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Liu C, Otsuka K, Kawai T. Recent advances in microscale separation techniques for glycome analysis. J Sep Sci 2024; 47:e2400170. [PMID: 38863084 DOI: 10.1002/jssc.202400170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/12/2024] [Accepted: 05/24/2024] [Indexed: 06/13/2024]
Abstract
The glycomic analysis holds significant appeal due to the diverse roles that glycans and glycoconjugates play, acting as modulators and mediators in cellular interactions, cell/organism structure, drugs, energy sources, glyconanomaterials, and more. The glycomic analysis relies on liquid-phase separation technologies for molecular purification, separation, and identification. As a miniaturized form of liquid-phase separation technology, microscale separation technologies offer various advantages such as environmental friendliness, high resolution, sensitivity, fast speed, and integration capabilities. For glycan analysis, microscale separation technologies are continuously evolving to address the increasing challenges in their unique manners. This review discusses the fundamentals and applications of microscale separation technologies for glycomic analysis. It covers liquid-phase separation technologies operating at scales generally less than 100 µm, including capillary electrophoresis, nanoflow liquid chromatography, and microchip electrophoresis. We will provide a brief overview of glycomic analysis and describe new strategies in microscale separation and their applications in glycan analysis from 2014 to 2023.
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Affiliation(s)
- Chenchen Liu
- Department of Chemistry, Faculty of Science, Kyushu University, Fukuoka, Japan
| | - Koji Otsuka
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
- Research Administration Center, Osaka Metropolitan University, Osaka, Japan
| | - Takayuki Kawai
- Department of Chemistry, Faculty of Science, Kyushu University, Fukuoka, Japan
- RIKEN Center for Biosystems Dynamics Research, Osaka, Japan
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2
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Xie Q, Liu S, Zhang S, Liao L, Xiao Z, Wang S, Zhang P. Research progress on the multi-omics and survival status of circulating tumor cells. Clin Exp Med 2024; 24:49. [PMID: 38427120 PMCID: PMC10907490 DOI: 10.1007/s10238-024-01309-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/08/2024] [Indexed: 03/02/2024]
Abstract
In the dynamic process of metastasis, circulating tumor cells (CTCs) emanate from the primary solid tumor and subsequently acquire the capacity to disengage from the basement membrane, facilitating their infiltration into the vascular system via the interstitial tissue. Given the pivotal role of CTCs in the intricate hematogenous metastasis, they have emerged as an essential resource for a deeper comprehension of cancer metastasis while also serving as a cornerstone for the development of new indicators for early cancer screening and new therapeutic targets. In the epoch of precision medicine, as CTC enrichment and separation technologies continually advance and reach full fruition, the domain of CTC research has transcended the mere straightforward detection and quantification. The rapid advancement of CTC analysis platforms has presented a compelling opportunity for in-depth exploration of CTCs within the bloodstream. Here, we provide an overview of the current status and research significance of multi-omics studies on CTCs, including genomics, transcriptomics, proteomics, and metabolomics. These studies have contributed to uncovering the unique heterogeneity of CTCs and identifying potential metastatic targets as well as specific recognition sites. We also review the impact of various states of CTCs in the bloodstream on their metastatic potential, such as clustered CTCs, interactions with other blood components, and the phenotypic states of CTCs after undergoing epithelial-mesenchymal transition (EMT). Within this context, we also discuss the therapeutic implications and potential of CTCs.
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Affiliation(s)
- Qingming Xie
- NHC Key Laboratory of Cancer Proteomics, Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Shilei Liu
- NHC Key Laboratory of Cancer Proteomics, Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Sai Zhang
- NHC Key Laboratory of Cancer Proteomics, Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Liqiu Liao
- Department of Breast Surgery, Hunan Clinical Meditech Research Center for Breast Cancer, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Zhi Xiao
- Department of Breast Surgery, Hunan Clinical Meditech Research Center for Breast Cancer, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Shouman Wang
- Department of Breast Surgery, Hunan Clinical Meditech Research Center for Breast Cancer, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.
| | - Pengfei Zhang
- NHC Key Laboratory of Cancer Proteomics, Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.
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3
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Slusher GA, Kottke PA, Culberson AL, Chilmonczyk MA, Fedorov AG. Microfluidics enabled multi-omics triple-shot mass spectrometry for cell-based therapies. BIOMICROFLUIDICS 2024; 18:011302. [PMID: 38268742 PMCID: PMC10807926 DOI: 10.1063/5.0175178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 01/01/2024] [Indexed: 01/26/2024]
Abstract
In recent years, cell-based therapies have transformed medical treatment. These therapies present a multitude of challenges associated with identifying the mechanism of action, developing accurate safety and potency assays, and achieving low-cost product manufacturing at scale. The complexity of the problem can be attributed to the intricate composition of the therapeutic products: living cells with complex biochemical compositions. Identifying and measuring critical quality attributes (CQAs) that impact therapy success is crucial for both the therapy development and its manufacturing. Unfortunately, current analytical methods and tools for identifying and measuring CQAs are limited in both scope and speed. This Perspective explores the potential for microfluidic-enabled mass spectrometry (MS) systems to comprehensively characterize CQAs for cell-based therapies, focusing on secretome, intracellular metabolome, and surfaceome biomarkers. Powerful microfluidic sampling and processing platforms have been recently presented for the secretome and intracellular metabolome, which could be implemented with MS for fast, locally sampled screening of the cell culture. However, surfaceome analysis remains limited by the lack of rapid isolation and enrichment methods. Developing innovative microfluidic approaches for surface marker analysis and integrating them with secretome and metabolome measurements using a common analytical platform hold the promise of enhancing our understanding of CQAs across all "omes," potentially revolutionizing cell-based therapy development and manufacturing for improved efficacy and patient accessibility.
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Affiliation(s)
| | - Peter A. Kottke
- The George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30318, USA
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4
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Pade LR, Stepler KE, Portero EP, DeLaney K, Nemes P. Biological mass spectrometry enables spatiotemporal 'omics: From tissues to cells to organelles. MASS SPECTROMETRY REVIEWS 2024; 43:106-138. [PMID: 36647247 PMCID: PMC10668589 DOI: 10.1002/mas.21824] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/14/2022] [Accepted: 09/17/2022] [Indexed: 06/17/2023]
Abstract
Biological processes unfold across broad spatial and temporal dimensions, and measurement of the underlying molecular world is essential to their understanding. Interdisciplinary efforts advanced mass spectrometry (MS) into a tour de force for assessing virtually all levels of the molecular architecture, some in exquisite detection sensitivity and scalability in space-time. In this review, we offer vignettes of milestones in technology innovations that ushered sample collection and processing, chemical separation, ionization, and 'omics analyses to progressively finer resolutions in the realms of tissue biopsies and limited cell populations, single cells, and subcellular organelles. Also highlighted are methodologies that empowered the acquisition and analysis of multidimensional MS data sets to reveal proteomes, peptidomes, and metabolomes in ever-deepening coverage in these limited and dynamic specimens. In pursuit of richer knowledge of biological processes, we discuss efforts pioneering the integration of orthogonal approaches from molecular and functional studies, both within and beyond MS. With established and emerging community-wide efforts ensuring scientific rigor and reproducibility, spatiotemporal MS emerged as an exciting and powerful resource to study biological systems in space-time.
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Affiliation(s)
- Leena R. Pade
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Kaitlyn E. Stepler
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Erika P. Portero
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Kellen DeLaney
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Peter Nemes
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
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5
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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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6
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Minegishi M, Kuchimaru T, Nishikawa K, Isagawa T, Iwano S, Iida K, Hara H, Miura S, Sato M, Watanabe S, Shiomi A, Mabuchi Y, Hamana H, Kishi H, Sato T, Sawaki D, Sato S, Hanazono Y, Suzuki A, Kohro T, Kadonosono T, Shimogori T, Miyawaki A, Takeda N, Shintaku H, Kizaka-Kondoh S, Nishimura S. Secretory GFP reconstitution labeling of neighboring cells interrogates cell-cell interactions in metastatic niches. Nat Commun 2023; 14:8031. [PMID: 38052804 DOI: 10.1038/s41467-023-43855-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/17/2023] [Indexed: 12/07/2023] Open
Abstract
Cancer cells inevitably interact with neighboring host tissue-resident cells during the process of metastatic colonization, establishing a metastatic niche to fuel their survival, growth, and invasion. However, the underlying mechanisms in the metastatic niche are yet to be fully elucidated owing to the lack of methodologies for comprehensively studying the mechanisms of cell-cell interactions in the niche. Here, we improve a split green fluorescent protein (GFP)-based genetically encoded system to develop secretory glycosylphosphatidylinositol-anchored reconstitution-activated proteins to highlight intercellular connections (sGRAPHIC) for efficient fluorescent labeling of tissue-resident cells that neighbor on and putatively interact with cancer cells in deep tissues. The sGRAPHIC system enables the isolation of metastatic niche-associated tissue-resident cells for their characterization using a single-cell RNA sequencing platform. We use this sGRAPHIC-leveraged transcriptomic platform to uncover gene expression patterns in metastatic niche-associated hepatocytes in a murine model of liver metastasis. Among the marker genes of metastatic niche-associated hepatocytes, we identify Lgals3, encoding galectin-3, as a potential pro-metastatic factor that accelerates metastatic growth and invasion.
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Affiliation(s)
- Misa Minegishi
- School of Life Science and Technology, Tokyo Institute of Technology, Kanagawa, Japan
- RIKEN Cluster for Pioneering Research, Saitama, Japan
| | - Takahiro Kuchimaru
- RIKEN Cluster for Pioneering Research, Saitama, Japan.
- Graduate School of Medicine, Jichi Medical University, Tochigi, Japan.
- Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan.
- Data Science Center, Jichi Medical University, Tochigi, Japan.
| | | | - Takayuki Isagawa
- Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
- Data Science Center, Jichi Medical University, Tochigi, Japan
| | - Satoshi Iwano
- RIKEN Center for Brain Science, Saitama, Japan
- Institute for Tenure Track Promotion, University of Miyazaki, Miyazaki, Japan
| | - Kei Iida
- Faculty of Science and Engineering, Kindai University, Osaka, Japan
| | - Hiromasa Hara
- Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
| | - Shizuka Miura
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Marika Sato
- MediGear International Corporation, Kanagawa, Japan
| | | | | | - Yo Mabuchi
- Graduate School of Medicine, Juntendo University, Tokyo, Japan
- School of Medicine, Fujita Health University, Aichi, Japan
| | - Hiroshi Hamana
- Department of Immunology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan
| | - Hiroyuki Kishi
- Department of Immunology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan
| | - Tatsuyuki Sato
- Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
| | - Daigo Sawaki
- Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
- Clinical Pharmacology, Jichi Medical University, Tochigi, Japan
| | - Shigeru Sato
- Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
| | - Yutaka Hanazono
- Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
| | - Atsushi Suzuki
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Takahide Kohro
- Data Science Center, Jichi Medical University, Tochigi, Japan
| | - Tetsuya Kadonosono
- School of Life Science and Technology, Tokyo Institute of Technology, Kanagawa, Japan
| | | | | | - Norihiko Takeda
- Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
| | | | - Shinae Kizaka-Kondoh
- School of Life Science and Technology, Tokyo Institute of Technology, Kanagawa, Japan
| | - Satoshi Nishimura
- Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
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7
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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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Kitagishi K, Kawai T, Tonouchi M, Serita K. An innovative detection technique for capillary electrophoresis: Localized terahertz emission-time domain spectroscopy. J Chromatogr A 2023; 1710:464384. [PMID: 37801940 DOI: 10.1016/j.chroma.2023.464384] [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: 07/03/2023] [Revised: 09/12/2023] [Accepted: 09/13/2023] [Indexed: 10/08/2023]
Abstract
Terahertz (THz) time-domain spectroscopy (TDS) is a recently emerging analysis method which can provide unique information on molecular vibration and rotation induced by inter/intra-molecular interactions. Although the application of THz-TDS to high-performance microscale separation methods like capillary electrophoresis (CE) has been anticipated, it has been hindered due to the diffraction limit of THz wave (typically, hundreds µm). In order to realize CE-THz-TDS, in this study, we placed a narrow open-tubular capillary on the surface of a GaAs semiconductor substrate as a "localized" THz-emitter. By focusing femtosecond pulsed laser beams at the surface of a gallium arsenide (GaAs) substrate closest to the capillary, THz waves were locally generated to pass through the capillary, so that THz absorbance spectra were obtained from the capillary which has narrower inner diameter than the diffraction limit. As a typical result from acetic acid analysis in the CE-THz-TDS platform, information on the refractive index and extinction coefficient was obtained, which showed non-linear and linear concentration dependence, respectively, similar to conventional THz-TDS using large liquid cells. Finally, CE-THz-TDS analysis of several carboxylic acids was demonstrated. Two acids were successfully separated and detected with THz-TDS, where their electrophoretic mobility values were estimated as close to those obtained with conventional contactless conductivity detection. Our proposed CE-THz-TDS showed the potential for the systematic analysis of inter/intra-molecular weak interactions like hydrogen bonds, which are unable to obtain with conventional detectors.
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Affiliation(s)
- Keiko Kitagishi
- Terahertz Photonics (THP) Group, Photon Beam Science Research Division, Institute of Laser Engineering, Osaka University, Suita, Osaka 565-0971, Japan.
| | - Takayuki Kawai
- Department of Chemistry, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan; RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-0874, Japan
| | - Masayoshi Tonouchi
- Terahertz Photonics (THP) Group, Photon Beam Science Research Division, Institute of Laser Engineering, Osaka University, Suita, Osaka 565-0971, Japan
| | - Kazunori Serita
- Terahertz Photonics (THP) Group, Photon Beam Science Research Division, Institute of Laser Engineering, Osaka University, Suita, Osaka 565-0971, Japan
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9
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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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10
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Li J, Huang L, Guo Y, Cupp-Sutton KA, Wu S. An automated spray-capillary platform for the microsampling and CE-MS analysis of picoliter- and nanoliter-volume samples. Anal Bioanal Chem 2023; 415:6961-6973. [PMID: 37581707 PMCID: PMC10843549 DOI: 10.1007/s00216-023-04870-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 07/01/2023] [Accepted: 07/04/2023] [Indexed: 08/16/2023]
Abstract
Capillary electrophoresis mass spectrometry (CE-MS) is an emerging analytical tool for microscale biological sample analysis that offers high separation resolution, low detection limit, and low sample consumption. We recently developed a novel microsampling device, "spray-capillary," for quantitative low-volume sample extraction (as low as 15 pL/s) and online CE-MS analysis. This platform can efficiently analyze picoliter samples (e.g., single cells) with minimal sample loss and no additional offline sample-handling steps. However, our original spray-capillary-based experiments required manual manipulation of the sample inlet for sample collection and separation, which is time consuming and requires proficiency in device handling. To optimize the performance of spray-capillary CE-MS analysis, we developed an automated platform for robust, high-throughput analysis of picoliter samples using a commercially available CE autosampler. Our results demonstrated high reproducibility among 50 continuous runs using the standard peptide angiotensin II (Ang II), with an RSD of 14.70% and 0.62% with respect to intensity and elution time, respectively. We also analyzed Ang II using varying injection times to evaluate the capability of the spray-capillary to perform quantitative sampling and found high linearity for peptide intensity with respect to injection time (R2 > 0.99). These results demonstrate the capability of the spray-capillary sampling platform for high-throughput quantitative analysis of low-volume, low-complexity samples using pressure elution (e.g., direct injection). To further evaluate and optimize the automated spray-capillary platform to analyze complex biological samples, we performed online CE-MS analysis on Escherichia coli lysate digest spiked with Ang II using varying injection times. We maintained high linearity of intensity with respect to injection time for Ang II and E. coli peptides (R2 > 0.97 in all cases). Furthermore, we observed good CE separation and high reproducibility between automated runs. Overall, we demonstrated that the automated spray-capillary CE-MS platform can efficiently and reproducibly sample picoliter and nanoliter biological samples for high-throughput proteomics analysis.
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Affiliation(s)
- Jiaxue Li
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Room 2210, Norman, OK, 73019, USA
| | - Lushuang Huang
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Room 2210, Norman, OK, 73019, USA
| | - Yanting Guo
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Room 2210, Norman, OK, 73019, USA
| | - Kellye A Cupp-Sutton
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Room 2210, Norman, OK, 73019, USA.
| | - Si Wu
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Room 2210, Norman, OK, 73019, USA.
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11
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Kelliher JM, Robinson AJ, Longley R, Johnson LYD, Hanson BT, Morales DP, Cailleau G, Junier P, Bonito G, Chain PSG. The endohyphal microbiome: current progress and challenges for scaling down integrative multi-omic microbiome research. MICROBIOME 2023; 11:192. [PMID: 37626434 PMCID: PMC10463477 DOI: 10.1186/s40168-023-01634-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 07/29/2023] [Indexed: 08/27/2023]
Abstract
As microbiome research has progressed, it has become clear that most, if not all, eukaryotic organisms are hosts to microbiomes composed of prokaryotes, other eukaryotes, and viruses. Fungi have only recently been considered holobionts with their own microbiomes, as filamentous fungi have been found to harbor bacteria (including cyanobacteria), mycoviruses, other fungi, and whole algal cells within their hyphae. Constituents of this complex endohyphal microbiome have been interrogated using multi-omic approaches. However, a lack of tools, techniques, and standardization for integrative multi-omics for small-scale microbiomes (e.g., intracellular microbiomes) has limited progress towards investigating and understanding the total diversity of the endohyphal microbiome and its functional impacts on fungal hosts. Understanding microbiome impacts on fungal hosts will advance explorations of how "microbiomes within microbiomes" affect broader microbial community dynamics and ecological functions. Progress to date as well as ongoing challenges of performing integrative multi-omics on the endohyphal microbiome is discussed herein. Addressing the challenges associated with the sample extraction, sample preparation, multi-omic data generation, and multi-omic data analysis and integration will help advance current knowledge of the endohyphal microbiome and provide a road map for shrinking microbiome investigations to smaller scales. Video Abstract.
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Affiliation(s)
| | | | - Reid Longley
- Los Alamos National Laboratory, Los Alamos, NM, USA
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12
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Bagwe K, Gould N, Johnson KR, Ivanov AR. Single-cell omic molecular profiling using capillary electrophoresis-mass spectrometry. Trends Analyt Chem 2023; 165:117117. [PMID: 37388554 PMCID: PMC10306258 DOI: 10.1016/j.trac.2023.117117] [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: 07/01/2023]
Abstract
Tissues and other cell populations are highly heterogeneous at the cellular level, owing to differences in expression and modifications of proteins, polynucleotides, metabolites, and lipids. The ability to assess this heterogeneity is crucial in understanding numerous biological phenomena, including various pathologies. Traditional analyses apply bulk-cell sampling, which masks the potentially subtle differences between cells that can be important in understanding of biological processes. These limitations due to cell heterogeneity inspired significant efforts and interest toward the analysis of smaller sample sizes, down to the level of individual cells. Among the emerging techniques, the unique capabilities of capillary electrophoresis coupled with mass spectrometry (CE-MS) made it a prominent technique for proteomics and metabolomics analysis at the single-cell level. In this review, we focus on the application of CE-MS in the proteomic and metabolomic profiling of single cells and highlight the recent advances in sample preparation, separation, MS acquisition, and data analysis.
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Affiliation(s)
- Ketki Bagwe
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, MA, 02115, United States
| | - Noah Gould
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, MA, 02115, United States
| | - Kendall R. Johnson
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, MA, 02115, United States
| | - Alexander R. Ivanov
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, MA, 02115, United States
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13
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Koganemaru S, Kawai T, Fuchigami H, Maeda N, Koyama K, Kuboki Y, Mukohara T, Doi T, Yasunaga M. Quantitative analysis of drug distribution in heterogeneous tissues using dual-stacking capillary electrophoresis-mass spectrometry. Br J Pharmacol 2023; 180:762-774. [PMID: 36377519 DOI: 10.1111/bph.15988] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 10/17/2022] [Accepted: 10/28/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND AND PURPOSE Intratumour heterogeneity frequently leads to drug resistance, which is a major issue in drug discovery. Drug distribution is one of the key factors for elucidating the resistance mechanism; however, quantitative and regional drug measurement is challenging. Here, we developed a novel ultra-sensitive analytical method and applied it to HER3-targeting antibody-drug conjugate patritumab deruxtecan (HER3-DXd), aiming to explore its payload (DXd) distribution within heterogeneous tissues. EXPERIMENTAL APPROACH The developed analytical method is named LDMS-CE-MS, a capillary electrophoresis-mass spectrometry (CE-MS) coupled with a novel sample preconcentration/separation method called "large-volume dual-sample stacking by micelle collapse and sweeping (LDMS)". First, the analytical performance of LDMS-CE-MS for DXd detection was evaluated. Subsequently, we evaluated the bystander effect of HER3-DXd, where tumour tissues were excised from xenograft models and clinical specimens after administration of HER3-DXd. HER3-high expression, adjacent, and HER3-low expression regions were then sampled by laser microdissection to quantify the released DXd. KEY RESULTS LDMS concentrated DXd by 1000-fold and separated it from the hydrophilic bio-matrix through continuous capture and release by the charged micelles, allowing quantification at sub-attomole-level. DXd concentrations decreased in the order of antigen-high expression > adjacent > antigen-low expression regions in the tumour xenograft model, whereas in clinical specimens, adjacent and antigen-high expression regions had approximately the same concentration. These distributions represent a bystander effect. CONCLUSIONS AND IMPLICATIONS Our LDMS-CE-MS successfully visualized the attomole-level drug distributions in heterogeneous clinical specimens. This new platform opens a new era of quantitative pharmacokinetic analysis, facilitating drug discovery and development.
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Affiliation(s)
- Shigehiro Koganemaru
- Department of Experimental Therapeutics, National Cancer Center Hospital East, Kashiwa, Japan
| | - Takayuki Kawai
- Department of Chemistry, Faculty of Science, Kyushu University, Fukuoka, Japan.,RIKEN Center for Biosystems Dynamics Research, Suita, Japan
| | - Hirobumi Fuchigami
- Division of Developmental Therapeutics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Japan
| | - Naoyuki Maeda
- Translational Science Department I, Daiichi Sankyo Co., Ltd., Tokyo, Japan
| | - Kumiko Koyama
- Translational Science Department I, Daiichi Sankyo Co., Ltd., Tokyo, Japan
| | - Yasutoshi Kuboki
- Department of Experimental Therapeutics, National Cancer Center Hospital East, Kashiwa, Japan
| | - Toru Mukohara
- Department of Medical Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Toshihiko Doi
- Department of Experimental Therapeutics, National Cancer Center Hospital East, Kashiwa, Japan
| | - Masahiro Yasunaga
- Division of Developmental Therapeutics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Japan
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14
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Hancock SE, Ding E, Johansson Beves E, Mitchell T, Turner N. FACS-assisted single-cell lipidome analysis of phosphatidylcholines and sphingomyelins in cells of different lineages. J Lipid Res 2023; 64:100341. [PMID: 36740022 PMCID: PMC10027561 DOI: 10.1016/j.jlr.2023.100341] [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: 09/26/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 02/05/2023] Open
Abstract
Recent advances in single-cell genomics and transcriptomics technologies have transformed our understanding of cellular heterogeneity in growth, development, ageing, and disease; however, methods for single-cell lipidomics have comparatively lagged behind in development. We have developed a method for the detection and quantification of a wide range of phosphatidylcholine and sphingomyelin species from single cells that combines fluorescence-assisted cell sorting with automated chip-based nanoESI and shotgun lipidomics. We show herein that our method is capable of quantifying more than 50 different phosphatidylcholine and sphingomyelin species from single cells and can easily distinguish between cells of different lineages or cells treated with exogenous fatty acids. Moreover, our method can detect more subtle differences in the lipidome between cell lines of the same cancer type. Our approach can be run in parallel with other single-cell technologies to deliver near-complete, high-throughput multi-omics data on cells with a similar phenotype and has the capacity to significantly advance our current knowledge on cellular heterogeneity.
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Affiliation(s)
- Sarah E Hancock
- Department of Pharmacology, School of Biomedical Sciences, UNSW Sydney, Australia; Cellular Bioenergetics Laboratory, Victor Chang Cardiac Research Institute, Sydney, NSW, Australia.
| | - Eileen Ding
- Department of Pharmacology, School of Biomedical Sciences, UNSW Sydney, Australia
| | | | - Todd Mitchell
- School of Medicine, University of Wollongong, Wollongong Australia; Molecular Horizons, University of Wollongong, Wollongong Australia
| | - Nigel Turner
- Department of Pharmacology, School of Biomedical Sciences, UNSW Sydney, Australia; Cellular Bioenergetics Laboratory, Victor Chang Cardiac Research Institute, Sydney, NSW, Australia.
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15
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Recent applications and chiral separation developments based on stationary phases in open tubular capillary electrochromatography (2019–2022). J Pharm Anal 2023; 13:323-339. [PMID: 37181297 PMCID: PMC10173184 DOI: 10.1016/j.jpha.2023.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 01/16/2023] [Accepted: 01/31/2023] [Indexed: 02/08/2023] Open
Abstract
Capillary electrochromatography (CEC) plays a significant role in chiral separation via the double separation principle, partition coefficient difference between the two phases, and electroosmotic flow-driven separation. Given the distinct properties of the inner wall stationary phase (SP), the separation ability of each SP differs from one another. Particularly, it provides large room for promising applications of open tubular capillary electrochromatography (OT-CEC). We divided the OT-CEC SPs developed over the past four years into six types: ionic liquids, nanoparticle materials, microporous materials, biomaterials, non-nanopolymers, and others, to mainly introduce their characteristics in chiral drug separation. There also added a few classic SPs that occurred within ten years as supplements to enrich the features of each SP. Additionally, we discuss their applications in metabolomics, food, cosmetics, environment, and biology as analytes in addition to chiral drugs. OT-CEC plays an increasingly significant role in chiral separation and may promote the development of capillary electrophoresis (CE) combined with other instruments in recent years, such as CE with mass spectrometry (CE/MS) and CE with ultraviolet light detector (CE/UV).
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16
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Advances in capillary electrophoresis mass spectrometry for metabolomics. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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17
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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: 31] [Impact Index Per Article: 15.5] [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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18
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KITAGAWA F, SOMA Y. Recent Applications of Dynamic On-Line Sample Preconcentration Techniques in Capillary Electrophoresis. CHROMATOGRAPHY 2022. [DOI: 10.15583/jpchrom.2022.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Fumihiko KITAGAWA
- Department of Frontier Materials Chemistry, Graduate School of Science and Technology, Hirosaki University
| | - Yuta SOMA
- Department of Frontier Materials Chemistry, Graduate School of Science and Technology, Hirosaki University
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19
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Recent progress in analytical capillary isotachophoresis (2018 - March 2022). J Chromatogr A 2022; 1677:463337. [PMID: 35868155 DOI: 10.1016/j.chroma.2022.463337] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/11/2022] [Accepted: 07/11/2022] [Indexed: 12/12/2022]
Abstract
This review brings a survey of papers on analytical capillary and microchip isotachophoresis published since 2018 until the first quarter of 2022. Theoretical papers extending fundamental knowledge include those on computer simulations that remain an important research tool useful in the design of electrolyte systems. Many papers are focused on instrumental aspects where new media including microfluidic devices and their hyphenation to various detection techniques bring remarkable results. Papers reporting analytical applications demonstrate the potential of contemporary analytical isotachophoresis. Although it is not being used on a mass scale, its special features are attracting continued interest resulting in applications of isotachophoresis both as a stand-alone analytical method and as a part of multidimensional separation techniques.
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20
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Portero EP, Pade L, Li J, Choi SB, Nemes P. Single-Cell Mass Spectrometry of Metabolites and Proteins for Systems and Functional Biology. NEUROMETHODS 2022; 184:87-114. [PMID: 36699808 PMCID: PMC9872963 DOI: 10.1007/978-1-0716-2525-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Molecular composition is intricately intertwined with cellular function, and elucidation of this relationship is essential for understanding life processes and developing next-generational therapeutics. Technological innovations in capillary electrophoresis (CE) and liquid chromatography (LC) mass spectrometry (MS) provide previously unavailable insights into cellular biochemistry by allowing for the unbiased detection and quantification of molecules with high specificity. This chapter presents our validated protocols integrating ultrasensitive MS with classical tools of cell, developmental, and neurobiology to assess the biological function of important biomolecules. We use CE and LC MS to measure hundreds of metabolites and thousands of proteins in single cells or limited populations of tissues in chordate embryos and mammalian neurons, revealing molecular heterogeneity between identified cells. By pairing microinjection and optical microscopy, we demonstrate cell lineage tracing and testing the roles the dysregulated molecules play in the formation and maintenance of cell heterogeneity and tissue specification in frog embryos (Xenopus laevis). Electrophysiology extends our workflows to characterizing neuronal activity in sections of mammalian brain tissues. The information obtained from these studies mutually strengthen chemistry and biology and highlight the importance of interdisciplinary research to advance basic knowledge and translational applications forward.
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Affiliation(s)
| | | | - Jie Li
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Sam B. Choi
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Peter Nemes
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
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21
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Elshamy YS, Strein TG, Holland LA, Li C, DeBastiani A, Valentine SJ, Li P, Lucas JA, Shaffer TA. Nanoflow Sheath Voltage-Free Interfacing of Capillary Electrophoresis and Mass Spectrometry for the Detection of Small Molecules. Anal Chem 2022; 94:11329-11336. [PMID: 35913997 PMCID: PMC9387528 DOI: 10.1021/acs.analchem.2c02074] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Coupling capillary electrophoresis (CE) to mass spectrometry (MS) is a powerful strategy to leverage a high separation efficiency with structural identification. Traditional CE-MS interfacing relies upon voltage to drive this process. Additionally, sheathless interfacing requires that the electrophoresis generates a sufficient volumetric flow to sustain the ionization process. Vibrating sharp-edge spray ionization (VSSI) is a new method to interface capillary electrophoresis to mass analyzers. In contrast to traditional interfacing, VSSI is voltage-free, making it straightforward for CE and MS. New nanoflow sheath CE-VSSI-MS is introduced in this work to reduce the reliance on the separation flow rate to facilitate the transfer of analyte to the MS. The nanoflow sheath VSSI spray ionization functions from 400 to 900 nL/min. Using the new nanoflow sheath reported here, volumetric flow rate through the separation capillary is less critical, allowing the use of a small (i.e., 20 to 25 μm) inner diameter separation capillary and enabling the use of higher separation voltages and faster analysis. Moreover, the use of a nanoflow sheath enables greater flexibility in the separation conditions. The nanoflow sheath is operated using aqueous solutions in the background electrolyte and in the sheath, demonstrating the separation can be performed under normal and reversed polarity in the presence or absence of electroosmotic flow. This includes the use of a wider pH range as well. The versatility of nanoflow sheath CE-VSSI-MS is demonstrated by separating cationic, anionic, and zwitterionic molecules under a variety of separation conditions. The detection sensitivity observed with nanoflow sheath CE-VSSI-MS is comparable to that obtained with sheathless CE-VSSI-MS as well as CE-MS separations with electrospray ionization interfacing. A bare fused silica capillary is used to separate cationic β-blockers with a near-neutral background electrolyte at concentrations ranging from 1.0 nM to 1.0 μM. Under acidic conditions, 13 amino acids are separated with normal polarity at a concentration ranging from 0.25 to 5 μM. Finally, separations of anionic compounds are demonstrated using reversed polarity under conditions of suppressed electroosmotic flow through the use of a semipermanent surface coating. With a near-neutral separation electrolyte, anionic nonsteroidal anti-inflammatory drugs are detected over a concentration range of 0.1 to 5.0 μM.
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Affiliation(s)
- Yousef S Elshamy
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26505, United States
| | - Timothy G Strein
- Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| | - Lisa A Holland
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26505, United States
| | - Chong Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26505, United States
| | - Anthony DeBastiani
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26505, United States
| | - Stephen J Valentine
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26505, United States
| | - Peng Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26505, United States
| | - John A Lucas
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26505, United States
| | - Tyler A Shaffer
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26505, United States
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22
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Zuo F, Yu J, He X. Single-Cell Metabolomics in Hematopoiesis and Hematological Malignancies. Front Oncol 2022; 12:931393. [PMID: 35912231 PMCID: PMC9326066 DOI: 10.3389/fonc.2022.931393] [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: 04/28/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
Aberrant metabolism contributes to tumor initiation, progression, metastasis, and drug resistance. Metabolic dysregulation has emerged as a hallmark of several hematologic malignancies. Decoding the molecular mechanism underlying metabolic rewiring in hematological malignancies would provide promising avenues for novel therapeutic interventions. Single-cell metabolic analysis can directly offer a meaningful readout of the cellular phenotype, allowing us to comprehensively dissect cellular states and access biological information unobtainable from bulk analysis. In this review, we first highlight the unique metabolic properties of hematologic malignancies and underscore potential metabolic vulnerabilities. We then emphasize the emerging single-cell metabolomics techniques, aiming to provide a guide to interrogating metabolism at single-cell resolution. Furthermore, we summarize recent studies demonstrating the power of single-cell metabolomics to uncover the roles of metabolic rewiring in tumor biology, cellular heterogeneity, immunometabolism, and therapeutic resistance. Meanwhile, we describe a practical view of the potential applications of single-cell metabolomics in hematopoiesis and hematological malignancies. Finally, we present the challenges and perspectives of single-cell metabolomics development.
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23
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Murphy SE, Sweedler JV. Metabolomics-based mass spectrometry methods to analyze the chemical content of 3D organoid models. Analyst 2022; 147:2918-2929. [PMID: 35660810 PMCID: PMC9533735 DOI: 10.1039/d2an00599a] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
Metabolomics, the study of metabolites present in biological samples, can provide a global view of sample state as well as insights into biological changes caused by disease or environmental interactions. Mass spectrometry (MS) is commonly used for metabolomics analysis given its high-throughput capabilities, high sensitivity, and capacity to identify multiple compounds in complex samples simultaneously. MS can be coupled to separation methods that can handle small volumes, making it well suited for analyzing the metabolome of organoids, miniaturized three-dimensional aggregates of stem cells that model in vivo organs. Organoids are being used in research efforts to study human disease and development, and in the design of personalized drug treatments. For organoid models to be useful, they need to recapitulate morphological and chemical aspects, such as the metabolome, of the parent tissue. This review highlights the separation- and imaging-based MS-based metabolomics methods that have been used to analyze the chemical contents of organoids. Future perspectives on how MS techniques can be optimized to determine the accuracy of organoid models and expand the field of organoid research are also discussed.
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Affiliation(s)
- Shannon E Murphy
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois, 61801, USA.
| | - Jonathan V Sweedler
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois, 61801, USA.
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24
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Lanekoff I, Sharma VV, Marques C. Single-cell metabolomics: where are we and where are we going? Curr Opin Biotechnol 2022; 75:102693. [DOI: 10.1016/j.copbio.2022.102693] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/12/2022] [Accepted: 01/20/2022] [Indexed: 12/11/2022]
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25
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Ramautar R. Capillary electrophoresis mass spectrometry for metabolomics: reflecting on the next steps. Bioanalysis 2022; 14:393-396. [PMID: 35311379 DOI: 10.4155/bio-2022-0031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- Rawi Ramautar
- Biomedical Microscale Analytics, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, Leiden, 2333 CC, The Netherlands
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26
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Wei D, Xu M, Wang Z, Tong J. The Development of Single-Cell Metabolism and Its Role in Studying Cancer Emergent Properties. Front Oncol 2022; 11:814085. [PMID: 35083160 PMCID: PMC8784738 DOI: 10.3389/fonc.2021.814085] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 12/16/2021] [Indexed: 12/13/2022] Open
Abstract
Metabolic reprogramming is one of the hallmarks of malignant tumors, which provides energy and material basis for tumor rapid proliferation, immune escape, as well as extensive invasion and metastasis. Blocking the energy and material supply of tumor cells is one of the strategies to treat tumor, however tumor cell metabolic heterogeneity prevents metabolic-based anti-cancer treatment. Therefore, searching for the key metabolic factors that regulate cell cancerous change and tumor recurrence has become a major challenge. Emerging technology––single-cell metabolomics is different from the traditional metabolomics that obtains average information of a group of cells. Single-cell metabolomics identifies the metabolites of single cells in different states by mass spectrometry, and captures the molecular biological information of the energy and substances synthesized in single cells, which provides more detailed information for tumor treatment metabolic target screening. This review will combine the current research status of tumor cell metabolism with the advantages of single-cell metabolomics technology, and explore the role of single-cell sequencing technology in searching key factors regulating tumor metabolism. The addition of single-cell technology will accelerate the development of metabolism-based anti-cancer strategies, which may greatly improve the prognostic survival rate of cancer patients.
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Affiliation(s)
- Dingju Wei
- School of Life Science, Central China Normal University, Wuhan, China
| | - Meng Xu
- School of Life Science, Central China Normal University, Wuhan, China
| | - Zhihua Wang
- Shenzhen Key Laboratory of Cardiovascular Disease, Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen, China.,State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jingjing Tong
- School of Life Science, Central China Normal University, Wuhan, China
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27
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Ye D, Li X, Shen J, Xia X. Microbial metabolomics: From novel technologies to diversified applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116540] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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28
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Kawai T, Matsumori N, Otsuka K. Recent advances in microscale separation techniques for lipidome analysis. Analyst 2021; 146:7418-7430. [PMID: 34787600 DOI: 10.1039/d1an00967b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This review paper highlights the recent research on liquid-phase microscale separation techniques for lipidome analysis over the last 10 years, mainly focusing on capillary liquid chromatography (LC) and capillary electrophoresis (CE) coupled with mass spectrometry (MS). Lipids are one of the most important classes of biomolecules which are involved in the cell membrane, energy storage, signal transduction, and so on. Since lipids include a variety of hydrophobic compounds including numerous structural isomers, lipidomes are a challenging target in bioanalytical chemistry. MS is the key technology that comprehensively identifies lipids; however, separation techniques like LC and CE are necessary prior to MS detection in order to avoid ionization suppression and resolve structural isomers. Separation techniques using μm-scale columns, such as a fused silica capillary and microfluidic device, are effective at realizing high-resolution separation. Microscale separation usually employs a nL-scale flow, which is also compatible with nanoelectrospray ionization-MS that achieves high sensitivity. Owing to such analytical advantages, microscale separation techniques like capillary/microchip LC and CE have been employed for more than 100 lipidome studies. Such techniques are still being evolved and achieving further higher resolution and wider coverage of lipidomes. Therefore, microscale separation techniques are promising as the fundamental technology in next-generation lipidome analysis.
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Affiliation(s)
- Takayuki Kawai
- Department of Chemistry, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Nobuaki Matsumori
- Department of Chemistry, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
| | - Koji Otsuka
- Department of Material Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
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29
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He B, Zhang W, Guled F, Harms A, Ramautar R, Hankemeier T. Analytical techniques for biomass-restricted metabolomics: An overview of the state-of-the-art. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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30
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Culberson AL, Chilmonczyk MA, Kottke PA, Bowles-Welch AC, Ghoshal D, Fedorov AG. Sample-to-analysis platform for rapid intracellular mass spectrometry from small numbers of cells. LAB ON A CHIP 2021; 21:4696-4706. [PMID: 34751694 PMCID: PMC8721559 DOI: 10.1039/d1lc00884f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Real-time, advanced diagnostics of the biochemical state within cells remains a significant challenge for research and development, production, and application of cell-based therapies. The fundamental biochemical processes and mechanisms of action of such advanced therapies are still largely unknown, including the critical quality attributes that correlate to therapeutic function, performance, and potency and the critical process parameters that impact quality throughout cell therapy manufacturing. An integrated microfluidic platform has been developed for in-line analysis of a small number of cells via direct infusion nano-electrospray ionization mass spectrometry. Central to this platform is a microfabricated cell processing device that prepares cells from limited sample volumes removed directly from cell culture systems. The sample-to-analysis workflow overcomes the labor intensive, time-consuming, and destructive nature of existing mass spectrometry approaches for analysis of cells. By providing rapid, high-throughput analyses of the intracellular state, this platform enables untargeted discovery of critical quality attributes and their real-time, in-process monitoring.
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Affiliation(s)
- Austin L Culberson
- The George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, USA.
| | - Mason A Chilmonczyk
- The George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, USA.
| | - Peter A Kottke
- The George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, USA.
| | - Annie C Bowles-Welch
- Marcus Center for Therapeutic Cell Characterization and Manufacturing, Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
| | - Delta Ghoshal
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Andrei G Fedorov
- The George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, USA.
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31
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Hong T, Liu X, Zhou Q, Liu Y, Guo J, Zhou W, Tan S, Cai Z. What the Microscale Systems "See" In Biological Assemblies: Cells and Viruses? Anal Chem 2021; 94:59-74. [PMID: 34812604 DOI: 10.1021/acs.analchem.1c04244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Tingting Hong
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu 213164, China
| | - Xing Liu
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu 213164, China
| | - Qi Zhou
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu 213164, China
| | - Yilian Liu
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu 213164, China
| | - Jing Guo
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu 213164, China
| | - Wenhu Zhou
- Xiangya School of Pharmaceutical Sciences, Central South University, 172 Tongzipo Road, Changsha, Hunan 410013, China
| | - Songwen Tan
- Xiangya School of Pharmaceutical Sciences, Central South University, 172 Tongzipo Road, Changsha, Hunan 410013, China.,Jiangsu Dawning Pharmaceutical Co., Ltd., Changzhou, Jiangsu 213100, China
| | - Zhiqiang Cai
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu 213164, China.,Jiangsu Dawning Pharmaceutical Co., Ltd., Changzhou, Jiangsu 213100, China
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32
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Zhu G, Shao Y, Liu Y, Pei T, Li L, Zhang D, Guo G, Wang X. Single-cell metabolite analysis by electrospray ionization mass spectrometry. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116351] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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33
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Xu S, Yang C, Yan X, Liu H. Towards high throughput and high information coverage: advanced single-cell mass spectrometric techniques. Anal Bioanal Chem 2021; 414:219-233. [PMID: 34435209 DOI: 10.1007/s00216-021-03624-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/13/2021] [Accepted: 08/17/2021] [Indexed: 12/23/2022]
Abstract
Mass spectrometry (MS) is attractive for single-cell analysis because of its high sensitivity, rich information, and large dynamic ranges, especially for the single-cell metabolome and proteome analysis. Efforts have been made to deal with the throughput and information coverage problems in typical manual single-cell MS techniques. In this review, advanced techniques to improve the automation and throughput for single-cell sampling and single-cell metabolome and proteome MS detection have been discussed. Furthermore, representative MS-based strategies that can increase the in-depth cellular information coverage and achieve the more comprehensive single-cell multiomics information during high throughput detection have been highlighted, providing an ongoing perspective of the MS performance for the single-cell research.
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Affiliation(s)
- Shuting Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China.,Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Cheng Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China.,Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Xiuping Yan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China. .,Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
| | - Huwei Liu
- Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
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34
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The limitless applications of single-cell metabolomics. Curr Opin Biotechnol 2021; 71:115-122. [PMID: 34339935 DOI: 10.1016/j.copbio.2021.07.015] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 07/08/2021] [Accepted: 07/11/2021] [Indexed: 12/28/2022]
Abstract
Single-cell metabolomics (SCM) is currently one of the most powerful tools for performing high-throughput metabolic analysis at the cellular level. The power of single-cell metabolomics to determine the metabolic profiles of individual cells makes it very suitable for decoding cell heterogeneity. SCM bears great potential in cell type identification and differentiation within cell colonies. With the development of various equipment and techniques, SCM analysis has become possible for a wide range of biological samples. Many fields have incorporated this cutting-edge analytic tool to generate fruitful findings. This review article pays close attention to the prevalent techniques utilized in SCM and the exciting new findings and applications developed by studies in phytology, neurology, and oncology using SCM.
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35
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Heidari Baladehi M, Hekmatara M, He Y, Bhaskar Y, Wang Z, Liu L, Ji Y, Xu J. Culture-Free Identification and Metabolic Profiling of Microalgal Single Cells via Ensemble Learning of Ramanomes. Anal Chem 2021; 93:8872-8880. [PMID: 34142549 DOI: 10.1021/acs.analchem.1c01015] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Microalgae are among the most genetically and metabolically diverse organisms on earth, yet their identification and metabolic profiling have generally been slow and tedious. Here, we established a reference ramanome database consisting of single-cell Raman spectra (SCRS) from >9000 cells of 27 phylogenetically diverse microalgal species, each under stationary and exponential states. When combined, prequenching ("pigment spectrum" (PS)) and postquenching ("whole spectrum" (WS)) signals can classify species and states with 97% accuracy via ensemble machine learning. Moreover, the biosynthetic profile of Raman-sensitive metabolites was unveiled at single cells, and their interconversion was detected via intra-ramanome correlation analysis. Furthermore, not-yet-cultured cells from the environment were functionally characterized via PS and WS and then phylogenetically identified by Raman-activated sorting and sequencing. This PS-WS combined approach for rapidly identifying and metabolically profiling single cells, either cultured or uncultured, greatly accelerates the mining of microalgae and their products.
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Affiliation(s)
- Mohammadhadi Heidari Baladehi
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101 Shandong, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266101 Shandong, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Maryam Hekmatara
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101 Shandong, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266101 Shandong, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuehui He
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101 Shandong, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266101 Shandong, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yogendra Bhaskar
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101 Shandong, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266101 Shandong, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zengbin Wang
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101 Shandong, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266101 Shandong, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lu Liu
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101 Shandong, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266101 Shandong, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuetong Ji
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101 Shandong, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266101 Shandong, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101 Shandong, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266101 Shandong, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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36
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Rosàs-Canyelles E, Modzelewski AJ, Gomez Martinez AE, Geldert A, Gopal A, He L, Herr AE. Multimodal detection of protein isoforms and nucleic acids from low starting cell numbers. LAB ON A CHIP 2021; 21:2427-2436. [PMID: 33978041 PMCID: PMC8206029 DOI: 10.1039/d1lc00073j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Protein isoforms play a key role in disease progression and arise from mechanisms involving multiple molecular subtypes, including DNA, mRNA and protein. Recently introduced multimodal assays successfully link genomes and transcriptomes to protein expression landscapes. However, the specificity of the protein measurement relies on antibodies alone, leading to major challenges when measuring different isoforms of the same protein. Here we utilize microfluidic design to perform same-cell profiling of DNA, mRNA and protein isoforms (triBlot) on low starting cell numbers (1-100 s of cells). After fractionation lysis, cytoplasmic proteins are resolved by molecular mass during polyacrylamide gel electrophoresis (PAGE), adding a degree of specificity to the protein measurement, while nuclei are excised from the device in sections termed "gel pallets" for subsequent off-chip nucleic acid analysis. By assaying TurboGFP-transduced glioblastoma cells, we observe a strong correlation between protein expression prior to lysis and immunoprobed protein. We measure both mRNA and DNA from retrieved nuclei, and find that mRNA levels correlate with protein abundance in TurboGFP-expressing cells. Furthermore, we detect the presence of TurboGFP isoforms differing by an estimated <1 kDa in molecular mass, demonstrating the ability to discern different proteoforms with the same antibody probe. By directly relating nucleic acid modifications to protein isoform expression in 1-100 s of cells, the triBlot assay holds potential as a screening tool for novel biomarkers in diseases driven by protein isoform expression.
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Affiliation(s)
- Elisabet Rosàs-Canyelles
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA. and The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, Berkeley, CA 94720, USA
| | - Andrew J Modzelewski
- Division of Cellular and Developmental Biology, Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ana E Gomez Martinez
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA. and The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, Berkeley, CA 94720, USA
| | - Alisha Geldert
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA. and The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, Berkeley, CA 94720, USA
| | - Anjali Gopal
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA. and The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, Berkeley, CA 94720, USA
| | - Lin He
- Division of Cellular and Developmental Biology, Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Amy E Herr
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA. and The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, Berkeley, CA 94720, USA and Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158, USA
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37
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Liu FL, Ye TT, Ding JH, Yin XM, Yang XK, Huang WH, Yuan BF, Feng YQ. Chemical Tagging Assisted Mass Spectrometry Analysis Enables Sensitive Determination of Phosphorylated Compounds in a Single Cell. Anal Chem 2021; 93:6848-6856. [PMID: 33882236 DOI: 10.1021/acs.analchem.1c00915] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Polar phosphorylated metabolites are involved in a variety of biological processes and play vital roles in energetic metabolism, cofactor regeneration, and nucleic acid synthesis. However, it is often challenging to interrogate polar phosphorylated metabolites and compounds from biological samples. Liquid chromatography-mass spectrometry (LC/MS) now plays a central role in metabolomic studies. However, LC/MS-based approaches have been hampered by the issues of the low ionization efficiencies, low in vivo concentrations, and less chemical stability of polar phosphorylated metabolites. In this work, we synthesized paired reagents of light and heavy isotopomers, 2-(diazomethyl)phenyl)(9-methyl-1,3,4,9-tetrahydro-2H-pyrido[3,4-b]indol-2-yl)methanone (DMPI) and d3-(2-(diazomethyl)phenyl)(9-methyl-1,3,4,9-tetrahydro-2H-pyrido[3,4-b]indol-2-yl)methanone (d3-DMPI). The paired reagents of DMPI and d3-DMPI carry diazo groups that can efficiently and selectively react with the phosphate group on polar phosphorylated metabolites under mild conditions. As a proof of concept, we found that the transfer of the indole heterocycle group from DMPI/d3-DMPI to ribonucleotides led to the significant increase of ionization efficiencies of ribonucleotides during LC/MS analysis. The detection sensitivities of these ribonucleotides increased by 25-1137-fold upon DMPI tagging with the limits of detection (LODs) being between 7 and 150 amol. With the developed method, we achieved the determination of all the 12 ribonucleotides from a single mammalian cell and from a single stamen of Arabidopsis thaliana. The method provides a valuable tool to investigate the dynamic changes of polar phosphorylated metabolites in a single cell under particular conditions.
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Affiliation(s)
- Fei-Long Liu
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Tian-Tian Ye
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Jiang-Hui Ding
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Xiao-Ming Yin
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Xiao-Ke Yang
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Wei-Hua Huang
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Bi-Feng Yuan
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China.,School of Health Sciences, Wuhan University, Wuhan 430071, China
| | - Yu-Qi Feng
- Sauvage Center for Molecular Sciences, Department of Chemistry, Wuhan University, Wuhan 430072, China.,School of Health Sciences, Wuhan University, Wuhan 430071, China
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38
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Mast DH, Liao HW, Romanova EV, Sweedler JV. Analysis of Peptide Stereochemistry in Single Cells by Capillary Electrophoresis-Trapped Ion Mobility Spectrometry Mass Spectrometry. Anal Chem 2021; 93:6205-6213. [PMID: 33825437 DOI: 10.1021/acs.analchem.1c00445] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Single cell analysis strives to probe molecular heterogeneity in morphologically similar cell populations through quantitative or qualitative measurements of genetic, proteomic, or metabolic products. Here, we applied mass analysis of single neurons to investigate cell-cell signaling peptides. The multiplicity of endogenous cell-cell signaling peptides is a common source of chemical diversity among cell populations. Certain peptides can undergo post-translational isomerization of select residues, which has important physiological consequences. The limited number of single cell analysis techniques that are sensitive to peptide stereochemistry make it challenging to study isomerization at the individual cell level. We performed capillary electrophoresis (CE) with mass spectrometry (MS) detection to characterize the peptide content of single cells. Using complementary trapped ion mobility spectrometry (TIMS) separations, we measured the stereochemical configurations of three neuropeptide gene products derived from the pleurin precursor in individual neurons (N = 3) isolated from the central nervous system of Aplysia californica. An analysis of the resultant mobility profiles indicated >98% of the detectable pleurin-derived peptides exist as the nonisomerized, all-l forms in individual neuron cell bodies. However, we observed 44% of the Plrn2 peptide from the pleurin precursor was present as the isomerized, d-residue-containing form in the nerve tissue. These findings demonstrate an unusual distribution of isomerized peptides in A. californica and establish CE-TIMS MS as a powerful analytical tool for investigating peptide stereochemistry at the single cell level.
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Affiliation(s)
- David H Mast
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,The Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Hsiao-Wei Liao
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Faculty of Pharmacy, National Yang-Ming University, No.155, Sec.2, Linong Street, Taipei 11221, Taiwan
| | - Elena V Romanova
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,The Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jonathan V Sweedler
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,The Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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39
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Huang L, Fang M, Cupp-Sutton KA, Wang Z, Smith K, Wu S. Spray-Capillary-Based Capillary Electrophoresis Mass Spectrometry for Metabolite Analysis in Single Cells. Anal Chem 2021; 93:4479-4487. [PMID: 33646748 PMCID: PMC8323477 DOI: 10.1021/acs.analchem.0c04624] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Single-cell capillary electrophoresis mass spectrometry (CE-MS) is a promising platform to analyze cellular contents and probe cell heterogeneity. However, current single-cell CE-MS methods often rely on offline microsampling processes and may demonstrate low sampling precision and accuracy. We have recently developed an electrospray-assisted device, spray-capillary, for low-volume sample extraction. With the spray-capillary, low-volume samples (pL-nL) are drawn into the sampling end of the device, which can be used directly for CE separation and online MS detection. Here, we redesigned the spray-capillary by utilizing a capillary with a <15 μm tapered tip so that it can be directly inserted into single cells for sample collection and on-capillary CE-MS analysis. We evaluated the performance of the modified spray-capillary by performing single-cell microsampling on single onion cells with varying sample injection times and direct MS analysis or online CE-MS analysis. We have demonstrated, for the first time, online sample collection and CE-MS for the analysis of single cells. This application of the modified spray-capillary device facilitates the characterization and relative quantification of hundreds of metabolites in single cells.
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Affiliation(s)
- Lushuang Huang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Mulin Fang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Kellye A Cupp-Sutton
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Zhe Wang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Kenneth Smith
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma 73104, United States
| | - Si Wu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
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40
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Kawai T, Mihara Y, Morita M, Ohkubo M, Asami T, Watanabe TM. Quantitation of Cell Membrane Permeability of Cyclic Peptides by Single-Cell Cytoplasm Mass Spectrometry. Anal Chem 2021; 93:3370-3377. [PMID: 33550808 DOI: 10.1021/acs.analchem.0c03901] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Cyclic peptides (CPs) have attracted attention as next-generation drugs because they possess both cell-permeable potential as small molecules and specific affinity similar to antibodies. As intracellular molecules are important targets of CPs, quantitation of the intracellular retention and transmembrane permeability of CPs is necessary for drug development. However, permeated CPs within cells cannot be directly assessed by conventional permeability assays using methods such as artificial membranes and cell monolayers. Here, we propose a new approach using single-cell cytoplasm mass spectrometry (SCC-MS). After cells were incubated with CPs, the cytoplasm was directly collected from a single cell using a microneedle followed by nanoelectrospray ionization mass spectrometry detection of the CPs. The height of the CP peak was plotted against time and fitted with a simple function, y = a(1 - e-bx), to calculate the apparent permeability coefficient (Papp) for both the influx and efflux directions. MCF-7 cells were selected as model cancer cells and cultured with cyclosporin A (CsA) and its demethylated analogs (dmCsA-1, -2, and -3) as model CPs. Papp values (10-6 cm/s) obtained from cells incubated with 50 μM CPs ranged from 0.017 to 0.121 for influx and 0.20 to 1.48 for efflux. The higher efflux ratio was possibly caused by efflux transporters such as P-glycoprotein, a well-known receptor of CsA. The equilibrated intracellular concentration of CPs was estimated to be as low as 4.1-6.8 μM, which showed good consistency with the high efflux ratio. SCC-MS is promising as a reliable permeability assay for next-generation CP-based pharmaceuticals.
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Affiliation(s)
- Takayuki Kawai
- RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-0874, Japan.,Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yasuhiro Mihara
- Research Headquarters, Taisho Pharmaceutical Co., LTD., Saitama-shi, Saitama 331-9530, Japan
| | - Makiko Morita
- RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-0874, Japan
| | - Masahiko Ohkubo
- Research Headquarters, Taisho Pharmaceutical Co., LTD., Saitama-shi, Saitama 331-9530, Japan
| | - Taiji Asami
- Research Headquarters, Taisho Pharmaceutical Co., LTD., Saitama-shi, Saitama 331-9530, Japan
| | - Tomonobu M Watanabe
- RIKEN Center for Biosystems Dynamics Research, Suita, Osaka 565-0874, Japan.,Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima City, Hiroshima 734-8553, Japan
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41
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Zhang W, Ramautar R. CE-MS for metabolomics: Developments and applications in the period 2018-2020. Electrophoresis 2021; 42:381-401. [PMID: 32906195 PMCID: PMC7891659 DOI: 10.1002/elps.202000203] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/30/2020] [Accepted: 09/01/2020] [Indexed: 02/06/2023]
Abstract
Capillary electrophoresis-mass spectrometry (CE-MS) is now a mature analytical technique in metabolomics, notably for the efficient profiling of polar and charged metabolites. Over the past few years, (further) progress has been made in the design of improved interfacing techniques for coupling CE to MS; also, in the development of CE-MS approaches for profiling metabolites in volume-restricted samples, and in strategies that further enhance the metabolic coverage. In this article, which is a follow-up of a previous review article covering the years 2016-2018 (Electrophoresis 2019, 40, 165-179), the main (technological) developments in CE-MS methods and strategies for metabolomics are discussed covering the literature from July 2018 to June 2020. Representative examples highlight the utility of CE-MS in the fields of biomedical, clinical, microbial, plant and food metabolomics. A complete overview of recent CE-MS-based metabolomics studies is given in a table, which provides information on sample type and pretreatment, capillary coatings, and MS detection mode. Finally, some general conclusions and perspectives are given.
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Affiliation(s)
- Wei Zhang
- Biomedical Microscale Analytics, Leiden Academic Centre for Drug ResearchLeiden UniversityLeidenThe Netherlands
| | - Rawi Ramautar
- Biomedical Microscale Analytics, Leiden Academic Centre for Drug ResearchLeiden UniversityLeidenThe Netherlands
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42
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Yamamoto K, Ota N, Tanaka Y. Nanofluidic Devices and Applications for Biological Analyses. Anal Chem 2021; 93:332-349. [PMID: 33125221 DOI: 10.1021/acs.analchem.0c03868] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Koki Yamamoto
- Laboratory for Integrated Biodevice, Center for Biosystems Dynamics Research (BDR), RIKEN, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Nobutoshi Ota
- Laboratory for Integrated Biodevice, Center for Biosystems Dynamics Research (BDR), RIKEN, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yo Tanaka
- Laboratory for Integrated Biodevice, Center for Biosystems Dynamics Research (BDR), RIKEN, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
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43
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Affiliation(s)
- Takayuki KAWAI
- RIKEN Center for Biosystems Dynamics Research
- Graduate School of Frontier Biosciences, Osaka University
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44
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Abstract
The ultimate goal of single-cell analyses is to obtain the biomolecular content for each cell in unicellular and multicellular organisms at different points of their life cycle under variable environmental conditions. These require an assessment of: a) the total number of cells, b) the total number of cell types, and c) the complete and quantitative single molecular detection and identification for all classes of biopolymers, and organic and inorganic compounds, in each individual cell. For proteins, glycans, lipids, and metabolites, whose sequences cannot be amplified by copying as in the case of nucleic acids, the detection limit by mass spectrometry is about 105 molecules. Therefore, proteomic, glycomic, lipidomic, and metabolomic analyses do not yet permit the assembly of the complete single-cell omes. The construction of novel nanoelectrophoretic arrays and nano in microarrays on a single 1-cm-diameter chip has shown proof of concept for a high throughput platform for parallel processing of thousands of individual cells. Combined with dynamic secondary ion mass spectrometry, with 3D scanning capability and lateral resolution of 50 nm, the sensitivity of single molecular quantification and identification for all classes of biomolecules could be reached. Further development and routine application of such technological and instrumentation solution would allow assembly of complete omes with a quantitative assessment of structural and functional cellular diversity at the molecular level.
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Xu X. Capillary Electrophoresis-Mass Spectrometry for Cancer Metabolomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1280:189-200. [PMID: 33791983 DOI: 10.1007/978-3-030-51652-9_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
This chapter presents the fundamentals, instrumentation, methodology, and applications of capillary electrophoresis-mass spectrometry (CE-MS) for cancer metabolomics. CE offers fast and high-resolution separation of charged analytes from a very small amount of sample. When coupled to MS, it represents a powerful analytical technique enabling identification and quantification of metabolites in biological samples. Several issues need to be addressed when combining CE with MS, especially the interface between CE and MS and the selection of a proper separation methodology, sample pretreatment, and capillary coatings. We will discuss these aspects of CE-MS and detail representative applications for cancer metabolomic analysis.
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Affiliation(s)
- Xiangdong Xu
- School of Public Health and Key Laboratory of Environment and Human Health, Hebei Medical University, Shijiazhuang, China.
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Choo SM, Almomani LM, Cho KH. Boolean Feedforward Neural Network Modeling of Molecular Regulatory Networks for Cellular State Conversion. Front Physiol 2020; 11:594151. [PMID: 33335489 PMCID: PMC7736109 DOI: 10.3389/fphys.2020.594151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 11/03/2020] [Indexed: 11/13/2022] Open
Abstract
The molecular regulatory network (MRN) within a cell determines cellular states and transitions between them. Thus, modeling of MRNs is crucial, but this usually requires extensive analysis of time-series measurements, which is extremely difficult to obtain from biological experiments. However, single-cell measurement data such as single-cell RNA-sequencing databases have recently provided a new insight into resolving this problem by ordering thousands of cells in pseudo-time according to their differential gene expressions. Neural network modeling can be employed by using temporal data as learning data. In contrast, Boolean network modeling of MRNs has a growing interest, as it is a parameter-free logical modeling and thereby robust to noisy data while still capturing essential dynamics of biological networks. In this study, we propose a Boolean feedforward neural network (FFN) modeling by combining neural network and Boolean network modeling approach to reconstruct a practical and useful MRN model from large temporal data. Furthermore, analyzing the reconstructed MRN model can enable us to identify control targets for potential cellular state conversion. Here, we show the usefulness of Boolean FFN modeling by demonstrating its applicability through a toy model and biological networks.
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Affiliation(s)
- Sang-Mok Choo
- Department of Mathematics, University of Ulsan, Ulsan, South Korea
| | | | - Kwang-Hyun Cho
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
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Domenick TM, Gill EL, Vedam-Mai V, Yost RA. Mass Spectrometry-Based Cellular Metabolomics: Current Approaches, Applications, and Future Directions. Anal Chem 2020; 93:546-566. [PMID: 33146525 DOI: 10.1021/acs.analchem.0c04363] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Taylor M Domenick
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Emily L Gill
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104-4283, United States.,Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104-4283, United States
| | - Vinata Vedam-Mai
- Department of Neurology, University of Florida, Gainesville, Florida 32610, United States
| | - Richard A Yost
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
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48
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Recent Advances in Single Cell Analysis Methods Based on Mass Spectrometry. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2020. [DOI: 10.1016/s1872-2040(20)60038-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Resolving Metabolic Heterogeneity in Experimental Models of the Tumor Microenvironment from a Stable Isotope Resolved Metabolomics Perspective. Metabolites 2020; 10:metabo10060249. [PMID: 32549391 PMCID: PMC7345423 DOI: 10.3390/metabo10060249] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/02/2020] [Accepted: 06/04/2020] [Indexed: 12/11/2022] Open
Abstract
The tumor microenvironment (TME) comprises complex interactions of multiple cell types that determines cell behavior and metabolism such as nutrient competition and immune suppression. We discuss the various types of heterogeneity that exist in solid tumors, and the complications this invokes for studies of TME. As human subjects and in vivo model systems are complex and difficult to manipulate, simpler 3D model systems that are compatible with flexible experimental control are necessary for studying metabolic regulation in TME. Stable Isotope Resolved Metabolomics (SIRM) is a valuable tool for tracing metabolic networks in complex systems, but at present does not directly address heterogeneous metabolism at the individual cell level. We compare the advantages and disadvantages of different model systems for SIRM experiments, with a focus on lung cancer cells, their interactions with macrophages and T cells, and their response to modulators in the immune microenvironment. We describe the experimental set up, illustrate results from 3D cultures and co-cultures of lung cancer cells with human macrophages, and outline strategies to address the heterogeneous TME.
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Wei X, Lu Y, Zhang X, Chen ML, Wang JH. Recent advances in single-cell ultra-trace analysis. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.115886] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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