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Bury A, Pyle A, Vincent AE, Actis P, Hudson G. Nanobiopsy investigation of the subcellular mtDNA heteroplasmy in human tissues. Sci Rep 2024; 14:13789. [PMID: 38877095 PMCID: PMC11178779 DOI: 10.1038/s41598-024-64455-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 06/10/2024] [Indexed: 06/16/2024] Open
Abstract
Mitochondrial function is critical to continued cellular vitality and is an important contributor to a growing number of human diseases. Mitochondrial dysfunction is typically heterogeneous, mediated through the clonal expansion of mitochondrial DNA (mtDNA) variants in a subset of cells in a given tissue. To date, our understanding of the dynamics of clonal expansion of mtDNA variants has been technically limited to the single cell-level. Here, we report the use of nanobiopsy for subcellular sampling from human tissues, combined with next-generation sequencing to assess subcellular mtDNA mutation load in human tissue from mitochondrial disease patients. The ability to map mitochondrial mutation loads within individual cells of diseased tissue samples will further our understanding of mitochondrial genetic diseases.
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Affiliation(s)
- Alexander Bury
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
- NIHR Biomedical Research Centre, Faculty of Medical Science, Newcastle University, Newcastle, UK
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, UK
- Bragg Centre for Materials Research, Leeds, UK
| | - Angela Pyle
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Amy E Vincent
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK.
- NIHR Biomedical Research Centre, Faculty of Medical Science, Newcastle University, Newcastle, UK.
| | - Paolo Actis
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, UK.
- Bragg Centre for Materials Research, Leeds, UK.
| | - Gavin Hudson
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK.
- NIHR Biomedical Research Centre, Faculty of Medical Science, Newcastle University, Newcastle, UK.
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2
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Bury AG, Pyle A, Marcuccio F, Turnbull DM, Vincent AE, Hudson G, Actis P. A subcellular cookie cutter for spatial genomics in human tissue. Anal Bioanal Chem 2022; 414:5483-5492. [PMID: 35233697 PMCID: PMC9242960 DOI: 10.1007/s00216-022-03944-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/23/2022] [Accepted: 01/31/2022] [Indexed: 11/30/2022]
Abstract
Intracellular heterogeneity contributes significantly to cellular physiology and, in a number of debilitating diseases, cellular pathophysiology. This is greatly influenced by distinct organelle populations and to understand the aetiology of disease, it is important to have tools able to isolate and differentially analyse organelles from precise location within tissues. Here, we report the development of a subcellular biopsy technology that facilitates the isolation of organelles, such as mitochondria, from human tissue. We compared the subcellular biopsy technology to laser capture microdissection (LCM) that is the state-of-the-art technique for the isolation of cells from their surrounding tissues. We demonstrate an operational limit of >20 µm for LCM and then, for the first time in human tissue, show that subcellular biopsy can be used to isolate mitochondria beyond this limit.
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Affiliation(s)
- Alexander G Bury
- Wellcome Centre for Mitochondrial Research, Medical School, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK.,Biosciences Institute, Medical School, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK.,Bragg Centre for Materials Research, University of Leeds, Leeds, LS2 9JT, UK.,School of Electronic and Electrical Engineering, University of Leeds, Leeds, LS2 9JT, UK
| | - Angela Pyle
- Wellcome Centre for Mitochondrial Research, Medical School, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK.,Translational and Clinical Research Institute, Medical School, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Fabio Marcuccio
- Bragg Centre for Materials Research, University of Leeds, Leeds, LS2 9JT, UK.,School of Electronic and Electrical Engineering, University of Leeds, Leeds, LS2 9JT, UK
| | - Doug M Turnbull
- Wellcome Centre for Mitochondrial Research, Medical School, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK.,Translational and Clinical Research Institute, Medical School, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Amy E Vincent
- Wellcome Centre for Mitochondrial Research, Medical School, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK. .,Translational and Clinical Research Institute, Medical School, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK.
| | - Gavin Hudson
- Wellcome Centre for Mitochondrial Research, Medical School, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK. .,Biosciences Institute, Medical School, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK.
| | - Paolo Actis
- Bragg Centre for Materials Research, University of Leeds, Leeds, LS2 9JT, UK. .,School of Electronic and Electrical Engineering, University of Leeds, Leeds, LS2 9JT, UK.
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3
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Qin S, Zhang Y, Tian Y, Xu F, Zhang P. Subcellular metabolomics: Isolation, measurement, and applications. J Pharm Biomed Anal 2021; 210:114557. [PMID: 34979492 DOI: 10.1016/j.jpba.2021.114557] [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: 06/30/2021] [Revised: 12/22/2021] [Accepted: 12/26/2021] [Indexed: 11/26/2022]
Abstract
Metabolomics, a technique that profiles global small molecules in biological samples, has been a pivotal tool for disease diagnosis and mechanism research. The sample type in metabolomics covers a wide range, including a variety of body fluids, tissues, and cells. However, little attention was paid to the smaller, relatively independent partition systems in cells, namely the organelles. The organelles are specific compartments/places where diverse metabolic activities are happening in an orderly manner. Metabolic disorders of organelles were found to occur in various pathological conditions such as inherited metabolic diseases, diabetes, cancer, and neurodegenerative diseases. However, at the cellular level, the metabolic outcomes of organelles and cytoplasm are superimposed interactively, making it difficult to describe the changes in subcellular compartments. Therefore, characterizing the metabolic pool in the compartmentalized system is of great significance for understanding the role of organelles in physiological functions and diseases. So far, there are very few research articles or reviews related to subcellular metabolomics. In this review, subcellular fractionation and metabolite analysis methods, as well as the application of subcellular metabolomics in the physiological and pathological studies are systematically reviewed, as a practical reference to promote the continued advancement in subcellular metabolomics.
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Affiliation(s)
- Siyuan Qin
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing 210009, PR China
| | - Yuxin Zhang
- Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, PR China
| | - Yuan Tian
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing 210009, PR China
| | - Fengguo Xu
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing 210009, PR China.
| | - Pei Zhang
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing 210009, PR China.
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4
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Siedlik MJ, Yang Z, Kadam PS, Eberwine J, Issadore D. Micro- and Nano-Devices for Studying Subcellular Biology. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2005793. [PMID: 33345457 PMCID: PMC8258219 DOI: 10.1002/smll.202005793] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/20/2020] [Indexed: 05/27/2023]
Abstract
Cells are complex machines whose behaviors arise from their internal collection of dynamically interacting organelles, supramolecular complexes, and cytoplasmic chemicals. The current understanding of the nature by which subcellular biology produces cell-level behaviors is limited by the technological hurdle of measuring the large number (>103 ) of small-sized (<1 μm) heterogeneous organelles and subcellular structures found within each cell. In this review, the emergence of a suite of micro- and nano-technologies for studying intracellular biology on the scale of organelles is described. Devices that use microfluidic and microelectronic components for 1) extracting and isolating subcellular structures from cells and lysate; 2) analyzing the physiology of individual organelles; and 3) recreating subcellular assembly and functions in vitro, are described. The authors envision that the continued development of single organelle technologies and analyses will serve as a foundation for organelle systems biology and will allow new insight into fundamental and clinically relevant biological questions.
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Affiliation(s)
- Michael J Siedlik
- Department of Bioengineering, 335 Skirkanich Hall, University of Pennsylvania, 210 South 33rd Street, Philadelphia, PA, 19104, USA
| | - Zijian Yang
- Department of Mechanical Engineering and Applied Science, 335 Skirkanich Hall, University of Pennsylvania, 210 South 33rd Street, Philadelphia, PA, 19104, USA
| | - Parnika S Kadam
- Systems Pharmacology and Translational Therapeutics, 38 John Morgan Building, University of Pennsylvania, 3620 Hamilton Walk, Philadelphia, PA, 19104, USA
| | - James Eberwine
- Systems Pharmacology and Translational Therapeutics, 38 John Morgan Building, University of Pennsylvania, 3620 Hamilton Walk, Philadelphia, PA, 19104, USA
| | - David Issadore
- Department of Bioengineering, 335 Skirkanich Hall, University of Pennsylvania, 210 South 33rd Street, Philadelphia, PA, 19104, USA
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5
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Friedrich R, Block S, Alizadehheidari M, Heider S, Fritzsche J, Esbjörner EK, Westerlund F, Bally M. A nano flow cytometer for single lipid vesicle analysis. LAB ON A CHIP 2017; 17:830-841. [PMID: 28128381 DOI: 10.1039/c6lc01302c] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We present a nanofluidic device for fluorescence-based detection and characterization of small lipid vesicles on a single particle basis. The device works like a nano flow cytometer where individual vesicles are visualized by fluorescence microscopy while passing through parallel nanochannels in a pressure-driven flow. An experiment requires less than 20 μl sample volume to quantify both the vesicle content and the fluorescence signals emitted by individual vesicles. We show that the device can be used to accurately count the number of fluorescent synthetic lipid vesicles down to a vesicle concentration of 170 fM. We also show that the size-distribution of the vesicles can be resolved from their fluorescence intensity distribution after calibration. We demonstrate the applicability of the assay in two different examples. In the first, we use the nanofluidic device to determine the particle concentration in a sample containing cell-derived extracellular vesicles labelled with a lipophilic dye. In the second, we demonstrate that dual-color detection can be used to probe peptide binding to synthetic lipid vesicles; we identify a positive membrane-curvature sensing behavior of an arginine enriched version of the Antennapedia homeodomain peptide penetratin. Altogether, these results illustrate the potential of this nanofluidic-based methodology for characterization and quantification of small biological vesicles and their interactors without ensemble averaging. The device is therefore likely to find use as a quantitative analytical tool in a variety of fields ranging from diagnostics to fundamental biology research. Moreover, our results have potential to facilitate further development of automated lab-on-a-chip devices for vesicle analysis.
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Affiliation(s)
- Remo Friedrich
- Department of Physics, Chalmers University of Technology, Gothenburg, Sweden.
| | - Stephan Block
- Department of Physics, Chalmers University of Technology, Gothenburg, Sweden.
| | | | - Susanne Heider
- Department of Physics, Chalmers University of Technology, Gothenburg, Sweden. and Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
| | - Joachim Fritzsche
- Department of Physics, Chalmers University of Technology, Gothenburg, Sweden.
| | - Elin K Esbjörner
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
| | - Marta Bally
- Department of Physics, Chalmers University of Technology, Gothenburg, Sweden. and Institut Curie, Centre de Recherche, CNRS, UMR168, Physico-Chimie Curie, Paris, France
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6
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Popkov VA, Plotnikov EY, Lyamzaev KG, Silachev DN, Zorova LD, Pevzner IB, Jankauskas SS, Zorov SD, Babenko VA, Zorov DB. Mitodiversity. BIOCHEMISTRY (MOSCOW) 2016; 80:532-41. [PMID: 26071770 DOI: 10.1134/s000629791505003x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Here, in addition to the previously coined term "mitobiota", we introduce the term "mitodiversity" for various phenotypic and genetic heterogeneities of mitochondria within the same cell or organ. Based on data on the mitochondrial transmembrane potential determined both in situ and in vitro under normal conditions and after organ ischemia/reperfusion, such heterogeneity is most evident under pathologic conditions. Herein, a part of the mitochondrial population with transmembrane potential typical of the normal state is sustained even under a pathological condition that, perhaps, underlies the development of ways of reversing pathology back to the normal state. The membrane potentials of isolated mitochondria were shown to directly correlate with the magnitude of side-scattered light depicting internal structure of mitochondria. We analyzed possible interpretations of data on mitochondrial membrane potential obtained using fluorescent probes. We suggest a possible mechanism underlying retention of fluorescent probes inside the cells and mitochondria.
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Affiliation(s)
- V A Popkov
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119991, Russia
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7
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Sarkar S, Cohen N, Sabhachandani P, Konry T. Phenotypic drug profiling in droplet microfluidics for better targeting of drug-resistant tumors. LAB ON A CHIP 2015; 15:4441-50. [PMID: 26456240 PMCID: PMC4666301 DOI: 10.1039/c5lc00923e] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Acquired drug resistance is a key factor in the failure of chemotherapy. Due to intratumoral heterogeneity, cancer cells depict variations in intracellular drug uptake and efflux at the single cell level, which may not be detectable in bulk assays. In this study we present a droplet microfluidics-based approach to assess the dynamics of drug uptake, efflux and cytotoxicity in drug-sensitive and drug-resistant breast cancer cells. An integrated droplet generation and docking microarray was utilized to encapsulate single cells as well as homotypic cell aggregates. Drug-sensitive cells showed greater death in the presence or absence of Doxorubicin (Dox) compared to the drug-resistant cells. We observed heterogeneous Dox uptake in individual drug-sensitive cells while the drug-resistant cells showed uniformly low uptake and retention. Dox-resistant cells were classified into distinct subsets based on their efflux properties. Cells that showed longer retention of extracellular reagents also demonstrated maximal death. We further observed homotypic fusion of both cell types in droplets, which resulted in increased cell survival in the presence of high doses of Dox. Our results establish the applicability of this microfluidic platform for quantitative drug screening in single cells and multicellular interactions.
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Affiliation(s)
- S Sarkar
- Department of Pharmaceutical Sciences, Northeastern University, 360 Huntington Avenue, Boston, 02115 MA, USA.
| | - N Cohen
- Department of Pharmaceutical Sciences, Northeastern University, 360 Huntington Avenue, Boston, 02115 MA, USA.
| | - P Sabhachandani
- Department of Pharmaceutical Sciences, Northeastern University, 360 Huntington Avenue, Boston, 02115 MA, USA.
| | - T Konry
- Department of Pharmaceutical Sciences, Northeastern University, 360 Huntington Avenue, Boston, 02115 MA, USA.
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8
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Quantification of protein copy number in single mitochondria: The Bcl-2 family proteins. Biosens Bioelectron 2015; 74:476-82. [DOI: 10.1016/j.bios.2015.06.057] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 06/23/2015] [Accepted: 06/25/2015] [Indexed: 01/06/2023]
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9
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Zhang X, Zhang S, Zhu S, Chen S, Han J, Gao K, Zeng JZ, Yan X. Identification of Mitochondria-Targeting Anticancer Compounds by an in Vitro Strategy. Anal Chem 2014; 86:5232-7. [DOI: 10.1021/ac500918g] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Xiang Zhang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, P. R. China
| | - Shuyue Zhang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, P. R. China
| | - Shaobin Zhu
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, P. R. China
| | - Sha Chen
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, P. R. China
| | - Jinyan Han
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, P. R. China
| | - Kaimin Gao
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, P. R. China
| | - Jin-zhang Zeng
- School
of Pharmaceutical Sciences and Institute for Biomedical Research, Xiamen University, Xiamen, Fujian 361005, P. R. China
| | - Xiaomei Yan
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, The Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, P. R. China
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10
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Deng B, Tian Y, Yu X, Song J, Guo F, Xiao Y, Zhang Z. Laminar flow mediated continuous single-cell analysis on a novel poly(dimethylsiloxane) microfluidic chip. Anal Chim Acta 2014; 820:104-11. [DOI: 10.1016/j.aca.2014.02.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 02/10/2014] [Accepted: 02/22/2014] [Indexed: 01/06/2023]
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11
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Taylor TH, Frost NW, Bowser MT, Arriaga EA. Analysis of individual mitochondria via fluorescent immunolabeling with Anti-TOM22 antibodies. Anal Bioanal Chem 2014; 406:1683-91. [PMID: 24481619 DOI: 10.1007/s00216-013-7593-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Revised: 12/11/2013] [Accepted: 12/19/2013] [Indexed: 01/08/2023]
Abstract
Mitochondria are responsible for maintaining a variety of cellular functions. One such function is the interaction and subsequent import of proteins into these organelles via the translocase of outer membrane (TOM) complex. Antibodies have been used to analyze the presence and function of proteins comprising this complex, but have not been used to investigate variations in the abundance of TOM complex in mitochondria. Here, we report on the feasibility of using capillary cytometry with laser-induced fluorescence to detect mitochondria labeled with antibodies targeting the TOM complex and to estimate the number of antibodies that bind to these organelles. Mitochondria were fluorescently labeled with DsRed2, while antibodies targeting the TOM22 protein, one of nine proteins comprising the TOM complex, were conjugated to the Atto-488 fluorophore. At typical labeling conditions, 94% of DsRed2 mitochondria were also immunofluorescently labeled with Atto-488 Anti-TOM22 antibodies. The calculated median number of Atto-488 Anti-TOM22 antibodies bound to the surface of mitochondria was ∼2,000 per mitochondrion. The combination of fluorescent immunolabeling and capillary cytometry could be further developed to include multicolor labeling experiments, which enable monitoring several molecular targets at the same time in the same or different organelle types.
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Affiliation(s)
- Thane H Taylor
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
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12
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Clède S, Policar C, Sandt C. Fourier transform infrared (FT-IR) spectromicroscopy to identify cell organelles: correlation with fluorescence staining in MCF-7 breast cancer cells. APPLIED SPECTROSCOPY 2014; 68:113-117. [PMID: 24405961 DOI: 10.1366/13-07139] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Biomolecules display specific vibrational signatures in the infrared (IR) range, and organelles that concentrate these biomolecules can be identified by these IR signatures. Subcellular identification and location of cell organelles using IR signatures is attractive as it does not require the use of any specific trackers and is thus non-invasive and non-destructive. We show here that endogenous IR absorptions are relevant to detecting and imaging the nucleus, the cytoplasm, and the Golgi apparatus/endoplasmic reticulum in MCF-7 breast cancer cells, and we compare these results with our previous work on the HeLa cell line. We correlate maps of fixed and dried cells obtained by synchrotron radiation Fourier transform infrared (SR FT-IR) spectromicroscopy with epifluorescence images using fluorescent trackers for Golgi apparatus and nucleus, namely BODIPY TR C5-ceramide complexed to BSA and DAPI, respectively. Interestingly, the ratios of the IR bands CH2 : CH3 (both asymmetric and symmetric) and CO((ester)):amide I were shown to be reliable gauges of the lipidic character of a cellular compartment, the -CH2 and the CO((ester)) absorptions increasing with the presence of inner membranes like in the Golgi apparatus.
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13
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Zand K, Pham T, Davila A, Wallace DC, Burke PJ. Nanofluidic platform for single mitochondria analysis using fluorescence microscopy. Anal Chem 2013; 85:6018-25. [PMID: 23678849 DOI: 10.1021/ac4010088] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Using nanofluidic channels in PDMS of cross section 500 nm × 2 μm, we demonstrate the trapping and interrogation of individual, isolated mitochondria. Fluorescence labeling demonstrates the immobilization of mitochondria at discrete locations along the channel. Interrogation of mitochondrial membrane potential with different potential sensitive dyes (JC-1 and TMRM) indicates the trapped mitochondria are vital in the respiration buffer. Fluctuations of the membrane potential can be observed at the single mitochondrial level. A variety of chemical challenges can be delivered to each individual mitochondrion in the nanofluidic system. As sample demonstrations, increases in the membrane potential are seen upon introduction of OXPHOS substrates into the nanofluidic channel. Introduction of Ca(2+) into the nanochannels induces mitochondrial membrane permeabilization (MMP), leading to depolarization, observed at the single mitochondrial level. A variety of applications in cancer biology, stem cell biology, apoptosis studies, and high throughput functional metabolomics studies can be envisioned using this technology.
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Affiliation(s)
- Katayoun Zand
- Integrated Nanosystem Research Facility, Electrical Engineering and Computer Science, University of California, Irvine, Irvine, California, USA
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14
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Dalhaimer P. Lipid droplet organelle distribution in populations of dividing cells studied by simulation. Phys Biol 2013; 10:036007. [DOI: 10.1088/1478-3975/10/3/036007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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15
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Liu Y, Barua D, Liu P, Wilson BS, Oliver JM, Hlavacek WS, Singh AK. Single-cell measurements of IgE-mediated FcεRI signaling using an integrated microfluidic platform. PLoS One 2013; 8:e60159. [PMID: 23544131 PMCID: PMC3609784 DOI: 10.1371/journal.pone.0060159] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 02/21/2013] [Indexed: 11/18/2022] Open
Abstract
Heterogeneity in responses of cells to a stimulus, such as a pathogen or allergen, can potentially play an important role in deciding the fate of the responding cell population and the overall systemic response. Measuring heterogeneous responses requires tools capable of interrogating individual cells. Cell signaling studies commonly do not have single-cell resolution because of the limitations of techniques used such as Westerns, ELISAs, mass spectrometry, and DNA microarrays. Microfluidics devices are increasingly being used to overcome these limitations. Here, we report on a microfluidic platform for cell signaling analysis that combines two orthogonal single-cell measurement technologies: on-chip flow cytometry and optical imaging. The device seamlessly integrates cell culture, stimulation, and preparation with downstream measurements permitting hands-free, automated analysis to minimize experimental variability. The platform was used to interrogate IgE receptor (FcεRI) signaling, which is responsible for triggering allergic reactions, in RBL-2H3 cells. Following on-chip crosslinking of IgE-FcεRI complexes by multivalent antigen, we monitored signaling events including protein phosphorylation, calcium mobilization and the release of inflammatory mediators. The results demonstrate the ability of our platform to produce quantitative measurements on a cell-by-cell basis from just a few hundred cells. Model-based analysis of the Syk phosphorylation data suggests that heterogeneity in Syk phosphorylation can be attributed to protein copy number variations, with the level of Syk phosphorylation being particularly sensitive to the copy number of Lyn.
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Affiliation(s)
- Yanli Liu
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, California, United States of America
| | - Dipak Barua
- Theoretical Biology and Biophysics Group, Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Peng Liu
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, California, United States of America
| | - Bridget S. Wilson
- Department of Pathology and Cancer Center, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Janet M. Oliver
- Department of Pathology and Cancer Center, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - William S. Hlavacek
- Theoretical Biology and Biophysics Group, Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Anup K. Singh
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, California, United States of America
- * E-mail:
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16
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Sandt C, Frederick J, Dumas P. Profiling pluripotent stem cells and organelles using synchrotron radiation infrared microspectroscopy. JOURNAL OF BIOPHOTONICS 2013; 6:60-72. [PMID: 23125135 DOI: 10.1002/jbio.201200139] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2012] [Revised: 09/27/2012] [Accepted: 10/01/2012] [Indexed: 05/22/2023]
Abstract
FTIR micro-spectroscopy is a sensitive, non-destructive and label-free method offering diffraction-limited resolution with high signal-to-noise ratios when combined with a synchrotron radiation source. The vibrational signature of individual cells was used to validate an alternative strategy for reprogramming induced pluripotent stem cells generated from amniocytes. The iPSC lines PB09 and PB10, were reprogrammed from the same amniocyte cell line using respectively the Oct54, Sox2, Lin28, and Nanog and the Oct4 and Sox2 transcription factor cocktail. We show that cells reprogrammed by the two different sets of transfection factors have similar spectral signatures after reprogramming, except for a small subpopulation of cells in one of the cell lines. Mapping HeLa cells at subcellular resolution, we show that the Golgi apparatus, the cytoplasm and the nucleus have a specific spectral signature. The CH(3):CH(2) ratio is the highest in the nucleus and the lowest in the Golgi apparatus/endoplasmic reticulum, in agreement with the membrane composition of these organelles. This is confirmed by specific staining of the organelles with fluorescent dyes. Subcellular differentiation of cell compartments is also demonstrated in living cells.
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Affiliation(s)
- Christophe Sandt
- Synchrotron SOLEIL, L'Orme des Merisiers, Gif-sur-Yvette, France
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