1
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Beck A, Muhoberac M, Randolph CE, Beveridge CH, Wijewardhane PR, Kenttämaa HI, Chopra G. Recent Developments in Machine Learning for Mass Spectrometry. ACS MEASUREMENT SCIENCE AU 2024; 4:233-246. [PMID: 38910862 PMCID: PMC11191731 DOI: 10.1021/acsmeasuresciau.3c00060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/27/2023] [Accepted: 01/22/2024] [Indexed: 06/25/2024]
Abstract
Statistical analysis and modeling of mass spectrometry (MS) data have a long and rich history with several modern MS-based applications using statistical and chemometric methods. Recently, machine learning (ML) has experienced a renaissance due to advents in computational hardware and the development of new algorithms for artificial neural networks (ANN) and deep learning architectures. Moreover, recent successes of new ANN and deep learning architectures in several areas of science, engineering, and society have further strengthened the ML field. Importantly, modern ML methods and architectures have enabled new approaches for tasks related to MS that are now widely adopted in several popular MS-based subdisciplines, such as mass spectrometry imaging and proteomics. Herein, we aim to provide an introductory summary of the practical aspects of ML methodology relevant to MS. Additionally, we seek to provide an up-to-date review of the most recent developments in ML integration with MS-based techniques while also providing critical insights into the future direction of the field.
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Affiliation(s)
- Armen
G. Beck
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Matthew Muhoberac
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Caitlin E. Randolph
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Connor H. Beveridge
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Prageeth R. Wijewardhane
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Hilkka I. Kenttämaa
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Gaurav Chopra
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
- Department
of Computer Science (by courtesy), Purdue University, West Lafayette, Indiana 47907, United States
- Purdue
Institute for Drug Discovery, Purdue Institute for Cancer Research,
Regenstrief Center for Healthcare Engineering, Purdue Institute for
Inflammation, Immunology and Infectious Disease, Purdue Institute for Integrative Neuroscience, West Lafayette, Indiana 47907 United States
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2
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Li XL, Zhang JQ, Li Y, Shen XJ, Yang HY, Yang L, Xu M, Bi QR, Yao CL, Guo DA. Medcheck: a novel software for automated de-formulation of traditional Chinese medicine (TCM) prescriptions by liquid chromatography-mass spectrometry. J Pharm Anal 2024; 14:100958. [PMID: 39005840 PMCID: PMC11246044 DOI: 10.1016/j.jpha.2024.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/06/2024] [Accepted: 02/25/2024] [Indexed: 07/16/2024] Open
Abstract
Image 1.
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Affiliation(s)
- Xiao-Lan Li
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jian-Qing Zhang
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yun Li
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Xuan-Jing Shen
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huan-Ya Yang
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Lin Yang
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Meng Xu
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Qi-Rui Bi
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Chang-Liang Yao
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - De-An Guo
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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3
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Yang C, Hsiao YC, Lee CC, Yu JS. Systematic Evaluation of Chromatographic Peak Quality for Targeted Mass Spectrometry via Variational Autoencoder. Anal Chem 2024. [PMID: 38336364 PMCID: PMC10882576 DOI: 10.1021/acs.analchem.3c03686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2024]
Abstract
Targeted mass spectrometry is a powerful technique for quantifying specific proteins or metabolites in complex biological samples. Accurate peak picking is a critical step as it determines the absolute abundance of each analyte by integrating the area under the picked peaks. Although automated software exists for handling such complex tasks, manual intervention is often required to rectify potential errors like misclassification or mis-picking events, which can significantly affect quantification accuracy. Therefore, it is necessary to develop objective scoring functions to evaluate peak-picking results and to identify problematic cases for further inspection. In this study, we present targeted mass spectrometry quality encoder (TMSQE), a data-driven scoring function that summarizes peak quality in three types: transition level, peak group level, and consistency level across samples. Through unsupervised learning from large data sets containing 1,703,827 peak groups, TMSQE establishes a reliable standard for systematic and objective evaluations of chromatographic peak quality in targeted mass spectrometry. TMSQE shows a high degree of consistency with expert experiences and can efficiently capture problematic cases after the automated software. Furthermore, we demonstrate the generalizability of TMSQE by successfully applying it to various data sets, including both peptide and metabolite data sets. Our proposed scoring approach provides a reliable solution for consistent and accurate peak quality evaluation, facilitating peak quality control for targeted mass spectrometry.
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Affiliation(s)
- Chi Yang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 33302, Taiwan
| | - Yung-Chin Hsiao
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 33302, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Department of Otolaryngology-Head and Neck Surgery, Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan
| | - Chi-Ching Lee
- Department of Computer Science and Information Engineering, Chang Gung University, Taoyuan 33302, Taiwan
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan
- Artificial Intelligence Research Center, Chang Gung University, Taoyuan 33302, Taiwan
| | - Jau-Song Yu
- Molecular Medicine Research Center, Chang Gung University, Taoyuan 33302, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Department of Otolaryngology-Head and Neck Surgery, Chang Gung Memorial Hospital, Taoyuan 33305, Taiwan
- Research Center for Food and Cosmetic Safety, College of Human Ecology, Chang Gung University of Science and Technology, 33302 Taoyuan, Taiwan
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4
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Villa M, Sanin DE, Apostolova P, Corrado M, Kabat AM, Cristinzio C, Regina A, Carrizo GE, Rana N, Stanczak MA, Baixauli F, Grzes KM, Cupovic J, Solagna F, Hackl A, Globig AM, Hässler F, Puleston DJ, Kelly B, Cabezas-Wallscheid N, Hasselblatt P, Bengsch B, Zeiser R, Sagar, Buescher JM, Pearce EJ, Pearce EL. Prostaglandin E 2 controls the metabolic adaptation of T cells to the intestinal microenvironment. Nat Commun 2024; 15:451. [PMID: 38200005 PMCID: PMC10781727 DOI: 10.1038/s41467-024-44689-2] [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: 03/14/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
Immune cells must adapt to different environments during the course of an immune response. Here we study the adaptation of CD8+ T cells to the intestinal microenvironment and how this process shapes the establishment of the CD8+ T cell pool. CD8+ T cells progressively remodel their transcriptome and surface phenotype as they enter the gut wall, and downregulate expression of mitochondrial genes. Human and mouse intestinal CD8+ T cells have reduced mitochondrial mass, but maintain a viable energy balance to sustain their function. We find that the intestinal microenvironment is rich in prostaglandin E2 (PGE2), which drives mitochondrial depolarization in CD8+ T cells. Consequently, these cells engage autophagy to clear depolarized mitochondria, and enhance glutathione synthesis to scavenge reactive oxygen species (ROS) that result from mitochondrial depolarization. Impairing PGE2 sensing promotes CD8+ T cell accumulation in the gut, while tampering with autophagy and glutathione negatively impacts the T cell pool. Thus, a PGE2-autophagy-glutathione axis defines the metabolic adaptation of CD8+ T cells to the intestinal microenvironment, to ultimately influence the T cell pool.
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Affiliation(s)
- Matteo Villa
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany.
- Division of Rheumatology and Immunology, Department of Internal Medicine, Medical University of Graz, 8036, Graz, Austria.
| | - David E Sanin
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany
- Bloomberg-Kimmel Institute of Immunotherapy, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Petya Apostolova
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany
- Bloomberg-Kimmel Institute of Immunotherapy, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Medicine I (Hematology and Oncology), University Medical Center Freiburg, 79106, Freiburg, Germany
| | - Mauro Corrado
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Agnieszka M Kabat
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany
- Bloomberg-Kimmel Institute of Immunotherapy, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Carmine Cristinzio
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany
- Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Annamaria Regina
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany
- Department of Life Sciences, University of Trieste, 34128, Trieste, Italy
| | - Gustavo E Carrizo
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Nisha Rana
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Michal A Stanczak
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Francesc Baixauli
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Katarzyna M Grzes
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Jovana Cupovic
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Francesca Solagna
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Alexandra Hackl
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Anna-Maria Globig
- Department of Medicine II, University Medical Center Freiburg, 79106, Freiburg, Germany
| | - Fabian Hässler
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Daniel J Puleston
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Beth Kelly
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | | | - Peter Hasselblatt
- Department of Medicine II, University Medical Center Freiburg, 79106, Freiburg, Germany
| | - Bertram Bengsch
- Department of Medicine II, University Medical Center Freiburg, 79106, Freiburg, Germany
- CIBSS Centre for Integrative Biological Signalling Studies, Freiburg, Germany
| | - Robert Zeiser
- Department of Medicine I (Hematology and Oncology), University Medical Center Freiburg, 79106, Freiburg, Germany
- CIBSS Centre for Integrative Biological Signalling Studies, Freiburg, Germany
| | - Sagar
- Department of Medicine II, University Medical Center Freiburg, 79106, Freiburg, Germany
| | - Joerg M Buescher
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany
| | - Edward J Pearce
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany
- Bloomberg-Kimmel Institute of Immunotherapy, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- CIBSS Centre for Integrative Biological Signalling Studies, Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Erika L Pearce
- Max Planck Institute for Immunobiology and Epigenetics, 79108, Freiburg, Germany.
- Bloomberg-Kimmel Institute of Immunotherapy, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- CIBSS Centre for Integrative Biological Signalling Studies, Freiburg, Germany.
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.
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5
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Lee CC, Lin YC, Pan TY, Yang CH, Li PH, Chen SY, Gao JJ, Yang C, Chu LJ, Huang PJ, Yeh YM, Tang P, Chang YS, Yu JS, Hsiao YC. HeapMS: An Automatic Peak-Picking Pipeline for Targeted Proteomic Data Powered by 2D Heatmap Transformation and Convolutional Neural Networks. Anal Chem 2023; 95:15486-15496. [PMID: 37820297 PMCID: PMC10603604 DOI: 10.1021/acs.analchem.3c01011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 09/20/2023] [Indexed: 10/13/2023]
Abstract
The process of peak picking and quality assessment for multiple reaction monitoring (MRM) data demands significant human effort, especially for signals with low abundance and high interference. Although multiple peak-picking software packages are available, they often fail to detect peaks with low quality and do not report cases with low confidence. Furthermore, visual examination of all chromatograms is still necessary to identify uncertain or erroneous cases. This study introduces HeapMS, a web service that uses artificial intelligence to assist with peak picking and the quality assessment of MRM chromatograms. HeapMS applies a rule-based filter to remove chromatograms with low interference and high-confidence peak boundaries detected by Skyline. Additionally, it transforms two histograms (representing light and heavy peptides) into a single encoded heatmap and performs a two-step evaluation (quality detection and peak picking) using image convolutional neural networks. HeapMS offers three categories of peak picking: uncertain peak picking that requires manual inspection, deletion peak picking that requires removal or manual re-examination, and automatic peak picking. HeapMS acquires the chromatogram and peak-picking boundaries directly from Skyline output. The output results are imported back into Skyline for further manual inspection, facilitating integration with Skyline. HeapMS offers the benefit of detecting chromatograms that should be deleted or require human inspection. Based on defined categories, it can significantly reduce human workload and provide consistent results. Furthermore, by using heatmaps instead of histograms, HeapMS can adapt to future updates in image recognition models. The HeapMS is available at: https://github.com/ccllabe/HeapMS.
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Affiliation(s)
- Chi-Ching Lee
- Department
of Computer Science and Information Engineering, Chang Gung University, 33302 Taoyuan, Taiwan
- Genomic
Medicine Core Laboratory, Chang Gung Memorial
Hospital, 33305 Taoyuan, Taiwan
- Artificial
Intelligence Research Center, Chang Gung
University, 33302 Taoyuan, Taiwan
| | - Yu-Chieh Lin
- Graduate
Institute of Artificial Intelligence, Chang
Gung University, 33302 Taoyuan, Taiwan
| | - Teng Yu Pan
- Department
of Computer Science and Information Engineering, Chang Gung University, 33302 Taoyuan, Taiwan
| | - Cheng Hann Yang
- Department
of Computer Science and Information Engineering, Chang Gung University, 33302 Taoyuan, Taiwan
| | - Pei-Hsuan Li
- Department
of Computer Science and Information Engineering, Chang Gung University, 33302 Taoyuan, Taiwan
| | - Sin You Chen
- Department
of Computer Science and Information Engineering, Chang Gung University, 33302 Taoyuan, Taiwan
- Artificial
Intelligence Research Center, Chang Gung
University, 33302 Taoyuan, Taiwan
| | - Jhih Jie Gao
- Department
of Computer Science and Information Engineering, Chang Gung University, 33302 Taoyuan, Taiwan
| | - Chi Yang
- Molecular
Medicine Research Center, Chang Gung University, 33302 Taoyuan, Taiwan
| | - Lichieh Julie Chu
- Molecular
Medicine Research Center, Chang Gung University, 33302 Taoyuan, Taiwan
- Graduate
Institute of Biomedical Sciences, College of Medicine, Chang Gung University, 33302 Taoyuan, Taiwan
- Department
of Otolaryngology-Head and Neck Surgery, Chang Gung Memorial Hospital, 33305 Taoyuan, Taiwan
| | - Po-Jung Huang
- Genomic
Medicine Core Laboratory, Chang Gung Memorial
Hospital, 33305 Taoyuan, Taiwan
- Department
of Biomedical Sciences, Chang Gung University, 33302 Taoyuan, Taiwan
| | - Yuan-Ming Yeh
- Genomic
Medicine Core Laboratory, Chang Gung Memorial
Hospital, 33305 Taoyuan, Taiwan
| | - Petrus Tang
- Molecular
Infectious Disease Research Center, Chang
Gung Memorial Hospital, 33305 Taoyuan, Taiwan
- Department
of Parasitology, College of Medicine, Chang
Gung University, 33302 Taoyuan, Taiwan
| | - Yu-Sun Chang
- Molecular
Medicine Research Center, Chang Gung University, 33302 Taoyuan, Taiwan
| | - Jau-Song Yu
- Molecular
Medicine Research Center, Chang Gung University, 33302 Taoyuan, Taiwan
- Graduate
Institute of Biomedical Sciences, College of Medicine, Chang Gung University, 33302 Taoyuan, Taiwan
- Department
of Otolaryngology-Head and Neck Surgery, Chang Gung Memorial Hospital, 33305 Taoyuan, Taiwan
- Research
Center for Food and Cosmetic Safety, College of Human Ecology, Chang Gung University of Science and Technology, 33302 Taoyuan, Taiwan
| | - Yung-Chin Hsiao
- Molecular
Medicine Research Center, Chang Gung University, 33302 Taoyuan, Taiwan
- Graduate
Institute of Biomedical Sciences, College of Medicine, Chang Gung University, 33302 Taoyuan, Taiwan
- Department
of Otolaryngology-Head and Neck Surgery, Chang Gung Memorial Hospital, 33305 Taoyuan, Taiwan
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6
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Villa M, Sanin DE, Apostolova P, Corrado M, Kabat AM, Cristinzio C, Regina A, Carrizo GE, Rana N, Stanczak MA, Baixauli F, Grzes KM, Cupovic J, Solagna F, Hackl A, Globig AM, Hässler F, Puleston DJ, Kelly B, Cabezas-Wallscheid N, Hasselblatt P, Bengsch B, Zeiser R, Sagar, Buescher JM, Pearce EJ, Pearce EL. Prostaglandin E 2 controls the metabolic adaptation of T cells to the intestinal microenvironment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.13.532431. [PMID: 36993703 PMCID: PMC10054978 DOI: 10.1101/2023.03.13.532431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Immune cells must adapt to different environments during the course of an immune response. We studied the adaptation of CD8 + T cells to the intestinal microenvironment and how this process shapes their residency in the gut. CD8 + T cells progressively remodel their transcriptome and surface phenotype as they acquire gut residency, and downregulate expression of mitochondrial genes. Human and mouse gut-resident CD8 + T cells have reduced mitochondrial mass, but maintain a viable energy balance to sustain their function. We found that the intestinal microenvironment is rich in prostaglandin E 2 (PGE 2 ), which drives mitochondrial depolarization in CD8 + T cells. Consequently, these cells engage autophagy to clear depolarized mitochondria, and enhance glutathione synthesis to scavenge reactive oxygen species (ROS) that result from mitochondrial depolarization. Impairing PGE 2 sensing promotes CD8 + T cell accumulation in the gut, while tampering with autophagy and glutathione negatively impacts the T cell population. Thus, a PGE 2 -autophagy-glutathione axis defines the metabolic adaptation of CD8 + T cells to the intestinal microenvironment, to ultimately influence the T cell pool.
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7
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Schönberger K, Mitterer M, Glaser K, Stecher M, Hobitz S, Schain-Zota D, Schuldes K, Lämmermann T, Rambold AS, Cabezas-Wallscheid N, Buescher JM. LC-MS-Based Targeted Metabolomics for FACS-Purified Rare Cells. Anal Chem 2023; 95:4325-4334. [PMID: 36812587 PMCID: PMC9996616 DOI: 10.1021/acs.analchem.2c04396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Metabolism plays a fundamental role in regulating cellular functions and fate decisions. Liquid chromatography-mass spectrometry (LC-MS)-based targeted metabolomic approaches provide high-resolution insights into the metabolic state of a cell. However, the typical sample size is in the order of 105-107 cells and thus not compatible with rare cell populations, especially in the case of a prior flow cytometry-based purification step. Here, we present a comprehensively optimized protocol for targeted metabolomics on rare cell types, such as hematopoietic stem cells and mast cells. Only 5000 cells per sample are required to detect up to 80 metabolites above background. The use of regular-flow liquid chromatography allows for robust data acquisition, and the omission of drying or chemical derivatization avoids potential sources of error. Cell-type-specific differences are preserved while the addition of internal standards, generation of relevant background control samples, and targeted metabolite with quantifiers and qualifiers ensure high data quality. This protocol could help numerous studies to gain thorough insights into cellular metabolic profiles and simultaneously reduce the number of laboratory animals and the time-consuming and costly experiments associated with rare cell-type purification.
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Affiliation(s)
- Katharina Schönberger
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany.,International Max Planck Research School for Immunobiology, Epigenetics and Metabolism (IMPRS-IEM), 79108 Freiburg, Germany.,Faculty of Biology, University of Freiburg, 79085 Freiburg, Germany
| | - Michael Mitterer
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Katharina Glaser
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany.,International Max Planck Research School for Immunobiology, Epigenetics and Metabolism (IMPRS-IEM), 79108 Freiburg, Germany.,Faculty of Biology, University of Freiburg, 79085 Freiburg, Germany
| | - Manuel Stecher
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany.,Faculty of Biology, University of Freiburg, 79085 Freiburg, Germany.,International Max Planck Research School for Immunobiology, Epigenetics and Metabolism (IMPRS-MCB), 79108 Freiburg, Germany
| | - Sebastian Hobitz
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Dominik Schain-Zota
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Konrad Schuldes
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Tim Lämmermann
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Angelika S Rambold
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | | | - Joerg M Buescher
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
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8
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Bunch DR, Durant TJ, Rudolf JW. Artificial Intelligence Applications in Clinical Chemistry. Clin Lab Med 2023; 43:47-69. [PMID: 36764808 DOI: 10.1016/j.cll.2022.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Artificial intelligence (AI) applications are an area of active investigation in clinical chemistry. Numerous publications have demonstrated the promise of AI across all phases of testing including preanalytic, analytic, and postanalytic phases; this includes novel methods for detecting common specimen collection errors, predicting laboratory results and diagnoses, and enhancing autoverification workflows. Although AI applications pose several ethical and operational challenges, these technologies are expected to transform the practice of the clinical chemistry laboratory in the near future.
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Affiliation(s)
- Dustin R Bunch
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, 700 Children's Drive, C1923, Columbus, OH 43205-2644, USA; Department of Pathology, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Thomas Js Durant
- Department of Laboratory Medicine, Yale School of Medicine, 55 Park Street, Room PS 502A, New Haven, CT 06510, USA
| | - Joseph W Rudolf
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; ARUP Laboratories, 500 Chipeta Way, MC 115, Salt Lake City, UT 84108, USA.
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9
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Quantitative challenges and their bioinformatic solutions in mass spectrometry-based metabolomics. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.117009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
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10
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Schönberger K, Mitterer M, Buescher JM, Cabezas-Wallscheid N. Targeted LC-MS/MS-based metabolomics and lipidomics on limited hematopoietic stem cell numbers. STAR Protoc 2022; 3:101408. [PMID: 35620073 PMCID: PMC9127697 DOI: 10.1016/j.xpro.2022.101408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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