS based methods.
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32
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Squeezing more value from the analytes we have: personal baselines for multiple analytes in serial DBS. Bioanalysis 2016; 8:1539-1542. [DOI: 10.4155/bio-2016-0088] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Monaghan PJ, Lord SJ, St John A, Sandberg S, Cobbaert CM, Lennartz L, Verhagen-Kamerbeek WDJ, Ebert C, Bossuyt PMM, Horvath AR. Biomarker development targeting unmet clinical needs. Clin Chim Acta 2016; 460:211-9. [PMID: 27374304 DOI: 10.1016/j.cca.2016.06.037] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 06/28/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND The introduction of new biomarkers can lead to inappropriate utilization of tests if they do not fill in existing gaps in clinical care. We aimed to define a strategy and checklist for identifying unmet needs for biomarkers. METHODS A multidisciplinary working group used a 4-step process: 1/ scoping literature review; 2/ face-to-face meetings to discuss scope, strategy and checklist items; 3/ iterative process of feedback and consensus to develop the checklist; 4/ testing and refinement of checklist items using case scenarios. RESULTS We used clinical pathway mapping to identify clinical management decisions linking biomarker testing to health outcomes and developed a 14-item checklist organized into 4 domains: 1/ identifying and 2/ verifying the unmet need; 3/ validating the intended use; and 4/ assessing the feasibility of the new biomarker to influence clinical practice and health outcome. We present an outcome-focused approach that can be used by multiple stakeholders for any medical test, irrespective of the purpose and role of testing. CONCLUSIONS The checklist intends to achieve more efficient biomarker development and translation into practice. We propose the checklist is field tested by stakeholders, and advocate the role of the clinical laboratory professional to foster trans-sector collaboration in this regard.
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Affiliation(s)
- Phillip J Monaghan
- Department of Clinical Biochemistry, The Christie Pathology Partnership, The Christie NHS Foundation Trust, Manchester, UK.
| | - Sarah J Lord
- School of Medicine, University of Notre Dame, Australia; National Health and Medical Research Council (NHMRC) Clinical Trials Centre, University of Sydney, Australia
| | | | - Sverre Sandberg
- The Norwegian Quality Improvement of Primary Care Laboratories (NOKLUS), Haraldsplass Deaconess Hospital, Bergen, Norway; Department of Public Health and Primary Health Care, University of Bergen, Norway; Laboratory of Clinical Biochemistry, Haukeland University Hospital, Bergen, Norway
| | - Christa M Cobbaert
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, The Netherlands
| | | | | | - Christoph Ebert
- Medical and Scientific Affairs, Roche Diagnostics GmbH, Penzberg, Germany
| | - Patrick M M Bossuyt
- Department of Clinical Epidemiology, Biostatistics & Bioinformatics, Academic Medical Center, University of Amsterdam, The Netherlands
| | - Andrea R Horvath
- SEALS Department of Clinical Chemistry and Endocrinology, Prince of Wales Hospital and School of Medical Sciences, University of New South Wales, Australia; Screening and Test Evaluation Program, School of Public Health, University of Sydney, Australia
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Zaslavsky BY, Uversky VN, Chait A. Analytical applications of partitioning in aqueous two-phase systems: Exploring protein structural changes and protein–partner interactions in vitro and in vivo by solvent interaction analysis method. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:622-44. [DOI: 10.1016/j.bbapap.2016.02.017] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 02/16/2016] [Accepted: 02/21/2016] [Indexed: 12/29/2022]
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Zaslavsky BY, Uversky VN, Chait A. Solvent interaction analysis as a proteomic approach to structure-based biomarker discovery and clinical diagnostics. Expert Rev Proteomics 2015; 13:9-17. [PMID: 26558960 DOI: 10.1586/14789450.2016.1116945] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Proteins have several measurable features in biological fluids that may change under pathological conditions. The current disease biomarker discovery is mostly based on protein concentration in the sample as the measurable feature. Changes in protein structures, such as post-translational modifications and in protein-partner interactions are known to accompany pathological processes. Changes in glycosylation profiles are well-established for many plasma proteins in various types of cancer and other diseases. The solvent interaction analysis method is based on protein partitioning in aqueous two-phase systems and is highly sensitive to changes in protein structure and protein-protein- and protein-partner interactions while independent of the protein concentration in the biological sample. It provides quantitative index: partition coefficient representing changes in protein structure and interactions with partners. The fundamentals of the method are presented with multiple examples of applications of the method to discover and monitor structural protein biomarkers as disease-specific diagnostic indicators.
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Affiliation(s)
- Boris Y Zaslavsky
- a Cleveland Diagnostics , 3615 Superior Avenue, Suite 4407B, Cleveland , OH 44114 , USA
| | - Vladimir N Uversky
- b Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine , University of South Florida , Tampa , FL 33612 , USA
| | - Arnon Chait
- a Cleveland Diagnostics , 3615 Superior Avenue, Suite 4407B, Cleveland , OH 44114 , USA
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36
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Abstract
Cardiovascular disease (CVD) is the most common cause of death and disability worldwide. Therefore, great importance has been placed on the discovery of novel risk factors and metabolic pathways relevant in the prevention and management of CVD. Such research is ongoing and may continue to lead to better risk stratification of individuals and/or the development of new intervention targets and treatment options. This review highlights emerging biomarkers related to lipid metabolism, glycemia, inflammation, and cardiac damage, some of which show promising associations with CVD risk and provide further understanding of the underlying pathophysiology. However, their measurement methodology and assays will require validation and standardization, and it will take time to accumulate evidence of their role in CVD in various population settings in order to fully assess their clinical utility. Several of the novel biomarkers represent intriguing, potentially game-changing targets for therapy.
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Affiliation(s)
- Leah E Cahill
- Department of Medicine, Dalhousie University, 5790 University Ave, Halifax, NS, B3H 1V7, Canada.
- Department of Nutrition, Harvard T. H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA, 02115, USA.
| | - Monica L Bertoia
- Department of Nutrition, Harvard T. H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA, 02115, USA.
| | - Sarah A Aroner
- Department of Nutrition, Harvard T. H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA, 02115, USA.
| | - Kenneth J Mukamal
- Beth Israel Deaconess Medical Center, 1309 Beacon Street, 2nd Floor, Brookline, Boston, MA, USA.
| | - Majken K Jensen
- Department of Nutrition, Harvard T. H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA, 02115, USA.
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37
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A critical analysis of cancer biobank practices in relation to biospecimen quality. Biophys Rev 2015; 7:369-378. [PMID: 28510101 DOI: 10.1007/s12551-015-0178-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 09/17/2015] [Indexed: 12/26/2022] Open
Abstract
There are concerns that a substantial proportion of published research data is not reproducible, which may partially explain the frequent failure to translate pre-clinical results to clinical care. High-quality cancer biospecimens are needed for robust, reproducible research findings, with most researchers obtaining these specimens from cancer biobanks or tumour banks. This review provides an overview of the types of quality control (QC) activities conducted within cancer biobanks that pertain to biospecimen quality and of biospecimen quality reporting tools, including SPREC and BRISQ. We examine how QC assay results and other biospecimen data are communicated from biobanks to researchers, and whether these activities lead to improved biospecimen quality reporting within the literature and/or to improved research outcomes. We also discuss operational factors that limit QC activities within biobanks and evidence gaps requiring further research. In summary, whereas the provision of quality biospecimens is a common aim of cancer biobanks, QC activities remain underreported and are rarely discussed in the literature, compared with other aspects of biobank operations. Further research is required to determine how biobanks can most efficiently optimise biospecimen quality, and how communication between biobanks and researchers can be improved.
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Shah AK, Cao KAL, Choi E, Chen D, Gautier B, Nancarrow D, Whiteman DC, Saunders NA, Barbour AP, Joshi V, Hill MM. Serum Glycoprotein Biomarker Discovery and Qualification Pipeline Reveals Novel Diagnostic Biomarker Candidates for Esophageal Adenocarcinoma. Mol Cell Proteomics 2015; 14:3023-39. [PMID: 26404905 DOI: 10.1074/mcp.m115.050922] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Indexed: 12/31/2022] Open
Abstract
We report an integrated pipeline for efficient serum glycoprotein biomarker candidate discovery and qualification that may be used to facilitate cancer diagnosis and management. The discovery phase used semi-automated lectin magnetic bead array (LeMBA)-coupled tandem mass spectrometry with a dedicated data-housing and analysis pipeline; GlycoSelector (http://glycoselector.di.uq.edu.au). The qualification phase used lectin magnetic bead array-multiple reaction monitoring-mass spectrometry incorporating an interactive web-interface, Shiny mixOmics (http://mixomics-projects.di.uq.edu.au/Shiny), for univariate and multivariate statistical analysis. Relative quantitation was performed by referencing to a spiked-in glycoprotein, chicken ovalbumin. We applied this workflow to identify diagnostic biomarkers for esophageal adenocarcinoma (EAC), a life threatening malignancy with poor prognosis in the advanced setting. EAC develops from metaplastic condition Barrett's esophagus (BE). Currently diagnosis and monitoring of at-risk patients is through endoscopy and biopsy, which is expensive and requires hospital admission. Hence there is a clinical need for a noninvasive diagnostic biomarker of EAC. In total 89 patient samples from healthy controls, and patients with BE or EAC were screened in discovery and qualification stages. Of the 246 glycoforms measured in the qualification stage, 40 glycoforms (as measured by lectin affinity) qualified as candidate serum markers. The top candidate for distinguishing healthy from BE patients' group was Narcissus pseudonarcissus lectin (NPL)-reactive Apolipoprotein B-100 (p value = 0.0231; AUROC = 0.71); BE versus EAC, Aleuria aurantia lectin (AAL)-reactive complement component C9 (p value = 0.0001; AUROC = 0.85); healthy versus EAC, Erythroagglutinin Phaseolus vulgaris (EPHA)-reactive gelsolin (p value = 0.0014; AUROC = 0.80). A panel of 8 glycoforms showed an improved AUROC of 0.94 to discriminate EAC from BE. Two biomarker candidates were independently verified by lectin magnetic bead array-immunoblotting, confirming the validity of the relative quantitation approach. Thus, we have identified candidate biomarkers, which, following large-scale clinical evaluation, can be developed into diagnostic blood tests. A key feature of the pipeline is the potential for rapid translation of the candidate biomarkers to lectin-immunoassays.
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Affiliation(s)
- Alok K Shah
- From the ‡The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Kim-Anh Lê Cao
- From the ‡The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Eunju Choi
- From the ‡The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia; §School of Veterinary Science, The University of Queensland, Gatton, Queensland, Australia
| | - David Chen
- ¶School of Information and Communication Technology, Griffith University, Brisbane, Queensland, Australia
| | - Benoît Gautier
- From the ‡The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Derek Nancarrow
- ‖QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - David C Whiteman
- ‖QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Nicholas A Saunders
- From the ‡The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Andrew P Barbour
- **School of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Virendra Joshi
- ‡‡Ochsner Health System, Gastroenterology, New Orleans, Louisiana
| | - Michelle M Hill
- From the ‡The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia;
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Chapoval AI, Legutki JB, Stafford P, Trebukhov AV, Johnston SA, Shoikhet YN, Lazarev AF. Immunosignature: Serum Antibody Profiling for Cancer Diagnostics. Asian Pac J Cancer Prev 2015; 16:4833-7. [DOI: 10.7314/apjcp.2015.16.12.4833] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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40
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Development of blood biomarkers for drug-induced liver injury: an evaluation of their potential for risk assessment and diagnostics. Mol Diagn Ther 2014; 17:343-54. [PMID: 23868512 DOI: 10.1007/s40291-013-0049-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Drug-induced liver injury (DILI) remains a rare but serious complication in drug therapy that is a primary cause of drug failure during clinical trials. Conventional biomarkers, particularly the serum transaminases and bilirubin, serve as useful indicators of hepatocellular or cholestatic liver injury, respectively, but only after substantial and sometimes irreversible tissue damage. Ideally, more sensitive biomarkers that respond very early before irreversible injury has occurred would offer improved outcomes. Novel biomarkers are initially being developed in animal models exposed to intrinsically hepatotoxic stimuli. However, the eventual translation to human populations, even those with known risk factors that predispose the liver to drug toxicity, would be the fundamental goal. Ultimately, some might even be applicable for the early identification of individuals predisposed to idiosyncratic hepatotoxicity potential. This article reviews recent progress in the discovery and qualification of novel biomarkers for DILI and delineates the path to eventual utilization for risk assessment. Some major categories of plasma or serum biomarkers surveyed include proteins, cytokines, circulating mRNAs, and microRNAs.
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41
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Huesgen PF, Lange PF, Overall CM. Ensembles of protein termini and specific proteolytic signatures as candidate biomarkers of disease. Proteomics Clin Appl 2014; 8:338-50. [PMID: 24497460 DOI: 10.1002/prca.201300104] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 12/04/2013] [Accepted: 12/09/2013] [Indexed: 12/23/2022]
Abstract
Early accurate diagnosis and personalized treatment are essential in order to treat complex or fatal diseases such as cancer and autoimmune, cardiovascular and neurodegenerative diseases. To realize this vision, new diagnostic and prognostic biomarkers are urgently required. MS-based proteomics is the most promising approach for protein biomarker identification, but suffers in clinical translation of biomarker candidates that show only quantitative differences from normal tissue. Indeed, success in translating proteomic data to biomarkers in the clinic has been disappointing. Here, we propose that protein termini provide a new opportunity for biomarker discovery due to qualitative differences in intact and new protein termini between diseased and normal tissues. Altered proteolysis occurs in most pathologies. Disease- and process-specific protein modifications, including proteolytic processing and subsequent modification of the terminal amino acids, frequently lead to altered protein activity that plays key roles in the disease process. Thus, mapping of ensembles of characteristic protein termini provides a proteolytic signature of high information content that shows both quantitative and most importantly qualitative differences in different diseases and stage of disease. These unique protein biomarkers have the added benefit of being mechanistically informative by revealing the activity state of the bioactive protein. Moreover, proteome-wide isolation of protein termini leads to generalized sample simplification, thereby enabling up to three orders of magnitude lower LODs compared to traditional shotgun proteomic approaches. We introduce the potential of protein termini for biomarker discovery, briefly review methods enabling large-scale studies of protein termini, and discuss how these may be integrated into a termini-oriented biomarker discovery pipeline from discovery to clinical application.
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Affiliation(s)
- Pitter F Huesgen
- Centre for Blood Research, University of British Columbia, Vancouver, Canada; Department of Oral Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada
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42
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Catch and measure-mass spectrometry-based immunoassays in biomarker research. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1844:927-32. [PMID: 24060810 DOI: 10.1016/j.bbapap.2013.09.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 08/28/2013] [Accepted: 09/16/2013] [Indexed: 12/21/2022]
Abstract
Mass spectrometry-based (MS) methods are effective tools for discovering protein biomarker candidates that can differentiate between physiological and pathophysiological states. Promising candidates are validated in studies comprising large patient cohorts. Here, targeted protein analytics are used to increase sample throughput. Methods involving antibodies, such as sandwich immunoassays or Western blots, are commonly applied at this stage. Highly-specific and sensitive mass spectrometry-based immunoassays that have been established in recent years offer a suitable alternative to sandwich immunoassays for quantifying proteins. Mass Spectrometric ImmunoAssays (MSIA) and Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA/iMALDI) are two prominent types of MS-based immunoassays in which the capture is done either at the protein or the peptide level. We present an overview of these emerging types of immunoassays and discuss their suitability for the discovery and validation of protein biomarkers. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge.
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43
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Kuehnbaum NL, Britz-McKibbin P. New Advances in Separation Science for Metabolomics: Resolving Chemical Diversity in a Post-Genomic Era. Chem Rev 2013; 113:2437-68. [DOI: 10.1021/cr300484s] [Citation(s) in RCA: 201] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Naomi L. Kuehnbaum
- Department of Chemistry
and Chemical Biology, McMaster University, Hamilton, Canada
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Diamandis EP, Bast RC, Gold P, Chu TM, Magnani JL. Reflection on the discovery of carcinoembryonic antigen, prostate-specific antigen, and cancer antigens CA125 and CA19-9. Clin Chem 2013; 59:22-31. [PMID: 23204222 PMCID: PMC3983776 DOI: 10.1373/clinchem.2012.187047] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Eleftherios P Diamandis
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada.
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