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El-Khoury V, Schritz A, Kim SY, Lesur A, Sertamo K, Bernardin F, Petritis K, Pirrotte P, Selinsky C, Whiteaker JR, Zhang H, Kennedy JJ, Lin C, Lee LW, Yan P, Tran NL, Inge LJ, Chalabi K, Decker G, Bjerkvig R, Paulovich AG, Berchem G, Kim YJ. Identification of a Blood-Based Protein Biomarker Panel for Lung Cancer Detection. Cancers (Basel) 2020; 12:cancers12061629. [PMID: 32575471 PMCID: PMC7352295 DOI: 10.3390/cancers12061629] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 06/09/2020] [Accepted: 06/13/2020] [Indexed: 12/24/2022] Open
Abstract
Lung cancer is the deadliest cancer worldwide, mainly due to its advanced stage at the time of diagnosis. A non-invasive method for its early detection remains mandatory to improve patients’ survival. Plasma levels of 351 proteins were quantified by Liquid Chromatography-Parallel Reaction Monitoring (LC-PRM)-based mass spectrometry in 128 lung cancer patients and 93 healthy donors. Bootstrap sampling and least absolute shrinkage and selection operator (LASSO) penalization were used to find the best protein combination for outcome prediction. The PanelomiX platform was used to select the optimal biomarker thresholds. The panel was validated in 48 patients and 49 healthy volunteers. A 6-protein panel clearly distinguished lung cancer from healthy individuals. The panel displayed excellent performance: area under the receiver operating characteristic curve (AUC) = 0.999, positive predictive value (PPV) = 0.992, negative predictive value (NPV) = 0.989, specificity = 0.989 and sensitivity = 0.992. The panel detected lung cancer independently of the disease stage. The 6-protein panel and other sub-combinations displayed excellent results in the validation dataset. In conclusion, we identified a blood-based 6-protein panel as a diagnostic tool in lung cancer. Used as a routine test for high- and average-risk individuals, it may complement currently adopted techniques in lung cancer screening.
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Affiliation(s)
- Victoria El-Khoury
- Department of Oncology, Luxembourg Institute of Health, 1 A-B Rue Thomas Edison, L-1445 Strassen, Luxembourg; (K.S.); (R.B.); (G.B.); (Y.J.K.)
- Correspondence: ; Tel.: +352-26970-932
| | - Anna Schritz
- Competence Center for Methodology and Statistics, Luxembourg Institute of Health, 1 A-B Rue Thomas Edison, L-1445 Strassen, Luxembourg;
| | - Sang-Yoon Kim
- Quantitative Biology Unit, Luxembourg Institute of Health, 1 A-B Rue Thomas Edison, L-1445 Strassen, Luxembourg; (S.-Y.K.); (A.L.); (F.B.)
| | - Antoine Lesur
- Quantitative Biology Unit, Luxembourg Institute of Health, 1 A-B Rue Thomas Edison, L-1445 Strassen, Luxembourg; (S.-Y.K.); (A.L.); (F.B.)
| | - Katriina Sertamo
- Department of Oncology, Luxembourg Institute of Health, 1 A-B Rue Thomas Edison, L-1445 Strassen, Luxembourg; (K.S.); (R.B.); (G.B.); (Y.J.K.)
| | - François Bernardin
- Quantitative Biology Unit, Luxembourg Institute of Health, 1 A-B Rue Thomas Edison, L-1445 Strassen, Luxembourg; (S.-Y.K.); (A.L.); (F.B.)
| | - Konstantinos Petritis
- Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, 445 N Fifth St., Phoenix, AZ 85004, USA; (K.P.); (P.P.); (C.S.)
| | - Patrick Pirrotte
- Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, 445 N Fifth St., Phoenix, AZ 85004, USA; (K.P.); (P.P.); (C.S.)
| | - Cheryl Selinsky
- Collaborative Center for Translational Mass Spectrometry, Translational Genomics Research Institute, 445 N Fifth St., Phoenix, AZ 85004, USA; (K.P.); (P.P.); (C.S.)
| | - Jeffrey R. Whiteaker
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109-1024, USA; (J.R.W.); (H.Z.); (J.J.K.); (C.L.); (L.W.L.); (P.Y.); (A.G.P.)
| | - Haizhen Zhang
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109-1024, USA; (J.R.W.); (H.Z.); (J.J.K.); (C.L.); (L.W.L.); (P.Y.); (A.G.P.)
| | - Jacob J. Kennedy
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109-1024, USA; (J.R.W.); (H.Z.); (J.J.K.); (C.L.); (L.W.L.); (P.Y.); (A.G.P.)
| | - Chenwei Lin
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109-1024, USA; (J.R.W.); (H.Z.); (J.J.K.); (C.L.); (L.W.L.); (P.Y.); (A.G.P.)
| | - Lik Wee Lee
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109-1024, USA; (J.R.W.); (H.Z.); (J.J.K.); (C.L.); (L.W.L.); (P.Y.); (A.G.P.)
| | - Ping Yan
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109-1024, USA; (J.R.W.); (H.Z.); (J.J.K.); (C.L.); (L.W.L.); (P.Y.); (A.G.P.)
| | - Nhan L. Tran
- Department of Cancer Biology, Mayo Clinic, 13400 E Shea Blvd, Scottsdale, AZ 85259, USA;
| | - Landon J. Inge
- Norton Thoracic Institute, St. Joseph’s Hospital and Medical Center, Phoenix, AZ 85013, USA;
| | - Khaled Chalabi
- Department of cardiac surgery, Institut national de chirurgie cardiaque et de cardiologie interventionnelle, 2A rue Nicolas-Ernest Barblé, L-1210 Luxembourg, Luxembourg;
| | - Georges Decker
- Zithaklinik, 46–48 rue d’Anvers, L-1130 Luxembourg, Luxembourg;
| | - Rolf Bjerkvig
- Department of Oncology, Luxembourg Institute of Health, 1 A-B Rue Thomas Edison, L-1445 Strassen, Luxembourg; (K.S.); (R.B.); (G.B.); (Y.J.K.)
- Department of Biomedicine, University of Bergen, Norway, Jonas Lies vei 91, N-5009 Bergen, Norway
| | - Amanda G. Paulovich
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109-1024, USA; (J.R.W.); (H.Z.); (J.J.K.); (C.L.); (L.W.L.); (P.Y.); (A.G.P.)
| | - Guy Berchem
- Department of Oncology, Luxembourg Institute of Health, 1 A-B Rue Thomas Edison, L-1445 Strassen, Luxembourg; (K.S.); (R.B.); (G.B.); (Y.J.K.)
- Centre Hospitalier de Luxembourg, 4 rue Nicolas-Ernest Barblé, L-1210 Luxembourg, Luxembourg
| | - Yeoun Jin Kim
- Department of Oncology, Luxembourg Institute of Health, 1 A-B Rue Thomas Edison, L-1445 Strassen, Luxembourg; (K.S.); (R.B.); (G.B.); (Y.J.K.)
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Kim YJ, Gallien S, El-Khoury V, Goswami P, Sertamo K, Schlesser M, Berchem G, Domon B. Quantification of SAA1 and SAA2 in lung cancer plasma using the isotype-specific PRM assays. Proteomics 2015; 15:3116-25. [PMID: 26177823 DOI: 10.1002/pmic.201400382] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 03/27/2015] [Accepted: 07/13/2015] [Indexed: 12/24/2022]
Abstract
The quantification of plasma proteins using the high resolution and accurate mass (HR/AM)-based parallel reaction monitoring (PRM) method provides an immediate benefit over the conventional SRM-based method in terms of selectivity. In this study, multiplexed PRM assays were developed to analyze isotypes of serum amyloid A (SAA) proteins in human plasma with a focus on SAA1 and SAA2. Elevated plasma levels of these proteins in patients diagnosed with lung cancer have been reported in previous studies. Since SAA1 and SAA2 are highly homologous, the available immunoassays tend to overestimate their concentrations due to cross-reactivity. On the other hand, when mass spectrometry (MS)-based assays are used, the presence of the several allelic variants may result in a problem of underestimation. In the present study, eight peptides that represent the target proteins at three different levels: isotype-specific (SAA1α, SAA 1β, SAA1γ, SAA2α, SAA2β), protein-specific (SAA1 or SAA2), and pan SAA (SAA1 and SAA2) were chosen to differentiate SAAs in lung cancer plasma samples using a panel of PRM assays. The measurement of specific isotypes, leveraging the analytical performance of PRM, allowed to quantify the allelic variants of both target proteins. The isotypes detected were corroborated with the genetic information obtained from the same samples. The combination of SAA2α and SAA2β assays representing the total SAA2 concentration demonstrated a superior analytical outcome than the previously used assay on the common peptide when applied to the detection of lung cancer.
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Affiliation(s)
- Yeoun Jin Kim
- Luxembourg Clinical Proteomics Center, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Sebastien Gallien
- Luxembourg Clinical Proteomics Center, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Victoria El-Khoury
- Laboratory of Experimental Hemato-Oncology, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Panchali Goswami
- Luxembourg Clinical Proteomics Center, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Katriina Sertamo
- Luxembourg Clinical Proteomics Center, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Marc Schlesser
- Service de Pneumologie, Centre Hospitalier du Luxembourg, Strassen, Luxembourg
| | - Guy Berchem
- Laboratory of Experimental Hemato-Oncology, Luxembourg Institute of Health, Strassen, Luxembourg.,Service d'Hémato-Cancérologie, Centre Hospitalier de Luxembourg, Strassen, Luxembourg
| | - Bruno Domon
- Luxembourg Clinical Proteomics Center, Luxembourg Institute of Health, Strassen, Luxembourg
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Kim YJ, Sertamo K, Pierrard MA, Mesmin C, Kim SY, Schlesser M, Berchem G, Domon B. Verification of the biomarker candidates for non-small-cell lung cancer using a targeted proteomics approach. J Proteome Res 2015; 14:1412-9. [PMID: 25597550 DOI: 10.1021/pr5010828] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Lung cancer, with its high metastatic potential and high mortality rate, is the worldwide leading cause of cancer-related deaths. High-throughput "omics"-based platforms have accelerated the discovery of biomarkers for lung cancer, and the resulting candidates are to be evaluated for their diagnostic potential as noninvasive biomarkers. The evaluation of the biomarker candidates involves the quantitative measurement of large numbers of proteins in bodily fluids using advanced mass spectrometric techniques. In this study, a robust pipeline based on targeted proteomics was developed for biomarker verification in plasma samples and applied to verifying lung cancer biomarker candidates. Highly multiplexed liquid chromatrography-selected reaction monitoring (LC-SRM) assays for 95 potential tumor markers for non-small-cell lung cancer (NSCLC) were generated to screen plasma samples obtained from 72, early to late stage, patients. A total of 17 proteins were verified as potent tumor markers detectable in plasma and, where available, verified by enzyme-linked immunosorbent assays (ELISAs). A novel plasma-based biomarker, zyxin, fulfilled the criteria for a potential early diagnostic marker for NSCLC.
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Affiliation(s)
- Yeoun Jin Kim
- Luxembourg Clinical Proteomics Center, Luxembourg Institute of Health , Strassen L-1445, Luxembourg
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