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Zhu L, Bai M, Xiao S, Liu Y, Zhu Q, Wang Z, Zhao J, Zhang W, Chen D. In-situ monitoring of cellular H 2O 2 within 3D cell clusters using conductive scaffolds. Talanta 2024; 279:126559. [PMID: 39018950 DOI: 10.1016/j.talanta.2024.126559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 06/23/2024] [Accepted: 07/11/2024] [Indexed: 07/19/2024]
Abstract
Accurately monitoring H2O2 concentrations in 3D cell clusters is challenging due to limited diffusion and rapid degradation of H2O2 in the culture medium. Despite the incorporation of three-dimensional cell culture approaches, the detection technology has largely remained as a 2D planar system. In this study, we present a versatile approach of 3D electrochemical sensing utilizing carbon nanotubes as conductive scaffolds for in-situ monitoring of H2O2 in cell clusters. These scaffolds enabled direct contact between H2O2 released from cells and the electrodes, thereby improving sensitivity and ensuring biocompatibility for cell aggregates. The scaffolds exhibited electrocatalytic behavior with a limit of detection of 6.7 nM H2O2. Additionally, the electrochemical responses of cell clusters with the scaffolds exhibited significantly higher current compared to clusters without scaffolds when stimulated with model drugs. This study underscores the potential of conductive scaffolds for real-time monitoring of H2O2 released from cell clusters in 3D microenvironments.
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Affiliation(s)
- Ling Zhu
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China
| | - Mingxia Bai
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China
| | - Shenghao Xiao
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China
| | - Yanhui Liu
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China
| | - Qin Zhu
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China
| | - Zixuan Wang
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China
| | - Jiaqian Zhao
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China; Key Laboratory of Elemene Class Anti-Cancer Medicines, Hangzhou Normal University, China
| | - Wei Zhang
- Medtronic Technology Center, Shanghai, China.
| | - Dajing Chen
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China; Key Laboratory of Elemene Class Anti-Cancer Medicines, Hangzhou Normal University, China.
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2
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Xie P, Zhang H, Wu P, Chen Y, Cai Z. Three-Dimensional Mass Spectrometry Imaging Reveals Distributions of Lipids and the Drug Metabolite Associated with the Enhanced Growth of Colon Cancer Cell Spheroids Treated with Triclosan. Anal Chem 2022; 94:13667-13675. [PMID: 36170179 PMCID: PMC9558077 DOI: 10.1021/acs.analchem.2c00768] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The application of mass spectrometry imaging (MSI) to explore the responses of cancer cell spheroids (CCS) after treatment of exogenous molecules has attracted growing attention. Increasing studies have utilized MSI to image the two-dimensional distributions of exogenous and endogenous molecules in planar CCS sections. However, because CCS are volumetric and heterogenous, maintaining their three-dimensional (3D) information is essential for acquiring a better understanding of the tumor microenvironment and mechanisms of action of exogenous molecules. Here, an established method of 3D MSI was applied to distinguish the distributions of triclosan sulfate and endogenous lipids in three microregions of colon CCS with an enhanced growth induced by the treatment of triclosan, a common antimicrobial agent. The results of 3D MSI showed that triclosan sulfate gradually accumulated from the periphery to the entire structure of CCS and finally localized in the core region. Spatial lipidomics analysis revealed that the upregulated phosphatidylethanolamine (fold change (FD) = 1.26, p = 0.0021), phosphatidylinositol (FD = 1.17, p = 0.0180), and phosphatidylcholine (FD = 1.22, p = 0.0178) species mainly distributed in the outer proliferative region, while the upregulated sphingomyelin (FD = 1.18, p = 0.024) species tended to distribute in the inner necrotic region. Our results suggest that a competitive mechanism between inhibiting and promoting CCS growth might be responsible for the proliferation of CCS treated with triclosan.
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Affiliation(s)
- Peisi Xie
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Kowloon 999077, Hong Kong SAR, China
| | - Hongna Zhang
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Kowloon 999077, Hong Kong SAR, China
| | - Pengfei Wu
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Kowloon 999077, Hong Kong SAR, China
| | - Yanyan Chen
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Kowloon 999077, Hong Kong SAR, China
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Kowloon 999077, Hong Kong SAR, China
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3
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Tobias F, Hummon AB. Lipidomic comparison of 2D and 3D colon cancer cell culture models. JOURNAL OF MASS SPECTROMETRY : JMS 2022; 57:e4880. [PMID: 36028991 PMCID: PMC9526240 DOI: 10.1002/jms.4880] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 07/21/2022] [Indexed: 06/10/2023]
Abstract
Altered lipid metabolism is one of the hallmarks of cancer. Cellular proliferation and de novo synthesis of lipids are related to cancer progression. In this study, we evaluated the lipidomic profile of two-dimensional (2D) monolayer and multicellular tumor spheroids from the HCT 116 colon carcinoma cell line. We utilized serial trypsinization on the spheroid samples to generate three cellular populations representing the proliferative, quiescent, and necrotic regions of the spheroid. This analysis enabled a comprehensive identification and quantification of lipids produced in each of the spheroid layer and 2D cultures. We show that lipid subclasses associated with lipid droplets form in oxygen-restricted and acidic regions of spheroids and are produced at higher levels than in 2D cultures. Additionally, sphingolipid production, which is implicated in cell death and survival pathways, is higher in spheroids relative to 2D cells. Finally, we show that increased numbers of lipids composed of polyunsaturated fatty acids (PUFAs) are produced in the quiescent and necrotic regions of the spheroid. The lipidomic signature for each region and cell culture type highlights the importance of understanding the spatial aspects of cancer biology. These results provide additional lipid biomarkers in colon cancer cells that can be further studied to target pivotal lipid production pathways.
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Affiliation(s)
- Fernando Tobias
- Department of Chemistry and BiochemistryThe Ohio State UniversityColumbusOhioUSA
| | - Amanda B. Hummon
- Department of Chemistry and BiochemistryThe Ohio State UniversityColumbusOhioUSA
- Comprehensive Cancer CenterThe Ohio State UniversityColumbusOhioUSA
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4
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Nguyen TD, Lan Y, Kane SS, Haffner JJ, Liu R, McCall LI, Yang Z. Single-Cell Mass Spectrometry Enables Insight into Heterogeneity in Infectious Disease. Anal Chem 2022; 94:10567-10572. [PMID: 35863111 PMCID: PMC10064790 DOI: 10.1021/acs.analchem.2c02279] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cellular heterogeneity is generally overlooked in infectious diseases. In this study, we investigated host cell heterogeneity during infection with Trypanosoma cruzi (T. cruzi) parasites, causative agents of Chagas disease (CD). In chronic-stage CD, only a few host cells are infected with a large load of parasites and symptoms may appear at sites distal to parasite colonization. Furthermore, recent work has revealed T. cruzi heterogeneity with regard to replication rates and drug susceptibility. However, the role of cellular-level metabolic heterogeneity in these processes has yet to be assessed. To fill this knowledge gap, we developed a Single-probe SCMS (single-cell mass spectrometry) method compatible with biosafety protocols, to acquire metabolomics data from individual cells during T. cruzi infection. This study revealed heterogeneity in the metabolic response of the host cells to T. cruzi infection in vitro. Our results showed that parasite-infected cells possessed divergent metabolism compared to control cells. Strikingly, some uninfected cells adjacent to infected cells showed metabolic impacts as well. Specific metabolic changes include increases in glycerophospholipids with infection. These results provide novel insight into the pathogenesis of CD. Furthermore, they represent the first application of bioanalytical SCMS to the study of mammalian-infectious agents, with the potential for broad applications to study infectious diseases.
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Affiliation(s)
- Tra D Nguyen
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Yunpeng Lan
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Shelley S Kane
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Jacob J Haffner
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, Oklahoma 73019, United States.,Department of Anthropology, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Renmeng Liu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Laura-Isobel McCall
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States.,Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, Oklahoma 73019, United States.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Zhibo Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
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5
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Sun M, Chen X, Yang Z. Single cell mass spectrometry studies reveal metabolomic features and potential mechanisms of drug-resistant cancer cell lines. Anal Chim Acta 2022; 1206:339761. [PMID: 35473873 PMCID: PMC9046687 DOI: 10.1016/j.aca.2022.339761] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 03/18/2022] [Accepted: 03/22/2022] [Indexed: 12/28/2022]
Abstract
Irinotecan (Iri) is a key drug to treat metastatic colorectal cancer, but its clinical activity is often limited by de novo and acquired drug resistance. Studying the underlying mechanisms of drug resistance is necessary for developing novel therapeutic strategies. In this study, we used both regular and irinotecan-resistant (Iri-resistant) colorectal cell lines as models, and performed single cell mass spectrometry (SCMS) metabolomics studies combined with analyses from cytotoxicity assay, western blot, flow cytometry, quantitative real-time polymerase chain reaction (qPCR), and reactive oxygen species (ROS). Our SCMS results indicate that Iri-resistant cancer cells possess higher levels of unsaturated lipids compared with the regular cancer cells. In addition, multiple protein biomarkers and their corresponding mRNAs of colon cancer stem cells are overexpressed in Iri-resistance cells. Particularly, stearoyl-CoA desaturase 1 (SCD1) is upregulated with the development of drug resistance in Iri-resistant cells, whereas inhibiting the activity of SCD1 efficiently increase their sensitivity to Iri treatment. In addition, we demonstrated that SCD1 directly regulates the expression of ALDH1A1, which contributes to the cancer stemness and ROS level in Iri-resistant cell lines.
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6
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A cellular chip-MS system for investigation of Lactobacillus rhamnosus GG and irinotecan synergistic effects on colorectal cancer. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.08.041] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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7
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Tian X, Zou Z, Yang Z. Extract Metabolomic Information from Mass Spectrometry Images Using Advanced Data Analysis. Methods Mol Biol 2022; 2437:253-272. [PMID: 34902154 DOI: 10.1007/978-1-0716-2030-4_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Mass spectrometry imaging (MSI) data generally contains large sizes and high-dimensional structures due to their inherent complex chemical and spatial information. A variety of data analysis methods have been developed to comprehensively analyze the MSI experimental results and extract essential information. Here, we describe the protocols of data preprocessing and emerging methods for data analyses, including multivariate analysis, machine learning, and image fusion, that have been applied to the data generated from the Single-probe MSI technique. These strategies and methods can be potentially applied to handling data produced from other MSI techniques.
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Affiliation(s)
- Xiang Tian
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
- Dynamic Omics, Center of Genomics Research (CGR), R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Zhu Zou
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Zhibo Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA.
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8
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Spatially resolved quantification of drug metabolism and efficacy in 3D paper-based tumor mimics. Anal Chim Acta 2021; 1186:339091. [PMID: 34756260 DOI: 10.1016/j.aca.2021.339091] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/10/2021] [Accepted: 09/20/2021] [Indexed: 11/23/2022]
Abstract
Paper-based cultures are an emerging platform for preparing three-dimensional (3D) tissue- and tumor-like structures. The ability to stack individual sheets of cell-containing paper affords a modular means of assembling structures with defined cellular compositions and microenvironments. These layered stacks are easily separated at the end of an experiment, providing spatially resolved populations of live cells for further analysis. Here we describe a workflow in which cell viability, drug penetration, and drug metabolism are quantified in a spatially resolved manner. Specifically, we mapped the distribution of the drug irinotecan and its bioactive metabolite SN38 in a colorectal cancer cell-containing stacked structure with liquid chromatography-mass spectrometry (LC-MS). This paper provides the first example of a 3D culture platform that quantifies viability and drug metabolism in a spatially resolved manner. Our data show that cells at the bottom of the stack are more drug-resistant than layers in contact with the culture medium, similar to cells in the nutrient-poor center of a proliferating tumor being more drug-resistant than the rapidly dividing cells at its periphery. The powerful combination of quantitative viability and drug metabolism measurements will enable future studies to determine the exact mechanism(s) of drug resistance in different regions of a tumor.
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9
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Chen Y, Wang T, Xie P, Song Y, Wang J, Cai Z. Mass spectrometry imaging revealed alterations of lipid metabolites in multicellular tumor spheroids in response to hydroxychloroquine. Anal Chim Acta 2021; 1184:339011. [PMID: 34625248 DOI: 10.1016/j.aca.2021.339011] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/24/2021] [Accepted: 08/30/2021] [Indexed: 12/11/2022]
Abstract
Three-dimensional (3D) multicellular tumor spheroids (MCTS) that mimic the complex tumor microenvironment provide a good platform for in vitro study of drug and endogenous metabolites. Hydroxychloroquine (HCQ) has shown anti-tumor activity in a variety of tumor models. However, the effect of the drug on the alteration of lipid metabolism spatial composition and distribution in the MCTS model is not clear. Herein, we utilized matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI) in the analysis of A549 lung cancer multicellular spheroids to investigate the in situ spatial distribution of HCQ and its effect on lipid metabolism. We have successfully observed the spatial variations of HCQ in the inner region of the spheroid at different drug-treated time points. The MSI results also demonstrated that HCQ treatment altered the spatial composition of lipids in the inner and outer regions of treated spheroids. Furthermore, the lipidomic results showed that the identified phosphatidylcholines (PC), lysophosphatidylcholines (LPC), phosphatidylethanolamines (PE), lysophosphatidylethanolamines (LPE), phosphatidylinositols (PI), ceramides (Cer), glucosylceramides (CerG), and diglycerides (DG) were significantly up-regulated, and phosphatidylglycerol (PG) and triglycerides (TG) were remarkable down-regulated. MSI method combined with LC-MS/MS profiling of endogenous metabolites can obtain more detailed information about how spheroids respond to drug and spatial distribution information, thus fostering a better understanding of the relationship between drug-altered lipid metabolism and cancer microenvironment.
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Affiliation(s)
- Yanyan Chen
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, China
| | - Tao Wang
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, China; Analysis Center, School of Pharmacy, Guangdong Medical University, Dongguan 523808, China
| | - Peisi Xie
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, China
| | - Yuanyuan Song
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, China
| | - Jianing Wang
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, China
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, China.
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10
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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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11
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Wang Y, Hummon AB. MS imaging of multicellular tumor spheroids and organoids as an emerging tool for personalized medicine and drug discovery. J Biol Chem 2021; 297:101139. [PMID: 34461098 PMCID: PMC8463860 DOI: 10.1016/j.jbc.2021.101139] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 08/26/2021] [Accepted: 08/26/2021] [Indexed: 12/22/2022] Open
Abstract
MS imaging (MSI) is a powerful tool in drug discovery because of its ability to interrogate a wide range of endogenous and exogenous molecules in a broad variety of samples. The impressive versatility of the approach, where almost any ionizable biomolecule can be analyzed, including peptides, proteins, lipids, carbohydrates, and nucleic acids, has been applied to numerous types of complex biological samples. While originally demonstrated with harvested organs from animal models and biopsies from humans, these models are time consuming and expensive, which makes it necessary to extend the approach to 3D cell culture systems. These systems, which include spheroid models, prepared from immortalized cell lines, and organoid cultures, grown from patient biopsies, can provide insight on the intersection of molecular information on a spatial scale. In particular, the investigation of drug compounds, their metabolism, and the subsequent distribution of their metabolites in 3D cell culture systems by MSI has been a promising area of study. This review summarizes the different ionization methods, sample preparation steps, and data analysis methods of MSI and focuses on several of the latest applications of MALDI-MSI for drug studies in spheroids and organoids. Finally, the application of this approach in patient-derived organoids to evaluate personalized medicine options is discussed.
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Affiliation(s)
- Yijia Wang
- Department of Chemistry and Biochemistry, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
| | - Amanda B Hummon
- Department of Chemistry and Biochemistry, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA.
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12
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Zang Q, Sun C, Chu X, Li L, Gan W, Zhao Z, Song Y, He J, Zhang R, Abliz Z. Spatially resolved metabolomics combined with multicellular tumor spheroids to discover cancer tissue relevant metabolic signatures. Anal Chim Acta 2021; 1155:338342. [PMID: 33766316 DOI: 10.1016/j.aca.2021.338342] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 02/05/2021] [Accepted: 02/16/2021] [Indexed: 12/18/2022]
Abstract
Spatially resolved metabolomics offers unprecedented opportunities for elucidating metabolic mechanisms during cancer progression. It facilitated the discovery of aberrant cellular metabolism with clinical application potential. Here, we developed a novel strategy to discover cancer tissue relevant metabolic signatures by high spatially resolved metabolomics combined with a multicellular tumor spheroid (MCTS) in vitro model. Esophageal cancer MCTS were generated using KYSE-30 human esophageal cancer cells to fully mimic the 3D microenvironment under physiological conditions. Then, the spatial features and temporal variation of metabolites and metabolic pathways in MCTS were accurately mapped by using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) with a spatial resolution at ∼12 μm. Metabolites, such as glutamate, tyrosine, inosine and various types of lipids displayed heterogeneous distributions in different microregions inside the MCTS, revealing the metabolic heterogenicity of cancer cells under different proliferative states. Subsequently, through joint analysis of metabolomic data of clinical cancer tissue samples, cancer tissue relevant metabolic signatures in esophageal cancer MCTS were identified, including glutamine metabolism, fatty acid metabolism, de novo synthesis phosphatidylcholine (PC) and phosphatidylethanolamine (PE), etc. In addition, the abnormal expression of the involved metabolic enzymes, i.e., GLS, FASN, CHKA and cPLA2, was further confirmed and showed similar tendencies in esophageal cancer MCTS and cancer tissues. The MALDI-MSI combined with MCTS approach offers molecular insights into cancer metabolism with real-word relevance, which would potentially benefit the biomarker discovery and metabolic mechanism studies.
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Affiliation(s)
- Qingce Zang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Chenglong Sun
- Key Laboratory for Applied Technology of Sophisticated Analytical Instruments of Shandong Province, Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, China
| | - Xiaoping Chu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Limei Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Wenqiang Gan
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Zitong Zhao
- State Key Laboratory of Molecular Oncology, Cancer Institute, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yongmei Song
- State Key Laboratory of Molecular Oncology, Cancer Institute, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jiuming He
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Ruiping Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
| | - Zeper Abliz
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China; Center for Imaging and Systems Biology, College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China.
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13
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Del Prete E, Facchiano A, Profumo A, Angelini C, Romano P. GeenaR: A Web Tool for Reproducible MALDI-TOF Analysis. Front Genet 2021; 12:635814. [PMID: 33854526 PMCID: PMC8039533 DOI: 10.3389/fgene.2021.635814] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/01/2021] [Indexed: 12/21/2022] Open
Abstract
Mass spectrometry is a widely applied technology with a strong impact in the proteomics field. MALDI-TOF is a combined technology in mass spectrometry with many applications in characterizing biological samples from different sources, such as the identification of cancer biomarkers, the detection of food frauds, the identification of doping substances in athletes’ fluids, and so on. The massive quantity of data, in the form of mass spectra, are often biased and altered by different sources of noise. Therefore, extracting the most relevant features that characterize the samples is often challenging and requires combining several computational methods. Here, we present GeenaR, a novel web tool that provides a complete workflow for pre-processing, analyzing, visualizing, and comparing MALDI-TOF mass spectra. GeenaR is user-friendly, provides many different functionalities for the analysis of the mass spectra, and supports reproducible research since it produces a human-readable report that contains function parameters, results, and the code used for processing the mass spectra. First, we illustrate the features available in GeenaR. Then, we describe its internal structure. Finally, we prove its capabilities in analyzing oncological datasets by presenting two case studies related to ovarian cancer and colorectal cancer. GeenaR is available at http://proteomics.hsanmartino.it/geenar/.
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Affiliation(s)
- Eugenio Del Prete
- Institute for Applied Mathematics, National Research Council, Naples, Italy
| | - Angelo Facchiano
- Institute of Food Sciences, National Research Council, Avellino, Italy
| | - Aldo Profumo
- Proteomica e Spettrometria di Massa, IRCCS Ospedale Policlinico San Martino IST, Genova, Italy
| | - Claudia Angelini
- Institute for Applied Mathematics, National Research Council, Naples, Italy
| | - Paolo Romano
- Proteomica e Spettrometria di Massa, IRCCS Ospedale Policlinico San Martino IST, Genova, Italy
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14
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Cintron-Diaz YL, Acanda de la Rocha AM, Castellanos A, Chambers JM, Fernandez-Lima F. Mapping chemotherapeutic drug distribution in cancer cell spheroids using 2D-TOF-SIMS and LESA-TIMS-MS. Analyst 2020; 145:7056-7062. [PMID: 32966375 DOI: 10.1039/c9an02245g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Three-dimensional (3D) cancer cell cultures grown in the form of spheroids are effective models for the study of in vivo-like processes simulating cancer tumor pharmacological dynamics and morphology. In this study, we show the advantages of Time-of-Flight Secondary Ion Mass Spectrometry (TOF-SIMS) combined with in situ Liquid Extraction Surface Analysis coupled to trapped Ion Mobility Spectrometry Mass Spectrometry (LESA-TIMS-TOF MS) for high spatial resolution mapping and quantitation of ABT-737, a chemotherapeutic drug, at the level of single human colon carcinoma cell spheroids (HCT 116 MCS). 2D-TOF-SIMS studies of consecutive sections (∼16 μm thick slices) showed that ABT-737 is homogenously distributed in the outer layers of the HCT 116 MCS. Complementary in situ LESA-TIMS-TOF MS/MS measurements confirmed the presence of the ABT-737 drug in the MCS slides by the observation of the molecular ion [M + H]+m/z and mobility, and the charateristic fragmentation pattern. LESA-TIMS-TOF MS allowed a quantitative assessment of the ABT-737 drug of the control MCS slice spiked with ABT-737 standard over the 0.4-4.1 ng range and MCS treated starting at 10 μM for 24 h. These experiments showcase an effective protocol for unambigous characterization and 3D mapping of chemotherapeutic drug distribution at the single MCS level.
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Affiliation(s)
- Yarixa L Cintron-Diaz
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th St., AHC4-233, Miami, FL 33199, USA.
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15
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Cao YQ, Zhang L, Zhang J, Guo YL. Single-Cell On-Probe Derivatization-Noncontact Nanocarbon Fiber Ionization: Unraveling Cellular Heterogeneity of Fatty Alcohol and Sterol Metabolites. Anal Chem 2020; 92:8378-8385. [PMID: 32420735 DOI: 10.1021/acs.analchem.0c00954] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Currently in single-cell mass spectrometry, the analysis of low-abundance cell metabolites such as fatty alcohols and sterols remains a challenge. In most research studies, single-cell samples are analyzed directly after sampling. However, this workflow may exclude many effective sample pretreatment methods such as derivatization for the improvement of detection sensitivity for specific cell metabolites in a single-cell sample. Metabolites in low abundance in a cell may not be detected. Herein on-probe derivatization coupled with noncontact nanocarbon fiber ionization is proposed for sensitive fatty alcohol and sterol metabolite analysis at the single-cell level. Fatty alcohol and sterol metabolites were rapidly quaternized by the single-cell on-probe derivatization method. The reaction products were directly ionized with no postreaction processing. Furthermore, a new ionization source for noncontact nanocarbon fiber ionization was developed to show good compatibility with dichloromethane, a low-polarity solvent used in on-probe derivatization. The quaternized fatty alcohols and sterols exhibited evidently enhanced ionization efficiency in mass spectra. In applications of the developed method, seven kinds of even-numbered-carbon fatty alcohols (C12-C22) and five kinds of sterols were detected in single L-02 and HepG2 cells. Then the L-02 and HepG2 cells were readily discriminated through principal component analysis. Additionally, a rough quantitative analysis of the detected fatty alcohols and sterols in single cells was performed. The mass intensities of fatty alcohols show a significant difference between L-02 and HepG2 cells while those of sterols remain stable.
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Affiliation(s)
- Yu-Qi Cao
- State Key Laboratory of Organometallic Chemistry and National Center for Organic Mass Spectrometry in Shanghai, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Li Zhang
- State Key Laboratory of Organometallic Chemistry and National Center for Organic Mass Spectrometry in Shanghai, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Jing Zhang
- State Key Laboratory of Organometallic Chemistry and National Center for Organic Mass Spectrometry in Shanghai, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Yin-Long Guo
- State Key Laboratory of Organometallic Chemistry and National Center for Organic Mass Spectrometry in Shanghai, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
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16
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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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17
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Zhu Y, Liu R, Yang Z. Redesigning the T-probe for mass spectrometry analysis of online lysis of non-adherent single cells. Anal Chim Acta 2019; 1084:53-59. [PMID: 31519234 PMCID: PMC6746249 DOI: 10.1016/j.aca.2019.07.059] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/25/2019] [Accepted: 07/28/2019] [Indexed: 12/16/2022]
Abstract
Single cell mass spectrometry (SCMS) allows for molecular analysis of individual cells while avoiding the inevitable drawbacks of using cell lysate prepared from populations of cells. Based on our previous design of the T-probe, a microscale sampling and ionization device for SCMS analysis, we further developed the device to perform online, and real time lysis of non-adherent live single cells for mass spectrometry (MS) analysis at ambient conditions. This redesigned T-probe includes three parts: a sampling probe with a small tip to withdraw a whole cell, a solvent-providing capillary to deliver lysis solution (i.e., acetonitrile), and a nano-ESI emitter in which rapid cell lysis and ionization occur followed by MS analysis. These three components are embedded between two polycarbonate slides and are jointed through a T-junction to form an integrated device. Colon cancer cells (HCT-116) under control and treatment (using anticancer drug irinotecan) conditions were analyzed. We detected a variety of intracellular species, and structural identification of selected ions was conducted using tandem MS (MS2). We further conducted statistical analysis (e.g., PLS-DA and t-test) to gain biological insights of cellular metabolism. Our results indicate that the influence of anticancer drugs on cellular metabolism of live non-adherent cells can be obtained using the SCMS experiments combined with statistical data analysis.
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Affiliation(s)
- Yanlin Zhu
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Renmeng Liu
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Zhibo Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA.
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18
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Tian X, Xie B, Zou Z, Jiao Y, Lin LE, Chen CL, Hsu CC, Peng J, Yang Z. Multimodal Imaging of Amyloid Plaques: Fusion of the Single-Probe Mass Spectrometry Image and Fluorescence Microscopy Image. Anal Chem 2019; 91:12882-12889. [PMID: 31536324 PMCID: PMC6885010 DOI: 10.1021/acs.analchem.9b02792] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Alzheimer's disease (AD) is one of the most common neurodegenerative diseases. The formation of amyloid plaques by aggregated amyloid beta (Aβ) peptides is a primary event in AD pathology. Understanding the metabolomic features and related pathways is critical for studying plaque-related pathological events (e.g., cell death and neuron dysfunction). Mass spectrometry imaging (MSI), due to its high sensitivity and ability to obtain the spatial distribution of metabolites, has been applied to AD studies. However, limited studies of metabolites in amyloid plaques have been performed due to the drawbacks of the commonly used techniques such as matrix-assisted laser desorption/ionization MSI. In the current study, we obtained high spatial resolution (∼17 μm) MS images of the AD mouse brain using the Single-probe, a microscale sampling and ionization device, coupled to a mass spectrometer under ambient conditions. The adjacent slices were used to obtain fluorescence microscopy images to locate amyloid plaques. The MS image and the fluorescence microscopy image were fused to spatially correlate histological protein hallmarks with metabolomic features. The fused images produced significantly improved spatial resolution (∼5 μm), allowing for the determination of fine structures in MS images and metabolomic biomarkers representing amyloid plaques.
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Affiliation(s)
- Xiang Tian
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Boer Xie
- Departments of Structural Biology and Developmental Neurobiology, Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Zhu Zou
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Yun Jiao
- Departments of Structural Biology and Developmental Neurobiology, Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Li-En Lin
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Chih-Lin Chen
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Cheng-Chih Hsu
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Zhibo Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
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19
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Pan N, Standke SJ, Kothapalli NR, Sun M, Bensen RC, Burgett AWG, Yang Z. Quantification of Drug Molecules in Live Single Cells Using the Single-Probe Mass Spectrometry Technique. Anal Chem 2019; 91:9018-9024. [PMID: 31246408 PMCID: PMC6677389 DOI: 10.1021/acs.analchem.9b01311] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Analyzing cellular constituents on the single-cell level through mass spectrometry (MS) allows for a wide range of compounds to be studied simultaneously. However, there is a need for quantitative single-cell mass spectrometry (qSCMS) methods to fully characterize drug efficacy from individual cells within cell populations. In this study, qSCMS experiments were carried out using the Single-probe MS technique. The method was successfully used to perform rapid absolute quantifications of the anticancer drug irinotecan in individual mammalian cancer cells under ambient conditions in real time. Traditional liquid chromatography/mass spectrometry (LC/MS) quantifications of irinotecan in cell lysate samples were used to compare the results from Single-probe qSCMS. This technique showcases heterogeneity of drug efficacy on the single-cell level.
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Affiliation(s)
- Ning Pan
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Shawna J. Standke
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Naga Rama Kothapalli
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Mei Sun
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Ryan C. Bensen
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Anthony W. G. Burgett
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Zhibo Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
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20
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Standke SJ, Colby DH, Bensen RC, Burgett AWG, Yang Z. Integrated Cell Manipulation Platform Coupled with the Single-probe for Mass Spectrometry Analysis of Drugs and Metabolites in Single Suspension Cells. J Vis Exp 2019. [PMID: 31282898 DOI: 10.3791/59875] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Single cell mass spectrometry (SCMS) enables sensitive detection and accurate analysis of broad ranges of cellular species on the individual-cell level. The single-probe, a microscale sampling and ionization device, can be coupled with a mass spectrometer for on-line, rapid SCMS analysis of cellular constituents under ambient conditions. Previously, the single-probe SCMS technique was primarily used to measure cells immobilized onto a substrate, limiting the types of cells for studies. In the current study, the single-probe SCMS technology has been integrated with a cell manipulation system, typically used for in vitro fertilization. This integrated cell manipulation and analysis platform uses a cell-selection probe to capture identified individual floating cells and transfer the cells to the single-probe tip for microscale lysis, followed by immediate mass spectrometry analysis. This capture and transfer process removes the cells from the surrounding solution prior to analysis, minimizing the introduction of matrix molecules in the mass spectrometry analysis. This integrated setup is capable of SCMS analysis of targeted patient-isolated cells present in body fluids samples (e.g., urine, blood, saliva, etc.), allowing for potential applications of SCMS analysis to human medicine and disease biology.
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Affiliation(s)
- Shawna J Standke
- Department of Chemistry and Biochemistry, University of Oklahoma
| | - Devon H Colby
- Department of Chemistry and Biochemistry, University of Oklahoma
| | - Ryan C Bensen
- Department of Chemistry and Biochemistry, University of Oklahoma
| | | | - Zhibo Yang
- Department of Chemistry and Biochemistry, University of Oklahoma;
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21
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Tian X, Zhang G, Zou Z, Yang Z. Anticancer Drug Affects Metabolomic Profiles in Multicellular Spheroids: Studies Using Mass Spectrometry Imaging Combined with Machine Learning. Anal Chem 2019; 91:5802-5809. [PMID: 30951294 PMCID: PMC6573030 DOI: 10.1021/acs.analchem.9b00026] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Multicellular spheroids (hereinafter referred to as spheroids) are 3D biological models. The metabolomic profiles inside spheroids provide crucial information reflecting the molecular phenotypes and microenvironment of cells. To study the influence of an anticancer drug on the spatially resolved metabolites, spheroids were cultured using HCT-116 colorectal cancer cells, treated with the anticancer drug Irinotecan under a series of time- and concentration-dependent conditions. The Single-probe mass spectrometry imaging (MSI) technique was utilized to conduct the experiments. The MSI data were analyzed using advanced data analysis methods to efficiently extract metabolomic information. Multivariate curve resolution alternating least square (MCR-ALS) was used to decompose each MS image into different components with grouped species. To improve the efficiency of data analysis, both supervised (Random Forest) and unsupervised (cluster large applications (CLARA)) machine learning (ML) methods were employed to cluster MS images according to their metabolomic features. Our results indicate that anticancer drug significantly affected the abundances of a variety of metabolites in different regions of spheroids. This integrated experiment and data analysis approach can facilitate the studies of metabolites in different types of 3D tumor models and tissues and potentially benefit the drug discovery, therapeutic resistance, and other biological research fields.
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Affiliation(s)
- Xiang Tian
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Genwei Zhang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Zhu Zou
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Zhibo Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
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22
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Cahill JF, Riba J, Kertesz V. Rapid, Untargeted Chemical Profiling of Single Cells in Their Native Environment. Anal Chem 2019; 91:6118-6126. [DOI: 10.1021/acs.analchem.9b00680] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- John F. Cahill
- Mass Spectrometry and Laser Spectroscopy Group, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6131, United States
| | - Julian Riba
- Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Georges-Köhler-Allee 103, 79110 Freiburg, Germany
- Cytena GmbH, Neuer Messplatz 3, 79108 Freiburg, Germany
| | - Vilmos Kertesz
- Mass Spectrometry and Laser Spectroscopy Group, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6131, United States
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23
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Abstract
Cancer stem cells (CSCs) are rare types of cells responsible for tumor development, relapse, and metastasis. However, current research in CSC biology is largely limited by the difficulty of obtaining sufficient CSCs. Single-cell analysis techniques are promising tools for CSC-related studies. Here, we used the Single-probe mass spectrometry (MS) technique to investigate the metabolic features of live colorectal CSCs at the single-cell level. Experimental data were analyzed using statistical analysis methods, including the t-test and partial least squares discriminant analysis. Our results indicate that the overall metabolic profiles of CSCs are distinct from non-stem cancer cells (NSCCs). Specifically, we demonstrated that tricarboxylic acid (TCA) cycle metabolites are more abundant in CSCs compared to NSCCs, indicating their major energy production pathways are different. Moreover, CSCs have relatively higher levels of unsaturated lipids. Inhibiting the activities of stearoyl-CoA desaturase-1 (SCD1), nuclear factor κB (NF-κB), and aldehyde dehydrogenases (ALDH1A1) in CSCs significantly reduced the abundances of unsaturated lipids and hindered the formation of spheroids, resulting in reduced stemness of CSCs. Our techniques and experimental protocols can be potentially used for metabolomic studies of other CSCs and rare types of cells and provide a new approach to discovering functional biomarkers as therapeutic targets.
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Affiliation(s)
- Mei Sun
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Zhibo Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
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24
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Standke SJ, Colby DH, Bensen RC, Burgett AWG, Yang Z. Mass Spectrometry Measurement of Single Suspended Cells Using a Combined Cell Manipulation System and a Single-Probe Device. Anal Chem 2019; 91:1738-1742. [PMID: 30644722 PMCID: PMC6640145 DOI: 10.1021/acs.analchem.8b05774] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Existing single cell mass spectrometry (SCMS) sampling platforms are largely designed to work only with immobilized cells and not the suspended cells isolated from patient samples. Here, we present a novel method that integrates a commercially available cell manipulation system commonly used for in vitro fertilization with the Single-probe SCMS sampling technology. The combined Single-probe SCMS/cell manipulating platform is capable of rapidly analyzing intracellular species in real time from a suspension leukemia cell line. A broad range of molecular species was detected, and species of interest were verified using tandem MS (MS/MS). Experimental results were analyzed utilizing statistical analyses such as principle component analysis (PCA) and t-tests. The developed SCMS/cell manipulation system is a versatile tool to provide rapid single cell analysis of broad types of patient cell samples.
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Affiliation(s)
- Shawna J. Standke
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Devon H. Colby
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Ryan C. Bensen
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Anthony W. G. Burgett
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Zhibo Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
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25
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Baker LA, Jagdale GS. On the intersection of electrochemistry and mass spectrometry. CURRENT OPINION IN ELECTROCHEMISTRY 2019; 13:140-146. [PMID: 33981910 PMCID: PMC8112614 DOI: 10.1016/j.coelec.2018.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The application of nanopipettes, developed first as a tool for electrochemistry and electrophysiology, as tools for mass spectrometry is considered. Recent examples of advances in electrospray ionization and sampling for mass spectrometry with nanopipettes is discussed. These examples show a scientific intersection that is ripe for further development.
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Affiliation(s)
- Lane A Baker
- Indiana University, Department of Chemistry, 800 E. Kirkwood Avenue, Bloomington, IN 47405, USA
| | - Gargi S Jagdale
- Indiana University, Department of Chemistry, 800 E. Kirkwood Avenue, Bloomington, IN 47405, USA
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26
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Surface-enhanced Raman spectroscopy based 3D spheroid culture for drug discovery studies. Talanta 2019; 191:390-399. [DOI: 10.1016/j.talanta.2018.08.087] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 08/27/2018] [Accepted: 08/31/2018] [Indexed: 12/26/2022]
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27
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Liu R, Pan N, Zhu Y, Yang Z. T-Probe: An Integrated Microscale Device for Online In Situ Single Cell Analysis and Metabolic Profiling Using Mass Spectrometry. Anal Chem 2018; 90:11078-11085. [PMID: 30119596 PMCID: PMC6583895 DOI: 10.1021/acs.analchem.8b02927] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The exploration of single cells reveals cell heterogeneity and biological principle of cellular metabolism. Although a number of mass spectrometry (MS) based single cell MS (SCMS) techniques have been dedicatedly developed with high efficiency and sensitivity, limitations still exist. In this work, we introduced a microscale multifunctional device, the T-probe, which integrates cellular contents extraction and immediate ionization, to implement online in situ SCMS analysis at ambient conditions with minimal sample preparation. With high sensitivity and reproducibility, the T-probe was employed for MS analysis of single HeLa cells under control and anticancer drug treatment conditions. Intracellular species and xenobiotic metabolites were detected, and changes of cellular metabolic profiles induced by drug treatment were measured. Combining SCMS experiments with statistical data analyses, including Orthogonal Partial Least Squares-Discriminant Analysis (OPLS-DA) and two-sample t-test, we provided biological insights into cellular metabolic response to drug treatment. Online MS/MS analysis was conducted at single cell level to identify species of interest, including endogenous metabolites and the drug compound. Using the T-probe SCMS technique combined with comprehensive data analyses, we provide an approach to understanding cellular metabolism and evaluate chemotherapies at the single cell level.
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Affiliation(s)
- Renmeng Liu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Ning Pan
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Yanlin Zhu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Zhibo Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
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28
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Tian X, Zhang G, Shao Y, Yang Z. Towards enhanced metabolomic data analysis of mass spectrometry image: Multivariate Curve Resolution and Machine Learning. Anal Chim Acta 2018; 1037:211-219. [PMID: 30292295 DOI: 10.1016/j.aca.2018.02.031] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 02/08/2018] [Accepted: 02/10/2018] [Indexed: 12/12/2022]
Abstract
Large amounts of data are generally produced from mass spectrometry imaging (MSI) experiments in obtaining the molecular and spatial information of biological samples. Traditionally, MS images are constructed using manually selected ions, and it is very challenging to comprehensively analyze MSI results due to their large data sizes and highly complex data structures. To overcome these barriers, it is obligatory to develop advanced data analysis approaches to handle the increasingly large MSI data. In the current study, we focused on the method development of using Multivariate Curve Resolution (MCR) and Machine Learning (ML) approaches. We aimed to effectively extract the essential information present in the large and complex MSI data and enhance the metabolomic data analysis of biological tissues. Multivariate Curve Resolution-Alternating Least Squares (MCR-ALS) algorithm was used to obtain major patterns of spatial distribution and grouped metabolites with the same spatial distribution patterns. In addition, both supervised and unsupervised ML methods were established to analyze the MSI data. In the supervised ML approach, Random Forest method was selected, and the model was trained using the selected datasets based on the distribution pattern obtained from MCR-ALS analyses. In the unsupervised ML approach, both DBSCAN (Density-based Spatial Clustering of Applications with Noise) and CLARA (Clustering Large Applications) were applied to cluster the MSI datasets. It is worth noting that similar patterns of spatial distribution were discovered through MSI data analysis using MCR-ALS, supervised ML, and unsupervised ML. Our protocols of data analysis can be applied to process the data acquired using many other types of MSI techniques, and to extract the overall features present in MSI results that are intractable using traditional data analysis approaches.
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Affiliation(s)
- Xiang Tian
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Genwei Zhang
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA.
| | - Zhibo Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA.
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29
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Sun M, Yang Z, Wawrik B. Metabolomic Fingerprints of Individual Algal Cells Using the Single-Probe Mass Spectrometry Technique. FRONTIERS IN PLANT SCIENCE 2018; 9:571. [PMID: 29760716 PMCID: PMC5936784 DOI: 10.3389/fpls.2018.00571] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 04/11/2018] [Indexed: 05/21/2023]
Abstract
Traditional approaches for the assessment of physiological responses of microbes in the environment rely on bulk filtration techniques that obscure differences among populations as well as among individual cells. Here, were report on the development on a novel micro-scale sampling device, referred to as the "Single-probe," which allows direct extraction of metabolites from living, individual phytoplankton cells for mass spectrometry (MS) analysis. The Single-probe is composed of dual-bore quartz tubing which is pulled using a laser pipette puller and fused to a silica capillary and a nano-ESI. For this study, we applied Single-probe MS technology to the marine dinoflagellate Scrippsiella trochoidea, assaying cells grown under different illumination levels and under nitrogen (N) limiting conditions as a proof of concept for the technology. In both experiments, significant differences in the cellular metabolome of individual cells could readily be identified, though the vast majority of detected metabolites could not be assigned to KEGG pathways. Using the same approach, significant changes in cellular lipid complements were observed, with individual lipids being both up- and down-regulated under light vs. dark conditions. Conversely, lipid content increased across the board under N limitation, consistent with an adjustment of Redfield stoichiometry to reflect higher C:N and C:P ratios. Overall, these data suggest that the Single-probe MS technique has the potential to allow for near in situ metabolomic analysis of individual phytoplankton cells, opening the door to targeted analyses that minimize cell manipulation and sampling artifacts, while preserving metabolic variability at the cellular level.
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Affiliation(s)
- Mei Sun
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, United States
| | - Zhibo Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, United States
| | - Boris Wawrik
- Department of Botany and Microbiology, University of Oklahoma, Norman, OK, United States
- *Correspondence: Boris Wawrik,
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