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Allcroft TJ, Duong JT, Skardal PS, Kovarik ML. Microfluidic single-cell measurements of oxidative stress as a function of cell cycle position. Anal Bioanal Chem 2023; 415:6481-6490. [PMID: 37682313 DOI: 10.1007/s00216-023-04924-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: 05/11/2023] [Revised: 07/24/2023] [Accepted: 08/28/2023] [Indexed: 09/09/2023]
Abstract
Single-cell measurements routinely demonstrate high levels of variation between cells, but fewer studies provide insight into the analytical and biological sources of this variation. This is particularly true of chemical cytometry, in which individual cells are lysed and their contents separated, compared to more established single-cell measurements of the genome and transcriptome. To characterize population-level variation and its sources, we analyzed oxidative stress levels in 1278 individual Dictyostelium discoideum cells as a function of exogenous stress level and cell cycle position. Cells were exposed to varying levels of oxidative stress via singlet oxygen generation using the photosensitizer Rose Bengal. Single-cell data reproduced the dose-response observed in ensemble measurements by CE-LIF, superimposed with high levels of heterogeneity. Through experiments and data analysis, we explored possible biological sources of this heterogeneity. No trend was observed between population variation and oxidative stress level, but cell cycle position was a major contributor to heterogeneity in oxidative stress. Cells synchronized to the same stage of cell division were less heterogeneous than unsynchronized cells (RSD of 37-51% vs 93%), and mitotic cells had higher levels of reactive oxygen species than interphase cells. While past research has proposed changes in cell size during the cell cycle as a source of biological noise, the measurements presented here use an internal standard to normalize for effects of cell volume, suggesting a more complex contribution of cell cycle to heterogeneity of oxidative stress.
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2
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Rodogiannis K, Duong JT, Kovarik ML. Microfluidic single-cell analysis of oxidative stress in Dictyostelium discoideum. Analyst 2019; 143:3643-3650. [PMID: 29969508 DOI: 10.1039/c8an00752g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Microfluidic chemical cytometry is a powerful technique for examining chemical contents of individual cells, but applications have focused on cells from multicellular organisms, especially mammals. We demonstrate the first use of microfluidic chemical cytometry to examine a unicellular organism, the social amoeba Dictyostelium discoideum. We used the reactive oxygen species indicator dichlorodihydrofluorescein diacetate to report on oxidative stress and controlled for variations in indicator loading and retention using carboxyfluorescein diacetate as an internal standard. After optimizing indicator concentration, we investigated the effect of peroxide treatment through single-cell measurements of 353 individual cells. The peak area ratio of dichlorofluorescein to carboxyfluorescein increased from 1.69 ± 0.89 for untreated cells to 5.19 ± 2.72 for cells treated with 40 mM hydrogen peroxide. Interestingly, the variance of the data also increased with oxidative stress. While preliminary, these results are consistent with the hypothesis that heterogeneous stress responses in unicellular organisms may be adaptive.
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Affiliation(s)
- Kathy Rodogiannis
- Department of Chemistry, Trinity College, 300 Summit St., Hartford, CT 06106, USA.
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3
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Chadha R, Kalminskii G, Tierney AJ, Knopf JD, Lazo de la Vega L, McElrath B, Kovarik ML. Effect of Loading Method on a Peptide Substrate Reporter in Intact Cells. Anal Chem 2018; 90:11344-11350. [PMID: 30175919 DOI: 10.1021/acs.analchem.8b02111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Studies of live cells often require loading of exogenous molecules through the cell membrane; however, effects of loading method on experimental results are poorly understood. Therefore, in this work, we compared three methods for loading a fluorescently labeled peptide into cells of the model organism Dictyostelium discoideum. We optimized loading by pinocytosis, electroporation, and myristoylation to maximize cell viability and characterized loading efficiency, localization, and uniformity. We also determined how the loading method affected measurements of enzyme activity on the peptide substrate reporter using capillary electrophoresis. Loading method had a strong effect on the stability and phosphorylation of the peptide. The half-life of the intact peptide in cells was 19 ± 2, 53 ± 15, and 12 ± 1 min, for pinocytosis, electroporation, and myristoylation, respectively. The peptide was phosphorylated only in cells loaded by electroporation. Fluorescence microscopy suggested that the differences between methods were likely due to differences in peptide localization.
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Affiliation(s)
- Rahuljeet Chadha
- Department of Chemistry , Trinity College , 300 Summit Street , Hartford , Connecticut 06106 , United States
| | - Grigorii Kalminskii
- Department of Chemistry , Trinity College , 300 Summit Street , Hartford , Connecticut 06106 , United States
| | - Allison J Tierney
- Department of Chemistry , Trinity College , 300 Summit Street , Hartford , Connecticut 06106 , United States
| | - Joshua D Knopf
- Department of Chemistry , Trinity College , 300 Summit Street , Hartford , Connecticut 06106 , United States
| | - Lorena Lazo de la Vega
- Department of Chemistry , Trinity College , 300 Summit Street , Hartford , Connecticut 06106 , United States
| | - Berjana McElrath
- Department of Chemistry , Trinity College , 300 Summit Street , Hartford , Connecticut 06106 , United States
| | - Michelle L Kovarik
- Department of Chemistry , Trinity College , 300 Summit Street , Hartford , Connecticut 06106 , United States
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4
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Proctor A, Sims CE, Allbritton NL. Chemical fixation to arrest phospholipid signaling for chemical cytometry. J Chromatogr A 2017; 1523:97-106. [PMID: 28528682 DOI: 10.1016/j.chroma.2017.05.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 04/28/2017] [Accepted: 05/07/2017] [Indexed: 12/18/2022]
Abstract
Chemical cytometry is a powerful tool for measuring biological processes such as enzymatic signaling at the single cell level. Among these technologies, single-cell capillary zone electrophoresis (CZE) has emerged as a powerful tool to assay a wide range of cellular metabolites. However, analysis of dynamic processes within cells remains challenging as signaling pathways are rapidly altered in response to changes in the cellular environment, including cell manipulation and storage. To address these limitations, we describe a method for chemical fixation of cells to stop the cellular reactions to preserve the integrity of key signaling molecules or reporters within the cell and to enable the cell to act as a storage reservoir for the reporter and its metabolites prior to assay by single-cell CZE. Fluorescent phosphatidylinositol 4,5-bisphosphate reporters were loaded into cells and the cells were chemically fixed and stored prior to analysis. The reporter and its metabolites were electrophoretically separated by single-cell CZE. Chemical fixation parameters such as fixative, fixation time, storage solution, storage duration, and extraction solution were optimized. When cells were loaded with a fluorescent C6- or C16-PIP2 followed by glutaraldehyde fixation and immediate analysis, 24±2% and 139±12% of the lipid was recoverable, respectively, when compared to an unfixed control. Storage of the cells for 24h yielded recoverable lipid of 61±3% (C6-PIP2) and 55±5% (C16-PIP2) when compared to cells analyzed immediately after fixation. The metabolites observed with and without fixation were identical. Measurement of phospholipase C activity in single leukemic cells in response to an agonist demonstrated the capability of chemical fixation coupled to single-cell CZE to yield an accurate snapshot of cellular reactions with the probe. This methodology enables cell assay with the reporter to be separated in space and time from reporter metabolite quantification while preserving assay integrity.
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Affiliation(s)
- Angela Proctor
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, United States.
| | - Christopher E Sims
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, United States.
| | - Nancy L Allbritton
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, United States; Joint Department of Biomedical Engineering, University of North Carolina, Chapel Hill, NC 27599, United States and North Carolina State University, Raleigh, NC 27695, United States.
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5
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Patabadige DEW, Sadeghi J, Kalubowilage M, Bossmann SH, Culbertson AH, Latifi H, Culbertson CT. Integrating Optical Fiber Bridges in Microfluidic Devices to Create Multiple Excitation/Detection Points for Single Cell Analysis. Anal Chem 2016; 88:9920-9925. [DOI: 10.1021/acs.analchem.6b03133] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Damith E. W. Patabadige
- Department
of Chemistry, Kansas State University, 1212 Mid-Campus Drive, Manhattan, Kansas 66506, United States
| | - Jalal Sadeghi
- Department
of Chemistry, Kansas State University, 1212 Mid-Campus Drive, Manhattan, Kansas 66506, United States
- Laser
and Plasma Research Institute, Shahid Beheshti University, Evin, Tehran, 1983963113, Iran
| | - Madumali Kalubowilage
- Department
of Chemistry, Kansas State University, 1212 Mid-Campus Drive, Manhattan, Kansas 66506, United States
| | - Stefan H. Bossmann
- Department
of Chemistry, Kansas State University, 1212 Mid-Campus Drive, Manhattan, Kansas 66506, United States
| | - Anne H. Culbertson
- Department
of Chemistry, Kansas State University, 1212 Mid-Campus Drive, Manhattan, Kansas 66506, United States
| | - Hamid Latifi
- Laser
and Plasma Research Institute, Shahid Beheshti University, Evin, Tehran, 1983963113, Iran
| | - Christopher T. Culbertson
- Department
of Chemistry, Kansas State University, 1212 Mid-Campus Drive, Manhattan, Kansas 66506, United States
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Patabadige DEW, Mickleburgh T, Ferris L, Brummer G, Culbertson AH, Culbertson CT. High‐throughput microfluidic device for single cell analysis using multiple integrated soft lithographic pumps. Electrophoresis 2016; 37:1337-44. [DOI: 10.1002/elps.201500557] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 02/08/2016] [Accepted: 02/09/2016] [Indexed: 01/07/2023]
Affiliation(s)
| | - Tom Mickleburgh
- Department of Chemistry Kansas State University Manhattan KS USA
| | - Lorin Ferris
- Department of Chemistry Kansas State University Manhattan KS USA
| | - Gage Brummer
- Department of Chemistry Kansas State University Manhattan KS USA
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7
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Turner AH, Lebhar MS, Proctor A, Wang Q, Lawrence DS, Allbritton NL. Rational Design of a Dephosphorylation-Resistant Reporter Enables Single-Cell Measurement of Tyrosine Kinase Activity. ACS Chem Biol 2016; 11:355-62. [PMID: 26587880 DOI: 10.1021/acschembio.5b00667] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Although peptide-based reporters of protein tyrosine kinase (PTK) activity have been used to study PTK enzymology in vitro, the application of these reporters to intracellular conditions is compromised by their dephosphorylation, preventing PTK activity measurements. Nonproteinogenic amino acids may be utilized to rationally design selective peptidic ligands by accessing greater chemical and structural diversity than is available using the native amino acids. We describe a peptidic reporter that, upon phosphorylation by the epidermal growth factor receptor (EGFR), is resistant to dephosphorylation both in vitro and in cellulo. The reporter contains a conformationally constrained phosphorylatable moiety (7-(S)-hydroxy-1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid) in the place of L-tyrosine and is efficiently phosphorylated in A431 epidermoid carcinoma cells. Dephosphorylation of the reporter occurs 3 orders of magnitude more slowly compared with that of the conventional tyrosine-containing reporter.
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Affiliation(s)
| | - Michael S. Lebhar
- 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
| | | | | | | | - Nancy L. Allbritton
- 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
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8
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Mainz ER, Dobes NC, Allbritton NL. Pronase E-Based Generation of Fluorescent Peptide Fragments: Tracking Intracellular Peptide Fate in Single Cells. Anal Chem 2015; 87:7987-95. [PMID: 26171808 PMCID: PMC6026012 DOI: 10.1021/acs.analchem.5b01929] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The ability to track intracellular peptide proteolysis at the single cell level is of growing interest, particularly as short peptide sequences continue to play important roles as biosensors, therapeutics, and endogenous participants in antigen processing and intracellular signaling. We describe a rapid and inexpensive methodology to generate fluorescent peptide fragments from a parent sequence with diverse chemical properties, including aliphatic, nonpolar, basic, acidic, and non-native amino acids. Four peptide sequences with existing biochemical applications were fragmented using incubation with Pronase E and/or formic acid, and in each case a complete set of fluorescent fragments was generated for use as proteolysis standards in chemical cytometry. Fragment formation and identity was monitored with capillary electrophoresis with laser-induced fluorescence detection (CE-LIF) and matrix assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-MS) to confirm the presence of all sequences and yield fragmentation profiles across Pronase E concentrations which can readily be used by others. As a pilot study, Pronase E-generated standards from an Abl kinase sensor and an ovalbumin antigenic peptide were then employed to identify proteolysis products arising from the metabolism of these sequences in single cells. The Abl kinase sensor fragmented at 4.2 ± 4.8 zmol μM(-1) s(-1) and the majority of cells possessed similar fragment identities. In contrast, an ovalbumin epitope peptide was degraded at 8.9 ± 0.1 zmol μM(-1) s(-1), but with differential fragment formation between individual cells. Overall, Pronase E-generated peptide standards were a rapid and efficient method to identify proteolysis products from cells.
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Affiliation(s)
- Emilie R. Mainz
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Nicholas C. Dobes
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Nancy L. Allbritton
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- Department of Biomedical Engineering, University of North Carolina, Chapel Hill, North Carolina 27599, USA and North Carolina State University, Raleigh, North Carolina 27695, US
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9
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Shehaj L, Lazo de la Vega L, Kovarik ML. Microfluidic Chemical Cytometry for Enzyme Assays of Single Cells. Methods Mol Biol 2015; 1346:221-38. [PMID: 26542725 DOI: 10.1007/978-1-4939-2987-0_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Cellular heterogeneity occurs, and should be probed, at multiple levels of cellular structure and physiology from the genome to enzyme activity. In particular, single-cell measures of protein levels are complemented by single-cell measurements of the activity of these proteins. Microfluidic assays of enzyme activity at the single-cell level combine moderate to high throughput with low dead volumes and the potential for automation. Herein, we describe the steps required to fabricate and operate a microfluidic device for chemical cytometry of fluorescent or fluorogenic reporters of enzyme activity in individual cells.
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Affiliation(s)
- Livia Shehaj
- Department of Chemistry, Trinity College, 300 Summit Street, Hartford, CT, 06106, USA
| | | | - Michelle L Kovarik
- Department of Chemistry, Trinity College, 300 Summit Street, Hartford, CT, 06106, USA.
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10
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Present state of microchip electrophoresis: state of the art and routine applications. J Chromatogr A 2014; 1382:66-85. [PMID: 25529267 DOI: 10.1016/j.chroma.2014.11.034] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 11/07/2014] [Accepted: 11/12/2014] [Indexed: 12/20/2022]
Abstract
Microchip electrophoresis (MCE) was one of the earliest applications of the micro-total analysis system (μ-TAS) concept, whose aim is to reduce analysis time and reagent and sample consumption while increasing throughput and portability by miniaturizing analytical laboratory procedures onto a microfluidic chip. More than two decades on, electrophoresis remains the most common separation technique used in microfluidic applications. MCE-based instruments have had some commercial success and have found application in many disciplines. This review will consider the present state of MCE including recent advances in technology and both novel and routine applications in the laboratory. We will also attempt to assess the impact of MCE in the scientific community and its prospects for the future.
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