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Yoo EJ, Kim JS, Stransky S, Spivack S, Sidoli S. Advances in proteomics methods for the analysis of exhaled breath condensate. MASS SPECTROMETRY REVIEWS 2024; 43:713-722. [PMID: 38149478 DOI: 10.1002/mas.21871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 12/28/2023]
Abstract
The analysis of exhaled breath condensate (EBC) demonstrates a promising avenue of minimally invasive biopsies for diagnostics. EBC is obtained by cooling exhaled air and collecting the condensation to be utilized for downstream analysis using various analytical methods. The aqueous phase of breath contains a large variety of miscible small compounds including polar electrolytes, amino acids, cytokines, chemokines, peptides, small proteins, metabolites, nucleic acids, and lipids/eicosanoids-however, these analytes are typically present at minuscule levels in EBC, posing a considerable technical challenge. Along with recent improvements in devices for breath collection, the sensitivity and resolution of liquid chromatography coupled to online mass spectrometry-based proteomics has attained subfemtomole sensitivity, vastly enhancing the quality of EBC sample analysis. As a result, proteomics analysis of EBC has been expanding the field of breath biomarker research. We present an au courant overview of the achievements in proteomics of EBC, the advancement of EBC collection devices, and the current and future applications for EBC biomarker analysis.
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Affiliation(s)
- Edwin J Yoo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Medicine, Division of Cardiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Julie S Kim
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Stephanie Stransky
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Simon Spivack
- Department of Medicine, Department of Epidemiology & Population Health, Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA
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Gade IL, Riddersholm SJ, Stilling-Vinther T, Brøndum RF, Bennike TB, Honoré B. A clinical proteomics study of exhaled breath condensate and biomarkers for pulmonary embolism. J Breath Res 2023; 18:016007. [PMID: 37939397 DOI: 10.1088/1752-7163/ad0aaa] [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: 06/23/2023] [Accepted: 11/07/2023] [Indexed: 11/10/2023]
Abstract
Pulmonary embolism (PE) can be a diagnostic challenge. Current diagnostic markers for PE are unspecific and new diagnostic tools are needed. The air we exhale is a possible new source for biomarkers which can be tapped into by analysing the exhaled breath condensate (EBC). We analysed the EBC from patients with PE and controls to investigate if the EBC is a useful source for new diagnostic biomarkers of PE. We collected and analysed EBC samples from patients with suspected PE and controls matched on age and sex. Patients in whom PE was ruled out after diagnostic work-up were included in the control group to increase the sensitivity and generalizability of the identified markers. EBC samples were collected using an RTube™. The protein composition of the EBCs were analysed using data dependent label-free quantitative nano liquid chromatography-tandem mass spectrometry. EBC samples from 28 patients with confirmed PE, and 49 controls were analysed. A total of 928 EBC proteins were identified in the 77 EBC samples. As expected, a low protein concentration was determined which resulted in many proteins with unmeasurable levels in several samples. The levels of HSPA5, PEBP1 and SFTPA2 were higher and levels of POF1B, EPPK1, PSMA4, ALDOA, and CFL1 were lower in PE compared with controls. In conclusion, the human EBC contained a variety of endogenous proteins and may be a source for new diagnostic markers of PE and other diseases.
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Affiliation(s)
- Inger Lise Gade
- Department of Hematology and Clinical Cancer Research Center, Aalborg University Hospital, 9000 Aalborg, Denmark
| | | | | | - Rasmus Froberg Brøndum
- Center for Clinical Data Science, Aalborg University and Aalborg University Hospital, 9260 Gistrup, Denmark
| | - Tue Bjerg Bennike
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Bent Honoré
- Department of Clinical Medicine, Aalborg University, 9000 Aalborg, Denmark
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
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Gade IL, Schultz JG, Brøndum RF, Kjærgaard B, Nielsen-Kudsk JE, Andersen A, Kristensen SR, Honoré B. Putative Biomarkers for Acute Pulmonary Embolism in Exhaled Breath Condensate. J Clin Med 2021; 10:5165. [PMID: 34768685 PMCID: PMC8584843 DOI: 10.3390/jcm10215165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/27/2021] [Accepted: 11/03/2021] [Indexed: 12/12/2022] Open
Abstract
Current diagnostic markers for pulmonary embolism (PE) are unspecific. We investigated the proteome of the exhaled breath condensate (EBC) in a porcine model of acute PE in order to identify putative diagnostic markers for PE. EBC was collected at baseline and after the induction of autologous intermediate-risk PE in 14 pigs, plus four negative control pigs. The protein profiles of the EBC were analyzed using label-free quantitative nano liquid chromatography-tandem mass spectrometry. A total of 897 proteins were identified in the EBCs from the pigs. Alterations were found in the levels of 145 different proteins after PE compared with the baseline and negative controls: albumin was among the most upregulated proteins, with 14-fold higher levels 2.5 h after PE (p-value: 0.02). The levels of 49 other proteins were between 1.3- and 17.1-fold higher after PE. The levels of 95 proteins were lower after PE. Neutrophil gelatinase-associated lipocalin (fold change 0.3, p-value < 0.01) was among the most reduced proteins 2.5 h after PE. A prediction model based on penalized regression identified five proteins including albumin and neutrophil gelatinase-associated lipocalin. The model was capable of discriminating baseline samples from EBC samples collected 2.5 h after PE correctly in 22 out of 27 samples. In conclusion, the EBC from pigs with acute PE contained several putative diagnostic markers of PE.
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Affiliation(s)
- Inger Lise Gade
- Department of Hematology and Clinical Cancer Research Center, Aalborg University Hospital, 9000 Aalborg, Denmark;
- Department of Clinical Medicine, Aalborg University, 9000 Aalborg, Denmark; (S.R.K.); (B.H.)
- Department of Clinical Biochemistry, Aalborg University Hospital, 9000 Aalborg, Denmark
| | - Jacob Gammelgaard Schultz
- Department of Cardiology, Aarhus University Hospital, 8200 Aarhus, Denmark; (J.G.S.); (J.E.N.-K.); (A.A.)
- Department of Clinical Medicine, Faculty of Health, Aarhus University, 8200 Aarhus, Denmark
| | - Rasmus Froberg Brøndum
- Department of Hematology and Clinical Cancer Research Center, Aalborg University Hospital, 9000 Aalborg, Denmark;
- Department of Clinical Medicine, Aalborg University, 9000 Aalborg, Denmark; (S.R.K.); (B.H.)
| | - Benedict Kjærgaard
- Department of Cardiothoracic Surgery, Aalborg University Hospital, 9000 Aalborg, Denmark;
| | - Jens Erik Nielsen-Kudsk
- Department of Cardiology, Aarhus University Hospital, 8200 Aarhus, Denmark; (J.G.S.); (J.E.N.-K.); (A.A.)
- Department of Clinical Medicine, Faculty of Health, Aarhus University, 8200 Aarhus, Denmark
| | - Asger Andersen
- Department of Cardiology, Aarhus University Hospital, 8200 Aarhus, Denmark; (J.G.S.); (J.E.N.-K.); (A.A.)
- Department of Clinical Medicine, Faculty of Health, Aarhus University, 8200 Aarhus, Denmark
| | - Søren Risom Kristensen
- Department of Clinical Medicine, Aalborg University, 9000 Aalborg, Denmark; (S.R.K.); (B.H.)
- Department of Clinical Biochemistry, Aalborg University Hospital, 9000 Aalborg, Denmark
| | - Bent Honoré
- Department of Clinical Medicine, Aalborg University, 9000 Aalborg, Denmark; (S.R.K.); (B.H.)
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
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Shao D, Huang L, Wang Y, Cui X, Li Y, Wang Y, Ma Q, Du W, Cui J. HBFP: a new repository for human body fluid proteome. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2021:6395039. [PMID: 34642750 PMCID: PMC8516408 DOI: 10.1093/database/baab065] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 09/23/2021] [Accepted: 09/28/2021] [Indexed: 12/15/2022]
Abstract
Body fluid proteome has been intensively studied as a primary source for disease
biomarker discovery. Using advanced proteomics technologies, early research
success has resulted in increasingly accumulated proteins detected in different
body fluids, among which many are promising biomarkers. However, despite a
handful of small-scale and specific data resources, current research is clearly
lacking effort compiling published body fluid proteins into a centralized and
sustainable repository that can provide users with systematic analytic tools. In
this study, we developed a new database of human body fluid proteome (HBFP) that
focuses on experimentally validated proteome in 17 types of human body fluids.
The current database archives 11 827 unique proteins reported by 164
scientific publications, with a maximal false discovery rate of 0.01 on both the
peptide and protein levels since 2001, and enables users to query, analyze and
download protein entries with respect to each body fluid. Three unique features
of this new system include the following: (i) the protein annotation page
includes detailed abundance information based on relative qualitative measures
of peptides reported in the original references, (ii) a new score is calculated
on each reported protein to indicate the discovery confidence and (iii) HBFP
catalogs 7354 proteins with at least two non-nested uniquely mapping peptides of
nine amino acids according to the Human Proteome Project Data Interpretation
Guidelines, while the remaining 4473 proteins have more than two unique peptides
without given sequence information. As an important resource for human protein
secretome, we anticipate that this new HBFP database can be a powerful tool that
facilitates research in clinical proteomics and biomarker discovery. Database URL:https://bmbl.bmi.osumc.edu/HBFP/
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Affiliation(s)
- Dan Shao
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, 122E Avery Hall, 1144 T St., Lincoln, NE 68588, USA.,Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, 2699 Qianjin Street, Changchun 130012, China.,Department of Computer Science and Technology, Changchun University, 6543 Weixing Road, Changchun 130022, China
| | - Lan Huang
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Yan Wang
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Xueteng Cui
- Department of Computer Science and Technology, Changchun University, 6543 Weixing Road, Changchun 130022, China
| | - Yufei Li
- Department of Computer Science and Technology, Changchun University, 6543 Weixing Road, Changchun 130022, China
| | - Yao Wang
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Qin Ma
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, 310G Lincoln tower, 1800 cannon drive, Columbus, OH 43210, USA
| | - Wei Du
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Juan Cui
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, 122E Avery Hall, 1144 T St., Lincoln, NE 68588, USA
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