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Richard VR, Gaither C, Popp R, Chaplygina D, Brzhozovskiy A, Kononikhin A, Mohammed Y, Zahedi RP, Nikolaev EN, Borchers CH. Early Prediction of COVID-19 Patient Survival by Targeted Plasma Multi-Omics and Machine Learning. Mol Cell Proteomics 2022; 21:100277. [PMID: 35931319 PMCID: PMC9345792 DOI: 10.1016/j.mcpro.2022.100277] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 07/05/2022] [Accepted: 07/27/2022] [Indexed: 01/18/2023] Open
Abstract
The recent surge of coronavirus disease 2019 (COVID-19) hospitalizations severely challenges healthcare systems around the globe and has increased the demand for reliable tests predictive of disease severity and mortality. Using multiplexed targeted mass spectrometry assays on a robust triple quadrupole MS setup which is available in many clinical laboratories, we determined the precise concentrations of hundreds of proteins and metabolites in plasma from hospitalized COVID-19 patients. We observed a clear distinction between COVID-19 patients and controls and, strikingly, a significant difference between survivors and nonsurvivors. With increasing length of hospitalization, the survivors' samples showed a trend toward normal concentrations, indicating a potential sensitive readout of treatment success. Building a machine learning multi-omic model that considers the concentrations of 10 proteins and five metabolites, we could predict patient survival with 92% accuracy (area under the receiver operating characteristic curve: 0.97) on the day of hospitalization. Hence, our standardized assays represent a unique opportunity for the early stratification of hospitalized COVID-19 patients.
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Key Words
- acd, acid citrate dextrose
- acn, acetonitrile
- auc, area under the receiver operating characteristic curve
- bqc19, biobanque quebecoise de la covid-19
- bsa, bovine serum albumin covid-19
- cptac, clinical proteomic tumor analysis consortium
- dtt, dithiothreitol
- fa, formic acid
- fdr, false discovery rate
- icu, intensive care unit
- lc/mrm-ms, liquid chromatography/multiple reaction monitoring mass spectrometry
- lc-ms, liquid chromatography-mass spectrometry
- lloq, lower limit of quantitation
- lysopc, lysophosphatidylcholine
- maldi, matrix-assisted laser desorption ionization
- meoh, methanol
- ms, mass spectrometry
- pbs, phosphatase buffered saline
- pcr, polymerase chain reaction
- pitc, phenylisothiocyanate
- qc, quality control
- rp-uhplc, reversed phase ultrahigh performance liquid chromatography
- sis, stable-isotope-labeled internal standard
- spe, solid-phase extraction
- svm, support vector machine
- trishcl, tris (hydroxymethyl) aminomethane hydrochloride
- uniprot, the universal protein resource
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Affiliation(s)
- Vincent R. Richard
- Segal Cancer Proteomics Centre, Lady Davis Institute for Medical Research, McGill University, Montreal, Quebec, Canada
| | | | | | - Daria Chaplygina
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Alexander Brzhozovskiy
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Alexey Kononikhin
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Yassene Mohammed
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands,Genome BC Proteomics Centre, University of Victoria, Victoria, Canada
| | - René P. Zahedi
- Segal Cancer Proteomics Centre, Lady Davis Institute for Medical Research, McGill University, Montreal, Quebec, Canada,Manitoba Centre for Proteomics & Systems Biology, John Buhler Research Centre, University of Manitoba, Winnipeg, Canada,Department of Internal Medicine, University of Manitoba, Winnipeg, Canada
| | - Evgeny N. Nikolaev
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Christoph H. Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute for Medical Research, McGill University, Montreal, Quebec, Canada,Gerald Bronfman Department of Oncology, Division of Experimental Medicine, Lady Davis Institute for Medical Research, McGill University, Montreal, Canada,Department of Pathology, McGill University, Montreal, Canada,For correspondence: Christoph H. Borchers
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Zeng H, Zhang X, Zhen Q, He Y, Wang H, Zhu Y, Sun Q, Ding M. Dual-Template Magnetic Molecularly Imprinted Polymer for Simultaneous Determination of Spot Urine Metanephrines and 3-Methoxytyramine for the Diagnosis of Pheochromocytomas and Paragangliomas. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27113520. [PMID: 35684457 PMCID: PMC9182035 DOI: 10.3390/molecules27113520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 05/27/2022] [Accepted: 05/28/2022] [Indexed: 11/16/2022]
Abstract
A novel dual-template magnetic molecularly imprinted polymer (MMIP) was synthesized to extract normetanephrine (NMN), metanephrine (MN) and 3-methoxytyramine (3-MT) from spot urine samples. As the adsorbent of dispersive solid-phase extraction (d-SPE), the MMIP was prepared using dopamine and MN as dual templates, methacrylic acid as the functional monomer, ethylene glycol dimethacrylate as the crosslinking reagent and magnetic nanoparticles as the magnetic core. NMN, MN, 3-MT and creatinine (Cr) in spot urine samples were selectively enriched by d-SPE and detected by HPLC-fluorescence detection/ultraviolet detection. The peak area (A) ratios of NMN, MN and 3-MT to Cr were used for the diagnosis of pheochromocytomas and paragangliomas (PPGLs). The results showed that the adsorption efficiencies of MMIP for target analytes were all higher than 89.0%, and the coefficient variation precisions of intra-assay and inter-assay for the analytes were within 4.9% and 6.3%, respectively. The recoveries of the analytes were from 93.2% to 112.8%. The MMIP was still functional within 14 days and could be reused at least seven times. The d-SPE and recommended solid-phase extraction (SPE) were both used to pretreat spot urine samples from 18 PPGLs patients and 22 healthy controls. The correlation coefficients of ANMN/ACr and AMN/ACr between d-SPE and SPE were both higher than 0.95. In addition, the areas under the receiver operator curves for spot urine ANMN/ACr, AMN/ACr and plasma free NMN and MN were 0.975, 0.773 and 0.990, 0.821, respectively, indicating the two methods had the similar performances. The d-SPE method took only 20 min, which was effective in clinical application.
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Affiliation(s)
- Hongyu Zeng
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China; (H.Z.); (X.Z.); (H.W.); (Y.Z.); (Q.S.)
| | - Xiaoqing Zhang
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China; (H.Z.); (X.Z.); (H.W.); (Y.Z.); (Q.S.)
| | - Qianna Zhen
- Department of Endocrinology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China; (Q.Z.); (Y.H.)
| | - Yifan He
- Department of Endocrinology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China; (Q.Z.); (Y.H.)
| | - Haoran Wang
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China; (H.Z.); (X.Z.); (H.W.); (Y.Z.); (Q.S.)
| | - Yang Zhu
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China; (H.Z.); (X.Z.); (H.W.); (Y.Z.); (Q.S.)
| | - Qi Sun
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China; (H.Z.); (X.Z.); (H.W.); (Y.Z.); (Q.S.)
| | - Min Ding
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, School of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China; (H.Z.); (X.Z.); (H.W.); (Y.Z.); (Q.S.)
- Correspondence:
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Song L, Cui R, Tian F, Liu Z. Structure engineering of lanthanide functionalized metal-organic frameworks: A versatile tool for the early diagnosis of pheochromocytomas and paragangliomas. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 264:120263. [PMID: 34454132 DOI: 10.1016/j.saa.2021.120263] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/08/2021] [Accepted: 08/03/2021] [Indexed: 06/13/2023]
Abstract
As a main extracellular metabolite of dopamine, 3-methoxytyramine (3-MT) is considered a potential biomarker of pheochromocytomas and paragangliomas. Therefore, the determination of 3-MT is of great significance in the early diagnosis of disease. However, it remains challenging for detecting 3-MT in consideration of sensitivity and accuracy. Here, a luminescent Eu3+ functionalized metal-organic frameworks (Eu3+@Al-MOF)with ultra-high chemical stability was constructed based on postsynthetic modification. Such a rational design greatly enhances the fluorescence signal of Eu3+@Al-MOF and it is endowed with excellent properties as a luminescent sensor to detect 3-MT in urine system. Intriguingly, the strong red emitting derived from antenna effect was significantly interdicted upon addition of 3-MT through the interaction between 3-MT and the ligand. The proposed sensing system exhibited many appealing analytical performances, such as excellent selectivity, high sensitivity and quick response. Remarkably, the developed paper-based sensor not only provides a portable and reliable strategy for direct detection of 3-MT but also expands the application of visual analysis tools. This work represents the first effort in designing a luminescent sensor to determine the metabolite biomarker 3-MT level and provides a new method for biomedical analysis.
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Affiliation(s)
- Lijun Song
- Inner Mongolia Key Laboratory of Chemistry and Physics of Rare Earth Materials, School of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot 010021, PR China
| | - Ruixue Cui
- Inner Mongolia Key Laboratory of Chemistry and Physics of Rare Earth Materials, School of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot 010021, PR China
| | - Fuli Tian
- Key Laboratory of Medicinal and Edible Plants Resources of Hainan Province, Hainan Vocational University of Science and Technology, Haikou 571126, PR China
| | - Zhiliang Liu
- Inner Mongolia Key Laboratory of Chemistry and Physics of Rare Earth Materials, School of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot 010021, PR China
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Smy L, Kushnir MM, Frank EL. A high sensitivity LC-MS/MS method for measurement of 3-methoxytyramine in plasma and associations between 3-methoxytyramine, metanephrines, and dopamine. J Mass Spectrom Adv Clin Lab 2021; 21:19-26. [PMID: 34820673 PMCID: PMC8601001 DOI: 10.1016/j.jmsacl.2021.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 08/02/2021] [Accepted: 08/02/2021] [Indexed: 11/27/2022] Open
Abstract
3-methoxytyramine (3MT) aids diagnosis of dopamine-producing tumors and metastases. A sensitive and specific LC-MS/MS method was developed to measure 3MT in plasma. 3MT was elevated in 46% of samples with elevated metanephrine and normetanephrine. 3MT concentrations correlated the strongest with normetanephrine concentrations.
Introduction Diagnosis of pheochromocytoma and paraganglioma (PPGL) is aided by the measurement of metanephrine (MN) and normetanephrine (NMN). Research suggests that 3-methoxytyramine (3MT), a dopamine (DA) metabolite, may serve as a biomarker of metastasis in patients with paraganglioma. Considering the very low endogenous plasma 3MT concentrations (<0.1 nM), highly sensitive and specific methods for 3MT are needed. Methods We developed a simple method for measurement of 3MT. Sample preparation was performed using solid phase micro-extraction with the eluates injected directly onto the LC-MS/MS. Data acquisition was performed in multiple reaction monitoring mode with an instrumental analysis time of 3 min per sample. We evaluated the method’s performance and analyzed samples from healthy individuals and pathological specimens. Results The limit of quantitation and upper limit of linearity were 0.03 nM and 20 nM, respectively. The intra-/inter-day imprecision for pooled plasma samples at concentrations of 0.04 nM, 0.2 nM, and 2 nM was 10.7%/18.3%, 4.5%/8.9%, and 3.1%/0.9%, respectively. Among samples with MN, NMN, or both MN and NMN above the reference intervals (RIs), 0%, 16% and 46%, respectively, showed 3MT greater than the proposed upper RI value of 0.1 nM; 12% of samples with DA above the RI had 3MT above 0.1 nM. Conclusions The developed method allowed accurate quantitation of 3MT in patient samples and would provide valuable information to clinicians diagnosing or monitoring patients with PPGL. High 3MT concentrations in patient samples with MN and NMN within the respective RIs may alert clinicians of the possibility of a DA-producing tumor.
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Key Words
- 3-Methoxytryamine
- 3MT, 3-methoxytyramine
- 3MT-d4, deuterated 3-methoxytyramine
- CE, collision energy
- CI, confidence interval
- COMT, catechol-O-methyltransferase
- CV, coefficient of variation
- CXP, collision cell exit potential
- DA, dopamine
- DBH, dopamine-β-hydroxylase
- DP, declustering potential
- Dopamine
- EDTA, ethylenediaminetetraacetic acid
- HCl, hydrochloride
- HPLC, high-performance liquid chromatography
- IQR, interquartile range
- IS, internal standard
- LC-MS/MS, liquid-chromatography tandem mass spectrometry
- LOQ, limit of quantification
- Liquid-chromatography tandem mass spectrometry
- MAO, monoamine oxidase
- MN, metanephrine
- MN-d3, deuterated metanephrine
- NMN, normetanephrine
- NMN-d3, deuterated normetanephrine
- PPGL, pheochromocytoma and paraganglioma
- Paraganglioma
- Pheochromocytoma
- Plasma
- RI, reference interval
- SD, standard deviation
- SDHx, succinate dehydrogenase genes
- SPE, solid phase extraction
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Affiliation(s)
- Laura Smy
- Department of Pathology, University of Utah Health School of Medicine, 500 Chipeta Way, Salt Lake City, UT 84108, USA
| | - Mark M Kushnir
- ARUP Institute for Clinical and Experimental Pathology, 500 Chipeta Way, Salt Lake City, UT 84108, USA
| | - Elizabeth L Frank
- Department of Pathology, University of Utah Health School of Medicine, 500 Chipeta Way, Salt Lake City, UT 84108, USA
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Gaspar VP, Ibrahim S, Zahedi RP, Borchers CH. Utility, promise, and limitations of liquid chromatography-mass spectrometry-based therapeutic drug monitoring in precision medicine. JOURNAL OF MASS SPECTROMETRY : JMS 2021; 56:e4788. [PMID: 34738286 PMCID: PMC8597589 DOI: 10.1002/jms.4788] [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: 08/03/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 05/03/2023]
Abstract
Therapeutic drug monitoring (TDM) is typically referred to as the measurement of the concentration of drugs in patient blood. Although in the past, TDM was restricted to drugs with a narrow therapeutic range in order to avoid drug toxicity, TDM has recently become a major tool for precision medicine being applied to many more drugs. Through compensating for interindividual differences in a drug's pharmacokinetics, improved dosing of individual patients based on TDM ensures maximum drug effectiveness while minimizing side effects. This is especially relevant for individuals that present a particularly high intervariability in pharmacokinetics, such as newborns, or for critically/severely ill patients. In this article, we will review the applications for and limitations of TDM, discuss for which patients TDM is most beneficial and why, examine which techniques are being used for TDM, and demonstrate how mass spectrometry is increasingly becoming a reliable and convenient alternative for the TDM of different classes of drugs. We will also highlight the advances, challenges, and limitations of the existing repertoire of TDM methods and discuss future opportunities for TDM-based precision medicine.
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Affiliation(s)
- Vanessa P. Gaspar
- Segal Cancer Proteomics CentreMcGill UniversityMontrealQuebecCanada
- Gerald Bronfman Department of OncologyMcGill UniversityMontrealQuebecCanada
| | - Sahar Ibrahim
- Segal Cancer Proteomics CentreMcGill UniversityMontrealQuebecCanada
- Division of Experimental MedicineMcGill UniversityMontrealQuebecCanada
- Clinical Pathology DepartmentMenoufia UniversityShibin el KomEgypt
| | - René P. Zahedi
- Segal Cancer Proteomics CentreMcGill UniversityMontrealQuebecCanada
- Center for Computational and Data‐Intensive Science and EngineeringSkolkovo Institute of Science and TechnologyMoscowRussia
| | - Christoph H. Borchers
- Segal Cancer Proteomics CentreMcGill UniversityMontrealQuebecCanada
- Gerald Bronfman Department of OncologyMcGill UniversityMontrealQuebecCanada
- Center for Computational and Data‐Intensive Science and EngineeringSkolkovo Institute of Science and TechnologyMoscowRussia
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