1
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Cerrato A, Cavaliere C, Laganà A, Montone CM, Piovesana S, Sciarra A, Taglioni E, Capriotti AL. First Proof of Concept of a Click Inverse Electron Demand Diels-Alder Reaction for Assigning the Regiochemistry of Carbon-Carbon Double Bonds in Untargeted Lipidomics. Anal Chem 2024. [PMID: 38874982 DOI: 10.1021/acs.analchem.4c02146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
Lipidomics by high-resolution mass spectrometry (HRMS) has become a prominent tool in clinical chemistry due to the proven connections between lipid dysregulation and the insurgence of pathologies. However, it is difficult to achieve structural characterization beyond the fatty acid level by HRMS, especially when it comes to the regiochemistry of carbon-carbon double bonds, which play a major role in determining the properties of cell membranes. Several approaches have been proposed for elucidating the regiochemistry of double bonds, such as derivatization before MS analysis by photochemical reactions, which have shown great potential for their versatility but have the unavoidable drawback of splitting the MS signal. Among other possible approaches for derivatizing electron-rich double bonds, the emerging inverse-electron-demand Diels-Alder (IEDDA) reaction with tetrazines stands out for its unmatchable kinetics and has found several applications in basic biology and protein imaging. In this study, a catalyst-free click IEDDA reaction was employed for the first time to pinpoint carbon-carbon double bonds in free and conjugated fatty acids. Fatty acid and glycerophospholipid regioisomers were analyzed alone and in combination, demonstrating that the IEDDA reaction had click character and allowed the obtention of diagnostic product ions following MS/MS fragmentation as well as the possibility of performing relative quantitation of lipid regioisomers. The IEDDA protocol was later employed in an untargeted lipidomics study on plasma samples of patients suffering from prostate cancer and benign prostatic conditions, confirming the applicability of the proposed reaction to complex matrices of clinical interest.
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Affiliation(s)
- Andrea Cerrato
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Chiara Cavaliere
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Aldo Laganà
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Carmela Maria Montone
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Susy Piovesana
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Alessandro Sciarra
- Department of Maternal and Child and Urological Sciences, Sapienza University of Rome, Viale del Policlinico 155, Rome 00161, Italy
| | - Enrico Taglioni
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Anna Laura Capriotti
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy
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2
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Logotheti S, Pavlopoulou A, Rudsari HK, Galow AM, Kafali Y, Kyrodimos E, Giotakis AI, Marquardt S, Velalopoulou A, Verginadis II, Koumenis C, Stiewe T, Zoidakis J, Balasingham I, David R, Georgakilas AG. Intercellular pathways of cancer treatment-related cardiotoxicity and their therapeutic implications: The paradigm of radiotherapy. Pharmacol Ther 2024:108670. [PMID: 38823489 DOI: 10.1016/j.pharmthera.2024.108670] [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: 11/11/2023] [Revised: 05/16/2024] [Accepted: 05/25/2024] [Indexed: 06/03/2024]
Abstract
Advances in cancer therapeutics have improved patient survival rates. However, cancer survivors may suffer from adverse events either at the time of therapy or later in life. Cardiovascular diseases (CVD) represent a clinically important, but mechanistically understudied complication, which interfere with the continuation of best-possible care, induce life-threatening risks, and/or lead to long-term morbidity. These concerns are exacerbated by the fact that targeted therapies and immunotherapies are frequently combined with radiotherapy, which induces durable inflammatory and immunogenic responses, thereby providing a fertile ground for the development of cardiovascular diseases (CVDs). Stressed and dying irradiated cells produce 'danger' signals including, but not limited to, major histocompatibility complexes, cell-adhesion molecules, proinflammatory cytokines, and damage-associated molecular patterns. These factors activate intercellular signaling pathways which have potentially detrimental effects on the heart tissue homeostasis. Herein, we present the clinical crosstalk between cancer and heart diseases, describe how it is potentiated by cancer therapies, and highlight the multifactorial nature of the underlying mechanisms. We particularly focus on radiotherapy, as a case known to often induce cardiovascular complications even decades after treatment. We provide evidence that the secretome of irradiated tumors entails factors that exert systemic, remote effects on the cardiac tissue, potentially predisposing it to CVDs. We suggest how diverse disciplines can utilize pertinent state-of-the-art methods in feasible experimental workflows, to shed light on the molecular mechanisms of radiotherapy-related cardiotoxicity at the organismal level and untangle the desirable immunogenic properties of cancer therapies from their detrimental effects on heart tissue. Results of such highly collaborative efforts hold promise to be translated to next-generation regimens that maximize tumor control, minimize cardiovascular complications, and support quality of life in cancer survivors.
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Affiliation(s)
- Stella Logotheti
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens (NTUA), Zografou, 15780, Athens, Greece.
| | - Athanasia Pavlopoulou
- Izmir Biomedicine and Genome Center, Izmir, Turkey; Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | | | - Anne-Marie Galow
- Institute for Genome Biology, Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany
| | - Yağmur Kafali
- Izmir Biomedicine and Genome Center, Izmir, Turkey; Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Efthymios Kyrodimos
- First Department of Otorhinolaryngology, Head and Neck Surgery, Hippocrateion General Hospital Athens, National and Kapodistrian University of Athens, Athens, Greece
| | - Aris I Giotakis
- First Department of Otorhinolaryngology, Head and Neck Surgery, Hippocrateion General Hospital Athens, National and Kapodistrian University of Athens, Athens, Greece
| | - Stephan Marquardt
- Institute of Translational Medicine for Health Care Systems, Medical School Berlin, Hochschule Für Gesundheit Und Medizin, 14197 Berlin, Germany
| | - Anastasia Velalopoulou
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ioannis I Verginadis
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Constantinos Koumenis
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Thorsten Stiewe
- Institute of Molecular Oncology, Philipps-University, 35043 Marburg, Germany; German Center for Lung Research (DZL), Universities of Giessen and Marburg Lung Center (UGMLC), 35043 Marburg, Germany; Genomics Core Facility, Philipps-University, 35043 Marburg, Germany; Institute for Lung Health (ILH), Justus Liebig University, 35392 Giessen, Germany
| | - Jerome Zoidakis
- Department of Biotechnology, Biomedical Research Foundation, Academy of Athens, Athens, Greece; Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Robert David
- Department of Cardiac Surgery, Rostock University Medical Center, 18057 Rostock, Germany; Department of Life, Light & Matter, Interdisciplinary Faculty, Rostock University, 18059 Rostock, Germany
| | - Alexandros G Georgakilas
- DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens (NTUA), Zografou, 15780, Athens, Greece.
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3
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Qin S, Zhang Y, Shi M, Miao D, Lu J, Wen L, Bai Y. In-depth organic mass cytometry reveals differential contents of 3-hydroxybutanoic acid at the single-cell level. Nat Commun 2024; 15:4387. [PMID: 38782922 PMCID: PMC11116506 DOI: 10.1038/s41467-024-48865-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 05/16/2024] [Indexed: 05/25/2024] Open
Abstract
Comprehensive single-cell metabolic profiling is critical for revealing phenotypic heterogeneity and elucidating the molecular mechanisms underlying biological processes. However, single-cell metabolomics remains challenging because of the limited metabolite coverage and inability to discriminate isomers. Herein, we establish a single-cell metabolomics platform for in-depth organic mass cytometry. Extended single-cell analysis time guarantees sufficient MS/MS acquisition for metabolite identification and the isomers discrimination while online sampling ensures the high-throughput of the method. The largest number of identified metabolites (approximately 600) are achieved in single cells and fine subtyping of MCF-7 cells is first demonstrated by an investigation on the differential levels of 3-hydroxybutanoic acid among clusters. Single-cell transcriptome analysis reveals differences in the expression of 3-hydroxybutanoic acid downstream antioxidative stress genes, such as metallothionein 2 (MT2A), while a fluorescence-activated cell sorting assay confirms the positive relationship between 3-hydroxybutanoic acid and target proteins; these results suggest that the heterogeneity of 3-hydroxybutanoic acid provides cancer cells with different ability to resist surrounding oxidative stress. Our method paves the way for deep single-cell metabolome profiling and investigations on the physiological and pathological processes that occur during cancer.
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Affiliation(s)
- Shaojie Qin
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Yi Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Mingying Shi
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Daiyu Miao
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Jiansen Lu
- Biomedical Pioneering Innovative Center, School of Life Sciences, Peking University, Beijing, China
| | - Lu Wen
- Biomedical Pioneering Innovative Center, School of Life Sciences, Peking University, Beijing, China
| | - Yu Bai
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
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4
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Cerrato A, Aita SE, Cannazza G, Cavaliere C, Cavazzini A, Citti C, Montone CM, Taglioni E, Laganà A. One-phase extraction coupled with photochemical reaction allows the in-depth lipid characterization of hempseeds by untargeted lipidomics. Talanta 2024; 271:125686. [PMID: 38244310 DOI: 10.1016/j.talanta.2024.125686] [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: 11/27/2023] [Revised: 01/10/2024] [Accepted: 01/15/2024] [Indexed: 01/22/2024]
Abstract
Due to their valuable nutritional content, several hemp-derived products from hempseeds have recently been placed in the market as food and food ingredients. In particular, the lipid composition of hempseeds has raised interest for their rich content in biologically active polyunsaturated fatty acids with an optimum ratio of omega-3 and omega-6 compounds. At present, however, the overall polar lipidome composition of hempseeds remains largely unknown. In the present work, an analytical platform was developed for the extraction, untargeted HRMS-based analysis, and detailed annotation of the lipid species. First, five one- and two-phase solid-liquid extraction protocols were tested and compared on a hempseed pool sample to select the method that allowed the overall highest efficiency as well as easy coupling with lipid derivatization by photochemical [2 + 2] cycloaddition with 6-azauracil. Underivatized lipids were annotated employing a data processing workflow on Compound Discoverer software that was specifically designed for polar lipidomics, whereas inspection of the MS/MS spectra of the derivatized lipids following the aza-Paternò-Büchi reaction allowed pinpointing the regiochemistry of carbon-carbon double bonds. A total of 184 lipids were annotated, i.e., 26 fatty acids and 158 phospholipids, including minor subclasses such as N-acylphosphatidylethanolamines. Once the platform was set up, the lipid extracts from nine hempseed samples from different hemp strains were characterized, with information on the regiochemistry of free and conjugated fatty acids. The overall analytical approach helped to fill a gap in the knowledge of the nutritional composition of hempseeds.
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Affiliation(s)
- Andrea Cerrato
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Sara Elsa Aita
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Giuseppe Cannazza
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, Modena, 41125, Italy; Institute of Nanotechnology - CNR NANOTEC, Campus Ecotekne, Via Monteroni, Lecce, 73100, Italy
| | - Chiara Cavaliere
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Alberto Cavazzini
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Via L. Borsari 46, Ferrara, 44121, Italy
| | - Cinzia Citti
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, Modena, 41125, Italy; Institute of Nanotechnology - CNR NANOTEC, Campus Ecotekne, Via Monteroni, Lecce, 73100, Italy
| | - Carmela Maria Montone
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy.
| | - Enrico Taglioni
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Aldo Laganà
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
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5
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Cheng S, Cao C, Qian Y, Yao H, Gong X, Dai X, Ouyang Z, Ma X. High-throughput single-cell mass spectrometry enables metabolic network analysis by resolving phospholipid C[double bond, length as m-dash]C isomers. Chem Sci 2024; 15:6314-6320. [PMID: 38699276 PMCID: PMC11062128 DOI: 10.1039/d3sc06573a] [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: 12/07/2023] [Accepted: 04/02/2024] [Indexed: 05/05/2024] Open
Abstract
Single-cell mass spectrometry (MS) is an essential technology for sensitive and multiplexed analysis of metabolites and lipids for cell phenotyping and pathway studies. However, the structural elucidation of lipids from single cells remains a challenge, especially in the high-throughput scenario. Technically, there is a contradiction between the inadequate sample amount (i.e. a single cell, 0.5-20 pL) for replicate or multiple analysis, on the one hand, and the high metabolite coverage and multidimensional structure analysis that needs to be performed for each single cell, on the other hand. Here, we have developed a high-throughput single-cell MS platform that can perform both lipid profiling and lipid carbon-carbon double bond (C[double bond, length as m-dash]C) location isomer resolution analysis, aided by C[double bond, length as m-dash]C activation in unsaturated lipids by the Paternò-Büchi (PB) reaction and tandem MS, termed single-cell structural lipidomics analysis. The method can achieve a single-cell analysis throughput of 51 cells per minute. A total of 145 lipids were structurally characterized at the subclass level, of which the relative abundance of 17 isomeric lipids differing in the location of C[double bond, length as m-dash]C from 5 lipid precursors was determined. While cell-to-cell variations in MS1-based lipid profiling can be large, an advantage of quantifying lipid C[double bond, length as m-dash]C location isomers is the significantly improved quantitation accuracy. For example, the relative standard deviations (RSDs) of the relative amounts of PC 34:1 C[double bond, length as m-dash]C position isomers in MDA-MB-468 cells are half smaller than those measured for PC 34:1 as a whole by MS1 abundance profiling. Taken together, the developed method can be effectively used for in-depth structural lipid metabolism network analysis by high-throughput analysis of 142 MDA-MB-468 human breast cancer cells.
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Affiliation(s)
- Simin Cheng
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology Bejing 100029 China
| | - Chenxi Cao
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University Beijing 100084 China
| | - Yao Qian
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University Beijing 100084 China
| | - Huan Yao
- Division of Chemical Metrology and Analytical Science, National Institute of Metrology Beijing 100029 China
| | - Xiaoyun Gong
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology Bejing 100029 China
| | - Xinhua Dai
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology Bejing 100029 China
| | - Zheng Ouyang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University Beijing 100084 China
| | - Xiaoxiao Ma
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University Beijing 100084 China
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6
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Yang L, Yuan J, Yu B, Hu S, Bai Y. Sample preparation for fatty acid analysis in biological samples with mass spectrometry-based strategies. Anal Bioanal Chem 2024; 416:2371-2387. [PMID: 38319358 DOI: 10.1007/s00216-024-05185-0] [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: 09/18/2023] [Revised: 01/05/2024] [Accepted: 01/29/2024] [Indexed: 02/07/2024]
Abstract
Fatty acids (FAs) have attracted many interests for their pivotal roles in many biological processes. Imbalance of FAs is related to a variety of diseases, which makes the measurement of them important in biological samples. Over the past two decades, mass spectrometry (MS) has become an indispensable technique for the analysis of FAs owing to its high sensitivity and precision. Due to complex matrix effect of biological samples and inherent poor ionization efficiency of FAs in MS, sample preparation including extraction and chemical derivatization prior to analysis are often employed. Here, we describe an updated overview of FA extraction techniques, as well as representative derivatization methods utilized in different MS platforms including gas chromatography-MS, liquid chromatography-MS, and mass spectrometry imaging based on different chain lengths of FAs. Derivatization strategies for the identification of double bond location in unsaturated FAs are also summarized and highlighted. The advantages, disadvantages, and prospects of these methods are compared and discussed. This review provides the development and valuable information for sample pretreatment approaches and qualitative and quantitative analysis of interested FAs using different MS-based platforms in complex biological matrices. Finally, the challenges of FA analysis are summarized and the future perspectives are prospected.
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Affiliation(s)
- Li Yang
- Department of Pharmacy, Shanxi Medical University, Taiyuan, 030001, People's Republic of China.
| | - Jie Yuan
- Department of Pharmacy, Shanxi Medical University, Taiyuan, 030001, People's Republic of China
| | - Bolin Yu
- Department of Pharmacy, Shanxi Medical University, Taiyuan, 030001, People's Republic of China
| | - Shuang Hu
- Department of Pharmacy, Shanxi Medical University, Taiyuan, 030001, People's Republic of China
| | - Yu Bai
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, 100871, People's Republic of China.
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7
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Erazo-Oliveras A, Muñoz-Vega M, Salinas ML, Wang X, Chapkin RS. Dysregulation of cellular membrane homeostasis as a crucial modulator of cancer risk. FEBS J 2024; 291:1299-1352. [PMID: 36282100 PMCID: PMC10126207 DOI: 10.1111/febs.16665] [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: 06/18/2022] [Revised: 09/09/2022] [Accepted: 10/24/2022] [Indexed: 11/07/2022]
Abstract
Cellular membranes serve as an epicentre combining extracellular and cytosolic components with membranous effectors, which together support numerous fundamental cellular signalling pathways that mediate biological responses. To execute their functions, membrane proteins, lipids and carbohydrates arrange, in a highly coordinated manner, into well-defined assemblies displaying diverse biological and biophysical characteristics that modulate several signalling events. The loss of membrane homeostasis can trigger oncogenic signalling. More recently, it has been documented that select membrane active dietaries (MADs) can reshape biological membranes and subsequently decrease cancer risk. In this review, we emphasize the significance of membrane domain structure, organization and their signalling functionalities as well as how loss of membrane homeostasis can steer aberrant signalling. Moreover, we describe in detail the complexities associated with the examination of these membrane domains and their association with cancer. Finally, we summarize the current literature on MADs and their effects on cellular membranes, including various mechanisms of dietary chemoprevention/interception and the functional links between nutritional bioactives, membrane homeostasis and cancer biology.
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Affiliation(s)
- Alfredo Erazo-Oliveras
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
| | - Mónica Muñoz-Vega
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
| | - Michael L. Salinas
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
| | - Xiaoli Wang
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
| | - Robert S. Chapkin
- Program in Integrative Nutrition and Complex Diseases; Texas A&M University; College Station, Texas, 77843; USA
- Department of Nutrition; Texas A&M University; College Station, Texas, 77843; USA
- Center for Environmental Health Research; Texas A&M University; College Station, Texas, 77843; USA
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8
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Sun X, Yu Y, Qian K, Wang J, Huang L. Recent Progress in Mass Spectrometry-Based Single-Cell Metabolic Analysis. SMALL METHODS 2024; 8:e2301317. [PMID: 38032130 DOI: 10.1002/smtd.202301317] [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: 09/27/2023] [Revised: 11/10/2023] [Indexed: 12/01/2023]
Abstract
Single-cell analysis enables the measurement of biomolecules at the level of individual cells, facilitating in-depth investigations into cellular heterogeneity and precise interpretation of the related biological mechanisms. Among these biomolecules, cellular metabolites exhibit remarkable sensitivity to environmental and biochemical changes, unveiling a hidden world underlying cellular heterogeneity and allowing for the determination of cell physiological states. However, the metabolic analysis of single cells is challenging due to the extremely low concentrations, substantial content variations, and rapid turnover rates of cellular metabolites. Mass spectrometry (MS), characterized by its high sensitivity, wide dynamic range, and excellent selectivity, is employed in single-cell metabolic analysis. This review focuses on recent advances and applications of MS-based single-cell metabolic analysis, encompassing three key steps of single-cell isolation, detection, and application. It is anticipated that MS will bring profound implications in biomedical practices, serving as advanced tools to depict the single-cell metabolic landscape.
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Affiliation(s)
- Xuming Sun
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
- School of Medical Engineering, Xinxiang Medical University, Xinxiang, 453003, P. R. China
- Engineering Technology Research Center of Neurosense and Control of Henan Province, Xinxiang Medical University, Xinxiang, 453003, P. R. China
- Xinxiang Key Laboratory of Neurobiosensor, Xinxiang Medical University, Xinxiang, 453003, P. R. China
| | - Yi Yu
- School of Medical Engineering, Xinxiang Medical University, Xinxiang, 453003, P. R. China
- Engineering Technology Research Center of Neurosense and Control of Henan Province, Xinxiang Medical University, Xinxiang, 453003, P. R. China
- Xinxiang Key Laboratory of Neurobiosensor, Xinxiang Medical University, Xinxiang, 453003, P. R. China
| | - Kun Qian
- School of Biomedical Engineering, Institute of Medical Robotics and Med X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Jiayi Wang
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
| | - Lin Huang
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
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9
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Schuurman AR, Chouchane O, Butler JM, Peters-Sengers H, Joosten S, Brands X, Haak BW, Otto NA, Uhel F, Klarenbeek A, van Linge CC, van Kampen A, Pras-Raves M, van Weeghel M, van Eijk M, Ferraz MJ, Faber DR, de Vos A, Scicluna BP, Vaz FM, Wiersinga WJ, van der Poll T. The shifting lipidomic landscape of blood monocytes and neutrophils during pneumonia. JCI Insight 2024; 9:e164400. [PMID: 38385743 DOI: 10.1172/jci.insight.164400] [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: 08/10/2022] [Accepted: 01/17/2024] [Indexed: 02/23/2024] Open
Abstract
The lipidome of immune cells during infection has remained unexplored, although evidence of the importance of lipids in the context of immunity is mounting. In this study, we performed untargeted lipidomic analysis of blood monocytes and neutrophils from patients hospitalized for pneumonia and age- and sex-matched noninfectious control volunteers. We annotated 521 and 706 lipids in monocytes and neutrophils, respectively, which were normalized to an extensive set of internal standards per lipid class. The cellular lipidomes were profoundly altered in patients, with both common and distinct changes between the cell types. Changes involved every level of the cellular lipidome: differential lipid species, class-wide shifts, and altered saturation patterns. Overall, differential lipids were mainly less abundant in monocytes and more abundant in neutrophils from patients. One month after hospital admission, lipidomic changes were fully resolved in monocytes and partially in neutrophils. Integration of lipidomic and concurrently collected transcriptomic data highlighted altered sphingolipid metabolism in both cell types. Inhibition of ceramide and sphingosine-1-phosphate synthesis in healthy monocytes and neutrophils resulted in blunted cytokine responses upon stimulation with lipopolysaccharide. These data reveal major lipidomic remodeling in immune cells during infection, and link the cellular lipidome to immune functionality.
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Affiliation(s)
- Alex R Schuurman
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Osoul Chouchane
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Joe M Butler
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Hessel Peters-Sengers
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Sebastiaan Joosten
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Xanthe Brands
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Bastiaan W Haak
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Natasja A Otto
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Fabrice Uhel
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, Netherlands
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker-Enfants Malades, Paris, France
- Médecine Intensive Réanimation, AP-HP, Hôpital Louis Mourier, DMU ESPRIT, Colombes, France
| | - Augustijn Klarenbeek
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Christine Ca van Linge
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Antoine van Kampen
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Mia Pras-Raves
- Core Facility Metabolomics, Amsterdam UMC, Amsterdam, Netherlands
- Department of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases, Emma Children's Hospital, Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Inborn Errors of Metabolism, Amsterdam, Netherlands
| | - Michel van Weeghel
- Core Facility Metabolomics, Amsterdam UMC, Amsterdam, Netherlands
- Department of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases, Emma Children's Hospital, Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Inborn Errors of Metabolism, Amsterdam, Netherlands
| | - Marco van Eijk
- Leiden Institute of Chemistry, University of Leiden, Netherlands
| | - Maria J Ferraz
- Leiden Institute of Chemistry, University of Leiden, Netherlands
| | - Daniël R Faber
- Department of Internal Medicine, BovenIJ Hospital, Amsterdam, Netherlands
| | - Alex de Vos
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Brendon P Scicluna
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, Netherlands
- Department of Applied Biomedical Science, Faculty of Health Sciences, Mater Dei Hospital, and
- Center for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Frédéric M Vaz
- Core Facility Metabolomics, Amsterdam UMC, Amsterdam, Netherlands
- Department of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases, Emma Children's Hospital, Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Inborn Errors of Metabolism, Amsterdam, Netherlands
| | - W Joost Wiersinga
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, Netherlands
- Division of Infectious Diseases, Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Tom van der Poll
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, Netherlands
- Division of Infectious Diseases, Amsterdam University Medical Centers - Location AMC, University of Amsterdam, Amsterdam, Netherlands
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10
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Yang J, Cheng R, Pan X, Pan S, Du M, Yao H, Hu Z, Zhang S, Zhang X. Single-Cell Unsaturated Lipid Profiling for Studying Chemoresistance Heterogeneity of Triple-Negative Breast Cancer Cells. Anal Chem 2024. [PMID: 38334074 DOI: 10.1021/acs.analchem.3c04887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Chemoresistance to triple-negative breast cancer (TNBC) is a critical issue in clinical practice. Lipid metabolism takes a unique role in breast cancer cells; especially, unsaturated lipids involving cell membrane fluidity and peroxidation are highly remarked. At present, for the lack of a high-resolution molecular recognition platform at the single-cell level, it is still hard to systematically study chemoresistance heterogeneity based on lipid unsaturation proportion. By designing a single-cell mass spectrometry workflow based on CyESI-MS, we profiled the unsaturated lipids of TNBC cells to evaluate lipidomic remodeling under platinum stress. Profiling revealed the heterogeneity of the polyunsaturated lipid proportion of TNBC cells under cisplatin treatment. A cluster of cells identified by polyunsaturated lipid accumulation was found to be involved in platinum sensitivity. Furthermore, we found that the chemoresistance of TNBC cells could be regulated by fatty acid supplementation, which determinates the composition of unsaturated lipids. These discoveries provide insights for monitoring and controlling cellular unsaturated lipid proportions to overcome chemoresistance in breast cancer.
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Affiliation(s)
- Jinlei Yang
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Runsong Cheng
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Xingyu Pan
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Siyuan Pan
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Murong Du
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Huan Yao
- National Institute of Metrology, Beijing 100029, China
- Key Laboratory of Chemical Metrology and Applications on Nutrition and Health for State Market Regulation, Beijing 100029, China
| | - Zhian Hu
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology, Beijing 100083, China
| | - Sichun Zhang
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Xinrong Zhang
- Department of Chemistry, Tsinghua University, Beijing 100084, China
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11
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Hao Y, Stuart T, Kowalski MH, Choudhary S, Hoffman P, Hartman A, Srivastava A, Molla G, Madad S, Fernandez-Granda C, Satija R. Dictionary learning for integrative, multimodal and scalable single-cell analysis. Nat Biotechnol 2024; 42:293-304. [PMID: 37231261 PMCID: PMC10928517 DOI: 10.1038/s41587-023-01767-y] [Citation(s) in RCA: 146] [Impact Index Per Article: 146.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 03/28/2023] [Indexed: 05/27/2023]
Abstract
Mapping single-cell sequencing profiles to comprehensive reference datasets provides a powerful alternative to unsupervised analysis. However, most reference datasets are constructed from single-cell RNA-sequencing data and cannot be used to annotate datasets that do not measure gene expression. Here we introduce 'bridge integration', a method to integrate single-cell datasets across modalities using a multiomic dataset as a molecular bridge. Each cell in the multiomic dataset constitutes an element in a 'dictionary', which is used to reconstruct unimodal datasets and transform them into a shared space. Our procedure accurately integrates transcriptomic data with independent single-cell measurements of chromatin accessibility, histone modifications, DNA methylation and protein levels. Moreover, we demonstrate how dictionary learning can be combined with sketching techniques to improve computational scalability and harmonize 8.6 million human immune cell profiles from sequencing and mass cytometry experiments. Our approach, implemented in version 5 of our Seurat toolkit ( http://www.satijalab.org/seurat ), broadens the utility of single-cell reference datasets and facilitates comparisons across diverse molecular modalities.
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Affiliation(s)
- Yuhan Hao
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Tim Stuart
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Madeline H Kowalski
- New York Genome Center, New York, NY, USA
- Institute for System Genetics, NYU Langone Medical Center, New York, NY, USA
| | - Saket Choudhary
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Paul Hoffman
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Austin Hartman
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Avi Srivastava
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | | | - Shaista Madad
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Carlos Fernandez-Granda
- Center for Data Science, New York University, New York, NY, USA
- Courant Institute of Mathematical Sciences, New York University, New York, NY, USA
| | - Rahul Satija
- Center for Genomics and Systems Biology, New York University, New York, NY, USA.
- New York Genome Center, New York, NY, USA.
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12
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Larson TS, DiProspero TJ, Glish GL, Lockett MR. Differential lipid analysis of oxaliplatin-sensitive and resistant HCT116 cells reveals different levels of drug-induced lipid droplet formation. Anal Bioanal Chem 2024; 416:151-162. [PMID: 37917349 PMCID: PMC10771862 DOI: 10.1007/s00216-023-05010-0] [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: 09/20/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 11/04/2023]
Abstract
Lipid droplets (LDs) are intracellular storage vesicles composed of a neutral lipid core surrounded by a glycerophospholipid membrane. LD accumulation is associated with different stages of cancer progression and stress responses resulting from chemotherapy. In previous work, a novel dual nano-electrospray ionization source and data-dependent acquisition method for measuring the relative abundances of lipid species between two extracts were described and validated. Here, this same source and method were used to determine if oxaliplatin-sensitive and resistant cells undergo similar lipid profile changes, with the goal of identifying potential signatures that could predict the effectiveness of an oxaliplatin-containing treatment. Oxaliplatin is commonly used in the treatment of colorectal cancer. When compared to a no-drug control, oxaliplatin dosing caused significant increases in triglyceride (TG) and cholesterol ester (CE) species. These increases were more pronounced in the oxaliplatin-sensitive cells than in oxaliplatin-resistant cells. The increased neutral lipid abundance correlated with LD formation, as confirmed by confocal micrographs of Nile Red-stained cells. Untargeted proteomic analyses also support LD formation after oxaliplatin treatment, with an increased abundance of LD-associated proteins in both the sensitive and resistant cells.
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Affiliation(s)
- Tyler S Larson
- Department of Chemistry, University of North Carolina at Chapel Hill, Kenan and Caudill Laboratories, Chapel Hill, NC, 27599-3290, USA
| | - Thomas J DiProspero
- Department of Chemistry, University of North Carolina at Chapel Hill, Kenan and Caudill Laboratories, Chapel Hill, NC, 27599-3290, USA
| | - Gary L Glish
- Department of Chemistry, University of North Carolina at Chapel Hill, Kenan and Caudill Laboratories, Chapel Hill, NC, 27599-3290, USA.
| | - Matthew R Lockett
- Department of Chemistry, University of North Carolina at Chapel Hill, Kenan and Caudill Laboratories, Chapel Hill, NC, 27599-3290, USA.
- Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-7295, USA.
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13
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Zhang D, Qiao L. Microfluidics Coupled Mass Spectrometry for Single Cell Multi-Omics. SMALL METHODS 2024; 8:e2301179. [PMID: 37840412 DOI: 10.1002/smtd.202301179] [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: 09/01/2023] [Revised: 10/02/2023] [Indexed: 10/17/2023]
Abstract
Population-level analysis masks significant heterogeneity between individual cells, making it difficult to accurately reflect the true intricacies of life activities. Microfluidics is a technique that can manipulate individual cells effectively and is commonly coupled with a variety of analytical methods for single-cell analysis. Single-cell omics provides abundant molecular information at the single-cell level, fundamentally revealing differences in cell types and biological states among cell individuals, leading to a deeper understanding of cellular phenotypes and life activities. Herein, this work summarizes the microfluidic chips designed for single-cell isolation, manipulation, trapping, screening, and sorting, including droplet microfluidic chips, microwell arrays, hydrodynamic microfluidic chips, and microchips with microvalves. This work further reviews the studies on single-cell proteomics, metabolomics, lipidomics, and multi-omics based on microfluidics and mass spectrometry. Finally, the challenges and future application of single-cell multi-omics are discussed.
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Affiliation(s)
- Dongxue Zhang
- Department of Chemistry, Institutes of Biomedical Sciences, and Minhang Hospital, Fudan University, Shanghai, 20000, China
| | - Liang Qiao
- Department of Chemistry, Institutes of Biomedical Sciences, and Minhang Hospital, Fudan University, Shanghai, 20000, China
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14
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Zhang Q, Lin L, Yi X, Xie T, Xing G, Li Y, Wang X, Lin JM. Microfluidic Sampling of Undissolved Components from Subcellular Regions of Living Single Cells for Mass Spectrometry Analysis. Anal Chem 2023; 95:18082-18090. [PMID: 38032315 DOI: 10.1021/acs.analchem.3c03086] [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: 12/01/2023]
Abstract
Precise sampling of undissolved chemical components from subcellular regions of living single cells is a prerequisite for their in-depth analysis, which could promote understanding of subtle early stage physiological or pathological processes. Here we report a microfluidic method to extract undissolved components from subcellular regions for MS analysis. The target single cell was isolated by the microchamber beneath the microfluidic probe and washed by the injected biocompatible isotonic glucose aqueous solution (IGAS). Then, the sampling solvent was injected to extract undissolved components from the expected subcellular region of the living single cell, where the position and size of the sampling region could be controlled. The components immobilized by undissolved cellular structures were proven to be successfully extracted. Since unextracted subcellular regions were protected by IGAS, the single cell could survive after a tiny part was extracted, providing the possibility of repetitive sampling of the same living cell. Phospholipids extracted from the subcellular regions were successfully identified. The results demonstrated the feasibility of our method for subcellular sampling and analysis.
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Affiliation(s)
- Qiang Zhang
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Ling Lin
- Department of Bioengineering, Beijing Technology and Business University, Beijing 100048, China
| | - Xizhen Yi
- Department of Chemistry, Tshinghua University, Beijing 100084, China
| | - Tianze Xie
- Department of Chemistry, Tshinghua University, Beijing 100084, China
| | - Gaowa Xing
- Department of Chemistry, Tshinghua University, Beijing 100084, China
| | - Yuxuan Li
- Department of Chemistry, Tshinghua University, Beijing 100084, China
| | - Xiaorui Wang
- Department of Bioengineering, Beijing Technology and Business University, Beijing 100048, China
| | - Jin-Ming Lin
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
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15
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Zeng Q, Xia MC, Yin X, Cheng S, Xue Z, Tan S, Gong X, Ye Z. Recent developments in ionization techniques for single-cell mass spectrometry. Front Chem 2023; 11:1293533. [PMID: 38130875 PMCID: PMC10733462 DOI: 10.3389/fchem.2023.1293533] [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: 09/13/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
The variation among individual cells plays a significant role in many biological functions. Single-cell analysis is advantageous for gaining insight into intricate biochemical mechanisms rarely accessible when studying tissues as a whole. However, measurement on a unicellular scale is still challenging due to unicellular complex composition, minute substance quantities, and considerable differences in compound concentrations. Mass spectrometry has recently gained extensive attention in unicellular analytical fields due to its exceptional sensitivity, throughput, and compound identification abilities. At present, single-cell mass spectrometry primarily concentrates on the enhancement of ionization methods. The principal ionization approaches encompass nanoelectrospray ionization (nano-ESI), laser desorption ionization (LDI), secondary ion mass spectrometry (SIMS), and inductively coupled plasma (ICP). This article summarizes the most recent advancements in ionization techniques and explores their potential directions within the field of single-cell mass spectrometry.
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Affiliation(s)
- Qingli Zeng
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Meng-Chan Xia
- National Anti-Drug Laboratory Beijing Regional Center, Beijing, China
| | - Xinchi Yin
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Simin Cheng
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Zhichao Xue
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Siyuan Tan
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Xiaoyun Gong
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Zihong Ye
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
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16
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Wevers D, Ramautar R, Clark C, Hankemeier T, Ali A. Opportunities and challenges for sample preparation and enrichment in mass spectrometry for single-cell metabolomics. Electrophoresis 2023; 44:2000-2024. [PMID: 37667867 DOI: 10.1002/elps.202300105] [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: 05/11/2023] [Revised: 08/08/2023] [Accepted: 08/19/2023] [Indexed: 09/06/2023]
Abstract
Single-cell heterogeneity in metabolism, drug resistance and disease type poses the need for analytical techniques for single-cell analysis. As the metabolome provides the closest view of the status quo in the cell, studying the metabolome at single-cell resolution may unravel said heterogeneity. A challenge in single-cell metabolome analysis is that metabolites cannot be amplified, so one needs to deal with picolitre volumes and a wide range of analyte concentrations. Due to high sensitivity and resolution, MS is preferred in single-cell metabolomics. Large numbers of cells need to be analysed for proper statistics; this requires high-throughput analysis, and hence automation of the analytical workflow. Significant advances in (micro)sampling methods, CE and ion mobility spectrometry have been made, some of which have been applied in high-throughput analyses. Microfluidics has enabled an automation of cell picking and metabolite extraction; image recognition has enabled automated cell identification. Many techniques have been used for data analysis, varying from conventional techniques to novel combinations of advanced chemometric approaches. Steps have been set in making data more findable, accessible, interoperable and reusable, but significant opportunities for improvement remain. Herein, advances in single-cell analysis workflows and data analysis are discussed, and recommendations are made based on the experimental goal.
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Affiliation(s)
- Dirk Wevers
- Wageningen University and Research, Wageningen, The Netherlands
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Rawi Ramautar
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Charlie Clark
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Thomas Hankemeier
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Ahmed Ali
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
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17
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Lu H, Zhang H, Li L. Chemical tagging mass spectrometry: an approach for single-cell omics. Anal Bioanal Chem 2023; 415:6901-6913. [PMID: 37466681 PMCID: PMC10729908 DOI: 10.1007/s00216-023-04850-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/20/2023]
Abstract
Single-cell (SC) analysis offers new insights into the study of fundamental biological phenomena and cellular heterogeneity. The superior sensitivity, high throughput, and rich chemical information provided by mass spectrometry (MS) allow MS to emerge as a leading technology for molecular profiling of SC omics, including the SC metabolome, lipidome, and proteome. However, issues such as ionization suppression, low concentration, and huge span of dynamic concentrations of SC components lead to poor MS response for certain types of molecules. It is noted that chemical tagging/derivatization has been adopted in SCMS analysis, and this strategy has been proven an effective solution to circumvent these issues in SCMS analysis. Herein, we review the basic principle and general strategies of chemical tagging/derivatization in SCMS analysis, along with recent applications of chemical derivatization to single-cell metabolomics and multiplexed proteomics, as well as SCMS imaging. Furthermore, the challenges and opportunities for the improvement of chemical derivatization strategies in SCMS analysis are discussed.
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Affiliation(s)
- Haiyan Lu
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Hua Zhang
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA.
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA.
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18
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Marques C, Friedrich F, Liu L, Castoldi F, Pietrocola F, Lanekoff I. Global and Spatial Metabolomics of Individual Cells Using a Tapered Pneumatically Assisted nano-DESI Probe. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2518-2524. [PMID: 37830184 PMCID: PMC10623638 DOI: 10.1021/jasms.3c00239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/26/2023] [Accepted: 09/29/2023] [Indexed: 10/14/2023]
Abstract
Single-cell metabolomics has the potential to reveal unique insights into intracellular mechanisms and biological processes. However, the detection of metabolites from individual cells is challenging due to their versatile chemical properties and concentrations. Here, we demonstrate a tapered probe for pneumatically assisted nanospray desorption electrospray ionization (PA nano-DESI) mass spectrometry that enables both chemical imaging of larger cells and global metabolomics of smaller 15 μm cells. Additionally, by depositing cells in predefined arrays, we show successful metabolomics from three individual INS-1 cells per minute, which enabled the acquisition of data from 479 individual cells. Several cells were used to optimize analytical conditions, and 93 or 97 cells were used to monitor metabolome alterations in INS-1 cells after exposure to a low or high glucose concentration, respectively. Our analytical approach offers insights into cellular heterogeneity and provides valuable information about cellular processes and responses in individual cells.
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Affiliation(s)
- Cátia Marques
- Department
of Chemistry—BMC, Uppsala University, 75123 Uppsala, Sweden
| | - Felix Friedrich
- Department
of Chemistry—BMC, Uppsala University, 75123 Uppsala, Sweden
| | - Liangwen Liu
- Department
of Medical Cell Biology, Uppsala University, 75123 Uppsala, Sweden
| | - Francesca Castoldi
- Department
of Biosciences and Nutrition, Karolinska
Institute, 14152 Huddinge, Sweden
| | - Federico Pietrocola
- Department
of Biosciences and Nutrition, Karolinska
Institute, 14152 Huddinge, Sweden
| | - Ingela Lanekoff
- Department
of Chemistry—BMC, Uppsala University, 75123 Uppsala, Sweden
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19
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Han J, Wang X, Wang W, Chen J, Xu B, Wei Z. Direct Analysis of Micro-biopsy Samples by Polarity Gradient Focusing Dip-and-Go Mass Spectrometry. Anal Chem 2023; 95:13266-13272. [PMID: 37610922 DOI: 10.1021/acs.analchem.3c02425] [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: 08/25/2023]
Abstract
Direct analysis of micro-biopsy samples by mass spectrometry at single-cell level still faces major challenges. In this work, we developed a polarity gradient focusing dip-and-go strategy (PGF-Dip&Go) during induced electrospray ionization mass spectrometry (iESI-MS) analysis for real-time enrichment and spatial separation of compounds such as lipids, alkaloids, fatty amines, and drugs. Compared with direct iESI-MS analysis, enrichment of analytes (enrichment factor of 5.0-100.0) and spatial separation between different analytes were achieved. Owing to the enrichment effect and salt cleanup effect, the sensitivity of PGF-Dip&Go has been improved by 25-10,000 times compared with direct iESI-MS. PGF-Dip&Go has been successfully applied for the analysis of lipids in a 200 pL micro-biopsy section from an individual fish egg. Lysophosphatidylcholine (LPC), phosphatidylcholine (PC), and triglyceride (TG) were significantly enriched and separated according to their polarity differences, proving the potential of PGF-Dip&Go to be a noninvasive and powerful analytical tool for in situ analysis of complex small volumes in the future.
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Affiliation(s)
- Jin Han
- College of Chemistry and Molecular Science, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Xiangyu Wang
- College of Chemistry and Molecular Science, Wuhan University, Wuhan, Hubei 430072, P. R. China
- School of Public Health, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Wenxin Wang
- College of Chemistry and Molecular Science, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Jianxiong Chen
- College of Chemistry and Molecular Science, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Bin Xu
- College of Chemistry and Molecular Science, Wuhan University, Wuhan, Hubei 430072, P. R. China
| | - Zhenwei Wei
- College of Chemistry and Molecular Science, Wuhan University, Wuhan, Hubei 430072, P. R. China
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20
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Abdelkader Y, Perez-Davalos L, LeDuc R, Zahedi RP, Labouta HI. Omics approaches for the assessment of biological responses to nanoparticles. Adv Drug Deliv Rev 2023; 200:114992. [PMID: 37414362 DOI: 10.1016/j.addr.2023.114992] [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: 02/28/2023] [Revised: 06/08/2023] [Accepted: 07/03/2023] [Indexed: 07/08/2023]
Abstract
Nanotechnology has enabled the development of innovative therapeutics, diagnostics, and drug delivery systems. Nanoparticles (NPs) can influence gene expression, protein synthesis, cell cycle, metabolism, and other subcellular processes. While conventional methods have limitations in characterizing responses to NPs, omics approaches can analyze complete sets of molecular entities that change upon exposure to NPs. This review discusses key omics approaches, namely transcriptomics, proteomics, metabolomics, lipidomics and multi-omics, applied to the assessment of biological responses to NPs. Fundamental concepts and analytical methods used for each approach are presented, as well as good practices for omics experiments. Bioinformatics tools are essential to analyze, interpret and visualize large omics data, and to correlate observations in different molecular layers. The authors envision that conducting interdisciplinary multi-omics analyses in future nanomedicine studies will reveal integrated cell responses to NPs at different omics levels, and the incorporation of omics into the evaluation of targeted delivery, efficacy, and safety will improve the development of nanomedicine therapies.
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Affiliation(s)
- Yasmin Abdelkader
- Unity Health Toronto - St. Michael's Hospital, University of Toronto, 209 Victoria St., Toronto, Ontario M5B 1T8, Canada; College of Pharmacy, Apotex Centre, University of Manitoba, 750 McDermot Av. W, Winnipeg, Manitoba R3E 0T5, Canada; Department of Cell Biology, Biotechnology Research Institute, National Research Centre, 33 El Buhouth St., Cairo 12622, Egypt
| | - Luis Perez-Davalos
- Unity Health Toronto - St. Michael's Hospital, University of Toronto, 209 Victoria St., Toronto, Ontario M5B 1T8, Canada; College of Pharmacy, Apotex Centre, University of Manitoba, 750 McDermot Av. W, Winnipeg, Manitoba R3E 0T5, Canada
| | - Richard LeDuc
- Children's Hospital Research Institute of Manitoba, 513 - 715 McDermot Av. W, Winnipeg, Manitoba R3E 3P4, Canada; Department of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Av., Winnipeg, Manitoba R3E 0J9, Canada
| | - Rene P Zahedi
- Department of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Av., Winnipeg, Manitoba R3E 0J9, Canada; Department of Internal Medicine, 715 McDermot Av., Winnipeg, Manitoba R3E 3P4, Canada; Manitoba Centre for Proteomics and Systems Biology, 799 JBRC, 715 McDermot Av., Winnipeg, Manitoba R3E 3P4, Canada; CancerCare Manitoba Research Institute, 675 McDermot Av., Manitoba R3E 0V9, Canada
| | - Hagar I Labouta
- Unity Health Toronto - St. Michael's Hospital, University of Toronto, 209 Victoria St., Toronto, Ontario M5B 1T8, Canada; College of Pharmacy, Apotex Centre, University of Manitoba, 750 McDermot Av. W, Winnipeg, Manitoba R3E 0T5, Canada; Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College St., Toronto, Ontario M5S 3M2, Canada; Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, M5S 3G9, Canada; Faculty of Pharmacy, Alexandria University, 1 Khartoum Square, Azarita, Alexandria, Egypt, 21521.
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21
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Yao M, Vaithiyanathan M, Allbritton NL. Analytical Techniques for Single-Cell Biochemical Assays of Lipids. Annu Rev Biomed Eng 2023; 25:281-309. [PMID: 37068764 PMCID: PMC11032153 DOI: 10.1146/annurev-bioeng-110220-034007] [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: 04/19/2023]
Abstract
Lipids are essential cellular components forming membranes, serving as energy reserves, and acting as chemical messengers. Dysfunction in lipid metabolism and signaling is associated with a wide range of diseases including cancer and autoimmunity. Heterogeneity in cell behavior including lipid signaling is increasingly recognized as a driver of disease and drug resistance. This diversity in cellular responses as well as the roles of lipids in health and disease drive the need to quantify lipids within single cells. Single-cell lipid assays are challenging due to the small size of cells (∼1 pL) and the large numbers of lipid species present at concentrations spanning orders of magnitude. A growing number of methodologies enable assay of large numbers of lipid analytes, perform high-resolution spatial measurements, or permit highly sensitive lipid assays in single cells. Covered in this review are mass spectrometry, Raman imaging, and fluorescence-based assays including microscopy and microseparations.
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Affiliation(s)
- Ming Yao
- Department of Bioengineering, University of Washington, Seattle, Washington, USA; , ,
| | | | - Nancy L Allbritton
- Department of Bioengineering, University of Washington, Seattle, Washington, USA; , ,
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22
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Iadecola C, Smith EE, Anrather J, Gu C, Mishra A, Misra S, Perez-Pinzon MA, Shih AY, Sorond FA, van Veluw SJ, Wellington CL. The Neurovasculome: Key Roles in Brain Health and Cognitive Impairment: A Scientific Statement From the American Heart Association/American Stroke Association. Stroke 2023; 54:e251-e271. [PMID: 37009740 PMCID: PMC10228567 DOI: 10.1161/str.0000000000000431] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
Abstract
BACKGROUND Preservation of brain health has emerged as a leading public health priority for the aging world population. Advances in neurovascular biology have revealed an intricate relationship among brain cells, meninges, and the hematic and lymphatic vasculature (the neurovasculome) that is highly relevant to the maintenance of cognitive function. In this scientific statement, a multidisciplinary team of experts examines these advances, assesses their relevance to brain health and disease, identifies knowledge gaps, and provides future directions. METHODS Authors with relevant expertise were selected in accordance with the American Heart Association conflict-of-interest management policy. They were assigned topics pertaining to their areas of expertise, reviewed the literature, and summarized the available data. RESULTS The neurovasculome, composed of extracranial, intracranial, and meningeal vessels, as well as lymphatics and associated cells, subserves critical homeostatic functions vital for brain health. These include delivering O2 and nutrients through blood flow and regulating immune trafficking, as well as clearing pathogenic proteins through perivascular spaces and dural lymphatics. Single-cell omics technologies have unveiled an unprecedented molecular heterogeneity in the cellular components of the neurovasculome and have identified novel reciprocal interactions with brain cells. The evidence suggests a previously unappreciated diversity of the pathogenic mechanisms by which disruption of the neurovasculome contributes to cognitive dysfunction in neurovascular and neurodegenerative diseases, providing new opportunities for the prevention, recognition, and treatment of these conditions. CONCLUSIONS These advances shed new light on the symbiotic relationship between the brain and its vessels and promise to provide new diagnostic and therapeutic approaches for brain disorders associated with cognitive dysfunction.
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23
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Zhu P, Bu G, Hu R, Ruan X, Fu R, Zhang Z, Wan Q, Liu X, Miao Y, Chen S. Lipidomic Characterization of Oocytes at Single-Cell Level Using Nanoflow Chromatography-Trapped Ion Mobility Spectrometry-Mass Spectrometry. Molecules 2023; 28:molecules28104202. [PMID: 37241942 DOI: 10.3390/molecules28104202] [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: 04/14/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Mass spectrometry (MS)-based lipidomic has become a powerful tool for studying lipids in biological systems. However, lipidome analysis at the single-cell level remains a challenge. Here, we report a highly sensitive lipidomic workflow based on nanoflow liquid chromatography and trapped ion mobility spectrometry (TIMS)-MS. This approach enables the high-coverage identification of lipidome landscape at the single-oocyte level. By using the proposed method, comprehensive lipid changes in porcine oocytes during their maturation were revealed. The results provide valuable insights into the structural changes of lipid molecules during porcine oocyte maturation, highlighting the significance of sphingolipids and glycerophospholipids. This study offers a new approach to the single-cell lipidomic.
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Affiliation(s)
- Pujia Zhu
- The Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Guowei Bu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Ruifeng Hu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Xianqin Ruan
- The Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Rongrong Fu
- The Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Zhourui Zhang
- The Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Qiongqiong Wan
- The Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Xin Liu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Yiliang Miao
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Suming Chen
- The Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
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24
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Conroy LR, Clarke HA, Allison DB, Valenca SS, Sun Q, Hawkinson TR, Young LEA, Ferreira JE, Hammonds AV, Dunne JB, McDonald RJ, Absher KJ, Dong BE, Bruntz RC, Markussen KH, Juras JA, Alilain WJ, Liu J, Gentry MS, Angel PM, Waters CM, Sun RC. Spatial metabolomics reveals glycogen as an actionable target for pulmonary fibrosis. Nat Commun 2023; 14:2759. [PMID: 37179348 PMCID: PMC10182559 DOI: 10.1038/s41467-023-38437-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
Matrix assisted laser desorption/ionization imaging has greatly improved our understanding of spatial biology, however a robust bioinformatic pipeline for data analysis is lacking. Here, we demonstrate the application of high-dimensionality reduction/spatial clustering and histopathological annotation of matrix assisted laser desorption/ionization imaging datasets to assess tissue metabolic heterogeneity in human lung diseases. Using metabolic features identified from this pipeline, we hypothesize that metabolic channeling between glycogen and N-linked glycans is a critical metabolic process favoring pulmonary fibrosis progression. To test our hypothesis, we induced pulmonary fibrosis in two different mouse models with lysosomal glycogen utilization deficiency. Both mouse models displayed blunted N-linked glycan levels and nearly 90% reduction in endpoint fibrosis when compared to WT animals. Collectively, we provide conclusive evidence that lysosomal utilization of glycogen is required for pulmonary fibrosis progression. In summary, our study provides a roadmap to leverage spatial metabolomics to understand foundational biology in pulmonary diseases.
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Affiliation(s)
- Lindsey R Conroy
- Department of Neuroscience, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
- Markey Cancer Center, Lexington, KY, 40536, USA
| | - Harrison A Clarke
- Department of Biochemistry & Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Derek B Allison
- Markey Cancer Center, Lexington, KY, 40536, USA
- Department of Pathology and Laboratory Medicine, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
| | - Samuel Santos Valenca
- Department of Physiology, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, KY, 40536, USA
| | - Qi Sun
- Department of Neuroscience, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
| | - Tara R Hawkinson
- Department of Biochemistry & Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Lyndsay E A Young
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
| | - Juanita E Ferreira
- Department of Pathology and Laboratory Medicine, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
| | - Autumn V Hammonds
- Department of Pathology and Laboratory Medicine, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
| | - Jaclyn B Dunne
- Department of Cell & Molecular Pharmacology & Experimental Therapeutics at the Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Robert J McDonald
- Department of Pathology and Laboratory Medicine, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
| | - Kimberly J Absher
- Department of Pathology and Laboratory Medicine, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
| | - Brittany E Dong
- Department of Physiology, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, KY, 40536, USA
| | - Ronald C Bruntz
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
| | - Kia H Markussen
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
| | - Jelena A Juras
- Department of Neuroscience, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
- Markey Cancer Center, Lexington, KY, 40536, USA
| | - Warren J Alilain
- Department of Neuroscience, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
- Spinal Cord and Brain Injury Research Center, Lexington, KY, 40536, USA
| | - Jinze Liu
- Department of Biostatistics, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Matthew S Gentry
- Markey Cancer Center, Lexington, KY, 40536, USA
- Department of Biochemistry & Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
- Center for Advanced Spatial Biomolecule Research, University of Florida, Gainesville, FL, 32610, USA
| | - Peggi M Angel
- Department of Cell & Molecular Pharmacology & Experimental Therapeutics at the Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Christopher M Waters
- Department of Physiology, University of Kentucky College of Medicine, Lexington, KY, 40536, USA.
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, KY, 40536, USA.
| | - Ramon C Sun
- Department of Neuroscience, University of Kentucky College of Medicine, Lexington, KY, 40536, USA.
- Markey Cancer Center, Lexington, KY, 40536, USA.
- Department of Biochemistry & Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA.
- Center for Advanced Spatial Biomolecule Research, University of Florida, Gainesville, FL, 32610, USA.
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25
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Ross DH, Lee JY, Bilbao A, Orton DJ, Eder JG, Burnet MC, Deatherage Kaiser BL, Kyle JE, Zheng X. LipidOz enables automated elucidation of lipid carbon-carbon double bond positions from ozone-induced dissociation mass spectrometry data. Commun Chem 2023; 6:74. [PMID: 37076550 PMCID: PMC10115790 DOI: 10.1038/s42004-023-00867-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 03/24/2023] [Indexed: 04/21/2023] Open
Abstract
Lipids play essential roles in many biological processes and disease pathology, but unambiguous identification of lipids is complicated by the presence of multiple isomeric species differing by fatty acyl chain length, stereospecifically numbered (sn) position, and position/stereochemistry of double bonds. Conventional liquid chromatography-mass spectrometry (LC-MS/MS) analyses enable the determination of fatty acyl chain lengths (and in some cases sn position) and number of double bonds, but not carbon-carbon double bond positions. Ozone-induced dissociation (OzID) is a gas-phase oxidation reaction that produces characteristic fragments from lipids containing double bonds. OzID can be incorporated into ion mobility spectrometry (IMS)-MS instruments for the structural characterization of lipids, including additional isomer separation and confident assignment of double bond positions. The complexity and repetitive nature of OzID data analysis and lack of software tool support have limited the application of OzID for routine lipidomics studies. Here, we present an open-source Python tool, LipidOz, for the automated determination of lipid double bond positions from OzID-IMS-MS data, which employs a combination of traditional automation and deep learning approaches. Our results demonstrate the ability of LipidOz to robustly assign double bond positions for lipid standard mixtures and complex lipid extracts, enabling practical application of OzID for future lipidomics.
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Affiliation(s)
- Dylan H Ross
- Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Joon-Yong Lee
- Pacific Northwest National Laboratory, Richland, WA, 99354, USA
- PrognomiQ, Inc, San Mateo, CA, 94403, USA
| | - Aivett Bilbao
- Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Daniel J Orton
- Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Josie G Eder
- Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Meagan C Burnet
- Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | | | - Jennifer E Kyle
- Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Xueyun Zheng
- Pacific Northwest National Laboratory, Richland, WA, 99354, USA.
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26
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Hartmann P, Trufa DI, Hohenberger K, Tausche P, Trump S, Mittler S, Geppert CI, Rieker RJ, Schieweck O, Sirbu H, Hartmann A, Finotto S. Contribution of serum lipids and cholesterol cellular metabolism in lung cancer development and progression. Sci Rep 2023; 13:5662. [PMID: 37024569 PMCID: PMC10079859 DOI: 10.1038/s41598-023-31575-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 03/14/2023] [Indexed: 04/08/2023] Open
Abstract
Neoplasms of the lungs are the leading cause of cancer incidence and mortality worldwide. Although immunotherapy has increased the overall survival of patients with lung cancer, there is the need to improve this treatment. At this regard, blood lipid levels are thought to be linked to cancer risk and thus a preventive intervention through regulation of the nutrition of patients with lung cancer is gaining much attention. In this study, we therefore asked about the contribution of serum lipids and cholesterol cellular metabolism in lung cancer development and progression. We measured different serum lipids and analyzed cholesterol synthesis enzymes 3-hydroxy-3-methyl-glutaryl-CoA reductase (HMGCR) and acetyl-coenzyme A cholesterol acetyltransferase 1 (ACAT1) as well as the cholesterol cellular export protein ATP-binding cassette (ABC) A-1 mRNA by quantitative PCR (qPCR) in the control and tumoral regions of post-surgery lung tissues to analyze the accumulation of cholesterol in cancer cells in a cohort of patients with lung adenocarcinoma (LUAD). We found that triglycerides in serum directly correlated with the body mass index (BMI) in patients with LUAD. By contrast, we found that high-density lipoprotein (HDL) cholesterol inversely correlated with the BMI, C-reactive protein (CRP) and overall survival and total cholesterol inversely correlated with the tumor diameter, serum CRP and overall survival in these LUAD patients. Functionally, the role of cholesterol is indispensable for the growth and development of normal animal cells where it is tightly regulated. Excess of cellular cholesterol regulated by HMGCR is converted to cholesteryl esters by the enzyme ACAT1 and exported extracellularly by the cholesterol transporter ABCA1. Here we found HMGCR and ACAT1 upregulated and ABCA1 downregulated in the lung's tumoral region of our LUAD cohort, indicating cholesterol dysregulated cellular export in lung tumor cells.
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Affiliation(s)
- Philipp Hartmann
- Department of Molecular Pneumology, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Universitätsklinikum Erlangen, 91052, Erlangen, Germany
| | - Denis I Trufa
- Department of Thoracic Surgery, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Universitätsklinikum Erlangen, 91052, Erlangen, Germany
| | - Katja Hohenberger
- Department of Molecular Pneumology, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Universitätsklinikum Erlangen, 91052, Erlangen, Germany
| | - Patrick Tausche
- Department of Molecular Pneumology, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Universitätsklinikum Erlangen, 91052, Erlangen, Germany
| | - Sonja Trump
- Department of Molecular Pneumology, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Universitätsklinikum Erlangen, 91052, Erlangen, Germany
| | - Susanne Mittler
- Department of Molecular Pneumology, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Universitätsklinikum Erlangen, 91052, Erlangen, Germany
| | - Carol I Geppert
- Institute of Pathology, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Universitätsklinikum Erlangen, 91052, Erlangen, Germany
| | - Ralf J Rieker
- Institute of Pathology, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Universitätsklinikum Erlangen, 91052, Erlangen, Germany
| | - Oliver Schieweck
- Laboratory of Clinic Medicine, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Universitätsklinikum Erlangen, 91052, Erlangen, Germany
| | - Horia Sirbu
- Department of Thoracic Surgery, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Universitätsklinikum Erlangen, 91052, Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany
| | - Arndt Hartmann
- Institute of Pathology, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Universitätsklinikum Erlangen, 91052, Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany
| | - Susetta Finotto
- Department of Molecular Pneumology, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Universitätsklinikum Erlangen, 91052, Erlangen, Germany.
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany.
- Laboratories of Cellular and Molecular Lung Immunology, Department of Molecular Pneumology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Hartmannstraße 14, 91052, Erlangen, Germany.
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27
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Qiu S, Cai Y, Yao H, Lin C, Xie Y, Tang S, Zhang A. Small molecule metabolites: discovery of biomarkers and therapeutic targets. Signal Transduct Target Ther 2023; 8:132. [PMID: 36941259 PMCID: PMC10026263 DOI: 10.1038/s41392-023-01399-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/22/2023] Open
Abstract
Metabolic abnormalities lead to the dysfunction of metabolic pathways and metabolite accumulation or deficiency which is well-recognized hallmarks of diseases. Metabolite signatures that have close proximity to subject's phenotypic informative dimension, are useful for predicting diagnosis and prognosis of diseases as well as monitoring treatments. The lack of early biomarkers could lead to poor diagnosis and serious outcomes. Therefore, noninvasive diagnosis and monitoring methods with high specificity and selectivity are desperately needed. Small molecule metabolites-based metabolomics has become a specialized tool for metabolic biomarker and pathway analysis, for revealing possible mechanisms of human various diseases and deciphering therapeutic potentials. It could help identify functional biomarkers related to phenotypic variation and delineate biochemical pathways changes as early indicators of pathological dysfunction and damage prior to disease development. Recently, scientists have established a large number of metabolic profiles to reveal the underlying mechanisms and metabolic networks for therapeutic target exploration in biomedicine. This review summarized the metabolic analysis on the potential value of small-molecule candidate metabolites as biomarkers with clinical events, which may lead to better diagnosis, prognosis, drug screening and treatment. We also discuss challenges that need to be addressed to fuel the next wave of breakthroughs.
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Affiliation(s)
- Shi Qiu
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China
| | - Ying Cai
- Graduate School, Heilongjiang University of Chinese Medicine, Harbin, 150040, China
| | - Hong Yao
- First Affiliated Hospital, Harbin Medical University, Harbin, 150081, China
| | - Chunsheng Lin
- Second Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin, 150001, China
| | - Yiqiang Xie
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China.
| | - Songqi Tang
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China.
| | - Aihua Zhang
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China.
- Graduate School, Heilongjiang University of Chinese Medicine, Harbin, 150040, China.
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28
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Mass Spectrometry Imaging for Single-Cell or Subcellular Lipidomics: A Review of Recent Advancements and Future Development. Molecules 2023; 28:molecules28062712. [PMID: 36985684 PMCID: PMC10057629 DOI: 10.3390/molecules28062712] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/14/2023] [Accepted: 03/14/2023] [Indexed: 03/19/2023] Open
Abstract
Mass Spectrometry Imaging (MSI) has emerged as a powerful imaging technique for the analysis of biological samples, providing valuable insights into the spatial distribution and structural characterization of lipids. The advancements in high-resolution MSI have made it an indispensable tool for single-cell or subcellular lipidomics. By preserving both intracellular and intercellular information, MSI enables a comprehensive analysis of lipidomics in individual cells and organelles. This enables researchers to delve deeper into the diversity of lipids within cells and to understand the role of lipids in shaping cell behavior. In this review, we aim to provide a comprehensive overview of recent advancements and future prospects of MSI for cellular/subcellular lipidomics. By keeping abreast of the cutting-edge studies in this field, we will continue to push the boundaries of the understanding of lipid metabolism and the impact of lipids on cellular behavior.
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29
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Balusu S, Praschberger R, Lauwers E, De Strooper B, Verstreken P. Neurodegeneration cell per cell. Neuron 2023; 111:767-786. [PMID: 36787752 DOI: 10.1016/j.neuron.2023.01.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/12/2022] [Accepted: 01/18/2023] [Indexed: 02/16/2023]
Abstract
The clinical definition of neurodegenerative diseases is based on symptoms that reflect terminal damage of specific brain regions. This is misleading as it tells little about the initial disease processes. Circuitry failures that underlie the clinical symptomatology are themselves preceded by clinically mostly silent, slowly progressing multicellular processes that trigger or are triggered by the accumulation of abnormally folded proteins such as Aβ, Tau, TDP-43, and α-synuclein, among others. Methodological advances in single-cell omics, combined with complex genetics and novel ways to model complex cellular interactions using induced pluripotent stem (iPS) cells, make it possible to analyze the early cellular phase of neurodegenerative disorders. This will revolutionize the way we study those diseases and will translate into novel diagnostics and cell-specific therapeutic targets, stopping these disorders in their early track before they cause difficult-to-reverse damage to the brain.
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Affiliation(s)
- Sriram Balusu
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium; KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
| | - Roman Praschberger
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium; KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
| | - Elsa Lauwers
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium; KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
| | - Bart De Strooper
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium; KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium; UK Dementia Research Institute, London, UK.
| | - Patrik Verstreken
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium; KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium.
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30
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Li Y, Jia K, Pan Y, Han J, Chen J, Wang Y, Ma X, Chen H, Wang S, Xie D, Xiong C, Nie Z. Pocket-Size Wireless Nanoelectrospray Ionization Mass Spectrometry for Metabolic Analysis of Salty Biofluids and Single Cells. Anal Chem 2023; 95:4612-4618. [PMID: 36862115 DOI: 10.1021/acs.analchem.2c04268] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Analysis of volume-limited biological samples such as single cells and biofluids not only benefits clinical purposes but also promotes fundamental research in life sciences. Detection of these samples, however, imposes strict requirements on measurement performance because of the minimal volume and concentrated salts of the samples. Herein, we developed a self-cleaning nanoelectrospray ionization device powered by a pocket-size "MasSpec Pointer" (MSP-nanoESI) for metabolic analysis of salty biological samples with limited volume. The self-cleaning effect induced by Maxwell-Wagner electric stress helps with keeping the borosilicate glass capillary tip free from clogging and thus increasing salt tolerance. This device possesses a high sample economy (about 0.1 μL per test) due to its pulsed high voltage supply, sampling method (dipping the nanoESI tip into analyte solution), and contact-free electrospray ionization (ESI) (the electrode does not touch the analyte solution during ESI). High repeatable results could be acquired by the device with a relative standard deviation (RSD) of 1.02% for voltage output and 12.94% for MS signals of caffeine standard. Single MCF-7 cells were metabolically analyzed directly from phosphate buffered saline, and two types of untreated cerebrospinal fluid from hydrocephalus patients were distinguished with 84% accuracy. MSP-nanoESI gets rid of the bulky apparatus and could be held in hand or put into one's pocket for transportation, and it could operate for more than 4 h without recharge. We believe this device will boost scientific research and clinical usage of volume-limited biological samples with high-concentration salts in a low-cost, convenient, and rapid manner.
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Affiliation(s)
- Yuze Li
- State Key Laboratory of High-efficiency Utilization of Coal and Green Chemical Engineering, College of Chemistry and Chemical Engineering, Ningxia University, Yinchuan 750021, China.,Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Ke Jia
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yixin Pan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Han
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Junyu Chen
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiran Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaobing Ma
- Aerospace Information Research Institute, Chinese Academy of Sciences Beijing 100094, China
| | - Hongwei Chen
- Department of Neurosurgery for Cerebrospinal Fluid Diseases, Aviation General Hospital, Beijing 100012, China
| | - Shengjie Wang
- Department of Neurosurgery for Cerebrospinal Fluid Diseases, Aviation General Hospital, Beijing 100012, China
| | - Dongcheng Xie
- Department of Neurosurgery for Cerebrospinal Fluid Diseases, Aviation General Hospital, Beijing 100012, China
| | - Caiqiao Xiong
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Zongxiu Nie
- State Key Laboratory of High-efficiency Utilization of Coal and Green Chemical Engineering, College of Chemistry and Chemical Engineering, Ningxia University, Yinchuan 750021, China.,Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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31
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Embracing lipidomics at single-cell resolution: Promises and pitfalls. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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32
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Song Y, Song Q, Liu W, Li J, Tu P. High-confidence structural identification of metabolites relying on tandem mass spectrometry through isomeric identification: A tutorial. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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33
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Protocol and Methods Applicable to Retinal Vascular Diseases. Methods Mol Biol 2023; 2625:71-78. [PMID: 36653633 DOI: 10.1007/978-1-0716-2966-6_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Lipidomics is a branch of omics biology that enables the characterization and determination of different lipid classes. Mass spectrometry is a widely used tool to identify and obtain qualitative and quantitative measurements of the range of lipid species in various cell/tissue types. Human retina is highly rich in different classes of lipids that are liable to undergo modification such as oxidation, isomerization, peroxidation, and hydroxylation due to continuous metabolic activity in response to light photons. Alterations in lipid metabolism are associated with retinal diseases such as age-related macular degeneration, diabetic retinopathy, and retinopathy of prematurity. However, a clear understanding on the type of lipids/alterations involved in these diseases is not established yet. The unavailability of suitable biological retinal tissue need for this research has prompted us to explore vitreous humor and tear film for studying lipidomic alterations in different ocular diseases. Subjecting the lipid extract to tandem mass spectrometry further gives qualitative and quantitative lipidome of the diseased tissue. While the mass spectrometry approaches for lipid profiling have been adequately described, the present chapter focusses on a simplified protocol for extracting sufficient lipids/metabolites from vitreous humor and tear samples obtained from patients and their subsequent mass spectrometry analysis.
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34
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Armbruster MR, Mostafa ME, Caldwell RN, Grady SF, Arnatt CK, Edwards JL. Isobaric 6-plex and tosyl dual tagging for the determination of positional isomers and quantitation of monounsaturated fatty acids using rapid UHPLC-MS/MS. Analyst 2023; 148:297-304. [PMID: 36533920 DOI: 10.1039/d2an01699k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Isobaric labelling of fatty acids is complicated by chromatographic co-elution of double bond isomers. This produces contaminated spectra which can mask important biological changes. Here two derivatization strategies are combined to improve throughput and produce MS2 reporters which change mass depending on double bond position. A 6-plex isobaric tag is attached to the acid group, followed by the tosylation of the double bond using chloramine-T. These two derivatizations allowed for the chromatographic resolution of nearly all investigated isomers using a 3.5 minute ultrafast method. Further isomer differentiation is achieved upon fragmentation as reporter masses scale with the double bond location. This occurs by a dual-fragmentation route which reveals the isobaric labelling and fragments along the double bond of each analyte. These unique fragments allowed for accurate quantitation of co-isolated double bond isomers where traditional isobaric tags would experience ratio distortion. Saturated and monounsaturated fatty acids were characterized by this rapid 6-plex method and produced an average signal RSD of 9.3% and R2 of 0.99. The method was then used to characterize fatty acid dysregulation upon inhibition of stearoyl CoA desaturase with CAY10566.
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Affiliation(s)
- Michael R Armbruster
- Department of Chemistry and Biochemistry, Saint Louis University, 3501 Laclede Ave, St. Louis, MO, 63103, USA.
| | - Mahmoud Elhusseiny Mostafa
- Department of Chemistry and Biochemistry, Saint Louis University, 3501 Laclede Ave, St. Louis, MO, 63103, USA.
| | - Rhea N Caldwell
- Department of Chemistry and Biochemistry, Saint Louis University, 3501 Laclede Ave, St. Louis, MO, 63103, USA.
| | - Scott F Grady
- Department of Chemistry and Biochemistry, Saint Louis University, 3501 Laclede Ave, St. Louis, MO, 63103, USA.
| | - Christopher K Arnatt
- Department of Chemistry and Biochemistry, Saint Louis University, 3501 Laclede Ave, St. Louis, MO, 63103, USA.
| | - James L Edwards
- Department of Chemistry and Biochemistry, Saint Louis University, 3501 Laclede Ave, St. Louis, MO, 63103, USA.
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35
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Ren J, Li HW, Chen L, Zhang M, Liu YX, Zhang BW, Xu R, Miao YY, Xu XM, Hua X, Sun XG, Yu RJ, Long YT, Hu SS. Mass Spectrometry Imaging-Based Single-Cell Lipidomics Profiles Metabolic Signatures of Heart Failure. RESEARCH 2023; 6:0019. [PMID: 37040505 PMCID: PMC10076023 DOI: 10.34133/research.0019] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 11/14/2022] [Indexed: 01/13/2023]
Abstract
Heart failure (HF), leading as one of the main causes of mortality, has become a serious public health issue with high prevalence around the world. Single cardiomyocyte (CM) metabolomics promises to revolutionize the understanding of HF pathogenesis since the metabolic remodeling in the human hearts plays a vital role in the disease progression. Unfortunately, current metabolic analysis is often limited by the dynamic features of metabolites and the critical needs for high-quality isolated CMs. Here, high-quality CMs were directly isolated from transgenic HF mice biopsies and further employed in the cellular metabolic analysis. The lipids landscape in individual CMs was profiled with a delayed extraction mode in time-of-flight secondary ion mass spectrometry. Specific metabolic signatures were identified to distinguish HF CMs from the control subjects, presenting as possible single-cell biomarkers. The spatial distributions of these signatures were imaged in single cells, and those were further found to be strongly associated with lipoprotein metabolism, transmembrane transport, and signal transduction. Taken together, we systematically studied the lipid metabolism of single CMs with a mass spectrometry imaging method, which directly benefited the identification of HF-associated signatures and a deeper understanding of HF-related metabolic pathways.
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Affiliation(s)
- Jie Ren
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medicine Science (CAMS) and Perking Union Medical College (PUMC), Beijing, 100037, P. R. China
| | - Hao-Wen Li
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Liang Chen
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medicine Science (CAMS) and Perking Union Medical College (PUMC), Beijing, 100037, P. R. China
| | - Min Zhang
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Yan-Xiang Liu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medicine Science (CAMS) and Perking Union Medical College (PUMC), Beijing, 100037, P. R. China
| | - Bo-Wen Zhang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medicine Science (CAMS) and Perking Union Medical College (PUMC), Beijing, 100037, P. R. China
| | - Rui Xu
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Yan-Yan Miao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Xue-Mei Xu
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Xin Hua
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, P. R. China
| | - Xiao-Gang Sun
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medicine Science (CAMS) and Perking Union Medical College (PUMC), Beijing, 100037, P. R. China
| | - Ru-Jia Yu
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| | - Yi-Tao Long
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| | - Sheng-Shou Hu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medicine Science (CAMS) and Perking Union Medical College (PUMC), Beijing, 100037, P. R. China
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36
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Lim MJ, Yagnik G, Henkel C, Frost SF, Bien T, Rothschild KJ. MALDI HiPLEX-IHC: multiomic and multimodal imaging of targeted intact proteins in tissues. Front Chem 2023; 11:1182404. [PMID: 37201132 PMCID: PMC10187789 DOI: 10.3389/fchem.2023.1182404] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 04/14/2023] [Indexed: 05/20/2023] Open
Abstract
Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) is one of the most widely used methods for imaging the spatial distribution of unlabeled small molecules such as metabolites, lipids and drugs in tissues. Recent progress has enabled many improvements including the ability to achieve single cell spatial resolution, 3D-tissue image reconstruction, and the precise identification of different isomeric and isobaric molecules. However, MALDI-MSI of high molecular weight intact proteins in biospecimens has thus far been difficult to achieve. Conventional methods normally require in situ proteolysis and peptide mass fingerprinting, have low spatial resolution, and typically detect only the most highly abundant proteins in an untargeted manner. In addition, MSI-based multiomic and multimodal workflows are needed which can image both small molecules and intact proteins from the same tissue. Such a capability can provide a more comprehensive understanding of the vast complexity of biological systems at the organ, tissue, and cellular levels of both normal and pathological function. A recently introduced top-down spatial imaging approach known as MALDI HiPLEX-IHC (MALDI-IHC for short) provides a basis for achieving this high-information content imaging of tissues and even individual cells. Based on novel photocleavable mass-tags conjugated to antibody probes, high-plex, multimodal and multiomic MALDI-based workflows have been developed to image both small molecules and intact proteins on the same tissue sample. Dual-labeled antibody probes enable multimodal mass spectrometry and fluorescent imaging of targeted intact proteins. A similar approach using the same photocleavable mass-tags can be applied to lectin and other probes. We detail here several examples of MALDI-IHC workflows designed to enable high-plex, multiomic and multimodal imaging of tissues at a spatial resolution as low as 5 µm. This approach is compared to other existing high-plex methods such as imaging mass cytometry, MIBI-TOF, GeoMx and CODEX. Finally, future applications of MALDI-IHC are discussed.
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Affiliation(s)
- Mark J. Lim
- AmberGen, Inc., Billerica, MA, United States
- *Correspondence: Mark J. Lim, ; Kenneth J. Rothschild,
| | | | | | | | - Tanja Bien
- Bruker Daltonics GmbH & Co. KG, Bremen, Germany
| | - Kenneth J. Rothschild
- AmberGen, Inc., Billerica, MA, United States
- Department of Physics and Photonics Center, Boston University, Boston, MA, United States
- *Correspondence: Mark J. Lim, ; Kenneth J. Rothschild,
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37
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Cheng S, Zhang D, Feng J, Hu Q, Tan A, Xie Z, Chen Q, Huang H, Wei Y, Ouyang Z, Ma X. Metabolic Pathway of Monounsaturated Lipids Revealed by In-Depth Structural Lipidomics by Mass Spectrometry. RESEARCH (WASHINGTON, D.C.) 2023; 6:0087. [PMID: 36951803 PMCID: PMC10026824 DOI: 10.34133/research.0087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 02/13/2023] [Indexed: 02/16/2023]
Abstract
The study of lipid metabolism relies on the characterization of the lipidome, which is quite complex due to the structure variations of the lipid species. New analytical tools have been developed recently for characterizing fine structures of lipids, with C=C location identification as one of the major improvements. In this study, we studied the lipid metabolism reprograming by analyzing glycerol phospholipid compositions in breast cancer cell lines with structural specification extended to the C=C location level. Inhibition of the lipid desaturase, stearoyl-CoA desaturase 1, increased the proportion of n-10 isomers that are produced via an alternative fatty acid desaturase 2 pathway. However, there were different variations of the ratio of n-9/n-7 isomers in C18:1-containing glycerol phospholipids after stearoyl-CoA desaturase 1 inhibition, showing increased tendency in MCF-7 cells, MDA-MB-468 cells, and BT-474 cells, but decreased tendency in MDA-MB-231 cells. No consistent change of the ratio of n-9/n-7 isomers was observed in SK-BR-3 cells. This type of heterogeneity in reprogrammed lipid metabolism can be rationalized by considering both lipid desaturation and fatty acid oxidation, highlighting the critical roles of comprehensive lipid analysis in both fundamental and biomedical applications.
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Affiliation(s)
- Simin Cheng
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument,
Tsinghua University, Beijing 100084, China
| | - Donghui Zhang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument,
Tsinghua University, Beijing 100084, China
| | - Jiaxin Feng
- Department of Chemistry,
Tsinghua University, Beijing 100084, China
| | - Qingyuan Hu
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument,
Tsinghua University, Beijing 100084, China
| | - Aolei Tan
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument,
Tsinghua University, Beijing 100084, China
| | - Zhuoning Xie
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument,
Tsinghua University, Beijing 100084, China
| | - Qinhua Chen
- Key Laboratory of TCM Clinical Pharmacy, Shenzhen Baoan Authentic TCM Therapy Hospital, Shenzhen, Guangdong 518101, China
| | - Huimin Huang
- Sinopharm Dongfeng General Hospital,
Hubei University of Medicine, Experiment center of medicine, Shiyan, Hubei 442008, China
| | - Ying Wei
- Sinopharm Dongfeng General Hospital,
Hubei University of Medicine, Experiment center of medicine, Shiyan, Hubei 442008, China
| | - Zheng Ouyang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument,
Tsinghua University, Beijing 100084, China
- *Address correspondence to: (Z.O.); (X.M.)
| | - Xiaoxiao Ma
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument,
Tsinghua University, Beijing 100084, China
- *Address correspondence to: (Z.O.); (X.M.)
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38
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Recent advances and typical applications in mass spectrometry-based technologies for single-cell metabolite analysis. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116763] [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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39
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Fu Z, Nilsson AK, Hellstrom A, Smith LEH. Retinopathy of prematurity: Metabolic risk factors. eLife 2022; 11:e80550. [PMID: 36420952 PMCID: PMC9691009 DOI: 10.7554/elife.80550] [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: 05/25/2022] [Accepted: 11/16/2022] [Indexed: 11/25/2022] Open
Abstract
At preterm birth, the retina is incompletely vascularized. Retinopathy of prematurity (ROP) is initiated by the postnatal suppression of physiological retinal vascular development that would normally occur in utero. As the neural retina slowly matures, increasing metabolic demand including in the peripheral avascular retina, leads to signals for compensatory but pathological neovascularization. Currently, only late neovascular ROP is treated. ROP could be prevented by promoting normal vascular growth. Early perinatal metabolic dysregulation is a strong but understudied risk factor for ROP and other long-term sequelae of preterm birth. We will discuss the metabolic and oxygen needs of retina, current treatments, and potential interventions to promote normal vessel growth including control of postnatal hyperglycemia, dyslipidemia and hyperoxia-induced retinal metabolic alterations. Early supplementation of missing nutrients and growth factors and control of supplemental oxygen promotes physiological retinal development. We will discuss the current knowledge gap in retinal metabolism after preterm birth.
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Affiliation(s)
- Zhongjie Fu
- Department of Ophthalmology, Boston Children’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Anders K Nilsson
- The Sahlgrenska Centre for Pediatric Ophthalmology Research, Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of GothenburgGothenburgSweden
| | - Ann Hellstrom
- The Sahlgrenska Centre for Pediatric Ophthalmology Research, Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of GothenburgGothenburgSweden
| | - Lois EH Smith
- Department of Ophthalmology, Boston Children’s Hospital, Harvard Medical SchoolBostonUnited States
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40
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Tajik M, Baharfar M, Donald WA. Single-cell mass spectrometry. Trends Biotechnol 2022; 40:1374-1392. [PMID: 35562238 DOI: 10.1016/j.tibtech.2022.04.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/04/2022] [Accepted: 04/09/2022] [Indexed: 01/21/2023]
Abstract
Owing to recent advances in mass spectrometry (MS), tens to hundreds of proteins, lipids, and small molecules can be measured in single cells. The ability to characterize the molecular heterogeneity of individual cells is necessary to define the full assortment of cell subtypes and identify their function. We review single-cell MS including high-throughput, targeted, mass cytometry-based approaches and antibody-free methods for broad profiling of the proteome and metabolome of single cells. The advantages and disadvantages of different methods are discussed, as well as the challenges and opportunities for further improvements in single-cell MS. These methods is being used in biomedicine in several applications including revealing tumor heterogeneity and high-content drug screening.
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Affiliation(s)
- Mohammad Tajik
- School of Chemistry, University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Mahroo Baharfar
- School of Chemical Engineering, University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - William A Donald
- School of Chemistry, University of New South Wales, Sydney, New South Wales, 2052, Australia.
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41
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Chen Y, Xie C, Wang X, Cao G, Ru Y, Song Y, Iyaswamy A, Li M, Wang J, Cai Z. 3-Acetylpyridine On-Tissue Paternò–Büchi Derivatization Enabling High Coverage Lipid C═C Location-Resolved MS Imaging in Biological Tissues. Anal Chem 2022; 94:15367-15376. [DOI: 10.1021/acs.analchem.2c03089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yanyan Chen
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Kowloon999077, Hong Kong SAR, China
| | - Chengyi Xie
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Kowloon999077, Hong Kong SAR, China
| | - Xiaoxiao Wang
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Kowloon999077, Hong Kong SAR, China
| | - Guodong Cao
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Kowloon999077, Hong Kong SAR, China
| | - Yi Ru
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Kowloon999077, Hong Kong SAR, China
| | - Yuanyuan Song
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Kowloon999077, Hong Kong SAR, China
| | - Ashok Iyaswamy
- Mr. & Mrs. Ko Chi-Ming Centre for Parkinson’s Disease Research, School of Chinese Medicine, Hong Kong Baptist University, Kowloon999077, Hong Kong SAR, China
| | - Min Li
- Mr. & Mrs. Ko Chi-Ming Centre for Parkinson’s Disease Research, School of Chinese Medicine, Hong Kong Baptist University, Kowloon999077, Hong Kong SAR, China
| | - Jianing Wang
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Kowloon999077, Hong Kong SAR, China
- Institute for Research and Continuing Education, Hong Kong Baptist University, Kowloon999077, Hong Kong SAR, China
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Kowloon999077, Hong Kong SAR, China
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42
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Ali A, Davidson S, Fraenkel E, Gilmore I, Hankemeier T, Kirwan JA, Lane AN, Lanekoff I, Larion M, McCall LI, Murphy M, Sweedler JV, Zhu C. Single cell metabolism: current and future trends. Metabolomics 2022; 18:77. [PMID: 36181583 PMCID: PMC10063251 DOI: 10.1007/s11306-022-01934-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 09/05/2022] [Indexed: 11/29/2022]
Abstract
Single cell metabolomics is an emerging and rapidly developing field that complements developments in single cell analysis by genomics and proteomics. Major goals include mapping and quantifying the metabolome in sufficient detail to provide useful information about cellular function in highly heterogeneous systems such as tissue, ultimately with spatial resolution at the individual cell level. The chemical diversity and dynamic range of metabolites poses particular challenges for detection, identification and quantification. In this review we discuss both significant technical issues of measurement and interpretation, and progress toward addressing them, with recent examples from diverse biological systems. We provide a framework for further directions aimed at improving workflow and robustness so that such analyses may become commonly applied, especially in combination with metabolic imaging and single cell transcriptomics and proteomics.
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Affiliation(s)
- Ahmed Ali
- Leiden Academic Centre for Drug Research, University of Leiden, Gorlaeus Building Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Shawn Davidson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Ernest Fraenkel
- Department of Biological Engineering and the Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ian Gilmore
- National Physical Laboratory, Teddington, TW11 0LW, Middlesex, UK
| | - Thomas Hankemeier
- Leiden Academic Centre for Drug Research, University of Leiden, Room number GW4.07, Gorlaeus Building, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Jennifer A Kirwan
- Berlin Institute of Health, Metabolomics Platform, Translational Research Unit of the Charite-Universitätsmedizin Berlin, Anna-Louisa-Karsch-Str 2, 10178, Berlin, Germany
| | - Andrew N Lane
- Department of Toxicology and Cancer Biology, and Center for Environmental and Systems Biochemistry, University of Kentucky, 789 S. Limestone St, Lexington, KY, 40536, USA.
| | - Ingela Lanekoff
- Department of Chemistry-BMC, Uppsala University, Husargatan 3 (576), 751 23, Uppsala, Sweden
| | - Mioara Larion
- Center for Cancer Research, National Cancer Institute, Building 37, Room 1136A, Bethesda, MD, 20892, USA
| | - Laura-Isobel McCall
- Department of Chemistry & Biochemistry, Department of Microbiology and Plant Biology, Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, 101 Stephenson Parkway, room 3750, Norman, OK, 73019-5251, USA
| | - Michael Murphy
- Departments of Biological Engineering, Department of Electrical Engineering, and Computer Science and the Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, USA
| | - Jonathan V Sweedler
- Department of Chemistry, and the Beckman Institute, University of Illinois Urbana-Champaign, 505 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Caigang Zhu
- Department of Biomedical Engineering, University of Kentucky, Lexington, KY, 40536, USA
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43
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Abstract
The immune system is highly complex and distributed throughout an organism, with hundreds to thousands of cell states existing in parallel with diverse molecular pathways interacting in a highly dynamic and coordinated fashion. Although the characterization of individual genes and molecules is of the utmost importance for understanding immune-system function, high-throughput, high-resolution omics technologies combined with sophisticated computational modeling and machine-learning approaches are creating opportunities to complement standard immunological methods with new insights into immune-system dynamics. Like systems immunology itself, immunology researchers must take advantage of these technologies and form their own diverse networks, connecting with researchers from other disciplines. This Review is an introduction and 'how-to guide' for immunologists with no particular experience in the field of omics but with the intention to learn about and apply these systems-level approaches, and for immunologists who want to make the most of interdisciplinary networks.
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44
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Cerrato A, Capriotti AL, Cavaliere C, Montone CM, Piovesana S, Laganà A. Novel Aza-Paternò-Büchi Reaction Allows Pinpointing Carbon-Carbon Double Bonds in Unsaturated Lipids by Higher Collisional Dissociation. Anal Chem 2022; 94:13117-13125. [PMID: 36121000 PMCID: PMC9523615 DOI: 10.1021/acs.analchem.2c02549] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The evaluation of double bond positions in fatty acyl
chains has
always been of great concern given their significance in the chemical
and biochemical role of lipids. Despite being the foremost technique
for lipidomics, it is difficult in practice to obtain identification
beyond the fatty acyl level by the sole high-resolution mass spectrometry.
Paternò–Büchi reactions of fatty acids (FAs)
with ketones have been successfully proposed for pinpointing double
bonds in FAs in combination with the collision-induced fragmentation
technique. In the present paper, an aza-Paternò–Büchi
(aPB) reaction of lipids with 6-azauracil (6-AU) was proposed for
the first time for the determination of carbon–carbon double
bonds in fatty acyl chains using higher collisional dissociation in
the negative ion mode. The method was optimized using free FA and
phospholipid analytical standards and compared to the standard Paternò–Büchi
reaction with acetone. The introduction of the 6-AU moiety allowed
enhancing the ionization efficiency of the FA precursor and diagnostic
product ions, thanks to the presence of ionizable sites on the derivatizing
agent. Moreover, the aPB derivatization allowed the obtention of deprotonated
ions of phosphatidylcholines, thanks to an intramolecular methyl transfer
from the phosphocholine polar heads during ionization. The workflow
was finally applied for pinpointing carbon–carbon double bonds
in 77 polar lipids from an yeast (Saccharomyces cerevisiae) extract.
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Affiliation(s)
- Andrea Cerrato
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Anna Laura Capriotti
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Chiara Cavaliere
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Carmela Maria Montone
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Susy Piovesana
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Aldo Laganà
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy
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45
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Jeong MH, Han H, Lagares D, Im H. Recent Advances in Molecular Diagnosis of Pulmonary Fibrosis for Precision Medicine. ACS Pharmacol Transl Sci 2022; 5:520-538. [DOI: 10.1021/acsptsci.2c00028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Indexed: 12/12/2022]
Affiliation(s)
- Mi Ho Jeong
- Center for Systems Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Hongwei Han
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - David Lagares
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Hyungsoon Im
- Center for Systems Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
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46
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Bien T, Koerfer K, Schwenzfeier J, Dreisewerd K, Soltwisch J. Mass spectrometry imaging to explore molecular heterogeneity in cell culture. Proc Natl Acad Sci U S A 2022; 119:e2114365119. [PMID: 35858333 PMCID: PMC9303856 DOI: 10.1073/pnas.2114365119] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 05/13/2022] [Indexed: 01/13/2023] Open
Abstract
Molecular analysis on the single-cell level represents a rapidly growing field in the life sciences. While bulk analysis from a pool of cells provides a general molecular profile, it is blind to heterogeneities between individual cells. This heterogeneity, however, is an inherent property of every cell population. Its analysis is fundamental to understanding the development, function, and role of specific cells of the same genotype that display different phenotypical properties. Single-cell mass spectrometry (MS) aims to provide broad molecular information for a significantly large number of cells to help decipher cellular heterogeneity using statistical analysis. Here, we present a sensitive approach to single-cell MS based on high-resolution MALDI-2-MS imaging in combination with MALDI-compatible staining and use of optical microscopy. Our approach allowed analyzing large amounts of unperturbed cells directly from the growth chamber. Confident coregistration of both modalities enabled a reliable compilation of single-cell mass spectra and a straightforward inclusion of optical as well as mass spectrometric features in the interpretation of data. The resulting multimodal datasets permit the use of various statistical methods like machine learning-driven classification and multivariate analysis based on molecular profile and establish a direct connection of MS data with microscopy information of individual cells. Displaying data in the form of histograms for individual signal intensities helps to investigate heterogeneous expression of specific lipids within the cell culture and to identify subpopulations intuitively. Ultimately, t-MALDI-2-MSI measurements at 2-µm pixel sizes deliver a glimpse of intracellular lipid distributions and reveal molecular profiles for subcellular domains.
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Affiliation(s)
- Tanja Bien
- Institute of Hygiene, University of Münster, 48149 Münster, Germany
- Interdisciplinary Center for Clinical Research (IZKF), University of Münster, 48149 Münster, Germany
| | - Krischan Koerfer
- Institute for Psychology, University of Münster, 48149 Münster, Germany
- Otto Creutzfeldt Center for Cognitive and Behavioural Neuroscience, University of Münster, 48149 Münster, Germany
| | - Jan Schwenzfeier
- Institute of Hygiene, University of Münster, 48149 Münster, Germany
| | - Klaus Dreisewerd
- Institute of Hygiene, University of Münster, 48149 Münster, Germany
- Interdisciplinary Center for Clinical Research (IZKF), University of Münster, 48149 Münster, Germany
| | - Jens Soltwisch
- Institute of Hygiene, University of Münster, 48149 Münster, Germany
- Interdisciplinary Center for Clinical Research (IZKF), University of Münster, 48149 Münster, Germany
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47
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Mao R, Li W, Jia P, Ding H, Teka T, Zhang L, Fu Z, Fu X, Kaushal S, Dou Z, Han L. An efficient and sensitive method on the identification of unsaturated fatty acids in biosamples: Total lipid extract from bovine liver as a case study. J Chromatogr A 2022; 1675:463176. [DOI: 10.1016/j.chroma.2022.463176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 05/15/2022] [Accepted: 05/24/2022] [Indexed: 12/14/2022]
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48
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Advances in Plant Metabolomics and Its Applications in Stress and Single-Cell Biology. Int J Mol Sci 2022; 23:ijms23136985. [PMID: 35805979 PMCID: PMC9266571 DOI: 10.3390/ijms23136985] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/19/2022] [Accepted: 06/19/2022] [Indexed: 02/04/2023] Open
Abstract
In the past two decades, the post-genomic era envisaged high-throughput technologies, resulting in more species with available genome sequences. In-depth multi-omics approaches have evolved to integrate cellular processes at various levels into a systems biology knowledge base. Metabolomics plays a crucial role in molecular networking to bridge the gaps between genotypes and phenotypes. However, the greater complexity of metabolites with diverse chemical and physical properties has limited the advances in plant metabolomics. For several years, applications of liquid/gas chromatography (LC/GC)-mass spectrometry (MS) and nuclear magnetic resonance (NMR) have been constantly developed. Recently, ion mobility spectrometry (IMS)-MS has shown utility in resolving isomeric and isobaric metabolites. Both MS and NMR combined metabolomics significantly increased the identification and quantification of metabolites in an untargeted and targeted manner. Thus, hyphenated metabolomics tools will narrow the gap between the number of metabolite features and the identified metabolites. Metabolites change in response to environmental conditions, including biotic and abiotic stress factors. The spatial distribution of metabolites across different organs, tissues, cells and cellular compartments is a trending research area in metabolomics. Herein, we review recent technological advancements in metabolomics and their applications in understanding plant stress biology and different levels of spatial organization. In addition, we discuss the opportunities and challenges in multiple stress interactions, multi-omics, and single-cell metabolomics.
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49
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Xie T, Zhang Q, Zhang W, Feng S, Lin JM. Inkjet-Patterned Microdroplets as Individual Microenvironments for Adherent Single Cell Culture. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2107992. [PMID: 35362237 DOI: 10.1002/smll.202107992] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/26/2022] [Indexed: 06/14/2023]
Abstract
Adhesion of single cells is the foundation of manifold cellular behaviors and life processes. However, investigating the function of a specific cell is still challenging due to deficiency of adhesion or interference from surrounding cells. Herein, an open microfluidic system is reported for culturing adherent single cells, implemented by a micrometer-scale droplet matrix on an inkjet-printed polylysine template. The target cells are isolated from any cell from other droplets, and their adhesion strength is determined to be comparable to conventional petri dishes via an in-situ investigation with a microfluidic extractor. On this proposed platform, isolated single cells are observed to display an entirely distinct spreading behavior featuring total absence of elongation, indicating drastic cell behavior change from their "singleness." This system has high versatility and compatibility for various assaying methods, assuring a promising potential in detailed single cell behavior and cell heterogeneity studies.
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Affiliation(s)
- Tianze Xie
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, P. R. China
| | - Qiang Zhang
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, P. R. China
| | - Weifei Zhang
- Division of Chemical Metrology and Analytical Science, National Institute of Metrology, N 3rd Ring Road E 18, Beijing, 100029, P. R. China
| | - Shuo Feng
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, P. R. China
| | - Jin-Ming Lin
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, P. R. China
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50
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Zhang W, Jian R, Zhao J, Liu Y, Xia Y. Deep-lipidotyping by mass spectrometry: recent technical advances and applications. J Lipid Res 2022; 63:100219. [PMID: 35489417 PMCID: PMC9213770 DOI: 10.1016/j.jlr.2022.100219] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 12/18/2022] Open
Abstract
In-depth structural characterization of lipids is an essential component of lipidomics. There has been a rapid expansion of mass spectrometry methods that are capable of resolving lipid isomers at various structural levels over the past decade. These developments finally make deep-lipidotyping possible, which provides new means to study lipid metabolism and discover new lipid biomarkers. In this review, we discuss recent advancements in tandem mass spectrometry (MS/MS) methods for identification of complex lipids beyond the species (known headgroup information) and molecular species (known chain composition) levels. These include identification at the levels of carbon-carbon double bond (C=C) location and sn-position as well as characterization of acyl chain modifications. We also discuss the integration of isomer-resolving MS/MS methods with different lipid analysis workflows and their applications in lipidomics. The results showcase the distinct capabilities of deep-lipidotyping in untangling the metabolism of individual isomers and sensitive phenotyping by using relative fractional quantitation of the isomers.
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Affiliation(s)
- Wenpeng Zhang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instruments, Tsinghua University, Beijing 100084, P. R. China
| | - Ruijun Jian
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biological, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Jing Zhao
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biological, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Yikun Liu
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instruments, Tsinghua University, Beijing 100084, P. R. China
| | - Yu Xia
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biological, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China.
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