1
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Bao K, Jiang X, Hu HM, Liu T, Zhang J. DEPICT-seq: Single-Cell Transcriptomic Analysis of Rare Cell Subsets Isolated via Nucleic Acid Cytometry. Anal Chem 2024. [PMID: 39287475 DOI: 10.1021/acs.analchem.4c03075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2024]
Abstract
The ability to dive deep into specific rare cell populations is critical for understanding tissue physiology and pathology across various biological domains. As single-cell RNA-seq flourishes, many newly discovered cell subtypes are defined by their transcriptomic markers. However, our ability to retrieve and analyze cells based on their nucleic acid markers remains underdeveloped. Here, we present Double Emulsion PCR-Initiated Cell sorting and Transcriptomic Sequencing (DEPICT-seq), a high-throughput droplet nucleic acid cytometry method that integrates batch cell fixation for cellular information preservation, double emulsion digital PCR-based cell sorting to target nucleic acid markers of interest, and in-depth full-length transcriptomic analyses at single-cell resolution. We utilize DEPICT-seq to isolate and characterize T cell receptor (TCR)-engineered T cells within a mixed population and also demonstrate a variation of the workflow by incorporating an RNase H-dependent PCR step to enrich full-length TCR sequences for paired single-cell TCR sequencing and transcriptomic profiling.
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Affiliation(s)
- Kaixuan Bao
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Department of Endocrinology and Metabolism, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | | | - Hong-Min Hu
- ImmuXell Biotech Ltd., Shanghai 201315, China
| | - Tiemin Liu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Department of Endocrinology and Metabolism, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
- School of Life Sciences, Inner Mongolia University, Hohhot, Inner Mongolia 010020, China
| | - Jingwei Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
- School of Exercise and Health, Shanghai University of Sport, Shanghai 200438, China
- Zhejiang Lab, Hangzhou, Zhejiang 311121, China
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2
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Belkina AC, Roe CE, Tang VA, Back JB, Bispo C, Conway A, Chakraborty U, Daniels KT, de la Cruz G, Ferrer-Font L, Filby A, Gravano DM, Gregory MD, Hall C, Kukat C, Mozes A, Ordoñez-Rueda D, Orlowski-Oliver E, Pesce I, Porat Z, Poulton NJ, Reifel KM, Rieger AM, Sheridan RTC, Van Isterdael G, Walker RV. Guidelines for establishing a cytometry laboratory. Cytometry A 2024; 105:88-111. [PMID: 37941128 DOI: 10.1002/cyto.a.24807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 08/10/2023] [Accepted: 10/03/2023] [Indexed: 11/10/2023]
Abstract
The purpose of this document is to provide guidance for establishing and maintaining growth and development of flow cytometry shared resource laboratories. While the best practices offered in this manuscript are not intended to be universal or exhaustive, they do outline key goals that should be prioritized to achieve operational excellence and meet the needs of the scientific community. Additionally, this document provides information on available technologies and software relevant to shared resource laboratories. This manuscript builds on the work of Barsky et al. 2016 published in Cytometry Part A and incorporates recent advancements in cytometric technology. A flow cytometer is a specialized piece of technology that require special care and consideration in its housing and operations. As with any scientific equipment, a thorough evaluation of the location, space requirements, auxiliary resources, and support is crucial for successful operation. This comprehensive resource has been written by past and present members of the International Society for Advancement of Cytometry (ISAC) Shared Resource Laboratory (SRL) Emerging Leaders Program https://isac-net.org/general/custom.asp?page=SRL-Emerging-Leaders with extensive expertise in managing flow cytometry SRLs from around the world in different settings including academia and industry. It is intended to assist in establishing a new flow cytometry SRL, re-purposing an existing space into such a facility, or adding a flow cytometer to an individual lab in academia or industry. This resource reviews the available cytometry technologies, the operational requirements, and best practices in SRL staffing and management.
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Affiliation(s)
- Anna C Belkina
- Flow Cytometry Core Facility, School of Medicine, Boston University, Boston, Massachusetts, USA
| | - Caroline E Roe
- Cancer and Immunology Core, Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Vera A Tang
- Faculty of Medicine, Department of Biochemistry, Microbiology, and Immunology, Flow Cytometry Core Facility, University of Ottawa, Ottawa, Ontario, Canada
| | - Jessica B Back
- Department of Oncology, Wayne State University, Detroit, Michigan, USA
| | - Claudia Bispo
- Flow Cytometry Core Lab, AbbVie Inc, South San Francisco, California, USA
| | | | - Uttara Chakraborty
- Manipal Institute of Regenerative Medicine, Bengaluru, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | | | - Gelo de la Cruz
- Flow Cytometry Platform, Novo Nordisk Foundation Center for Stem Cell Medicine - reNEW, Copenhagen, Denmark
| | - Laura Ferrer-Font
- Hugh Green Cytometry Centre, Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Andrew Filby
- Flow Cytometry Core Facility and Innovation, Methodology and Application Research Theme, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - David M Gravano
- Stem Cell Instrumentation Foundry, University of California Merced, Merced, California, USA
| | - Michael D Gregory
- Cleveland Clinic, Florida Research and Innovation Center, Port St. Lucie, Florida, USA
| | - Christopher Hall
- Flow Cytometry Facility, Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Christian Kukat
- FACS & Imaging Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - André Mozes
- Flow Cytometry Platform, Champalimaud Foundation, Lisbon, Portugal
| | - Diana Ordoñez-Rueda
- Flow Cytometry Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | - Isabella Pesce
- Cell Analysis and Separation Core Facility, Department of Cellular Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Ziv Porat
- Flow Cytometry Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Nicole J Poulton
- Center for Aquatic Cytometry, Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, USA
| | - Kristen M Reifel
- Flow Cytometry Core Facility, Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Aja M Rieger
- Flow Cytometry Core Facility, University of Alberta, Alberta, Canada
| | | | - Gert Van Isterdael
- VIB Flow Core, VIB Center for Inflammation Research, Belgium & Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Rachael V Walker
- Flow Cytometry Facility, Babraham Institute, Babraham Research Campus, Cambridge, UK
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3
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Kosyrkova AV, Gusev DV, Goryainov SA, Kravchuk AD, Aristov AA, Batalov AI, Zakharova NE, Shugai SV, Pavlova GV, Pronin IN. [National and world experience in functioning of centers for collective use of biological resource collections of tumors of the central nervous system]. ZHURNAL VOPROSY NEIROKHIRURGII IMENI N. N. BURDENKO 2024; 88:59-64. [PMID: 38881017 DOI: 10.17116/neiro20248803159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Collective use center is an organization or structural unit with unique resource providing access to this resource for internal and third-party users. Collective use centers are a relatively new phenomenon in bioresource collections, especially collections of human biological material due to some ethical and legal issues. At the same time, the demand for human biological material continues to grow in fundamental and applied researches. The collective use center «Bioresource collection of tissues and cell cultures of tumors of the human nervous system for fundamental and applied researches» has worked since October 14, 2022. This center has access to unique collection of the Laboratory of Neurosurgical Anatomy and Conservation of Human Biological Tissues of the Burdenko Neurosurgical Center. OBJECTIVE To analyze the experience of collective use center and biobank of the Burdenko Neurosurgical Center compared to national and international data on functioning of collective use centers specializing in tumors of the human central nervous system. MATERIAL AND METHODS We reviewed the PubMed and e-Library databases using the following keywords: core facilities brain tumors, repository of collective use brain tumors, biobank of CNS tumors, central nervous system tumor collection centers. We also analyzed the organizations registered on the portal of scientific and technical infrastructure of the Russian Federation. RESULTS We analyzed 275 publications devoted to collective use centers and biobanks. These biobanks do not position themselves as collective use centers but actively realize biological material for researches. Structure of institutions presented on the portal of scientific and technical infrastructure of the Russian Federation is characterized. The collective use center «Bioresource collection of tissues and cell cultures of tumors of the human nervous system for fundamental and applied researches» has access to biobank of the Burdenko Neurosurgical Center. To date, the biobank contains more than 8478 aliquots of tumor tissue frozen at ultra-low temperature (-196°C) and obtained from 1993 patients. Considering available data, we established the basic principles of work in collective use centers with bioresource collections. CONCLUSION Collective use centers with bioresource collections of tumors of the central nervous system are rare. There is only one collective use center organized at the Burdenko Neurosurgical Center on the portal of scientific and technical infrastructure of the Russian Federation. At the same time, there is an urgent need to increase their number and activity in Russia and other countries worldwide. You can use the resource of brain tumor collections by leaving a request on the official website of this organization in the «Collective use center» section.
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Affiliation(s)
| | - D V Gusev
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - S A Goryainov
- Burdenko Neurosurgical Center, Moscow, Russia
- Kant Baltic Federal University, Kaliningrad, Russia
| | | | - A A Aristov
- Burdenko Neurosurgical Center, Moscow, Russia
| | - A I Batalov
- Burdenko Neurosurgical Center, Moscow, Russia
| | | | - S V Shugai
- Burdenko Neurosurgical Center, Moscow, Russia
| | - G V Pavlova
- Burdenko Neurosurgical Center, Moscow, Russia
- Institute of Higher Nervous Activity and Neurophysiology of the Russian Academy of Sciences, Moscow, Russia
| | - I N Pronin
- Burdenko Neurosurgical Center, Moscow, Russia
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4
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Cheetham M, Davies D, Hall C, Petersen CC, Schulte R, Walker R. Practicalities of Cell Sorting. Methods Mol Biol 2024; 2779:125-143. [PMID: 38526785 DOI: 10.1007/978-1-0716-3738-8_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Cell sorting is a technique commonly used in academic and biotechnology laboratories in order to separate out cells or particles of interest from heterogeneous populations. Cell sorters use the same principles as flow cytometry analyzers, but instead of cell populations passing to the waste of the instrument, they can be collected for further studies including DNA sequencing as well as other genomic, in vitro and in vivo experiments. This chapter aims to give an overview of cell sorting, the different types of cell sorters, details on how a cell sorter works, as well as protocols that are useful when embarking on a journey with cell sorting.
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Affiliation(s)
| | | | | | | | - Reiner Schulte
- Flow Cytometry Facility, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Rachael Walker
- Flow Cytometry Facility, Babraham Institute, Cambridge, UK.
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5
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Cohen M, Laux J, Douagi I. Cytometry in High-Containment Laboratories. Methods Mol Biol 2024; 2779:425-456. [PMID: 38526798 DOI: 10.1007/978-1-0716-3738-8_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
The emergence of new pathogens continues to fuel the need for advanced high-containment laboratories across the globe. Here we explore challenges and opportunities for integration of cytometry, a central technology for cell analysis, within high-containment laboratories. We review current applications in infectious disease, vaccine research, and biosafety. Considerations specific to cytometry within high-containment laboratories, such as biosafety requirements, and sample containment strategies are also addressed. We further tour the landscape of emerging technologies, including combination of cytometry with other omics, the application of automation, and artificial intelligence. Finally, we propose a framework to fast track the immersion of advanced technologies into the high-containment research setting to improve global preparedness for new emerging diseases.
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Affiliation(s)
- Melanie Cohen
- Flow Cytometry Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Julie Laux
- Flow Cytometry Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Iyadh Douagi
- Flow Cytometry Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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6
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Aspland AM, Douagi I, Filby A, Jellison ER, Martinez L, Shinko D, Smith AL, Tang VA, Thornton S. Biosafety during a pandemic: shared resource laboratories rise to the challenge. Cytometry A 2021; 99:68-80. [PMID: 33289290 PMCID: PMC7753791 DOI: 10.1002/cyto.a.24280] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/21/2020] [Accepted: 11/29/2020] [Indexed: 01/19/2023]
Abstract
Biosafety has always been an important aspect of daily work in any research institution, particularly for cytometry Shared Resources Laboratories (SRLs). SRLs are common‐use spaces that facilitate the sharing of knowledge, expertise, and ideas. This sharing inescapably involves contact and interaction of all those within this working environment on a daily basis. The current pandemic caused by SARS‐CoV‐2 has prompted the re‐evaluation of many policies governing the operations of SRLs. Here we identify and review the unique challenges SRLs face in maintaining biosafety standards, highlighting the potential risks associated with not only cytometry instrumentation and samples, but also the people working with them. We propose possible solutions to safety issues raised by the COVID‐19 pandemic and provide tools for facilities to adapt to evolving guidelines and future challenges.
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Affiliation(s)
- Avrill M Aspland
- Sydney Cytometry Core Research Facility, Centenary Institute, The University of Sydney, Sydney, New South Wales, Australia
| | - Iyadh Douagi
- Flow Cytometry Section, Research Technologies Branch, NIAID, NIH, Bethesda, Maryland, USA
| | - Andrew Filby
- Innovation, Methodology and Application Research Theme, Newcastle University, Newcastle upon Tyne, UK
| | - Evan R Jellison
- Department of Immunology, UCONN School of Medicine, Farmington, Connecticut, USA
| | - Lola Martinez
- Biotechnology Programme, Flow Cytometry Core Unit, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Diana Shinko
- Sydney Cytometry Core Research Facility, Centenary Institute, The University of Sydney, Sydney, New South Wales, Australia
| | - Adrian L Smith
- Sydney Cytometry Core Research Facility, Centenary Institute, The University of Sydney, Sydney, New South Wales, Australia
| | - Vera A Tang
- Faculty of Medicine, Department of Biochemistry, Microbiology, and Immunology, Flow Cytometry and Virometry Core Facility, University of Ottawa, Ottawa, Ontario, Canada
| | - Sherry Thornton
- Division of Rheumatology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati Medical Center, Cincinnati, Ohio, USA
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7
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Carson CF, Inglis TJJ. Air sampling to assess potential generation of aerosolized viable bacteria during flow cytometric analysis of unfixed bacterial suspensions. Gates Open Res 2018; 1:2. [PMID: 29608197 PMCID: PMC5873458 DOI: 10.12688/gatesopenres.12759.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/16/2018] [Indexed: 01/31/2024] Open
Abstract
This study investigated aerosolized viable bacteria in a university research laboratory during operation of an acoustic-assisted flow cytometer for antimicrobial susceptibility testing by sampling room air before, during and after flow cytometer use. The aim was to assess the risk associated with use of an acoustic-assisted flow cytometer analyzing unfixed bacterial suspensions. Air sampling in a nearby clinical laboratory was conducted during the same period to provide context for the existing background of microorganisms that would be detected in the air. The three species of bacteria undergoing analysis by flow cytometer in the research laboratory were Klebsiella pneumoniae, Burkholderia thailandensis and Streptococcus pneumoniae. None of these was detected from multiple 1000 L air samples acquired in the research laboratory environment. The main cultured bacteria in both locations were skin commensal and environmental bacteria, presumed to have been disturbed or dispersed in laboratory air by personnel movements during routine laboratory activities. The concentrations of bacteria detected in research laboratory air samples were reduced after interventional cleaning measures were introduced and were lower than those in the diagnostic clinical microbiology laboratory. We conclude that our flow cytometric analyses of unfixed suspensions of K. pneumoniae, B. thailandensis and S. pneumoniae do not pose a risk to cytometer operators or other personnel in the laboratory but caution against extrapolation of our results to other bacteria and/or different flow cytometric experimental procedures.
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Affiliation(s)
- Christine F Carson
- School of Biomedical Sciences (M504), Faculty of Health and Medical Sciences, University of Western Australia, Crawley, WA, Australia
| | - Timothy JJ Inglis
- School of Biomedical Sciences (M504), Faculty of Health and Medical Sciences, University of Western Australia, Crawley, WA, Australia
- School of Medicine, Faculty of Health and Medical Sciences, University of Western Australia, Crawley, WA, Australia
- Department of Microbiology, PathWest Laboratory Medicine WA, Queen Elizabeth II Medical Centre, Nedlands, WA, Australia
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8
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Carson CF, Inglis TJ. Air sampling to assess potential generation of aerosolized viable bacteria during flow cytometric analysis of unfixed bacterial suspensions. Gates Open Res 2018; 1:2. [PMID: 29608197 PMCID: PMC5873458 DOI: 10.12688/gatesopenres.12759.2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/16/2018] [Indexed: 11/20/2022] Open
Abstract
This study investigated aerosolized viable bacteria in a university research laboratory during operation of an acoustic-assisted flow cytometer for antimicrobial susceptibility testing by sampling room air before, during and after flow cytometer use. The aim was to assess the risk associated with use of an acoustic-assisted flow cytometer analyzing unfixed bacterial suspensions. Air sampling in a nearby clinical laboratory was conducted during the same period to provide context for the existing background of microorganisms that would be detected in the air. The three species of bacteria undergoing analysis by flow cytometer in the research laboratory were
Klebsiella pneumoniae, Burkholderia thailandensis and
Streptococcus pneumoniae. None of these was detected from multiple 1000 L air samples acquired in the research laboratory environment. The main cultured bacteria in both locations were skin commensal and environmental bacteria, presumed to have been disturbed or dispersed in laboratory air by personnel movements during routine laboratory activities. The concentrations of bacteria detected in research laboratory air samples were reduced after interventional cleaning measures were introduced and were lower than those in the diagnostic clinical microbiology laboratory. We conclude that our flow cytometric analyses of unfixed suspensions of
K. pneumoniae, B. thailandensis and
S. pneumoniae do not pose a risk to cytometer operators or other personnel in the laboratory but caution against extrapolation of our results to other bacteria and/or different flow cytometric experimental procedures.
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Affiliation(s)
- Christine F Carson
- School of Biomedical Sciences (M504), Faculty of Health and Medical Sciences, University of Western Australia, Crawley, WA, Australia
| | - Timothy Jj Inglis
- School of Biomedical Sciences (M504), Faculty of Health and Medical Sciences, University of Western Australia, Crawley, WA, Australia.,School of Medicine, Faculty of Health and Medical Sciences, University of Western Australia, Crawley, WA, Australia.,Department of Microbiology, PathWest Laboratory Medicine WA, Queen Elizabeth II Medical Centre, Nedlands, WA, Australia
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9
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Mariotti S, Pardini M, Teloni R, Gagliardi MC, Fraziano M, Nisini R. A method permissive to fixation and permeabilization for the multiparametric analysis of apoptotic and necrotic cell phenotype by flow cytometry. Cytometry A 2017; 91:1115-1124. [DOI: 10.1002/cyto.a.23268] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 09/07/2017] [Accepted: 09/28/2017] [Indexed: 12/17/2022]
Affiliation(s)
- Sabrina Mariotti
- Dipartimento di Malattie Infettive, Istituto Superiore di Sanità; Roma Italy
| | - Manuela Pardini
- Dipartimento di Malattie Infettive, Istituto Superiore di Sanità; Roma Italy
| | - Raffaela Teloni
- Dipartimento di Malattie Infettive, Istituto Superiore di Sanità; Roma Italy
| | | | | | - Roberto Nisini
- Dipartimento di Malattie Infettive, Istituto Superiore di Sanità; Roma Italy
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10
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Cell-type-specific Jumonji histone demethylase gene expression in the healthy rat CNS: detection by a novel flow cytometry method. ASN Neuro 2014; 6:193-207. [PMID: 24735454 PMCID: PMC4034710 DOI: 10.1042/an20130050] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Our understanding of how histone demethylation contributes to the regulation of basal gene expression in the brain is largely unknown in any injury model, and especially in the healthy adult brain. Although Jumonji genes are often regulated transcriptionally, cell-specific gene expression of Jumonji histone demethylases in the brain remains poorly understood. Thus, in the present study we profiled the mRNA levels of 26 Jumonji genes in microglia (CD11b+), neurons (NeuN+) and astrocytes (GFAP+) from the healthy adult rat brain. We optimized a method combining a mZBF (modified zinc-based fixative) and FCM (flow cytometry) to simultaneously sort cells from non-transgenic animals. We evaluated cell-surface, intracellular and nuclear proteins, including histones, as well as messenger- and micro-RNAs in different cell types simultaneously from a single-sorted sample. We found that 12 Jumonji genes were differentially expressed between adult microglia, neurons and astrocytes. While JMJD2D was neuron-restricted, PHF8 and JMJD1C were expressed in all three cell types although the expression was highest in neurons. JMJD3 and JMJD5 were expressed in all cell types, but were highly enriched in microglia; astrocytes had the lowest expression of UTX and JHDM1D. Levels of global H3K27 (H3 lysine 27) methylation varied among cell types and appeared to be lowest in microglia, indicating that differences in basal gene expression of specific Jumonji histone demethylases may contribute to cell-specific gene expression in the CNS (central nervous system). This multiparametric technique will be valuable for simultaneously assaying chromatin modifications and gene regulation in the adult CNS.
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11
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Holmes KL, Fontes B, Hogarth P, Konz R, Monard S, Pletcher CH, Wadley RB, Schmid I, Perfetto SP. International Society for the Advancement of Cytometry cell sorter biosafety standards. Cytometry A 2014; 85:434-53. [PMID: 24634405 PMCID: PMC4117398 DOI: 10.1002/cyto.a.22454] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 01/17/2014] [Accepted: 02/16/2014] [Indexed: 11/09/2022]
Abstract
Flow cytometric cell sorting of biological specimens has become prevalent in basic and clinical research laboratories. These specimens may contain known or unknown infectious agents, necessitating precautions to protect instrument operators and the environment from biohazards arising from the use of sorters. To this end the International Society of Analytical Cytology (ISAC) was proactive in establishing biosafety guidelines in 1997 (Schmid et al., Cytometry 1997;28:99-117) and subsequently published revised biosafety standards for cell sorting of unfixed samples in 2007 (Schmid et al., Cytometry Part A J Int Soc Anal Cytol 2007;71A:414-437). Since their publication, these documents have become recognized worldwide as the standard of practice and safety precautions for laboratories performing cell sorting experiments. However, the field of cytometry has progressed since 2007, and the document requires an update. The new Standards provides guidance: (1) for laboratory design for cell sorter laboratories; (2) for the creation of laboratory or instrument specific Standard Operating Procedures (SOP); and (3) on procedures for the safe operation of cell sorters, including personal protective equipment (PPE) and validation of aerosol containment.
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Affiliation(s)
- Kevin L. Holmes
- Flow Cytometry Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Benjamin Fontes
- Environmental Health and Safety, Yale University, New Haven, Connecticut
| | - Philip Hogarth
- Flow Cytometry Facility, Animal Health and Veterinary Laboratories Agency, Weybridge, United Kingdom
| | - Richard Konz
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Simon Monard
- The Cytometry Laboratory, Walter and Eliza Hall Institute, Parkville, Victoria, Australia
| | - Charles H. Pletcher
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Robert B. Wadley
- Dendritic Cell Program, Mater Medical Research Institute, South Brisbane, Queensland, Australia
| | - Ingrid Schmid
- Department of Hematology-Oncology, UCLA, David Geffen School of Medicine, Los Angeles, California
| | - Stephen P. Perfetto
- Flow Cytometry Core Facility, Vaccine Research Center, National Institutes of Health, Bethesda, Maryland
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12
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Fitzsimons MS, Novotny M, Lo CC, Dichosa AEK, Yee-Greenbaum JL, Snook JP, Gu W, Chertkov O, Davenport KW, McMurry K, Reitenga KG, Daughton AR, He J, Johnson SL, Gleasner CD, Wills PL, Parson-Quintana B, Chain PS, Detter JC, Lasken RS, Han CS. Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome. Genome Res 2013; 23:878-88. [PMID: 23493677 PMCID: PMC3638143 DOI: 10.1101/gr.142208.112] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The majority of microbial genomic diversity remains unexplored. This is largely due to our inability to culture most microorganisms in isolation, which is a prerequisite for traditional genome sequencing. Single-cell sequencing has allowed researchers to circumvent this limitation. DNA is amplified directly from a single cell using the whole-genome amplification technique of multiple displacement amplification (MDA). However, MDA from a single chromosome copy suffers from amplification bias and a large loss of specificity from even very small amounts of DNA contamination, which makes assembling a genome difficult and completely finishing a genome impossible except in extraordinary circumstances. Gel microdrop cultivation allows culturing of a diverse microbial community and provides hundreds to thousands of genetically identical cells as input for an MDA reaction. We demonstrate the utility of this approach by comparing sequencing results of gel microdroplets and single cells following MDA. Bias is reduced in the MDA reaction and genome sequencing, and assembly is greatly improved when using gel microdroplets. We acquired multiple near-complete genomes for two bacterial species from human oral and stool microbiome samples. A significant amount of genome diversity, including single nucleotide polymorphisms and genome recombination, is discovered. Gel microdroplets offer a powerful and high-throughput technology for assembling whole genomes from complex samples and for probing the pan-genome of naturally occurring populations.
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Affiliation(s)
- Michael S Fitzsimons
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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13
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Schmid I. How to develop a standard operating procedure for sorting unfixed cells. Methods 2012; 57:392-7. [PMID: 22381383 PMCID: PMC3380136 DOI: 10.1016/j.ymeth.2012.02.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 01/27/2012] [Accepted: 02/08/2012] [Indexed: 11/30/2022] Open
Abstract
Written standard operating procedures (SOPs) are an important tool to assure that recurring tasks in a laboratory are performed in a consistent manner. When the procedure covered in the SOP involves a high-risk activity such as sorting unfixed cells using a jet-in-air sorter, safety elements are critical components of the document. The details on sort sample handling, sorter set-up, validation, operation, troubleshooting, and maintenance, personal protective equipment (PPE), and operator training, outlined in the SOP are to be based on careful risk assessment of the procedure. This review provides background information on the hazards associated with sorting of unfixed cells and the process used to arrive at the appropriate combination of facility design, instrument placement, safety equipment, and practices to be followed.
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Affiliation(s)
- Ingrid Schmid
- David Geffen School of Medicine at UCLA, Department of Hematology/Oncology, Los Angeles, USA.
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Perfetto SP, Ambrozak DR, Nguyen R, Roederer M, Koup RA, Holmes KL. Standard practice for cell sorting in a BSL-3 facility. Methods Mol Biol 2011; 699:449-69. [PMID: 21116997 PMCID: PMC4789760 DOI: 10.1007/978-1-61737-950-5_22] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2024]
Abstract
Over the past decade, there has been a rapid growth in the number of BSL-3 and BSL-4 laboratories in the USA and an increase in demand for infectious cell sorting in BSL-3 laboratories. In 2007, the International Society for Advancement of Cytometry (ISAC) Biosafety Committee published standards for the sorting of unfixed cells and is an important resource for biosafety procedures when performing infectious cell sorting. Following a careful risk assessment, if it is determined that a cell sorter must be located within a BSL-3 laboratory, there are a variety of factors to be considered prior to the establishment of the laboratory. This chapter outlines procedures for infectious cell sorting in a BSL-3 environment to facilitate the establishment and safe operation of a BSL-3 cell sorting laboratory. Subjects covered include containment verification, remote operation, disinfection, personal protective equipment (PPE), and instrument-specific modifications for enhanced aerosol evacuation.
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Affiliation(s)
- Stephen P Perfetto
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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Schmid I, Lambert C, Ambrozak D, Perfetto SP. Standard safety practices for sorting of unfixed cells. ACTA ACUST UNITED AC 2008; Chapter 3:Unit3.6. [PMID: 18770851 DOI: 10.1002/0471142956.cy0306s39] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Cell sorting of viable biological specimens has become widespread in laboratories involved in basic and clinical research. As these samples can contain infectious agents, precautions to protect instrument operators and the environment from hazards arising from the use of sorters are paramount. This unit presents a revised and updated version of the biosafety guidelines for sorting of unfixed cells established in 1977 by the International Society of Analytical Cytology (ISAC), whose recommendations have become recognized worldwide as the standard practices and safety precautions for laboratories performing viable cell-sorting experiments. The unit contains background information on the biohazard potential of sorting and the hazard classification of infectious agents as well as recommendations on (1) sample handling, (2) operator training and personal protection, (3) laboratory design, (4) cell sorter setup, maintenance, and decontamination, and (5) testing the instrument for the efficiency of aerosol containment.
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Affiliation(s)
- Ingrid Schmid
- David Geffen School of Medicine at UCLA, Los Angeles, California, USA
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Evidence-based biosafety: a review of the principles and effectiveness of microbiological containment measures. Clin Microbiol Rev 2008; 21:403-25. [PMID: 18625678 DOI: 10.1128/cmr.00014-08] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
We examined the available evidence on the effectiveness of measures aimed at protecting humans and the environment against the risks of working with genetically modified microorganisms (GMOs) and with non-GMO pathogenic microorganisms. A few principles and methods underlie the current biosafety practice: risk assessment, biological containment, concentration and enclosure, exposure minimization, physical containment, and hazard minimization. Many of the current practices are based on experience and expert judgment. The effectiveness of biosafety measures may be evaluated at the level of single containment equipment items and procedures, at the level of the laboratory as a whole, or at the clinical-epidemiological level. Data on the containment effectiveness of equipment and laboratories are scarce and fragmented. Laboratory-acquired infections (LAIs) are therefore important for evaluating the effectiveness of biosafety. For the majority of LAIs there appears to be no direct cause, suggesting that failures of biosafety were not noticed or that containment may have been insufficient. The number of reported laboratory accidents associated with GMOs is substantially lower than that of those associated with non-GMOs. It is unknown to what extent specific measures contribute to the overall level of biosafety. We therefore recommend that the evidence base of biosafety practice be strengthened.
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Schmid I, Lambert C, Ambrozak D, Marti GE, Moss DM, Perfetto SP. International Society for Analytical Cytology biosafety standard for sorting of unfixed cells. Cytometry A 2007; 71:414-37. [PMID: 17385740 DOI: 10.1002/cyto.a.20390] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
BACKGROUND Cell sorting of viable biological specimens has become very prevalent in laboratories involved in basic and clinical research. As these samples can contain infectious agents, precautions to protect instrument operators and the environment from hazards arising from the use of sorters are paramount. To this end the International Society of Analytical Cytology (ISAC) took a lead in establishing biosafety guidelines for sorting of unfixed cells (Schmid et al., Cytometry 1997;28:99-117). During the time period these recommendations have been available, they have become recognized worldwide as the standard practices and safety precautions for laboratories performing viable cell sorting experiments. However, the field of cytometry has progressed since 1997, and the document requires an update. METHODS Initially, suggestions about the document format and content were discussed among members of the ISAC Biosafety Committee and were incorporated into a draft version that was sent to all committee members for review. Comments were collected, carefully considered, and incorporated as appropriate into a draft document that was posted on the ISAC web site to invite comments from the flow cytometry community at large. The revised document was then submitted to ISAC Council for review. Simultaneously, further comments were sought from newly-appointed ISAC Biosafety committee members. RESULTS This safety standard for performing viable cell sorting experiments was recently generated. The document contains background information on the biohazard potential of sorting and the hazard classification of infectious agents as well as recommendations on (1) sample handling, (2) operator training and personal protection, (3) laboratory design, (4) cell sorter set-up, maintenance, and decontamination, and (5) testing the instrument for the efficiency of aerosol containment. CONCLUSIONS This standard constitutes an updated and expanded revision of the 1997 biosafety guideline document. It is intended to provide laboratories involved in cell sorting with safety practices that take into account the enhanced hazard potential of high-speed sorting. Most importantly, it states that droplet-based sorting of infectious or hazardous biological material requires a higher level of containment than the one recommended for the risk group classification of the pathogen. The document also provides information on safety features of novel instrumentation, new options for personal protective equipment, and recently developed methods for testing the efficiency of aerosol containment.
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Affiliation(s)
- Ingrid Schmid
- Department of Hematology/Oncology, David Geffen School of Medicine at UCLA, Los Angeles, California 90095, USA.
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Lennartz K, Lu M, Flasshove M, Moritz T, Kirstein U. Improving the biosafety of cell sorting by adaptation of a cell sorting system to a biosafety cabinet. Cytometry A 2005; 66:119-27. [PMID: 15973698 DOI: 10.1002/cyto.a.20157] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND The jet-in-air cell sorters currently available are not very suitable for sorting potentially biohazardous material under optimal conditions because they do not protect operators and samples as recommended in the guidelines for safe biotechnology. To solve this problem we have adapted a cell sorting system to a special biosafety cabinet that satisfies the requirements for class II cabinets. With aid of this unit, sorting can be performed in conformance with the recommendations for biosafety level 2. METHODS After integrating a modified fluorescence-activated cell sorter (FACS) Vantage into a special biosafety cabinet, we investigated the influence of the laminar air flow (LAF) inside the cabinet on side stream stability and the analytical precision of the cell sorter. In addition to the routine electronic counting of microparticles, we carried out tests on the containment of aerosols, using T4 bacteriophage as indicators, to demonstrate the efficiency of the biosafety cabinet for sorting experiments performed under biosafety level 2 conditions. RESULTS The experiments showed that LAF, which is necessary to build up sterile conditions in a biosafety cabinet, does not influence the conditions for side stream stability or the analytical precision of the FACS Vantage cell sorting system. In addition, tests performed to assess aerosol containment during operation of the special biosafety cabinet demonstrated that the cabinet-integrated FACS Vantage unit (CIF) satisfies the conditions for class II cabinets. In the context of gene transfer experiments, the CIF facility was used to sort hematopoietic progenitor cells under biosafety level 2 conditions. CONCLUSIONS The newly designed biosafety cabinet offers a practical modality for improving biosafety for operators and samples during cell sorting procedures. It can thus also be used for sorting experiments with genetically modified organisms in conformance with current biosafety regulations and guidelines.
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Affiliation(s)
- Klaus Lennartz
- Institute of Cell Biology (Cancer Research), West German Cancer Center Essen, University of Duisburg-Essen, Medical School, Essen, Germany
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Affiliation(s)
- Ingrid Schmid
- David Geffen School of Medicine, University of California Los Angeles, Department of Hematology/Oncology, Los Angeles, California 90095, USA
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