1
|
Liu Y, Zhao H, Fu B, Jiang S, Wang J, Wan Y. Mapping Cell Phenomics with Multiparametric Flow Cytometry Assays. PHENOMICS (CHAM, SWITZERLAND) 2022; 2:272-281. [PMID: 36939758 PMCID: PMC9590532 DOI: 10.1007/s43657-021-00031-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 09/28/2021] [Accepted: 10/11/2021] [Indexed: 11/26/2022]
Abstract
Phenomics explores the complex interactions among genes, epigenetics, symbiotic microorganisms, diet, and environmental exposure based on the physical, chemical, and biological characteristics of individuals and groups. Increasingly efficient and comprehensive phenotyping techniques have been integrated into modern phenomics-related research. Multicolor flow cytometry technology provides more measurement parameters than conventional flow cytometry. Based on detailed descriptions of cell phenotypes, rare cell populations and cell subsets can be distinguished, new cell phenotypes can be discovered, and cell apoptosis characteristics can be detected, which will expand the potential of cell phenomics research. Based on the enhancements in multicolor flow cytometry hardware, software, reagents, and method design, the present review summarizes the recent advances and applications of multicolor flow cytometry in cell phenomics, illuminating the potential of applying phenomics in future studies.
Collapse
Affiliation(s)
- Yang Liu
- Biomedical Analysis Center, Army Medical University, Chongqing, 400038 China
- Chongqing Key Laboratory of Cytomics, Chongqing, 400038 China
| | - Haichu Zhao
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518055 China
| | - Boqiang Fu
- National Institute of Metrology, Beijing, 100029 China
| | - Shan Jiang
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518055 China
| | - Jing Wang
- National Institute of Metrology, Beijing, 100029 China
| | - Ying Wan
- Biomedical Analysis Center, Army Medical University, Chongqing, 400038 China
- Chongqing Key Laboratory of Cytomics, Chongqing, 400038 China
| |
Collapse
|
2
|
Mitra-Kaushik S, Mehta-Damani A, Stewart JJ, Green C, Litwin V, Gonneau C. The Evolution of Single-Cell Analysis and Utility in Drug Development. AAPS JOURNAL 2021; 23:98. [PMID: 34389904 PMCID: PMC8363238 DOI: 10.1208/s12248-021-00633-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 07/27/2021] [Indexed: 02/07/2023]
Abstract
This review provides a brief history of the advances of cellular analysis tools focusing on instrumentation, detection probes, and data analysis tools. The interplay of technological advancement and a deeper understanding of cellular biology are emphasized. The relevance of this topic to drug development is that the evaluation of cellular biomarkers has become a critical component of the development strategy for novel immune therapies, cell therapies, gene therapies, antiviral therapies, and vaccines. Moreover, recent technological advances in single-cell analysis are providing more robust cellular measurements and thus accelerating the advancement of novel therapies. Graphical abstract
![]()
Collapse
Affiliation(s)
| | | | | | - Cherie Green
- Development Sciences, Genentech, Inc., A Member of the Roche Group, South San Francisco, California, USA
| | | | - Christèle Gonneau
- Central Laboratory Services, Labcorp Drug Development, Geneva, Switzerland.
| |
Collapse
|
3
|
Algar WR, Massey M, Rees K, Higgins R, Krause KD, Darwish GH, Peveler WJ, Xiao Z, Tsai HY, Gupta R, Lix K, Tran MV, Kim H. Photoluminescent Nanoparticles for Chemical and Biological Analysis and Imaging. Chem Rev 2021; 121:9243-9358. [PMID: 34282906 DOI: 10.1021/acs.chemrev.0c01176] [Citation(s) in RCA: 123] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Research related to the development and application of luminescent nanoparticles (LNPs) for chemical and biological analysis and imaging is flourishing. Novel materials and new applications continue to be reported after two decades of research. This review provides a comprehensive and heuristic overview of this field. It is targeted to both newcomers and experts who are interested in a critical assessment of LNP materials, their properties, strengths and weaknesses, and prospective applications. Numerous LNP materials are cataloged by fundamental descriptions of their chemical identities and physical morphology, quantitative photoluminescence (PL) properties, PL mechanisms, and surface chemistry. These materials include various semiconductor quantum dots, carbon nanotubes, graphene derivatives, carbon dots, nanodiamonds, luminescent metal nanoclusters, lanthanide-doped upconversion nanoparticles and downshifting nanoparticles, triplet-triplet annihilation nanoparticles, persistent-luminescence nanoparticles, conjugated polymer nanoparticles and semiconducting polymer dots, multi-nanoparticle assemblies, and doped and labeled nanoparticles, including but not limited to those based on polymers and silica. As an exercise in the critical assessment of LNP properties, these materials are ranked by several application-related functional criteria. Additional sections highlight recent examples of advances in chemical and biological analysis, point-of-care diagnostics, and cellular, tissue, and in vivo imaging and theranostics. These examples are drawn from the recent literature and organized by both LNP material and the particular properties that are leveraged to an advantage. Finally, a perspective on what comes next for the field is offered.
Collapse
Affiliation(s)
- W Russ Algar
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Melissa Massey
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Kelly Rees
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Rehan Higgins
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Katherine D Krause
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Ghinwa H Darwish
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - William J Peveler
- School of Chemistry, Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, U.K
| | - Zhujun Xiao
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Hsin-Yun Tsai
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Rupsa Gupta
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Kelsi Lix
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Michael V Tran
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Hyungki Kim
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| |
Collapse
|
4
|
Abstract
Flow cytometry and sorting represents a valuable and mature experimental platform for the analysis of cellular populations. Applications involving higher plants started to emerge around 40 years ago and are now widely employed both to provide unique information regarding basic and applied questions in the biosciences and to advance agricultural productivity in practical ways. Further development of this platform is being actively pursued, and this promises additional progress in our understanding of the interactions of cells within complex tissues and organs. Higher plants offer unique challenges in terms of flow cytometric analysis, first since their organs and tissues are, almost without exception, three-dimensional assemblies of different cell types held together by tough cell walls, and, second, because individual plant cells are generally larger than those of mammals.This chapter, which updates work last reviewed in 2014 [Galbraith DW (2014) Flow cytometry and sorting in Arabidopsis. In: Sanchez Serrano JJ, Salinas J (eds) Arabidopsis Protocols, 3rd ed. Methods in molecular biology, vol 1062. Humana Press, Totowa, pp 509-537], describes the application of techniques of flow cytometry and sorting to the model plant species Arabidopsis thaliana, in particular emphasizing (a) fluorescence labeling in vivo of specific cell types and of subcellular components, (b) analysis using both conventional cytometers and spectral analyzers, (c) fluorescence-activated sorting of protoplasts and nuclei, and (d) transcriptome analyses using sorted protoplasts and nuclei, focusing on population analyses at the level of single protoplasts and nuclei. Since this is an update, details of new experimental methods are emphasized.
Collapse
Affiliation(s)
- David W Galbraith
- University of Arizona, School of Plant Sciences and Bio5 Institute, Tucson, AZ, USA. .,Henan University, Institute of Plant Stress Biology, School of Life Sciences, Kaifeng, China.
| | - Guiling Sun
- Henan University, Institute of Plant Stress Biology, School of Life Sciences, Kaifeng, China
| |
Collapse
|
5
|
Rana R, Chang Q, Bassan J, Chow S, Hedley D, Nitz M. An Iodinated DAPI-Based Reagent for Mass Cytometry. Chembiochem 2020; 22:532-538. [PMID: 32897623 DOI: 10.1002/cbic.202000369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/02/2020] [Indexed: 01/04/2023]
Abstract
Multiparametric single-cell analysis has seen dramatic improvements with the introduction of mass cytometry (MC) and imaging mass cytometry (IMC™ ). These technologies expanded the number of biomarkers that can be identified simultaneously by using heavy-isotope-tagged antibody reagents. Small-molecule probes bearing heavy isotopes are emerging as additional useful functional reporters of cellular features. Realizing this, we explored the iodination of DAPI to produce a heavy-atom-substituted derivative of the commonly used fluorescent DNA stain. Although exhibiting a drastically reduced fluorescence emission profile, I-DAPI retains strong binding affinity for DNA. I-DAPI was used to detect cellular DNA in MC and IMC™ assays with comparable efficiency to known Ir-containing DNA intercalators. This work suggests repurposing well-known colorimetric stains through simple reactions could be an effective strategy to develop new, functional MC and IMC™ reagents.
Collapse
Affiliation(s)
- Rahul Rana
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Qing Chang
- Fluidigm Canada Inc., 1380 Rodick Road, Markham, ON L3R 4G5, Canada
| | - Jay Bassan
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada.,BIMDAQ Ltd, 9 Lessness Avenue, Bexleyheath, DA7 5SH, UK
| | - Sue Chow
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON M5G 2 M9, Canada
| | - David Hedley
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON M5G 2 M9, Canada
| | - Mark Nitz
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| |
Collapse
|
6
|
Lannigan J. Is there a Pot of Gold at the End of the Spectrum? Cytometry A 2020; 97:1105-1108. [PMID: 32629526 DOI: 10.1002/cyto.a.24186] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 06/26/2020] [Indexed: 12/27/2022]
Abstract
Full spectrum flow cytometry: Is there a pot of gold at the end of the spectrum?
Collapse
Affiliation(s)
- Joanne Lannigan
- Flow Cytometry Support Services, LLC, Alexandria, Virginia, 22314, USA
| |
Collapse
|
7
|
Chattopadhyay PK, Winters AF, Lomas WE, Laino AS, Woods DM. High-Parameter Single-Cell Analysis. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2019; 12:411-430. [PMID: 30699035 DOI: 10.1146/annurev-anchem-061417-125927] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Thousands of transcripts and proteins confer function and discriminate cell types in the body. Using high-parameter technologies, we can now measure many of these markers at once, and multiple platforms are now capable of analysis on a cell-by-cell basis. Three high-parameter single-cell technologies have particular potential for discovering new biomarkers, revealing disease mechanisms, and increasing our fundamental understanding of cell biology. We review these three platforms (high-parameter flow cytometry, mass cytometry, and a new class of technologies called integrated molecular cytometry platforms) in this article. We describe the underlying hardware and instrumentation, the reagents involved, and the limitations and advantages of each platform. We also highlight the emerging field of high-parameter single-cell data analysis, providing an accessible overview of the data analysis process and choice of tools.
Collapse
Affiliation(s)
- Pratip K Chattopadhyay
- Precision Immunology Laboratory, Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA;
| | - Aidan F Winters
- Precision Immunology Laboratory, Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA;
| | - Woodrow E Lomas
- Precision Immunology Laboratory, Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA;
| | - Andressa S Laino
- Precision Immunology Laboratory, Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA;
| | - David M Woods
- Precision Immunology Laboratory, Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA;
| |
Collapse
|
8
|
Flores-Montero J, Kalina T, Corral-Mateos A, Sanoja-Flores L, Pérez-Andrés M, Martin-Ayuso M, Sedek L, Rejlova K, Mayado A, Fernández P, van der Velden V, Bottcher S, van Dongen JJM, Orfao A. Fluorochrome choices for multi-color flow cytometry. J Immunol Methods 2019; 475:112618. [PMID: 31181212 DOI: 10.1016/j.jim.2019.06.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 05/29/2019] [Accepted: 06/04/2019] [Indexed: 12/21/2022]
Abstract
Fluorochrome selection is a key step in designing multi-color antibody panels. The list of available fluorochromes is continuously growing, fitting current needs in clinical flow cytometry to simultaneously use more markers to better define multiple leukocyte subpopulations in a single tube. Several criteria guide fluorochrome selection: i) the fluorescence profiles (excitation and emission), ii) relative brightness, iii) fluorescence overlap, iv) fluorochrome stability, and v) reproducible conjugation to antibodies. Here we used 75 samples (45 bone marrow and 30 blood) to illustrate EuroFlow strategies for evaluation of compatible fluorochromes, and how the results obtained guide fluorochrome selection as a critical step in the antibody-panel building process. Our results allowed identification of optimal fluorescence profiles (e.g. higher fluorescence intensity and/or resolution with limited fluorescence overlap into neighbor channels) for brilliant violet (BV)421 and BV510 in the violet laser and allophycocyanin (APC) hilite 7 (H7) or APC C750 in the red laser vs. other candidate fluorochromes generally applied for the same detectors and here evaluated. Moreover, evaluation of the same characteristics for another group of fluorochromes (e.g. BV605, BV650, PE CF594, AF700 or APC AF700) guided selection of the most appropriate fluorochrome conjugates to be combined in a multi-color antibody panel. Albeit this is a demanding approach, it could be successfully applied for selection of fluorochrome combinations for the EuroFlow antibody panels for diagnosis, classification and monitoring of hematological malignancies and primary immunodeficiencies. Consequently, sets of 8-, 10- and 12-color fluorochrome combinations are proposed as frame of reference for initial antibody panel design.
Collapse
Affiliation(s)
- Juan Flores-Montero
- Cancer Research Center (IBMCC-CSIC/USAL-IBSAL), Cytometry Service (NUCLEUS) and Department of Medicine, University of Salamanca, Salamanca, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBER-ONC) CB16/12/00400, Instituto de Salud Carlos III, Madrid, Spain
| | - Tomas Kalina
- CLIP Cytometry, Department of Pediatric Hematology and Oncology, 2nd Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Alba Corral-Mateos
- Cancer Research Center (IBMCC-CSIC/USAL-IBSAL), Cytometry Service (NUCLEUS) and Department of Medicine, University of Salamanca, Salamanca, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBER-ONC) CB16/12/00400, Instituto de Salud Carlos III, Madrid, Spain
| | - Luzalba Sanoja-Flores
- Cancer Research Center (IBMCC-CSIC/USAL-IBSAL), Cytometry Service (NUCLEUS) and Department of Medicine, University of Salamanca, Salamanca, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBER-ONC) CB16/12/00400, Instituto de Salud Carlos III, Madrid, Spain
| | - Martin Pérez-Andrés
- Cancer Research Center (IBMCC-CSIC/USAL-IBSAL), Cytometry Service (NUCLEUS) and Department of Medicine, University of Salamanca, Salamanca, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBER-ONC) CB16/12/00400, Instituto de Salud Carlos III, Madrid, Spain
| | | | - Lukasz Sedek
- Department of Pediatric Hematology and Oncology, Medical University of Silesia in Katowice, Zabrze, Poland
| | - Katerina Rejlova
- CLIP Cytometry, Department of Pediatric Hematology and Oncology, 2nd Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Andrea Mayado
- Cancer Research Center (IBMCC-CSIC/USAL-IBSAL), Cytometry Service (NUCLEUS) and Department of Medicine, University of Salamanca, Salamanca, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBER-ONC) CB16/12/00400, Instituto de Salud Carlos III, Madrid, Spain
| | - Paula Fernández
- FACS/Stem cell Laboratory, Institute of Laboratory Medicine, Kantonsspital Aarau AG, Aarau, Switzerland
| | - Vincent van der Velden
- Department of Immunology, Erasmus MC, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Sebastian Bottcher
- Rostock University Medical Center, Division of Internal Medicine, Medical Clinic III, Hematology, Oncology and Palliative Medicine, Special Hematology Laboratory, Rostock, Germany
| | - Jaques J M van Dongen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands.
| | - Alberto Orfao
- Cancer Research Center (IBMCC-CSIC/USAL-IBSAL), Cytometry Service (NUCLEUS) and Department of Medicine, University of Salamanca, Salamanca, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBER-ONC) CB16/12/00400, Instituto de Salud Carlos III, Madrid, Spain..
| |
Collapse
|
9
|
Francis JE, Mason D, Lévy R. Evaluation of quantum dot conjugated antibodies for immunofluorescent labelling of cellular targets. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2017; 8:1238-1249. [PMID: 28685124 PMCID: PMC5480344 DOI: 10.3762/bjnano.8.125] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 05/09/2017] [Indexed: 05/20/2023]
Abstract
Semiconductor quantum dots (Qdots) have been utilised as probes in fluorescence microscopy and provide an alternative to fluorescent dyes and fluorescent proteins due to their brightness, photostability, and the possibility to excite different Qdots with a single wavelength. In spite of these attractive properties, their implemenation by biologists has been somewhat limited and only a few Qdot conjugates are commercially available for the labelling of cellular targets. Although many protocols have been reported for the specific labelling of proteins with Qdots, the majority of these relied on Qdot-conjugated antibodies synthesised specifically by the authors (and therefore not widely available), which limits the scope of applications and complicates replication. Here, the specificity of a commercially available, Qdot-conjugated secondary antibody (Qdot-Ab) was tested against several primary IgG antibodies. The antigens were labelled simultaneously with a fluorescent dye coupled to a secondary antibody (Dye-Ab) and the Qdot-Ab. Although, the Dye-Ab labelled all of the intended target proteins, the Qdot-Ab was found bound to only some of the protein targets in the cytosol and could not reach the nucleus, even after extensive cell permeabilisation.
Collapse
Affiliation(s)
- Jennifer E Francis
- Department of Biochemistry, Institute of Integrative Biology, Biosciences Building, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - David Mason
- Centre for Cell Imaging, Institute of Integrative Biology, Biosciences Building, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Raphaël Lévy
- Department of Biochemistry, Institute of Integrative Biology, Biosciences Building, Crown Street, Liverpool, L69 7ZB, United Kingdom
| |
Collapse
|
10
|
Lo Giudice MC, Herda LM, Polo E, Dawson KA. In situ characterization of nanoparticle biomolecular interactions in complex biological media by flow cytometry. Nat Commun 2016; 7:13475. [PMID: 27845346 PMCID: PMC5116075 DOI: 10.1038/ncomms13475] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 10/06/2016] [Indexed: 12/13/2022] Open
Abstract
Nanoparticles interacting with, or derived from, living organisms are almost invariably coated in a variety of biomolecules presented in complex biological milieu, which produce a bio-interface or 'biomolecular corona' conferring a biological identity to the particle. Biomolecules at the surface of the nanoparticle-biomolecule complex present molecular fragments that may be recognized by receptors of cells or biological barriers, potentially engaging with different biological pathways. Here we demonstrate that using intense fluorescent reporter binders, in this case antibodies bound to quantum dots, we can map out the availability of such recognition fragments, allowing for a rapid and meaningful biological characterization. The application in microfluidic flow, in small detection volumes, with appropriate thresholding of the detection allows the study of even complex nanoparticles in realistic biological milieu, with the emerging prospect of making direct connection to conditions of cell level and in vivo experiments.
Collapse
Affiliation(s)
- Maria Cristina Lo Giudice
- Centre for BioNano Interactions, School of Chemistry and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
| | - Luciana M. Herda
- Centre for BioNano Interactions, School of Chemistry and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
| | - Ester Polo
- Centre for BioNano Interactions, School of Chemistry and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
| | - Kenneth A. Dawson
- Centre for BioNano Interactions, School of Chemistry and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
| |
Collapse
|
11
|
Brilliant violet fluorochromes in simultaneous multicolor flow cytometry-fluorescence in situ hybridization measurement of monocyte subsets and telomere length in heart failure. J Transl Med 2016; 96:1223-1230. [PMID: 27617397 DOI: 10.1038/labinvest.2016.100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Revised: 08/18/2016] [Accepted: 08/22/2016] [Indexed: 12/28/2022] Open
Abstract
Conventional analytical methods to determine telomere length (TL) have been replaced by more precise and reproducible procedures, such as fluorescence in situ hybridization coupled with flow cytometry (flow-FISH). However, simultaneous measurement of TL and cell phenotype remains difficult. Relatively expensive and time-consuming cell-sorting purification is needed to counteract the loss, due to stringent FISH conditions, of prehybridization fluorescence by the organic fluorochromes conventionally used in the phenotyping step. Here, we sought to assess whether the newly developed Brilliant Violet (BV) dyes are valuable to specifically and simultaneously assess the distribution and telomere attrition of monocyte subsets circulating in the blood of a cohort of patients with heart failure. We performed flow-FISH on blood samples from 28 patients with heart failure. To differentiate among monocyte subsets, we used BV and conventional fluorochromes conjugated to antibodies against CD86, CD14, CD16, and CD15. We simultaneously assessed the TLs of the monocyte subsets with a telomere-specific peptide nucleic acid probe labeled with fluorescein isothiocyanate. The BV dyes completely tolerated the harsh conditions required for adequate DNA denaturation and simultaneously provided accurate identification of monocyte subpopulations and respective TLs. The presented protocol may be faster and less expensive than those used currently for purposes such as establishing associations among patient categories, disease progression, monocyte heterogeneity, and aging in the context of heart failure.
Collapse
|
12
|
Fuller KA, Bennett S, Hui H, Chakera A, Erber WN. Development of a robust immuno-S-FISH protocol using imaging flow cytometry. Cytometry A 2016; 89:720-30. [DOI: 10.1002/cyto.a.22852] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 03/03/2016] [Accepted: 03/09/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Kathryn A. Fuller
- Translational Cancer Pathology Laboratory, School of Pathology and Laboratory Medicine; The University of Western Australia; Crawley Australia
| | - Sophia Bennett
- Translational Renal Research Group; Harry Perkins Institute of Medical Research; Nedlands Australia
| | - Henry Hui
- Translational Cancer Pathology Laboratory, School of Pathology and Laboratory Medicine; The University of Western Australia; Crawley Australia
| | - Aron Chakera
- Translational Renal Research Group; Harry Perkins Institute of Medical Research; Nedlands Australia
| | - Wendy N. Erber
- Translational Cancer Pathology Laboratory, School of Pathology and Laboratory Medicine; The University of Western Australia; Crawley Australia
- PathWest Laboratory Medicine; Nedlands Australia
| |
Collapse
|
13
|
Telford WG. Near infrared lasers in flow cytometry. Methods 2015; 82:12-20. [PMID: 25814439 PMCID: PMC8363084 DOI: 10.1016/j.ymeth.2015.03.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 02/19/2015] [Accepted: 03/18/2015] [Indexed: 01/25/2023] Open
Abstract
Technology development in flow cytometry has closely tracked laser technology, the light source that flow cytometers almost exclusively use to excite fluorescent probes. The original flow cytometers from the 1970s and 1980s used large water-cooled lasers to produce only one or two laser lines at a time. Modern cytometers can take advantage of the revolution in solid state laser technology to use almost any laser wavelength ranging from the ultraviolet to the near infrared. Commercial cytometers can now be equipped with many small solid state lasers, providing almost any wavelength needed for cellular analysis. Flow cytometers are now equipped to analyze 20 or more fluorescent probes simultaneously, requiring multiple laser wavelengths. Instrument developers are now trying to increase this number by designing fluorescent probes that can be excited by laser wavelength at the "edges" of the visible light range, in the near ultraviolet and near-infrared region. A variety of fluorescent probes have been developed that excite with violet and long wavelength ultraviolet light; however, the near-infrared range (660-800 nm) has yet seen only exploitation in flow cytometry. Fortunately, near-infrared laser diodes and other solid state laser technologies appropriate for flow cytometry have been in existence for some time, and can be readily incorporated into flow cytometers to accelerate fluorescent probe development. The near infrared region represents one of the last "frontiers" to maximize the number of fluorescent probes that can be analyzed by flow cytometry. In addition, near infrared fluorescent probes used in biomedical tracking and imaging could also be employed for flow cytometry with the correct laser wavelengths. This review describes the available technology, including lasers, fluorescent probes and detector technology optimal for near infrared signal detection.
Collapse
Affiliation(s)
- William G Telford
- Experimental Transplantation and Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
14
|
Sands B, Jenkins P, Peria WJ, Naivar M, Houston JP, Brent R. Measuring and sorting cell populations expressing isospectral fluorescent proteins with different fluorescence lifetimes. PLoS One 2014; 9:e109940. [PMID: 25302964 PMCID: PMC4193854 DOI: 10.1371/journal.pone.0109940] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 09/04/2014] [Indexed: 01/03/2023] Open
Abstract
Study of signal transduction in live cells benefits from the ability to visualize and quantify light emitted by fluorescent proteins (XFPs) fused to different signaling proteins. However, because cell signaling proteins are often present in small numbers, and because the XFPs themselves are poor fluorophores, the amount of emitted light, and the observable signal in these studies, is often small. An XFP's fluorescence lifetime contains additional information about the immediate environment of the fluorophore that can augment the information from its weak light signal. Here, we constructed and expressed in Saccharomyces cerevisiae variants of Teal Fluorescent Protein (TFP) and Citrine that were isospectral but had shorter fluorescence lifetimes, ∼1.5 ns vs ∼3 ns. We modified microscopic and flow cytometric instruments to measure fluorescence lifetimes in live cells. We developed digital hardware and a measure of lifetime called a “pseudophasor” that we could compute quickly enough to permit sorting by lifetime in flow. We used these abilities to sort mixtures of cells expressing TFP and the short-lifetime TFP variant into subpopulations that were respectively 97% and 94% pure. This work demonstrates the feasibility of using information about fluorescence lifetime to help quantify cell signaling in living cells at the high throughput provided by flow cytometry. Moreover, it demonstrates the feasibility of isolating and recovering subpopulations of cells with different XFP lifetimes for subsequent experimentation.
Collapse
Affiliation(s)
- Bryan Sands
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Patrick Jenkins
- Department of Chemical Engineering, New Mexico State University, Las Cruces, New Mexico, United States of America
| | - William J. Peria
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Mark Naivar
- Darkling X, LLC, Los Alamos, New Mexico, United States of America
| | - Jessica P. Houston
- Department of Chemical Engineering, New Mexico State University, Las Cruces, New Mexico, United States of America
| | - Roger Brent
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail:
| |
Collapse
|
15
|
Nanotechnology in reproductive medicine: Emerging applications of nanomaterials. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2014; 10:921-38. [DOI: 10.1016/j.nano.2014.01.001] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 12/09/2013] [Accepted: 01/09/2014] [Indexed: 12/21/2022]
|
16
|
Abstract
Flow cytometry, and the accompanying technology of cell sorting, represents an established and valuable experimental platform for the analysis of cellular populations. Applications involving higher plants, which started to emerge around 30 years ago, are now widely employed both to provide unique information regarding fundamental questions in basic and applied bioscience and to advance agricultural productivity in practical ways. Further developments of this platform are being actively pursued, promising additional advances in our understanding of the interactions of cells within the complex tissues and organs. Higher plants offer unique challenges in terms of flow cytometric analysis, first since their organs and tissues are, almost without exception, three-dimensional assemblies of different cell types and second that their individual cells are generally larger than those of mammals. This chapter focuses on the use of flow cytometry and cell sorting with the model species Arabidopsis thaliana, in particular addressing (1) fluorescence in vivo labeling of specific cell types, (2) fluorescence-activated sorting of protoplasts and nuclei, and (3) transcriptome analyses using sorted protoplasts and nuclei.
Collapse
|
17
|
Akinfieva O, Nabiev I, Sukhanova A. New directions in quantum dot-based cytometry detection of cancer serum markers and tumor cells. Crit Rev Oncol Hematol 2013; 86:1-14. [DOI: 10.1016/j.critrevonc.2012.09.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 07/18/2012] [Accepted: 09/05/2012] [Indexed: 10/27/2022] Open
|
18
|
Studying the human immunome: the complexity of comprehensive leukocyte immunophenotyping. Curr Top Microbiol Immunol 2013; 377:23-60. [PMID: 23975032 DOI: 10.1007/82_2013_336] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A comprehensive study of the cellular components of the immune system requires both deep and broad immunophenotyping of numerous cell populations in an efficient and practical manner. In this chapter, we describe the technical aspects of studying the human immunome using high-dimensional (15 color) fluorescence-based immunophenotyping. We focus on the technical aspects of polychromatic flow cytometry and the initial stages in developing a panel for comprehensive leukocyte immunophenotyping (CLIP). We also briefly discuss how this panel is being used and the challenges of encyclopedic analysis of these rich data sets.
Collapse
|
19
|
Yu HW, Kim IS, Niessner R, Knopp D. Multiplex competitive microbead-based flow cytometric immunoassay using quantum dot fluorescent labels. Anal Chim Acta 2012; 750:191-8. [PMID: 23062440 DOI: 10.1016/j.aca.2012.05.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Revised: 05/11/2012] [Accepted: 05/12/2012] [Indexed: 01/03/2023]
Abstract
In answer to the ever-increasing need to perform the simultaneous analysis of environmental hazards, microcarrier-based multiplex technologies show great promise. Further integration with biofunctionalized quantum dots (QDs) creates new opportunities to extend the capabilities of multicolor flow cytometry with their unique fluorescence properties. Here, we have developed a competitive microbead-based flow cytometric immunoassay using QDs fluorescent labels for simultaneous detection of two analytes, bringing the benefits of sensitive, rapid and easy-of-manipulation analytical tool for environmental contaminants. As model target compounds, the cyanobacterial toxin microcystin-LR and the polycyclic aromatic hydrocarbon compound benzo[a]pyrene were selected. The assay was carried out in two steps: the competitive immunological reaction of multiple targets using their exclusive sensing elements of QD/antibody detection probes and antigen-coated microsphere, and the subsequent flow cytometric analysis. The fluorescence of the QD-encoded microsphere was thus found to be inversely proportional to target analyte concentration. Under optimized conditions, the proposed assay performed well within 30 min for the identification and quantitative analysis of the two environmental contaminants. For microcystin-LR and benzo[a]pyrene, dose-response curves with IC(50) values of 5 μg L(-1) and 1.1 μg L(-1) and dynamic ranges of 0.52-30 μg L(-1) and 0.13-10 μg L(-1) were obtained, respectively. Recovery was 92.6-106.5% for 5 types of water samples like bottled water, tap water, surface water and seawater using only filtration as sample pretreatment.
Collapse
Affiliation(s)
- Hye-Weon Yu
- School of Environmental Science and Engineering, Gwangju Institute of Science and Technology, 261 Cheomdan-gwagiro, Buk-gu, Gwangju, South Korea
| | | | | | | |
Collapse
|
20
|
Chattopadhyay PK, Gaylord B, Palmer A, Jiang N, Raven MA, Lewis G, Reuter MA, Nur-ur Rahman AKM, Price DA, Betts MR, Roederer M. Brilliant violet fluorophores: a new class of ultrabright fluorescent compounds for immunofluorescence experiments. Cytometry A 2012; 81:456-66. [PMID: 22489009 DOI: 10.1002/cyto.a.22043] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Revised: 02/12/2012] [Accepted: 02/28/2012] [Indexed: 01/11/2023]
Abstract
The Nobel Prize in Chemistry was awarded in 2000 for the discovery of conductive organic polymers, which have subsequently been adapted for applications in ultrasensitive biological detection. Here, we report the first use of this new class of fluorescent probes in a diverse range of cytometric and imaging applications. We demonstrate that these "Brilliant Violet" reporters are dramatically brighter than other UV-violet excitable dyes, and are of similar utility to phycoerythrin (PE) and allophycocyanin (APC). They are thus ideally suited for cytometric assays requiring high sensitivity, such as MHC-multimer staining or detection of intracellular antigens. Furthermore, these reporters are sensitive and spectrally distinct options for fluorescence imaging, two-photon microscopy and imaging cytometry. These ultra-bright materials provide the first new high-sensitivity fluorescence probes in over 25 years and will have a dramatic impact on the design and implementation of multicolor panels for high-sensitivity immunofluorescence assays.
Collapse
Affiliation(s)
- Pratip K Chattopadhyay
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, Maryland 20892, USA.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Abstract
The development of quantum dot (QD) technology represents one of the most dramatic advances in flow cytometry history, offering the opportunity for highly multiplexed experiments and allowing better resolution of dimly staining markers. Here, we guide users through the technical aspects of using QDs (including instrumentation and antibody conjugation), demonstrate why QDs are useful in multicolor flow cytometry, and describe some of the challenges investigators may face when adopting this technology.
Collapse
|
22
|
Abstract
Cytometric techniques are continually being improved, refined, and adapted to new applications. This chapter briefly outlines recent advances in the field of cytometry with the main focus on new instrumentations in flow and image cytometry as well as new probes suitable for multiparametric analyses. There is a remarkable trend for miniaturizing cytometers, developing label-free and fluorescence-free analytical approaches, and designing "intelligent" probes. Furthermore, new methods for analyzing complex data for extracting relevant information are reviewed.
Collapse
|