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Yao M, Vaithiyanathan M, Allbritton NL. Analytical Techniques for Single-Cell Biochemical Assays of Lipids. Annu Rev Biomed Eng 2023; 25:281-309. [PMID: 37068764 PMCID: PMC11032153 DOI: 10.1146/annurev-bioeng-110220-034007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
Lipids are essential cellular components forming membranes, serving as energy reserves, and acting as chemical messengers. Dysfunction in lipid metabolism and signaling is associated with a wide range of diseases including cancer and autoimmunity. Heterogeneity in cell behavior including lipid signaling is increasingly recognized as a driver of disease and drug resistance. This diversity in cellular responses as well as the roles of lipids in health and disease drive the need to quantify lipids within single cells. Single-cell lipid assays are challenging due to the small size of cells (∼1 pL) and the large numbers of lipid species present at concentrations spanning orders of magnitude. A growing number of methodologies enable assay of large numbers of lipid analytes, perform high-resolution spatial measurements, or permit highly sensitive lipid assays in single cells. Covered in this review are mass spectrometry, Raman imaging, and fluorescence-based assays including microscopy and microseparations.
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Affiliation(s)
- Ming Yao
- Department of Bioengineering, University of Washington, Seattle, Washington, USA; , ,
| | | | - Nancy L Allbritton
- Department of Bioengineering, University of Washington, Seattle, Washington, USA; , ,
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Gallion LA, Wang Y, Massaro A, Yao M, Petersen BV, Zhang Q, Huang W, Carr AJ, Zhang Q, Allbritton NL. "Fix and Click" for Assay of Sphingolipid Signaling in Single Primary Human Intestinal Epithelial Cells. Anal Chem 2022; 94:1594-1600. [PMID: 35020354 PMCID: PMC8931668 DOI: 10.1021/acs.analchem.1c03503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Capillary electrophoresis with fluorescence detection (CE-F) is a powerful method to measure enzyme activation in single cells. However, cellular enzymatic assays used in CE-F routinely utilize reporter substrates that possess a bulky fluorophore that may impact enzyme kinetics. To address these challenges, we describe a "fix and click" method utilizing an alkyne-terminated enzyme activation reporter, aldehyde-based fixation, and a click chemistry reaction to attach a fluorophore prior to analysis by single-cell CE-F. The "fix and click" strategy was utilized to investigate sphingolipid signaling in both immortalized cell lines and primary human colonic epithelial cells. When the sphingosine alkyne reporter was loaded into cells, this reporter was metabolized to ceramide (31.6 ± 3.3% peak area) without the production of sphingosine-1-phosphate. In contrast, when the reporter sphingosine fluorescein was introduced into cells, sphingosine fluorescein was converted to sphingosine-1-phosphate and downstream products (32.8 ± 5.7% peak area) without the formation of ceramide. Sphingolipid metabolism was measured in single cells from both differentiated and stem/proliferative human colonic epithelium using "fix and click" paired with CE-F to highlight the diversity of sphingosine metabolism in single cells from primary human colonic epithelium. This novel method will find widespread utility for the performance of single-cell enzyme assays by virtue of its ability to temporally and spatially separate cellular reactions with alkyne-terminated reporters, followed by the assay of enzyme activation at a later time and place.
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Affiliation(s)
- Luke A. Gallion
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina, 27514, United States of America,Department of Bioengineering, University of Washington, Seattle, Washington, 98105, United States of America
| | - Yuli Wang
- Department of Bioengineering, University of Washington, Seattle, Washington, 98105, United States of America
| | - Angelo Massaro
- Department of Bioengineering, University of Washington, Seattle, Washington, 98105, United States of America
| | - Ming Yao
- Department of Bioengineering, University of Washington, Seattle, Washington, 98105, United States of America
| | - Brae V. Petersen
- Department of Bioengineering, University of Washington, Seattle, Washington, 98105, United States of America
| | - Quanzheng Zhang
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, Chapel Hill, North Carolina, 27514, United States of America
| | - Weigang Huang
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, Chapel Hill, North Carolina, 27514, United States of America
| | - Adam J. Carr
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, Chapel Hill, North Carolina, 27514, United States of America
| | - Qisheng Zhang
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, Chapel Hill, North Carolina, 27514, United States of America
| | - Nancy L. Allbritton
- Department of Bioengineering, University of Washington, Seattle, Washington, 98105, United States of America,Correspondence: Nancy L. Allbritton, Department of Bioengineering, University of Washington, Seattle, Washington, 98105, United States of America;
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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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Gallion LA, Anttila MM, Abraham DH, Proctor A, Allbritton NL. Preserving Single Cells in Space and Time for Analytical Assays. Trends Analyt Chem 2020; 122:115723. [PMID: 32153309 PMCID: PMC7061724 DOI: 10.1016/j.trac.2019.115723] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Analytical assays performed within clinical laboratories influence roughly 70% of all medical decisions by facilitating disease detection, diagnosis, and management. Both in clinical and academic research laboratories, single-cell assays permit measurement of cell diversity and identification of rare cells, both of which are important in the understanding of disease pathogenesis. For clinically utility, the single-cell assays must be compatible with the clinical workflow steps of sample collection, sample transportation, pre-analysis processing, and single-cell assay; therefore, it is paramount to preserve cells in a state that resembles that in vivo rather than measuring signaling behaviors initiated in response to stressors such as sample collection and processing. To address these challenges, novel cell fixation (and more broadly, cell preservation) techniques incorporate programmable fixation times, reversible bond formation and cleavage, chemoselective reactions, and improved analyte recovery. These technologies will further the development of individualized, precision therapies for patients to yield improved clinical outcomes.
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Affiliation(s)
- Luke A. Gallion
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Matthew M. Anttila
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - David H. Abraham
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Angela Proctor
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Nancy L. Allbritton
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
- Joint Department of Biomedical Engineering, University of North Carolina, Chapel Hill, NC 27599, USA and North Carolina State University, Raleigh, NC 27695, USA
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Abraham DH, Anttila MM, Gallion LA, Petersen BV, Proctor A, Allbritton NL. Design of an automated capillary electrophoresis platform for single-cell analysis. Methods Enzymol 2019; 628:191-221. [PMID: 31668230 DOI: 10.1016/bs.mie.2019.06.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Single-cell analysis of cellular contents by highly sensitive analytical instruments is known as chemical cytometry. A chemical cytometer typically samples one cell at a time, quantifies the cellular contents of interest, and then processes and reports that data. Automation adds the potential to perform this entire sequence of events with minimal intervention, increasing throughput and repeatability. In this chapter, we discuss the design considerations for an automated capillary electrophoresis-based instrument for assay of enzymatic activity within single cells. We describe the key requirements of the microscope base and capillary electrophoresis platforms. We also provide detailed protocols and schematic designs of our cell isolation, lysis, sampling, and detection strategies. Additionally, we describe our signal processing and instrument automation workflows. The described automated system has demonstrated single-cell throughput at rates above 100cells/h and analyte limits of detection as low as 10-20mol.
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Affiliation(s)
- David H Abraham
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, United States
| | - Matthew M Anttila
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, United States
| | - Luke A Gallion
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, United States
| | - Brae V Petersen
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, United States
| | - Angela Proctor
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, United States
| | - Nancy L Allbritton
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, United States; Joint Department of Biomedical Engineering, University of North Carolina, Chapel and North Carolina State University, Raleigh, NC, USA.
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Proctor A, Allbritton NL. "Fix and assay": separating in-cellulo sphingolipid reactions from analytical assay in time and space using an aldehyde-based fixative. Analyst 2019; 144:961-971. [PMID: 30207332 DOI: 10.1039/c8an01353e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Chemical cytometry using capillary electrophoresis (CE) is a powerful tool for measuring single-cell enzyme activity. However, these measurements are often confounding as dynamic processes within cells rapidly change depending on environment, meaning that cell handling, transport, and storage can affect signaling pathways and alter results. To meet these challenges, we describe a method utilizing aldehyde fixation to simultaneously terminate cellular reactions across a population, freezing reaction results in time prior to analytical analysis. Fluorescent sphingosine was loaded into cells of different lineages (leukemia and lymphoma cell lines and primary leukemia cells) and allowed to react before fixing. The remaining sphingosine and any products formed were then quantified with chemical cytometry utilizing CE. When cells were loaded with sphingosine followed by glyoxal fixation and immediate analysis, 55 ± 5% of lipid was recoverable compared to an unfixed control. Storage of fixed cells for 24 h showed no statistical differences in total amount of recoverable sphingolipid compared to samples analyzed immediately after fixation-though there was a difference in recovery of low-abundance products. Sphingosine kinase activity decreased in response to inhibitor treatment compared to treatment with a DMSO vehicle (21 ± 3% product formed in inhibitor-treated cells vs. 57 ± 2% in control cells), which was mirrored in single-cell measurements. This "fix and assay" strategy enables measurement of sphingosine kinase activity in single cells followed by subsequent analytical assay separated in space and time from reaction initiation, enabling greater temporal control over intracellular reactions and improving future compatibility with clinical workflow.
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Affiliation(s)
- Angela Proctor
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, USA
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DeLaney K, Sauer CS, Vu NQ, Li L. Recent Advances and New Perspectives in Capillary Electrophoresis-Mass Spectrometry for Single Cell "Omics". Molecules 2018; 24:molecules24010042. [PMID: 30583525 PMCID: PMC6337428 DOI: 10.3390/molecules24010042] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 12/20/2018] [Accepted: 12/21/2018] [Indexed: 12/31/2022] Open
Abstract
Accurate clinical therapeutics rely on understanding the metabolic responses of individual cells. However, the high level of heterogeneity between cells means that simply sampling from large populations of cells is not necessarily a reliable approximation of an individual cell's response. As a result, there have been numerous developments in the field of single-cell analysis to address this lack of knowledge. Many of these developments have focused on the coupling of capillary electrophoresis (CE), a separation technique with low sample consumption and high resolving power, and mass spectrometry (MS), a sensitive detection method for interrogating all ions in a sample in a single analysis. In recent years, there have been many notable advancements at each step of the single-cell CE-MS analysis workflow, including sampling, manipulation, separation, and MS analysis. In each of these areas, the combined improvements in analytical instrumentation and achievements of numerous researchers have served to drive the field forward to new frontiers. Consequently, notable biological discoveries have been made possible by the implementation of these methods. Although there is still room in the field for numerous further advances, researchers have effectively minimized various limitations in detection of analytes, and it is expected that there will be many more developments in the near future.
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Affiliation(s)
- Kellen DeLaney
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA.
| | - Christopher S Sauer
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA.
| | - Nhu Q Vu
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA.
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA.
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA.
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Vickerman BM, Anttila MM, Petersen BV, Allbritton NL, Lawrence DS. Design and Application of Sensors for Chemical Cytometry. ACS Chem Biol 2018; 13:1741-1751. [PMID: 29376326 DOI: 10.1021/acschembio.7b01009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The bulk cell population response to a stimulus, be it a growth factor or a cytotoxic agent, neglects the cell-to-cell variability that can serve as a friend or as a foe in human biology. Biochemical variations among closely related cells furnish the basis for the adaptability of the immune system but also act as the root cause of resistance to chemotherapy by tumors. Consequently, the ability to probe for the presence of key biochemical variables at the single-cell level is now recognized to be of significant biological and biomedical impact. Chemical cytometry has emerged as an ultrasensitive single-cell platform with the flexibility to measure an array of cellular components, ranging from metabolite concentrations to enzyme activities. We briefly review the various chemical cytometry strategies, including recent advances in reporter design, probe and metabolite separation, and detection instrumentation. We also describe strategies for improving intracellular delivery, biochemical specificity, metabolic stability, and detection sensitivity of probes. Recent applications of these strategies to small molecules, lipids, proteins, and other analytes are discussed. Finally, we assess the current scope and limitations of chemical cytometry and discuss areas for future development to meet the needs of single-cell research.
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Affiliation(s)
- Brianna M. Vickerman
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Matthew M. Anttila
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Brae V. Petersen
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Nancy L. Allbritton
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Joint Department of Biomedical Engineering, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, and North Carolina State University,
Raleigh, North Carolina 27695, United States
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - David S. Lawrence
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Division of Chemical Biology and Medicinal Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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