1
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Kuhn TM, Paulsen M, Cuylen-Haering S. Accessible high-speed image-activated cell sorting. Trends Cell Biol 2024; 34:657-670. [PMID: 38789300 DOI: 10.1016/j.tcb.2024.04.007] [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] [Received: 09/06/2023] [Revised: 04/15/2024] [Accepted: 04/23/2024] [Indexed: 05/26/2024]
Abstract
Over the past six decades, fluorescence-activated cell sorting (FACS) has become an essential technology for basic and clinical research by enabling the isolation of cells of interest in high throughput. Recent technological advancements have started a new era of flow cytometry. By combining the spatial resolution of microscopy with high-speed cell sorting, new instruments allow cell sorting based on simple image-derived parameters or sophisticated image analysis algorithms, thereby greatly expanding the scope of applications. In this review, we discuss the systems that are commercially available or have been described in enough methodological and engineering detail to allow their replication. We summarize their strengths and limitations and highlight applications that have the potential to transform various fields in basic life science research and clinical settings.
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Affiliation(s)
- Terra M Kuhn
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Malte Paulsen
- Novo Nordisk Foundation Center for Stem Cell Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Sara Cuylen-Haering
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
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2
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Gholamzad A, Khakpour N, Khosroshahi EM, Asadi S, Koohpar ZK, Matinahmadi A, Jebali A, Rashidi M, Hashemi M, Sadi FH, Gholamzad M. Cancer stem cells: The important role of CD markers, Signaling pathways, and MicroRNAs. Pathol Res Pract 2024; 256:155227. [PMID: 38490099 DOI: 10.1016/j.prp.2024.155227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/23/2024] [Accepted: 02/25/2024] [Indexed: 03/17/2024]
Abstract
For the first time, a subset of small cancer cells identified in acute myeloid leukemia has been termed Cancer Stem Cells (CSCs). These cells are notorious for their robust proliferation, self-renewal abilities, significant tumor-forming potential, spread, and resistance to treatments. CSCs are a global concern, as it found in numerous types of cancer, posing a real-world challenge today. Our review encompasses research on key CSC markers, signaling pathways, and MicroRNA in three types of cancer: breast, colon, and liver. These factors play a critical role in either promoting or inhibiting cancer cell growth. The reviewed studies have shown that as cells undergo malignant transformation, there can be an increase or decrease in the expression of different Cluster of Differentiation (CD) markers on their surface. Furthermore, alterations in essential signaling pathways, such as Wnt and Notch1, may impact CSC proliferation, survival, and movement, while also providing potential targets for cancer therapies. Additionally, some research has focused on MicroRNAs due to their dual role as potential therapeutic biomarkers and their ability to enhance CSCs' response to anti-cancer drugs. MicroRNAs also regulate a wide array of cellular processes, including the self-renewal and pluripotency of CSCs, and influence gene transcription. Thus, these studies indicate that MicroRNAs play a significant role in the malignancy of various tumors. Although the gathered information suggests that specific CSC markers, signaling pathways, and MicroRNAs are influential in determining the destiny of cancer cells and could be advantageous for therapeutic strategies, their precise roles and impacts remain incompletely defined, necessitating further investigation.
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Affiliation(s)
- Amir Gholamzad
- Department of Microbiology and Immunology, Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical sciences, Islamic Azad University, Tehran, Iran
| | - Niloofar Khakpour
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Elaheh Mohandesi Khosroshahi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical sciences, Islamic Azad University, Tehran, Iran
| | - Saba Asadi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical sciences, Islamic Azad University, Tehran, Iran
| | - Zeinab Khazaei Koohpar
- Department of Cell and Molecular Biology, Faculty of Biological Sciences,Tonekabon Branch,Islamic Azad University, Tonekabon, Iran
| | - Arash Matinahmadi
- Department of Cellular and Molecular Biology, Nicolaus Copernicus,Torun,Poland
| | - Ali Jebali
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical sciences, Islamic Azad University, Tehran, Iran; Deprtment of Medical Nanotechnology,Faculty of Advanced Sciences and Technology,Tehran Medical Sciences,Islamic Azad University, Tehran, Iran
| | - Mohsen Rashidi
- Department Pharmacology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran; The Health of Plant and Livestock Products Research Center, Mazandaran University of Medical Sciences, Sari, Iran.
| | - Mehrdad Hashemi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical sciences, Islamic Azad University, Tehran, Iran.
| | | | - Mehrdad Gholamzad
- Department of Microbiology and Immunology, Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
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3
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Lazarski CA, Hanley PJ. Review of flow cytometry as a tool for cell and gene therapy. Cytotherapy 2024; 26:103-112. [PMID: 37943204 PMCID: PMC10872958 DOI: 10.1016/j.jcyt.2023.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 11/10/2023]
Abstract
Quality control testing and analytics are critical for the development and manufacture of cell and gene therapies, and flow cytometry is a key quality control and analytical assay that is used extensively. However, the technical scope of characterization assays and safety assays must keep apace as the breadth of cell therapy products continues to expand beyond hematopoietic stem cell products into producing novel adoptive immune therapies and gene therapy products. Flow cytometry services are uniquely positioned to support the evolving needs of cell therapy facilities, as access to flow cytometers, new antibody clones and improved fluorochrome reagents becomes more egalitarian. This report will outline the features, logistics, limitations and the current state of flow cytometry within the context of cellular therapy.
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Affiliation(s)
- Christopher A Lazarski
- Program for Cell Enhancement and Technology for Immunotherapy, Center for Cancer and Immunology Research, Children's National Hospital, Washington, DC, USA; The George Washington University, Washington, DC, USA.
| | - Patrick J Hanley
- Program for Cell Enhancement and Technology for Immunotherapy, Center for Cancer and Immunology Research, Children's National Hospital, Washington, DC, USA; The George Washington University, Washington, DC, USA.
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4
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Clausen BE, Amon L, Backer RA, Berod L, Bopp T, Brand A, Burgdorf S, Chen L, Da M, Distler U, Dress RJ, Dudziak D, Dutertre CA, Eich C, Gabele A, Geiger M, Ginhoux F, Giusiano L, Godoy GJ, Hamouda AEI, Hatscher L, Heger L, Heidkamp GF, Hernandez LC, Jacobi L, Kaszubowski T, Kong WT, Lehmann CHK, López-López T, Mahnke K, Nitsche D, Renkawitz J, Reza RA, Sáez PJ, Schlautmann L, Schmitt MT, Seichter A, Sielaff M, Sparwasser T, Stoitzner P, Tchitashvili G, Tenzer S, Tochoedo NR, Vurnek D, Zink F, Hieronymus T. Guidelines for mouse and human DC functional assays. Eur J Immunol 2023; 53:e2249925. [PMID: 36563126 DOI: 10.1002/eji.202249925] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 10/25/2022] [Accepted: 10/26/2022] [Indexed: 12/24/2022]
Abstract
This article is part of the Dendritic Cell Guidelines article series, which provides a collection of state-of-the-art protocols for the preparation, phenotype analysis by flow cytometry, generation, fluorescence microscopy, and functional characterization of mouse and human dendritic cells (DC) from lymphoid organs and various non-lymphoid tissues. Recent studies have provided evidence for an increasing number of phenotypically distinct conventional DC (cDC) subsets that on one hand exhibit a certain functional plasticity, but on the other hand are characterized by their tissue- and context-dependent functional specialization. Here, we describe a selection of assays for the functional characterization of mouse and human cDC. The first two protocols illustrate analysis of cDC endocytosis and metabolism, followed by guidelines for transcriptomic and proteomic characterization of cDC populations. Then, a larger group of assays describes the characterization of cDC migration in vitro, ex vivo, and in vivo. The final guidelines measure cDC inflammasome and antigen (cross)-presentation activity. While all protocols were written by experienced scientists who routinely use them in their work, this article was also peer-reviewed by leading experts and approved by all co-authors, making it an essential resource for basic and clinical DC immunologists.
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Affiliation(s)
- Björn E Clausen
- Research Center for Immunotherapy (FZI), University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
- Institute for Molecular Medicine, Paul Klein Center for Immune Intervention, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Lukas Amon
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Germany
| | - Ronald A Backer
- Research Center for Immunotherapy (FZI), University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
- Institute for Molecular Medicine, Paul Klein Center for Immune Intervention, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Luciana Berod
- Research Center for Immunotherapy (FZI), University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
- Institute of Molecular Medicine, University Medical Center of the Johannes Gutenberg-University Mainz, Germany
| | - Tobias Bopp
- Research Center for Immunotherapy (FZI), University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
- Institute of Immunology, Paul Klein Center for Immune Intervention, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
| | - Anna Brand
- Institute for Molecular Medicine, Paul Klein Center for Immune Intervention, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Sven Burgdorf
- Laboratory of Cellular Immunology, LIMES Institute, University of Bonn, Bonn, Germany
| | - Luxia Chen
- Department of Dermatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Meihong Da
- Department of Dermatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Ute Distler
- Research Center for Immunotherapy (FZI), University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
- Institute of Immunology, Paul Klein Center for Immune Intervention, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
| | - Regine J Dress
- Institute of Systems Immunology, Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Diana Dudziak
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Germany
- Medical Immunology Campus Erlangen (MICE), Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Germany
| | - Charles-Antoine Dutertre
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | - Christina Eich
- Institute for Molecular Medicine, Paul Klein Center for Immune Intervention, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Anna Gabele
- Research Center for Immunotherapy (FZI), University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
- Institute of Immunology, Paul Klein Center for Immune Intervention, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
| | - Melanie Geiger
- Institute for Biomedical Engineering, Department of Cell Biology, RWTH Aachen University, Medical Faculty, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Florent Ginhoux
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Lucila Giusiano
- Institute of Medical Microbiology and Hygiene, University Medical Center of the Johannes Gutenberg-University Mainz, Germany
| | - Gloria J Godoy
- Institute of Medical Microbiology and Hygiene, University Medical Center of the Johannes Gutenberg-University Mainz, Germany
| | - Ahmed E I Hamouda
- Institute for Biomedical Engineering, Department of Cell Biology, RWTH Aachen University, Medical Faculty, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Lukas Hatscher
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Germany
| | - Lukas Heger
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Germany
| | - Gordon F Heidkamp
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Germany
| | - Lola C Hernandez
- Cell Communication and Migration Laboratory, Institute of Biochemistry and Molecular Cell Biology, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lukas Jacobi
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Germany
| | - Tomasz Kaszubowski
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Germany
| | - Wan Ting Kong
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | - Christian H K Lehmann
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Germany
- Medical Immunology Campus Erlangen (MICE), Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Germany
| | - Tamara López-López
- Cell Communication and Migration Laboratory, Institute of Biochemistry and Molecular Cell Biology, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Karsten Mahnke
- Department of Dermatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Dominik Nitsche
- Laboratory of Cellular Immunology, LIMES Institute, University of Bonn, Bonn, Germany
| | - Jörg Renkawitz
- Biomedical Center (BMC), Walter Brendel Center of Experimental Medicine, Institute of Cardiovascular Physiology and Pathophysiology, Klinikum der Universität, LMU Munich, Munich, Germany
| | - Rifat A Reza
- Biomedical Center (BMC), Walter Brendel Center of Experimental Medicine, Institute of Cardiovascular Physiology and Pathophysiology, Klinikum der Universität, LMU Munich, Munich, Germany
| | - Pablo J Sáez
- Cell Communication and Migration Laboratory, Institute of Biochemistry and Molecular Cell Biology, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Laura Schlautmann
- Laboratory of Cellular Immunology, LIMES Institute, University of Bonn, Bonn, Germany
| | - Madeleine T Schmitt
- Biomedical Center (BMC), Walter Brendel Center of Experimental Medicine, Institute of Cardiovascular Physiology and Pathophysiology, Klinikum der Universität, LMU Munich, Munich, Germany
| | - Anna Seichter
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Germany
| | - Malte Sielaff
- Research Center for Immunotherapy (FZI), University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
- Institute of Immunology, Paul Klein Center for Immune Intervention, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
| | - Tim Sparwasser
- Research Center for Immunotherapy (FZI), University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
- Institute of Medical Microbiology and Hygiene, University Medical Center of the Johannes Gutenberg-University Mainz, Germany
| | - Patrizia Stoitzner
- Department of Dermatology, Venerology & Allergology, Medical University Innsbruck, Innsbruck, Austria
| | - Giorgi Tchitashvili
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Germany
| | - Stefan Tenzer
- Research Center for Immunotherapy (FZI), University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
- Institute of Immunology, Paul Klein Center for Immune Intervention, University Medical Center of the Johannes-Gutenberg University Mainz, Mainz, Germany
- Helmholtz Institute for Translational Oncology Mainz (HI-TRON Mainz), Mainz, Germany
| | - Nounagnon R Tochoedo
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Germany
| | - Damir Vurnek
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Germany
| | - Fabian Zink
- Laboratory of Cellular Immunology, LIMES Institute, University of Bonn, Bonn, Germany
| | - Thomas Hieronymus
- Institute for Biomedical Engineering, Department of Cell Biology, RWTH Aachen University, Medical Faculty, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
- Institute of Cell and Tumor Biology, RWTH Aachen University, Medical Faculty, Germany
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5
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Brune-Ingebretsen S, Høgestøl EA, de Rosbo NK, Berg-Hansen P, Brunborg C, Blennow K, Zetterberg H, Paul F, Uccelli A, Villoslada P, Harbo HF, Berge T. Immune cell subpopulations and serum neurofilament light chain are associated with increased risk of disease worsening in multiple sclerosis. J Neuroimmunol 2023; 382:578175. [PMID: 37573634 DOI: 10.1016/j.jneuroim.2023.578175] [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] [Received: 03/13/2023] [Revised: 05/18/2023] [Accepted: 08/06/2023] [Indexed: 08/15/2023]
Abstract
Changes is lymphocyte subpopulations in peripheral blood have been proposed as biomarkers for evaluation of disease activity in multiple sclerosis (MS). Serum neurofilament light chain (sNfL) is a biomarker reflecting neuro-axonal injury in MS that could be used to monitor disease activity, response to drugs and to prognosticate disease course. Here we show a moderate correlation between sNfL and lymphocyte cell subpopulations, and our data furthermore suggest that sNfL and specific immune cell subpopulations together could predict future disease worsening in MS.
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Affiliation(s)
- Synne Brune-Ingebretsen
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Neurology, Oslo University Hospital, Oslo, Norway.
| | - Einar A Høgestøl
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Neurology, Oslo University Hospital, Oslo, Norway; Department of Psychology, University of Oslo, Oslo, Norway
| | - Nicole Kerlero de Rosbo
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy; TomaLab, Institute of Nanotechnology, National Research Council (CNR), Rome, Italy
| | - Pål Berg-Hansen
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Cathrine Brunborg
- Oslo Centre for Biostatistics and Epidemiology, Oslo University Hospital, Oslo, Norway
| | - Kaj Blennow
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden; Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Henrik Zetterberg
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden; Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden; Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, United Kingdom; UK Dementia Research Institute at UCL, London, United Kingdom; Hong Kong Center for Neurodegenerative Diseases, Clear Water Bay, Hong Kong, China; Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Friedemann Paul
- Experimental and Clinical Research Center, Max Delbrueck Center for Molecular Medicine and Charité-Universitaetsmedizin Berlin, Berlin, Germany; NeuroCure Clinical Research Center, Charité-Universitaetsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Berlin, Germany
| | - Antonio Uccelli
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy; Center of Excellence for Biomedical Research, University of Genoa, Genoa, Italy; IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Pablo Villoslada
- Institut d'Investigacions Biomediques August Pi Sunyer, Barcelona, Spain
| | - Hanne F Harbo
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Tone Berge
- Department of Research, Innovation and Education, Oslo University Hospital, Oslo, Norway; Department of Mechanical, Electronic and Chemical Engineering, Oslo Metropolitan University, Oslo, Norway
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6
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Gerling T, Godino N, Pfisterer F, Hupf N, Kirschbaum M. High-precision, low-complexity, high-resolution microscopy-based cell sorting. LAB ON A CHIP 2023. [PMID: 37314345 DOI: 10.1039/d3lc00242j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Continuous flow cell sorting based on image analysis is a powerful concept that exploits spatially-resolved features in cells, such as subcellular protein localisation or cell and organelle morphology, to isolate highly specialised cell types that were previously inaccessible to biomedical research, biotechnology, and medicine. Recently, sorting protocols have been proposed that achieve impressive throughput by combining ultra-high flow rates with sophisticated imaging and data processing protocols. However, moderate image quality and high complex experimental setups still prevent the full potential of image-activated cell sorting from being a general-purpose tool. Here, we present a new low-complexity microfluidic approach based on high numerical aperture wide-field microscopy and precise dielectrophoretic cell handling. It provides high-quality images with unprecedented resolution in image-activated cell sorting (i.e., 216 nm). In addition, it also allows long image processing times of several hundred milliseconds for thorough image analysis, while ensuring reliable and low-loss cell processing. Using our approach, we sorted live T cells based on subcellular localisation of fluorescence signals and demonstrated that purities above 80% are possible while targeting maximum yields and sample volume throughputs in the range of μl min-1. We were able to recover 85% of the target cells analysed. Finally, we ensure and quantify the full vitality of the sorted cells cultivating the cells for a period of time and through colorimetric viability tests.
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Affiliation(s)
- Tobias Gerling
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses IZI-BB, Am Muehlenberg 13, 14476 Potsdam, Germany.
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany
| | - Neus Godino
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses IZI-BB, Am Muehlenberg 13, 14476 Potsdam, Germany.
| | - Felix Pfisterer
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses IZI-BB, Am Muehlenberg 13, 14476 Potsdam, Germany.
| | - Nina Hupf
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses IZI-BB, Am Muehlenberg 13, 14476 Potsdam, Germany.
| | - Michael Kirschbaum
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses IZI-BB, Am Muehlenberg 13, 14476 Potsdam, Germany.
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7
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El-Hajjar L, Ali Ahmad F, Nasr R. A Guide to Flow Cytometry: Components, Basic Principles, Experimental Design, and Cancer Research Applications. Curr Protoc 2023; 3:e721. [PMID: 36946745 DOI: 10.1002/cpz1.721] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Flow cytometry (FCM) is a state-of-the-art technique for the qualitative and quantitative assessment of cells and other particles' physical and biological properties. These cells are suspended within a high-velocity fluid stream and pass through a laser beam in single file. The main principle of the FCM instrument is the light scattering and fluorescence emission upon the interaction of the fluorescent particle with the laser beam. It also allows for the physical sorting of particles depending on different parameters. A flow cytometer comprises different components, including fluidic, optics, and electronics systems. This article briefly explains the mechanism of all components of a flow cytometer to clarify the FCM technique's general principles, provides some useful guidelines for the proper design of FCM panels, and highlights some general applications and important applications in cancer research. © 2023 Wiley Periodicals LLC.
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Affiliation(s)
- Layal El-Hajjar
- Office of Basic/Translational Research and Graduate Studies, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Fatima Ali Ahmad
- Office of Basic/Translational Research and Graduate Studies, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Rihab Nasr
- Office of Basic/Translational Research and Graduate Studies, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Department of Anatomy, Cell Biology, and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
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8
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Elshari ZS, Nepesov S, Tahrali I, Kiykim A, Camcioglu Y, Deniz G, Kucuksezer UC. Comparison of mitogen-induced proliferation in child and adult healthy groups by flow cytometry revealed similarities. Immunol Res 2023; 71:51-59. [PMID: 36261686 DOI: 10.1007/s12026-022-09328-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 10/07/2022] [Indexed: 01/27/2023]
Abstract
The proliferation of antigen-specific lymphocyte clones, the initial step in acquired immunity, is vital for effector functions. Proliferation tests both in immunology research and diagnosis are gaining attendance gradually, while the use of adult healthy individuals as controls of pediatric patients is a question. This study aimed to investigate and compare mitogen-stimulated proliferation responses of total lymphocytes and T- and B-lymphocyte subsets in adult and children healthy donors. Nineteen children and 20 adult healthy donors were enrolled in this study. Peripheral blood mononuclear cells (PBMCs) purified from peripheral blood samples of the donors, by Ficoll gradient centrifugation, were stained with CFSE and were cultured in a 37 ℃ CO2 incubator for 120 h with the absence or existence of polyclonal activators: PHA and CD-Mix. After cell culture, PBMCs were stained with monoclonal antibodies against CD4 and CD19, and proliferation percentages of CD4+ T and CD19+ B cells, together with total lymphocytes were determined by flow cytometry. This study revealed similarities between children and adult age groups, concerning mitogenic stimulation of the lymphocytes. The only difference was a significantly high proliferation of pediatric CD4+ T cells in response to PHA. CD4+ T cell responses against PHA were inversely correlated with altering age. When pediatric individuals were distributed into age groups of 0-2 years, 3-5 years, and 6-18 years, PHA responses of CD4+ cells were found to be diminished with advancing age. These findings propose the possibility of enrollment of adult healthy individuals as controls for pediatric patients.
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Affiliation(s)
- Zakya Shoub Elshari
- Graduate School of Health Sciences, Istanbul University, Vakif Gureba St. 34093, Fatih, Istanbul, Turkey.,Department of Immunology, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Vakif Gureba St. 34093, Fatih, Istanbul, Turkey
| | - Serdar Nepesov
- Department of Pediatrics, Division of Pediatric Allergy and Immunology, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey.,Department of Pediatrics, Division of Pediatric Allergy and Immunology, Medical Park Goztepe Hospital, Istanbul, Turkey
| | - Ilhan Tahrali
- Department of Immunology, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Vakif Gureba St. 34093, Fatih, Istanbul, Turkey
| | - Ayca Kiykim
- Department of Pediatrics, Division of Pediatric Allergy and Immunology, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Yildiz Camcioglu
- Department of Pediatrics, Division of Pediatric Allergy and Immunology, Cerrahpasa Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Gunnur Deniz
- Department of Immunology, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Vakif Gureba St. 34093, Fatih, Istanbul, Turkey
| | - Umut Can Kucuksezer
- Department of Immunology, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Vakif Gureba St. 34093, Fatih, Istanbul, Turkey.
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9
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Soh KT, Conway A, Liu X, Wallace PK. Development of a 27-color panel for the detection of measurable residual disease in patients diagnosed with acute myeloid leukemia. Cytometry A 2022; 101:970-983. [PMID: 35716345 DOI: 10.1002/cyto.a.24667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 04/26/2022] [Accepted: 06/15/2022] [Indexed: 01/27/2023]
Abstract
Acute myeloid leukemia (AML) measurable residual disease (MRD) evaluated by multiparametric flow cytometry (MFC) is a surrogate for progression-free and overall survival in clinical trials and patient management. Due to the limited number of detection channels available in conventional flow cytometers, panels used for assessing AML MRD are typically split into multiple tubes. This cripples the simultaneous and correlated assessment of all myeloblast measurements. In response, we prototyped a single-tube 27-color MFC assay for the evaluation of AML MRD, incorporating all recommended markers. Marrow aspirates from 22 patients were processed for analysis using full spectrum flow cytometry (FSFC). The signal resolution of each marker was compared between samples stained with single antibody vs. the fully stained panel. The analytical accuracy for quantifying hematopoietic cells between our established 8-color assay and the new 27-color method were compared. Variations within an operator and between separate operators were assessed to evaluate the assays reproducibility. The limited of blank (LOB), limit of detection (LOD), and lower limit of quantification (LLOQ) of the 27-color method were empirically determined using limiting dilution experiments. The stability of antibody cocktails over a period of 120 h was also studied using cryopreserved marrow cells. The stain indices for all antibodies were lower in the fully stained panel compared to cells stained with one antibody but clear separations between negative and positive signals were achieved for all antibodies. Our results demonstrated a high concordance between the established 8-color method and the new 27-color assay for enumerating myeloblasts and MRD interpretation within and between operators. The data further showed that the single-tube 27-color assay easily achieved the minimum required detection sensitivity of 0.1%. When antibodies were combined, however, expression intensity of some antigens deteriorated significantly when stored. Our single-tube 27-color panel is a suitable, high sensitivity flow cytometric approach that can be used for AML MRD testing, which improves the correlation of aberrant antigens and detection of asynchronous differentiation patterns. Based on the stability study, we recommend the full panel be made prior to staining.
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Affiliation(s)
- Kah Teong Soh
- Department of Flow and Image Cytometry, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Alexis Conway
- Department of Flow and Image Cytometry, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Xiaojun Liu
- Department of Flow and Image Cytometry, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Paul K Wallace
- Department of Flow and Image Cytometry, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
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10
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Rozowsky JS, Meesters-Ensing JI, Lammers JAS, Belle ML, Nierkens S, Kranendonk MEG, Kester LA, Calkoen FG, van der Lugt J. A Toolkit for Profiling the Immune Landscape of Pediatric Central Nervous System Malignancies. Front Immunol 2022; 13:864423. [PMID: 35464481 PMCID: PMC9022116 DOI: 10.3389/fimmu.2022.864423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/11/2022] [Indexed: 11/13/2022] Open
Abstract
The prognosis of pediatric central nervous system (CNS) malignancies remains dismal due to limited treatment options, resulting in high mortality rates and long-term morbidities. Immunotherapies, including checkpoint inhibition, cancer vaccines, engineered T cell therapies, and oncolytic viruses, have promising results in some hematological and solid malignancies, and are being investigated in clinical trials for various high-grade CNS malignancies. However, the role of the tumor immune microenvironment (TIME) in CNS malignancies is mostly unknown for pediatric cases. In order to successfully implement immunotherapies and to eventually predict which patients would benefit from such treatments, in-depth characterization of the TIME at diagnosis and throughout treatment is essential. In this review, we provide an overview of techniques for immune profiling of CNS malignancies, and detail how they can be utilized for different tissue types and studies. These techniques include immunohistochemistry and flow cytometry for quantifying and phenotyping the infiltrating immune cells, bulk and single-cell transcriptomics for describing the implicated immunological pathways, as well as functional assays. Finally, we aim to describe the potential benefits of evaluating other compartments of the immune system implicated by cancer therapies, such as cerebrospinal fluid and blood, and how such liquid biopsies are informative when designing immune monitoring studies. Understanding and uniformly evaluating the TIME and immune landscape of pediatric CNS malignancies will be essential to eventually integrate immunotherapy into clinical practice.
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Affiliation(s)
| | | | | | - Muriël L. Belle
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Stefan Nierkens
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | | | | | - Friso G. Calkoen
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
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11
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Pedersen CB, Dam SH, Barnkob MB, Leipold MD, Purroy N, Rassenti LZ, Kipps TJ, Nguyen J, Lederer JA, Gohil SH, Wu CJ, Olsen LR. cyCombine allows for robust integration of single-cell cytometry datasets within and across technologies. Nat Commun 2022; 13:1698. [PMID: 35361793 PMCID: PMC8971492 DOI: 10.1038/s41467-022-29383-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 03/14/2022] [Indexed: 12/21/2022] Open
Abstract
Combining single-cell cytometry datasets increases the analytical flexibility and the statistical power of data analyses. However, in many cases the full potential of co-analyses is not reached due to technical variance between data from different experimental batches. Here, we present cyCombine, a method to robustly integrate cytometry data from different batches, experiments, or even different experimental techniques, such as CITE-seq, flow cytometry, and mass cytometry. We demonstrate that cyCombine maintains the biological variance and the structure of the data, while minimizing the technical variance between datasets. cyCombine does not require technical replicates across datasets, and computation time scales linearly with the number of cells, allowing for integration of massive datasets. Robust, accurate, and scalable integration of cytometry data enables integration of multiple datasets for primary data analyses and the validation of results using public datasets.
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Affiliation(s)
- Christina Bligaard Pedersen
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
- Center for Genomic Medicine, Rigshospitalet-Copenhagen University Hospital, Copenhagen, Denmark
| | - Søren Helweg Dam
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Mike Bogetofte Barnkob
- Centre for Cellular Immunotherapy of Haematological Cancer Odense (CITCO), Department of Clinical Immunology, Odense University Hospital, University of Southern Denmark, Odense, Denmark
| | - Michael D Leipold
- Human Immune Monitoring Center, Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Noelia Purroy
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- AstraZeneca, Waltham, MA, USA
| | - Laura Z Rassenti
- Division of Hematology-Oncology, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Thomas J Kipps
- Division of Hematology-Oncology, Department of Medicine, Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Jennifer Nguyen
- Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - James Arthur Lederer
- Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Satyen Harish Gohil
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Academic Haematology, University College London, London, UK
- Department of Haematology, University College London Hospitals NHS Trust, London, UK
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lars Rønn Olsen
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark.
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12
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Sheng J, Hod EA, Vlad G, Chavez A. Quantifying protein abundance on single cells using split-pool sequencing on DNA-barcoded antibodies for diagnostic applications. Sci Rep 2022; 12:884. [PMID: 35042926 PMCID: PMC8766443 DOI: 10.1038/s41598-022-04842-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 01/03/2022] [Indexed: 12/11/2022] Open
Abstract
Proteins play critical roles across all facets of biology, with their abundance frequently used as markers of cell identity and state. The most popular method for detecting proteins on single cells, flow cytometry, is limited by considerations of fluorescent spectral overlap. While mass cytometry (CyTOF) allows for the detection of upwards of 40 epitopes simultaneously, it requires local access to specialized instrumentation not commonly accessible to many laboratories. To overcome these limitations, we independently developed a method to quantify multiple protein targets on single cells without the need for specialty equipment other than access to widely available next generation sequencing (NGS) services. We demonstrate that this combinatorial indexing method compares favorably to traditional flow-cytometry, and allows over two dozen target proteins to be assayed at a time on single cells. To showcase the potential of the technique, we analyzed peripheral blood and bone marrow aspirates from human clinical samples, and identified pathogenic cellular subsets with high fidelity. The ease of use of this technique makes it a promising technology for high-throughput proteomics and for interrogating complex samples such as those from patients with leukemia.
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Affiliation(s)
- Jenny Sheng
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Eldad A Hod
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - George Vlad
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Alejandro Chavez
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA.
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13
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Gökçe F, Ravaynia PS, Modena MM, Hierlemann A. What is the future of electrical impedance spectroscopy in flow cytometry? BIOMICROFLUIDICS 2021; 15:061302. [PMID: 34917226 PMCID: PMC8651262 DOI: 10.1063/5.0073457] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/23/2021] [Indexed: 05/02/2023]
Abstract
More than 20 years ago, electrical impedance spectroscopy (EIS) was proposed as a potential characterization method for flow cytometry. As the setup is comparably simple and the method is label-free, EIS has attracted considerable interest from the research community as a potential alternative to standard optical methods, such as fluorescence-activated cell sorting (FACS). However, until today, FACS remains by and large the laboratory standard with highly developed capabilities and broad use in research and clinical settings. Nevertheless, can EIS still provide a complement or alternative to FACS in specific applications? In this Perspective, we will give an overview of the current state of the art of EIS in terms of technologies and capabilities. We will then describe recent advances in EIS-based flow cytometry, compare the performance to that of FACS methods, and discuss potential prospects of EIS in flow cytometry.
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Affiliation(s)
- Furkan Gökçe
- Bioengineering Laboratory, Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Paolo S. Ravaynia
- Bioengineering Laboratory, Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Mario M. Modena
- Bioengineering Laboratory, Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Andreas Hierlemann
- Bioengineering Laboratory, Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
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14
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Abstract
Flow cytometry is a laser-based technology generating a scattered and a fluorescent light signal that enables rapid analysis of the size and granularity of a particle or single cell. In addition, it offers the opportunity to phenotypically characterize and collect the cell with the use of a variety of fluorescent reagents. These reagents include but are not limited to fluorochrome-conjugated antibodies, fluorescent expressing protein-, viability-, and DNA-binding dyes. Major developments in reagents, electronics, and software within the last 30 years have greatly expanded the ability to combine up to 50 antibodies in one single tube. However, these advances also harbor technical risks and interpretation issues in the identification of certain cell populations which will be summarized in this viewpoint article. It will further provide an overview of different potential applications of flow cytometry in research and its possibilities to be used in the clinic.
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15
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Fernández-Bañares F, López-Palacios N, Corzo M, Arau B, Rubio M, Fernández-Prieto M, Tristán E, Pujals M, Farrais S, Horta S, Hernández JM, Gomez-Perosanz M, Reche PA, Esteve M, Núñez C. Activated gut-homing CD8 + T cells for coeliac disease diagnosis on a gluten-free diet. BMC Med 2021; 19:237. [PMID: 34610833 PMCID: PMC8493675 DOI: 10.1186/s12916-021-02116-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 09/01/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The diagnosis of coeliac disease (CD) in individuals that have started a gluten-free diet (GFD) without an adequate previous diagnostic work-out is a challenge. Several immunological assays such as IFN-γ ELISPOT have been developed to avoid the need of prolonged gluten challenge to induce the intestinal damage. We aimed to evaluate the diagnostic accuracy of activated gut-homing CD8+ and TCRγδ+ T cells in blood after a 3-day gluten challenge and to compare it with the performance of IFN-γ ELISPOT in a HLA-DQ2.5 subsample. METHODS A total of 22 CD patients and 48 non-CD subjects, all of them following a GFD, underwent a 3-day 10-g gluten challenge. The percentage of two T cell subsets (CD8+ CD103+ β7hi CD38+/total CD8+ and TCRγδ+ CD103+ β7hi CD38+/total TCRγδ+) in fresh peripheral blood drawn baseline and 6 days after the challenge was determined by flow cytometry. IFN-γ ELISPOT assays were also performed in HLA-DQ2.5 participants. ROC curve analysis was used to assess the diagnostic performance of the CD8+ T cell response and IFN-γ ELISPOT. RESULTS Significant differences between the percentage of the two studied subsets of CD8+ and TCRγδ+ cells at days 0 and 6 were found only when considering CD patients (p < 10-3 vs. non-CD subjects). Measuring activated CD8+ T cells provided accurate CD diagnosis with 95% specificity and 97% sensitivity, offering similar results than IFN-γ ELISPOT. CONCLUSIONS The results provide a highly accurate blood test for CD diagnosis in patients on a GFD of easy implementation in daily clinical practice.
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Affiliation(s)
- Fernando Fernández-Bañares
- Department of Gastroenterology, Hospital Universitari Mutua Terrassa, Terrassa, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Natalia López-Palacios
- Servicio de Aparato Digestivo, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), 28040, Madrid, Spain
| | - María Corzo
- Laboratorio de Investigación en Genética de enfermedades complejas, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), 28040, Madrid, Spain
| | - Beatriz Arau
- Department of Gastroenterology, Hospital Universitari Mutua Terrassa, Terrassa, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Mercedes Rubio
- Laboratorio de Investigación en Genética de enfermedades complejas, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), 28040, Madrid, Spain
| | - Marta Fernández-Prieto
- Laboratorio de Investigación en Genética de enfermedades complejas, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), 28040, Madrid, Spain
| | - Eva Tristán
- Department of Gastroenterology, Hospital Universitari Mutua Terrassa, Terrassa, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Mar Pujals
- Department of Gastroenterology, Hospital Universitari Mutua Terrassa, Terrassa, Barcelona, Spain
| | - Sergio Farrais
- Servicio de Aparato Digestivo, Hospital Universitario Fundación Jiménez Díaz, 28040, Madrid, Spain
| | - Saúl Horta
- Laboratorio de Investigación en Genética de enfermedades complejas, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), 28040, Madrid, Spain
| | - Juana María Hernández
- Department of Gastroenterology, Hospital Universitari Mutua Terrassa, Terrassa, Barcelona, Spain
| | - Marta Gomez-Perosanz
- Facultad de Medicina, Laboratorio de Inmunomedicina, Departamento de Inmunología, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Pedro A Reche
- Facultad de Medicina, Laboratorio de Inmunomedicina, Departamento de Inmunología, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - María Esteve
- Department of Gastroenterology, Hospital Universitari Mutua Terrassa, Terrassa, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Concepción Núñez
- Laboratorio de Investigación en Genética de enfermedades complejas, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), 28040, Madrid, Spain.
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16
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Courtney SJ, Stromberg ZR, Myers y Gutiérrez A, Jacobsen D, Stromberg LR, Lenz KD, Theiler J, Foley BT, Gans J, Yusim K, Kubicek-Sutherland JZ. Optical Biosensor Platforms Display Varying Sensitivity for the Direct Detection of Influenza RNA. BIOSENSORS 2021; 11:367. [PMID: 34677323 PMCID: PMC8534094 DOI: 10.3390/bios11100367] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 12/28/2022]
Abstract
Detection methods that do not require nucleic acid amplification are advantageous for viral diagnostics due to their rapid results. These platforms could provide information for both accurate diagnoses and pandemic surveillance. Influenza virus is prone to pandemic-inducing genetic mutations, so there is a need to apply these detection platforms to influenza diagnostics. Here, we analyzed the Fast Evaluation of Viral Emerging Risks (FEVER) pipeline on ultrasensitive detection platforms, including a waveguide-based optical biosensor and a flow cytometry bead-based assay. The pipeline was also evaluated in silico for sequence coverage in comparison to the U.S. Centers for Disease Control and Prevention's (CDC) influenza A and B diagnostic assays. The influenza FEVER probe design had a higher tolerance for mismatched bases than the CDC's probes, and the FEVER probes altogether had a higher detection rate for influenza isolate sequences from GenBank. When formatted for use as molecular beacons, the FEVER probes detected influenza RNA as low as 50 nM on the waveguide-based optical biosensor and 1 nM on the flow cytometer. In addition to molecular beacons, which have an inherently high background signal we also developed an exonuclease selection method that could detect 500 pM of RNA. The combination of high-coverage probes developed using the FEVER pipeline coupled with ultrasensitive optical biosensors is a promising approach for future influenza diagnostic and biosurveillance applications.
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Affiliation(s)
- Samantha J. Courtney
- Physical Chemistry and Applied Spectroscopy, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (S.J.C.); (Z.R.S.); (D.J.); (L.R.S.); (K.D.L.)
| | - Zachary R. Stromberg
- Physical Chemistry and Applied Spectroscopy, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (S.J.C.); (Z.R.S.); (D.J.); (L.R.S.); (K.D.L.)
| | - Adán Myers y Gutiérrez
- Biosecurity and Public Health, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (A.M.y.G.); (J.G.)
| | - Daniel Jacobsen
- Physical Chemistry and Applied Spectroscopy, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (S.J.C.); (Z.R.S.); (D.J.); (L.R.S.); (K.D.L.)
| | - Loreen R. Stromberg
- Physical Chemistry and Applied Spectroscopy, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (S.J.C.); (Z.R.S.); (D.J.); (L.R.S.); (K.D.L.)
| | - Kiersten D. Lenz
- Physical Chemistry and Applied Spectroscopy, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (S.J.C.); (Z.R.S.); (D.J.); (L.R.S.); (K.D.L.)
| | - James Theiler
- Space Data Science and Systems, Los Alamos National Laboratory, Los Alamos, NM 87545, USA;
| | - Brian T. Foley
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA;
| | - Jason Gans
- Biosecurity and Public Health, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (A.M.y.G.); (J.G.)
| | - Karina Yusim
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA;
| | - Jessica Z. Kubicek-Sutherland
- Physical Chemistry and Applied Spectroscopy, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (S.J.C.); (Z.R.S.); (D.J.); (L.R.S.); (K.D.L.)
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17
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Shi J, Mu RQ, Wang P, Geng WQ, Jiang YJ, Zhao M, Shang H, Zhang ZN. The development of autoverification system of lymphocyte subset assays on the flow cytometry platform. Clin Chem Lab Med 2021; 60:92-100. [PMID: 34533003 DOI: 10.1515/cclm-2021-0736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 09/04/2021] [Indexed: 11/15/2022]
Abstract
OBJECTIVES Peripheral blood lymphocyte subsets are important parameters for monitoring immune status; however, lymphocyte subset detection is time-consuming and error-prone. This study aimed to explore a highly efficient and clinically useful autoverification system for lymphocyte subset assays performed on the flow cytometry platform. METHODS A total of 94,402 lymphocyte subset test results were collected. To establish the limited-range rules, 80,427 results were first used (69,135 T lymphocyte subset tests and 11,292 NK, B, T lymphocyte tests), of which 15,000 T lymphocyte subset tests from human immunodeficiency virus (HIV) infected patients were used to set customized limited-range rules for HIV infected patients. Subsequently, 13,975 results were used for historical data validation and online test validation. RESULTS Three key autoverification rules were established, including limited-range, delta-check, and logical rules. Guidelines for addressing the issues that trigger these rules were summarized. The historical data during the validation phase showed that the total autoverification passing rate of lymphocyte subset assays was 69.65% (6,941/9,966), with a 67.93% (5,268/7,755) passing rate for T lymphocyte subset tests and 75.67% (1,673/2,211) for NK, B, T lymphocyte tests. For online test validation, the total autoverification passing rate was 75.26% (3,017/4,009), with 73.23% (2,191/2,992) for the T lymphocyte subset test and 81.22% (826/1,017) for the NK, B, T lymphocyte test. The turnaround time (TAT) was reduced from 228 to 167 min using the autoverification system. CONCLUSIONS The autoverification system based on the laboratory information system for lymphocyte subset assays reduced TAT and the number of error reports and helped in the identification of abnormal cell populations that may offer clues for clinical interventions.
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Affiliation(s)
- Jue Shi
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, P. R. China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, P. R. China
| | - Run-Qing Mu
- Department of Laboratory Medicine, National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, P. R. China
| | - Pan Wang
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, P. R. China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, P. R. China
| | - Wen-Qing Geng
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, P. R. China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, P. R. China
| | - Yong-Jun Jiang
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, P. R. China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, P. R. China
| | - Min Zhao
- Department of Laboratory Medicine, National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, P. R. China
| | - Hong Shang
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, P. R. China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, P. R. China.,Department of Laboratory Medicine, National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, P. R. China
| | - Zi-Ning Zhang
- NHC Key Laboratory of AIDS Immunology (China Medical University), National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, P. R. China.,Key Laboratory of AIDS Immunology, Chinese Academy of Medical Sciences, Shenyang, P. R. China
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18
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Lee K, Kim SE, Doh J, Kim K, Chung WK. User-friendly image-activated microfluidic cell sorting technique using an optimized, fast deep learning algorithm. LAB ON A CHIP 2021; 21:1798-1810. [PMID: 33734252 DOI: 10.1039/d0lc00747a] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Image-activated cell sorting is an essential biomedical research technique for understanding the unique characteristics of single cells. Deep learning algorithms can be used to extract hidden cell features from high-content image information to enable the discrimination of cell-to-cell differences in image-activated cell sorters. However, such systems are challenging to implement from a technical perspective due to the advanced imaging and sorting requirements and the long processing times of deep learning algorithms. Here, we introduce a user-friendly image-activated microfluidic sorting technique based on a fast deep learning model under the TensorRT framework to enable sorting decisions within 3 ms. The proposed sorter employs a significantly simplified operational procedure based on the use of a syringe connected to a piezoelectric actuator. The sorter has a 2.5 ms latency. The utility of the sorter was demonstrated through real-time sorting of fluorescent polystyrene beads and cells. The sorter achieved 98.0%, 95.1%, and 94.2% sorting purities for 15 μm and 10 μm beads, HL-60 and Jurkat cells, and HL-60 and K562 cells, respectively, with a throughput of up to 82.8 events per second (eps).
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Affiliation(s)
- Keondo Lee
- Department of Mechanical Engineering, Pohang University of Science and Technology, Pohang (POSTECH), 77, Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea.
| | - Seong-Eun Kim
- Department of Mechanical Engineering, Pohang University of Science and Technology, Pohang (POSTECH), 77, Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea.
| | - Junsang Doh
- Department of Materials Science and Engineering, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Keehoon Kim
- Department of Mechanical Engineering, Pohang University of Science and Technology, Pohang (POSTECH), 77, Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea.
| | - Wan Kyun Chung
- Department of Mechanical Engineering, Pohang University of Science and Technology, Pohang (POSTECH), 77, Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, South Korea.
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Nissim N, Dudaie M, Barnea I, Shaked NT. Real-Time Stain-Free Classification of Cancer Cells and Blood Cells Using Interferometric Phase Microscopy and Machine Learning. Cytometry A 2020; 99:511-523. [PMID: 32910546 DOI: 10.1002/cyto.a.24227] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 07/29/2020] [Accepted: 09/07/2020] [Indexed: 12/14/2022]
Abstract
We present a method for real-time visualization and automatic processing for detection and classification of untreated cancer cells in blood during stain-free imaging flow cytometry using digital holographic microscopy and machine learning in throughput of 15 cells per second. As a preliminary model for circulating tumor cells in the blood, following an initial label-free rapid enrichment stage based on the cell size, we applied our holographic imaging approach, providing the quantitative optical thickness profiles of the cells during flow. We automatically classified primary and metastatic colon cancer cells, where the two types of cancer cells were isolated from the same individual, as well as four types of blood cells. We used low-coherence off-axis interferometric phase microscopy and a microfluidic channel to image cells during flow quantitatively. The acquired images were processed and classified based on their morphology and quantitative phase features during the cell flow. We achieved high accuracy of 92.56% for distinguishing between the cells, enabling further automatic enrichment and cancer-cell grading from blood. © 2020 International Society for Advancement of Cytometry.
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Affiliation(s)
- Noga Nissim
- Department of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv, Ramat Aviv, Israel
| | - Matan Dudaie
- Department of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv, Ramat Aviv, Israel
| | - Itay Barnea
- Department of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv, Ramat Aviv, Israel
| | - Natan T Shaked
- Department of Biomedical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv, Ramat Aviv, Israel
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Mfarrej B, Gaude J, Couquiaud J, Calmels B, Chabannon C, Lemarie C. Validation of a flow cytometry-based method to quantify viable lymphocyte subtypes in fresh and cryopreserved hematopoietic cellular products. Cytotherapy 2020; 23:77-87. [PMID: 32718876 DOI: 10.1016/j.jcyt.2020.06.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/27/2020] [Accepted: 06/22/2020] [Indexed: 12/23/2022]
Abstract
BACKGROUND AIMS Adoptive cellular therapy with immune effector cells (IECs) has shown promising efficacy against some neoplastic diseases as well as potential in immune regulation. Both inherent variability in starting material and variations in cell composition produced by the manufacturing process must be thoroughly evaluated with a validated method established to quantify viable lymphocyte subtypes. Currently, commercialized immunophenotyping methods determine cell viability with significant errors in thawed products since they do not include any viability staining. We hereby report on the validation of a flow cytometry-based method for quantifying viable lymphocyte immunophenotypes in fresh and cryopreserved hematopoietic cellular products. METHODS Using fresh or frozen cellular products and stabilized blood, we report on the validation parameters accuracy, uncertainty, precision, sensitivity, robustness and contamination between samples for quantification of viable CD3+, CD4+ T cells, CD8+ T cells, CD3-CD56+CD16+/- NK cells, CD19+ B cells and CD14+ monocytes of relevance to fresh and cryopreserved hematopoietic cellular products using the Cytomics FC500 cytometer (Beckman Coulter). RESULTS The acceptance criteria set in the validation plan were all met. The method is able to accommodate the variability in absolute numbers of cells in starting materials collected or cryopreserved from patients or healthy donors (uncertainty of ≤20% at three different concentrations), stability over time (compliance over 3 years during regular inter-laboratory comparisons) and confidence in meaningful changes during cell processing and manufacturing (intra-assay and intermediate precision of 10% coefficient of variation). Furthermore, the method can accurately report on the efficacy of cell depletion since the lower limit of quantification was established (CD3+, CD4+ and CD8+ cells at 9, 8 and 8 cells/µL, respectively). The method complies with Foundation for the Accreditation of Cellular Therapy (FACT) standards for IEC, FACT-Joint Accreditation Committee of ISCT-EBMT (JACIE) hematopoietic cell therapy standards, International Council for Harmonisation of Technical Requirements for Pharmaceuticals for Human Use Q2(R1) and International Organization for Standardization 15189 standards. Furthermore, it complies with Ligand Binding Assay Bioanalytical Focus Group/American Association of Pharmaceutical Scientists, International Council for Standardization of Hematology/International Clinical Cytometry Society and European Bioanalysis Forum recommendations for validating such methods. CONCLUSIONS The implications of this effort include standardization of viable cell immunophenotyping of starting material for cell manufacturing, cell selection and in-process quality controls or dosing of IECs. This method also complies with all relevant standards, particularly FACT-JACIE standards, in terms of enumerating and reporting on the viability of the "clinically relevant cell populations."
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Affiliation(s)
- Bechara Mfarrej
- Centre de Thérapie Cellulaire, Institut Paoli-Calmettes, Marseille, France.
| | - Julie Gaude
- Centre de Thérapie Cellulaire, Institut Paoli-Calmettes, Marseille, France
| | - Jerome Couquiaud
- Centre de Thérapie Cellulaire, Institut Paoli-Calmettes, Marseille, France
| | - Boris Calmels
- Centre de Thérapie Cellulaire, Institut Paoli-Calmettes, Marseille, France
| | | | - Claude Lemarie
- Centre de Thérapie Cellulaire, Institut Paoli-Calmettes, Marseille, France
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Bovine serum albumin conjugation on poly(methyl methacrylate) nanoparticles for targeted drug delivery applications. J Drug Deliv Sci Technol 2020. [DOI: 10.1016/j.jddst.2019.101490] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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22
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Cellerino M, Ivaldi F, Pardini M, Rotta G, Vila G, Bäcker-Koduah P, Berge T, Laroni A, Lapucci C, Novi G, Boffa G, Sbragia E, Palmeri S, Asseyer S, Høgestøl E, Campi C, Piana M, Inglese M, Paul F, Harbo HF, Villoslada P, Kerlero de Rosbo N, Uccelli A. Impact of treatment on cellular immunophenotype in MS: A cross-sectional study. NEUROLOGY-NEUROIMMUNOLOGY & NEUROINFLAMMATION 2020; 7:7/3/e693. [PMID: 32139439 PMCID: PMC7136062 DOI: 10.1212/nxi.0000000000000693] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 01/05/2020] [Indexed: 12/22/2022]
Abstract
Objective To establish cytometry profiles associated with disease stages and immunotherapy in MS. Methods Demographic/clinical data and peripheral blood samples were collected from 227 patients with MS and 82 sex- and age-matched healthy controls (HCs) enrolled in a cross-sectional study at 4 European MS centers (Spain, Italy, Germany, and Norway). Flow cytometry of isolated peripheral blood mononuclear cells was performed in each center using specifically prepared antibody-cocktail Lyotubes; data analysis was centralized at the Genoa center. Differences in immune cell subsets were assessed between groups of untreated patients with relapsing-remitting or progressive MS (RRMS or PMS) and HCs and between groups of patients with RRMS taking 6 commonly used disease-modifying drugs. Results In untreated patients with MS, significantly higher frequencies of Th17 cells in the RRMS population compared with HC and lower frequencies of B-memory/B-regulatory cells as well as higher percentages of B-mature cells in patients with PMS compared with HCs emerged. Overall, the greatest deviation in immunophenotype in MS was observed by treatment rather than disease course, with the strongest impact found in fingolimod-treated patients. Fingolimod induced a decrease in total CD4+ T cells and in B-mature and B-memory cells and increases in CD4+ and CD8+ T-regulatory and B-regulatory cells. Conclusions Our highly standardized, multisite cytomics data provide further understanding of treatment impact on MS immunophenotype and could pave the way toward monitoring immune cells to help clinical management of MS individuals.
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Affiliation(s)
- Maria Cellerino
- From the Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (M.C., F.I., M.P., A.L., C.L., G.N., G.B., E.S., S.P., M.I., N.K.d.R.) and Center of Excellence for Biomedical Research (A.U.), University of Genoa, Italy; BD Biosciences Italy (G.R.), Milan; Institut d'Investigacions Biomediques August Pi Sunyer (G.V., P.V.), Barcelona, Spain; Charité Universitaetsmedizin Berlin and Max Delbrueck Center for Molecular Medicine (P.B.-K., S.A., F.P.), Germany; Department of Research, Innovation and Education (T.B.), Neuroscience Research Unit, Oslo University Hospital; Department of Mechanical Electronics and Chemical Engineering (T.B.), Oslo Metropolitan University, Norway; University of Oslo (E.H., H.F.H.) and Oslo University Hospital (H.F.H.), Norway; Department of Mathematics and Padova Neuroscience Center (C.C.), University of Padua, Italy; Department of Mathematics (M.P.), University of Genoa, Italy; and IRCCS Ospedale Policlinico San Martino (A.L., M.P., M.I., A.U.), Genoa, Italy
| | - Federico Ivaldi
- From the Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (M.C., F.I., M.P., A.L., C.L., G.N., G.B., E.S., S.P., M.I., N.K.d.R.) and Center of Excellence for Biomedical Research (A.U.), University of Genoa, Italy; BD Biosciences Italy (G.R.), Milan; Institut d'Investigacions Biomediques August Pi Sunyer (G.V., P.V.), Barcelona, Spain; Charité Universitaetsmedizin Berlin and Max Delbrueck Center for Molecular Medicine (P.B.-K., S.A., F.P.), Germany; Department of Research, Innovation and Education (T.B.), Neuroscience Research Unit, Oslo University Hospital; Department of Mechanical Electronics and Chemical Engineering (T.B.), Oslo Metropolitan University, Norway; University of Oslo (E.H., H.F.H.) and Oslo University Hospital (H.F.H.), Norway; Department of Mathematics and Padova Neuroscience Center (C.C.), University of Padua, Italy; Department of Mathematics (M.P.), University of Genoa, Italy; and IRCCS Ospedale Policlinico San Martino (A.L., M.P., M.I., A.U.), Genoa, Italy
| | - Matteo Pardini
- From the Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (M.C., F.I., M.P., A.L., C.L., G.N., G.B., E.S., S.P., M.I., N.K.d.R.) and Center of Excellence for Biomedical Research (A.U.), University of Genoa, Italy; BD Biosciences Italy (G.R.), Milan; Institut d'Investigacions Biomediques August Pi Sunyer (G.V., P.V.), Barcelona, Spain; Charité Universitaetsmedizin Berlin and Max Delbrueck Center for Molecular Medicine (P.B.-K., S.A., F.P.), Germany; Department of Research, Innovation and Education (T.B.), Neuroscience Research Unit, Oslo University Hospital; Department of Mechanical Electronics and Chemical Engineering (T.B.), Oslo Metropolitan University, Norway; University of Oslo (E.H., H.F.H.) and Oslo University Hospital (H.F.H.), Norway; Department of Mathematics and Padova Neuroscience Center (C.C.), University of Padua, Italy; Department of Mathematics (M.P.), University of Genoa, Italy; and IRCCS Ospedale Policlinico San Martino (A.L., M.P., M.I., A.U.), Genoa, Italy
| | - Gianluca Rotta
- From the Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (M.C., F.I., M.P., A.L., C.L., G.N., G.B., E.S., S.P., M.I., N.K.d.R.) and Center of Excellence for Biomedical Research (A.U.), University of Genoa, Italy; BD Biosciences Italy (G.R.), Milan; Institut d'Investigacions Biomediques August Pi Sunyer (G.V., P.V.), Barcelona, Spain; Charité Universitaetsmedizin Berlin and Max Delbrueck Center for Molecular Medicine (P.B.-K., S.A., F.P.), Germany; Department of Research, Innovation and Education (T.B.), Neuroscience Research Unit, Oslo University Hospital; Department of Mechanical Electronics and Chemical Engineering (T.B.), Oslo Metropolitan University, Norway; University of Oslo (E.H., H.F.H.) and Oslo University Hospital (H.F.H.), Norway; Department of Mathematics and Padova Neuroscience Center (C.C.), University of Padua, Italy; Department of Mathematics (M.P.), University of Genoa, Italy; and IRCCS Ospedale Policlinico San Martino (A.L., M.P., M.I., A.U.), Genoa, Italy
| | - Gemma Vila
- From the Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (M.C., F.I., M.P., A.L., C.L., G.N., G.B., E.S., S.P., M.I., N.K.d.R.) and Center of Excellence for Biomedical Research (A.U.), University of Genoa, Italy; BD Biosciences Italy (G.R.), Milan; Institut d'Investigacions Biomediques August Pi Sunyer (G.V., P.V.), Barcelona, Spain; Charité Universitaetsmedizin Berlin and Max Delbrueck Center for Molecular Medicine (P.B.-K., S.A., F.P.), Germany; Department of Research, Innovation and Education (T.B.), Neuroscience Research Unit, Oslo University Hospital; Department of Mechanical Electronics and Chemical Engineering (T.B.), Oslo Metropolitan University, Norway; University of Oslo (E.H., H.F.H.) and Oslo University Hospital (H.F.H.), Norway; Department of Mathematics and Padova Neuroscience Center (C.C.), University of Padua, Italy; Department of Mathematics (M.P.), University of Genoa, Italy; and IRCCS Ospedale Policlinico San Martino (A.L., M.P., M.I., A.U.), Genoa, Italy
| | - Priscilla Bäcker-Koduah
- From the Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (M.C., F.I., M.P., A.L., C.L., G.N., G.B., E.S., S.P., M.I., N.K.d.R.) and Center of Excellence for Biomedical Research (A.U.), University of Genoa, Italy; BD Biosciences Italy (G.R.), Milan; Institut d'Investigacions Biomediques August Pi Sunyer (G.V., P.V.), Barcelona, Spain; Charité Universitaetsmedizin Berlin and Max Delbrueck Center for Molecular Medicine (P.B.-K., S.A., F.P.), Germany; Department of Research, Innovation and Education (T.B.), Neuroscience Research Unit, Oslo University Hospital; Department of Mechanical Electronics and Chemical Engineering (T.B.), Oslo Metropolitan University, Norway; University of Oslo (E.H., H.F.H.) and Oslo University Hospital (H.F.H.), Norway; Department of Mathematics and Padova Neuroscience Center (C.C.), University of Padua, Italy; Department of Mathematics (M.P.), University of Genoa, Italy; and IRCCS Ospedale Policlinico San Martino (A.L., M.P., M.I., A.U.), Genoa, Italy
| | - Tone Berge
- From the Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (M.C., F.I., M.P., A.L., C.L., G.N., G.B., E.S., S.P., M.I., N.K.d.R.) and Center of Excellence for Biomedical Research (A.U.), University of Genoa, Italy; BD Biosciences Italy (G.R.), Milan; Institut d'Investigacions Biomediques August Pi Sunyer (G.V., P.V.), Barcelona, Spain; Charité Universitaetsmedizin Berlin and Max Delbrueck Center for Molecular Medicine (P.B.-K., S.A., F.P.), Germany; Department of Research, Innovation and Education (T.B.), Neuroscience Research Unit, Oslo University Hospital; Department of Mechanical Electronics and Chemical Engineering (T.B.), Oslo Metropolitan University, Norway; University of Oslo (E.H., H.F.H.) and Oslo University Hospital (H.F.H.), Norway; Department of Mathematics and Padova Neuroscience Center (C.C.), University of Padua, Italy; Department of Mathematics (M.P.), University of Genoa, Italy; and IRCCS Ospedale Policlinico San Martino (A.L., M.P., M.I., A.U.), Genoa, Italy
| | - Alice Laroni
- From the Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (M.C., F.I., M.P., A.L., C.L., G.N., G.B., E.S., S.P., M.I., N.K.d.R.) and Center of Excellence for Biomedical Research (A.U.), University of Genoa, Italy; BD Biosciences Italy (G.R.), Milan; Institut d'Investigacions Biomediques August Pi Sunyer (G.V., P.V.), Barcelona, Spain; Charité Universitaetsmedizin Berlin and Max Delbrueck Center for Molecular Medicine (P.B.-K., S.A., F.P.), Germany; Department of Research, Innovation and Education (T.B.), Neuroscience Research Unit, Oslo University Hospital; Department of Mechanical Electronics and Chemical Engineering (T.B.), Oslo Metropolitan University, Norway; University of Oslo (E.H., H.F.H.) and Oslo University Hospital (H.F.H.), Norway; Department of Mathematics and Padova Neuroscience Center (C.C.), University of Padua, Italy; Department of Mathematics (M.P.), University of Genoa, Italy; and IRCCS Ospedale Policlinico San Martino (A.L., M.P., M.I., A.U.), Genoa, Italy
| | - Caterina Lapucci
- From the Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (M.C., F.I., M.P., A.L., C.L., G.N., G.B., E.S., S.P., M.I., N.K.d.R.) and Center of Excellence for Biomedical Research (A.U.), University of Genoa, Italy; BD Biosciences Italy (G.R.), Milan; Institut d'Investigacions Biomediques August Pi Sunyer (G.V., P.V.), Barcelona, Spain; Charité Universitaetsmedizin Berlin and Max Delbrueck Center for Molecular Medicine (P.B.-K., S.A., F.P.), Germany; Department of Research, Innovation and Education (T.B.), Neuroscience Research Unit, Oslo University Hospital; Department of Mechanical Electronics and Chemical Engineering (T.B.), Oslo Metropolitan University, Norway; University of Oslo (E.H., H.F.H.) and Oslo University Hospital (H.F.H.), Norway; Department of Mathematics and Padova Neuroscience Center (C.C.), University of Padua, Italy; Department of Mathematics (M.P.), University of Genoa, Italy; and IRCCS Ospedale Policlinico San Martino (A.L., M.P., M.I., A.U.), Genoa, Italy
| | - Giovanni Novi
- From the Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (M.C., F.I., M.P., A.L., C.L., G.N., G.B., E.S., S.P., M.I., N.K.d.R.) and Center of Excellence for Biomedical Research (A.U.), University of Genoa, Italy; BD Biosciences Italy (G.R.), Milan; Institut d'Investigacions Biomediques August Pi Sunyer (G.V., P.V.), Barcelona, Spain; Charité Universitaetsmedizin Berlin and Max Delbrueck Center for Molecular Medicine (P.B.-K., S.A., F.P.), Germany; Department of Research, Innovation and Education (T.B.), Neuroscience Research Unit, Oslo University Hospital; Department of Mechanical Electronics and Chemical Engineering (T.B.), Oslo Metropolitan University, Norway; University of Oslo (E.H., H.F.H.) and Oslo University Hospital (H.F.H.), Norway; Department of Mathematics and Padova Neuroscience Center (C.C.), University of Padua, Italy; Department of Mathematics (M.P.), University of Genoa, Italy; and IRCCS Ospedale Policlinico San Martino (A.L., M.P., M.I., A.U.), Genoa, Italy
| | - Giacomo Boffa
- From the Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (M.C., F.I., M.P., A.L., C.L., G.N., G.B., E.S., S.P., M.I., N.K.d.R.) and Center of Excellence for Biomedical Research (A.U.), University of Genoa, Italy; BD Biosciences Italy (G.R.), Milan; Institut d'Investigacions Biomediques August Pi Sunyer (G.V., P.V.), Barcelona, Spain; Charité Universitaetsmedizin Berlin and Max Delbrueck Center for Molecular Medicine (P.B.-K., S.A., F.P.), Germany; Department of Research, Innovation and Education (T.B.), Neuroscience Research Unit, Oslo University Hospital; Department of Mechanical Electronics and Chemical Engineering (T.B.), Oslo Metropolitan University, Norway; University of Oslo (E.H., H.F.H.) and Oslo University Hospital (H.F.H.), Norway; Department of Mathematics and Padova Neuroscience Center (C.C.), University of Padua, Italy; Department of Mathematics (M.P.), University of Genoa, Italy; and IRCCS Ospedale Policlinico San Martino (A.L., M.P., M.I., A.U.), Genoa, Italy
| | - Elvira Sbragia
- From the Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (M.C., F.I., M.P., A.L., C.L., G.N., G.B., E.S., S.P., M.I., N.K.d.R.) and Center of Excellence for Biomedical Research (A.U.), University of Genoa, Italy; BD Biosciences Italy (G.R.), Milan; Institut d'Investigacions Biomediques August Pi Sunyer (G.V., P.V.), Barcelona, Spain; Charité Universitaetsmedizin Berlin and Max Delbrueck Center for Molecular Medicine (P.B.-K., S.A., F.P.), Germany; Department of Research, Innovation and Education (T.B.), Neuroscience Research Unit, Oslo University Hospital; Department of Mechanical Electronics and Chemical Engineering (T.B.), Oslo Metropolitan University, Norway; University of Oslo (E.H., H.F.H.) and Oslo University Hospital (H.F.H.), Norway; Department of Mathematics and Padova Neuroscience Center (C.C.), University of Padua, Italy; Department of Mathematics (M.P.), University of Genoa, Italy; and IRCCS Ospedale Policlinico San Martino (A.L., M.P., M.I., A.U.), Genoa, Italy
| | - Serena Palmeri
- From the Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (M.C., F.I., M.P., A.L., C.L., G.N., G.B., E.S., S.P., M.I., N.K.d.R.) and Center of Excellence for Biomedical Research (A.U.), University of Genoa, Italy; BD Biosciences Italy (G.R.), Milan; Institut d'Investigacions Biomediques August Pi Sunyer (G.V., P.V.), Barcelona, Spain; Charité Universitaetsmedizin Berlin and Max Delbrueck Center for Molecular Medicine (P.B.-K., S.A., F.P.), Germany; Department of Research, Innovation and Education (T.B.), Neuroscience Research Unit, Oslo University Hospital; Department of Mechanical Electronics and Chemical Engineering (T.B.), Oslo Metropolitan University, Norway; University of Oslo (E.H., H.F.H.) and Oslo University Hospital (H.F.H.), Norway; Department of Mathematics and Padova Neuroscience Center (C.C.), University of Padua, Italy; Department of Mathematics (M.P.), University of Genoa, Italy; and IRCCS Ospedale Policlinico San Martino (A.L., M.P., M.I., A.U.), Genoa, Italy
| | - Susanna Asseyer
- From the Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (M.C., F.I., M.P., A.L., C.L., G.N., G.B., E.S., S.P., M.I., N.K.d.R.) and Center of Excellence for Biomedical Research (A.U.), University of Genoa, Italy; BD Biosciences Italy (G.R.), Milan; Institut d'Investigacions Biomediques August Pi Sunyer (G.V., P.V.), Barcelona, Spain; Charité Universitaetsmedizin Berlin and Max Delbrueck Center for Molecular Medicine (P.B.-K., S.A., F.P.), Germany; Department of Research, Innovation and Education (T.B.), Neuroscience Research Unit, Oslo University Hospital; Department of Mechanical Electronics and Chemical Engineering (T.B.), Oslo Metropolitan University, Norway; University of Oslo (E.H., H.F.H.) and Oslo University Hospital (H.F.H.), Norway; Department of Mathematics and Padova Neuroscience Center (C.C.), University of Padua, Italy; Department of Mathematics (M.P.), University of Genoa, Italy; and IRCCS Ospedale Policlinico San Martino (A.L., M.P., M.I., A.U.), Genoa, Italy
| | - Einar Høgestøl
- From the Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (M.C., F.I., M.P., A.L., C.L., G.N., G.B., E.S., S.P., M.I., N.K.d.R.) and Center of Excellence for Biomedical Research (A.U.), University of Genoa, Italy; BD Biosciences Italy (G.R.), Milan; Institut d'Investigacions Biomediques August Pi Sunyer (G.V., P.V.), Barcelona, Spain; Charité Universitaetsmedizin Berlin and Max Delbrueck Center for Molecular Medicine (P.B.-K., S.A., F.P.), Germany; Department of Research, Innovation and Education (T.B.), Neuroscience Research Unit, Oslo University Hospital; Department of Mechanical Electronics and Chemical Engineering (T.B.), Oslo Metropolitan University, Norway; University of Oslo (E.H., H.F.H.) and Oslo University Hospital (H.F.H.), Norway; Department of Mathematics and Padova Neuroscience Center (C.C.), University of Padua, Italy; Department of Mathematics (M.P.), University of Genoa, Italy; and IRCCS Ospedale Policlinico San Martino (A.L., M.P., M.I., A.U.), Genoa, Italy
| | - Cristina Campi
- From the Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (M.C., F.I., M.P., A.L., C.L., G.N., G.B., E.S., S.P., M.I., N.K.d.R.) and Center of Excellence for Biomedical Research (A.U.), University of Genoa, Italy; BD Biosciences Italy (G.R.), Milan; Institut d'Investigacions Biomediques August Pi Sunyer (G.V., P.V.), Barcelona, Spain; Charité Universitaetsmedizin Berlin and Max Delbrueck Center for Molecular Medicine (P.B.-K., S.A., F.P.), Germany; Department of Research, Innovation and Education (T.B.), Neuroscience Research Unit, Oslo University Hospital; Department of Mechanical Electronics and Chemical Engineering (T.B.), Oslo Metropolitan University, Norway; University of Oslo (E.H., H.F.H.) and Oslo University Hospital (H.F.H.), Norway; Department of Mathematics and Padova Neuroscience Center (C.C.), University of Padua, Italy; Department of Mathematics (M.P.), University of Genoa, Italy; and IRCCS Ospedale Policlinico San Martino (A.L., M.P., M.I., A.U.), Genoa, Italy
| | - Michele Piana
- From the Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (M.C., F.I., M.P., A.L., C.L., G.N., G.B., E.S., S.P., M.I., N.K.d.R.) and Center of Excellence for Biomedical Research (A.U.), University of Genoa, Italy; BD Biosciences Italy (G.R.), Milan; Institut d'Investigacions Biomediques August Pi Sunyer (G.V., P.V.), Barcelona, Spain; Charité Universitaetsmedizin Berlin and Max Delbrueck Center for Molecular Medicine (P.B.-K., S.A., F.P.), Germany; Department of Research, Innovation and Education (T.B.), Neuroscience Research Unit, Oslo University Hospital; Department of Mechanical Electronics and Chemical Engineering (T.B.), Oslo Metropolitan University, Norway; University of Oslo (E.H., H.F.H.) and Oslo University Hospital (H.F.H.), Norway; Department of Mathematics and Padova Neuroscience Center (C.C.), University of Padua, Italy; Department of Mathematics (M.P.), University of Genoa, Italy; and IRCCS Ospedale Policlinico San Martino (A.L., M.P., M.I., A.U.), Genoa, Italy
| | - Matilde Inglese
- From the Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (M.C., F.I., M.P., A.L., C.L., G.N., G.B., E.S., S.P., M.I., N.K.d.R.) and Center of Excellence for Biomedical Research (A.U.), University of Genoa, Italy; BD Biosciences Italy (G.R.), Milan; Institut d'Investigacions Biomediques August Pi Sunyer (G.V., P.V.), Barcelona, Spain; Charité Universitaetsmedizin Berlin and Max Delbrueck Center for Molecular Medicine (P.B.-K., S.A., F.P.), Germany; Department of Research, Innovation and Education (T.B.), Neuroscience Research Unit, Oslo University Hospital; Department of Mechanical Electronics and Chemical Engineering (T.B.), Oslo Metropolitan University, Norway; University of Oslo (E.H., H.F.H.) and Oslo University Hospital (H.F.H.), Norway; Department of Mathematics and Padova Neuroscience Center (C.C.), University of Padua, Italy; Department of Mathematics (M.P.), University of Genoa, Italy; and IRCCS Ospedale Policlinico San Martino (A.L., M.P., M.I., A.U.), Genoa, Italy
| | - Friedemann Paul
- From the Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (M.C., F.I., M.P., A.L., C.L., G.N., G.B., E.S., S.P., M.I., N.K.d.R.) and Center of Excellence for Biomedical Research (A.U.), University of Genoa, Italy; BD Biosciences Italy (G.R.), Milan; Institut d'Investigacions Biomediques August Pi Sunyer (G.V., P.V.), Barcelona, Spain; Charité Universitaetsmedizin Berlin and Max Delbrueck Center for Molecular Medicine (P.B.-K., S.A., F.P.), Germany; Department of Research, Innovation and Education (T.B.), Neuroscience Research Unit, Oslo University Hospital; Department of Mechanical Electronics and Chemical Engineering (T.B.), Oslo Metropolitan University, Norway; University of Oslo (E.H., H.F.H.) and Oslo University Hospital (H.F.H.), Norway; Department of Mathematics and Padova Neuroscience Center (C.C.), University of Padua, Italy; Department of Mathematics (M.P.), University of Genoa, Italy; and IRCCS Ospedale Policlinico San Martino (A.L., M.P., M.I., A.U.), Genoa, Italy
| | - Hanne F Harbo
- From the Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (M.C., F.I., M.P., A.L., C.L., G.N., G.B., E.S., S.P., M.I., N.K.d.R.) and Center of Excellence for Biomedical Research (A.U.), University of Genoa, Italy; BD Biosciences Italy (G.R.), Milan; Institut d'Investigacions Biomediques August Pi Sunyer (G.V., P.V.), Barcelona, Spain; Charité Universitaetsmedizin Berlin and Max Delbrueck Center for Molecular Medicine (P.B.-K., S.A., F.P.), Germany; Department of Research, Innovation and Education (T.B.), Neuroscience Research Unit, Oslo University Hospital; Department of Mechanical Electronics and Chemical Engineering (T.B.), Oslo Metropolitan University, Norway; University of Oslo (E.H., H.F.H.) and Oslo University Hospital (H.F.H.), Norway; Department of Mathematics and Padova Neuroscience Center (C.C.), University of Padua, Italy; Department of Mathematics (M.P.), University of Genoa, Italy; and IRCCS Ospedale Policlinico San Martino (A.L., M.P., M.I., A.U.), Genoa, Italy
| | - Pablo Villoslada
- From the Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (M.C., F.I., M.P., A.L., C.L., G.N., G.B., E.S., S.P., M.I., N.K.d.R.) and Center of Excellence for Biomedical Research (A.U.), University of Genoa, Italy; BD Biosciences Italy (G.R.), Milan; Institut d'Investigacions Biomediques August Pi Sunyer (G.V., P.V.), Barcelona, Spain; Charité Universitaetsmedizin Berlin and Max Delbrueck Center for Molecular Medicine (P.B.-K., S.A., F.P.), Germany; Department of Research, Innovation and Education (T.B.), Neuroscience Research Unit, Oslo University Hospital; Department of Mechanical Electronics and Chemical Engineering (T.B.), Oslo Metropolitan University, Norway; University of Oslo (E.H., H.F.H.) and Oslo University Hospital (H.F.H.), Norway; Department of Mathematics and Padova Neuroscience Center (C.C.), University of Padua, Italy; Department of Mathematics (M.P.), University of Genoa, Italy; and IRCCS Ospedale Policlinico San Martino (A.L., M.P., M.I., A.U.), Genoa, Italy
| | - Nicole Kerlero de Rosbo
- From the Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (M.C., F.I., M.P., A.L., C.L., G.N., G.B., E.S., S.P., M.I., N.K.d.R.) and Center of Excellence for Biomedical Research (A.U.), University of Genoa, Italy; BD Biosciences Italy (G.R.), Milan; Institut d'Investigacions Biomediques August Pi Sunyer (G.V., P.V.), Barcelona, Spain; Charité Universitaetsmedizin Berlin and Max Delbrueck Center for Molecular Medicine (P.B.-K., S.A., F.P.), Germany; Department of Research, Innovation and Education (T.B.), Neuroscience Research Unit, Oslo University Hospital; Department of Mechanical Electronics and Chemical Engineering (T.B.), Oslo Metropolitan University, Norway; University of Oslo (E.H., H.F.H.) and Oslo University Hospital (H.F.H.), Norway; Department of Mathematics and Padova Neuroscience Center (C.C.), University of Padua, Italy; Department of Mathematics (M.P.), University of Genoa, Italy; and IRCCS Ospedale Policlinico San Martino (A.L., M.P., M.I., A.U.), Genoa, Italy
| | - Antonio Uccelli
- From the Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (M.C., F.I., M.P., A.L., C.L., G.N., G.B., E.S., S.P., M.I., N.K.d.R.) and Center of Excellence for Biomedical Research (A.U.), University of Genoa, Italy; BD Biosciences Italy (G.R.), Milan; Institut d'Investigacions Biomediques August Pi Sunyer (G.V., P.V.), Barcelona, Spain; Charité Universitaetsmedizin Berlin and Max Delbrueck Center for Molecular Medicine (P.B.-K., S.A., F.P.), Germany; Department of Research, Innovation and Education (T.B.), Neuroscience Research Unit, Oslo University Hospital; Department of Mechanical Electronics and Chemical Engineering (T.B.), Oslo Metropolitan University, Norway; University of Oslo (E.H., H.F.H.) and Oslo University Hospital (H.F.H.), Norway; Department of Mathematics and Padova Neuroscience Center (C.C.), University of Padua, Italy; Department of Mathematics (M.P.), University of Genoa, Italy; and IRCCS Ospedale Policlinico San Martino (A.L., M.P., M.I., A.U.), Genoa, Italy.
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23
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Nobori T, Kawamura M, Yoshida R, Joichi T, Kamino K, Kishimura A, Baba E, Mori T, Katayama Y. Fluorescence Signal Amplification by Using β-Galactosidase for Flow Cytometry; Advantages of an Endogenous Activity-Free Enzyme. Anal Chem 2020; 92:3069-3076. [PMID: 31971376 DOI: 10.1021/acs.analchem.9b04471] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We previously proposed using a hydrolysis enzyme for fluorescent signal amplification in flow cytometric detection of antigen proteins, which was named the catalyzed reporter penetration (CARP) method. In this method, antigen proteins are labeled with enzyme-modified antibodies, and then fluorophore-modified substrates stain cells by penetrating the cell membrane upon hydrolysis of the substrate. We proved the concept by using alkaline phosphatase (AP) as the hydrolysis enzyme. However, a required prior inactivation process of endogenous AP activity on the cell surface risked disrupting recognition of antigen proteins by antibodies. In this report, the CARP method was extended to β-galactosidase (β-gal) as an amplification enzyme, which circumvented the requirement of an initial inactivation process because endogenous β-gal activity on the surface of examined cells was found to be negligible. The substrate structure for β-gal was optimized and used for the CARP method. The CARP method showed significantly higher fluorescent signals than a conventional method using fluorophore-modified antibodies. Moreover, the degree of amplification of the fluorescence signal was higher for antigens with low expression levels, showing that the CARP method is a suitable signal amplification method over current conventional approaches.
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Affiliation(s)
- Takanobu Nobori
- Department of Applied Chemistry, Faculty of Engineering , Kyushu University , 744 Motooka , Nishi-Ku, Fukuoka 819-0395 , Japan
| | - Masumi Kawamura
- Graduate School of Systems Life Sciences , Kyushu University , 744 Motooka , Nishi-Ku, Fukuoka 819-0395 , Japan
| | - Ryosuke Yoshida
- Graduate School of Systems Life Sciences , Kyushu University , 744 Motooka , Nishi-Ku, Fukuoka 819-0395 , Japan
| | - Taisei Joichi
- Graduate School of Systems Life Sciences , Kyushu University , 744 Motooka , Nishi-Ku, Fukuoka 819-0395 , Japan
| | - Kenta Kamino
- Graduate School of Systems Life Sciences , Kyushu University , 744 Motooka , Nishi-Ku, Fukuoka 819-0395 , Japan
| | - Akihiro Kishimura
- Department of Applied Chemistry, Faculty of Engineering , Kyushu University , 744 Motooka , Nishi-Ku, Fukuoka 819-0395 , Japan.,Graduate School of Systems Life Sciences , Kyushu University , 744 Motooka , Nishi-Ku, Fukuoka 819-0395 , Japan.,Center for Future Chemistry , Kyushu University , 744 Motooka , Nishi-Ku, Fukuoka 819-0395 , Japan.,Institute of Systems , Information Technologies and Nanotechnologies , 203-1 Motooka , Nishi-Ku, Fukuoka 819-0385 , Japan
| | - Eishi Baba
- Department of Cmprehensive Clinical Oncology, Faculty of Medical Sciences , Kyushu University , 3-1-1 Maidashi, Higashi-Ku , Fukuoka 812-8581 , Japan
| | - Takeshi Mori
- Department of Applied Chemistry, Faculty of Engineering , Kyushu University , 744 Motooka , Nishi-Ku, Fukuoka 819-0395 , Japan.,Graduate School of Systems Life Sciences , Kyushu University , 744 Motooka , Nishi-Ku, Fukuoka 819-0395 , Japan.,Center for Future Chemistry , Kyushu University , 744 Motooka , Nishi-Ku, Fukuoka 819-0395 , Japan
| | - Yoshiki Katayama
- Department of Applied Chemistry, Faculty of Engineering , Kyushu University , 744 Motooka , Nishi-Ku, Fukuoka 819-0395 , Japan.,Graduate School of Systems Life Sciences , Kyushu University , 744 Motooka , Nishi-Ku, Fukuoka 819-0395 , Japan.,Center for Future Chemistry , Kyushu University , 744 Motooka , Nishi-Ku, Fukuoka 819-0395 , Japan.,Institute of Systems , Information Technologies and Nanotechnologies , 203-1 Motooka , Nishi-Ku, Fukuoka 819-0385 , Japan.,International Research Center for Molecular Systems , Kyushu University , 744 Motooka , Nishi-Ku, Fukuoka 819-0395 , Japan.,Center for Advanced Medical Innovation , Kyushu University , 744 Motooka , Nishi-Ku, Fukuoka 819-0395 , Japan.,Department of Biomedical Engineering , Chung Yuan Christian University , Taoyuan , Taiwan
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24
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Gaipa G, Erba E, Danova M, Mazzini G, Venditti A, Buldini B, Specchia G, Maglia O, Kunkl A, Ciriello MM, Arpinati M, Mannelli F, Lanza F, Riccioni R, Pistotti V, Apolone G. Health technology assessment-based approach to flow cytometric immunophenotyping of acute leukemias: a literature classification. TUMORI JOURNAL 2020; 106:300891620904412. [PMID: 32056511 DOI: 10.1177/0300891620904412] [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: 11/17/2022]
Abstract
OBJECTIVE Acute leukemia (AL) is a broad, heterogeneous group of malignant diseases. The diagnostic workup of AL is based on several clinical and laboratory findings, including flow cytometric immunophenotyping. However, the role of this assay in the diagnosis of AL has not been systematically investigated. The aim of this study was to determine the accuracy and utility of flow cytometric immunophenotyping in the identification, characterization, and staging of AL. METHODS We performed a systematic selection and classification of the literature since 1980, focused on flow cytometric immunophenotyping of AL. We applied a 6-variables model to cover both the technical capabilities and the clinical value of flow cytometric immunophenotyping in the diagnosis of AL. RESULTS Using 3 key words (acute leukemia, immunophenotyping, flow cytometry), we screened the literature from January 1985 to April 2015 in PubMed and Embase databases and found 1010 articles. A total of 363 were selected and submitted to the expert panel, which selected a final data set of 248 articles to be analyzed. Of these, 160 were focused on clinical and biological issues, 55 were technical articles, and 31 were reviews. These 248 articles were then analyzed according to the 6-variables model and definitively classified. CONCLUSIONS We assessed the literature on flow cytometric immunophenotyping of AL over 3 decades as the first step toward an evidence-based analysis of the impact of this technology on the clinical management of patients with AL.
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Affiliation(s)
- Giuseppe Gaipa
- M. Tettamanti Research Center, Pediatric Clinic, University of Milano Bicocca, Monza, Italy
| | - Eugenio Erba
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Dipartimento di Oncologia, Milan, Italy
| | - Marco Danova
- Department of Internal Medicine and Oncology, ASST of Pavia, Pavia, Italy
| | - Giuliano Mazzini
- Molecular Genetics Institute, National Research Council and Biology and Biotechnology, Department "L. Spallanzani," University of Pavia, Pavia, Italy
| | - Adriano Venditti
- Hematology, Department of Biomedicine and Prevention, University of Rome "Tor Vergata," Rome, Italy
| | - Barbara Buldini
- Laboratory of Hematology-Oncology, Department of Woman and Child Health, University of Padova, Padova, Italy
| | - Giorgina Specchia
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, Bari, Italy
| | - Oscar Maglia
- M. Tettamanti Research Center, Pediatric Clinic, University of Milano Bicocca, Monza, Italy
| | - Annalisa Kunkl
- Clinical Flow Cytometry Unit, Anatomic Pathology Department, IRCCS San Martino Polyclinic University Hospital, Genoa, Italy
| | | | - Mario Arpinati
- Department of Experimental, Diagnostic, and Specialty Medicine, Hematopathology & Hematology Sections, Molecular Pathology Laboratory, S. Orsola-Malpighi Hospital, Bologna University, Bologna, Italy
| | - Francesco Mannelli
- Anna Meyer Children's University Hospital, Department of Hematology, Florence, Italy
| | | | - Roberta Riccioni
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Vanna Pistotti
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Dipartimento di Oncologia, Milan, Italy
| | - Giovanni Apolone
- Fondazione IRCCS Istituto Nazionale dei Tumori, Direzione Scientifica, Milan, Italy
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25
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Bhola RK, Das PK, Pradhan S, Chakraborty K, Mohapatra D, Samal P, Patra PC, Panda SS, Mishra SK. Multiplexing 8 colors with 12 antibodies in a single lymphoid screening tube by flow cytometry for evaluating suspected chronic lymphoproliferative disorders (CLPD). J Hematop 2019. [DOI: 10.1007/s12308-019-00376-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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26
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Hesselink L, Spijkerman R, van Wessem KJP, Koenderman L, Leenen LPH, Huber-Lang M, Hietbrink F. Neutrophil heterogeneity and its role in infectious complications after severe trauma. World J Emerg Surg 2019; 14:24. [PMID: 31164913 PMCID: PMC6542247 DOI: 10.1186/s13017-019-0244-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 05/13/2019] [Indexed: 02/06/2023] Open
Abstract
Background Trauma leads to a complex inflammatory cascade that induces both immune activation and a refractory immune state in parallel. Although both components are deemed necessary for recovery, the balance is tight and easily lost. Losing the balance can lead to life-threatening infectious complications as well as long-term immunosuppression with recurrent infections. Neutrophils are known to play a key role in these processes. Therefore, this review focuses on neutrophil characteristics and function after trauma and how these features can be used to identify trauma patients at risk for infectious complications. Results Distinct neutrophil subtypes exist that play their own role in the recovery and/or development of infectious complications after trauma. Furthermore, the refractory immune state is related to the risk of infectious complications. These findings change the initial concepts of the immune response after trauma and give rise to new biomarkers for monitoring and predicting inflammatory complications in severely injured patients. Conclusion For early recognition of patients at risk, the immune system should be monitored. Several neutrophil biomarkers show promising results and analysis of these markers has become accessible to such extent that they can be used for point-of-care decision making after trauma.
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Affiliation(s)
- Lillian Hesselink
- Department of Trauma Surgery, University Medical Centre Utrecht, Utrecht, The Netherlands
- Laboratory of Translational Immunology and Department of Respiratory Medicine, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Roy Spijkerman
- Department of Trauma Surgery, University Medical Centre Utrecht, Utrecht, The Netherlands
- Laboratory of Translational Immunology and Department of Respiratory Medicine, University Medical Centre Utrecht, Utrecht, The Netherlands
| | | | - Leo Koenderman
- Laboratory of Translational Immunology and Department of Respiratory Medicine, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Luke P. H. Leenen
- Department of Trauma Surgery, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Markus Huber-Lang
- Institute of Clinical and Experimental Trauma Immunology, University Hospital of Ulm, Ulm, Germany
| | - Falco Hietbrink
- Department of Trauma Surgery, University Medical Centre Utrecht, Utrecht, The Netherlands
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27
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Liu Y, Yao J, Walther-Antonio M. Whole genome amplification of single epithelial cells dissociated from snap-frozen tissue samples in microfluidic platform. BIOMICROFLUIDICS 2019; 13:034109. [PMID: 31149320 PMCID: PMC6520095 DOI: 10.1063/1.5090235] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/28/2019] [Indexed: 05/04/2023]
Abstract
Single cell sequencing is a technology capable of analyzing the genome of a single cell within a population. This technology is mostly integrated with microfluidics for precise cell manipulation and fluid handling. So far, most of the microfluidic-based single cell genomic studies have been focused on lab-cultured species or cell lines that are relatively easy to handle following standard microfluidic-based protocols without additional adjustments. The major challenges for performing single cell sequencing on clinical samples is the complex nature of the samples which requires additional sample processing steps to obtain intact single cells of interest without using amplification-inhibitive agents. Fluorescent-activated cell sorting is a common option to obtain single cells from clinical samples for single cell applications but requires >100 000 viable cells in suspension and the need for specialized laboratory and personnel. In this work, we present a protocol that can be used to obtain intact epithelial cells from snap-frozen postsurgical human endometrial tissues for single cell whole genome amplification. Our protocol includes sample thawing, cell dissociation, and labeling for genome amplification of targeted cells. Between 80% and 100% of single cell replicates lead to >25 ng of DNA after amplification with no measurable contamination, sufficient for downstream sequencing.
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28
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Roy S, Lin HY, Chou CY, Huang CH, Small J, Sadik N, Ayinon CM, Lansbury E, Cruz L, Yekula A, Jones PS, Balaj L, Carter BS. Navigating the Landscape of Tumor Extracellular Vesicle Heterogeneity. Int J Mol Sci 2019; 20:ijms20061349. [PMID: 30889795 PMCID: PMC6471355 DOI: 10.3390/ijms20061349] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 03/08/2019] [Accepted: 03/08/2019] [Indexed: 01/01/2023] Open
Abstract
The last decade has seen a rapid expansion of interest in extracellular vesicles (EVs) released by cells and proposed to mediate intercellular communication in physiological and pathological conditions. Considering that the genetic content of EVs reflects that of their respective parent cell, many researchers have proposed EVs as a source of biomarkers in various diseases. So far, the question of heterogeneity in given EV samples is rarely addressed at the experimental level. Because of their relatively small size, EVs are difficult to reliably isolate and detect within a given sample. Consequently, standardized protocols that have been optimized for accurate characterization of EVs are lacking despite recent advancements in the field. Continuous improvements in pre-analytical parameters permit more efficient assessment of EVs, however, methods to more objectively distinguish EVs from background, and to interpret multiple single-EV parameters are lacking. Here, we review EV heterogeneity according to their origin, mode of release, membrane composition, organelle and biochemical content, and other factors. In doing so, we also provide an overview of currently available and potentially applicable methods for single EV analysis. Finally, we examine the latest findings from experiments that have analyzed the issue at the single EV level and discuss potential implications.
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Affiliation(s)
- Sabrina Roy
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
| | - Hsing-Ying Lin
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
- Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
| | - Chung-Yu Chou
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
- Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan City 32001, Taiwan.
| | - Chen-Han Huang
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan City 32001, Taiwan.
| | - Julia Small
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
| | - Noah Sadik
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
- Department of Biomedical Engineering, Columbia University, New York City, NY 10027, USA.
| | - Caroline M Ayinon
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
| | - Elizabeth Lansbury
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
| | - Lilian Cruz
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
| | - Anudeep Yekula
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
| | - Pamela S Jones
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
| | - Leonora Balaj
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
| | - Bob S Carter
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
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29
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Abstract
Flow cytometry is one of the most suitable techniques for analyzing and classifying different cell suspensions derived from blood or others compartments. The characterization of all different cellular subtypes is made with different antibodies that detect surface or intracytoplasmic antigens. Here we describe the technique to thoroughly characterize immune cells from tumor infiltrates and proceed to isolation using single-cell sorting.
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Affiliation(s)
- Davide Brusa
- Flow Cytometry Platform, Institute of Experimental and Clinical Research (IREC), Université Catholique de Louvain (UCL), Brussels, Belgium.
| | - Jean-Luc Balligand
- Pole of Pharmacology and Therapeutics, Institute of Experimental and Clinical Research (IREC), Medical School, Université Catholique de Louvain (UCL), Brussels, Belgium
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30
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Momen-Heravi F, Getting SJ, Moschos SA. Extracellular vesicles and their nucleic acids for biomarker discovery. Pharmacol Ther 2018; 192:170-187. [PMID: 30081050 DOI: 10.1016/j.pharmthera.2018.08.002] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Extracellular vesicles (EVs) are a heterogenous population of vesicles originate from cells. EVs are found in different biofluids and carry different macromolecules, including proteins, lipids, and nucleic acids, providing a snap shot of the parental cells at the time of release. EVs have the ability to transfer molecular cargoes to other cells and can initiate different physiological and pathological processes. Mounting lines of evidence demonstrated that EVs' cargo and machinery is affected in disease states, positioning EVs as potential sources for the discovery of novel biomarkers. In this review, we demonstrate a conceptual overview of the EV field with particular focus on their nucleic acid cargoes. Current knowledge of EV subtypes, nucleic acid cargo and pathophysiological roles are outlined, with emphasis placed on advantages against competing analytes. We review the utility of EVs and their nucleic acid cargoes as biomarkers and critically assess the newly available advances in the field of EV biomarkers and high throughput technologies. Challenges to achieving the diagnostic potential of EVs, including sample handling, EV isolation, methodological considerations, and bioassay reproducibility are discussed. Future implementation of 'omics-based technologies and integration of systems biology approaches for the development of EV-based biomarkers and personalized medicine are also considered.
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Affiliation(s)
- Fatemeh Momen-Heravi
- Division of Periodontics, Section of Oral and Diagnostic Sciences, Columbia University, College of Dental Medicine, New York, NY, USA; Department of Biomedical Sciences, University of Westminster, London, UK.
| | - Stephen J Getting
- Department of Biomedical Sciences, University of Westminster, London, UK; Department of Life Sciences, University of Westminster, London, UK
| | - Sterghios Athanasios Moschos
- Department of Biomedical Sciences, University of Westminster, London, UK; Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle, UK
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31
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Kim B, Oh S, Shin S, Yim SG, Yang SY, Hahn YK, Choi S. Pumpless Microflow Cytometry Enabled by Viscosity Modulation and Immunobead Labeling. Anal Chem 2018; 90:8254-8260. [PMID: 29874050 DOI: 10.1021/acs.analchem.8b01804] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Major challenges of miniaturizing flow cytometry include obviating the need for bulky, expensive, and complex pump-based fluidic and laser-based optical systems while retaining the ability to detect target cells based on their unique surface receptors. We addressed these critical challenges by (i) using a viscous liquid additive to control flow rate passively, without external pumping equipment, and (ii) adopting an immunobead assay that can be quantified with a portable fluorescence cell counter based on a blue light-emitting diode. Such novel features enable pumpless microflow cytometry (pFC) analysis by simply dropping a sample solution onto the inlet reservoir of a disposable cell-counting chamber. With our pFC platform, we achieved reliable cell counting over a dynamic range of 9-298 cells/μL. We demonstrated the practical utility of the platform by identifying a type of cancer cell based on CD326, the epithelial cell adhesion molecule. This portable microflow cytometry platform can be applied generally to a range of cell types using immunobeads labeled with specific antibodies, thus making it valuable for cell-based and point-of-care diagnostics.
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Affiliation(s)
- Byeongyeon Kim
- Department of Biomedical Engineering , Kyung Hee University , Yongin-si , Gyeonggi-do 17104 , Republic of Korea
| | - Sein Oh
- Department of Biomedical Engineering , Kyung Hee University , Yongin-si , Gyeonggi-do 17104 , Republic of Korea
| | - Suyeon Shin
- Department of Biomedical Engineering , Kyung Hee University , Yongin-si , Gyeonggi-do 17104 , Republic of Korea
| | - Sang-Gu Yim
- Department of Biomaterials Science, Life and Industry Convergence Institute , Pusan National University , 1268-50 Samrangjin-ro , Miryang 50463 , Republic of Korea
| | - Seung Yun Yang
- Department of Biomaterials Science, Life and Industry Convergence Institute , Pusan National University , 1268-50 Samrangjin-ro , Miryang 50463 , Republic of Korea
| | - Young Ki Hahn
- Department of New Biology , Daegu Gyeongbuk Institute of Science & Technology (DGIST) , Daegu 42988 , Republic of Korea
| | - Sungyoung Choi
- Department of Biomedical Engineering , Kyung Hee University , Yongin-si , Gyeonggi-do 17104 , Republic of Korea
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32
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Individually addressable and dynamic DNA gates for multiplexed cell sorting. Proc Natl Acad Sci U S A 2018; 115:4357-4362. [PMID: 29632190 DOI: 10.1073/pnas.1714820115] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ability to analyze and isolate cells based on the expression of specific surface markers has increased our understanding of cell biology and produced numerous applications for biomedicine. However, established cell-sorting platforms rely on labels that are limited in number due to biophysical constraints, such as overlapping emission spectra of fluorophores in FACS. Here, we establish a framework built on a system of orthogonal and extensible DNA gates for multiplexed cell sorting. These DNA gates label target cell populations by antibodies to allow magnetic bead isolation en masse and then selectively unlock by strand displacement to sort cells. We show that DNA gated sorting (DGS) is triggered to completion within minutes on the surface of cells and achieves target cell purity, viability, and yield equivalent to that of commercial magnetic sorting kits. We demonstrate multiplexed sorting of three distinct immune cell populations (CD8+, CD4+, and CD19+) from mouse splenocytes to high purity and show that recovered CD8+ T cells retain proliferative potential and target cell-killing activity. To broaden the utility of this platform, we implement a double positive sorting scheme using DNA gates on peptide-MHC tetramers to isolate antigen-specific CD8+ T cells from mice infected with lymphocytic choriomeningitis virus (LCMV). DGS can potentially be expanded with fewer biophysical constraints to large families of DNA gates for applications that require analysis of complex cell populations, such as host immune responses to disease.
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33
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Galkowski D, Ratajczak MZ, Kocki J, Darzynkiewicz Z. Of Cytometry, Stem Cells and Fountain of Youth. Stem Cell Rev Rep 2018; 13:465-481. [PMID: 28364326 DOI: 10.1007/s12015-017-9733-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Outlined are advances of cytometry applications to identify and sort stem cells, of laser scanning cytometry and ImageStream imaging instrumentation to further analyze morphometry of these cells, and of mass cytometry to classify a multitude of cellular markers in large cell populations. Reviewed are different types of stem cells, including potential candidates for cancer stem cells, with respect to their "stemness", and other characteristics. Appraised is further progress in identification and isolation of the "very small embryonic-like stem cells" (VSELs) and their autogenous transplantation for tissue repair and geroprotection. Also assessed is a function of hyaluronic acid, the major stem cells niche component, as a guardian and controller of stem cells. Briefly appraised are recent advances and challenges in the application of stem cells in regenerative medicine and oncology and their future role in different disciplines of medicine, including geriatrics.
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Affiliation(s)
| | - Mariusz Z Ratajczak
- Stem Cell Institute at James Graham Brown Cancer Center, University of Louisville, Louisville, KY, 40202, USA
| | - Janusz Kocki
- Department of Clinical Genetics, Medical University in Lublin, 20-080, Lublin, Poland
| | - Zbigniew Darzynkiewicz
- Brander Cancer Research Institute and Department of Pathology, New York Medical College, Valhalla, NY, 10095, USA.
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Bhagwat N, Dulmage K, Pletcher CH, Wang L, DeMuth W, Sen M, Balli D, Yee SS, Sa S, Tong F, Yu L, Moore JS, Stanger BZ, Dixon EP, Carpenter EL. An integrated flow cytometry-based platform for isolation and molecular characterization of circulating tumor single cells and clusters. Sci Rep 2018; 8:5035. [PMID: 29568081 PMCID: PMC5864750 DOI: 10.1038/s41598-018-23217-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/07/2018] [Indexed: 01/06/2023] Open
Abstract
Comprehensive molecular analysis of rare circulating tumor cells (CTCs) and cell clusters is often hampered by low throughput and purity, as well as cell loss. To address this, we developed a fully integrated platform for flow cytometry-based isolation of CTCs and clusters from blood that can be combined with whole transcriptome analysis or targeted RNA transcript quantification. Downstream molecular signature can be linked to cell phenotype through index sorting. This newly developed platform utilizes in-line magnetic particle-based leukocyte depletion, and acoustic cell focusing and washing to achieve >98% reduction of blood cells and non-cellular debris, along with >1.5 log-fold enrichment of spiked tumor cells. We could also detect 1 spiked-in tumor cell in 1 million WBCs in 4/7 replicates. Importantly, the use of a large 200μm nozzle and low sheath pressure (3.5 psi) minimized shear forces, thereby maintaining cell viability and integrity while allowing for simultaneous recovery of single cells and clusters from blood. As proof of principle, we isolated and transcriptionally characterized 63 single CTCs from a genetically engineered pancreatic cancer mouse model (n = 12 mice) and, using index sorting, were able to identify distinct epithelial and mesenchymal sub-populations based on linked single cell protein and gene expression.
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Affiliation(s)
- Neha Bhagwat
- Division of Gastroenterology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Keely Dulmage
- BD Technologies and Innovation, Research Triangle Park, NC, USA
| | - Charles H Pletcher
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ling Wang
- BD Technologies and Innovation, Research Triangle Park, NC, USA
| | - William DeMuth
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Moen Sen
- Division of Hematology and Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David Balli
- Division of Gastroenterology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Stephanie S Yee
- Division of Hematology and Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Silin Sa
- BD Biosciences, San Jose, CA, USA
| | - Frances Tong
- BD Technologies and Innovation, Research Triangle Park, NC, USA
| | | | - Jonni S Moore
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ben Z Stanger
- Division of Gastroenterology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Eric P Dixon
- BD Technologies and Innovation, Research Triangle Park, NC, USA
| | - Erica L Carpenter
- Division of Hematology and Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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Nobori T, Tosaka K, Kawamura A, Joichi T, Kamino K, Kishimura A, Baba E, Mori T, Katayama Y. Alkaline Phosphatase-Catalyzed Amplification of a Fluorescence Signal for Flow Cytometry. Anal Chem 2017; 90:1059-1062. [DOI: 10.1021/acs.analchem.7b03893] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Takanobu Nobori
- Department
of Applied Chemistry, Faculty of Engineering, Kyushu University, 744
Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Kenta Tosaka
- Graduate
School of Systems Life Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Akira Kawamura
- Graduate
School of Systems Life Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Taisei Joichi
- Graduate
School of Systems Life Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Kenta Kamino
- Graduate
School of Systems Life Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Akihiro Kishimura
- Department
of Applied Chemistry, Faculty of Engineering, Kyushu University, 744
Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
- Graduate
School of Systems Life Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
- International
Research Center for Molecular Systems, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Eishi Baba
- Department
of Comprehensive Clinical Oncology, Faculty of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Takeshi Mori
- Department
of Applied Chemistry, Faculty of Engineering, Kyushu University, 744
Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
- Graduate
School of Systems Life Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Yoshiki Katayama
- Department
of Applied Chemistry, Faculty of Engineering, Kyushu University, 744
Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
- Graduate
School of Systems Life Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
- International
Research Center for Molecular Systems, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
- Center
for Advanced Medical Innovation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
- Department
of Biomedical Engineering, Chung Yuan Christian University, 200 Chung
Pei Road, Chung Li, 32023 ROC, Taiwan
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36
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Abstract
The majority of cancer-related deaths result from metastasis, the process by which cancer cells escape the primary tumor site and enter into the blood circulation in order to disseminate to secondary locations throughout the body. Tumor cells found within the circulation are referred to as circulating tumor cells (CTCs), and their detection and enumeration correlate with poor prognosis. The epithelial-to-mesenchymal transition (EMT) is a dynamic process that imparts epithelial cells with mesenchymal-like properties, thus facilitating tumor cell dissemination and contributing to metastasis. However, EMT also results in the downregulation of various epithelial proteins typically utilized by CTC technologies for enrichment and detection of these rare cells, resulting in reduced detection of some CTCs, potentially those with a more metastatic phenotype. In addition to the current clinical role of CTCs as a prognostic biomarker, they also have potential as a predictive biomarker via CTC characterization. However, CTC characterization is complicated by the unknown biological significance of CTCs possessing an EMT-like phenotype, and the ability to capture and understand this CTC subpopulation is an essential step in the utilization of CTCs for patient management. This chapter will review the process of EMT and its contribution to metastasis; discusses current and future clinical applications of CTCs; and describes both traditional and novel methods for CTC enrichment, detection, and characterization with a specific focus on CTCs with an EMT phenotype.
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Surface marker profiling of SH-SY5Y cells enables small molecule screens identifying BMP4 as a modulator of neuroblastoma differentiation. Sci Rep 2017; 7:13612. [PMID: 29051534 PMCID: PMC5648761 DOI: 10.1038/s41598-017-13497-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 09/25/2017] [Indexed: 01/08/2023] Open
Abstract
Neuroblastoma is the most common extra-cranial solid tumor in children. Its broad spectrum of clinical outcomes reflects the underlying inherent cellular heterogeneity. As current treatments often do not lead to tumor eradication, there is a need to better define therapy-resistant neuroblastoma and to identify new modulatory molecules. To this end, we performed the first comprehensive flow cytometric characterization of surface molecule expression in neuroblastoma cell lines. Exploiting an established clustering algorithm (SPADE) for unbiased visualization of cellular subsets, we conducted a multiwell screen for small molecule modulators of neuroblastoma phenotype. In addition to SH-SY5Y cells, the SH-EP, BE(2)-M17 and Kelly lines were included in follow-up analysis as in vitro models of neuroblastoma. A combinatorial detection of glycoprotein epitopes (CD15, CD24, CD44, CD57, TrkA) and the chemokine receptor CXCR4 (CD184) enabled the quantitative identification of SPADE-defined clusters differentially responding to small molecules. Exposure to bone morphogenetic protein (BMP)-4 was found to enhance a TrkAhigh/CD15−/CD184− neuroblastoma cellular subset, accompanied by a reduction in doublecortin-positive neuroblasts and of NMYC protein expression in SH-SY5Y cells. Beyond yielding novel marker candidates for studying neuroblastoma pathology, our approach may provide tools for improved pharmacological screens towards developing novel avenues of neuroblastoma diagnosis and treatment.
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38
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Kalb DM, Fencl FA, Woods TA, Swanson A, Maestas GC, Juárez JJ, Edwards BS, Shreve AP, Graves SW. Line-Focused Optical Excitation of Parallel Acoustic Focused Sample Streams for High Volumetric and Analytical Rate Flow Cytometry. Anal Chem 2017; 89:9967-9975. [PMID: 28823146 PMCID: PMC6134836 DOI: 10.1021/acs.analchem.7b02319] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Flow cytometry provides highly sensitive multiparameter analysis of cells and particles but has been largely limited to the use of a single focused sample stream. This limits the analytical rate to ∼50K particles/s and the volumetric rate to ∼250 μL/min. Despite the analytical prowess of flow cytometry, there are applications where these rates are insufficient, such as rare cell analysis in high cellular backgrounds (e.g., circulating tumor cells and fetal cells in maternal blood), detection of cells/particles in large dilute samples (e.g., water quality, urine analysis), or high-throughput screening applications. Here we report a highly parallel acoustic flow cytometer that uses an acoustic standing wave to focus particles into 16 parallel analysis points across a 2.3 mm wide optical flow cell. A line-focused laser and wide-field collection optics are used to excite and collect the fluorescence emission of these parallel streams onto a high-speed camera for analysis. With this instrument format and fluorescent microsphere standards, we obtain analysis rates of 100K/s and flow rates of 10 mL/min, while maintaining optical performance comparable to that of a commercial flow cytometer. The results with our initial prototype instrument demonstrate that the integration of key parallelizable components, including the line-focused laser, particle focusing using multinode acoustic standing waves, and a spatially arrayed detector, can increase analytical and volumetric throughputs by orders of magnitude in a compact, simple, and cost-effective platform. Such instruments will be of great value to applications in need of high-throughput yet sensitive flow cytometry analysis.
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Affiliation(s)
- Daniel M. Kalb
- Center for Biomedical Engineering & Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM 87131
| | - Frank A. Fencl
- Center for Biomedical Engineering & Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM 87131
| | - Travis A. Woods
- Center for Biomedical Engineering & Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM 87131
- Center for Molecular Discovery, Innovation Discovery and Training Center, Health Sciences Center, University of New Mexico, Albuquerque, New Mexico, 87131-0001 United States
| | | | - Gian C. Maestas
- Center for Biomedical Engineering & Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM 87131
| | - Jaime J. Juárez
- Center for Biomedical Engineering & Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM 87131
| | - Bruce S. Edwards
- Center for Molecular Discovery, Innovation Discovery and Training Center, Health Sciences Center, University of New Mexico, Albuquerque, New Mexico, 87131-0001 United States
| | - Andrew P. Shreve
- Center for Biomedical Engineering & Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM 87131
| | - Steven W. Graves
- Center for Biomedical Engineering & Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM 87131
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39
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Roitshtain D, Wolbromsky L, Bal E, Greenspan H, Satterwhite LL, Shaked NT. Quantitative phase microscopy spatial signatures of cancer cells. Cytometry A 2017; 91:482-493. [DOI: 10.1002/cyto.a.23100] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Revised: 02/09/2017] [Accepted: 03/03/2017] [Indexed: 12/29/2022]
Affiliation(s)
- Darina Roitshtain
- Department of Biomedical Engineering; Faculty of Engineering, Tel Aviv University; Tel Aviv 69978 Israel
| | - Lauren Wolbromsky
- Department of Biomedical Engineering; Faculty of Engineering, Tel Aviv University; Tel Aviv 69978 Israel
| | - Evgeny Bal
- Department of Biomedical Engineering; Faculty of Engineering, Tel Aviv University; Tel Aviv 69978 Israel
| | - Hayit Greenspan
- Department of Biomedical Engineering; Faculty of Engineering, Tel Aviv University; Tel Aviv 69978 Israel
| | - Lisa L. Satterwhite
- Department of Biomedical Engineering; Duke University; Durham North Carolina 27708
| | - Natan T. Shaked
- Department of Biomedical Engineering; Faculty of Engineering, Tel Aviv University; Tel Aviv 69978 Israel
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40
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41
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Poudineh M, Aldridge PM, Ahmed S, Green BJ, Kermanshah L, Nguyen V, Tu C, Mohamadi RM, Nam RK, Hansen A, Sridhar SS, Finelli A, Fleshner NE, Joshua AM, Sargent EH, Kelley SO. Tracking the dynamics of circulating tumour cell phenotypes using nanoparticle-mediated magnetic ranking. NATURE NANOTECHNOLOGY 2017; 12:274-281. [PMID: 27870841 DOI: 10.1038/nnano.2016.239] [Citation(s) in RCA: 169] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 10/03/2016] [Indexed: 05/07/2023]
Abstract
Profiling the heterogeneous phenotypes of rare circulating tumour cells (CTCs) in whole blood is critical to unravelling the complex and dynamic properties of these potential clinical markers. This task is challenging because these cells are present at parts per billion levels among normal blood cells. Here we report a new nanoparticle-enabled method for CTC characterization, called magnetic ranking cytometry, which profiles CTCs on the basis of their surface expression phenotype. We achieve this using a microfluidic chip that successfully processes whole blood samples. The approach classifies CTCs with single-cell resolution in accordance with their expression of phenotypic surface markers, which is read out using magnetic nanoparticles. We deploy this new technique to reveal the dynamic phenotypes of CTCs in unprocessed blood from mice as a function of tumour growth and aggressiveness. We also test magnetic ranking cytometry using blood samples collected from cancer patients.
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Affiliation(s)
- Mahla Poudineh
- Department of Electrical and Computer Engineering, Faculty of Engineering, University of Toronto, Toronto, Ontario M5S 3G4, Canada
| | - Peter M Aldridge
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Sharif Ahmed
- Department of Pharmaceutical Science, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Brenda J Green
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Leyla Kermanshah
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Vivian Nguyen
- Department of Pharmaceutical Science, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Carmen Tu
- Department of Pharmaceutical Science, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Reza M Mohamadi
- Department of Pharmaceutical Science, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Robert K Nam
- Sunnybrook Health Sciences Centre, Sunnybrook Research Institute, University of Toronto, Toronto, Ontario M4N 3M5, Canada
| | - Aaron Hansen
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario M5G 2M9, Canada
| | - Srikala S Sridhar
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario M5G 2M9, Canada
| | - Antonio Finelli
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario M5G 2M9, Canada
| | - Neil E Fleshner
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario M5G 2M9, Canada
| | - Anthony M Joshua
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario M5G 2M9, Canada
| | - Edward H Sargent
- Department of Electrical and Computer Engineering, Faculty of Engineering, University of Toronto, Toronto, Ontario M5S 3G4, Canada
| | - Shana O Kelley
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3M2, Canada
- Department of Pharmaceutical Science, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
- Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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42
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Abstract
Cell death and its recently discovered regulated form ferroptosis are characterized by distinct morphological, electrophysiological, and pharmacological features. In particular ferroptosis can be induced by experimental compounds and clinical drugs (i.e., erastin, sulfasalazine, sorafenib, and artesunate) in various cell types and cancer cells. Pharmacologically, this cell death process can be inhibited by iron chelators and lipid peroxidation inhibitors. Relevance of this specific cell death form has been found in different pathological conditions such as cancer, neurotoxicity, neurodegeneration, and ischemia. Distinguishing cell viability and cell death is essential for experimental and clinical applications and a key component in flow cytometry experiments. Dead cells can compromise the integrity of the data by nonspecific binding of antibodies and dyes. Therefore it is essential that dead cells are robustly and reproducibly identified and characterized by means of cytometry application. Here we describe a procedure to detect and quantify cell death and its specific form ferroptosis based on standard flow cytometry techniques.
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43
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Janczuk M, Richter Ł, Hoser G, Kawiak J, Łoś M, Niedziółka-Jönsson J, Paczesny J, Hołyst R. Bacteriophage-Based Bioconjugates as a Flow Cytometry Probe for Fast Bacteria Detection. Bioconjug Chem 2016; 28:419-425. [DOI: 10.1021/acs.bioconjchem.6b00596] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marta Janczuk
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Łukasz Richter
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Grażyna Hoser
- Laboratory
of Flow Cytometry, Medical Center of Postgraduate Education, Marymoncka
99/103, 01-813 Warsaw, Poland
| | - Jerzy Kawiak
- Department
of Biomedical Systems and Technologies, Nalecz Institute of Biocybernetics
and Biomedical Engineering, Polish Academy of Sciences, Trojdena
4, 02-109 Warsaw, Poland
| | - Marcin Łoś
- Department
of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
- Phage Consultants, Partyzantów
10/18, 80-254 Gdansk, Poland
| | | | - Jan Paczesny
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Robert Hołyst
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
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44
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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.
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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
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45
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Altered Expression of Natural Cytotoxicity Receptors and NKG2D on Peripheral Blood NK Cell Subsets in Breast Cancer Patients. Transl Oncol 2016; 9:384-391. [PMID: 27641642 PMCID: PMC5024335 DOI: 10.1016/j.tranon.2016.07.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 07/10/2016] [Accepted: 07/13/2016] [Indexed: 12/13/2022] Open
Abstract
Human natural killer (NK) cells are considered professional cytotoxic cells that are integrated into the effector branch of innate immunity during antiviral and antitumoral responses. The purpose of this study was to examine the peripheral distribution and expression of NK cell activation receptors from the fresh peripheral blood mononuclear cells of 30 breast cancer patients prior to any form of treatment (including surgery, chemotherapy, and radiotherapy), 10 benign breast pathology patients, and 24 control individuals. CD3−CD56dimCD16bright NK cells (CD56dim NK) and CD3−CD56brightCD16dim/− NK cells (CD56bright NK) were identified using flow cytometry. The circulating counts of CD56dim and CD56bright NK cells were not significantly different between the groups evaluated, nor were the counts of other leukocyte subsets between the breast cancer patients and benign breast pathology patients. However, in CD56dim NK cells, NKp44 expression was higher in breast cancer patients (P = .0302), whereas NKp30 (P = .0005), NKp46 (P = .0298), and NKG2D (P = .0005) expression was lower with respect to healthy donors. In CD56bright NK cells, NKp30 (P = .0007), NKp46 (P = .0012), and NKG2D (P = .0069) expression was lower in breast cancer patients compared with control group. Only NKG2D in CD56bright NK cells (P = .0208) and CD56dim NK cells (P = .0439) showed difference between benign breast pathology and breast cancer patients. Collectively, the current study showed phenotypic alterations in activation receptors on CD56dim and CD56bright NK cells, suggesting that breast cancer patients have decreased NK cell cytotoxicity.
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Abstract
The onset of the AIDS pandemic in the early 1980s coincided with the convergence of technologies now collectively known as flow cytometry (FCM). Major advances in FCM led significantly toward our understanding of the pathogenicity of the disease, which in turn led to wider adoption of the technology, including using it effectively in a variety of diagnostics. CD4+ T lymphocyte population counts, along with human immunodeficiency virus (HIV) viral load, remain the gold standard in diagnosis and continue to play a major role in the monitoring of advanced retroviral therapies. Arguably, the spread of AIDS (acquired immunodeficiency syndrome), the HIV virus, and the toll of the virus on humanity have been considerably altered by the concurrent development of FCM, the details of which are presented herein.
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Affiliation(s)
- Ian C Clift
- Indiana University South Bend School of Applied Health Sciences, South Bend, IN
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47
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Pellegrino M, Sciambi A, Yates JL, Mast JD, Silver C, Eastburn DJ. RNA-Seq following PCR-based sorting reveals rare cell transcriptional signatures. BMC Genomics 2016; 17:361. [PMID: 27189161 PMCID: PMC4869385 DOI: 10.1186/s12864-016-2694-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 05/04/2016] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Rare cell subtypes can profoundly impact the course of human health and disease, yet their presence within a sample is often missed with bulk molecular analysis. Single-cell analysis tools such as FACS, FISH-FC and single-cell barcode-based sequencing can investigate cellular heterogeneity; however, they have significant limitations that impede their ability to identify and transcriptionally characterize many rare cell subpopulations. RESULTS PCR-activated cell sorting (PACS) is a novel cytometry method that uses single-cell TaqMan PCR reactions performed in microfluidic droplets to identify and isolate cell subtypes with high-throughput. Here, we extend this method and demonstrate that PACS enables high-dimensional molecular profiling on TaqMan-targeted cells. Using a random priming RNA-Seq strategy, we obtained high-fidelity transcriptome measurements following PACS sorting of prostate cancer cells from a heterogeneous population. The sequencing data revealed prostate cancer gene expression profiles that were obscured in the unsorted populations. Single-cell expression analysis with PACS was subsequently used to confirm a number of the differentially expressed genes identified with RNA sequencing. CONCLUSIONS PACS requires minimal sample processing, uses readily available TaqMan assays and can isolate cell subtypes with high sensitivity. We have now validated a method for performing next-generation sequencing on mRNA obtained from PACS isolated cells. This capability makes PACS well suited for transcriptional profiling of rare cells from complex populations to obtain maximal biological insight into cell states and behaviors.
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Affiliation(s)
| | - Adam Sciambi
- Mission Bio, Inc., 953 Indiana St., San Francisco, California, 94107, USA
| | - Jamie L Yates
- Mission Bio, Inc., 953 Indiana St., San Francisco, California, 94107, USA
| | - Joshua D Mast
- Mission Bio, Inc., 953 Indiana St., San Francisco, California, 94107, USA
| | - Charles Silver
- Mission Bio, Inc., 953 Indiana St., San Francisco, California, 94107, USA
| | - Dennis J Eastburn
- Mission Bio, Inc., 953 Indiana St., San Francisco, California, 94107, USA.
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48
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Multiplexed labeling system for high-throughput cell sorting. Anal Biochem 2016; 508:124-8. [PMID: 27181032 DOI: 10.1016/j.ab.2016.05.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 04/28/2016] [Accepted: 05/04/2016] [Indexed: 11/23/2022]
Abstract
Flow cytometry and fluorescence activated cell sorting techniques were designed to realize configurable classification and separation of target cells. A number of cell phenotypes with different functionalities have recently been revealed. Before simultaneous selective capture of cells, it is desirable to label different samples with the corresponding dyes in a multiplexing manner to allow for a single analysis. However, few methods to obtain multiple fluorescent colors for various cell types have been developed. Even when restricted laser sources are employed, a small number of color codes can be expressed simultaneously. In this study, we demonstrate the ability to manifest DNA nanostructure-based multifluorescent colors formed by a complex of dyes. Highly precise self-assembly of fluorescent dye-conjugated oligonucleotides gives anisotropic DNA nanostructures, Y- and tree-shaped DNA (Y-DNA and T-DNA, respectively), which may be used as platforms for fluorescent codes. As a proof of concept, we have demonstrated seven different fluorescent codes with only two different fluorescent dyes using T-DNA. This method provides maximum efficiency for current flow cytometry. We are confident that this system will provide highly efficient multiplexed fluorescent detection for bioanalysis compared with one-to-one fluorescent correspondence for specific marker detection.
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Kverneland AH, Streitz M, Geissler E, Hutchinson J, Vogt K, Boës D, Niemann N, Pedersen AE, Schlickeiser S, Sawitzki B. Age and gender leucocytes variances and references values generated using the standardized ONE-Study protocol. Cytometry A 2016; 89:543-64. [PMID: 27144459 DOI: 10.1002/cyto.a.22855] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Revised: 03/02/2016] [Accepted: 03/17/2016] [Indexed: 01/10/2023]
Abstract
Flow cytometry is now accepted as an ideal technology to reveal changes in immune cell composition and function. However, it is also an error-prone and variable technology, which makes it difficult to reproduce findings across laboratories. We have recently developed a strategy to standardize whole blood flow cytometry. The performance of our protocols was challenged here by profiling samples from healthy volunteers to reveal age- and gender-dependent differences and to establish a standardized reference cohort for use in clinical trials. Whole blood samples from two different cohorts were analyzed (first cohort: n = 52, second cohort: n = 46, both 20-84 years with equal gender distribution). The second cohort was run as a validation cohort by a different operator. The "ONE Study" panels were applied to analyze expression of >30 different surface markers to enumerate proportional and absolute numbers of >50 leucocyte subsets. Indeed, analysis of the first cohort revealed significant age-dependent changes in subsets e.g. increased activated and differentiated CD4(+) and CD8(+) T cell subsets, acquisition of a memory phenotype for Tregs as well as decreased MDC2 and Marginal Zone B cells. Males and females showed different dynamics in age-dependent T cell activation and differentiation, indicating faster immunosenescence in males. Importantly, although both cohorts consisted of a small sample size, our standardized approach enabled validation of age-dependent changes with the second cohort. Thus, we have proven the utility of our strategy and generated reproducible reference ranges accounting for age- and gender-dependent differences, which are crucial for a better patient monitoring and individualized therapy. © 2016 International Society for Advancement of Cytometry.
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Affiliation(s)
- Anders H Kverneland
- Institute of Medical Immunology, Charité Universitätsmedizin Berlin, Germany.,Department of International Health, Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, København, Denmark
| | - Mathias Streitz
- Institute of Medical Immunology, Charité Universitätsmedizin Berlin, Germany
| | | | | | - Katrin Vogt
- Institute of Medical Immunology, Charité Universitätsmedizin Berlin, Germany
| | - David Boës
- Institute of Medical Immunology, Charité Universitätsmedizin Berlin, Germany
| | - Nadja Niemann
- Institute of Medical Immunology, Charité Universitätsmedizin Berlin, Germany
| | - Anders Elm Pedersen
- Department of International Health, Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, København, Denmark
| | | | - Birgit Sawitzki
- Institute of Medical Immunology, Charité Universitätsmedizin Berlin, Germany
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50
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Monaco G, Chen H, Poidinger M, Chen J, de Magalhães JP, Larbi A. flowAI: automatic and interactive anomaly discerning tools for flow cytometry data. Bioinformatics 2016; 32:2473-80. [DOI: 10.1093/bioinformatics/btw191] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 04/04/2016] [Indexed: 12/25/2022] Open
Abstract
Abstract
Motivation: Flow cytometry (FCM) is widely used in both clinical and basic research to characterize cell phenotypes and functions. The latest FCM instruments analyze up to 20 markers of individual cells, producing high-dimensional data. This requires the use of the latest clustering and dimensionality reduction techniques to automatically segregate cell sub-populations in an unbiased manner. However, automated analyses may lead to false discoveries due to inter-sample differences in quality and properties.
Results: We present an R package, flowAI, containing two methods to clean FCM files from unwanted events: (i) an automatic method that adopts algorithms for the detection of anomalies and (ii) an interactive method with a graphical user interface implemented into an R shiny application. The general approach behind the two methods consists of three key steps to check and remove suspected anomalies that derive from (i) abrupt changes in the flow rate, (ii) instability of signal acquisition and (iii) outliers in the lower limit and margin events in the upper limit of the dynamic range. For each file analyzed our software generates a summary of the quality assessment from the aforementioned steps. The software presented is an intuitive solution seeking to improve the results not only of manual but also and in particular of automatic analysis on FCM data.
Availability and implementation: R source code available through Bioconductor: http://bioconductor.org/packages/flowAI/
Contacts: mongianni1@gmail.com or Anis_Larbi@immunol.a-star.edu.sg
Supplementary information: Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Gianni Monaco
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Singapore 138648, Singapore
- Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Hao Chen
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Singapore 138648, Singapore
| | - Michael Poidinger
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Singapore 138648, Singapore
| | - Jinmiao Chen
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Singapore 138648, Singapore
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Anis Larbi
- Singapore Immunology Network (SIgN), Agency for Science Technology and Research (A*STAR), Singapore 138648, Singapore
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