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Vlachová M, Pečinka L, Gregorová J, Moráň L, Růžičková T, Kovačovicová P, Almáši M, Pour L, Štork M, Hájek R, Jelínek T, Popková T, Večeřa M, Havel J, Vaňhara P, Ševčíková S. Liquid biopsy of peripheral blood using mass spectrometry detects primary extramedullary disease in multiple myeloma patients. Sci Rep 2024; 14:18777. [PMID: 39138296 PMCID: PMC11322162 DOI: 10.1038/s41598-024-69408-1] [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: 04/28/2024] [Accepted: 08/05/2024] [Indexed: 08/15/2024] Open
Abstract
Multiple myeloma (MM) is the second most prevalent hematological malignancy, characterized by infiltration of the bone marrow by malignant plasma cells. Extramedullary disease (EMD) represents a more aggressive condition involving the migration of a subclone of plasma cells to paraskeletal or extraskeletal sites. Liquid biopsies could improve and speed diagnosis, as they can better capture the disease heterogeneity while lowering patients' discomfort due to minimal invasiveness. Recent studies have confirmed alterations in the proteome across various malignancies, suggesting specific changes in protein classes. In this study, we show that MALDI-TOF mass spectrometry fingerprinting of peripheral blood can differentiate between MM and primary EMD patients. We constructed a predictive model using a supervised learning method, partial least squares-discriminant analysis (PLS-DA) and evaluated its generalization performance on a test dataset. The outcome of this analysis is a method that predicts specifically primary EMD with high sensitivity (86.4%), accuracy (78.4%), and specificity (72.4%). Given the simplicity of this approach and its minimally invasive character, this method provides rapid identification of primary EMD and could prove helpful in clinical practice.
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Affiliation(s)
- Monika Vlachová
- Babak Myeloma Group, Department of Pathophysiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Lukáš Pečinka
- Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Jana Gregorová
- Babak Myeloma Group, Department of Pathophysiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Lukáš Moráň
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Tereza Růžičková
- Babak Myeloma Group, Department of Pathophysiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Petra Kovačovicová
- International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czech Republic
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Martina Almáši
- Department of Clinical Hematology, University Hospital Brno, Brno, Czech Republic
| | - Luděk Pour
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno, Brno, Czech Republic
| | - Martin Štork
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno, Brno, Czech Republic
| | - Roman Hájek
- Department of Hematooncology, University Hospital Ostrava, Ostrava, Czech Republic
- Department of Hematooncology, Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
| | - Tomáš Jelínek
- Department of Hematooncology, University Hospital Ostrava, Ostrava, Czech Republic
- Department of Hematooncology, Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
| | - Tereza Popková
- Department of Hematooncology, University Hospital Ostrava, Ostrava, Czech Republic
- Department of Hematooncology, Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
| | - Marek Večeřa
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Josef Havel
- Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Petr Vaňhara
- Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Sabina Ševčíková
- Babak Myeloma Group, Department of Pathophysiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.
- Department of Clinical Hematology, University Hospital Brno, Brno, Czech Republic.
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Pečinka L, Vlachová M, Moráň L, Gregorová J, Porokh V, Kovačovicová P, Almáši M, Pour L, Štork M, Havel J, Ševčíková S, Vaňhara P. Improved Screening of Monoclonal Gammopathy Patients by MALDI-TOF Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2646-2653. [PMID: 37994781 DOI: 10.1021/jasms.3c00166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
Monoclonal gammopathies are a group of blood diseases characterized by presence of abnormal immunoglobulins in peripheral blood and/or urine of patients. Multiple myeloma and plasma cell leukemia are monoclonal gammopathies with unclear etiology, caused by malignant transformation of bone marrow plasma cells. Mass spectrometry with matrix-assisted laser desorption/ionization and time-of-flight detection is commonly used for investigation of the peptidome and small proteome of blood plasma with high accuracy, robustness, and cost-effectivity. In addition, mass spectrometry coupled with advanced statistics can be used for molecular profiling, classification, and diagnosis of liquid biopsies and tissue specimens in various malignancies. Despite the fact there have been fully optimized protocols for mass spectrometry of normal blood plasma available for decades, in monoclonal gammopathy patients, the massive alterations of biophysical and biochemical parameters of peripheral blood plasma often limit the mass spectrometry measurements. In this paper, we present a new two-step extraction protocol and demonstrated the enhanced resolution and intensity (>50×) of mass spectra obtained from extracts of peripheral blood plasma from monoclonal gammopathy patients. When coupled with advanced statistics and machine learning, the mass spectra profiles enabled the direct identification, classification, and discrimination of multiple myeloma and plasma cell leukemia patients with high accuracy and precision. A model based on PLS-DA achieved the best performance with 71.5% accuracy (95% confidence interval, CI = 57.1-83.3%) when the 10× repeated 5-fold CV was performed. In summary, the two-step extraction protocol improved the analysis of monoclonal gammopathy peripheral blood plasma samples by mass spectrometry and provided a tool for addressing the complex molecular etiology of monoclonal gammopathies.
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Affiliation(s)
- Lukáš Pečinka
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno, Pekařská 53, 656 91 Brno, Czech Republic
| | - Monika Vlachová
- Babak Myeloma Group, Department of Pathophysiology, Faculty of Medicine, Masaryk University, Kamenice 3, 625 00 Brno, Czech Republic
| | - Lukáš Moráň
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Kamenice 3, 625 00 Brno, Czech Republic
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, Žlutý kopec 7, 602 00 Brno, Czech Republic
| | - Jana Gregorová
- Babak Myeloma Group, Department of Pathophysiology, Faculty of Medicine, Masaryk University, Kamenice 3, 625 00 Brno, Czech Republic
| | - Volodymyr Porokh
- International Clinical Research Center, St. Anne's University Hospital Brno, Pekařská 53, 656 91 Brno, Czech Republic
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Kamenice 3, 625 00 Brno, Czech Republic
| | - Petra Kovačovicová
- International Clinical Research Center, St. Anne's University Hospital Brno, Pekařská 53, 656 91 Brno, Czech Republic
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Kamenice 3, 625 00 Brno, Czech Republic
| | - Martina Almáši
- Department of Clinical Hematology, University Hospital Brno, Jihlavská 20, 625 00 Brno, Czech Republic
| | - Luděk Pour
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno, Jihlavská 20, 625 00 Brno, Czech Republic
| | - Martin Štork
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno, Jihlavská 20, 625 00 Brno, Czech Republic
| | - Josef Havel
- Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital Brno, Pekařská 53, 656 91 Brno, Czech Republic
| | - Sabina Ševčíková
- Babak Myeloma Group, Department of Pathophysiology, Faculty of Medicine, Masaryk University, Kamenice 3, 625 00 Brno, Czech Republic
- Department of Clinical Hematology, University Hospital Brno, Jihlavská 20, 625 00 Brno, Czech Republic
| | - Petr Vaňhara
- International Clinical Research Center, St. Anne's University Hospital Brno, Pekařská 53, 656 91 Brno, Czech Republic
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Kamenice 3, 625 00 Brno, Czech Republic
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Liquid biopsy: an evolving paradigm for the biological characterisation of plasma cell disorders. Leukemia 2021; 35:2771-2783. [PMID: 34262132 DOI: 10.1038/s41375-021-01339-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 05/14/2021] [Accepted: 06/25/2021] [Indexed: 02/06/2023]
Abstract
Liquid biopsies-a source of circulating cell-free nucleic acids, proteins and extracellular vesicles-are currently being explored for the quantitative and qualitative characterisation of the tumour genome and as a mode of non-invasive therapeutic monitoring in cancer. Emerging data suggest that liquid biopsies might offer a potentially simple, non-invasive, repeatable strategy for diagnosis, prognostication and therapeutic decision making in a genetically heterogeneous disease like multiple myeloma (MM), with particular applicability in subsets of patients where conventional markers of disease burden may be less informative. In this review, we describe the emerging utility of the evaluation of circulating tumour DNA, extracellular RNA, cell-free proteins and metabolites and extracellular vesicles in MM.
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Gomila RM, Martorell G, Fraile-Ribot PA, Doménech-Sánchez A, Albertí M, Oliver A, García-Gasalla M, Albertí S. Use of Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry Analysis of Serum Peptidome to Classify and Predict Coronavirus Disease 2019 Severity. Open Forum Infect Dis 2021; 8:ofab222. [PMID: 34109258 PMCID: PMC8135799 DOI: 10.1093/ofid/ofab222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 04/27/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Classification and early detection of severe coronavirus disease 2019 (COVID-19) patients is required to establish an effective treatment. We tested the utility of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) to classify and predict the severity of COVID-19. METHODS We used MALDI-TOF MS to analyze the serum peptidome from 72 patients with COVID-19 (training cohort), clinically classified as mild (28), severe (23), and critical (21), and 20 healthy controls. The resulting matrix of peak intensities was used for Machine Learning (ML) approaches to classify and predict COVID-19 severity of 22 independent patients (validation cohort). Finally, we analyzed all sera by liquid chromatography mass spectrometry (LC-MS/MS) to identify the most relevant proteins associated with disease severity. RESULTS We found a clear variability of the serum peptidome profile depending on COVID-19 severity. Forty-two peaks exhibited a log fold change ≥1 and 17 were significantly different and at least 4-fold more intense in the set of critical patients than in the mild ones. The ML approach classified clinical stable patients according to their severity with 100% accuracy and correctly predicted the evolution of the nonstable patients in all cases. The LC-MS/MS identified 5 proteins that were significantly upregulated in the critical patients. They included the serum amyloid protein A2, which probably yielded the most intense peak detected by MALDI-TOF MS. CONCLUSIONS We demonstrate the potential of the MALDI-TOF MS as a bench to bedside technology to aid clinicians in their decision making regarding patients with COVID-19.
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Affiliation(s)
- Rosa M Gomila
- Servicios Científico-Técnicos, Universidad de las Islas Baleares, Palma de Mallorca, Spain
| | - Gabriel Martorell
- Servicios Científico-Técnicos, Universidad de las Islas Baleares, Palma de Mallorca, Spain
| | - Pablo A Fraile-Ribot
- Servicio de Microbiología, Hospital Universitario Son Espases, Palma de Mallorca, Spain
- Instituto de Investigación Sanitaria de las Islas Baleares (IDISBA), Palma de Mallorca, Spain
| | - Antonio Doménech-Sánchez
- Instituto de Investigación Sanitaria de las Islas Baleares (IDISBA), Palma de Mallorca, Spain
- IUNICS, Universidad de las Islas Baleares, Palma de Mallorca, Spain
| | - Miguel Albertí
- Escuela Politécnica Superior, Universidad de las Islas Baleares, Palma de Mallorca, Spain
| | - Antonio Oliver
- Servicio de Microbiología, Hospital Universitario Son Espases, Palma de Mallorca, Spain
- Instituto de Investigación Sanitaria de las Islas Baleares (IDISBA), Palma de Mallorca, Spain
| | - Mercedes García-Gasalla
- Instituto de Investigación Sanitaria de las Islas Baleares (IDISBA), Palma de Mallorca, Spain
- Servicio de Medicina Interna. Hospital Universitario Son Espases, Palma de Mallorca, Spain
| | - Sebastián Albertí
- Servicios Científico-Técnicos, Universidad de las Islas Baleares, Palma de Mallorca, Spain
- Instituto de Investigación Sanitaria de las Islas Baleares (IDISBA), Palma de Mallorca, Spain
- IUNICS, Universidad de las Islas Baleares, Palma de Mallorca, Spain
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Challenges and Opportunities in Clinical Applications of Blood-Based Proteomics in Cancer. Cancers (Basel) 2020; 12:cancers12092428. [PMID: 32867043 PMCID: PMC7564506 DOI: 10.3390/cancers12092428] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/23/2020] [Accepted: 08/25/2020] [Indexed: 12/12/2022] Open
Abstract
Simple Summary The traditional approach in identifying cancer related protein biomarkers has focused on evaluation of a single peptide/protein in tissue or circulation. At best, this approach has had limited success for clinical applications, since multiple pathological tumor pathways may be involved during initiation or progression of cancer which diminishes the significance of a single candidate protein/peptide. Emerging sensitive proteomic based technologies like liquid chromatography mass spectrometry (LC-MS)-based quantitative proteomics can provide a platform for evaluating serial serum or plasma samples to interrogate secreted products of tumor–host interactions, thereby revealing a more “complete” repertoire of biological variables encompassing heterogeneous tumor biology. However, several challenges need to be met for successful application of serum/plasma based proteomics. These include uniform pre-analyte processing of specimens, sensitive and specific proteomic analytical platforms and adequate attention to study design during discovery phase followed by validation of discovery-level signatures for prognostic, predictive, and diagnostic cancer biomarker applications. Abstract Blood is a readily accessible biofluid containing a plethora of important proteins, nucleic acids, and metabolites that can be used as clinical diagnostic tools in diseases, including cancer. Like the on-going efforts for cancer biomarker discovery using the liquid biopsy detection of circulating cell-free and cell-based tumor nucleic acids, the circulatory proteome has been underexplored for clinical cancer biomarker applications. A comprehensive proteome analysis of human serum/plasma with high-quality data and compelling interpretation can potentially provide opportunities for understanding disease mechanisms, although several challenges will have to be met. Serum/plasma proteome biomarkers are present in very low abundance, and there is high complexity involved due to the heterogeneity of cancers, for which there is a compelling need to develop sensitive and specific proteomic technologies and analytical platforms. To date, liquid chromatography mass spectrometry (LC-MS)-based quantitative proteomics has been a dominant analytical workflow to discover new potential cancer biomarkers in serum/plasma. This review will summarize the opportunities of serum proteomics for clinical applications; the challenges in the discovery of novel biomarkers in serum/plasma; and current proteomic strategies in cancer research for the application of serum/plasma proteomics for clinical prognostic, predictive, and diagnostic applications, as well as for monitoring minimal residual disease after treatments. We will highlight some of the recent advances in MS-based proteomics technologies with appropriate sample collection, processing uniformity, study design, and data analysis, focusing on how these integrated workflows can identify novel potential cancer biomarkers for clinical applications.
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Prediction of malaria transmission drivers in Anopheles mosquitoes using artificial intelligence coupled to MALDI-TOF mass spectrometry. Sci Rep 2020; 10:11379. [PMID: 32647135 PMCID: PMC7347643 DOI: 10.1038/s41598-020-68272-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 06/16/2020] [Indexed: 11/21/2022] Open
Abstract
Vector control programmes are a strategic priority in the fight against malaria. However, vector control interventions require rigorous monitoring. Entomological tools for characterizing malaria transmission drivers are limited and are difficult to establish in the field. To predict Anopheles drivers of malaria transmission, such as mosquito age, blood feeding and Plasmodium infection, we evaluated artificial neural networks (ANNs) coupled to matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) and analysed the impact on the proteome of laboratory-reared Anopheles stephensi mosquitoes. ANNs were sensitive to Anopheles proteome changes and specifically recognized spectral patterns associated with mosquito age (0–10 days, 11–20 days and 21–28 days), blood feeding and P. berghei infection, with best prediction accuracies of 73%, 89% and 78%, respectively. This study illustrates that MALDI-TOF MS coupled to ANNs can be used to predict entomological drivers of malaria transmission, providing potential new tools for vector control. Future studies must assess the field validity of this new approach in wild-caught adult Anopheles. A similar approach could be envisaged for the identification of blood meal source and the detection of insecticide resistance in Anopheles and to other arthropods and pathogens.
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