1
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Girel S, Meister I, Glauser G, Rudaz S. Hyphenation of microflow chromatography with electrospray ionization mass spectrometry for bioanalytical applications focusing on low molecular weight compounds: A tutorial review. MASS SPECTROMETRY REVIEWS 2024. [PMID: 38952056 DOI: 10.1002/mas.21898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 06/10/2024] [Accepted: 06/20/2024] [Indexed: 07/03/2024]
Abstract
Benefits of miniaturized chromatography with various detection modes, such as increased sensitivity, chromatographic efficiency, and speed, were recognized nearly 50 years ago. Over the past two decades, this approach has experienced rapid growth, driven by the emergence of mass spectrometry applications serving -omics sciences and the need for analyzing minute volumes of precious samples with ever higher sensitivity. While nanoscale liquid chromatography (flow rates <1 μL/min) has gained widespread recognition in proteomics, the adoption of microscale setups (flow rates ranging from 1 to 100 μL/min) for low molecular weight compound applications, including metabolomics, has been surprisingly slow, despite the inherent advantages of the approach. Highly heterogeneous matrices and chemical structures accompanied by a relative lack of options for both selective sample preparation and user-friendly equipment are usually reported as major hindrances. To facilitate the wider implementation of microscale analyses, we present here a comprehensive tutorial encompassing important theoretical and practical considerations. We provide fundamental principles in micro-chromatography and guide the reader through the main elements of a microflow workflow, from LC pumps to ionization devices. Finally, based on both our literature overview and experience, illustrated by some in-house data, we highlight the critical importance of the ionization source design and its careful optimization to achieve significant sensitivity improvement.
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Affiliation(s)
- Sergey Girel
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Isabel Meister
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- Swiss Center of Applied Human Toxicology (SCAHT), Basel, Switzerland
| | - Gaetan Glauser
- Neuchâtel Platform of Analytical Chemistry, University of Neuchâtel, Neuchâtel, Switzerland
| | - Serge Rudaz
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- Swiss Center of Applied Human Toxicology (SCAHT), Basel, Switzerland
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2
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Lin W, Ji J, Su KJ, Qiu C, Tian Q, Zhao LJ, Luo Z, Wu C, Shen H, Deng H. omicsMIC: a comprehensive benchmarking platform for robust comparison of imputation methods in mass spectrometry-based omics data. NAR Genom Bioinform 2024; 6:lqae071. [PMID: 38881578 PMCID: PMC11177553 DOI: 10.1093/nargab/lqae071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 04/25/2024] [Accepted: 05/30/2024] [Indexed: 06/18/2024] Open
Abstract
Mass spectrometry is a powerful and widely used tool for generating proteomics, lipidomics and metabolomics profiles, which is pivotal for elucidating biological processes and identifying biomarkers. However, missing values in mass spectrometry-based omics data may pose a critical challenge for the comprehensive identification of biomarkers and elucidation of the biological processes underlying human complex disorders. To alleviate this issue, various imputation methods for mass spectrometry-based omics data have been developed. However, a comprehensive comparison of these imputation methods is still lacking, and researchers are frequently confronted with a multitude of options without a clear rationale for method selection. To address this pressing need, we developed omicsMIC (mass spectrometry-based omics with Missing values Imputation methods Comparison platform), an interactive platform that provides researchers with a versatile framework to evaluate the performance of 28 diverse imputation methods. omicsMIC offers a nuanced perspective, acknowledging the inherent heterogeneity in biological data and the unique attributes of each dataset. Our platform empowers researchers to make data-driven decisions in imputation method selection based on real-time visualizations of the outcomes associated with different imputation strategies. The comprehensive benchmarking and versatility of omicsMIC make it a valuable tool for the scientific community engaged in mass spectrometry-based omics research. omicsMIC is freely available at https://github.com/WQLin8/omicsMIC.
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Affiliation(s)
- Weiqiang Lin
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Jiadong Ji
- Institute for Financial Studies, Shandong University, Jinan, Shandong 250100, China
| | - Kuan-Jui Su
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Chuan Qiu
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Qing Tian
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Lan-Juan Zhao
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Zhe Luo
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Chong Wu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77230, USA
| | - Hui Shen
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Hongwen Deng
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA
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3
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Lin W, Ji J, Su KJ, Qiu C, Tian Q, Zhao LJ, Luo Z, Shen H, Wu C, Deng H. omicsMIC: a Comprehensive Benchmarking Platform for Robust Comparison of Imputation Methods in Mass Spectrometry-based Omics Data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.12.557189. [PMID: 37745599 PMCID: PMC10515867 DOI: 10.1101/2023.09.12.557189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Mass spectrometry is a powerful and widely used tool for generating proteomics, lipidomics, and metabolomics profiles, which is pivotal for elucidating biological processes and identifying biomarkers. However, missing values in spectrometry-based omics data may pose a critical challenge for the comprehensive identification of biomarkers and elucidation of the biological processes underlying human complex disorders. To alleviate this issue, various imputation methods for mass spectrometry-based omics data have been developed. However, a comprehensive and systematic comparison of these imputation methods is still lacking, and researchers are frequently confronted with a multitude of options without a clear rationale for method selection. To address this pressing need, we developed omicsMIC (mass spectrometry-based omics with Missing values Imputation methods Comparison platform), an interactive platform that provides researchers with a versatile framework to simulate and evaluate the performance of 28 diverse imputation methods. omicsMIC offers a nuanced perspective, acknowledging the inherent heterogeneity in biological data and the unique attributes of each dataset. Our platform empowers researchers to make data-driven decisions in imputation method selection based on real-time visualizations of the outcomes associated with different imputation strategies. The comprehensive benchmarking and versatility of omicsMIC make it a valuable tool for the scientific community engaged in mass spectrometry-based omics research. OmicsMIC is freely available at https://github.com/WQLin8/omicsMIC.
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Affiliation(s)
- Weiqiang Lin
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Jiadong Ji
- Institute for Financial Studies, Shandong University, Jinan 250100, China
| | - Kuan-Jui Su
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Chuan Qiu
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Qing Tian
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Lan-Juan Zhao
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Zhe Luo
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Hui Shen
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Chong Wu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hongwen Deng
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA
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4
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Hsieh YC, Lin CY, Lin HY, Kuo CT, Yin SY, Hsu YH, Yeh HF, Wang J, Wan D. Controllable-Swelling Microneedle-Assisted Ultrasensitive Paper Sensing Platforms for Personal Health Monitoring. Adv Healthc Mater 2023; 12:e2300321. [PMID: 37037493 DOI: 10.1002/adhm.202300321] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/07/2023] [Indexed: 04/12/2023]
Abstract
Microneedle (MN) patches, which allow the extraction of skin interstitial fluid (ISF) without a pain sensation, are powerful tools for minimally invasive biofluid sampling. Herein, an MN-assisted paper-based sensing platform that enables rapid and painless biofluid analysis with ultrasensitive molecular recognition capacity is developed. First, a controllable-swelling MN patch is constructed through the engineering of a poly(ethylene glycol) diacrylate/methacrylated hyaluronic acid hydrogel; it combines rapid, sufficient extraction of ISF with excellent structural integrity. Notably, the analyte molecules in the needles can be recovered into a moist cellulose paper through spontaneous diffusion. More importantly, the paper can be functionalized with enzymatic colorimetric reagents or a plasmonic array, enabling a desired detection capacity-for example, the use of paper-based surface-enhanced Raman spectroscopy sensors leads to label-free, trace detection (sub-ppb level) of a diverse set of molecules (cefazolin, nicotine, paraquat, methylene blue). Finally, nicotine is selected as a model drug to evaluate the painless monitoring of three human volunteers. The changes in the nicotine levels can be tracked, with the levels varying significantly in response to the metabolism of drug in different volunteers. This as-designed minimally invasive sensing system should open up new opportunities for precision medicine, especially for personal healthcare monitoring.
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Affiliation(s)
- Yi-Chia Hsieh
- Institute of Biomedical Engineering and Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu, 300044, Taiwan
| | - Chih-Yu Lin
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 300044, Taiwan
| | - Hsin-Yao Lin
- Institute of Biomedical Engineering and Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu, 300044, Taiwan
- Division of Neurosurgery, Department of Surgery, MacKay Memorial Hospital, Taipei, 104217, Taiwan
- Institute of Nanoengineering and Microsystems, National Tsing Hua University, Hsinchu, 300044, Taiwan
| | - Chun-Ting Kuo
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 300044, Taiwan
| | - Shin-Yi Yin
- Department of Research and Development, Win Coat Corporation, Hsinchu, 30078, Taiwan
| | - Ying-Hua Hsu
- Department of Research and Development, Win Coat Corporation, Hsinchu, 30078, Taiwan
| | - Hsiu-Feng Yeh
- Department of Research and Development, Win Coat Corporation, Hsinchu, 30078, Taiwan
| | - Jane Wang
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, 300044, Taiwan
| | - Dehui Wan
- Institute of Biomedical Engineering and Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu, 300044, Taiwan
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5
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Hristova J, Svinarov D. Enhancing precision medicine through clinical mass spectrometry platform. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2053342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Julieta Hristova
- Alexander University Hospital, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Dobrin Svinarov
- Alexander University Hospital, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
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6
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Kong W, Hui HWH, Peng H, Goh WWB. Dealing with missing values in proteomics data. Proteomics 2022; 22:e2200092. [PMID: 36349819 DOI: 10.1002/pmic.202200092] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/15/2022] [Accepted: 10/11/2022] [Indexed: 11/10/2022]
Abstract
Proteomics data are often plagued with missingness issues. These missing values (MVs) threaten the integrity of subsequent statistical analyses by reduction of statistical power, introduction of bias, and failure to represent the true sample. Over the years, several categories of missing value imputation (MVI) methods have been developed and adapted for proteomics data. These MVI methods perform their tasks based on different prior assumptions (e.g., data is normally or independently distributed) and operating principles (e.g., the algorithm is built to address random missingness only), resulting in varying levels of performance even when dealing with the same dataset. Thus, to achieve a satisfactory outcome, a suitable MVI method must be selected. To guide decision making on suitable MVI method, we provide a decision chart which facilitates strategic considerations on datasets presenting different characteristics. We also bring attention to other issues that can impact proper MVI such as the presence of confounders (e.g., batch effects) which can influence MVI performance. Thus, these too, should be considered during or before MVI.
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Affiliation(s)
- Weijia Kong
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Harvard Wai Hann Hui
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Hui Peng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Wilson Wen Bin Goh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,Centre for Biomedical Informatics, Nanyang Technological University, Singapore, Singapore
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7
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NAUREEN ZAKIRA, CRISTONI SIMONE, DONATO KEVIN, MEDORI MARIACHIARA, SAMAJA MICHELE, HERBST KARENL, AQUILANTI BARBARA, VELLUTI VALERIA, MATERA GIUSEPPINA, FIORETTI FRANCESCO, IACONELLI AMERIGO, PERRONE MARCOALFONSO, DI GIULIO LORENZO, GREGORACE EMANUELE, CHIURAZZI PIETRO, NODARI SAVINA, CONNELLY STEPHENTHADDEUS, BERTELLI MATTEO. Metabolomics application for the design of an optimal diet. JOURNAL OF PREVENTIVE MEDICINE AND HYGIENE 2022; 63:E142-E149. [PMID: 36479478 PMCID: PMC9710392 DOI: 10.15167/2421-4248/jpmh2022.63.2s3.2755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Precision nutrition is an emerging branch of nutrition science that aims to use modern omics technologies (genomics, proteomics, and metabolomics) to assess an individual's response to specific foods or dietary patterns and thereby determine the most effective diet or lifestyle interventions to prevent or treat specific diseases. Metabolomics is vital to nearly every aspect of precision nutrition. It can be targeted or untargeted, and it has many applications. Indeed, it can be used to comprehensively characterize the thousands of chemicals in foods, identify food by-products in human biofluids or tissues, characterize nutrient deficiencies or excesses, monitor biochemical responses to dietary interventions, track long- or short-term dietary habits, and guide the development of nutritional therapies. Indeed, metabolomics can be coupled with genomics and proteomics to study and advance the field of precision nutrition. Integrating omics with epidemiological and clinical data will begin to define the beneficial effects of human food metabolites. In this review, we present the metabolome and its relationship to precision nutrition. Moreover, we describe the different techniques used in metabolomics and present how metabolomics has been applied to advance the field of precision nutrition by providing notable examples and cases.
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Affiliation(s)
| | - SIMONE CRISTONI
- ISB Ion Source & Biotechnologies srl, Italy, Bresso, Milano, Italy
| | | | | | | | - KAREN L. HERBST
- Total Lipedema Care, Beverly Hills California and Tucson Arizona, USA
| | - BARBARA AQUILANTI
- UOSD Medicina Bariatrica, Fondazione Policlinico Agostino Gemelli IRCCS, Rome, Italy
| | - VALERIA VELLUTI
- UOSD Medicina Bariatrica, Fondazione Policlinico Agostino Gemelli IRCCS, Rome, Italy
| | - GIUSEPPINA MATERA
- UOSD Medicina Bariatrica, Fondazione Policlinico Agostino Gemelli IRCCS, Rome, Italy
| | - FRANCESCO FIORETTI
- Department of Cardiology, University of Brescia and ASST “Spedali Civili” Hospital, Brescia, Italy
| | - AMERIGO IACONELLI
- UOSD Medicina Bariatrica, Fondazione Policlinico Agostino Gemelli IRCCS, Rome, Italy
| | | | - LORENZO DI GIULIO
- Department of Vascular Surgery, University of Rome Tor Vergata, Rome Italy
| | - EMANUELE GREGORACE
- Department of Cardiology and CardioLab, University of Rome Tor Vergata, Rome, Italy
| | - PIETRO CHIURAZZI
- Istituto di Medicina Genomica, Università Cattolica del Sacro Cuore, Rome, Italy
- UOC Genetica Medica, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, Rome, Italy
| | - SAVINA NODARI
- Department of Cardiology, University of Brescia and ASST “Spedali Civili” Hospital, Brescia, Italy
| | - STEPHEN THADDEUS CONNELLY
- San Francisco Veterans Affairs Health Care System, Department of Oral & Maxillofacial Surgery, University of California, San Francisco, CA, USA
| | - MATTEO BERTELLI
- MAGI EUREGIO, Bolzano, Italy
- MAGI’S LAB, Rovereto (TN), Italy
- Total Lipedema Care, Beverly Hills California and Tucson Arizona, USA
- MAGISNAT, Peachtree Corners (GA), USA
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8
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Yaari Z, Horoszko CP, Antman-Passig M, Kim M, Nguyen FT, Heller DA. Emerging technologies in cancer detection. Cancer Biomark 2022. [DOI: 10.1016/b978-0-12-824302-2.00011-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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9
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Hu Y, Wang Z, Liu L, Zhu J, Zhang D, Xu M, Zhang Y, Xu F, Chen Y. Mass spectrometry-based chemical mapping and profiling toward molecular understanding of diseases in precision medicine. Chem Sci 2021; 12:7993-8009. [PMID: 34257858 PMCID: PMC8230026 DOI: 10.1039/d1sc00271f] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/15/2021] [Indexed: 12/11/2022] Open
Abstract
Precision medicine has been strongly promoted in recent years. It is used in clinical management for classifying diseases at the molecular level and for selecting the most appropriate drugs or treatments to maximize efficacy and minimize adverse effects. In precision medicine, an in-depth molecular understanding of diseases is of great importance. Therefore, in the last few years, much attention has been given to translating data generated at the molecular level into clinically relevant information. However, current developments in this field lack orderly implementation. For example, high-quality chemical research is not well integrated into clinical practice, especially in the early phase, leading to a lack of understanding in the clinic of the chemistry underlying diseases. In recent years, mass spectrometry (MS) has enabled significant innovations and advances in chemical research. As reported, this technique has shown promise in chemical mapping and profiling for answering "what", "where", "how many" and "whose" chemicals underlie the clinical phenotypes, which are assessed by biochemical profiling, MS imaging, molecular targeting and probing, biomarker grading disease classification, etc. These features can potentially enhance the precision of disease diagnosis, monitoring and treatment and thus further transform medicine. For instance, comprehensive MS-based biochemical profiling of ovarian tumors was performed, and the results revealed a number of molecular insights into the pathways and processes that drive ovarian cancer biology and the ways that these pathways are altered in correspondence with clinical phenotypes. Another study demonstrated that quantitative biomarker mapping can be predictive of responses to immunotherapy and of survival in the supposedly homogeneous group of breast cancer patients, allowing for stratification of patients. In this context, our article attempts to provide an overview of MS-based chemical mapping and profiling, and a perspective on their clinical utility to improve the molecular understanding of diseases for advancing precision medicine.
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Affiliation(s)
- Yechen Hu
- School of Pharmacy, Nanjing Medical University Nanjing 211166 China
| | - Zhongcheng Wang
- School of Pharmacy, Nanjing Medical University Nanjing 211166 China
| | - Liang Liu
- School of Pharmacy, Nanjing Medical University Nanjing 211166 China
- Department of Pharmacy, Zhongnan Hospital of Wuhan University Wuhan 430071 China
| | - Jianhua Zhu
- School of Pharmacy, Nanjing Medical University Nanjing 211166 China
| | - Dongxue Zhang
- School of Pharmacy, Nanjing Medical University Nanjing 211166 China
| | - Mengying Xu
- School of Pharmacy, Nanjing Medical University Nanjing 211166 China
| | - Yuanyuan Zhang
- School of Pharmacy, Nanjing Medical University Nanjing 211166 China
| | - Feifei Xu
- School of Pharmacy, Nanjing Medical University Nanjing 211166 China
| | - Yun Chen
- School of Pharmacy, Nanjing Medical University Nanjing 211166 China
- State Key Laboratory of Reproductive Medicine, Key Laboratory of Cardiovascular & Cerebrovascular Medicine Nanjing 210029 China
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10
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Quantitative analysis of docetaxel by surface-enhanced Raman spectroscopy (SERS) combined with chemometric models and Ag@ZnO nanoparticles substrates. Microchem J 2020. [DOI: 10.1016/j.microc.2019.104373] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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11
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Fenwick A, Woodworth A, Yu M. An Unexpected Result of Meconium Drug Testing. Clin Chem 2019; 64:1671-1672. [PMID: 30377181 DOI: 10.1373/clinchem.2018.293209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 07/25/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Alexander Fenwick
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Kentucky, Lexington, KY
| | - Alison Woodworth
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Kentucky, Lexington, KY
| | - Min Yu
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Kentucky, Lexington, KY.
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12
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Cremers S, Guha N, Shine B. Therapeutic drug monitoring in the era of precision medicine: opportunities! Br J Clin Pharmacol 2018; 82:900-2. [PMID: 27612297 DOI: 10.1111/bcp.13047] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 06/16/2016] [Indexed: 12/30/2022] Open
Affiliation(s)
- Serge Cremers
- Departments of Pathology & Cell Biology and Medicine, Columbia University Medical Center, New York, NY, USA.
| | - Nishan Guha
- Department of Clinical Biochemistry, John Radcliffe Hospital and Nuffield Department of Clinical Laboratory Sciences, University of Oxford, Oxford, UK
| | - Brian Shine
- Department of Clinical Biochemistry, John Radcliffe Hospital and Nuffield Department of Clinical Laboratory Sciences, University of Oxford, Oxford, UK
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13
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Modak AS. Point-of-care companion diagnostic tests for personalizing psychiatric medications: fulfilling an unmet clinical need. J Breath Res 2017; 12:017101. [PMID: 28920579 DOI: 10.1088/1752-7163/aa8d2e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Over the last decade stable isotope-labeled substrates have been used as probes for rapid, point-of-care, non-invasive and user-friendly phenotype breath tests to evaluate activity of drug metabolizing enzymes. These diagnostic breath tests can potentially be used as companion diagnostics by physicians to personalize medications, especially psychiatric drugs with narrow therapeutic windows, to monitor the progress of disease severity, medication efficacy and to study in vivo the pharmacokinetics of xenobiotics. Several genotype tests have been approved by the FDA over the last 15 years for both cytochrome P450 2D6 and 2C19 enzymes, however they have not been cleared for use in personalizing medications since they fall woefully short in identifying all non-responders to drugs, especially for the CYP450 enzymes. CYP2D6 and CYP2C19 are among the most extensively studied drug metabolizing enzymes, involved in the metabolism of approximately 30% of FDA-approved drugs in clinical use, associated with large individual differences in medication efficacy or tolerability essentially due to phenoconversion. The development and commercialization via FDA approval of the non-invasive, rapid (<60 min), in vivo, phenotype diagnostic breath tests to evaluate polymorphic CYP2D6 and CYP2C19 enzyme activity by measuring exhaled 13CO2 as a biomarker in breath will effectively resolve the currently unmet clinical need for individualized psychiatric drug therapy. Clinicians could personalize treatment options for patients based on the CYP2D6 and CYP2C19 phenotype by selecting the optimal medication at the right initial and subsequent maintenance dose for the desired clinical outcome (i.e. greatest efficacy and minimal side effects).
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Affiliation(s)
- Anil S Modak
- Cambridge Isotope Laboratories, Inc., 3 Highwood Drive, Tewksbury, MA 01876, United States of America
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14
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Rajoriya N, Combet C, Zoulim F, Janssen HLA. How viral genetic variants and genotypes influence disease and treatment outcome of chronic hepatitis B. Time for an individualised approach? J Hepatol 2017; 67:1281-1297. [PMID: 28736138 DOI: 10.1016/j.jhep.2017.07.011] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 06/27/2017] [Accepted: 07/12/2017] [Indexed: 12/12/2022]
Abstract
Chronic hepatitis B virus (HBV) infection remains a global problem. Several HBV genotypes exist with different biology and geographical prevalence. Whilst the future aim of HBV treatment remains viral eradication, current treatment strategies aim to suppress the virus and prevent the progression of liver disease. Current strategies also involve identification of patients for treatment, namely those at risk of progressive liver disease. Identification of HBV genotype, HBV mutants and other predictive factors allow for tailoured treatments, and risk-surveillance pathways, such as hepatocellular cancer screening. In the future, these factors may enable stratification not only of treatment decisions, but also of patients at risk of higher relapse rates when current therapies are discontinued. Newer technologies, such as next-generation sequencing, to assess drug-resistant or immune escape variants and quasi-species heterogeneity in patients, may allow for more information-based treatment decisions between the clinician and the patient. This article serves to discuss how HBV genotypes and genetic variants impact not only upon the disease course and outcomes, but also current treatment strategies. Adopting a personalised genotypic approach may play a role in future strategies to combat the disease. Herein, we discuss new technologies that may allow more informed decision-making for response guided therapy in the battle against HBV.
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Affiliation(s)
- Neil Rajoriya
- Toronto Centre for Liver Diseases, Toronto General Hospital, 200 Elizabeth Street, Toronto, Ontario M5G 2C4, Canada
| | - Christophe Combet
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Lyon 69XXX, France
| | - Fabien Zoulim
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Lyon 69XXX, France; Department of Hepatology, Groupement Hospitalier Nord, Hospices Civils de Lyon, Lyon, France
| | - Harry L A Janssen
- Toronto Centre for Liver Diseases, Toronto General Hospital, 200 Elizabeth Street, Toronto, Ontario M5G 2C4, Canada.
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15
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Woo HI, Lee SK, Kim J, Kim SW, Yu J, Bae SY, Lee JE, Nam SJ, Lee SY. Variations in plasma concentrations of tamoxifen metabolites and the effects of genetic polymorphisms on tamoxifen metabolism in Korean patients with breast cancer. Oncotarget 2017; 8:100296-100311. [PMID: 29245979 PMCID: PMC5725021 DOI: 10.18632/oncotarget.22220] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 10/12/2017] [Indexed: 12/16/2022] Open
Abstract
Inter-individual variation in tamoxifen metabolism in breast cancer patients is caused by various genetic and clinical factors. We measured the plasma concentrations of tamoxifen and its metabolites and investigated genetic polymorphisms influencing those concentrations. We measured the concentrations of tamoxifen, endoxifen, N-desmethyltamoxifen (NDM), and 4-hydroxytamoxifen (4-OH tamoxifen) in 550 plasma specimens from 281 breast cancer patients treated with tamoxifen. Duplicate or triplicate specimens were obtained from 179 patients at 3-month intervals. In 80 patients, genotyping for tamoxifen metabolizing enzymes was performed using the DMET Plus array and long-range PCR. Plasma concentrations of tamoxifen and its metabolites showed wide variations among patients. The following genetic polymorphisms were associated with the plasma concentrations when body mass index and tamoxifen concentrations were considered as co-variables: CYP1A2 -2467delT, CYP2B6 genotype, CYP2D6 activity score (AS), and FMO3 441C>T. CYP2D6 AS and three variants in the SULT1E1 gene showed correlation with ratios of tamoxifen metabolites. CYP2D6 AS was the only variable that showed associations with both metabolite concentration and ratio: endoxifen (P < 0.001), NDM (P < 0.001), endoxifen/NDM (P < 0.001), NDM/tamoxifen (P < 0.001), and 4-OH tamoxifen/tamoxifen (P = 0.005). Serial measurements of 448 plasma concentrations in 179 patients at 3-month intervals showed wide intra-individual variation. Our study showed that genetic polymorphisms can in part determine the baseline concentrations of tamoxifen and its metabolites. However, marked intra-individual variations during follow-up monitoring were observed, and this could not be explained by genotype. Therefore, serial measurements of tamoxifen and its metabolites would be helpful in monitoring in vivo tamoxifen metabolic status.
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Affiliation(s)
- Hye In Woo
- Department of Laboratory Medicine, Samsung Changwon Hospital, Sungkyunkwan University School of Medicine, Changwon, Korea
| | - Se Kyung Lee
- Division of Breast Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jiyoung Kim
- Department of Surgery, Jeju National University School of Medicine, Jeju National University Hospital, Jeju, Korea
| | - Seok Won Kim
- Division of Breast Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jonghan Yu
- Division of Breast Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Soo Youn Bae
- Division of Breast and Endocrine Surgery, Department of Surgery, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Korea
| | - Jeong Eon Lee
- Division of Breast Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Seok Jin Nam
- Division of Breast Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Soo-Youn Lee
- Department of Clinical Pharmacology & Therapeutics, Samsung Medical Center, Seoul, Korea.,Department of Laboratory Medicine & Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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16
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The achievements of clinical chemistry testing: 1967–2017. Clin Biochem 2017; 50:165-167. [DOI: 10.1016/j.clinbiochem.2016.11.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 11/18/2016] [Indexed: 11/22/2022]
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17
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Decosterd L, Widmer N, André P, Aouri M, Buclin T. The emerging role of multiplex tandem mass spectrometry analysis for therapeutic drug monitoring and personalized medicine. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2016.03.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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18
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Shipkova M, Svinarov D. LC–MS/MS as a tool for TDM services: Where are we? Clin Biochem 2016; 49:1009-23. [DOI: 10.1016/j.clinbiochem.2016.05.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Revised: 04/23/2016] [Accepted: 05/01/2016] [Indexed: 12/23/2022]
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19
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Annesley TM, Cooks RG, Herold DA, Hoofnagle AN. Clinical Mass Spectrometry—Achieving Prominence in Laboratory Medicine. Clin Chem 2016; 62:1-3. [DOI: 10.1373/clinchem.2015.251272] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Thomas M Annesley
- Department of Pathology, University of Michigan Health System, Ann Arbor, MI
| | - R Graham Cooks
- Department of Chemistry and Center for Analytical Instrumentation Development, Purdue University, West Lafayette, IN
| | - David A Herold
- Department of Pathology, University of California San Diego, La Jolla, CA
| | - Andrew N Hoofnagle
- Departments of Laboratory Medicine and Medicine, University of Washington, Seattle, WA
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