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Shi C, Cheng L, Yu Y, Chen S, Dai Y, Yang J, Zhang H, Chen J, Geng N. Multi-omics integration analysis: Tools and applications in environmental toxicology. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 360:124675. [PMID: 39103035 DOI: 10.1016/j.envpol.2024.124675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 07/08/2024] [Accepted: 08/03/2024] [Indexed: 08/07/2024]
Abstract
Nowadays, traditional single-omics study is not enough to explain the causality between molecular alterations and toxicity endpoints for environmental pollutants. With the development of high-throughput sequencing technology and high-resolution mass spectrometry technology, the integrative analysis of multi-omics has become an efficient strategy to understand holistic biological mechanisms and to uncover the regulation network in specific biological processes. This review summarized sample preparation methods, integration analysis tools and the application of multi-omics integration analyses in environmental toxicology field. Currently, omics methods have been widely applied being as the sensitivity of early biological response, especially for low-dose and long-term exposure to environmental pollutants. Integrative omics can reveal the overall changes of genes, proteins, and/or metabolites in the cells, tissues or organisms, which provide new insights into revealing the overall toxicity effects, screening the toxic targets, and exploring the underlying molecular mechanism of pollutants.
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Affiliation(s)
- Chengcheng Shi
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; College of Environmental Science and Engineering, Dalian Maritime University, Dalian, 116026, China
| | - Lin Cheng
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Ying Yu
- College of Environmental Science and Engineering, Dalian Maritime University, Dalian, 116026, China
| | - Shuangshuang Chen
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; College of Environmental Science and Engineering, Dalian Maritime University, Dalian, 116026, China
| | - Yubing Dai
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Jiajia Yang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; College of Materials Science and Engineering, Hebei University of Engineering, Handan, 056038, China
| | - Haijun Zhang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Jiping Chen
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Ningbo Geng
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
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2
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Petrak J, Tevosian SG, Richter S, Ghayee HK. Metabolomics and proteomics in pheochromocytoma and paraganglioma: Translating biochemistry and biology to bedside. Best Pract Res Clin Endocrinol Metab 2024:101935. [PMID: 39299859 DOI: 10.1016/j.beem.2024.101935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
The complexity of omes - the key cellular ensembles (genome and epigenome, transcriptome, proteome, and metabolome) - is becoming increasingly understood in terms of big-data analysis, the omics. Amongst these, proteomics provides a global description of quantitative and qualitative alterations of protein expression (or protein abundance in body fluids) in response to physiologic or pathologic processes while metabolomics offers a functional portrait of the physiological state by quantifying metabolite abundances in biological samples. Here, we summarize how different techniques of proteomic and metabolic analysis can be used to define key biochemical characteristics of pheochromocytomas/paragangliomas (PPGL). The significance of omics in understanding features of PPGL biology that might translate to improved diagnosis and treatment will be highlighted.
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Affiliation(s)
- Jiri Petrak
- BIOCEV, First Faculty of Medicine, Charles University, Vestec, Czech Republic.
| | - Sergei G Tevosian
- Department of Physiological Sciences, University of Florida, Gainesville, FL, USA
| | - Susan Richter
- Institute of Clinical Chemistry and Laboratory Medicine, Medical Faculty Carl Gustav Carus, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Hans K Ghayee
- Department of Medicine, Division of Endocrinology & Metabolism, Malcom Randall VA Medical Center, University of Florida, Gainesville, FL, USA.
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3
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Hu Y, Zou Y, Qiao L, Lin L. Integrative proteomic and metabolomic elucidation of cardiomyopathy with in vivo and in vitro models and clinical samples. Mol Ther 2024:S1525-0016(24)00586-0. [PMID: 39233439 DOI: 10.1016/j.ymthe.2024.08.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/16/2024] [Accepted: 08/30/2024] [Indexed: 09/06/2024] Open
Abstract
Cardiomyopathy is a prevalent cardiovascular disease that affects individuals of all ages and can lead to life-threatening heart failure. Despite its variety in types, each with distinct characteristics and causes, our understanding of cardiomyopathy at a systematic biology level remains incomplete. Mass spectrometry-based techniques have emerged as powerful tools, providing a comprehensive view of the molecular landscape and aiding in the discovery of biomarkers and elucidation of mechanisms. This review highlights the significant potential of integrating proteomic and metabolomic approaches with specialized databases to identify biomarkers and therapeutic targets across different types of cardiomyopathies. In vivo and in vitro models, such as genetically modified mice, patient-derived or induced pluripotent stem cells, and organ chips, are invaluable in exploring the pathophysiological complexities of this disease. By integrating omics approaches with these sophisticated modeling systems, our comprehension of the molecular underpinnings of cardiomyopathy can be greatly enhanced, facilitating the development of diagnostic markers and therapeutic strategies. Among the promising therapeutic targets are those involved in extracellular matrix remodeling, sarcomere damage, and metabolic remodeling. These targets hold the potential to advance precision therapy in cardiomyopathy, offering hope for more effective treatments tailored to the specific molecular profiles of patients.
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Affiliation(s)
- Yiwei Hu
- Department of Chemistry, Zhongshan Hospital, and Minhang Hospital, Fudan University, Shanghai 200000, China
| | - Yunzeng Zou
- Department of Chemistry, Zhongshan Hospital, and Minhang Hospital, Fudan University, Shanghai 200000, China.
| | - Liang Qiao
- Department of Chemistry, Zhongshan Hospital, and Minhang Hospital, Fudan University, Shanghai 200000, China.
| | - Ling Lin
- Department of Chemistry, Zhongshan Hospital, and Minhang Hospital, Fudan University, Shanghai 200000, China.
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4
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Pergande MR, Osterbauer KJ, Buck KM, Roberts DS, Wood NN, Balasubramanian P, Mann MW, Rossler KJ, Diffee GM, Colman RJ, Anderson RM, Ge Y. Mass Spectrometry-Based Multiomics Identifies Metabolic Signatures of Sarcopenia in Rhesus Monkey Skeletal Muscle. J Proteome Res 2024; 23:2845-2856. [PMID: 37991985 PMCID: PMC11109024 DOI: 10.1021/acs.jproteome.3c00474] [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] [Indexed: 11/24/2023]
Abstract
Sarcopenia is a progressive disorder characterized by age-related loss of skeletal muscle mass and function. Although significant progress has been made over the years to identify the molecular determinants of sarcopenia, the precise mechanisms underlying the age-related loss of contractile function remains unclear. Advances in "omics" technologies, including mass spectrometry-based proteomic and metabolomic analyses, offer great opportunities to better understand sarcopenia. Herein, we performed mass spectrometry-based analyses of the vastus lateralis from young, middle-aged, and older rhesus monkeys to identify molecular signatures of sarcopenia. In our proteomic analysis, we identified proteins that change with age, including those involved in adenosine triphosphate and adenosine monophosphate metabolism as well as fatty acid beta oxidation. In our untargeted metabolomic analysis, we identified metabolites that changed with age largely related to energy metabolism including fatty acid beta oxidation. Pathway analysis of age-responsive proteins and metabolites revealed changes in muscle structure and contraction as well as lipid, carbohydrate, and purine metabolism. Together, this study discovers new metabolic signatures and offers new insights into the molecular mechanisms underlying sarcopenia for the evaluation and monitoring of a therapeutic treatment of sarcopenia.
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Affiliation(s)
- Melissa R. Pergande
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Katie J. Osterbauer
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Kevin M. Buck
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - David S. Roberts
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Nina N. Wood
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
| | | | - Morgan W. Mann
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Kalina J. Rossler
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Gary M. Diffee
- Department of Kinesiology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ricki J. Colman
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Rozalyn M. Anderson
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
- Geriatric Research Education and Clinical Center, William S. Middleton Memorial Veterans Hospital, Madison, WI 53705, USA
| | - Ying Ge
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
- Human Proteomics Program, University of Wisconsin-Madison, Madison, WI 53705, USA
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5
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Hemmati M, Wudy SI, Hackbarth F, Mittermeier-Kleßinger VK, Coleman OI, Haller D, Ludwig C, Dawid C, Kleigrewe K. Development of a Global Metabo-Lipid-Prote-omics Workflow to Compare Healthy Proximal and Distal Colonic Epithelium in Mice. J Proteome Res 2024; 23:3124-3140. [PMID: 39052308 DOI: 10.1021/acs.jproteome.3c00771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
A multimetabo-lipid-prote-omics workflow was developed to characterize the molecular interplay within proximal (PC) and distal (DC) colonic epithelium of healthy mice. This multiomics data set lays the foundation to better understand the two tissue types and can be used to study, for example, colon-related diseases like colorectal cancer or inflammatory bowel disease. First, the methyl tert-butyl ether extraction method was optimized, so that from a single tissue biopsy >350 reference-matched metabolites, >1850 reference-matched lipids, and >4500 proteins were detected by using targeted and untargeted metabolomics, untargeted lipidomics, and proteomics. Next, each omics-data set was analyzed individually and then merged with the additional omics disciplines to generate a deep understanding of the underlying complex regulatory network within the colon. Our data demonstrates, for example, differences in mucin formation, detected on substrate level as well as on enzyme level, and altered lipid metabolism by the detection of phospholipases hydrolyzing sphingomyelins to ceramides. In conclusion, the combination of the three mass spectrometry-based omics techniques can better entangle the functional and regional differences between PC and DC tissue compared to each single omics technique.
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Affiliation(s)
- Maryam Hemmati
- Bavarian Center for Biomolecular Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Susanne I Wudy
- Bavarian Center for Biomolecular Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Franziska Hackbarth
- Bavarian Center for Biomolecular Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Verena K Mittermeier-Kleßinger
- Chair of Food Chemistry and Molecular Sensory Science, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Olivia I Coleman
- Chair of Nutrition and Immunology, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Dirk Haller
- Chair of Nutrition and Immunology, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
- ZIEL Institute for Food and Health, Technical University of Munich, 85354 Freising, Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Corinna Dawid
- Bavarian Center for Biomolecular Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
- Chair of Food Chemistry and Molecular Sensory Science, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
- Professorship for Functional Phytometabolomics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
- ZIEL Institute for Food and Health, Technical University of Munich, 85354 Freising, Germany
| | - Karin Kleigrewe
- Bavarian Center for Biomolecular Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
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6
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Boggi B, Sharpen JDA, Taylor G, Drosou K. A novel integrated extraction protocol for multi-omic studies in heavily degraded samples. Sci Rep 2024; 14:17477. [PMID: 39080329 PMCID: PMC11289452 DOI: 10.1038/s41598-024-67104-8] [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: 01/19/2024] [Accepted: 07/08/2024] [Indexed: 08/02/2024] Open
Abstract
The combination of multi-omic techniques, such as genomics, transcriptomics, proteomics, metabolomics and epigenomics, has revolutionised studies in medical research. These techniques are employed to support biomarker discovery, better understand molecular pathways and identify novel drug targets. Despite concerted efforts in integrating omic datasets, there is an absence of protocols that integrate all four biomolecules in a single extraction process. Here, we demonstrate for the first time a minimally destructive integrated protocol for the simultaneous extraction of artificially degraded DNA, proteins, lipids and metabolites from pig brain samples. We used an MTBE-based approach to separate lipids and metabolites, followed by subsequent isolation of DNA and proteins. We have validated this protocol against standalone extraction protocols and show comparable or higher yields of all four biomolecules. This integrated protocol is key to facilitating the preservation of irreplaceable samples while promoting downstream analyses and successful data integration by removing bias from univariate dataset noise and varied distribution characteristics.
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Affiliation(s)
- Byron Boggi
- Faculty of Biology, Medicine and Health, Division of Cell Matrix Biology and Regenerative Medicine, University of Manchester, Manchester, M13 9PL, UK
| | - Jack D A Sharpen
- Faculty of Biology, Medicine and Health, Division of Cell Matrix Biology and Regenerative Medicine, University of Manchester, Manchester, M13 9PL, UK
| | - George Taylor
- Faculty of Biology, Medicine and Health, Research and Innovation, University of Manchester, Manchester, M13 9PG, UK
| | - Konstantina Drosou
- Faculty of Biology, Medicine and Health, Division of Cell Matrix Biology and Regenerative Medicine, University of Manchester, Manchester, M13 9PL, UK.
- Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK.
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7
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Vu N, Maile TM, Gollapudi S, Gaun A, Seitzer P, O'Brien JJ, Hackett SR, Zavala-Solorio J, McAllister FE, Kolumam G, Keyser R, Bennett BD. Automated preparation of plasma lipids, metabolites, and proteins for LC/MS-based analysis of a high-fat diet in mice. J Lipid Res 2024; 65:100607. [PMID: 39067520 PMCID: PMC11399584 DOI: 10.1016/j.jlr.2024.100607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Accepted: 07/19/2024] [Indexed: 07/30/2024] Open
Abstract
Blood plasma is one of the most commonly analyzed and easily accessible biological samples. Here, we describe an automated liquid-liquid extraction platform that generates accurate, precise, and reproducible samples for metabolomic, lipidomic, and proteomic analyses from a single aliquot of plasma while minimizing hands-on time and avoiding contamination from plasticware. We applied mass spectrometry to examine the metabolome, lipidome, and proteome of 90 plasma samples to determine the effects of age, time of day, and a high-fat diet in mice. From 25 μl of mouse plasma, we identified 907 lipid species from 16 different lipid classes and subclasses, 233 polar metabolites, and 344 proteins. We found that the high-fat diet induced only mild changes in the polar metabolome, upregulated apolipoproteins, and induced substantial shifts in the lipidome, including a significant increase in arachidonic acid and a decrease in eicosapentaenoic acid content across all lipid classes.
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Affiliation(s)
- Ngoc Vu
- Calico Life Sciences LLC, South San Francisco, CA, USA
| | | | | | | | | | | | | | | | | | | | - Rob Keyser
- Calico Life Sciences LLC, South San Francisco, CA, USA
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8
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Gegner HM, Naake T, Aljakouch K, Dugourd A, Kliewer G, Müller T, Schilling D, Schneider MA, Kunze-Rohrbach N, Grünewald TGP, Hell R, Saez-Rodriguez J, Huber W, Poschet G, Krijgsveld J. A single-sample workflow for joint metabolomic and proteomic analysis of clinical specimens. Clin Proteomics 2024; 21:49. [PMID: 38969985 PMCID: PMC11225228 DOI: 10.1186/s12014-024-09501-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 06/26/2024] [Indexed: 07/07/2024] Open
Abstract
Understanding the interplay of the proteome and the metabolome helps to understand cellular regulation and response. To enable robust inferences from such multi-omics analyses, we introduced and evaluated a workflow for combined proteome and metabolome analysis starting from a single sample. Specifically, we integrated established and individually optimized protocols for metabolomic and proteomic profiling (EtOH/MTBE and autoSP3, respectively) into a unified workflow (termed MTBE-SP3), and took advantage of the fact that the protein residue of the metabolomic sample can be used as a direct input for proteome analysis. We particularly evaluated the performance of proteome analysis in MTBE-SP3, and demonstrated equivalence of proteome profiles irrespective of prior metabolite extraction. In addition, MTBE-SP3 combines the advantages of EtOH/MTBE and autoSP3 for semi-automated metabolite extraction and fully automated proteome sample preparation, respectively, thus advancing standardization and scalability for large-scale studies. We showed that MTBE-SP3 can be applied to various biological matrices (FFPE tissue, fresh-frozen tissue, plasma, serum and cells) to enable implementation in a variety of clinical settings. To demonstrate applicability, we applied MTBE-SP3 and autoSP3 to a lung adenocarcinoma cohort showing consistent proteomic alterations between tumour and non-tumour adjacent tissue independent of the method used. Integration with metabolomic data obtained from the same samples revealed mitochondrial dysfunction in tumour tissue through deregulation of OGDH, SDH family enzymes and PKM. In summary, MTBE-SP3 enables the facile and reliable parallel measurement of proteins and metabolites obtained from the same sample, benefiting from reduced sample variation and input amount. This workflow is particularly applicable for studies with limited sample availability and offers the potential to enhance the integration of metabolomic and proteomic datasets.
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Affiliation(s)
- Hagen M Gegner
- Centre for Organismal Studies (COS), Metabolomics Core Technology Platform, Heidelberg University, Im Neuenheimer Feld 360, 69120, Heidelberg, Germany
| | - Thomas Naake
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117, Heidelberg, Germany
| | - Karim Aljakouch
- Faculty of Medicine, Heidelberg University, 69120, Heidelberg, Germany
- Division Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany
| | - Aurelien Dugourd
- Institute for Computational Biomedicine, Bioquant, Faculty of Medicine, Heidelberg University and Heidelberg University Hospital, Im Neuenheimer Feld 130, 69120, Heidelberg, Germany
| | - Georg Kliewer
- Faculty of Medicine, Heidelberg University, 69120, Heidelberg, Germany
- Division Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany
| | - Torsten Müller
- Faculty of Medicine, Heidelberg University, 69120, Heidelberg, Germany
- Division Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany
| | - Dustin Schilling
- Institute for Computational Biomedicine, Bioquant, Faculty of Medicine, Heidelberg University and Heidelberg University Hospital, Im Neuenheimer Feld 130, 69120, Heidelberg, Germany
| | - Marc A Schneider
- Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, Röntgenstraße 1, 69126, Heidelberg, Germany
- Translational Research Center Heidelberg (TLRC), Member of The German Center for Lung Research (DZL), Im Neuenheimer Feld 156, 69120, Heidelberg, Germany
| | - Nina Kunze-Rohrbach
- Centre for Organismal Studies (COS), Metabolomics Core Technology Platform, Heidelberg University, Im Neuenheimer Feld 360, 69120, Heidelberg, Germany
| | - Thomas G P Grünewald
- Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany
- Institute of Pathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, DKFZ and Heidelberg University Hospital, Heidelberg, Germany
| | - Rüdiger Hell
- Centre for Organismal Studies (COS), Metabolomics Core Technology Platform, Heidelberg University, Im Neuenheimer Feld 360, 69120, Heidelberg, Germany
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Bioquant, Faculty of Medicine, Heidelberg University and Heidelberg University Hospital, Im Neuenheimer Feld 130, 69120, Heidelberg, Germany
| | - Wolfgang Huber
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117, Heidelberg, Germany
| | - Gernot Poschet
- Centre for Organismal Studies (COS), Metabolomics Core Technology Platform, Heidelberg University, Im Neuenheimer Feld 360, 69120, Heidelberg, Germany.
| | - Jeroen Krijgsveld
- Faculty of Medicine, Heidelberg University, 69120, Heidelberg, Germany.
- Division Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany.
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9
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Michel L, Ferdinandy P, Rassaf T. Cellular Alterations in Immune Checkpoint Inhibitor Therapy-Related Cardiac Dysfunction. Curr Heart Fail Rep 2024; 21:214-223. [PMID: 38430308 PMCID: PMC11090976 DOI: 10.1007/s11897-024-00652-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/26/2024] [Indexed: 03/03/2024]
Abstract
PURPOSE OF REVIEW Immune checkpoint inhibitor (ICI) therapy has emerged as a pivotal advancement in cancer treatment, but the widespread adoption has given rise to a growing number of reports detailing significant cardiovascular toxicity. This review concentrates on elucidating the mechanisms behind ICI-related cardiovascular complications, emphasizing preclinical and mechanistic data. RECENT FINDINGS Accumulating evidence indicates a more significant role of immune checkpoints in maintaining cardiac integrity than previously understood, and new key scientific data are available to improve our understanding of ICI-related cardiovascular toxicity, including hidden cardiotoxicity. New avenues for innovative concepts are hypothesized, and opportunities to leverage the knowledge from ICI-therapy for pioneering approaches in related scientific domains can be derived from the latest scientific projects. Cardiotoxicity from ICI therapy is a paramount challenge for cardio-oncology. Understanding the underlying effects builds the foundation for tailored cardioprotective approaches in the growing collective at risk for severe cardiovascular complications.
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Affiliation(s)
- Lars Michel
- Department of Cardiology and Vascular Medicine, West German Heart and Vascular Center, University Hospital Essen, Hufelandstr. 55, 45147, Essen, Germany.
| | - Peter Ferdinandy
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Pharmahungary Group, Szeged, Hungary
| | - Tienush Rassaf
- Department of Cardiology and Vascular Medicine, West German Heart and Vascular Center, University Hospital Essen, Hufelandstr. 55, 45147, Essen, Germany
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10
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Glotzbach A, Rohlf K, Gonscharow A, Lüke S, Demirci Ö, Begher-Tibbe B, Overbeck N, Reinders J, Cadenas C, Hengstler JG, Edlund K, Marchan R. EDI3 knockdown in ER-HER2+ breast cancer cells reduces tumor burden and improves survival in two mouse models of experimental metastasis. Breast Cancer Res 2024; 26:87. [PMID: 38816770 PMCID: PMC11138102 DOI: 10.1186/s13058-024-01849-y] [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: 11/02/2023] [Accepted: 05/23/2024] [Indexed: 06/01/2024] Open
Abstract
BACKGROUND Despite progress understanding the mechanisms underlying tumor spread, metastasis remains a clinical challenge. We identified the choline-producing glycerophosphodiesterase, EDI3 and reported its association with metastasis-free survival in endometrial cancer. We also observed that silencing EDI3 slowed cell migration and other cancer-relevant phenotypes in vitro. Recent work demonstrated high EDI3 expression in ER-HER2+ breast cancer compared to the other molecular subtypes. Silencing EDI3 in ER-HER2+ cells significantly reduced cell survival in vitro and decreased tumor growth in vivo. However, a role for EDI3 in tumor metastasis in this breast cancer subtype was not explored. Therefore, in the present work we investigate whether silencing EDI3 in ER-HER2+ breast cancer cell lines alters phenotypes linked to metastasis in vitro, and metastasis formation in vivo using mouse models of experimental metastasis. METHODS To inducibly silence EDI3, luciferase-expressing HCC1954 cells were transduced with lentiviral particles containing shRNA oligos targeting EDI3 under the control of doxycycline. The effect on cell migration, adhesion, colony formation and anoikis was determined in vitro, and significant findings were confirmed in a second ER-HER2+ cell line, SUM190PT. Doxycycline-induced HCC1954-luc shEDI3 cells were injected into the tail vein or peritoneum of immunodeficient mice to generate lung and peritoneal metastases, respectively and monitored using non-invasive bioluminescence imaging. Metabolite levels in cells and tumor tissue were analyzed using targeted mass spectrometry and MALDI mass spectrometry imaging (MALDI-MSI), respectively. RESULTS Inducibly silencing EDI3 reduced cell adhesion and colony formation, as well as increased susceptibility to anoikis in HCC1954-luc cells, which was confirmed in SUM190PT cells. No influence on cell migration was observed. Reduced luminescence was seen in lungs and peritoneum of mice injected with cells expressing less EDI3 after tail vein and intraperitoneal injection, respectively, indicative of reduced metastasis. Importantly, mice injected with EDI3-silenced cells survived longer. Closer analysis of the peritoneal organs revealed that silencing EDI3 had no effect on metastatic organotropism but instead reduced metastatic burden. Finally, metabolic analyses revealed significant changes in choline and glycerophospholipid metabolites in cells and in pancreatic metastases in vivo. CONCLUSIONS Reduced metastasis upon silencing supports EDI3's potential as a treatment target in metastasizing ER-HER2+ breast cancer.
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Affiliation(s)
- Annika Glotzbach
- Leibniz Research Centre for Working Environment and Human Factors at the TU Dortmund (IfADo), Ardeystrasse 67, 44139, Dortmund, Germany
| | - Katharina Rohlf
- Leibniz Research Centre for Working Environment and Human Factors at the TU Dortmund (IfADo), Ardeystrasse 67, 44139, Dortmund, Germany
| | - Anastasia Gonscharow
- Leibniz Research Centre for Working Environment and Human Factors at the TU Dortmund (IfADo), Ardeystrasse 67, 44139, Dortmund, Germany
| | - Simon Lüke
- Leibniz Research Centre for Working Environment and Human Factors at the TU Dortmund (IfADo), Ardeystrasse 67, 44139, Dortmund, Germany
| | - Özlem Demirci
- Leibniz Research Centre for Working Environment and Human Factors at the TU Dortmund (IfADo), Ardeystrasse 67, 44139, Dortmund, Germany
- Department of Biology, Science Faculty, Dicle University, Diyarbakir, Turkey
| | - Brigitte Begher-Tibbe
- Leibniz Research Centre for Working Environment and Human Factors at the TU Dortmund (IfADo), Ardeystrasse 67, 44139, Dortmund, Germany
| | - Nina Overbeck
- Leibniz Research Centre for Working Environment and Human Factors at the TU Dortmund (IfADo), Ardeystrasse 67, 44139, Dortmund, Germany
| | - Jörg Reinders
- Leibniz Research Centre for Working Environment and Human Factors at the TU Dortmund (IfADo), Ardeystrasse 67, 44139, Dortmund, Germany
| | - Cristina Cadenas
- Leibniz Research Centre for Working Environment and Human Factors at the TU Dortmund (IfADo), Ardeystrasse 67, 44139, Dortmund, Germany
| | - Jan G Hengstler
- Leibniz Research Centre for Working Environment and Human Factors at the TU Dortmund (IfADo), Ardeystrasse 67, 44139, Dortmund, Germany
| | - Karolina Edlund
- Leibniz Research Centre for Working Environment and Human Factors at the TU Dortmund (IfADo), Ardeystrasse 67, 44139, Dortmund, Germany
| | - Rosemarie Marchan
- Leibniz Research Centre for Working Environment and Human Factors at the TU Dortmund (IfADo), Ardeystrasse 67, 44139, Dortmund, Germany.
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11
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Wu J, Xu QQ, Jiang YR, Chen JB, Ying WX, Fan QX, Wang HF, Wang Y, Shi SW, Pan JZ, Fang Q. One-Shot Single-Cell Proteome and Metabolome Analysis Strategy for the Same Single Cell. Anal Chem 2024; 96:5499-5508. [PMID: 38547315 DOI: 10.1021/acs.analchem.3c05659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
Characterizing the profiles of proteome and metabolome at the single-cell level is of great significance in single-cell multiomic studies. Herein, we proposed a novel strategy called one-shot single-cell proteome and metabolome analysis (scPMA) to acquire the proteome and metabolome information in a single-cell individual in one injection of LC-MS/MS analysis. Based on the scPMA strategy, a total workflow was developed to achieve the single-cell capture, nanoliter-scale sample pretreatment, one-shot LC injection and separation of the enzyme-digested peptides and metabolites, and dual-zone MS/MS detection for proteome and metabolome profiling. Benefiting from the scPMA strategy, we realized dual-omic analysis of single tumor cells, including A549, HeLa, and HepG2 cells with 816, 578, and 293 protein groups and 72, 91, and 148 metabolites quantified on average. A single-cell perspective experiment for investigating the doxorubicin-induced antitumor effects in both the proteome and metabolome aspects was also performed.
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Affiliation(s)
- Jie Wu
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Qin-Qin Xu
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Yi-Rong Jiang
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Jian-Bo Chen
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Wei-Xin Ying
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Qian-Xi Fan
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Hui-Feng Wang
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311200, China
| | - Yu Wang
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311200, China
| | - Shao-Wen Shi
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311200, China
| | - Jian-Zhang Pan
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311200, China
| | - Qun Fang
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311200, China
- Key Laboratory for Biomedical Engineering of Ministry of Education, Cancer Center, Zhejiang University, Hangzhou 310007, China
- Key Laboratory of Excited-State Materials of Zhejiang Province, Zhejiang University, Hangzhou 310007, China
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
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12
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Huang Y, Swarge BN, Roseboom W, Bleeker JD, Brul S, Setlow P, Kramer G. Integrative Metabolomics and Proteomics Allow the Global Intracellular Characterization of Bacillus subtilis Cells and Spores. J Proteome Res 2024; 23:596-608. [PMID: 38190553 PMCID: PMC10845140 DOI: 10.1021/acs.jproteome.3c00386] [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: 06/29/2023] [Revised: 12/01/2023] [Accepted: 12/08/2023] [Indexed: 01/10/2024]
Abstract
Reliable and comprehensive multi-omics analysis is essential for researchers to understand and explore complex biological systems more completely. Bacillus subtilis (B. subtilis) is a model organism for Gram-positive spore-forming bacteria, and in-depth insight into the physiology and molecular basis of spore formation and germination in this organism requires advanced multilayer molecular data sets generated from the same sample. In this study, we evaluated two monophasic methods for polar and nonpolar compound extraction (acetonitrile/methanol/water; isopropanol/water, and 60% ethanol) and two biphasic methods (chloroform/methanol/water, and methyl tert-butyl ether/methanol/water) on coefficients of variation of analytes, identified metabolite composition, and the quality of proteomics profiles. The 60% EtOH protocol proved to be the easiest in sample processing and was more amenable to automation. Collectively, we annotated 505 and 484 metabolites and identified 1665 and 1562 proteins in B. subtilis vegetative cells and spores, respectively. We also show differences between vegetative cells and spores from a multi-omics perspective and demonstrate that an integrative multi-omics analysis can be implemented from one sample using the 60% EtOH protocol. The results obtained by the 60% EtOH protocol provide comprehensive insight into differences in the metabolic and protein makeup of B. subtilis vegetative cells and spores.
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Affiliation(s)
- Yixuan Huang
- Laboratory
for Mass Spectrometry of Biomolecules, Swammerdam Institute for Life
Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
- Molecular
Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Bhagyashree N. Swarge
- Laboratory
for Mass Spectrometry of Biomolecules, Swammerdam Institute for Life
Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
- Molecular
Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Winfried Roseboom
- Laboratory
for Mass Spectrometry of Biomolecules, Swammerdam Institute for Life
Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Jurre D. Bleeker
- Laboratory
for Mass Spectrometry of Biomolecules, Swammerdam Institute for Life
Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Stanley Brul
- Molecular
Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Peter Setlow
- Department
of Molecular Biology and Biophysics, UConn
Health, Farmington, Connecticut 06030-3305, United States
| | - Gertjan Kramer
- Laboratory
for Mass Spectrometry of Biomolecules, Swammerdam Institute for Life
Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
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13
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Gadara D, Berka V, Spacil Z. High-Throughput Microbore LC-MS Lipidomics to Investigate APOE Phenotypes. Anal Chem 2024; 96:59-66. [PMID: 38113351 PMCID: PMC10782415 DOI: 10.1021/acs.analchem.3c02652] [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: 06/18/2023] [Revised: 11/13/2023] [Accepted: 11/16/2023] [Indexed: 12/21/2023]
Abstract
Microflow liquid chromatography interfaced with mass spectrometry (μLC-MS/MS) is increasingly applied for high-throughput profiling of biological samples and has been proven to have an acceptable trade-off between sensitivity and reproducibility. However, lipidomics applications are scarce. We optimized a μLC-MS/MS system utilizing a 1 mm inner diameter × 100 mm column coupled to a triple quadrupole mass spectrometer to establish a sensitive, high-throughput, and robust single-shot lipidomics workflow. Compared to conventional lipidomics methods, we achieve a ∼4-fold increase in response, facilitating quantification of 351 lipid species from a single iPSC-derived cerebral organoid during a 15 min LC-MS analysis. Consecutively, we injected 303 samples over ∼75 h to prove the robustness and reproducibility of the microflow separation. As a proof of concept, μLC-MS/MS analysis of Alzheimer's disease patient-derived iPSC cerebral organoid reveals differential lipid metabolism depending on APOE phenotype (E3/3 vs E4/4). Microflow separation proves to be an environmentally friendly and cost-effective method as it reduces the consumption of harmful solvents. Also, the data demonstrate robust, in-depth, high-throughput performance to enable routine clinical or biomedical applications.
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Affiliation(s)
- Darshak Gadara
- RECETOX
Centre, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
| | - Vratislav Berka
- RECETOX
Centre, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
| | - Zdenek Spacil
- RECETOX
Centre, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
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14
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Mok JH, Joo M, Cho S, Duong VA, Song H, Park JM, Lee H. Optimizing MS-Based Multi-Omics: Comparative Analysis of Protein, Metabolite, and Lipid Extraction Techniques. Metabolites 2024; 14:34. [PMID: 38248837 PMCID: PMC10820684 DOI: 10.3390/metabo14010034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 12/29/2023] [Accepted: 12/30/2023] [Indexed: 01/23/2024] Open
Abstract
Multi-omics integrates diverse types of biological information from genomic, proteomic, and metabolomics experiments to achieve a comprehensive understanding of complex cellular mechanisms. However, this approach is also challenging due to technical issues such as limited sample quantities, the complexity of data pre-processing, and reproducibility concerns. Furthermore, existing studies have primarily focused on technical performance assessment and the presentation of modified protocols through quantitative comparisons of the identified protein counts. Nevertheless, the specific differences in these comparisons have been minimally investigated. Here, findings obtained from various omics approaches were profiled using various extraction methods (methanol extraction, the Folch method, and Matyash methods for metabolites and lipids) and two digestion methods (filter-aided sample preparation (FASP) and suspension traps (S-Trap)) for resuspended proteins. FASP was found to be more effective for the identification of membrane-related proteins, whereas S-Trap excelled in isolating nuclear-related and RNA-processing proteins. Thus, FASP may be suitable for investigating the immune response and bacterial infection pathways, whereas S-Trap may be more effective for studies focused on the mechanisms of neurodegenerative diseases. Moreover, regarding the choice of extraction method, the single-phase method identified organic compounds and compounds related to fatty acids, whereas the two-phase extraction method identified more hydrophilic compounds such as nucleotides. Lipids with strong hydrophobicity, such as ChE and TG, were identified in the two-phase extraction results. These findings highlight that significant differences among small molecules are primarily identified due to the varying polarities of extraction solvents. These results, obtained by considering variables such as human error and batch effects in the sample preparation step, offer comprehensive and detailed results not previously provided by existing studies, thereby aiding in the selection of the most suitable pre-processing approach.
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Affiliation(s)
- Jeong-Hun Mok
- Department of Medical Device Management and Research, SAIHST, Sungkyunkwan University, 115, Irwon-ro, Gangnam-gu, Seoul 06355, Republic of Korea;
| | - Minjoong Joo
- Basilbiotech, 157-20, Sinsong-ro, Yeonsu-gu, Incheon 22002, Republic of Korea; (M.J.); (S.C.)
| | - Seonghyeon Cho
- Basilbiotech, 157-20, Sinsong-ro, Yeonsu-gu, Incheon 22002, Republic of Korea; (M.J.); (S.C.)
| | - Van-An Duong
- College of Pharmacy, Gachon University, 191, Hambangmoe-ro, Yeonsu-gu, Incheon 21936, Republic of Korea; (V.-A.D.); (H.S.)
| | - Haneul Song
- College of Pharmacy, Gachon University, 191, Hambangmoe-ro, Yeonsu-gu, Incheon 21936, Republic of Korea; (V.-A.D.); (H.S.)
| | - Jong-Moon Park
- Basilbiotech, 157-20, Sinsong-ro, Yeonsu-gu, Incheon 22002, Republic of Korea; (M.J.); (S.C.)
| | - Hookeun Lee
- College of Pharmacy, Gachon University, 191, Hambangmoe-ro, Yeonsu-gu, Incheon 21936, Republic of Korea; (V.-A.D.); (H.S.)
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15
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Pade LR, Stepler KE, Portero EP, DeLaney K, Nemes P. Biological mass spectrometry enables spatiotemporal 'omics: From tissues to cells to organelles. MASS SPECTROMETRY REVIEWS 2024; 43:106-138. [PMID: 36647247 PMCID: PMC10668589 DOI: 10.1002/mas.21824] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/14/2022] [Accepted: 09/17/2022] [Indexed: 06/17/2023]
Abstract
Biological processes unfold across broad spatial and temporal dimensions, and measurement of the underlying molecular world is essential to their understanding. Interdisciplinary efforts advanced mass spectrometry (MS) into a tour de force for assessing virtually all levels of the molecular architecture, some in exquisite detection sensitivity and scalability in space-time. In this review, we offer vignettes of milestones in technology innovations that ushered sample collection and processing, chemical separation, ionization, and 'omics analyses to progressively finer resolutions in the realms of tissue biopsies and limited cell populations, single cells, and subcellular organelles. Also highlighted are methodologies that empowered the acquisition and analysis of multidimensional MS data sets to reveal proteomes, peptidomes, and metabolomes in ever-deepening coverage in these limited and dynamic specimens. In pursuit of richer knowledge of biological processes, we discuss efforts pioneering the integration of orthogonal approaches from molecular and functional studies, both within and beyond MS. With established and emerging community-wide efforts ensuring scientific rigor and reproducibility, spatiotemporal MS emerged as an exciting and powerful resource to study biological systems in space-time.
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Affiliation(s)
- Leena R. Pade
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Kaitlyn E. Stepler
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Erika P. Portero
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Kellen DeLaney
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Peter Nemes
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
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16
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Kale D, Fatangare A, Phapale P, Sickmann A. Blood-Derived Lipid and Metabolite Biomarkers in Cardiovascular Research from Clinical Studies: A Recent Update. Cells 2023; 12:2796. [PMID: 38132115 PMCID: PMC10741540 DOI: 10.3390/cells12242796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/24/2023] [Accepted: 12/01/2023] [Indexed: 12/23/2023] Open
Abstract
The primary prevention, early detection, and treatment of cardiovascular disease (CVD) have been long-standing scientific research goals worldwide. In the past decades, traditional blood lipid profiles have been routinely used in clinical practice to estimate the risk of CVDs such as atherosclerotic cardiovascular disease (ASCVD) and as treatment targets for the primary prevention of adverse cardiac events. These blood lipid panel tests often fail to fully predict all CVD risks and thus need to be improved. A comprehensive analysis of molecular species of lipids and metabolites (defined as lipidomics and metabolomics, respectively) can provide molecular insights into the pathophysiology of the disease and could serve as diagnostic and prognostic indicators of disease. Mass spectrometry (MS) and nuclear magnetic resonance (NMR)-based lipidomics and metabolomics analysis have been increasingly used to study the metabolic changes that occur during CVD pathogenesis. In this review, we provide an overview of various MS-based platforms and approaches that are commonly used in lipidomics and metabolomics workflows. This review summarizes the lipids and metabolites in human plasma/serum that have recently (from 2018 to December 2022) been identified as promising CVD biomarkers. In addition, this review describes the potential pathophysiological mechanisms associated with candidate CVD biomarkers. Future studies focused on these potential biomarkers and pathways will provide mechanistic clues of CVD pathogenesis and thus help with the risk assessment, diagnosis, and treatment of CVD.
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Affiliation(s)
- Dipali Kale
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44139 Dortmund, Germany; (A.F.); (P.P.)
| | | | | | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44139 Dortmund, Germany; (A.F.); (P.P.)
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17
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He Y, Yuan H, Liang Y, Liu X, Zhang X, Ji Y, Zhao B, Yang K, Zhang J, Zhang S, Zhang Y, Zhang L. On-capillary alkylation micro-reactor: a facile strategy for proteo-metabolome profiling in the same single cells. Chem Sci 2023; 14:13495-13502. [PMID: 38033888 PMCID: PMC10686037 DOI: 10.1039/d3sc05047e] [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: 09/26/2023] [Accepted: 11/02/2023] [Indexed: 12/02/2023] Open
Abstract
Single-cell multi-omics analysis can provide comprehensive insights to study cell-to-cell heterogeneity in normal and disease physiology. However, due to the lack of amplification technique, the measurement of proteome and metabolome in the same cell is challenging. Herein, a novel on-capillary alkylation micro-reactor (OCAM) was developed to achieve proteo-metabolome profiling in the same single cells, by which proteins were first covalently bound to an iodoacetic acid functionalized open-tubular capillary micro-reactor via sulfhydryl alkylation reaction, and metabolites were rapidly eluted, followed by on-column digestion of captured proteins. Compared with existing methods for low-input proteome sample preparation, OCAM exhibited improved efficiency, anti-interference ability and recovery, enabling the identification of an average of 1509 protein groups in single HeLa cells. This strategy was applied to single-cell proteo-metabolome analysis of mouse oocytes at different stages, 3457 protein groups and 171 metabolites were identified in single oocytes, which is the deepest coverage of proteome and metabolome from single mouse oocytes to date, achieving complementary characterization of metabolic patterns during oocyte maturation.
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Affiliation(s)
- Yingyun He
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Huiming Yuan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Yu Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Xinxin Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Xiaozhe Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Yahui Ji
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Baofeng Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Kaiguang Yang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Jue Zhang
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA Changsha 410013 China
| | - Shen Zhang
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA Changsha 410013 China
| | - Yukui Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
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18
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Koh J, Woo YD, Yoo HJ, Choi JP, Kim SH, Chang YS, Jung KC, Kim JH, Jeon YK, Kim HY, Chung DH. De novo fatty-acid synthesis protects invariant NKT cells from cell death, thereby promoting their homeostasis and pathogenic roles in airway hyperresponsiveness. eLife 2023; 12:RP87536. [PMID: 37917548 PMCID: PMC10622147 DOI: 10.7554/elife.87536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023] Open
Abstract
Invariant natural-killer T (iNKT) cells play pathogenic roles in allergic asthma in murine models and possibly also humans. While many studies show that the development and functions of innate and adaptive immune cells depend on their metabolic state, the evidence for this in iNKT cells is very limited. It is also not clear whether such metabolic regulation of iNKT cells could participate in their pathogenic activities in asthma. Here, we showed that acetyl-coA-carboxylase 1 (ACC1)-mediated de novo fatty-acid synthesis is required for the survival of iNKT cells and their deleterious functions in allergic asthma. ACC1, which is a key fatty-acid synthesis enzyme, was highly expressed by lung iNKT cells from WT mice that were developing asthma. Cd4-Cre::Acc1fl/fl mice failed to develop OVA-induced and HDM-induced asthma. Moreover, iNKT cell-deficient mice that were reconstituted with ACC1-deficient iNKT cells failed to develop asthma, unlike when WT iNKT cells were transferred. ACC1 deficiency in iNKT cells associated with reduced expression of fatty acid-binding proteins (FABPs) and peroxisome proliferator-activated receptor (PPAR)γ, but increased glycolytic capacity that promoted iNKT-cell death. Furthermore, circulating iNKT cells from allergic-asthma patients expressed higher ACC1 and PPARG levels than the corresponding cells from non-allergic-asthma patients and healthy individuals. Thus, de novo fatty-acid synthesis prevents iNKT-cell death via an ACC1-FABP-PPARγ axis, which contributes to their homeostasis and their pathogenic roles in allergic asthma.
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Affiliation(s)
- Jaemoon Koh
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Laboratory of Immune Regulation in Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yeon Duk Woo
- Laboratory of Immune Regulation in Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hyun Jung Yoo
- Laboratory of Immunology and Vaccine Innovation, Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Jun-Pyo Choi
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Sae Hoon Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
- Institute of Allergy and Clinical Immunology, Seoul National University Medical Research Council, Seoul, Republic of Korea
| | - Yoon-Seok Chang
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
- Institute of Allergy and Clinical Immunology, Seoul National University Medical Research Council, Seoul, Republic of Korea
| | - Kyeong Cheon Jung
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ji Hyung Kim
- Laboratory of Immunology and Vaccine Innovation, Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Yoon Kyung Jeon
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hye Young Kim
- Laboratory of Immune Regulation in Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Doo Hyun Chung
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Laboratory of Immune Regulation in Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
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19
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Troppmair N, Kopczynski D, Assinger A, Lehmann R, Coman C, Ahrends R. Accurate Sphingolipid Quantification Reducing Fragmentation Bias by Nonlinear Models. Anal Chem 2023; 95:15227-15235. [PMID: 37782305 PMCID: PMC10585660 DOI: 10.1021/acs.analchem.3c02445] [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: 06/06/2023] [Accepted: 09/07/2023] [Indexed: 10/03/2023]
Abstract
Quantitative sphingolipid analysis is crucial for understanding the roles of these bioactive molecules in various physiological and pathological contexts. Molecular sphingolipid species are typically quantified using sphingoid base-derived fragments relative to a class-specific internal standard. However, the commonly employed "one standard per class" strategy fails to account for fragmentation differences presented by the structural diversity of sphingolipids. To address this limitation, we developed a novel approach for quantitative sphingolipid analysis. This approach utilizes fragmentation models to correct for structural differences and thus overcomes the limitations associated with using a limited number of standards for quantification. Importantly, our method is independent of the internal standard, instrumental setup, and collision energy. Furthermore, we integrated this method into a user-friendly KNIME workflow. The validation results illustrate the effectiveness of our approach in accurately quantifying ceramide subclasses from various biological matrices. This breakthrough opens up new avenues for exploring sphingolipid metabolism and gaining insights into its implications.
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Affiliation(s)
- Nina Troppmair
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
- Vienna
Doctoral School in Chemistry, University
of Vienna, 1090 Vienna, Austria
| | - Dominik Kopczynski
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Alice Assinger
- Department
of Vascular Biology and Thrombosis Research, Center of Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Rainer Lehmann
- Institute
for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic
Laboratory Medicine, University Hospital
Tuebingen, 72076 Tuebingen, Germany
| | - Cristina Coman
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Robert Ahrends
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
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20
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de Jonckheere B, Kollotzek F, Münzer P, Göb V, Fischer M, Mott K, Coman C, Troppmair NN, Manke MC, Zdanyte M, Harm T, Sigle M, Kopczynski D, Bileck A, Gerner C, Hoffmann N, Heinzmann D, Assinger A, Gawaz M, Stegner D, Schulze H, Borst O, Ahrends R. Critical shifts in lipid metabolism promote megakaryocyte differentiation and proplatelet formation. NATURE CARDIOVASCULAR RESEARCH 2023; 2:835-852. [PMID: 38075556 PMCID: PMC7615361 DOI: 10.1038/s44161-023-00325-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 07/27/2023] [Indexed: 08/29/2024]
Abstract
During megakaryopoiesis, megakaryocytes (MK) undergo cellular morphological changes with strong modification of membrane composition and lipid signaling. Here we adopt a lipid-centric multiomics approach to create a quantitative map of the MK lipidome during maturation and proplatelet formation. Data reveal that MK differentiation is driven by an increased fatty acyl import and de novo lipid synthesis, resulting in an anionic membrane phenotype. Pharmacological perturbation of fatty acid import and phospholipid synthesis blocked membrane remodeling and directly reduced MK polyploidization and proplatelet formation resulting in thrombocytopenia. The anionic lipid shift during megakaryopoiesis was paralleled by lipid-dependent relocalization of the scaffold protein CKIP-1 and recruitment of the kinase CK2α to the plasma membrane, which seems to be essential for sufficient platelet biogenesis. Overall, this study provides a framework to understand how the MK lipidome is altered during maturation and the impact of MK membrane lipid remodeling on MK kinase signaling involved in thrombopoiesis.
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Affiliation(s)
- Bianca de Jonckheere
- Institute of Analytical Chemistry, University of Vienna, Austria
- Vienna Doctoral School in Chemistry, University of Vienna, Austria
| | - Ferdinand Kollotzek
- DFG Heisenberg Group Cardiovascular Thromboinflammation and Translational Thrombocardiology, University of Tübingen, Germany
- Department of Cardiology and Angiology, University of Tübingen, Germany
| | - Patrick Münzer
- DFG Heisenberg Group Cardiovascular Thromboinflammation and Translational Thrombocardiology, University of Tübingen, Germany
- Department of Cardiology and Angiology, University of Tübingen, Germany
| | - Vanessa Göb
- Institute for Experimental Biomedicine, University Hospital Würzburg, Germany
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Würzburg, Germany
| | - Melina Fischer
- DFG Heisenberg Group Cardiovascular Thromboinflammation and Translational Thrombocardiology, University of Tübingen, Germany
- Department of Cardiology and Angiology, University of Tübingen, Germany
| | - Kristina Mott
- Institute for Experimental Biomedicine, University Hospital Würzburg, Germany
| | - Cristina Coman
- Institute of Analytical Chemistry, University of Vienna, Austria
| | - Nina Nicole Troppmair
- Institute of Analytical Chemistry, University of Vienna, Austria
- Vienna Doctoral School in Chemistry, University of Vienna, Austria
| | - Mailin-Christin Manke
- DFG Heisenberg Group Cardiovascular Thromboinflammation and Translational Thrombocardiology, University of Tübingen, Germany
- Department of Cardiology and Angiology, University of Tübingen, Germany
| | - Monika Zdanyte
- DFG Heisenberg Group Cardiovascular Thromboinflammation and Translational Thrombocardiology, University of Tübingen, Germany
- Department of Cardiology and Angiology, University of Tübingen, Germany
| | - Tobias Harm
- Department of Cardiology and Angiology, University of Tübingen, Germany
| | - Manuel Sigle
- Department of Cardiology and Angiology, University of Tübingen, Germany
| | | | - Andrea Bileck
- Institute of Analytical Chemistry, University of Vienna, Austria
- Joint Metabolome Facility, University of Vienna and Medical University of Vienna, Austria
| | - Christopher Gerner
- Institute of Analytical Chemistry, University of Vienna, Austria
- Joint Metabolome Facility, University of Vienna and Medical University of Vienna, Austria
| | - Nils Hoffmann
- Institute of Analytical Chemistry, University of Vienna, Austria
- Forschungszentrum Jülich GmbH, Institute for Bio- and Geosciences (IBG-5) Jülich, Germany
| | - David Heinzmann
- Department of Cardiology and Angiology, University of Tübingen, Germany
| | - Alice Assinger
- Institute of Physiology, Centre of Physiology and Pharmacology, Medical University of Vienna, Austria
| | - Meinrad Gawaz
- Department of Cardiology and Angiology, University of Tübingen, Germany
| | - David Stegner
- Institute for Experimental Biomedicine, University Hospital Würzburg, Germany
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Würzburg, Germany
| | - Harald Schulze
- Institute for Experimental Biomedicine, University Hospital Würzburg, Germany
| | - Oliver Borst
- DFG Heisenberg Group Cardiovascular Thromboinflammation and Translational Thrombocardiology, University of Tübingen, Germany
- Department of Cardiology and Angiology, University of Tübingen, Germany
| | - Robert Ahrends
- Institute of Analytical Chemistry, University of Vienna, Austria
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21
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Kelliher JM, Robinson AJ, Longley R, Johnson LYD, Hanson BT, Morales DP, Cailleau G, Junier P, Bonito G, Chain PSG. The endohyphal microbiome: current progress and challenges for scaling down integrative multi-omic microbiome research. MICROBIOME 2023; 11:192. [PMID: 37626434 PMCID: PMC10463477 DOI: 10.1186/s40168-023-01634-7] [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: 03/01/2023] [Accepted: 07/29/2023] [Indexed: 08/27/2023]
Abstract
As microbiome research has progressed, it has become clear that most, if not all, eukaryotic organisms are hosts to microbiomes composed of prokaryotes, other eukaryotes, and viruses. Fungi have only recently been considered holobionts with their own microbiomes, as filamentous fungi have been found to harbor bacteria (including cyanobacteria), mycoviruses, other fungi, and whole algal cells within their hyphae. Constituents of this complex endohyphal microbiome have been interrogated using multi-omic approaches. However, a lack of tools, techniques, and standardization for integrative multi-omics for small-scale microbiomes (e.g., intracellular microbiomes) has limited progress towards investigating and understanding the total diversity of the endohyphal microbiome and its functional impacts on fungal hosts. Understanding microbiome impacts on fungal hosts will advance explorations of how "microbiomes within microbiomes" affect broader microbial community dynamics and ecological functions. Progress to date as well as ongoing challenges of performing integrative multi-omics on the endohyphal microbiome is discussed herein. Addressing the challenges associated with the sample extraction, sample preparation, multi-omic data generation, and multi-omic data analysis and integration will help advance current knowledge of the endohyphal microbiome and provide a road map for shrinking microbiome investigations to smaller scales. Video Abstract.
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Affiliation(s)
| | | | - Reid Longley
- Los Alamos National Laboratory, Los Alamos, NM, USA
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22
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Costa AC, Riça LB, van de Bilt M, Zandonadi FS, Gattaz WF, Talib LL, Sussulini A. Application of Lipidomics in Psychiatry: Plasma-Based Potential Biomarkers in Schizophrenia and Bipolar Disorder. Metabolites 2023; 13:metabo13050600. [PMID: 37233641 DOI: 10.3390/metabo13050600] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/19/2023] [Accepted: 04/24/2023] [Indexed: 05/27/2023] Open
Abstract
In this study, we obtained a lipidomic profile of plasma samples from drug-naïve patients with schizophrenia (SZ) and bipolar disorder (BD) in comparison to healthy controls. The sample cohort consisted of 30 BD and 30 SZ patients and 30 control individuals. An untargeted lipidomics strategy using liquid chromatography coupled with high-resolution mass spectrometry was employed to obtain the lipid profiles. Data were preprocessed, then univariate (t-test) and multivariate (principal component analysis and orthogonal partial least squares discriminant analysis) statistical tools were applied to select differential lipids, which were putatively identified. Afterward, multivariate receiver operating characteristic tests were performed, and metabolic pathway networks were constructed, considering the differential lipids. Our results demonstrate alterations in distinct lipid pathways, especially in glycerophospholipids, sphingolipids and glycerolipids, between SZ and BD patients. The results obtained in this study may serve as a basis for differential diagnosis, which is crucial for effective treatment and improving the quality of life of patients with psychotic disorders.
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Affiliation(s)
- Alana C Costa
- Laboratory of Neuroscience (LIM-27), Department and Institute of Psychiatry, University of Sao Paulo Medical School, Sao Paulo 05403903, Brazil
- Instituto Nacional de Biomarcadores em Neuropsiquiatria (INBioN), Conselho Nacional de Desenvolvimento Científico e Tecnológico, Sao Paulo 05403903, Brazil
| | - Larissa B Riça
- Laboratory of Bioanalytics and Integrated Omics (LaBIOmics), Institute of Chemistry, University of Campinas (UNICAMP), Campinas 13083970, Brazil
| | - Martinus van de Bilt
- Laboratory of Neuroscience (LIM-27), Department and Institute of Psychiatry, University of Sao Paulo Medical School, Sao Paulo 05403903, Brazil
- Instituto Nacional de Biomarcadores em Neuropsiquiatria (INBioN), Conselho Nacional de Desenvolvimento Científico e Tecnológico, Sao Paulo 05403903, Brazil
| | - Flávia S Zandonadi
- Laboratory of Bioanalytics and Integrated Omics (LaBIOmics), Institute of Chemistry, University of Campinas (UNICAMP), Campinas 13083970, Brazil
| | - Wagner F Gattaz
- Laboratory of Neuroscience (LIM-27), Department and Institute of Psychiatry, University of Sao Paulo Medical School, Sao Paulo 05403903, Brazil
- Instituto Nacional de Biomarcadores em Neuropsiquiatria (INBioN), Conselho Nacional de Desenvolvimento Científico e Tecnológico, Sao Paulo 05403903, Brazil
| | - Leda L Talib
- Laboratory of Neuroscience (LIM-27), Department and Institute of Psychiatry, University of Sao Paulo Medical School, Sao Paulo 05403903, Brazil
- Instituto Nacional de Biomarcadores em Neuropsiquiatria (INBioN), Conselho Nacional de Desenvolvimento Científico e Tecnológico, Sao Paulo 05403903, Brazil
| | - Alessandra Sussulini
- Laboratory of Bioanalytics and Integrated Omics (LaBIOmics), Institute of Chemistry, University of Campinas (UNICAMP), Campinas 13083970, Brazil
- Instituto Nacional de Ciência e Tecnologia de Bioanalítica (INCTBio), Institute of Chemistry, University of Campinas (UNICAMP), Campinas 13083970, Brazil
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23
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Schäfer JA, Sutandy FXR, Münch C. Omics-based approaches for the systematic profiling of mitochondrial biology. Mol Cell 2023; 83:911-926. [PMID: 36931258 DOI: 10.1016/j.molcel.2023.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 02/06/2023] [Accepted: 02/14/2023] [Indexed: 03/18/2023]
Abstract
Mitochondria are essential for cellular functions such as metabolism and apoptosis. They dynamically adapt to the changing environmental demands by adjusting their protein, nucleic acid, metabolite, and lipid contents. In addition, the mitochondrial components are modulated on different levels in response to changes, including abundance, activity, and interaction. A wide range of omics-based approaches has been developed to be able to explore mitochondrial adaptation and how mitochondrial function is compromised in disease contexts. Here, we provide an overview of the omics methods that allow us to systematically investigate the different aspects of mitochondrial biology. In addition, we show examples of how these methods have provided new biological insights. The emerging use of these toolboxes provides a more comprehensive understanding of the processes underlying mitochondrial function.
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Affiliation(s)
- Jasmin Adriana Schäfer
- Institute of Biochemistry II, Goethe University Frankfurt, Theodor-Stern-Kai 7, Haus 75, 60590 Frankfurt am Main, Germany
| | - F X Reymond Sutandy
- Institute of Biochemistry II, Goethe University Frankfurt, Theodor-Stern-Kai 7, Haus 75, 60590 Frankfurt am Main, Germany
| | - Christian Münch
- Institute of Biochemistry II, Goethe University Frankfurt, Theodor-Stern-Kai 7, Haus 75, 60590 Frankfurt am Main, Germany.
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24
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Kao CY, Chang CT, Kuo PY, Lin CJ, Chiu HH, Liao HW. Sequential isolation of metabolites and lipids from a single sample to achieve multiomics by using TRIzol reagent. Talanta 2023; 258:124416. [PMID: 36889188 DOI: 10.1016/j.talanta.2023.124416] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 02/13/2023] [Accepted: 03/02/2023] [Indexed: 03/06/2023]
Abstract
Simultaneous extraction of various types of biomolecule from a single sample can be beneficial for multiomics studies of unique specimens. An efficient and convenient sample preparation approach must be developed that can comprehensively isolate and extract biomolecules from one sample. TRIzol reagent is widely used in biological studies for DNA, RNA, and protein isolation. This study evaluated the feasibility of using TRIzol reagent for the simultaneous isolation of not only DNA, RNA, and proteins but also metabolites and lipids from a single sample. Through the comparison of known metabolites and lipids obtained using the conventional methanol (MeOH) and methyl-tert-butyl ether (MTBE) extraction methods, we determined the presence of metabolites and lipids in the supernatant during TRIzol sequential isolation. Finally, we performed untargeted metabolomics and lipidomics to examine metabolite and lipid alterations associated with the jhp0417 mutation in Helicobacter pylori by using the TRIzol sequential isolation protocol and MeOH and MTBE extraction methods. Metabolites and lipids with significant differences isolated using the TRIzol sequential isolation protocol were consistent with those obtained using the conventional MeOH and MTBE extraction methods. These results indicated that TRIzol reagent can be used to simultaneously isolate metabolites and lipids from a single sample. Thus, TRIzol reagent can be used in biological and clinical research, especially in multiomics studies.
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Affiliation(s)
- Cheng-Yen Kao
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
| | - Chung-Te Chang
- Institute of Biochemistry and Molecular Biology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
| | - Pei-Yun Kuo
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
| | - Chia-Jen Lin
- Department of Pharmacy, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
| | - Huai-Hsuan Chiu
- The Metabolomics Core Laboratory, Centers of Genomic and Precision Medicine, National Taiwan University, Taipei, 10617, Taiwan; Department of Medical Research, National Taiwan University Hospital, Taipei, 10617, Taiwan
| | - Hsiao-Wei Liao
- Department of Pharmacy, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan.
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25
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van Pijkeren A, Egger AS, Hotze M, Zimmermann E, Kipura T, Grander J, Gollowitzer A, Koeberle A, Bischoff R, Thedieck K, Kwiatkowski M. Proteome Coverage after Simultaneous Proteo-Metabolome Liquid-Liquid Extraction. J Proteome Res 2023; 22:951-966. [PMID: 36763818 PMCID: PMC9990123 DOI: 10.1021/acs.jproteome.2c00758] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Proteomics and metabolomics are essential in systems biology, and simultaneous proteo-metabolome liquid-liquid extraction (SPM-LLE) allows isolation of the metabolome and proteome from the same sample. Since the proteome is present as a pellet in SPM-LLE, it must be solubilized for quantitative proteomics. Solubilization and proteome extraction are critical factors in the information obtained at the proteome level. In this study, we investigated the performance of two surfactants (sodium deoxycholate (SDC), sodium dodecyl sulfate (SDS)) and urea in terms of proteome coverage and extraction efficiency of an interphase proteome pellet generated by methanol-chloroform based SPM-LLE. We also investigated how the performance differs when the proteome is extracted from the interphase pellet or by direct cell lysis. We quantified 12 lipids covering triglycerides and various phospholipid classes, and 25 polar metabolites covering central energy metabolism in chloroform and methanol extracts. Our study reveals that the proteome coverages between the two surfactants and urea for the SPM-LLE interphase pellet were similar, but the extraction efficiencies differed significantly. While SDS led to enrichment of basic proteins, which were mainly ribosomal and ribonuclear proteins, urea was the most efficient extraction agent for simultaneous proteo-metabolome analysis. The results of our study also show that the performance of surfactants for quantitative proteomics is better when the proteome is extracted through direct cell lysis rather than an interphase pellet. In contrast, the performance of urea for quantitative proteomics was significantly better when the proteome was extracted from an interphase pellet than by direct cell lysis. We demonstrated that urea is superior to surfactants for proteome extraction from SPM-LLE interphase pellets, with a particularly good performance for the extraction of proteins associated with metabolic pathways. Data are available via ProteomeXchange with identifier PXD027338.
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Affiliation(s)
- Alienke van Pijkeren
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, A-6020, Austria.,Department of Analytical Biochemistry and Interfaculty Mass Spectrometry Center, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, 9713 AV, The Netherlands
| | - Anna-Sophia Egger
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, A-6020, Austria
| | - Madlen Hotze
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, A-6020, Austria
| | - Elisabeth Zimmermann
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, A-6020, Austria
| | - Tobias Kipura
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, A-6020, Austria
| | - Julia Grander
- Michael Popp Institute and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, A-6020, Innsbruck, Austria
| | - André Gollowitzer
- Michael Popp Institute and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, A-6020, Innsbruck, Austria
| | - Andreas Koeberle
- Michael Popp Institute and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, A-6020, Innsbruck, Austria
| | - Rainer Bischoff
- Department of Analytical Biochemistry and Interfaculty Mass Spectrometry Center, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, 9713 AV, The Netherlands
| | - Kathrin Thedieck
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, A-6020, Austria.,Laboratory of Pediatrics, Section Systems Medicine of Metabolism and Signaling, University of Groningen, University Medical Center Groningen, Groningen, 9713 AV, The Netherlands.,Department for Neuroscience, School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, 26129, Germany
| | - Marcel Kwiatkowski
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, A-6020, Austria
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26
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Faugere J, Brunet TA, Clément Y, Espeyte A, Geffard O, Lemoine J, Chaumot A, Degli-Esposti D, Ayciriex S, Salvador A. Development of a multi-omics extraction method for ecotoxicology: investigation of the reproductive cycle of Gammarus fossarum. Talanta 2023; 253:123806. [PMID: 36113334 DOI: 10.1016/j.talanta.2022.123806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 07/24/2022] [Accepted: 07/29/2022] [Indexed: 12/13/2022]
Abstract
Omics study exemplified by proteomics, lipidomics or metabolomics, provides the opportunity to get insight of the molecular modifications occurring in living organisms in response to contaminants or in different physiological conditions. However, individual omics discloses only a single layer of information leading to a partial image of the biological complexity. Multiplication of samples preparation and processing can generate analytical variations resulting from several extractions and instrumental runs. To get all the -omics information at the proteins, metabolites and lipids level coming from a unique sample, a specific sample preparation must be optimized. In this study, we streamlined a biphasic extraction procedure based on a MTBE/Methanol mixture to provide the simultaneous extraction of polar (proteins, metabolites) and apolar compounds (lipids) for multi-omics analyses from a unique biological sample by a liquid chromatography (LC)/mass spectrometry (MS)/MS-based targeted approach. We applied the methodology for the study of female amphipod Gammarus fossarum during the reproductive cycle. Multivariate data analyses including Partial Least Squares Discriminant Analysis and multiple factor analysis were applied for the integration of the multi-omics data sets and highlighted molecular signatures, specific to the different stages.
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Affiliation(s)
- Julien Faugere
- Université de Lyon, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, CNRS UMR 5280, 5 Rue de La Doua, F-69100, Villeurbanne, France
| | - Thomas Alexandre Brunet
- Université de Lyon, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, CNRS UMR 5280, 5 Rue de La Doua, F-69100, Villeurbanne, France
| | - Yohann Clément
- Université de Lyon, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, CNRS UMR 5280, 5 Rue de La Doua, F-69100, Villeurbanne, France
| | - Anabelle Espeyte
- INRAE, UR RiverLy, Laboratoire D'écotoxicologie, F-69625, Villeurbanne, France
| | - Olivier Geffard
- INRAE, UR RiverLy, Laboratoire D'écotoxicologie, F-69625, Villeurbanne, France
| | - Jérôme Lemoine
- Université de Lyon, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, CNRS UMR 5280, 5 Rue de La Doua, F-69100, Villeurbanne, France
| | - Arnaud Chaumot
- INRAE, UR RiverLy, Laboratoire D'écotoxicologie, F-69625, Villeurbanne, France
| | | | - Sophie Ayciriex
- Université de Lyon, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, CNRS UMR 5280, 5 Rue de La Doua, F-69100, Villeurbanne, France
| | - Arnaud Salvador
- Université de Lyon, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, CNRS UMR 5280, 5 Rue de La Doua, F-69100, Villeurbanne, France.
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27
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Muehlbauer LK, Jen A, Zhu Y, He Y, Shishkova E, Overmyer KA, Coon JJ. Rapid Multi-Omics Sample Preparation for Mass Spectrometry. Anal Chem 2023; 95:659-667. [PMID: 36594155 PMCID: PMC10026941 DOI: 10.1021/acs.analchem.2c02042] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Multi-omics analysis is a powerful and increasingly utilized approach to gain insight into complex biological systems. One major hindrance with multi-omics, however, is the lengthy and wasteful sample preparation process. Preparing samples for mass spectrometry (MS)-based multi-omics involves extraction of metabolites and lipids with organic solvents, precipitation of proteins, and overnight digestion of proteins. These existing workflows are disparate and laborious. Here, we present a simple, efficient, and unified approach to prepare lipids, metabolites, and proteins for MS analysis. Our approach, termed the Bead-enabled Accelerated Monophasic Multi-omics (BAMM) method, combines an n-butanol-based monophasic extraction with unmodified magnetic beads and accelerated protein digestion. We demonstrate that the BAMM method affords comparable depth, quantitative reproducibility, and recovery of biomolecules as state-of-the-art multi-omics methods (e.g., Matyash extraction and overnight protein digestion). However, the BAMM method only requires about 3 h to perform, which saves 11 steps and 19 h on average compared to published multi-omics methods. Furthermore, we validate the BAMM method for multiple sample types and formats (biofluid, culture plate, and pellet) and show that in all cases, it produces high biomolecular coverage and data quality.
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Affiliation(s)
- Laura K. Muehlbauer
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Annie Jen
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Yunyun Zhu
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Yuchen He
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Evgenia Shishkova
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Katherine A. Overmyer
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Joshua J. Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
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28
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Evaluation of Two Simultaneous Metabolomic and Proteomic Extraction Protocols Assessed by Ultra-High-Performance Liquid Chromatography Tandem Mass Spectrometry. Int J Mol Sci 2023; 24:ijms24021354. [PMID: 36674867 PMCID: PMC9865896 DOI: 10.3390/ijms24021354] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 12/31/2022] [Accepted: 01/01/2023] [Indexed: 01/13/2023] Open
Abstract
Untargeted multi-omics analysis of plasma is an emerging tool for the identification of novel biomarkers for evaluating disease prognosis, and for developing a better understanding of molecular mechanisms underlying human disease. The successful application of metabolomic and proteomic approaches relies on reproducibly quantifying a wide range of metabolites and proteins. Herein, we report the results of untargeted metabolomic and proteomic analyses from blood plasma samples following analyte extraction by two frequently-used solvent systems: chloroform/methanol and methanol-only. Whole blood samples were collected from participants (n = 6) at University Hospital Sharjah (UHS) hospital, then plasma was separated and extracted by two methods: (i) methanol precipitation and (ii) 4:3 methanol:chloroform extraction. The coverage and reproducibility of the two methods were assessed by ultra-high-performance liquid chromatography-electrospray ionization quadrupole time-of-flight mass spectrometry (UHPLC-ESI-QTOF-MS). The study revealed that metabolite extraction by methanol-only showed greater reproducibility for both metabolomic and proteomic quantifications than did methanol/chloroform, while yielding similar peptide coverage. However, coverage of extracted metabolites was higher with the methanol/chloroform precipitation.
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29
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Henne A, Vigh A, Märtens A, Nonnenmacher Y, Ohm M, Hosseini S, More TH, Lauterbach MA, Garritsen H, Korte M, He W, Hiller K. SiMeEx, a simplified method for metabolite extraction of adherent mammalian cells. Front Mol Biosci 2022; 9:1084060. [PMID: 36619169 PMCID: PMC9812552 DOI: 10.3389/fmolb.2022.1084060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
A reliable method for metabolite extraction is central to mass spectrometry-based metabolomics. However, existing methods are lengthy, mostly due to the step of scraping cells from cell culture vessels, which restricts metabolomics in broader application such as lower cell numbers and high-throughput studies. Here, we present a simplified metabolite extraction (SiMeEx) method, to efficiently and quickly extract metabolites from adherent mammalian cells. Our method excludes the cell scraping step and therefore allows for a more efficient extraction of polar metabolites in less than 30 min per 12-well plate. We demonstrate that SiMeEx achieves the same metabolite recovery as using a standard method containing a scraping step, in various immortalized and primary cells. Omitting cell scraping does not compromise the performance of non-targeted and targeted GC-MS analysis, but enables metabolome analysis of cell culture on smaller well sizes down to 96-well plates. Therefore, SiMeEx demonstrates advantages not only on time and resources, but also on the applicability in high-throughput studies.
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Affiliation(s)
- Antonia Henne
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Anna Vigh
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Andre Märtens
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Yannic Nonnenmacher
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Melanie Ohm
- Department of Cellular Neurobiology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
| | - Shirin Hosseini
- Department of Cellular Neurobiology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
| | - Tushar H. More
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Mario A. Lauterbach
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Hendrikus Garritsen
- Institute of Transfusion Medicine, Klinikum Braunschweig, Braunschweig, Germany,Fraunhofer Institute for Surface Engineering and Thin Films IST, Braunschweig, Germany
| | - Martin Korte
- Department of Cellular Neurobiology, Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany,Neuroinflammation and Neurodegeneration Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Wei He
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Karsten Hiller
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology, Technische Universität Braunschweig, Braunschweig, Germany,*Correspondence: Karsten Hiller,
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30
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Hohenwallner K, Troppmair N, Panzenboeck L, Kasper C, El Abiead Y, Koellensperger G, Lamp LM, Hartler J, Egger D, Rampler E. Decoding Distinct Ganglioside Patterns of Native and Differentiated Mesenchymal Stem Cells by a Novel Glycolipidomics Profiling Strategy. JACS AU 2022; 2:2466-2480. [PMID: 36465531 PMCID: PMC9709940 DOI: 10.1021/jacsau.2c00230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 10/01/2022] [Accepted: 10/03/2022] [Indexed: 06/17/2023]
Abstract
Gangliosides are an indispensable glycolipid class concentrated on cell surfaces with a critical role in stem cell differentiation. Nonetheless, owing to the lack of suitable methods for scalable analysis covering the full scope of ganglioside molecular diversity, their mechanistic properties in signaling and differentiation remain undiscovered to a large extent. This work introduces a sensitive and comprehensive ganglioside assay based on liquid chromatography, high-resolution mass spectrometry, and multistage fragmentation. Complemented by an open-source data evaluation workflow, we provide automated in-depth lipid species-level and molecular species-level annotation based on decision rule sets for all major ganglioside classes. Compared to conventional state-of-the-art methods, the presented ganglioside assay offers (1) increased sensitivity, (2) superior structural elucidation, and (3) the possibility to detect novel ganglioside species. A major reason for the highly improved sensitivity is the optimized spectral readout based on the unique capability of two parallelizable mass analyzers for multistage fragmentation. We demonstrated the high-throughput universal capability of our novel analytical strategy by identifying 254 ganglioside species. As a proof of concept, 137 unique gangliosides were annotated in native and differentiated human mesenchymal stem cells including 78 potential cell-state-specific markers and 38 previously unreported gangliosides. A general increase of the ganglioside numbers upon differentiation was observed as well as cell-state-specific clustering based on the ganglioside species patterns. The combination of the developed glycolipidomics assay with the extended automated annotation tool enables comprehensive in-depth ganglioside characterization as shown on biological samples of interest. Our results suggest ganglioside patterns as a promising quality control tool for stem cells and their differentiation products. Additionally, we believe that our analytical workflow paves the way for probing glycolipid-based biochemical processes shedding light on the enigmatic processes of gangliosides and glycolipids in general.
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Affiliation(s)
- Katharina Hohenwallner
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
- Vienna
Doctoral School in Chemistry (DoSChem), University of Vienna, Vienna 1090, Austria
| | - Nina Troppmair
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
- Vienna
Doctoral School in Chemistry (DoSChem), University of Vienna, Vienna 1090, Austria
| | - Lisa Panzenboeck
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
- Vienna
Doctoral School in Chemistry (DoSChem), University of Vienna, Vienna 1090, Austria
| | - Cornelia Kasper
- Institute
of Cell and Tissue Culture Technologies, University of Natural Resources and Life Sciences, Vienna 1190, Austria
| | - Yasin El Abiead
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
| | - Gunda Koellensperger
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
| | - Leonida M. Lamp
- Institute
of Pharmaceutical Sciences, University of
Graz, Graz 8010, Austria
| | - Jürgen Hartler
- Institute
of Pharmaceutical Sciences, University of
Graz, Graz 8010, Austria
- Field
of Excellence BioHealth − University
of Graz, Graz 8010, Austria
| | - Dominik Egger
- Institute
of Cell and Tissue Culture Technologies, University of Natural Resources and Life Sciences, Vienna 1190, Austria
| | - Evelyn Rampler
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna 1090, Austria
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31
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Chen W, Huang W, Pather SR, Chang W, Sung L, Wu H, Liao M, Lee C, Wu H, Wu C, Liao K, Lin C, Yang S, Lin H, Lai P, Ng C, Hu C, Chen I, Chuang C, Lai C, Lin P, Lee Y, Schuyler SC, Schambach A, Lu FL, Lu J. Podocalyxin-Like Protein 1 Regulates Pluripotency through the Cholesterol Biosynthesis Pathway. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 10:e2205451. [PMID: 36373710 PMCID: PMC9811443 DOI: 10.1002/advs.202205451] [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: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Deciphering signaling mechanisms critical for the extended pluripotent stem cell (EPSC) state and primed pluripotency is necessary for understanding embryonic development. Here, a membrane protein, podocalyxin-like protein 1 (PODXL) as being essential for extended and primed pluripotency, is identified. Alteration of PODXL expression levels affects self-renewal, protein expression of c-MYC and telomerase, and induced pluripotent stem cell (iPSC) and EPSC colony formation. PODXL is the first membrane protein reported to regulate de novo cholesterol biosynthesis, and human pluripotent stem cells (hPSCs) are more sensitive to cholesterol depletion than fibroblasts. The addition of exogenous cholesterol fully restores PODXL knockdown-mediated loss of pluripotency. PODXL affects lipid raft dynamics via the regulation of cholesterol. PODXL recruits the RAC1/CDC42/actin network to regulate SREBP1 and SREBP2 maturation and lipid raft dynamics. Single-cell RNA sequencing reveals PODXL overexpression enhanced chimerism between human cells in mouse host embryos (hEPSCs 57%). Interestingly, in the human-mouse chimeras, laminin and collagen signaling-related pathways are dominant in PODXL overexpressing cells. It is concluded that cholesterol regulation via PODXL signaling is critical for ESC/EPSC.
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Affiliation(s)
- Wei‐Ju Chen
- Genomics Research CenterAcademia SinicaGenome and Systems Biology Degree ProgramCollege of Life ScienceNational Taiwan UniversityTaipei10617Taiwan
- Genomics Research CenterAcademia SinicaTaipei11529Taiwan
| | - Wei‐Kai Huang
- Center for Genomic MedicineMassachusetts General HospitalBostonMA02114USA
| | - Sarshan R. Pather
- Cell and Molecular Biology Graduate GroupPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPA19104USA
| | - Wei‐Fang Chang
- Institute of BiotechnologyNational Taiwan UniversityTaipei10617Taiwan
| | - Li‐Ying Sung
- Institute of BiotechnologyNational Taiwan UniversityTaipei10617Taiwan
- Agricultural Biotechnology Research CenterAcademia SinicaTaipei11529Taiwan
- Animal Resource CenterNational Taiwan UniversityTaipei10617Taiwan
| | - Han‐Chung Wu
- Institute of Cellular and Organismic BiologyAcademia SinicaTaipei11529Taiwan
- Biomedical Translation Research Center (BioTReC)Academia SinicaTaipei11529Taiwan
| | - Mei‐Ying Liao
- Institute of Cellular and Organismic BiologyAcademia SinicaTaipei11529Taiwan
| | - Chi‐Chiu Lee
- Institute of Cellular and Organismic BiologyAcademia SinicaTaipei11529Taiwan
| | - Hsuan‐Hui Wu
- Institute of Cellular and Organismic BiologyAcademia SinicaTaipei11529Taiwan
| | - Chung‐Yi Wu
- Genomics Research CenterAcademia SinicaTaipei11529Taiwan
| | | | - Chun‐Yu Lin
- Genomics Research CenterAcademia SinicaTaipei11529Taiwan
| | | | - Hsuan Lin
- Genomics Research CenterAcademia SinicaTaipei11529Taiwan
| | - Pei‐Lun Lai
- Genomics Research CenterAcademia SinicaTaipei11529Taiwan
| | - Chi‐Hou Ng
- Genomics Research CenterAcademia SinicaTaipei11529Taiwan
| | - Chun‐Mei Hu
- Genomics Research CenterAcademia SinicaTaipei11529Taiwan
| | - I‐Chih Chen
- Genomics Research CenterAcademia SinicaTaipei11529Taiwan
| | | | - Chien‐Ying Lai
- Genomics Research CenterAcademia SinicaTaipei11529Taiwan
| | - Po‐Yu Lin
- Genomics Research CenterAcademia SinicaTaipei11529Taiwan
| | - Yueh‐Chang Lee
- Department of OphthalmologyHualien Tzu Chi HospitalBuddhist Tzu Chi Medical FoundationHualien97004Taiwan
| | - Scott C. Schuyler
- Department of Biomedical SciencesCollege of MedicineChang Gung UniversityDivision of Head and Neck SurgeryDepartment of OtolaryngologyChang Gung Memorial HospitalTaoyuan33302Taiwan
| | - Axel Schambach
- Institute of Experimental HematologyHannover Medical School30625HannoverGermany
| | - Frank Leigh Lu
- Department of PediatricsNational Taiwan University Hospital and National Taiwan University Medical CollegeTaipei10051Taiwan
| | - Jean Lu
- Genomics Research CenterAcademia SinicaGenome and Systems Biology Degree ProgramCollege of Life ScienceNational Taiwan UniversityTaipei10617Taiwan
- Genomics Research CenterAcademia SinicaTaipei11529Taiwan
- National RNAi Platform/ National Core Facility Program for BiotechnologyTaipei11529Taiwan
- Department of Life ScienceTzu Chi UniversityHualien97004Taiwan
- Graduate Institute of Medical SciencesNational Defense Medical CenterTaipei11490Taiwan
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32
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Toward building mass spectrometry-based metabolomics and lipidomics atlases for biological and clinical research. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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33
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Song WS, Lee JS, Lim JW, Kim J, Jo SH, Kwon JE, Park JH, Choi SH, Jang D, Kim IW, Jeong JH, Kim YG. Multiomics characterization of dose- and time-dependent effects of ionizing radiation on human skin keratinocytes. KOREAN J CHEM ENG 2022. [DOI: 10.1007/s11814-022-1095-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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34
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Endo- and Exometabolome Crosstalk in Mesenchymal Stem Cells Undergoing Osteogenic Differentiation. Cells 2022; 11:cells11081257. [PMID: 35455937 PMCID: PMC9024772 DOI: 10.3390/cells11081257] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/03/2022] [Accepted: 04/05/2022] [Indexed: 02/04/2023] Open
Abstract
This paper describes, for the first time to our knowledge, a lipidome and exometabolome characterization of osteogenic differentiation for human adipose tissue stem cells (hAMSCs) using nuclear magnetic resonance (NMR) spectroscopy. The holistic nature of NMR enabled the time-course evolution of cholesterol, mono- and polyunsaturated fatty acids (including ω-6 and ω-3 fatty acids), several phospholipids (phosphatidylcholine, phosphatidylethanolamine, sphingomyelins, and plasmalogens), and mono- and triglycerides to be followed. Lipid changes occurred almost exclusively between days 1 and 7, followed by a tendency for lipidome stabilization after day 7. On average, phospholipids and longer and more unsaturated fatty acids increased up to day 7, probably related to plasma membrane fluidity. Articulation of lipidome changes with previously reported polar endometabolome profiling and with exometabolome changes reported here in the same cells, enabled important correlations to be established during hAMSC osteogenic differentiation. Our results supported hypotheses related to the dynamics of membrane remodelling, anti-oxidative mechanisms, protein synthesis, and energy metabolism. Importantly, the observation of specific up-taken or excreted metabolites paves the way for the identification of potential osteoinductive metabolites useful for optimized osteogenic protocols.
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35
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Tikunov AP, Tipton JD, Garrett TJ, Shinde SV, Kim HJ, Gerber DA, Herring LE, Graves LM, Macdonald JM. Green Chemistry Preservation and Extraction of Biospecimens for Multi-omic Analyses. Methods Mol Biol 2022; 2394:267-298. [PMID: 35094334 DOI: 10.1007/978-1-0716-1811-0_17] [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] [Indexed: 05/16/2023]
Abstract
The Environmental Protection Agency's definition of "Green Chemistry" is "the design of chemical products and processes that reduces or eliminates the use or generation of hazardous substances. Green chemistry applies across the life cycle of a chemical product, including its design, manufacture, use, and ultimate disposal." Conventional omic tissue extraction procedures use solvents that are toxic and carcinogenic, such as chloroform and methyl-tert-butyl ether for lipidomics, or caustic chaotropic solutions for genomics and transcriptomics, such as guanidine or urea. A common preservation solution for pathology is formaldehyde, which is a carcinogen. Use of acetonitrile as a universal biospecimen preservation and extraction solvent will reduce these hazardous wastes, because it is less toxic and more environmentally friendly than the conventional solvents used in biorepository and biospecimen research. A new extraction method never applied to multi-omic, system biology research, called cold-induced phase separation (CIPS), uses freezing point temperatures to induce a phase separation of acetonitrile-water mixtures. Also, the CO2 exposure during CIPS will acidify the water precipitating DNA out of aqueous phase. The resulting phase separation brings hydrophobic lipids to the top acetonitrile fraction that is easily decanted from the bottom aqueous fraction, especially when the water is frozen. This CIPS acetonitrile extract contains the lipidome (lipids), the bottom aqueous fraction is sampled to obtain the transcriptome (RNA) fraction, and the remaining water and pellet is extracted with 60% acetonitrile to isolate the metabolome (<1 kD polar molecules). Finally, steps 4 and 5 use a TRIzol™ liquid-liquid extraction SOP of the pellet to isolate the genome (DNA) and proteome (proteins). This chapter details the multi-omic sequential extraction SOP and potential problems associated with each of the 5 steps, with steps 2, 4, and 5 still requiring validation. The metabolomic and lipidomic extraction efficiencies using the CIPS SOP is compared to conventional solvent extraction SOPs and is analyzed by nuclear magnetic resonance (NMR) spectroscopy and liquid chromatography-mass spectrometry (LC-MS), respectively. Acetonitrile biospecimen preservation combined with the CIPS multi-omic extraction SOP is green chemistry technology that will eliminate the generation of the hazardous substances associated with biospecimen processing and permits separation and safe disposal of acetonitrile avoiding environmental contamination.
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Affiliation(s)
- Andrey P Tikunov
- Departments of Biomedical Engineering, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Jeremiah D Tipton
- Departments of Biomedical Engineering, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, College of Medicine, Gainesville, FL, USA
| | - Timothy J Garrett
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, College of Medicine, Gainesville, FL, USA
| | - Sachi V Shinde
- Departments of Biomedical Engineering, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Hong Jin Kim
- Departments of Surgery, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - David A Gerber
- Departments of Surgery, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Laura E Herring
- Departments of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Lee M Graves
- Departments of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Jeffrey M Macdonald
- Departments of Biomedical Engineering, University of North Carolina School of Medicine, Chapel Hill, NC, USA.
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36
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Chen Z, Chen Z, Zhu J, He J, Liu Q, Zhu H, Lei A, Wang J. Proteomic Responses of Dark-Adapted Euglena gracilis and Bleached Mutant Against Light Stimuli. Front Bioeng Biotechnol 2022; 10:843414. [PMID: 35309998 PMCID: PMC8927018 DOI: 10.3389/fbioe.2022.843414] [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: 12/25/2021] [Accepted: 01/25/2022] [Indexed: 11/29/2022] Open
Abstract
Euglena gracilis (E. gracilis) has secondary endosymbiotic chloroplasts derived from ancient green algae. Its chloroplasts are easily lost under numerous conditions to become permanently bleached mutants. Green cells adapted in the dark contain undeveloped proplastids and they will develop into mature chloroplasts after 3 days of light exposure. Thus, E. gracilis is an ideal model species for a chloroplast development study. Previous studies about chloroplast development in E. gracilis focused on morphology and physiology, whereas few studies have addressed the regulatory processes induced by light in the proteome. In this study, the whole-genome proteome of dark-adapted E. gracilis (WT) and permanently ofloxacin-bleached mutant (B2) was compared under the light exposure after 0, 12, and 72 h. The results showed that the photosynthesis-related proteins were up-regulated over time in both WT and B2. The B2 strain, with losing functional chloroplasts, seemed to possess a complete photosynthetic function system. Both WT and B2 exhibited significant light responses with similar alternation patterns, suggesting the sensitive responses to light in proteomic levels. The main metabolic activities for the utilization of carbon and energy in WT were up-regulated, while the proteins with calcium ion binding, cell cycle, and non-photosynthetic carbon fixation were down-regulated in B2. This study confirmed light-induced chloroplast development in WT from dark, and also for the first time investigates the light responses of a bleached mutant B2, providing more information about the unknown functions of residual plastids in Euglena bleached mutants.
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Affiliation(s)
- Zhenfan Chen
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
- College of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, China
| | - Zixi Chen
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Jiayi Zhu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Jiayi He
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Qiong Liu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Shenzhen-Hong Kong Institute of Brain Science, Shenzhen, China
| | - Hui Zhu
- College of Food Engineering and Biotechnology, Hanshan Normal University, Chaozhou, China
| | - Anping Lei
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Jiangxin Wang
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- *Correspondence: Jiangxin Wang,
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37
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Multi-Omic Analysis to Characterize Metabolic Adaptation of the E. coli Lipidome in Response to Environmental Stress. Metabolites 2022; 12:metabo12020171. [PMID: 35208246 PMCID: PMC8880424 DOI: 10.3390/metabo12020171] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 12/17/2022] Open
Abstract
As an adaptive survival response to exogenous stress, bacteria undergo dynamic remodelling of their lipid metabolism pathways to alter the composition of their cellular membranes. Here, using Escherichia coli as a well characterised model system, we report the development and application of a ‘multi-omics’ strategy for comprehensive quantitative analysis of the temporal changes in the lipidome and proteome profiles that occur under exponential growth phase versus stationary growth phase conditions i.e., nutrient depletion stress. Lipidome analysis performed using ‘shotgun’ direct infusion-based ultra-high resolution accurate mass spectrometry revealed a quantitative decrease in total lipid content under stationary growth phase conditions, along with a significant increase in the mol% composition of total cardiolipin, and an increase in ‘odd-numbered’ acyl-chain length containing glycerophospholipids. The inclusion of field asymmetry ion mobility spectrometry was shown to enable the enrichment and improved depth of coverage of low-abundance cardiolipins, while ultraviolet photodissociation-tandem mass spectrometry facilitated more complete lipid structural characterisation compared with conventional collision-induced dissociation, including unambiguous assignment of the odd-numbered acyl-chains as containing cyclopropyl modifications. Proteome analysis using data-dependent acquisition nano-liquid chromatography mass spectrometry and tandem mass spectrometry analysis identified 83% of the predicted E. coli lipid metabolism enzymes, which enabled the temporal dependence associated with the expression of key enzymes responsible for the observed adaptive lipid metabolism to be determined, including those involved in phospholipid metabolism (e.g., ClsB and Cfa), fatty acid synthesis (e.g., FabH) and degradation (e.g., FadA/B,D,E,I,J and M), and proteins involved in the oxidative stress response resulting from the generation of reactive oxygen species during β-oxidation or lipid degradation.
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38
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Garikapati V, Colasante C, Baumgart-Vogt E, Spengler B. Sequential lipidomic, metabolomic, and proteomic analyses of serum, liver, and heart tissue specimens from peroxisomal biogenesis factor 11α knockout mice. Anal Bioanal Chem 2022; 414:2235-2250. [PMID: 35083512 PMCID: PMC8821073 DOI: 10.1007/s00216-021-03860-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 11/25/2021] [Accepted: 12/20/2021] [Indexed: 12/16/2022]
Abstract
Peroxisomes are versatile single membrane-enclosed cytoplasmic organelles, involved in reactive oxygen species (ROS) and lipid metabolism and diverse other metabolic processes. Peroxisomal disorders result from mutations in Pex genes-encoded proteins named peroxins (PEX proteins) and single peroxisomal enzyme deficiencies. The PEX11 protein family (α, β, and γ isoforms) plays an important role in peroxisomal proliferation and fission. However, their specific functions and the metabolic impact caused by their deficiencies have not been precisely characterized. To understand the systemic molecular alterations caused by peroxisomal defects, here we utilized untreated peroxisomal biogenesis factor 11α knockout (Pex11α KO) mouse model and performed serial relative-quantitative lipidomic, metabolomic, and proteomic analyses of serum, liver, and heart tissue homogenates. We demonstrated significant specific changes in the abundances of multiple lipid species, polar metabolites, and proteins and dysregulated metabolic pathways in distinct biological specimens of the Pex11α KO adult mice in comparison to the wild type (WT) controls. Overall, the present study reports comprehensive semi-quantitative molecular omics information of the Pex11α KO mice, which might serve in the future as a reference for a better understanding of the roles of Pex11α and underlying pathophysiological mechanisms of peroxisomal biogenesis disorders.
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Affiliation(s)
- Vannuruswamy Garikapati
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, 35392, Giessen, Germany.,Institute for Anatomy and Cell Biology II, Division of Medical Cell Biology, Justus Liebig University Giessen, 35392, Giessen, Germany
| | - Claudia Colasante
- Institute for Anatomy and Cell Biology II, Division of Medical Cell Biology, Justus Liebig University Giessen, 35392, Giessen, Germany
| | - Eveline Baumgart-Vogt
- Institute for Anatomy and Cell Biology II, Division of Medical Cell Biology, Justus Liebig University Giessen, 35392, Giessen, Germany.
| | - Bernhard Spengler
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, 35392, Giessen, Germany.
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39
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Lim SY, Ng BH, Vermulapalli D, Lau H, Carrasco Laserna AK, Yang X, Tan SH, Chan MY, Li SFY. Simultaneous Polar Metabolite and N-Glycan Extraction Workflow for Joint-Omics Analysis: A Synergistic Approach for Novel Insights into Diseases. J Proteome Res 2022; 21:643-653. [DOI: 10.1021/acs.jproteome.1c00676] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Si Ying Lim
- NUS Graduate School for Integrative Sciences & Engineering (NGS), National University of Singapore, University Hall, Tan Chin Tuan Wing, Singapore 119077
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Bao Hui Ng
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Dhruti Vermulapalli
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Hazel Lau
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), Fusionopolis Way, Innovis, #08-03, Singapore 138634
| | - Anna Karen Carrasco Laserna
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
- Central Instrumentation Facility (Laguna Campus), Office of the Vice Chancellor for Research and Innovation, De La Salle University, 2041 Taft Avenue, Manila 1004, Philippines
| | - Xiaoxun Yang
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599
| | - Sock Hwee Tan
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599
| | - Mark Y. Chan
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599
| | - Sam Fong Yau Li
- NUS Graduate School for Integrative Sciences & Engineering (NGS), National University of Singapore, University Hall, Tan Chin Tuan Wing, Singapore 119077
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
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40
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Serrato LAM, Bilella A, Blanchoud S. Noninvasive Intravascular Microtransfusion in Colonial Tunicates. Methods Mol Biol 2022; 2450:399-415. [PMID: 35359320 PMCID: PMC9761924 DOI: 10.1007/978-1-0716-2172-1_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Tunicates are a diverse group of worldwide marine filter-feeders that are vertebrates' closest invertebrate relatives. Colonial tunicates are the only know chordates that have been shown to undergo whole-body regeneration (WBR). Botrylloides in particular can regenerate one fully functional adult from a minute fragment of their vascular system in as little as 10 days. This regenerative process relies on the proliferation of circulating stem cells, likely supported by the activity of some of the 11 identified types of hemocytes. To study and challenge WBR, it is thus important to have the capacity to isolate, analyze, and manipulate hemolymph in regenerating colonies. Here we present a microtransfusion technique that permits the collection of pure hemocytes, the quantification of their purity, their labeling, and reinjection into colonial tunicates. To exemplify our approach, we present in addition a protocol to analyze the isolated hemocytes using flow cytometry. Our approach is minimally invasive, does not induce lethality, and therefore allows repeated transfusion into exactly the same colony with minimal disruption to the process being studied.
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Affiliation(s)
| | | | - Simon Blanchoud
- Department of Biology, University of Fribourg, Fribourg, Switzerland.
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Lim SY, Selvaraji S, Lau H, Li SFY. Application of omics beyond the central dogma in coronary heart disease research: A bibliometric study and literature review. Comput Biol Med 2022; 140:105069. [PMID: 34847384 DOI: 10.1016/j.compbiomed.2021.105069] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/22/2021] [Accepted: 11/22/2021] [Indexed: 12/12/2022]
Abstract
Despite remarkable progress in disease diagnosis and treatment, coronary heart disease (CHD) remains the number one leading cause of death worldwide. Many practical challenges still faced in clinical settings necessitates the pursuit of omics studies to identify alternative/orthogonal biomarkers, as well as to discover novel insights into disease mechanisms. Albeit relatively nascent as compared to the omics frontrunners (genomics, transcriptomics, and proteomics), omics beyond the central dogma (OBCD; e.g., metabolomics, lipidomics, glycomics, and metallomics) have undeniable contributions and prospects in CHD research. In this bibliometric study, we characterised the global trends in publication/citation outputs, collaborations, and research hotspots concerning OBCD-CHD, with a focus on the more prolific fields of metabolomics and lipidomics. As for glycomics and metallomics, there were insufficient publication records on their applications in CHD research for quantitative bibliometrics analysis. Thus, we reviewed their applications in health/disease research in general, discussed and justified their potential in CHD research, and suggested important/promising research avenues. By summarising evidence obtained both quantitatively and qualitatively, this study offers a first and comprehensive picture of OBCD applications in CHD, facilitating the establishment of future research directions.
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Affiliation(s)
- Si Ying Lim
- Integrative Sciences & Engineering Programme, NUS Graduate School, National University of Singapore, University Hall, Tan Chin Tuan Wing, Singapore 119077, Singapore; Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Sharmelee Selvaraji
- Integrative Sciences & Engineering Programme, NUS Graduate School, National University of Singapore, University Hall, Tan Chin Tuan Wing, Singapore 119077, Singapore; Department of Physiology, Yong Loo Lin School of Medicine, 2 Medical Drive MD9, National University of Singapore, Singapore 117593, Singapore
| | - Hazel Lau
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Sam Fong Yau Li
- Integrative Sciences & Engineering Programme, NUS Graduate School, National University of Singapore, University Hall, Tan Chin Tuan Wing, Singapore 119077, Singapore; Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore.
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Blum BC, Lin W, Lawton ML, Liu Q, Kwan J, Turcinovic I, Hekman R, Hu P, Emili A. Multiomic Metabolic Enrichment Network Analysis Reveals Metabolite-Protein Physical Interaction Subnetworks Altered in Cancer. Mol Cell Proteomics 2022; 21:100189. [PMID: 34933084 PMCID: PMC8761777 DOI: 10.1016/j.mcpro.2021.100189] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 12/04/2021] [Accepted: 12/16/2021] [Indexed: 11/25/2022] Open
Abstract
Metabolism is recognized as an important driver of cancer progression and other complex diseases, but global metabolite profiling remains a challenge. Protein expression profiling is often a poor proxy since existing pathway enrichment models provide an incomplete mapping between the proteome and metabolism. To overcome these gaps, we introduce multiomic metabolic enrichment network analysis (MOMENTA), an integrative multiomic data analysis framework for more accurately deducing metabolic pathway changes from proteomics data alone in a gene set analysis context by leveraging protein interaction networks to extend annotated metabolic models. We apply MOMENTA to proteomic data from diverse cancer cell lines and human tumors to demonstrate its utility at revealing variation in metabolic pathway activity across cancer types, which we verify using independent metabolomics measurements. The novel metabolic networks we uncover in breast cancer and other tumors are linked to clinical outcomes, underscoring the pathophysiological relevance of the findings.
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Affiliation(s)
- Benjamin C Blum
- Center for Network Systems Biology, Boston University, Boston, Massachusetts, USA; Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Weiwei Lin
- Center for Network Systems Biology, Boston University, Boston, Massachusetts, USA; Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Matthew L Lawton
- Center for Network Systems Biology, Boston University, Boston, Massachusetts, USA; Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Qian Liu
- Departments of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Julian Kwan
- Center for Network Systems Biology, Boston University, Boston, Massachusetts, USA; Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Isabella Turcinovic
- Center for Network Systems Biology, Boston University, Boston, Massachusetts, USA
| | - Ryan Hekman
- Center for Network Systems Biology, Boston University, Boston, Massachusetts, USA; Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Pingzhao Hu
- Departments of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Andrew Emili
- Center for Network Systems Biology, Boston University, Boston, Massachusetts, USA; Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA; Department of Biology, Boston University, Boston, Massachusetts, USA.
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Li T, Hentschel A, Ahrends R. Analytical comparison of absolute quantification strategies to investigate the Insulin signaling pathway in fat cells. Proteomics 2021; 22:e2100136. [PMID: 34964541 DOI: 10.1002/pmic.202100136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 11/08/2022]
Abstract
So far, mass spectrometry based targeted proteomics is the most sensitive approach to answer and address specific biological questions in an accurate and quantitative fashion. However, the data analysis design used for such quantification varies in the field leading to discrepancies in the reported values. In this study, different quantification strategies based on calibration curves were evaluated and compared. The best accuracy and coefficient of variation was achieved by ratio to ratio calibration curves. We applied the ratio to ratio quantification approach to analyze very low abundant insulin signaling proteins such as PIK3RA (0.10-0.93 fmol/μg), AKT1 (0.1-0.39 fmol/μg) and the Insulin receptor (0.22 -2.62 fmol/μg) in a fat cell model and demonstrated the adaptation of this pathway at different states of insulin sensitivity. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Tingting Li
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e. V., Otto-Hahn-Straße 6b, Dortmund, 44227, Germany
| | - Andreas Hentschel
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e. V., Otto-Hahn-Straße 6b, Dortmund, 44227, Germany
| | - Robert Ahrends
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e. V., Otto-Hahn-Straße 6b, Dortmund, 44227, Germany.,Department of Analytical Chemistry, University of Vienna, Währinger Straße 38, Vienna, 1090, Austria
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Imbert A, Rompais M, Selloum M, Castelli F, Mouton-Barbosa E, Brandolini-Bunlon M, Chu-Van E, Joly C, Hirschler A, Roger P, Burger T, Leblanc S, Sorg T, Ouzia S, Vandenbrouck Y, Médigue C, Junot C, Ferro M, Pujos-Guillot E, de Peredo AG, Fenaille F, Carapito C, Herault Y, Thévenot EA. ProMetIS, deep phenotyping of mouse models by combined proteomics and metabolomics analysis. Sci Data 2021; 8:311. [PMID: 34862403 PMCID: PMC8642540 DOI: 10.1038/s41597-021-01095-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 11/02/2021] [Indexed: 01/20/2023] Open
Abstract
Genes are pleiotropic and getting a better knowledge of their function requires a comprehensive characterization of their mutants. Here, we generated multi-level data combining phenomic, proteomic and metabolomic acquisitions from plasma and liver tissues of two C57BL/6 N mouse models lacking the Lat (linker for activation of T cells) and the Mx2 (MX dynamin-like GTPase 2) genes, respectively. Our dataset consists of 9 assays (1 preclinical, 2 proteomics and 6 metabolomics) generated with a fully non-targeted and standardized approach. The data and processing code are publicly available in the ProMetIS R package to ensure accessibility, interoperability, and reusability. The dataset thus provides unique molecular information about the physiological role of the Lat and Mx2 genes. Furthermore, the protocols described herein can be easily extended to a larger number of individuals and tissues. Finally, this resource will be of great interest to develop new bioinformatic and biostatistic methods for multi-omics data integration.
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Affiliation(s)
- Alyssa Imbert
- CEA, LIST, Laboratoire Sciences des Données et de la Décision, IFB, MetaboHUB, Gif-sur-Yvette, France.
- IFB-core, UMS3601, Genoscope, Evry, France.
| | - Magali Rompais
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, ProFI, Strasbourg, France
| | - Mohammed Selloum
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris, Phenomin-ICS, Illkirch, France
| | - Florence Castelli
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), MetaboHUB, Gif-sur-Yvette, France
| | - Emmanuelle Mouton-Barbosa
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, ProFI, Toulouse, France
| | - Marion Brandolini-Bunlon
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB, Clermont-Ferrand, France
| | - Emeline Chu-Van
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), MetaboHUB, Gif-sur-Yvette, France
| | - Charlotte Joly
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB, Clermont-Ferrand, France
| | - Aurélie Hirschler
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, ProFI, Strasbourg, France
| | - Pierrick Roger
- CEA, LIST, Laboratoire Intelligence Artificielle et Apprentissage Automatique, MetaboHUB, Gif-sur-Yvette, France
| | - Thomas Burger
- Université Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, FR2048, ProFI, Grenoble, France
| | - Sophie Leblanc
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris, Phenomin-ICS, Illkirch, France
| | - Tania Sorg
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris, Phenomin-ICS, Illkirch, France
| | - Sadia Ouzia
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), MetaboHUB, Gif-sur-Yvette, France
| | - Yves Vandenbrouck
- Université Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, FR2048, ProFI, Grenoble, France
| | - Claudine Médigue
- IFB-core, UMS3601, Genoscope, Evry, France
- Laboratoire d'Analyses Bioinformatique en Génomique et Métabolisme (LABGeM), CNRS & CEA/DRF/IFJ, UMR8030, Evry, France
| | - Christophe Junot
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), MetaboHUB, Gif-sur-Yvette, France
| | - Myriam Ferro
- Université Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, FR2048, ProFI, Grenoble, France
| | - Estelle Pujos-Guillot
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB, Clermont-Ferrand, France
| | - Anne Gonzalez de Peredo
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, ProFI, Toulouse, France
| | - François Fenaille
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), MetaboHUB, Gif-sur-Yvette, France
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, ProFI, Strasbourg, France
| | - Yann Herault
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris, Phenomin-ICS, Illkirch, France
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique Biologie Moléculaire et Cellulaire, IGBMC, Illkirch, France
| | - Etienne A Thévenot
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), MetaboHUB, Gif-sur-Yvette, France.
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Muselius B, Durand SL, Geddes-McAlister J. Proteomics of Cryptococcus neoformans: From the Lab to the Clinic. Int J Mol Sci 2021; 22:12390. [PMID: 34830272 PMCID: PMC8618913 DOI: 10.3390/ijms222212390] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/12/2021] [Accepted: 11/15/2021] [Indexed: 12/12/2022] Open
Abstract
Fungal pathogens cause an array of diseases by targeting both immunocompromised and immunocompetent hosts. Fungi overcome our current arsenal of antifungals through the emergence and evolution of resistance. In particular, the human fungal pathogen, Cryptococcus neoformans is found ubiquitously within the environment and causes severe disease in immunocompromised individuals around the globe with limited treatment options available. To uncover fundamental knowledge about this fungal pathogen, as well as investigate new detection and treatment strategies, mass spectrometry-based proteomics provides a plethora of tools and applications, as well as bioinformatics platforms. In this review, we highlight proteomics approaches within the laboratory to investigate changes in the cellular proteome, secretome, and extracellular vesicles. We also explore regulation by post-translational modifications and the impact of protein-protein interactions. Further, we present the development and comprehensive assessment of murine models of cryptococcal infection, which provide valuable tools to define the dynamic relationship between the host and pathogen during disease. Finally, we explore recent quantitative proteomics studies that begin to extrapolate the findings from the bench to the clinic for improved methods of fungal detection and monitoring. Such studies support a framework for personalized medical approaches to eradicate diseases caused by C. neoformans.
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Affiliation(s)
| | | | - Jennifer Geddes-McAlister
- Molecular and Cellular Biology Department, University of Guelph, Guelph, ON N1G 2W1, Canada; (B.M.); (S.-L.D.)
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Hello from the other side: Membrane contact of lipid droplets with other organelles and subsequent functional implications. Prog Lipid Res 2021; 85:101141. [PMID: 34793861 DOI: 10.1016/j.plipres.2021.101141] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/10/2021] [Accepted: 11/10/2021] [Indexed: 02/06/2023]
Abstract
Lipid droplets (LDs) are ubiquitous organelles that play crucial roles in response to physiological and environmental cues. The identification of several neutral lipid synthesizing and regulatory protein complexes have propelled significant advance on the mechanisms of LD biogenesis in the endoplasmic reticulum (ER). Increasing evidence suggests that distinct proteins and regulatory factors, which localize to membrane contact sites (MCS), are involved not only in interorganellar lipid exchange and transport, but also function in other important cellular processes, including autophagy, mitochondrial dynamics and inheritance, ion signaling and inter-regulation of these MCS. More and more tethers and molecular determinants are associated to MCS and to a diversity of cellular and pathophysiological processes, demonstrating the dynamics and importance of these junctions in health and disease. The conjugation of lipids with proteins in supramolecular complexes is known to be paramount for many biological processes, namely membrane biosynthesis, cell homeostasis, regulation of organelle division and biogenesis, and cell growth. Ultimately, this physical organization allows the contact sites to function as crucial metabolic hubs that control the occurrence of chemical reactions. This leads to biochemical and metabolite compartmentalization for the purposes of energetic efficiency and cellular homeostasis. In this review, we will focus on the structural and functional aspects of LD-organelle interactions and how they ensure signaling exchange and metabolites transfer between organelles.
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Letertre MPM, Giraudeau P, de Tullio P. Nuclear Magnetic Resonance Spectroscopy in Clinical Metabolomics and Personalized Medicine: Current Challenges and Perspectives. Front Mol Biosci 2021; 8:698337. [PMID: 34616770 PMCID: PMC8488110 DOI: 10.3389/fmolb.2021.698337] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 08/30/2021] [Indexed: 12/12/2022] Open
Abstract
Personalized medicine is probably the most promising area being developed in modern medicine. This approach attempts to optimize the therapies and the patient care based on the individual patient characteristics. Its success highly depends on the way the characterization of the disease and its evolution, the patient’s classification, its follow-up and the treatment could be optimized. Thus, personalized medicine must combine innovative tools to measure, integrate and model data. Towards this goal, clinical metabolomics appears as ideally suited to obtain relevant information. Indeed, the metabolomics signature brings crucial insight to stratify patients according to their responses to a pathology and/or a treatment, to provide prognostic and diagnostic biomarkers, and to improve therapeutic outcomes. However, the translation of metabolomics from laboratory studies to clinical practice remains a subsequent challenge. Nuclear magnetic resonance spectroscopy (NMR) and mass spectrometry (MS) are the two key platforms for the measurement of the metabolome. NMR has several advantages and features that are essential in clinical metabolomics. Indeed, NMR spectroscopy is inherently very robust, reproducible, unbiased, quantitative, informative at the structural molecular level, requires little sample preparation and reduced data processing. NMR is also well adapted to the measurement of large cohorts, to multi-sites and to longitudinal studies. This review focus on the potential of NMR in the context of clinical metabolomics and personalized medicine. Starting with the current status of NMR-based metabolomics at the clinical level and highlighting its strengths, weaknesses and challenges, this article also explores how, far from the initial “opposition” or “competition”, NMR and MS have been integrated and have demonstrated a great complementarity, in terms of sample classification and biomarker identification. Finally, a perspective discussion provides insight into the current methodological developments that could significantly raise NMR as a more resolutive, sensitive and accessible tool for clinical applications and point-of-care diagnosis. Thanks to these advances, NMR has a strong potential to join the other analytical tools currently used in clinical settings.
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Affiliation(s)
| | | | - Pascal de Tullio
- Metabolomics Group, Center for Interdisciplinary Research of Medicine (CIRM), Department of Pharmacy, Université de Liège, Liège, Belgique
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48
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Borgmeyer M, Coman C, Has C, Schött HF, Li T, Westhoff P, Cheung YFH, Hoffmann N, Yuanxiang P, Behnisch T, Gomes GM, Dumenieu M, Schweizer M, Chocholoušková M, Holčapek M, Mikhaylova M, Kreutz MR, Ahrends R. Multiomics of synaptic junctions reveals altered lipid metabolism and signaling following environmental enrichment. Cell Rep 2021; 37:109797. [PMID: 34610315 DOI: 10.1016/j.celrep.2021.109797] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 04/12/2021] [Accepted: 09/15/2021] [Indexed: 12/30/2022] Open
Abstract
Membrane lipids and their metabolism have key functions in neurotransmission. Here we provide a quantitative lipid inventory of mouse and rat synaptic junctions. To this end, we developed a multiomics extraction and analysis workflow to probe the interplay of proteins and lipids in synaptic signal transduction from the same sample. Based on this workflow, we generate hypotheses about novel mechanisms underlying complex changes in synaptic connectivity elicited by environmental stimuli. As a proof of principle, this approach reveals that in mice exposed to an enriched environment, reduced endocannabinoid synthesis and signaling is linked to increased surface expression of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) in a subset of Cannabinoid-receptor 1 positive synapses. This mechanism regulates synaptic strength in an input-specific manner. Thus, we establish a compartment-specific multiomics workflow that is suitable to extract information from complex lipid and protein networks involved in synaptic function and plasticity.
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Affiliation(s)
- Maximilian Borgmeyer
- Leibniz Group 'Dendritic Organelles and Synaptic Function,' University Medical Center Hamburg-Eppendorf, Center for Molecular Neurobiology, ZMNH, 20251 Hamburg, Germany; RG Neuroplasticity, Leibniz Institute for Neurobiology, 39118 Magdeburg, Germany
| | - Cristina Coman
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227 Dortmund, Germany; Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Wien, Austria
| | - Canan Has
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227 Dortmund, Germany
| | - Hans-Frieder Schött
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227 Dortmund, Germany
| | - Tingting Li
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227 Dortmund, Germany
| | - Philipp Westhoff
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227 Dortmund, Germany
| | - Yam F H Cheung
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227 Dortmund, Germany
| | - Nils Hoffmann
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227 Dortmund, Germany
| | - PingAn Yuanxiang
- RG Neuroplasticity, Leibniz Institute for Neurobiology, 39118 Magdeburg, Germany
| | - Thomas Behnisch
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai 200032, China
| | - Guilherme M Gomes
- RG Neuroplasticity, Leibniz Institute for Neurobiology, 39118 Magdeburg, Germany
| | - Mael Dumenieu
- RG Neuroplasticity, Leibniz Institute for Neurobiology, 39118 Magdeburg, Germany
| | - Michaela Schweizer
- Morphology and Electron Microscopy, University Medical Center Hamburg-Eppendorf, Center for Molecular Neurobiology, ZMNH, 20251 Hamburg, Germany
| | - Michaela Chocholoušková
- University of Pardubice, Department of Analytical Chemistry, CZ-532 10 Pardubice, Czech Republic
| | - Michal Holčapek
- University of Pardubice, Department of Analytical Chemistry, CZ-532 10 Pardubice, Czech Republic
| | - Marina Mikhaylova
- Emmy Noether Group 'Neuronal Protein Transport,' University Medical Center Hamburg-Eppendorf, Center for Molecular Neurobiology, ZMNH, 20251 Hamburg, Germany; AG Optobiology, Institute for Biology, Humboldt Universität zu Berlin, 10115 Berlin, Germany
| | - Michael R Kreutz
- Leibniz Group 'Dendritic Organelles and Synaptic Function,' University Medical Center Hamburg-Eppendorf, Center for Molecular Neurobiology, ZMNH, 20251 Hamburg, Germany; RG Neuroplasticity, Leibniz Institute for Neurobiology, 39118 Magdeburg, Germany; German Center for Neurodegenerative Diseases (DZNE), 39120 Magdeburg, Germany; Center for Behavioral Brain Sciences, 30120 Magdeburg, Germany.
| | - Robert Ahrends
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227 Dortmund, Germany; Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Wien, Austria.
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Bayne EF, Simmons AD, Roberts DS, Zhu Y, Aballo TJ, Wancewicz B, Palecek SP, Ge Y. Multiomics Method Enabled by Sequential Metabolomics and Proteomics for Human Pluripotent Stem-Cell-Derived Cardiomyocytes. J Proteome Res 2021; 20:4646-4654. [PMID: 34499502 PMCID: PMC8714023 DOI: 10.1021/acs.jproteome.1c00611] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human pluripotent stem-cell-derived cardiomyocytes (hPSC-CMs) show immense promise for patient-specific disease modeling, cardiotoxicity screening, and regenerative therapy development. However, thus far, hPSC-CMs in culture have not recapitulated the structural or functional properties of adult CMs in vivo. To gain global insight into hPSC-CM biology, we established a multiomics method for analyzing the hPSC-CM metabolome and proteome from the same cell culture, creating multidimensional profiles of hPSC-CMs. Specifically, we developed a sequential extraction to capture metabolites and proteins from the same hPSC-CM monolayer cultures and analyzed these extracts using high-resolution mass spectrometry. Using this method, we annotated 205 metabolites/lipids and 4319 proteins from 106 cells with high reproducibility. We further integrated the proteome and metabolome measurements to create network profiles of molecular phenotypes for hPSC-CMs. Out of 310 pathways identified using metabolomics and proteomics, 40 pathways were considered significantly overrepresented (false-discovery-rate-corrected p ≤ 0.05). Highly populated pathways included those involved in protein synthesis (ribosome, spliceosome), ATP generation (oxidative phosphorylation), and cardiac muscle contraction. This multiomics method achieves a deep coverage of metabolites and proteins, creating a multidimensional view of the hPSC-CM phenotype, which provides a strong technological foundation to advance the understanding of hPSC-CM biology. Raw data are available in the MassIVE repository with identifier MSV000088010.
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Affiliation(s)
- Elizabeth F. Bayne
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Aaron D. Simmons
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - David S. Roberts
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Yanlong Zhu
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Timothy J. Aballo
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Benjamin Wancewicz
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Sean P. Palecek
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
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Michel L, Helfrich I, Hendgen-Cotta UB, Mincu RI, Korste S, Mrotzek SM, Spomer A, Odersky A, Rischpler C, Herrmann K, Umutlu L, Coman C, Ahrends R, Sickmann A, Löffek S, Livingstone E, Ugurel S, Zimmer L, Gunzer M, Schadendorf D, Totzeck M, Rassaf T. Targeting early stages of cardiotoxicity from anti-PD1 immune checkpoint inhibitor therapy. Eur Heart J 2021; 43:316-329. [PMID: 34389849 DOI: 10.1093/eurheartj/ehab430] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/25/2021] [Accepted: 06/25/2021] [Indexed: 12/13/2022] Open
Abstract
AIMS Cardiac immune-related adverse events (irAEs) from immune checkpoint inhibition (ICI) targeting programmed death 1 (PD1) are of growing concern. Once cardiac irAEs become clinically manifest, fatality rates are high. Cardio-oncology aims to prevent detrimental effects before manifestation of severe complications by targeting early pathological changes. We therefore aimed to investigate early consequences of PD1 inhibition for cardiac integrity to prevent the development of overt cardiac disease. METHODS AND RESULTS We investigated cardiac-specific consequences from anti-PD1 therapy in a combined biochemical and in vivo phenotyping approach. Mouse hearts showed broad expression of the ligand PDL1 on cardiac endothelial cells as a main mediator of immune-crosstalk. Using a novel melanoma mouse model, we assessed that anti-PD1 therapy promoted myocardial infiltration with CD4+ and CD8+ T cells, the latter being markedly activated. Left ventricular (LV) function was impaired during pharmacological stress, as shown by pressure-volume catheterization. This was associated with a dysregulated myocardial metabolism, including the proteome and the lipidome. Analogous to the experimental approach, in patients with metastatic melanoma (n = 7) receiving anti-PD1 therapy, LV function in response to stress was impaired under therapy. Finally, we identified that blockade of tumour necrosis factor alpha (TNFα) preserved LV function without attenuating the anti-cancer efficacy of anti-PD1 therapy. CONCLUSIONS Anti-PD1 therapy induces a disruption of cardiac immune homeostasis leading to early impairment of myocardial functional integrity, with potential prognostic effects on the growing number of treated patients. Blockade of TNFα may serve as an approach to prevent the manifestation of ICI-related cardiotoxicity.
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Affiliation(s)
- Lars Michel
- Department of Cardiology and Vascular Medicine, West German Heart and Vascular Center, University Hospital Essen, Hufelandstraße 55, Essen 45147, Germany
| | - Iris Helfrich
- Department of Dermatology, University Hospital Essen, Hufelandstraße 55, Essen 45147, Germany.,German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, Essen 45147, Germany.,Medical Faculty of the Ludwig Maximilian University of Munich, Department of Dermatology and Allergology, Frauenlobstrasse 9-11, Munich 80377, Germany
| | - Ulrike Barbara Hendgen-Cotta
- Department of Cardiology and Vascular Medicine, West German Heart and Vascular Center, University Hospital Essen, Hufelandstraße 55, Essen 45147, Germany
| | - Raluca-Ileana Mincu
- Department of Cardiology and Vascular Medicine, West German Heart and Vascular Center, University Hospital Essen, Hufelandstraße 55, Essen 45147, Germany
| | - Sebastian Korste
- Department of Cardiology and Vascular Medicine, West German Heart and Vascular Center, University Hospital Essen, Hufelandstraße 55, Essen 45147, Germany
| | - Simone Maria Mrotzek
- Department of Cardiology and Vascular Medicine, West German Heart and Vascular Center, University Hospital Essen, Hufelandstraße 55, Essen 45147, Germany
| | - Armin Spomer
- Department of Cardiology and Vascular Medicine, West German Heart and Vascular Center, University Hospital Essen, Hufelandstraße 55, Essen 45147, Germany
| | - Andrea Odersky
- Department of Cardiology and Vascular Medicine, West German Heart and Vascular Center, University Hospital Essen, Hufelandstraße 55, Essen 45147, Germany
| | - Christoph Rischpler
- Department of Nuclear Medicine, University Hospital Essen, Hufelandstraße 55, Essen 45147, Germany
| | - Ken Herrmann
- Department of Nuclear Medicine, University Hospital Essen, Hufelandstraße 55, Essen 45147, Germany
| | - Lale Umutlu
- Department of Diagnostic and Interventional Radiology and Neuroradiology, University Hospital Essen, Hufelandstraße 55, Essen 45147, Germany
| | - Cristina Coman
- Institute for Analytical Chemistry, Waehringer Straße 38, Vienna A-1090, Austria.,Leibniz Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Straße 6b, Dortmund 44227, Germany
| | - Robert Ahrends
- Institute for Analytical Chemistry, Waehringer Straße 38, Vienna A-1090, Austria.,Leibniz Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Straße 6b, Dortmund 44227, Germany
| | - Albert Sickmann
- Leibniz Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Straße 6b, Dortmund 44227, Germany.,Medizinische Fakultät, Medizinisches Proteom-Center (MPC), Ruhr-Universität Bochum, Bochum 44801, Germany.,Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen AB243FX, Scotland
| | - Stefanie Löffek
- Department of Dermatology, University Hospital Essen, Hufelandstraße 55, Essen 45147, Germany.,German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, Essen 45147, Germany
| | - Elisabeth Livingstone
- Department of Dermatology, University Hospital Essen, Hufelandstraße 55, Essen 45147, Germany.,German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, Essen 45147, Germany
| | - Selma Ugurel
- Department of Dermatology, University Hospital Essen, Hufelandstraße 55, Essen 45147, Germany.,German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, Essen 45147, Germany
| | - Lisa Zimmer
- Department of Dermatology, University Hospital Essen, Hufelandstraße 55, Essen 45147, Germany.,German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, Essen 45147, Germany
| | - Matthias Gunzer
- Leibniz Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Straße 6b, Dortmund 44227, Germany.,Institute for Experimental Immunology and Imaging, University Hospital Essen, Hufelandstraße 55, Essen 45147, Germany
| | - Dirk Schadendorf
- Department of Dermatology, University Hospital Essen, Hufelandstraße 55, Essen 45147, Germany.,German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, Essen 45147, Germany
| | - Matthias Totzeck
- Department of Cardiology and Vascular Medicine, West German Heart and Vascular Center, University Hospital Essen, Hufelandstraße 55, Essen 45147, Germany
| | - Tienush Rassaf
- Department of Cardiology and Vascular Medicine, West German Heart and Vascular Center, University Hospital Essen, Hufelandstraße 55, Essen 45147, Germany
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