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Pilkington KR. Autofluorescence: From burden to benefit. Cytometry A 2024. [PMID: 38984776 DOI: 10.1002/cyto.a.24885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 06/11/2024] [Accepted: 06/14/2024] [Indexed: 07/11/2024]
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2
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Roet JEG, Mikula AM, de Kok M, Chadick CH, Garcia Vallejo JJ, Roest HP, van der Laan LJW, de Winde CM, Mebius RE. Unbiased method for spectral analysis of cells with great diversity of autofluorescence spectra. Cytometry A 2024. [PMID: 38863410 DOI: 10.1002/cyto.a.24856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 03/12/2024] [Accepted: 05/29/2024] [Indexed: 06/13/2024]
Abstract
Autofluorescence is an intrinsic feature of cells, caused by the natural emission of light by photo-excitatory molecular content, which can complicate analysis of flow cytometry data. Different cell types have different autofluorescence spectra and, even within one cell type, heterogeneity of autofluorescence spectra can be present, for example, as a consequence of activation status or metabolic changes. By using full spectrum flow cytometry, the emission spectrum of a fluorochrome is captured by a set of photo detectors across a range of wavelengths, creating an unique signature for that fluorochrome. This signature is then used to identify, or unmix, that fluorochrome's unique spectrum from a multicolor sample containing different fluorescent molecules. Importantly, this means that this technology can also be used to identify intrinsic autofluorescence signal of an unstained sample, which can be used for unmixing purposes and to separate the autofluorescence signal from the fluorophore signals. However, this only works if the sample has a singular, relatively homogeneous and bright autofluorescence spectrum. To analyze samples with heterogeneous autofluorescence spectral profiles, we setup an unbiased workflow to more quickly identify differing autofluorescence spectra present in a sample to include as "autofluorescence signatures" during the unmixing of the full stained samples. First, clusters of cells with similar autofluorescence spectra are identified by unbiased dimensional reduction and clustering of unstained cells. Then, unique autofluorescence clusters are determined and are used to improve the unmixing accuracy of the full stained sample. Independent of the intensity of the autofluorescence and immunophenotyping of cell subsets, this unbiased method allows for the identification of most of the distinct autofluorescence spectra present in a sample, leading to less confounding autofluorescence spillover and spread into extrinsic phenotyping markers. Furthermore, this method is equally useful for spectral analysis of different biological samples, including tissue cell suspensions, peripheral blood mononuclear cells, and in vitro cultures of (primary) cells.
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Affiliation(s)
- Janna E G Roet
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
| | - Aleksandra M Mikula
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
| | - Michael de Kok
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
- Microscopy and Cytometry Core Facility, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Cora H Chadick
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
- Microscopy and Cytometry Core Facility, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Juan J Garcia Vallejo
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
- Microscopy and Cytometry Core Facility, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Henk P Roest
- Department of Surgery, Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Luc J W van der Laan
- Department of Surgery, Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Charlotte M de Winde
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
- Cancer Biology and Immunology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Reina E Mebius
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
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Paul Robinson J, Rajwa B. Spectral flow cytometry: Fundamentals and future impact. Methods Cell Biol 2024; 186:311-332. [PMID: 38705605 DOI: 10.1016/bs.mcb.2024.02.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
Spectral flow cytometry has emerged as a significant player in the cytometry marketplace, with the potential for rapid growth. Despite a slow start, the technology has made significant strides in advancing various areas of single-cell analysis utilized by the scientific community. The integration of spectral cytometry into clinical laboratories and diagnostic processes is currently underway and is expected to garner a significant level of widespread acceptance in the near future. However, incorporating a new methodological approach into existing research programs can lead to misunderstandings or even misuse. This chapter offers an introductory yet comprehensive explanation of the scientific principles that form the foundation of spectral cytometry. Specifically, it delves into the unmixing processes that are utilized for data analysis. This overview is designed for those who are new to the field and seeking an informative guide to this exciting emerging technology.
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Affiliation(s)
- J Paul Robinson
- Weldon School of Biomedical Engineering, College of Engineering, Purdue University, West Lafayette, IN, United States; Department of Basic Medical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN, United States.
| | - Bartek Rajwa
- Bindley Bioscience Center, Purdue University, West Lafayette, IN, United States
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Iyengar SN, Robinson JP. Spectral analysis and sorting of microbial organisms using a spectral sorter. Methods Cell Biol 2024; 186:189-212. [PMID: 38705599 DOI: 10.1016/bs.mcb.2024.02.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
This chapter discusses the problems related to the application of conventional flow cytometers to microbiology. To address some of those limitations, the concept of spectral flow cytometry is introduced and the advantages over conventional flow cytometry for bacterial sorting are presented. We demonstrate by using ThermoFisher's Bigfoot spectral sorter where the spectral signatures of different stains for staining bacteria are demonstrated with an example of performing unmixing on spectral datasets. In addition to the Bigfoot's spectral analysis, the special biosafety features of this instrument are discussed. Utilizing these biosafety features, the sorting and patterning at the single cell level is optimized using non-pathogenic bacteria. Finally, the chapter is concluded by presenting a novel, label free, non-destructive, and rapid phenotypic method called Elastic Light Scattering (ELS) technology for identification of the patterned bacterial cells based on their unique colony scatter patterns.
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Affiliation(s)
- Sharath Narayana Iyengar
- Department of Basic Medical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN, United States
| | - J Paul Robinson
- Department of Basic Medical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN, United States; Weldon School of Biomedical Engineering, College of Engineering, Purdue University, West Lafayette, IN, United States.
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Ferrer-Font L, Small SJ, Hyde E, Pilkington KR, Price KM. Panel Design and Optimization for Full Spectrum Flow Cytometry. Methods Mol Biol 2024; 2779:99-124. [PMID: 38526784 DOI: 10.1007/978-1-0716-3738-8_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Technological advancements in fluorescence flow cytometry and an ever-expanding understanding of the complexity of the immune system have led to the development of large flow cytometry panels, reaching up to 40 markers at the single-cell level. Full spectrum flow cytometry, which measures the full emission range of all the fluorophores present in the panel instead of only the emission peaks, is now routinely used in laboratories around the world, and the demand for this technology is rapidly increasing. With the ability to use larger and more complex staining panels, optimized protocols are vital for achieving the best panel design, panel optimization, and high-dimensional data analysis outcomes. In addition, a better understanding of how to fully characterize the autofluorescence of the sample, coupled with an intelligent panel design approach, allows improved marker resolution on highly autofluorescent tissues or cells. Here, we provide optimized step-by-step protocols for full spectrum flow cytometry, covering panel design and optimization, autofluorescence evaluation and strategy selection, and methods for performing longitudinal studies.
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Affiliation(s)
- Laura Ferrer-Font
- Hugh Green Cytometry Centre, Malaghan Institute of Medical Research, Wellington, New Zealand.
| | - Sam J Small
- Hugh Green Cytometry Centre, Malaghan Institute of Medical Research, Wellington, New Zealand
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Evelyn Hyde
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | | | - Kylie M Price
- Hugh Green Cytometry Centre, Malaghan Institute of Medical Research, Wellington, New Zealand
- Malaghan Institute of Medical Research, Wellington, New Zealand
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Cohen M, Laux J, Douagi I. Cytometry in High-Containment Laboratories. Methods Mol Biol 2024; 2779:425-456. [PMID: 38526798 DOI: 10.1007/978-1-0716-3738-8_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
The emergence of new pathogens continues to fuel the need for advanced high-containment laboratories across the globe. Here we explore challenges and opportunities for integration of cytometry, a central technology for cell analysis, within high-containment laboratories. We review current applications in infectious disease, vaccine research, and biosafety. Considerations specific to cytometry within high-containment laboratories, such as biosafety requirements, and sample containment strategies are also addressed. We further tour the landscape of emerging technologies, including combination of cytometry with other omics, the application of automation, and artificial intelligence. Finally, we propose a framework to fast track the immersion of advanced technologies into the high-containment research setting to improve global preparedness for new emerging diseases.
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Affiliation(s)
- Melanie Cohen
- Flow Cytometry Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Julie Laux
- Flow Cytometry Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Iyadh Douagi
- Flow Cytometry Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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Robinson JP, Ostafe R, Iyengar SN, Rajwa B, Fischer R. Flow Cytometry: The Next Revolution. Cells 2023; 12:1875. [PMID: 37508539 PMCID: PMC10378642 DOI: 10.3390/cells12141875] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/06/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Unmasking the subtleties of the immune system requires both a comprehensive knowledge base and the ability to interrogate that system with intimate sensitivity. That task, to a considerable extent, has been handled by an iterative expansion in flow cytometry methods, both in technological capability and also in accompanying advances in informatics. As the field of fluorescence-based cytomics matured, it reached a technological barrier at around 30 parameter analyses, which stalled the field until spectral flow cytometry created a fundamental transformation that will likely lead to the potential of 100 simultaneous parameter analyses within a few years. The simultaneous advance in informatics has now become a watershed moment for the field as it competes with mature systematic approaches such as genomics and proteomics, allowing cytomics to take a seat at the multi-omics table. In addition, recent technological advances try to combine the speed of flow systems with other detection methods, in addition to fluorescence alone, which will make flow-based instruments even more indispensable in any biological laboratory. This paper outlines current approaches in cell analysis and detection methods, discusses traditional and microfluidic sorting approaches as well as next-generation instruments, and provides an early look at future opportunities that are likely to arise.
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Affiliation(s)
- J Paul Robinson
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN 47907, USA
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Raluca Ostafe
- Molecular Evolution, Protein Engineering and Production Facility (PI4D), Purdue University, West Lafayette, IN 47907, USA
| | | | - Bartek Rajwa
- Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA
| | - Rainer Fischer
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute of Inflammation, Immunology and Infectious Diseases, Purdue University, West Lafayette, IN 47907, USA
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Spurgeon BEJ, Frelinger AL. Platelet Phenotyping by Full Spectrum Flow Cytometry. Curr Protoc 2023; 3:e687. [PMID: 36779850 DOI: 10.1002/cpz1.687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
Platelets play key roles in hemostasis, immunity, and inflammation, and tests of platelet phenotype and function are useful in studies of disease biology and pathology. Full spectrum flow cytometry offers distinct advantages over standard tests and enables the sensitive and simultaneous detection of many biomarkers. A typical assay provides a wealth of information on platelet biology and allows the assessment of in vivo activation and in vitro reactivity, as well as the discovery of novel phenotypes. Here, we describe the analysis of platelets by full spectrum flow cytometry and discuss a range of controls and methods for interpreting results. © 2023 Wiley Periodicals LLC. Basic Protocol: Platelet phenotyping by full spectrum flow cytometry Support Protocol 1: Spectral unmixing Support Protocol 2: Data preprocessing.
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Affiliation(s)
- Benjamin E J Spurgeon
- Center for Platelet Research Studies, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts
| | - Andrew L Frelinger
- Center for Platelet Research Studies, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts
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Chao Z, Han Y, Jiao Z, You Z, Zhao J. Prism Design for Spectral Flow Cytometry. MICROMACHINES 2023; 14:315. [PMID: 36838016 PMCID: PMC9966954 DOI: 10.3390/mi14020315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 01/09/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Flow cytometers are instruments used for the rapid quantitative analysis of cell suspension. Traditional flow cytometry uses multi-channel filters to detect fluorescence, whereas full-spectrum fluorescence based on dispersion detection is a more effective and accurate method. The application of various dispersion schemes in flow cytometry spectroscopy has been studied. From the perspective of modern detectors and demand for the miniaturization of flow cytometry, prism dispersion exhibits higher and more uniform light energy utilization, meaning that it is a more suitable dispersion method for small flow cytometers, such as microfluidic flow cytometers. Prism dispersion designs include the size, number, and placement of prisms. By deducing the formula of the final position of light passing through the prism and combining it with the formula of transmittance, the design criteria of the top angle and the incident angle of the prism in pursuit of the optimum transmittance and dispersion index can be obtained. Considering the case of multiple prisms, under the premise of pursuing a smaller size, the optimal design criteria for dispersion system composed of multiple prisms can be obtained. The design of prism dispersion fluorescence detection was demonstrated with a microfluidic flow cytometer, and the effectiveness of the design results was verified by microsphere experiments and practical biological experiments. This design criterion developed in this study is generally applicable to spectral flow cytometers.
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Affiliation(s)
- Zixi Chao
- Department of Precision Instruments, Tsinghua University, Beijing 100084, China
| | - Yong Han
- Department of Precision Instruments, Tsinghua University, Beijing 100084, China
| | - Zeheng Jiao
- Department of Precision Instruments, Tsinghua University, Beijing 100084, China
| | - Zheng You
- Department of Precision Instruments, Tsinghua University, Beijing 100084, China
| | - Jingjing Zhao
- Department of Structural Biology, School of Medicine, Stanford University, Stanford, CA 94305, USA
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