1
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Mohammed Y, Tran K, Carlsten C, Ryerson C, Wong A, Lee T, Cheng MP, Vinh DC, Lee TC, Winston BW, Sweet D, Boyd JH, Walley KR, Haljan G, McGeer A, Lamontagne F, Fowler R, Maslove D, Singer J, Patrick DM, Marshall JC, Murthy S, Jain F, Borchers CH, Goodlett DR, Levin A, Russell JA. Proteomic Evolution from Acute to Post-COVID-19 Conditions. J Proteome Res 2024; 23:52-70. [PMID: 38048423 PMCID: PMC10775146 DOI: 10.1021/acs.jproteome.3c00324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 10/30/2023] [Accepted: 11/13/2023] [Indexed: 12/06/2023]
Abstract
Many COVID-19 survivors have post-COVID-19 conditions, and females are at a higher risk. We sought to determine (1) how protein levels change from acute to post-COVID-19 conditions, (2) whether females have a plasma protein signature different from that of males, and (3) which biological pathways are associated with COVID-19 when compared to restrictive lung disease. We measured protein levels in 74 patients on the day of admission and at 3 and 6 months after diagnosis. We determined protein concentrations by multiple reaction monitoring (MRM) using a panel of 269 heavy-labeled peptides. The predicted forced vital capacity (FVC) and diffusing capacity of the lungs for carbon monoxide (DLCO) were measured by routine pulmonary function testing. Proteins associated with six key lipid-related pathways increased from admission to 3 and 6 months; conversely, proteins related to innate immune responses and vasoconstriction-related proteins decreased. Multiple biological functions were regulated differentially between females and males. Concentrations of eight proteins were associated with FVC, %, and they together had c-statistics of 0.751 (CI:0.732-0.779); similarly, concentrations of five proteins had c-statistics of 0.707 (CI:0.676-0.737) for DLCO, %. Lipid biology may drive evolution from acute to post-COVID-19 conditions, while activation of innate immunity and vascular regulation pathways decreased over that period. (ProteomeXchange identifiers: PXD041762, PXD029437).
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Affiliation(s)
- Yassene Mohammed
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Leiden 2333 ZA, The Netherlands
- UVic-Genome
BC Proteomics Centre, University of Victoria, Victoria V8Z 5N3, BC Canada
- Gerald
Bronfman Department of Oncology, McGill
University, Montreal, QC H3A 0G4, Canada
| | - Karen Tran
- Division
of General Internal Medicine, Vancouver
General Hospital and University of British Columbia, 2775 Laurel St, Vancouver, BC V5Z 1M9, Canada
| | - Chris Carlsten
- Division
of Respiratory Medicine, Vancouver General Hospital, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Christopher Ryerson
- Division
of Respiratory Medicine, Vancouver General Hospital, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Alyson Wong
- Division
of Respiratory Medicine, Vancouver General Hospital, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Terry Lee
- Centre for
Health Evaluation and Outcome Science (CHEOS), St. Paul’s Hospital, University of British Columbia, 1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada
| | - Matthew P. Cheng
- Division
of Infectious Diseases, Department of Medicine, McGill University Health Centre, Montreal, PQ H4A 3J1, Canada
| | - Donald C. Vinh
- Division
of Infectious Diseases, Department of Medicine, McGill University Health Centre, Montreal, PQ H4A 3J1, Canada
| | - Todd C. Lee
- Division
of Infectious Diseases, Department of Medicine, McGill University Health Centre, Montreal, PQ H4A 3J1, Canada
| | - Brent W. Winston
- Departments
of Critical Care Medicine, Medicine and Biochemistry and Molecular
Biology, Foothills Medical Centre and University
of Calgary, 1403 29 Street
NW, Calgary, Alberta T2N 4N1, Canada
| | - David Sweet
- Division
of Critical Care Medicine, Vancouver General
Hospital, 2775 Laurel St, Vancouver, BC V5Z 1M9, Canada
| | - John H. Boyd
- Centre
for Heart Lung Innovation, St. Paul’s Hospital, University of British Columbia, 1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada
- Division of Critical Care Medicine, St.
Paul’s Hospital, University of British
Columbia, 1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada
| | - Keith R. Walley
- Centre
for Heart Lung Innovation, St. Paul’s Hospital, University of British Columbia, 1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada
- Division of Critical Care Medicine, St.
Paul’s Hospital, University of British
Columbia, 1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada
| | - Greg Haljan
- Department of Medicine, Surrey Memorial
Hospital, 13750 96th
Avenue, Surrey, BC V3V 1Z2, Canada
| | - Allison McGeer
- Mt. Sinai Hospital and University of Toronto, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | | | - Robert Fowler
- Sunnybrook Health Sciences Centre, 2075 Bayview Avenue, Toronto, ON M4N 3M5, Canada
| | - David Maslove
- Department
of Critical Care, Kingston General Hospital
and Queen’s University, 76 Stuart Street, Kingston, ON K7L 2V7, Canada
| | - Joel Singer
- Centre for
Health Evaluation and Outcome Science (CHEOS), St. Paul’s Hospital, University of British Columbia, 1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada
| | - David M. Patrick
- British Columbia Centre for Disease Control
(BCCDC) and University
of British Columbia, 655 West 12th Avenue, Vancouver, BC V5Z 4R4, Canada
| | - John C. Marshall
- Department of Surgery, St. Michael’s
Hospital, 30 Bond Street, Toronto, ON M5B
1W8, Canada
| | - Srinivas Murthy
- BC Children’s Hospital and University of British Columbia, 4500 Oak Street, Vancouver, BC V6H 3N1, Canada
| | - Fagun Jain
- Black Tusk Research Group, Vancouver, BC V6Z 2C7, Canada
| | - Christoph H. Borchers
- Segal Cancer Proteomics, Centre, Lady Davis
Institute
for Medical Research, McGill University, Montreal, QC H3T 1E2, Canada
- Gerald Bronfman Department of Oncology, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
- Division of Experimental Medicine, McGill
University, Montreal, QC H3T 1E2, Canada
- Department of Pathology, McGill
University, Montreal, QC H3T 1E2, Canada
| | - David R. Goodlett
- UVic-Genome
BC Proteomics Centre, University of Victoria, Victoria V8Z 5N3, BC Canada
| | - Adeera Levin
- Division of Nephrology, St.
Paul’s Hospital, 1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada
| | - James A. Russell
- Centre
for Heart Lung Innovation, St. Paul’s Hospital, University of British Columbia, 1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada
- Division of Critical Care Medicine, St.
Paul’s Hospital, University of British
Columbia, 1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada
| | - ARBs CORONA I Consortium
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Leiden 2333 ZA, The Netherlands
- UVic-Genome
BC Proteomics Centre, University of Victoria, Victoria V8Z 5N3, BC Canada
- Gerald
Bronfman Department of Oncology, McGill
University, Montreal, QC H3A 0G4, Canada
- Division
of General Internal Medicine, Vancouver
General Hospital and University of British Columbia, 2775 Laurel St, Vancouver, BC V5Z 1M9, Canada
- Division
of Respiratory Medicine, Vancouver General Hospital, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
- Centre for
Health Evaluation and Outcome Science (CHEOS), St. Paul’s Hospital, University of British Columbia, 1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada
- Division
of Infectious Diseases, Department of Medicine, McGill University Health Centre, Montreal, PQ H4A 3J1, Canada
- Departments
of Critical Care Medicine, Medicine and Biochemistry and Molecular
Biology, Foothills Medical Centre and University
of Calgary, 1403 29 Street
NW, Calgary, Alberta T2N 4N1, Canada
- Division
of Critical Care Medicine, Vancouver General
Hospital, 2775 Laurel St, Vancouver, BC V5Z 1M9, Canada
- Centre
for Heart Lung Innovation, St. Paul’s Hospital, University of British Columbia, 1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada
- Division of Critical Care Medicine, St.
Paul’s Hospital, University of British
Columbia, 1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada
- Department of Medicine, Surrey Memorial
Hospital, 13750 96th
Avenue, Surrey, BC V3V 1Z2, Canada
- Mt. Sinai Hospital and University of Toronto, 600 University Avenue, Toronto, ON M5G 1X5, Canada
- University of Sherbrooke, Sherbrooke, PQ J1K 2R1, Canada
- Sunnybrook Health Sciences Centre, 2075 Bayview Avenue, Toronto, ON M4N 3M5, Canada
- Department
of Critical Care, Kingston General Hospital
and Queen’s University, 76 Stuart Street, Kingston, ON K7L 2V7, Canada
- British Columbia Centre for Disease Control
(BCCDC) and University
of British Columbia, 655 West 12th Avenue, Vancouver, BC V5Z 4R4, Canada
- Department of Surgery, St. Michael’s
Hospital, 30 Bond Street, Toronto, ON M5B
1W8, Canada
- BC Children’s Hospital and University of British Columbia, 4500 Oak Street, Vancouver, BC V6H 3N1, Canada
- Black Tusk Research Group, Vancouver, BC V6Z 2C7, Canada
- Segal Cancer Proteomics, Centre, Lady Davis
Institute
for Medical Research, McGill University, Montreal, QC H3T 1E2, Canada
- Gerald Bronfman Department of Oncology, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
- Division of Experimental Medicine, McGill
University, Montreal, QC H3T 1E2, Canada
- Department of Pathology, McGill
University, Montreal, QC H3T 1E2, Canada
- Division of Nephrology, St.
Paul’s Hospital, 1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada
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2
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Mohammed Y, Goodlett D, Borchers CH. Bioinformatics Tools and Knowledgebases to Assist Generating Targeted Assays for Plasma Proteomics. Methods Mol Biol 2023; 2628:557-577. [PMID: 36781806 DOI: 10.1007/978-1-0716-2978-9_32] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
In targeted proteomics experiments, selecting the appropriate proteotypic peptides as surrogate for the target protein is a crucial pre-acquisition step. This step is largely a bioinformatics exercise that involves integrating information on the peptides and proteins and using various software tools and knowledgebases. We present here a few resources that automate and simplify the selection process to a great degree. These tools and knowledgebases were developed primarily to streamline targeted proteomics assay development and include PeptidePicker, PeptidePickerDB, MRMAssayDB, MouseQuaPro, and PeptideTracker. We have used these tools to develop and document thousands of targeted proteomics assays, many of them for plasma proteins with focus on human and mouse. An important aspect in all these resources is the integrative approach on which they are based. Using these tools in the first steps of designing a singleplexed or multiplexed targeted proteomic experiment can reduce the necessary experimental steps tremendously. All the tools and knowledgebases we describe here are Web-based and freely accessible so scientists can query the information conveniently from the browser. This chapter provides an overview of these software tools and knowledgebases, their content, and how to use them for targeted plasma proteomics. We further demonstrate how to use them with the results of the HUPO Human Plasma Proteome Project to produce a new database of 3.8 k targeted assays for known human plasma proteins. Upon experimental validation, these assays should help in the further quantitative characterizing of the plasma proteome.
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Affiliation(s)
- Yassene Mohammed
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, ZA, Netherlands. .,University of Victoria - Genome BC Proteomics Centre, Victoria, BC, Canada. .,Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada.
| | - David Goodlett
- University of Victoria - Genome BC Proteomics Centre, Victoria, BC, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada.,University of Gdansk, International Centre for Cancer Vaccine Science, Gdansk, Poland
| | - Christoph H Borchers
- Proteomics Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada.,Gerald Bronfman Department of Oncology, Jewish General Hospital, Montreal, QC, Canada.,Division of Experimental Medicine, McGill University, Montreal, QC, Canada.,Department of Pathology, McGill University, Montreal, QC, Canada
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3
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Edfors F, Iglesias MJ, Butler LM, Odeberg J. Proteomics in thrombosis research. Res Pract Thromb Haemost 2022; 6:e12706. [PMID: 35494505 PMCID: PMC9039028 DOI: 10.1002/rth2.12706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 11/24/2022] Open
Abstract
A State of the Art lecture titled “Proteomics in Thrombosis Research” was presented at the ISTH Congress in 2021. In clinical practice, there is a need for improved plasma biomarker‐based tools for diagnosis and risk prediction of venous thromboembolism (VTE). Analysis of blood, to identify plasma proteins with potential utility for such tools, could enable an individualized approach to treatment and prevention. Technological advances to study the plasma proteome on a large scale allows broad screening for the identification of novel plasma biomarkers, both by targeted and nontargeted proteomics methods. However, assay limitations need to be considered when interpreting results, with orthogonal validation required before conclusions are drawn. Here, we review and provide perspectives on the application of affinity‐ and mass spectrometry‐based methods for the identification and analysis of plasma protein biomarkers, with potential application in the field of VTE. We also provide a future perspective on discovery strategies and emerging technologies for targeted proteomics in thrombosis research. Finally, we summarize relevant new data on this topic, presented during the 2021 ISTH Congress.
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Affiliation(s)
- Fredrik Edfors
- Science for Life Laboratory Department of Protein Science CBH KTH Royal Institute of Technology Stockholm Sweden
- Karolinska University Laboratory Karolinska University Hospital Stockholm Sweden
| | - Maria Jesus Iglesias
- Science for Life Laboratory Department of Protein Science CBH KTH Royal Institute of Technology Stockholm Sweden
| | - Lynn M. Butler
- Science for Life Laboratory Department of Protein Science CBH KTH Royal Institute of Technology Stockholm Sweden
- Clinical Chemistry and Blood Coagulation Research Department of Molecular Medicine and Surgery Karolinska Institute Stockholm Sweden
- Clinical Chemistry Karolinska University Laboratory Karolinska University Hospital Stockholm Sweden
- Department of Clinical Medicine The Arctic University of Norway Tromsø Norway
| | - Jacob Odeberg
- Science for Life Laboratory Department of Protein Science CBH KTH Royal Institute of Technology Stockholm Sweden
- Department of Clinical Medicine The Arctic University of Norway Tromsø Norway
- Division of Internal Medicine University Hospital of North Norway Tromsø Norway
- Coagulation Unit Department of Hematology Karolinska University Hospital Stockholm Sweden
- Department of Medicine Solna Karolinska Institute Stockholm Sweden
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4
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Mohammed Y, Goodlett DR, Cheng MP, Vinh DC, Lee TC, Mcgeer A, Sweet D, Tran K, Lee T, Murthy S, Boyd JH, Singer J, Walley KR, Patrick DM, Quan C, Ismail S, Amar L, Pal A, Bassawon R, Fesdekjian L, Gou K, Lamontagne F, Marshall J, Haljan G, Fowler R, Winston BW, Russell JA. Longitudinal Plasma Proteomics Analysis Reveals Novel Candidate Biomarkers in Acute COVID-19. J Proteome Res 2022; 21:975-992. [PMID: 35143212 PMCID: PMC8864781 DOI: 10.1021/acs.jproteome.1c00863] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Indexed: 12/15/2022]
Abstract
The host response to COVID-19 pathophysiology over the first few days of infection remains largely unclear, especially the mechanisms in the blood compartment. We report on a longitudinal proteomic analysis of acute-phase COVID-19 patients, for which we used blood plasma, multiple reaction monitoring with internal standards, and data-independent acquisition. We measured samples on admission for 49 patients, of which 21 had additional samples on days 2, 4, 7, and 14 after admission. We also measured 30 externally obtained samples from healthy individuals for comparison at baseline. The 31 proteins differentiated in abundance between acute COVID-19 patients and healthy controls belonged to acute inflammatory response, complement activation, regulation of inflammatory response, and regulation of protein activation cascade. The longitudinal analysis showed distinct profiles revealing increased levels of multiple lipid-associated functions, a rapid decrease followed by recovery for complement activation, humoral immune response, and acute inflammatory response-related proteins, and level fluctuation in the regulation of smooth muscle cell proliferation, secretory mechanisms, and platelet degranulation. Three proteins were differentiated between survivors and nonsurvivors. Finally, increased levels of fructose-bisphosphate aldolase B were determined in patients with exposure to angiotensin receptor blockers versus decreased levels in those exposed to angiotensin-converting enzyme inhibitors. Data are available via ProteomeXchange PXD029437.
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Affiliation(s)
- Yassene Mohammed
- Genome BC Proteomics Centre, University
of Victoria, Victoria V8Z 5N3, British Columbia,
Canada
- Center for Proteomics and Metabolomics,
Leiden University Medical Center, Leiden 2333 ZA,
Netherlands
| | - David R. Goodlett
- Genome BC Proteomics Centre, University
of Victoria, Victoria V8Z 5N3, British Columbia,
Canada
- Department of Biochemistry and Microbiology,
University of Victoria, Victoria V8W 2Y2, British Columbia,
Canada
- International Centre for Cancer Vaccine Science,
University of Gdansk, Gdansk 80-822, European Union,
Poland
| | - Matthew P. Cheng
- Division of Infectious Diseases (Department of
Medicine), Division of Medical Microbiology (Department of Pathology and Laboratory
Medicine), McGill University Health Centre, Montreal H4A 3J1,
Quebec, Canada
| | - Donald C. Vinh
- Division of Infectious Diseases (Department of
Medicine), Division of Medical Microbiology (Department of Pathology and Laboratory
Medicine), McGill University Health Centre, Montreal H4A 3J1,
Quebec, Canada
| | - Todd C. Lee
- Department of Medicine, McGill
University, Montreal H4A 3J1, Quebec, Canada
| | - Allison Mcgeer
- Mt. Sinai Hospital and University of
Toronto, University Avenue, Toronto M5G 1X5, Ontario,
Canada
| | - David Sweet
- Division of Critical Care Medicine, Department of
Emergency Medicine, Vancouver General Hospital and University of British
Columbia, Vancouver V5Z 1M9, British Columbia,
Canada
| | - Karen Tran
- Division of General Internal Medicine,
Vancouver General Hospital and University of British
Columbia, Vancouver V5Z 1M9, British Columbia,
Canada
| | - Terry Lee
- Centre for Health Evaluation and Outcome Science
(CHEOS), St. Paul’s Hospital, University of British
Columbia, 1081 Burrard Street, Vancouver V6Z 1Y6, British Columbia,
Canada
| | - Srinivas Murthy
- BC Children’s Hospital,
University of British Columbia, Vancouver V6H 3N1, British Columbia,
Canada
| | - John H. Boyd
- Centre for Heart Lung Innovation, St.
Paul’s Hospital, University of British Columbia, 1081 Burrard
Street, Vancouver V6Z 1Y6, British Columbia, Canada
- Division of Critical Care Medicine, St.
Paul’s Hospital, University of British Columbia, 1081 Burrard
Street, Vancouver V6Z 1Y6, British Columbia, Canada
| | - Joel Singer
- Centre for Health Evaluation and Outcome Science
(CHEOS), St. Paul’s Hospital, University of British
Columbia, 1081 Burrard Street, Vancouver V6Z 1Y6, British Columbia,
Canada
| | - Keith R. Walley
- Centre for Heart Lung Innovation, St.
Paul’s Hospital, University of British Columbia, 1081 Burrard
Street, Vancouver V6Z 1Y6, British Columbia, Canada
- Division of Critical Care Medicine, St.
Paul’s Hospital, University of British Columbia, 1081 Burrard
Street, Vancouver V6Z 1Y6, British Columbia, Canada
| | - David M. Patrick
- British Columbia Centre for Disease
Control (BCCDC) and University of British Columbia, Vancouver V5Z 4R4,
British Columbia, Canada
| | - Curtis Quan
- Department of Medicine, McGill
University, Montreal H4A 3J1, Quebec, Canada
| | - Sara Ismail
- Department of Medicine, McGill
University, Montreal H4A 3J1, Quebec, Canada
| | - Laetitia Amar
- Department of Medicine, McGill
University, Montreal H4A 3J1, Quebec, Canada
| | - Aditya Pal
- Department of Medicine, McGill
University, Montreal H4A 3J1, Quebec, Canada
| | - Rayhaan Bassawon
- Department of Medicine, McGill
University, Montreal H4A 3J1, Quebec, Canada
| | - Lara Fesdekjian
- Department of Medicine, McGill
University, Montreal H4A 3J1, Quebec, Canada
| | - Karine Gou
- Department of Medicine, McGill
University, Montreal H4A 3J1, Quebec, Canada
| | | | - John Marshall
- Department of Surgery, St.
Michael’s Hospital, Toronto M5B 1W8, Ontario,
Canada
| | - Greg Haljan
- Division of Critical Care, Surrey
Memorial Hospital and University of British Columbia, Surrey V3V 1Z2,
British Columbia, Canada
| | - Robert Fowler
- Sunnybrook Health Sciences
Centre, Toronto M4N 3M5, Ontario, Canada
| | - Brent W. Winston
- Departments of Critical Care Medicine, Medicine and
Biochemistry and Molecular Biology, University of Calgary,
Calgary T2N 4N1, Alberta, Canada
| | - James A. Russell
- Centre for Heart Lung Innovation, St.
Paul’s Hospital, University of British Columbia, 1081 Burrard
Street, Vancouver V6Z 1Y6, British Columbia, Canada
- Division of Critical Care Medicine, St.
Paul’s Hospital, University of British Columbia, 1081 Burrard
Street, Vancouver V6Z 1Y6, British Columbia, Canada
| | - ARBs CORONA I
- Genome BC Proteomics Centre, University
of Victoria, Victoria V8Z 5N3, British Columbia,
Canada
- Center for Proteomics and Metabolomics,
Leiden University Medical Center, Leiden 2333 ZA,
Netherlands
- Department of Biochemistry and Microbiology,
University of Victoria, Victoria V8W 2Y2, British Columbia,
Canada
- International Centre for Cancer Vaccine Science,
University of Gdansk, Gdansk 80-822, European Union,
Poland
- Department of Medicine, McGill
University, Montreal H4A 3J1, Quebec, Canada
- Mt. Sinai Hospital and University of
Toronto, University Avenue, Toronto M5G 1X5, Ontario,
Canada
- Division of Critical Care Medicine, Department of
Emergency Medicine, Vancouver General Hospital and University of British
Columbia, Vancouver V5Z 1M9, British Columbia,
Canada
- Division of General Internal Medicine,
Vancouver General Hospital and University of British
Columbia, Vancouver V5Z 1M9, British Columbia,
Canada
- Centre for Health Evaluation and Outcome Science
(CHEOS), St. Paul’s Hospital, University of British
Columbia, 1081 Burrard Street, Vancouver V6Z 1Y6, British Columbia,
Canada
- BC Children’s Hospital,
University of British Columbia, Vancouver V6H 3N1, British Columbia,
Canada
- Centre for Heart Lung Innovation, St.
Paul’s Hospital, University of British Columbia, 1081 Burrard
Street, Vancouver V6Z 1Y6, British Columbia, Canada
- Division of Critical Care Medicine, St.
Paul’s Hospital, University of British Columbia, 1081 Burrard
Street, Vancouver V6Z 1Y6, British Columbia, Canada
- British Columbia Centre for Disease
Control (BCCDC) and University of British Columbia, Vancouver V5Z 4R4,
British Columbia, Canada
- University of Sherbrooke,
Sherbrooke J1K 2R1, Quebec, Canada
- Department of Surgery, St.
Michael’s Hospital, Toronto M5B 1W8, Ontario,
Canada
- Division of Critical Care, Surrey
Memorial Hospital and University of British Columbia, Surrey V3V 1Z2,
British Columbia, Canada
- Sunnybrook Health Sciences
Centre, Toronto M4N 3M5, Ontario, Canada
- Departments of Critical Care Medicine, Medicine and
Biochemistry and Molecular Biology, University of Calgary,
Calgary T2N 4N1, Alberta, Canada
- Division of Infectious Diseases (Department of
Medicine), Division of Medical Microbiology (Department of Pathology and Laboratory
Medicine), McGill University Health Centre, Montreal H4A 3J1,
Quebec, Canada
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5
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Schmidt A, Schreiner D. Quantitative Detection of Protein Splice Variants by Selected Reaction Monitoring (SRM) Mass Spectrometry. Methods Mol Biol 2022; 2537:231-246. [PMID: 35895268 DOI: 10.1007/978-1-0716-2521-7_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Molecular diversification of the cellular proteome through alternative splicing has emerged as an important biological principle. However, the lack of tools to specifically detect and quantify proteoforms (Smith et al., Nat Methods 10:186-187, 2013) is a major impediment to functional studies. Recently, biological mass spectrometry (MS) has undergone impressive advances (Mann, Nat Rev Mol Cell Biol 17:678, 2016), including the generation of a highly diverse set of biological applications (Aebersold and Mann, Nature 537:347-355, 2016), and has demonstrated to be an essential tool to address many biological questions (Savitski et al., Science 346:1255784, 2014; Rinner et al., Nat Methods 5:315-318, 2008). In particular, targeted LC-MS, with its high selectivity and specificity, is ideally suited for the precise and sensitive quantification of specific proteins and their proteoforms (Picotti and Aebersold, Nat Methods 9:555-566, 2012). We describe in detail the application of this workflow applied to dissect the molecular diversity of the synaptic adhesion proteins and their splicing-derived proteoforms (Schreiner et al., Elife 4:e07794, 2015).
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6
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Demichev V, Tober-Lau P, Nazarenko T, Lemke O, Kaur Aulakh S, Whitwell HJ, Röhl A, Freiwald A, Mittermaier M, Szyrwiel L, Ludwig D, Correia-Melo C, Lippert LJ, Helbig ET, Stubbemann P, Olk N, Thibeault C, Grüning NM, Blyuss O, Vernardis S, White M, Messner CB, Joannidis M, Sonnweber T, Klein SJ, Pizzini A, Wohlfarter Y, Sahanic S, Hilbe R, Schaefer B, Wagner S, Machleidt F, Garcia C, Ruwwe-Glösenkamp C, Lingscheid T, Bosquillon de Jarcy L, Stegemann MS, Pfeiffer M, Jürgens L, Denker S, Zickler D, Spies C, Edel A, Müller NB, Enghard P, Zelezniak A, Bellmann-Weiler R, Weiss G, Campbell A, Hayward C, Porteous DJ, Marioni RE, Uhrig A, Zoller H, Löffler-Ragg J, Keller MA, Tancevski I, Timms JF, Zaikin A, Hippenstiel S, Ramharter M, Müller-Redetzky H, Witzenrath M, Suttorp N, Lilley K, Mülleder M, Sander LE, Kurth F, Ralser M. A proteomic survival predictor for COVID-19 patients in intensive care. PLOS DIGITAL HEALTH 2022; 1:e0000007. [PMID: 36812516 PMCID: PMC9931303 DOI: 10.1371/journal.pdig.0000007] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 11/18/2021] [Indexed: 02/07/2023]
Abstract
Global healthcare systems are challenged by the COVID-19 pandemic. There is a need to optimize allocation of treatment and resources in intensive care, as clinically established risk assessments such as SOFA and APACHE II scores show only limited performance for predicting the survival of severely ill COVID-19 patients. Additional tools are also needed to monitor treatment, including experimental therapies in clinical trials. Comprehensively capturing human physiology, we speculated that proteomics in combination with new data-driven analysis strategies could produce a new generation of prognostic discriminators. We studied two independent cohorts of patients with severe COVID-19 who required intensive care and invasive mechanical ventilation. SOFA score, Charlson comorbidity index, and APACHE II score showed limited performance in predicting the COVID-19 outcome. Instead, the quantification of 321 plasma protein groups at 349 timepoints in 50 critically ill patients receiving invasive mechanical ventilation revealed 14 proteins that showed trajectories different between survivors and non-survivors. A predictor trained on proteomic measurements obtained at the first time point at maximum treatment level (i.e. WHO grade 7), which was weeks before the outcome, achieved accurate classification of survivors (AUROC 0.81). We tested the established predictor on an independent validation cohort (AUROC 1.0). The majority of proteins with high relevance in the prediction model belong to the coagulation system and complement cascade. Our study demonstrates that plasma proteomics can give rise to prognostic predictors substantially outperforming current prognostic markers in intensive care.
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Affiliation(s)
- Vadim Demichev
- Charité–Universitätsmedizin Berlin, Department of Biochemistry, Berlin, Germany
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, United Kingdom
- The University of Cambridge, Department of Biochemistry and Cambridge Centre for Proteomics, Cambridge, United Kingdom
| | - Pinkus Tober-Lau
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Tatiana Nazarenko
- University College London, Department of Mathematics, London, United Kingdom
- University College London, Department of Women’s Cancer, EGA Institute for Women’s Health, London, United Kingdom
| | - Oliver Lemke
- Charité–Universitätsmedizin Berlin, Department of Biochemistry, Berlin, Germany
| | - Simran Kaur Aulakh
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, United Kingdom
| | - Harry J. Whitwell
- National Phenome Centre and Imperial Clinical Phenotyping Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
- Lobachevsky University, Laboratory of Systems Medicine of Healthy Ageing, Nizhny Novgorod, Russia
- Imperial College London, Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, London, United Kingdom
| | - Annika Röhl
- Charité–Universitätsmedizin Berlin, Department of Biochemistry, Berlin, Germany
| | - Anja Freiwald
- Charité–Universitätsmedizin Berlin, Department of Biochemistry, Berlin, Germany
| | - Mirja Mittermaier
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Lukasz Szyrwiel
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, United Kingdom
| | - Daniela Ludwig
- Charité–Universitätsmedizin Berlin, Department of Biochemistry, Berlin, Germany
| | - Clara Correia-Melo
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, United Kingdom
| | - Lena J. Lippert
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Elisa T. Helbig
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Paula Stubbemann
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Nadine Olk
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Charlotte Thibeault
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Nana-Maria Grüning
- Charité–Universitätsmedizin Berlin, Department of Biochemistry, Berlin, Germany
| | - Oleg Blyuss
- Lobachevsky University, Department of Applied Mathematics, Nizhny Novgorod, Russia
- University of Hertfordshire, School of Physics, Astronomy and Mathematics, Hatfield, United Kingdom
- Sechenov First Moscow State Medical University, Department of Paediatrics and Paediatric Infectious Diseases, Moscow, Russia
| | - Spyros Vernardis
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, United Kingdom
| | - Matthew White
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, United Kingdom
| | - Christoph B. Messner
- Charité–Universitätsmedizin Berlin, Department of Biochemistry, Berlin, Germany
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, United Kingdom
| | - Michael Joannidis
- Medical University Innsbruck, Division of Intensive Care and Emergency Medicine, Department of Internal Medicine, Innsbruck, Austria
| | - Thomas Sonnweber
- Medical University of Innsbruck, Department of Internal Medicine II, Innsbruck, Austria
| | - Sebastian J. Klein
- Medical University Innsbruck, Division of Intensive Care and Emergency Medicine, Department of Internal Medicine, Innsbruck, Austria
| | - Alex Pizzini
- Medical University of Innsbruck, Department of Internal Medicine II, Innsbruck, Austria
| | - Yvonne Wohlfarter
- Medical University of Innsbruck, Institute of Human Genetics, Innsbruck, Austria
| | - Sabina Sahanic
- Medical University of Innsbruck, Department of Internal Medicine II, Innsbruck, Austria
| | - Richard Hilbe
- Medical University of Innsbruck, Department of Internal Medicine II, Innsbruck, Austria
| | - Benedikt Schaefer
- Medical University of Innsbruck, Christian Doppler Laboratory for Iron and Phosphate Biology, Department of Internal Medicine I, Innsbruck, Austria
| | - Sonja Wagner
- Medical University of Innsbruck, Christian Doppler Laboratory for Iron and Phosphate Biology, Department of Internal Medicine I, Innsbruck, Austria
| | - Felix Machleidt
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Carmen Garcia
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Christoph Ruwwe-Glösenkamp
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Tilman Lingscheid
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Laure Bosquillon de Jarcy
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Miriam S. Stegemann
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Moritz Pfeiffer
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Linda Jürgens
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Sophy Denker
- Charité–Universitätsmedizin Berlin, Medical Department of Hematology, Oncology & Tumor Immunology, Virchow Campus & Molekulares Krebsforschungszentrum, Berlin, Germany
| | - Daniel Zickler
- Charité–Universitätsmedizin Berlin, Department of Nephrology and Internal Intensive Care Medicine, Berlin, Germany
| | - Claudia Spies
- Charité–Universitätsmedizin Berlin, Department of Anesthesiology and Intensive Care, Berlin, Germany
| | - Andreas Edel
- Charité–Universitätsmedizin Berlin, Department of Anesthesiology and Intensive Care, Berlin, Germany
| | - Nils B. Müller
- Charité–Universitätsmedizin Berlin, Department of Nephrology and Internal Intensive Care Medicine, Berlin, Germany
| | - Philipp Enghard
- Charité–Universitätsmedizin Berlin, Department of Nephrology and Internal Intensive Care Medicine, Berlin, Germany
| | - Aleksej Zelezniak
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, United Kingdom
- Chalmers University of Technology, Department of Biology and Biological Engineering, Gothenburg, Sweden
| | - Rosa Bellmann-Weiler
- Medical University of Innsbruck, Department of Internal Medicine II, Innsbruck, Austria
| | - Günter Weiss
- Medical University of Innsbruck, Department of Internal Medicine II, Innsbruck, Austria
| | - Archie Campbell
- University of Edinburgh, Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, United Kingdom
- University of Edinburgh, Usher Institute, Edinburgh, United Kingdom
| | - Caroline Hayward
- University of Edinburgh, MRC Human Genetics Unit, Institute of Genetics and Cancer, Edinburgh, United Kingdom
| | - David J. Porteous
- University of Edinburgh, Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, United Kingdom
- University of Edinburgh, Usher Institute, Edinburgh, United Kingdom
| | - Riccardo E. Marioni
- University of Edinburgh, Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, United Kingdom
| | - Alexander Uhrig
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Heinz Zoller
- Medical University of Innsbruck, Christian Doppler Laboratory for Iron and Phosphate Biology, Department of Internal Medicine I, Innsbruck, Austria
| | - Judith Löffler-Ragg
- Medical University of Innsbruck, Department of Internal Medicine II, Innsbruck, Austria
| | - Markus A. Keller
- Medical University of Innsbruck, Institute of Human Genetics, Innsbruck, Austria
| | - Ivan Tancevski
- Medical University of Innsbruck, Department of Internal Medicine II, Innsbruck, Austria
| | - John F. Timms
- University College London, Department of Women’s Cancer, EGA Institute for Women’s Health, London, United Kingdom
| | - Alexey Zaikin
- University College London, Department of Mathematics, London, United Kingdom
- University College London, Department of Women’s Cancer, EGA Institute for Women’s Health, London, United Kingdom
- Lobachevsky University, Laboratory of Systems Medicine of Healthy Ageing, Nizhny Novgorod, Russia
- Centre for Analysis of Complex Systems, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Stefan Hippenstiel
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
- German Centre for Lung Research, Germany
| | - Michael Ramharter
- Bernhard Nocht Institute for Tropical Medicine, Department of Tropical Medicine, and University Medical Center Hamburg-Eppendorf, Department of Medicine, Hamburg, Germany
| | - Holger Müller-Redetzky
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
| | - Martin Witzenrath
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
- German Centre for Lung Research, Germany
| | - Norbert Suttorp
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
- German Centre for Lung Research, Germany
| | - Kathryn Lilley
- The University of Cambridge, Department of Biochemistry and Cambridge Centre for Proteomics, Cambridge, United Kingdom
| | - Michael Mülleder
- Charité–Universitätsmedizin Berlin, Core Facility—High-Throughput Mass Spectrometry, Berlin, Germany
| | - Leif Erik Sander
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
- German Centre for Lung Research, Germany
| | | | - Florian Kurth
- Charité–Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany
- Bernhard Nocht Institute for Tropical Medicine, Department of Tropical Medicine, and University Medical Center Hamburg-Eppendorf, Department of Medicine, Hamburg, Germany
- * E-mail:
| | - Markus Ralser
- Charité–Universitätsmedizin Berlin, Department of Biochemistry, Berlin, Germany
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, United Kingdom
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7
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Demichev V, Tober-Lau P, Lemke O, Nazarenko T, Thibeault C, Whitwell H, Röhl A, Freiwald A, Szyrwiel L, Ludwig D, Correia-Melo C, Aulakh SK, Helbig ET, Stubbemann P, Lippert LJ, Grüning NM, Blyuss O, Vernardis S, White M, Messner CB, Joannidis M, Sonnweber T, Klein SJ, Pizzini A, Wohlfarter Y, Sahanic S, Hilbe R, Schaefer B, Wagner S, Mittermaier M, Machleidt F, Garcia C, Ruwwe-Glösenkamp C, Lingscheid T, Bosquillon de Jarcy L, Stegemann MS, Pfeiffer M, Jürgens L, Denker S, Zickler D, Enghard P, Zelezniak A, Campbell A, Hayward C, Porteous DJ, Marioni RE, Uhrig A, Müller-Redetzky H, Zoller H, Löffler-Ragg J, Keller MA, Tancevski I, Timms JF, Zaikin A, Hippenstiel S, Ramharter M, Witzenrath M, Suttorp N, Lilley K, Mülleder M, Sander LE, Ralser M, Kurth F. A time-resolved proteomic and prognostic map of COVID-19. Cell Syst 2021; 12:780-794.e7. [PMID: 34139154 PMCID: PMC8201874 DOI: 10.1016/j.cels.2021.05.005] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 03/24/2021] [Accepted: 05/07/2021] [Indexed: 12/14/2022]
Abstract
COVID-19 is highly variable in its clinical presentation, ranging from asymptomatic infection to severe organ damage and death. We characterized the time-dependent progression of the disease in 139 COVID-19 inpatients by measuring 86 accredited diagnostic parameters, such as blood cell counts and enzyme activities, as well as untargeted plasma proteomes at 687 sampling points. We report an initial spike in a systemic inflammatory response, which is gradually alleviated and followed by a protein signature indicative of tissue repair, metabolic reconstitution, and immunomodulation. We identify prognostic marker signatures for devising risk-adapted treatment strategies and use machine learning to classify therapeutic needs. We show that the machine learning models based on the proteome are transferable to an independent cohort. Our study presents a map linking routinely used clinical diagnostic parameters to plasma proteomes and their dynamics in an infectious disease.
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Affiliation(s)
- Vadim Demichev
- Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany; The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, UK; The University of Cambridge, Department of Biochemistry and Cambridge Centre for Proteomics, Cambridge CB21GA, UK
| | - Pinkus Tober-Lau
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Oliver Lemke
- Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany
| | - Tatiana Nazarenko
- University College London, Department of Mathematics, London WC1E 6BT, UK; University College London, Department of Women's Cancer, EGA Institute for Women'S Health, London WC1E 6BT, UK
| | - Charlotte Thibeault
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Harry Whitwell
- National Phenome Centre and Imperial Clinical Phenotyping Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London SW72AZ, UK; Lobachevsky University, Department of Applied Mathematics, Nizhny Novgorod 603105, Russia; Imperial College London, Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, London SW7 2AZ, UK
| | - Annika Röhl
- Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany
| | - Anja Freiwald
- Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany
| | - Lukasz Szyrwiel
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, UK
| | - Daniela Ludwig
- Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany
| | - Clara Correia-Melo
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, UK
| | - Simran Kaur Aulakh
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, UK
| | - Elisa T Helbig
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Paula Stubbemann
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Lena J Lippert
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Nana-Maria Grüning
- Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany
| | - Oleg Blyuss
- Lobachevsky University, Department of Applied Mathematics, Nizhny Novgorod 603105, Russia; University of Hertfordshire, School of Physics, Astronomy and Mathematics, Hatfield AL10 9AB, UK; Sechenov First Moscow State Medical University, Department of Paediatrics and Paediatric Infectious Diseases, Moscow 119435, Russia
| | - Spyros Vernardis
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, UK
| | - Matthew White
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, UK
| | - Christoph B Messner
- Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany; The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, UK
| | - Michael Joannidis
- Medical University Innsbruck, Division of Intensive Care and Emergency Medicine, Department of Internal Medicine, 6020 Innsbruck, Austria
| | - Thomas Sonnweber
- Medical University of Innsbruck, Department of Internal Medicine II, 6020 Innsbruck, Austria
| | - Sebastian J Klein
- Medical University Innsbruck, Division of Intensive Care and Emergency Medicine, Department of Internal Medicine, 6020 Innsbruck, Austria
| | - Alex Pizzini
- Medical University of Innsbruck, Department of Internal Medicine II, 6020 Innsbruck, Austria
| | - Yvonne Wohlfarter
- Medical University of Innsbruck, Institute of Human Genetics, 6020 Innsbruck, Austria
| | - Sabina Sahanic
- Medical University of Innsbruck, Department of Internal Medicine II, 6020 Innsbruck, Austria
| | - Richard Hilbe
- Medical University of Innsbruck, Department of Internal Medicine II, 6020 Innsbruck, Austria
| | - Benedikt Schaefer
- Medical University of Innsbruck, Christian Doppler Laboratory for Iron and Phosphate Biology, Department of Internal Medicine I, 6020 Innsbruck, Austria
| | - Sonja Wagner
- Medical University of Innsbruck, Christian Doppler Laboratory for Iron and Phosphate Biology, Department of Internal Medicine I, 6020 Innsbruck, Austria
| | - Mirja Mittermaier
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany; Berlin Institute of Health, 10178 Berlin, Germany
| | - Felix Machleidt
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Carmen Garcia
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Christoph Ruwwe-Glösenkamp
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Tilman Lingscheid
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Laure Bosquillon de Jarcy
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Miriam S Stegemann
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Moritz Pfeiffer
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Linda Jürgens
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Sophy Denker
- Charité Universitätsmedizin Berlin, Medical Department of Hematology, Oncology & Tumor Immunology, Virchow Campus & Molekulares Krebsforschungszentrum, 13353 Berlin, Germany; Berlin Institute of Health, 10178 Berlin, Germany
| | - Daniel Zickler
- Charité Universitätsmedizin Berlin, Department of Nephrology and Internal Intensive Care Medicine, 10117 Berlin, Germany
| | - Philipp Enghard
- Charité Universitätsmedizin Berlin, Department of Nephrology and Internal Intensive Care Medicine, 10117 Berlin, Germany
| | - Aleksej Zelezniak
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, UK; Chalmers Tekniska Högskola, Department of Biology and Biological Engineering, SE-412 96 Gothenburg, Sweden
| | - Archie Campbell
- University of Edinburgh, Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, Edinburgh EH4 2XU, UK; University of Edinburgh, Usher Institute, Edinburgh EH16 4UX, UK
| | - Caroline Hayward
- University of Edinburgh, MRC Human Genetics Unit, Institute of Genetics and Cancer, Edinburgh EH4 2XU, UK
| | - David J Porteous
- University of Edinburgh, Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, Edinburgh EH4 2XU, UK; University of Edinburgh, Usher Institute, Edinburgh EH16 4UX, UK
| | - Riccardo E Marioni
- University of Edinburgh, Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, Edinburgh EH4 2XU, UK
| | - Alexander Uhrig
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Holger Müller-Redetzky
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany
| | - Heinz Zoller
- Medical University of Innsbruck, Christian Doppler Laboratory for Iron and Phosphate Biology, Department of Internal Medicine I, 6020 Innsbruck, Austria
| | - Judith Löffler-Ragg
- Medical University of Innsbruck, Department of Internal Medicine II, 6020 Innsbruck, Austria
| | - Markus A Keller
- Medical University of Innsbruck, Institute of Human Genetics, 6020 Innsbruck, Austria
| | - Ivan Tancevski
- Medical University of Innsbruck, Department of Internal Medicine II, 6020 Innsbruck, Austria
| | - John F Timms
- University College London, Department of Women's Cancer, EGA Institute for Women'S Health, London WC1E 6BT, UK
| | - Alexey Zaikin
- University College London, Department of Mathematics, London WC1E 6BT, UK; University College London, Department of Women's Cancer, EGA Institute for Women'S Health, London WC1E 6BT, UK; Lobachevsky University, Laboratory of Systems Medicine of Healthy Ageing, Nizhny Novgorod 603105, Russia
| | - Stefan Hippenstiel
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany; German Centre for Lung Research, 35392 Gießen, Germany
| | - Michael Ramharter
- Bernhard Nocht Institute for Tropical Medicine, Department of Tropical Medicine, and University Medical Center Hamburg-Eppendorf, Department of Medicine, 20359 Hamburg, Germany
| | - Martin Witzenrath
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany; German Centre for Lung Research, 35392 Gießen, Germany
| | - Norbert Suttorp
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany; German Centre for Lung Research, 35392 Gießen, Germany
| | - Kathryn Lilley
- The University of Cambridge, Department of Biochemistry and Cambridge Centre for Proteomics, Cambridge CB21GA, UK
| | - Michael Mülleder
- Charité - Universitätsmedizin Berlin, Core Facility - High-Throughput Mass Spectrometry, 10117 Berlin, Germany
| | - Leif Erik Sander
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany; German Centre for Lung Research, 35392 Gießen, Germany
| | - Markus Ralser
- Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany; The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, UK.
| | - Florian Kurth
- Charité Universitätsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany; Bernhard Nocht Institute for Tropical Medicine, Department of Tropical Medicine, and University Medical Center Hamburg-Eppendorf, Department of Medicine, 20359 Hamburg, Germany
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8
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Whiteaker JR, Sharma K, Hoffman MA, Kuhn E, Zhao L, Cocco AR, Schoenherr RM, Kennedy JJ, Voytovich U, Lin C, Fang B, Bowers K, Whiteley G, Colantonio S, Bocik W, Roberts R, Hiltke T, Boja E, Rodriguez H, McCormick F, Holderfield M, Carr SA, Koomen JM, Paulovich AG. Targeted mass spectrometry-based assays enable multiplex quantification of receptor tyrosine kinase, MAP Kinase, and AKT signaling. CELL REPORTS METHODS 2021; 1:100015. [PMID: 34671754 PMCID: PMC8525888 DOI: 10.1016/j.crmeth.2021.100015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 02/16/2021] [Accepted: 05/07/2021] [Indexed: 02/07/2023]
Abstract
SUMMARY A primary goal of the US National Cancer Institute's Ras initiative at the Frederick National Laboratory for Cancer Research is to develop methods to quantify RAS signaling to facilitate development of novel cancer therapeutics. We use targeted proteomics technologies to develop a community resource consisting of 256 validated multiple reaction monitoring (MRM)-based, multiplexed assays for quantifying protein expression and phosphorylation through the receptor tyrosine kinase, MAPK, and AKT signaling networks. As proof of concept, we quantify the response of melanoma (A375 and SK-MEL-2) and colorectal cancer (HCT-116 and HT-29) cell lines to BRAF inhibition by PLX-4720. These assays replace over 60 Western blots with quantitative mass spectrometry-based assays of high molecular specificity and quantitative precision, showing the value of these methods for pharmacodynamic measurements and mechanism of action studies. Methods, fit-for-purpose validation, and results are publicly available as a resource for the community at assays.cancer.gov. MOTIVATION A lack of quantitative, multiplexable assays for phosphosignaling limits comprehensive investigation of aberrant signaling in cancer and evaluation of novel treatments. To alleviate this limitation, we sought to develop assays using targeted mass spectrometry for quantifying protein expression and phosphorylation through the receptor tyrosine kinase, MAPK, and AKT signaling networks. The resulting assays provide a resource for replacing over 60 Western blots in examining cancer signaling and tumor biology with high molecular specificity and quantitative rigor.
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Affiliation(s)
- Jeffrey R. Whiteaker
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Kanika Sharma
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Melissa A. Hoffman
- Proteomics and Metabolomics Core, Department of Molecular Oncology, and Department of Tumor Biology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Eric Kuhn
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Lei Zhao
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Alexandra R. Cocco
- Gillings School of Global Public Health, Kenan-Flagler Business School, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Regine M. Schoenherr
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jacob J. Kennedy
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Ulianna Voytovich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Chenwei Lin
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Bin Fang
- Proteomics and Metabolomics Core, Department of Molecular Oncology, and Department of Tumor Biology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Kiah Bowers
- Proteomics and Metabolomics Core, Department of Molecular Oncology, and Department of Tumor Biology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Gordon Whiteley
- Antibody Characterization Laboratory, Leidos Biochemical Research Inc, Frederick National Laboratory for Cancer Research ATRF, Frederick, MD 21701, USA
| | - Simona Colantonio
- Antibody Characterization Laboratory, Leidos Biochemical Research Inc, Frederick National Laboratory for Cancer Research ATRF, Frederick, MD 21701, USA
| | - William Bocik
- Antibody Characterization Laboratory, Leidos Biochemical Research Inc, Frederick National Laboratory for Cancer Research ATRF, Frederick, MD 21701, USA
| | - Rhonda Roberts
- Antibody Characterization Laboratory, Leidos Biochemical Research Inc, Frederick National Laboratory for Cancer Research ATRF, Frederick, MD 21701, USA
| | - Tara Hiltke
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Emily Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Frank McCormick
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Matthew Holderfield
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
- Department of Biology, Revolution Medicines, Inc., Redwood City, CA 94063, USA
| | - Steven A. Carr
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - John M. Koomen
- Proteomics and Metabolomics Core, Department of Molecular Oncology, and Department of Tumor Biology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Amanda G. Paulovich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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9
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Bhowmick P, Roome S, Borchers CH, Goodlett DR, Mohammed Y. An Update on MRMAssayDB: A Comprehensive Resource for Targeted Proteomics Assays in the Community. J Proteome Res 2021; 20:2105-2115. [PMID: 33683131 PMCID: PMC8041396 DOI: 10.1021/acs.jproteome.0c00961] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Precise multiplexed
quantification of proteins in biological samples
can be achieved by targeted proteomics using multiple or parallel
reaction monitoring (MRM/PRM). Combined with internal standards, the
method achieves very good repeatability and reproducibility enabling
excellent protein quantification and allowing longitudinal and cohort
studies. A laborious part of performing such experiments lies in the
preparation steps dedicated to the development and validation of individual
protein assays. Several public repositories host information on targeted
proteomics assays, including NCI’s Clinical Proteomic Tumor
Analysis Consortium assay portals, PeptideAtlas SRM Experiment Library,
SRMAtlas, PanoramaWeb, and PeptideTracker, with all offering varying
levels of details. We introduced MRMAssayDB in 2018 as an integrated
resource for targeted proteomics assays. The Web-based application
maps and links the assays from the repositories, includes comprehensive
up-to-date protein and sequence annotations, and provides multiple
visualization options on the peptide and protein level. We have extended
MRMAssayDB with more assays and extensive annotations. Currently it
contains >828 000 assays covering >51 000 proteins
from
94 organisms, of which >17 000 proteins are present in >2400
biological pathways, and >48 000 mapping to >21 000
Gene Ontology terms. This is an increase of about four times the number
of assays since introduction. We have expanded annotations of interaction,
biological pathways, and disease associations. A newly added visualization
module for coupled molecular structural annotation browsing allows
the user to interactively examine peptide sequence and any known PTMs
and disease mutations, and map all to available protein 3D structures.
Because of its integrative approach, MRMAssayDB enables a holistic
view of suitable proteotypic peptides and commonly used transitions
in empirical data. Availability: http://mrmassaydb.proteincentre.com.
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Affiliation(s)
- Pallab Bhowmick
- University of Victoria - Genome BC Proteomics Centre, Victoria, British Columbia V8Z 7X8, Canada.,University of Victoria, Victoria, British Columbia V8P 5C2, Canada
| | - Simon Roome
- University of Victoria - Genome BC Proteomics Centre, Victoria, British Columbia V8Z 7X8, Canada.,University of Victoria, Victoria, British Columbia V8P 5C2, Canada
| | - Christoph H Borchers
- Proteomics Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec H3T 1E2, Canada.,Gerald Bronfman Department of Oncology, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada.,Department of Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Skolkovo Innovation Center, Nobel Street, Moscow 121205, Russia
| | - David R Goodlett
- University of Victoria - Genome BC Proteomics Centre, Victoria, British Columbia V8Z 7X8, Canada.,University of Victoria, Victoria, British Columbia V8P 5C2, Canada.,University of Gdansk, International Centre for Cancer Vaccine Science, 80-309 Gdansk, Poland
| | - Yassene Mohammed
- University of Victoria - Genome BC Proteomics Centre, Victoria, British Columbia V8Z 7X8, Canada.,University of Victoria, Victoria, British Columbia V8P 5C2, Canada.,Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA Leiden, Netherlands
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10
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Gillespie MA, Palii CG, Sanchez-Taltavull D, Perkins TJ, Brand M, Ranish JA. Absolute quantification of transcription factors in human erythropoiesis using selected reaction monitoring mass spectrometry. STAR Protoc 2020; 1:100216. [PMID: 33377109 PMCID: PMC7757672 DOI: 10.1016/j.xpro.2020.100216] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Quantitative changes in transcription factor (TF) abundance regulate dynamic cellular processes, including cell fate decisions. Protein copy number provides information about the relative stoichiometry of TFs that can be used to determine how quantitative changes in TF abundance influence gene regulatory networks. In this protocol, we describe a targeted selected reaction monitoring (SRM)-based mass-spectrometry method to systematically measure the absolute protein concentration of nuclear TFs as human hematopoietic stem and progenitor cells differentiate along the erythropoietic lineage. For complete details on the use and execution of this protocol, please refer to Gillespie et al. (2020). Protocol for absolute quantification of TFs in human erythropoiesis Selected reaction monitoring mass-spectrometry parameters for each peptide Validated SRM assays corresponding to >100 TFs Copy number reveals the relative stoichiometries of TFs during erythropoiesis
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Affiliation(s)
- Mark A. Gillespie
- Institute for Systems Biology, Seattle, WA 98109, USA
- Corresponding author
| | - Carmen G. Palii
- Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Corresponding author
| | - Daniel Sanchez-Taltavull
- Visceral Surgery and Medicine, Inselspital, Bern University Hospital, Department for BioMedical Research, University of Bern, Murtenstrasse 35, 3008 Bern, Switzerland
| | - Theodore J. Perkins
- Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Marjorie Brand
- Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Jeffrey A. Ranish
- Institute for Systems Biology, Seattle, WA 98109, USA
- Corresponding author
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11
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An Exploratory Pilot Study with Plasma Protein Signatures Associated with Response of Patients with Depression to Antidepressant Treatment for 10 Weeks. Biomedicines 2020; 8:biomedicines8110455. [PMID: 33126421 PMCID: PMC7692261 DOI: 10.3390/biomedicines8110455] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 10/26/2020] [Accepted: 10/26/2020] [Indexed: 12/11/2022] Open
Abstract
Major depressive disorder (MDD) is a leading cause of global disability with a chronic and recurrent course. Recognition of biological markers that could predict and monitor response to drug treatment could personalize clinical decision-making, minimize unnecessary drug exposure, and achieve better outcomes. Four longitudinal plasma samples were collected from each of ten patients with MDD treated with antidepressants for 10 weeks. Plasma proteins were analyzed qualitatively and quantitatively with a nanoflow LC−MS/MS technique. Of 1153 proteins identified in the 40 longitudinal plasma samples, 37 proteins were significantly associated with response/time and clustered into six according to time and response by the linear mixed model. Among them, three early-drug response markers (PHOX2B, SH3BGRL3, and YWHAE) detectable within one week were verified by liquid chromatography-multiple reaction monitoring/mass spectrometry (LC-MRM/MS) in the well-controlled 24 patients. In addition, 11 proteins correlated significantly with two or more psychiatric measurement indices. This pilot study might be useful in finding protein marker candidates that can monitor response to antidepressant treatment during follow-up visits within 10 weeks after the baseline visit.
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12
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Mohammed Y, Kootte RS, Kopatz WF, Borchers CH, Büller HR, Versteeg HH, Nieuwdorp M, van Mens TE. The intestinal microbiome potentially affects thrombin generation in human subjects. J Thromb Haemost 2020; 18:642-650. [PMID: 31808596 PMCID: PMC7065057 DOI: 10.1111/jth.14699] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 11/06/2019] [Accepted: 11/27/2019] [Indexed: 12/15/2022]
Abstract
BACKGROUND The intestinal microbiome plays a versatile role in the etiology of arterial thrombosis. In venous thrombosis, driven chiefly by plasma coagulation, no such role has yet been established. We hypothesized that the intestinal microbiome composition affects coagulation in humans. METHODS We used healthy donor fecal microbiota transplant (FMT) to experimentally change the microbiome composition in metabolic syndrome patients. Thirty-five subjects were randomized in a blinded fashion to healthy donor FMT or autologous FMT as a control in a 2:1 ratio. We measured thrombin generation at baseline and after 6 weeks using automated calibrated thrombinography, and we determined plasma abundance of 32 coagulation related proteins using a targeted mass spectrometry-based quantitative proteomics assay with heavy labeled internal standards. RESULTS Healthy donor FMT prolonged the thrombinography lag time (median delta 0.0 versus 0.25 minutes, P = .039). The other thrombinography parameters showed no significant difference. Unsupervised cluster analysis suggested overall downregulation of coagulation related plasma proteins in subject clusters containing predominantly subjects that had a metabolic response to healthy donor FMT. FMT treatment status itself showed no clear clustering pattern with up- or downregulation, however, and proteins did not cluster according to an apparent biological grouping. DISCUSSION A single healthy donor FMT tends to modestly suppress the onset thrombin generation in metabolic syndrome patients, representing initial proof-of-principle that the intestinal microbiota composition might affect the coagulation system in humans. The findings merit external validation as a role for intestinal microbiota in coagulation can have clinically important implications.
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Affiliation(s)
- Yassene Mohammed
- Center for Proteomics and MetabolomicsLeiden University Medical CenterLeidenthe Netherlands
- University of Victoria‐Genome BC Proteomics CentreUniversity of VictoriaVictoriaBCCanada
- Division of Medical SciencesUniversity of VictoriaVictoriaBCCanada
| | - Ruud S. Kootte
- Department of Vascular MedicineAmsterdam Cardiovascular SciencesAmsterdam UMC, University of AmsterdamAmsterdamthe Netherlands
| | - Wil F. Kopatz
- Department of Vascular MedicineAmsterdam Cardiovascular SciencesAmsterdam UMC, University of AmsterdamAmsterdamthe Netherlands
| | - Christoph H. Borchers
- University of Victoria‐Genome BC Proteomics CentreUniversity of VictoriaVictoriaBCCanada
- Department of Biochemistry and MicrobiologyUniversity of VictoriaVictoriaBCCanada
- Proteomics CentreSegal Cancer CentreLady Davis InstituteJewish General HospitalMcGill UniversityMontrealQCCanada
| | - Harry R. Büller
- Department of Vascular MedicineAmsterdam Cardiovascular SciencesAmsterdam UMC, University of AmsterdamAmsterdamthe Netherlands
| | - Henri H. Versteeg
- Department of Internal MedicineEinthoven Laboratory for Experimental Vascular MedicineLeiden University Medical CenterLeidenthe Netherlands
| | - Max Nieuwdorp
- Department of Vascular MedicineAmsterdam Cardiovascular SciencesAmsterdam UMC, University of AmsterdamAmsterdamthe Netherlands
| | - Thijs E. van Mens
- Department of Vascular MedicineAmsterdam Cardiovascular SciencesAmsterdam UMC, University of AmsterdamAmsterdamthe Netherlands
- Department of Vascular MedicineAmsterdam Reproduction and DevelopmentAmsterdam UMCUniversity of AmsterdamAmsterdamthe Netherlands
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13
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Tang J, Wang Y, Li Y, Zhang Y, Zhang R, Xiao Z, Luo Y, Guo X, Tao L, Lou Y, Xue W, Zhu F. Recent Technological Advances in the Mass Spectrometry-based Nanomedicine Studies: An Insight from Nanoproteomics. Curr Pharm Des 2019; 25:1536-1553. [PMID: 31258068 DOI: 10.2174/1381612825666190618123306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 06/11/2019] [Indexed: 11/22/2022]
Abstract
Nanoscience becomes one of the most cutting-edge research directions in recent years since it is gradually matured from basic to applied science. Nanoparticles (NPs) and nanomaterials (NMs) play important roles in various aspects of biomedicine science, and their influences on the environment have caused a whole range of uncertainties which require extensive attention. Due to the quantitative and dynamic information provided for human proteome, mass spectrometry (MS)-based quantitative proteomic technique has been a powerful tool for nanomedicine study. In this article, recent trends of progress and development in the nanomedicine of proteomics were discussed from quantification techniques and publicly available resources or tools. First, a variety of popular protein quantification techniques including labeling and label-free strategies applied to nanomedicine studies are overviewed and systematically discussed. Then, numerous protein profiling tools for data processing and postbiological statistical analysis and publicly available data repositories for providing enrichment MS raw data information sources are also discussed.
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Affiliation(s)
- Jing Tang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, China.,School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
| | - Yunxia Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, China
| | - Yi Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, China
| | - Yang Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, China.,School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
| | - Runyuan Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, China
| | - Ziyu Xiao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, China
| | - Yongchao Luo
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, China
| | - Xueying Guo
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, China
| | - Lin Tao
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicine of Zhejiang Province, School of Medicine, Hangzhou Normal University, Hangzhou 310036, China
| | - Yan Lou
- Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, Zhejiang University, 79 QingChun Road, Hangzhou, Zhejiang 310000, China
| | - Weiwei Xue
- School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 401331, China.,School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing 401331, China
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14
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Zhang B, Whiteaker JR, Hoofnagle AN, Baird GS, Rodland KD, Paulovich AG. Clinical potential of mass spectrometry-based proteogenomics. Nat Rev Clin Oncol 2019; 16:256-268. [PMID: 30487530 PMCID: PMC6448780 DOI: 10.1038/s41571-018-0135-7] [Citation(s) in RCA: 130] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Cancer genomics research aims to advance personalized oncology by finding and targeting specific genetic alterations associated with cancers. In genome-driven oncology, treatments are selected for individual patients on the basis of the findings of tumour genome sequencing. This personalized approach has prolonged the survival of subsets of patients with cancer. However, many patients do not respond to the predicted therapies based on the genomic profiles of their tumours. Furthermore, studies pairing genomic and proteomic analyses of samples from the same tumours have shown that the proteome contains novel information that cannot be discerned through genomic analysis alone. This observation has led to the concept of proteogenomics, in which both types of data are leveraged for a more complete view of tumour biology that might enable patients to be more successfully matched to effective treatments than they would using genomics alone. In this Perspective, we discuss the added value of proteogenomics over the current genome-driven approach to the clinical characterization of cancers and summarize current efforts to incorporate targeted proteomic measurements based on selected/multiple reaction monitoring (SRM/MRM) mass spectrometry into the clinical laboratory to facilitate clinical proteogenomics.
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Affiliation(s)
- Bing Zhang
- Department of Molecular and Human Genetics, Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Jeffrey R Whiteaker
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Andrew N Hoofnagle
- Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Geoffrey S Baird
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
- Department of Cell, Development and Cancer Biology, Oregon Health & Sciences University, Portland, OR, USA
| | - Amanda G Paulovich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Division of Medical Oncology, University of Washington School of Medicine, Seattle, WA, USA.
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15
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Gibbons BC, Fillmore TL, Gao Y, Moore RJ, Liu T, Nakayasu ES, Metz TO, Payne SH. Rapidly Assessing the Quality of Targeted Proteomics Experiments through Monitoring Stable-Isotope Labeled Standards. J Proteome Res 2018; 18:694-699. [PMID: 30525668 DOI: 10.1021/acs.jproteome.8b00688] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Targeted proteomics experiments based on selected reaction monitoring (SRM) have gained wide adoption in the use of clinical biomarkers, cellular modeling, and numerous other biological experiments due to their highly accurate and reproducible quantification. The quantitative accuracy in targeted proteomics experiments is reliant on the stable-isotope, heavy-labeled peptide standards that are spiked into a sample and used as a reference when calculating the abundance of endogenous peptides. Therefore, the quality of measurement for these standards is a critical factor in determining whether data acquisition was successful. With improved mass spectrometry (MS) instrumentation that enables the monitoring of hundreds of peptides in hundreds to thousands of samples, quality assessment is increasingly important and cannot be performed manually. We present Q4SRM, a software tool that rapidly checks the signal from all heavy-labeled peptides and flags those that fail quality-control metrics. Using four metrics, the tool detects problems with both individual SRM transitions and the collective group of transitions that monitor a single peptide. The program's speed and simplicity enable its use at the point of data acquisition and can be ideally run immediately upon the completion of a liquid chromatography-SRM-MS analysis.
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Affiliation(s)
- Bryson C Gibbons
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland Washington 99336 , United States
| | - Thomas L Fillmore
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland Washington 99336 , United States
| | - Yuqian Gao
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland Washington 99336 , United States
| | - Ronald J Moore
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland Washington 99336 , United States
| | - Tao Liu
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland Washington 99336 , United States
| | - Ernesto S Nakayasu
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland Washington 99336 , United States
| | - Thomas O Metz
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland Washington 99336 , United States
| | - Samuel H Payne
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland Washington 99336 , United States
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