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Xu YL, Li XJ, Cai W, Yu WY, Chen J, Lee Q, Choi YJ, Wu F, Lou YJ, Ying HZ, Yu CH, Wu QF. Diosmetin-7-O-β-D-glucopyranoside from Pogostemonis Herba alleviated SARS-CoV-2-induced pneumonia by reshaping macrophage polarization and limiting viral replication. JOURNAL OF ETHNOPHARMACOLOGY 2025; 336:118704. [PMID: 39182703 DOI: 10.1016/j.jep.2024.118704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 08/04/2024] [Accepted: 08/16/2024] [Indexed: 08/27/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Viral pneumonia is the leading cause of death after SARS-CoV-2 infection. Despite effective at early stage, long-term treatment with glucocorticoids can lead to a variety of adverse effects and limited benefits. The Chinese traditional herb Pogostemonis Herba is the aerial part of Pogostemon Cablin (Blanco) Benth., which has potent antiviral, antibacterial, anti-inflammatory, and anticancer effects. It was used widely for treating various throat and respiratory diseases, including COVID-19, viral infection, cough, allergic asthma, acute lung injury and lung cancer. AIM OF THE STUDY To investigate the antiviral and anti-inflammatory effects of chemical compounds from Pogostemonis Herba in SARS-CoV-2-infected hACE2-overexpressing mouse macrophage RAW264.7 cells and hACE2 transgenic mice. MATERIALS AND METHODS The hACE2-overexpressing RAW264.7 cells were exposed with SARS-CoV-2. The cell viability was detected by CCK8 assay and cell apoptotic rate was by flow cytometric assay. The expressions of macrophage M1 phenotype markers (TNF-α and IL-6) and M2 markers (IL-10 and Arg-1) as well as the viral loads were detected by qPCR. The mice were inoculated intranasally with SARS-CoV-2 omicron variant to induce viral pneumonia. The levels of macrophages, neutrophils, and T cells in the lung tissues of infected mice were analyzed by full spectrum flow cytometry. The expressions of key proteins were detected by Western blot assay. RESULTS Diosmetin-7-O-β-D-glucopyranoside (DG) presented the strongest anti-SARS-CoV-2 activity. Intervention with DG at the concentrations of 0.625-2.5 μM not only reduced the viral replication, cell apoptosis, and the productions of inflammatory cytokines (IL-6 and TNF-α) in SARS-CoV-2-infected RAW264.7 cells, but also reversed macrophage polarity from M1 to M2 phenotype. Furthermore, treatment with DG (25-100 mg/kg) alleviated acute lung injury, and reduced macrophage infiltration in SARS-COV-2-infected mice. Mechanistically, DG inhibited SARS-COV-2 gene expression and HK3 translation via targeting YTHDF1, resulting in the inactivation of glycolysis-mediated NF-κB pathway. CONCLUSIONS DG exerted the potent antiviral and anti-inflammatory activities. It reduced pneumonia in SARS-COV-2-infected mice via inhibiting the viral replication and accelerating M2 macrophage polarization via targeting YTHDF1, indicating its potential for COVID-19 treatment.
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Affiliation(s)
- Yun-Lu Xu
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Xue-Jian Li
- Key Laboratory of Experimental Animal and Safety Evaluation, Hangzhou Medical College, Hangzhou, 310013, China; Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310018, China
| | - Wei Cai
- College of Chinese Medicine, Zhejiang Pharmaceutical University, Ningbo, 315500, China
| | - Wen-Ying Yu
- Key Laboratory of Experimental Animal and Safety Evaluation, Hangzhou Medical College, Hangzhou, 310013, China
| | - Jing Chen
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Qin Lee
- Key Laboratory of Experimental Animal and Safety Evaluation, Hangzhou Medical College, Hangzhou, 310013, China; Department of Biochemistry, College of Medicine, Gachon University, Incheon, 21999, Republic of Korea
| | - Yong-Jun Choi
- Department of Biochemistry, College of Medicine, Gachon University, Incheon, 21999, Republic of Korea
| | - Fang Wu
- Key Laboratory of Experimental Animal and Safety Evaluation, Hangzhou Medical College, Hangzhou, 310013, China
| | - Ying-Jun Lou
- Key Laboratory of Experimental Animal and Safety Evaluation, Hangzhou Medical College, Hangzhou, 310013, China
| | - Hua-Zhong Ying
- Key Laboratory of Experimental Animal and Safety Evaluation, Hangzhou Medical College, Hangzhou, 310013, China
| | - Chen-Huan Yu
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, 310018, China.
| | - Qiao-Feng Wu
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China.
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Vardaman D, Ali MA, Bolding C, Tidwell H, Stephens H, Tyrrell DJ. Development of a Spectral Flow Cytometry Analysis Pipeline for High-Dimensional Immune Cell Characterization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.19.599633. [PMID: 38948780 PMCID: PMC11213029 DOI: 10.1101/2024.06.19.599633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Flow cytometry is a widely used technique for immune cell analysis, offering insights into cell composition and function. Spectral flow cytometry allows for high-dimensional analysis of immune cells, overcoming limitations of conventional flow cytometry. However, analyzing data from large antibody panels can be challenging using traditional bi-axial gating strategies. Here, we present a novel analysis pipeline designed to improve analysis of spectral flow cytometry. We employ this method to identify rare T cell populations in aging. We isolated splenocytes from young (2-3 months) and aged (18-19 months) female mice then stained these with a panel of 20 fluorescently labeled antibodies. Spectral flow cytometry was performed, followed by data processing and analysis using Python within a Jupyter Notebook environment to perform batch correction, unsupervised clustering, dimensionality reduction, and differential expression analysis. Our analysis of 3,776,804 T cells from 11 spleens revealed 34 distinct T cell clusters identified by surface marker expression. We observed significant differences between young and aged mice, with certain clusters enriched in one age group over the other. Naïve, effector memory, and central memory CD8+ and CD4+ T cell subsets exhibited age-associated changes in abundance and marker expression. Additionally, γδ T cell clusters showed differential abundance between age groups. By leveraging high-dimensional analysis methods borrowed from single-cell RNA sequencing analysis, we identified age-related differences in T cell subsets, providing insights into the immune aging process. This approach offers a robust, free, and easily implemented analysis pipeline for spectral flow cytometry data that may facilitate the discovery of novel therapeutic targets for age-related immune dysfunction.
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Affiliation(s)
- Donald Vardaman
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, 35205 USA
| | - Md Akkas Ali
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, 35205 USA
- Biochemistry and Structural Biology Theme, Graduate Biomedical Sciences, University of Alabama at Birmingham, Birmingham, AL, 35205 USA
| | - Chase Bolding
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, 35205 USA
| | - Harrison Tidwell
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, 35205 USA
| | - Holly Stephens
- Department of Nutrition Sciences, University of Alabama at Birmingham, Birmingham, AL, 35205 USA
- Immunology Theme, Graduate Biomedical Sciences, University of Alabama at Birmingham, Birmingham, AL, 35205 USA
| | - Daniel J. Tyrrell
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, 35205 USA
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Roet JEG, Mikula AM, de Kok M, Chadick CH, Garcia Vallejo JJ, Roest HP, van der Laan LJW, de Winde CM, Mebius RE. Unbiased method for spectral analysis of cells with great diversity of autofluorescence spectra. Cytometry A 2024. [PMID: 38863410 DOI: 10.1002/cyto.a.24856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 03/12/2024] [Accepted: 05/29/2024] [Indexed: 06/13/2024]
Abstract
Autofluorescence is an intrinsic feature of cells, caused by the natural emission of light by photo-excitatory molecular content, which can complicate analysis of flow cytometry data. Different cell types have different autofluorescence spectra and, even within one cell type, heterogeneity of autofluorescence spectra can be present, for example, as a consequence of activation status or metabolic changes. By using full spectrum flow cytometry, the emission spectrum of a fluorochrome is captured by a set of photo detectors across a range of wavelengths, creating an unique signature for that fluorochrome. This signature is then used to identify, or unmix, that fluorochrome's unique spectrum from a multicolor sample containing different fluorescent molecules. Importantly, this means that this technology can also be used to identify intrinsic autofluorescence signal of an unstained sample, which can be used for unmixing purposes and to separate the autofluorescence signal from the fluorophore signals. However, this only works if the sample has a singular, relatively homogeneous and bright autofluorescence spectrum. To analyze samples with heterogeneous autofluorescence spectral profiles, we setup an unbiased workflow to more quickly identify differing autofluorescence spectra present in a sample to include as "autofluorescence signatures" during the unmixing of the full stained samples. First, clusters of cells with similar autofluorescence spectra are identified by unbiased dimensional reduction and clustering of unstained cells. Then, unique autofluorescence clusters are determined and are used to improve the unmixing accuracy of the full stained sample. Independent of the intensity of the autofluorescence and immunophenotyping of cell subsets, this unbiased method allows for the identification of most of the distinct autofluorescence spectra present in a sample, leading to less confounding autofluorescence spillover and spread into extrinsic phenotyping markers. Furthermore, this method is equally useful for spectral analysis of different biological samples, including tissue cell suspensions, peripheral blood mononuclear cells, and in vitro cultures of (primary) cells.
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Affiliation(s)
- Janna E G Roet
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
| | - Aleksandra M Mikula
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
| | - Michael de Kok
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
- Microscopy and Cytometry Core Facility, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Cora H Chadick
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
- Microscopy and Cytometry Core Facility, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Juan J Garcia Vallejo
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
- Microscopy and Cytometry Core Facility, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Henk P Roest
- Department of Surgery, Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Luc J W van der Laan
- Department of Surgery, Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Charlotte M de Winde
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
- Cancer Biology and Immunology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Reina E Mebius
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Immunology and Infectious Diseases, Amsterdam, The Netherlands
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Mosebarger A, Vidal MS, Bento GFC, Lintao RCV, Severino MEL, Kumar Kammala A, Menon R. Immune cells at the feto-maternal interface: Comprehensive characterization and insights into term labor. J Reprod Immunol 2024; 163:104239. [PMID: 38493591 DOI: 10.1016/j.jri.2024.104239] [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: 11/05/2023] [Revised: 02/05/2024] [Accepted: 03/07/2024] [Indexed: 03/19/2024]
Abstract
Immune cells at the feto-maternal interface play an important role in pregnancy; starting at implantation, maintenance of pregnancy, and parturition. The role of decidual immune cells in induction of labor still needs to be understood. Published reports on this topic show heterogeneity in methods of cell isolation, assay, analysis and cellular characterization making it difficult to collate available information in order to understand the contribution of immune cells at term leading to parturition. In the present study, available literature was reviewed to study the differences in immune cells between the decidua basalis and decidua parietalis, as well as between immune cells in term and preterm labor. Additionally, immune cells at the decidua parietalis were isolated from term not in labor (TNL) or term in labor (TL) samples and characterized via flow cytometry using a comprehensive, high-dimensional antibody panel. This allowed a full view of immune cell differences without combining multiple studies, which must include variation in isolation and analysis methods, for more conclusive data. The ratio of cells found in decidua parietalis in this study generally matched those reported in the literature, although we report a lower percentage of natural killer (NK) cells at term. We report that CD4 expression on CD8- NK cells decreased in term labor compared to not in labor samples, suggesting that natural killer cells may be migrating to other sites during labor. Also, we report a decrease in CD38 expression on CD8+ CD57+ T cells in labor, indicative of cytotoxic T cell senescence. Our study provides a comprehensive status of immune cells at the decidua-chorion interface at term.
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Affiliation(s)
- Angela Mosebarger
- Division of Basic and Translational Research, Department of Obstetrics and Gynecology, University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Manuel S Vidal
- Division of Basic and Translational Research, Department of Obstetrics and Gynecology, University of Texas Medical Branch at Galveston, Galveston, TX, USA; Department of Biochemistry and Molecular Biology, College of Medicine, University of Philippines Manila, Manila, Philippines
| | | | - Ryan C V Lintao
- Division of Basic and Translational Research, Department of Obstetrics and Gynecology, University of Texas Medical Branch at Galveston, Galveston, TX, USA; Department of Biochemistry and Molecular Biology, College of Medicine, University of Philippines Manila, Manila, Philippines
| | - Mary Elise L Severino
- Division of Basic and Translational Research, Department of Obstetrics and Gynecology, University of Texas Medical Branch at Galveston, Galveston, TX, USA; Department of Biochemistry and Molecular Biology, College of Medicine, University of Philippines Manila, Manila, Philippines
| | - Ananth Kumar Kammala
- Division of Basic and Translational Research, Department of Obstetrics and Gynecology, University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Ramkumar Menon
- Division of Basic and Translational Research, Department of Obstetrics and Gynecology, University of Texas Medical Branch at Galveston, Galveston, TX, USA.
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Konecny AJ, Mage P, Tyznik AJ, Prlic M, Mair F. OMIP-102: 50-color phenotyping of the human immune system with in-depth assessment of T cells and dendritic cells. Cytometry A 2024; 105:430-436. [PMID: 38634730 PMCID: PMC11178442 DOI: 10.1002/cyto.a.24841] [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: 01/19/2024] [Revised: 03/27/2024] [Accepted: 04/02/2024] [Indexed: 04/19/2024]
Abstract
We report the development of an optimized 50-color spectral flow cytometry panel designed for the in-depth analysis of the immune system in human blood and tissues, with the goal of maximizing the amount of information that can be collected using currently available flow cytometry platforms. We established and tested this panel using peripheral blood mononuclear cells (PBMCs), but included CD45 to enable its future use for the analysis of human tissue samples. The panel contains lineage markers for all major immune cell subsets, and an extensive set of phenotyping markers focused on the activation and differentiation status of the T cell and dendritic cell (DC) compartment. We outline the biological insight that can be gained from the simultaneous measurement of such a large number of proteins and propose that this approach provides a unique opportunity for the comprehensive exploration of the immune status in human samples with a limited number of cells. Of note, we tested the panel to be compatible with cell sorting for further downstream applications. Furthermore, to facilitate the wide-spread implementation of such a panel across different cohorts and samples, we established a trimmed-down 45-color version which can be used with different spectral cytometry platforms. Finally, to generate this panel, we utilized not only existing panel design guidelines, but also developed new metrics to systematically identify the optimal combination of 50 fluorochromes and evaluate fluorochrome-specific resolution in the context of a 50-color unmixing matrix.
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Affiliation(s)
- Andrew J. Konecny
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle WA, 98109, USA
- Department of Immunology, University of Washington, Seattle, WA 98195, USA
| | - Peter Mage
- Advanced Technology Group, BD Biosciences, San Jose, CA 95131, USA
| | - Aaron J. Tyznik
- Applied Research & Technology, Medical and Scientific Affairs, BD Biosciences, San Diego, CA 92037, USA
| | - Martin Prlic
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle WA, 98109, USA
- Department of Immunology, University of Washington, Seattle, WA 98195, USA
| | - Florian Mair
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle WA, 98109, USA
- Flow Cytometry Core Facility, Institute of Molecular Health Sciences, ETH Zurich, 8093 Zurich, Switzerland
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Shevchenko Y, Lurje I, Tacke F, Hammerich L. Fluorochrome-dependent specific changes in spectral profiles using different compensation beads or primary cells in full spectrum cytometry. Cytometry A 2024; 105:458-463. [PMID: 38511720 DOI: 10.1002/cyto.a.24836] [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: 11/08/2023] [Revised: 03/01/2024] [Accepted: 03/12/2024] [Indexed: 03/22/2024]
Abstract
Full spectrum flow cytometry is a powerful tool for immune monitoring on a single-cell level and with currently available machines, panels of 40 or more markers per sample are possible. However, with an increased panel size, spectral unmixing issues arise, and appropriate single stain reference controls are required for accurate experimental results and to avoid unmixing errors. In contrast to conventional flow cytometry, full spectrum flow cytometry takes into account even minor differences in spectral signatures and requires the full spectrum of each fluorochrome to be identical in the reference control and the fully stained sample to ensure accurate and reliable results. In general, using the cells of interest is considered optimal, but certain markers may not be expressed at sufficient levels to generate a reliable positive control. In this case, compensation beads show some significant advantages as they bind a consistent amount of antibody independent of its specificity. In this study, we evaluated two types of manufactured compensation beads for use as reference controls for 30 of the most commonly used and commercially available fluorochromes in full spectrum cytometry and compared them to human and murine primary leukocytes. While most fluorochromes show the same spectral profile on beads and cells, we demonstrate that specific fluorochromes show a significantly different spectral profile depending on which type of compensation beads is used, and some fluorochromes should be used on cells exclusively. Here, we provide a list of important considerations when selecting optimal reference controls for full spectrum flow cytometry.
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Affiliation(s)
- Yaroslava Shevchenko
- Department of Hepatology and Gastroenterology, Charité-Universitätsmedizin Berlin, Campus Virchow-Klinikum (CVK) and Campus Charité Mitte (CCM), Berlin, Germany
| | - Isabella Lurje
- Department of Hepatology and Gastroenterology, Charité-Universitätsmedizin Berlin, Campus Virchow-Klinikum (CVK) and Campus Charité Mitte (CCM), Berlin, Germany
| | - Frank Tacke
- Department of Hepatology and Gastroenterology, Charité-Universitätsmedizin Berlin, Campus Virchow-Klinikum (CVK) and Campus Charité Mitte (CCM), Berlin, Germany
| | - Linda Hammerich
- Department of Hepatology and Gastroenterology, Charité-Universitätsmedizin Berlin, Campus Virchow-Klinikum (CVK) and Campus Charité Mitte (CCM), Berlin, Germany
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Guo K, Feng X, Xu L, Li C, Ma Y, Peng M. Within- and between-subject biological variation estimates for the enumeration of lymphocyte deep immunophenotyping and monocyte subsets. Clin Chem Lab Med 2024; 0:cclm-2024-0371. [PMID: 38815136 DOI: 10.1515/cclm-2024-0371] [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: 03/21/2024] [Accepted: 05/05/2024] [Indexed: 06/01/2024]
Abstract
OBJECTIVES This study aimed to deliver biological variation (BV) estimates for 25 types of lymphocyte subpopulations subjected to deep immunophenotyping (memory T/B cells, regulatory T cells, etc.) and classical, intermediate, and nonclassical monocyte subsets based on the full spectrum flow cytometry (FS-FCM) and a Biological Variation Data Critical Appraisal Checklist (BIVAC) design. METHODS Samples were collected biweekly from 60 healthy Chinese adults over 10 consecutive two-week periods. Each sample was measured in duplicate within a single run for lymphocyte deep immunophenotyping and monocyte subset determination using FS-FCM, including the percentage (%) and absolute count (cells/μL). After trend adjustment, a Bayesian model was applied to deliver the within-subject BV (CVI) and between-subject BV (CVG) estimates with 95 % credibility intervals. RESULTS Enumeration (% and cells/μL) for 25 types of lymphocyte deep immunophenotyping and three types of monocyte subset percentages showed considerable variability in terms of CVI and CVG. CVI ranged from 4.23 to 47.47 %. Additionally, CVG ranged between 10.32 and 101.30 %, except for CD4+ effector memory T cells re-expressing CD45RA. No significant differences were found between males and females for CVI and CVG estimates. Nevertheless, the CVGs of PD-1+ T cells (%) may be higher in females than males. Based on the desired analytical performance specification, the maximum allowable imprecision immune parameter was the CD8+PD-1+ T cell (cells/μL), with 23.7 %. CONCLUSIONS This is the first study delivering BV estimates for 25 types of lymphocyte subpopulations subjected to deep immunophenotyping, along with classical, intermediate, and nonclassical monocyte subsets, using FS-FCM and adhering to the BIVAC design.
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Affiliation(s)
- Kai Guo
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, P.R. China
- 12501 National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing, P.R. China
| | - Xiaoran Feng
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, P.R. China
- 12501 National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing, P.R. China
| | - Lei Xu
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, P.R. China
- 12501 National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing, P.R. China
| | - Chenbin Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, P.R. China
| | - Yating Ma
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, P.R. China
| | - Mingting Peng
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, P.R. China
- 12501 National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing, P.R. China
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Sharma P, Bose P, Mallik N, Gupta DG, Rachagiri S, Kumar A, Kaur J, Malhotra P, Varma N, Sachdeva MUS. FLAER as a standalone reagent for paroxysmal nocturnal hemoglobinuria: Do we need to reconsider the guidelines for testing? Int J Lab Hematol 2024; 46:383-389. [PMID: 38069562 DOI: 10.1111/ijlh.14213] [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: 06/01/2023] [Accepted: 11/22/2023] [Indexed: 03/20/2024]
Abstract
INTRODUCTION Flow cytometry-based paroxysmal nocturnal hemoglobinuria (PNH) testing involves utilization of monoclonal antibodies against GPI-linked proteins and FLAER. The ability of FLAER to bind to a wide variety of GPI-linked structures and to be utilized across different leukocyte subsets is remarkable. We hypothesize that FLAER as a standalone reagent may be equally effective for detecting PNH clones. The present study intends to compare the results of a FLAER alone-based strategy to the recommended FLAER+GPI-linked protein-based approach for applicability in clinical settings. METHODS EDTA-anticoagulated blood samples from patients for PNH workup were tested for PNH by multiparametric flow cytometry. A conventional panel comprising gating markers (CD45 for WBC, CD15 for granulocytes, and CD64 for monocytes) and a combination of FLAER and GPI-linked markers, such as CD24 and CD14, henceforth referred to as the "routine panel," was employed. Second, a "FLAER-only panel" comprising the gating markers and FLAER alone (excluding the GPI-linked markers CD24 and CD14) was set up. The samples were processed using the lyse-wash-stain-wash technique, and events were acquired on BC Navios Ex flow cytometer (Beckman Coulter, Inc., USA) and analyzed on Kaluza Software 2.1. The presence of a PNH clone was reported at a value of ≥0.01%. RESULTS A total of 209 patients were tested. Both panels found a PNH clone in 20.1% of patients (n = 42/209) with a 100% concordance rate. The PNH clone range for granulocytes was 0.01%-89.68%, and for monocyte was 0.04%-96.09% in the routine panel. The range in the FLAER-only panel for granulocytes was 0.01%-89.61%, and for monocytes, it was 0.01%-96.05%. Pearson correlation statistics revealed a significant correlation between the size of the PNH clone of granulocytes and monocytes among the two panels tested (granulocytes r = 0.9999, p < 0.0001, 95% CI = 0.9999 to 1.000; monocytes r = 0.9974, p < 0.0001, 95% CI = 0.9966-0.9980). CONCLUSION Based on our results, FLAER as a standalone marker is specific and sensitive for identifying PNH clones in granulocytes and monocytes, even for high-sensitivity PNH assay. The proposed "FLAER-only panel" panel is efficient and cost-effective for highly sensitive PNH testing in two different cell lineages, especially in resource-limited clinical settings.
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Affiliation(s)
- Praveen Sharma
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Parveen Bose
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Nabhajit Mallik
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Dikshat Gopal Gupta
- Department of Urology, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Suneel Rachagiri
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Arun Kumar
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Jasbir Kaur
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Pankaj Malhotra
- Department of Clinical Hematology & Medical Oncology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Neelam Varma
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Man Updesh Singh Sachdeva
- Department of Hematology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
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Ferrer-Font L, Burn OK, Mayer JU, Price KM. Immunophenotyping challenging tissue types using high-dimensional full spectrum flow cytometry. Methods Cell Biol 2024; 186:51-90. [PMID: 38705606 DOI: 10.1016/bs.mcb.2024.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
Technological advancements in fluorescence flow cytometry and an ever-expanding understanding of the complexity of the immune system, have led to the development of large flow cytometry panels, reaching up to 40 markers at the single-cell level. Full spectrum flow cytometry, that measures the full emission range of all the fluorophores present in the panel instead of only the emission peaks is now routinely used in many laboratories internationally, and the demand for this technology is rapidly increasing. With the capacity to use larger and more complex staining panels, optimized protocols are required for the best panel design, panel validation and high-dimensional data analysis outcomes. In addition, for ex vivo experiments, tissue preparation methods for single-cell analysis should also be optimized to ensure that samples are of the highest quality and are truly representative of tissues in situ. Here we provide optimized step-by-step protocols for full spectrum flow cytometry panel design, tissue digestion and panel optimization to facilitate the analysis of challenging tissue types.
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Affiliation(s)
- Laura Ferrer-Font
- Hugh Green Cytometry Centre, Malaghan Institute of Medical Research, Wellington, New Zealand.
| | - Olivia K Burn
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Johannes U Mayer
- Department of Dermatology, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Kylie M Price
- Hugh Green Cytometry Centre, Malaghan Institute of Medical Research, Wellington, New Zealand
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10
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Fokken H, Waclawski J, Kattre N, Kloos A, Müller S, Ettinger M, Kacprowski T, Heuser M, Maetzig T, Schwarzer A. A 19-color single-tube full spectrum flow cytometry assay for the detection of measurable residual disease in acute myeloid leukemia. Cytometry A 2024; 105:181-195. [PMID: 37984809 DOI: 10.1002/cyto.a.24811] [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: 07/10/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 11/22/2023]
Abstract
Multiparameter flow cytometry (MFC) has emerged as a standard method for quantifying measurable residual disease (MRD) in acute myeloid leukemia. However, the limited number of available channels on conventional flow cytometers requires the division of a diagnostic sample into several tubes, restricting the number of cells and the complexity of immunophenotypes that can be analyzed. Full spectrum flow cytometers overcome this limitation by enabling the simultaneous use of up to 40 fluorescent markers. Here, we used this approach to develop a good laboratory practice-conform single-tube 19-color MRD detection assay that complies with recommendations of the European LeukemiaNet Flow-MRD Working Party. We based our assay on clinically-validated antibody clones and evaluated its performance on an IVD-certified full spectrum flow cytometer. We measured MRD and normal bone marrow samples and compared the MRD data to a widely used reference MRD-MFC panel generating highly concordant results. Using our newly developed single-tube panel, we established reference values in healthy bone marrow for 28 consensus leukemia-associated immunophenotypes and introduced a semi-automated dimensionality-reduction, clustering and cell type identification approach that aids the unbiased detection of aberrant cells. In summary, we provide a comprehensive full spectrum MRD-MFC workflow with the potential for rapid implementation for routine diagnostics due to reduced cell requirements and ease of data analysis with increased reproducibility in comparison to conventional FlowMRD routines.
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Affiliation(s)
- Hendrik Fokken
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Julian Waclawski
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Nadine Kattre
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Arnold Kloos
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Sebastian Müller
- Division Data Science in Biomedicine, Peter L. Reichertz Institute for Medical Informatics of TU Braunschweig and Hannover Medical School, Braunschweig, Germany
- Braunschweig Integrated Centre for Systems Biology (BRICS), TU Braunschweig, Braunschweig, Germany
| | - Max Ettinger
- Department of Orthopedic Surgery, Hannover Medical School, Hannover, Germany
| | - Tim Kacprowski
- Division Data Science in Biomedicine, Peter L. Reichertz Institute for Medical Informatics of TU Braunschweig and Hannover Medical School, Braunschweig, Germany
- Braunschweig Integrated Centre for Systems Biology (BRICS), TU Braunschweig, Braunschweig, Germany
| | - Michael Heuser
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Tobias Maetzig
- Department of Pediatric Hematology, Hannover Medical School, Hannover, Germany
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | - Adrian Schwarzer
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
- CCC-MV and Department of Internal Medicine C, University Medicine Greifswald, Greifswald, Germany
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11
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Spiteri AG, Pilkington KR, Wishart CL, Macia L, King NJC. High-Dimensional Methods of Single-Cell Microglial Profiling to Enhance Understanding of Neuropathological Disease. Curr Protoc 2024; 4:e985. [PMID: 38439574 DOI: 10.1002/cpz1.985] [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] [Indexed: 03/06/2024]
Abstract
Microglia are the innate myeloid cells of the central nervous system (CNS) parenchyma, functionally implicated in almost every defined neuroinflammatory and neurodegenerative disorder. Current understanding of disease pathogenesis for many neuropathologies is limited and/or lacks reliable diagnostic markers, vaccines, and treatments. With the increasing aging of society and rise in neurogenerative diseases, improving our understanding of their pathogenesis is essential. Analysis of microglia from murine disease models provides an investigative tool to unravel disease processes. In many neuropathologies, bone-marrow-derived monocytes are recruited to the CNS, adopting a phenotype similar to that of microglia. This significantly confounds the accurate identification of cell-type-specific functions and downstream therapeutic targeting. The increased capacity to analyze more phenotypic markers using spectral-cytometry-based technologies allows improved separation of microglia from monocyte-derived cells. Full-spectrum profiling enables enhanced marker resolution, time-efficient analysis of >40 fluorescence parameters, and extraction of cellular autofluorescence parameters. Coupling this system with additional cytometric technologies, including cell sorting and high-parameter imaging, can improve the understanding of microglial phenotypes in disease. To this end, we provide detailed, step-by-step protocols for the analysis of murine brain tissue by high-parameter ex vivo cytometric analysis using the Aurora spectral cytometer (Cytek), including best practices for unmixing and autofluorescence extraction, cell sorting for single-cell RNA analysis, and imaging mass cytometry. Together, this provides a toolkit for researchers to comprehensively investigate microglial disease processes at protein, RNA, and spatial levels for the identification of therapeutic targets in neuropathology. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Processing the mouse brain into a single-cell suspension for microglia isolation Basic Protocol 2: Staining single-cell mouse brain suspensions for microglial phenotyping by spectral cytometry Basic Protocol 3: Flow cytometric sorting of mouse microglia for ex vivo analysis Basic Protocol 4: Processing the mouse brain for imaging mass cytometry for spatial microglia analysis.
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Affiliation(s)
- Alanna G Spiteri
- Viral Immunopathology Laboratory, Infection, Immunity and Inflammation Research Theme, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | | | - Claire L Wishart
- Viral Immunopathology Laboratory, Infection, Immunity and Inflammation Research Theme, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | - Laurence Macia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
- Sydney Cytometry, The University of Sydney and Centenary Institute, Sydney, Australia
| | - Nicholas J C King
- Viral Immunopathology Laboratory, Infection, Immunity and Inflammation Research Theme, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
- Sydney Cytometry, The University of Sydney and Centenary Institute, Sydney, Australia
- The University of Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, Australia
- The University of Sydney Nano Institute, The University of Sydney, Sydney, Australia
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12
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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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13
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Ferrer-Font L, Small SJ, Hyde E, Pilkington KR, Price KM. Panel Design and Optimization for Full Spectrum Flow Cytometry. Methods Mol Biol 2024; 2779:99-124. [PMID: 38526784 DOI: 10.1007/978-1-0716-3738-8_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Technological advancements in fluorescence flow cytometry and an ever-expanding understanding of the complexity of the immune system have led to the development of large flow cytometry panels, reaching up to 40 markers at the single-cell level. Full spectrum flow cytometry, which measures the full emission range of all the fluorophores present in the panel instead of only the emission peaks, is now routinely used in laboratories around the world, and the demand for this technology is rapidly increasing. With the ability to use larger and more complex staining panels, optimized protocols are vital for achieving the best panel design, panel optimization, and high-dimensional data analysis outcomes. In addition, a better understanding of how to fully characterize the autofluorescence of the sample, coupled with an intelligent panel design approach, allows improved marker resolution on highly autofluorescent tissues or cells. Here, we provide optimized step-by-step protocols for full spectrum flow cytometry, covering panel design and optimization, autofluorescence evaluation and strategy selection, and methods for performing longitudinal studies.
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Affiliation(s)
- Laura Ferrer-Font
- Hugh Green Cytometry Centre, Malaghan Institute of Medical Research, Wellington, New Zealand.
| | - Sam J Small
- Hugh Green Cytometry Centre, Malaghan Institute of Medical Research, Wellington, New Zealand
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Evelyn Hyde
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | | | - Kylie M Price
- Hugh Green Cytometry Centre, Malaghan Institute of Medical Research, Wellington, New Zealand
- Malaghan Institute of Medical Research, Wellington, New Zealand
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14
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Shi X, Fan W, Mehrpouyan M, Chen Y, D'Cruz LM, Widmann SJ, Tyznik AJ. Flow cytometry analysis of protein expression using antibody-derived tags followed by CITE-Seq. Cytometry A 2024; 105:62-73. [PMID: 37772953 DOI: 10.1002/cyto.a.24792] [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: 02/19/2023] [Revised: 05/13/2023] [Accepted: 09/04/2023] [Indexed: 09/30/2023]
Abstract
Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-Seq) is a single-cell phenotyping method that uses antibody-derived tags (ADTs) to quantitatively detect cell surface protein expression and generate transcriptomic data at the single-cell level. Despite the increased popularity of this technique to study cellular heterogeneity and dynamics, detailed methods on how to choose ADT markers and ensuring reagent performance in biological relevant systems prior to sequencing is not available. Here we describe a novel and easy-to-use multiplex flow proxy assay in which multiple protein markers can be measured simultaneously using a combination of ADT reagents and dye-oligo conjugates by flow cytometry. Using dye-oligo conjugates with sequences complementary to the ADT reagents, we can achieve specific binding and evaluate protein marker expression in a multiplex way. This quality control assay is useful for guiding ADT marker choice and confirming protein expression prior to sequencing. Importantly, the labeled cells can be directly isolated based on the specific fluorescence from dye-oligo conjugates using a flow cytometry cell sorter and processed for downstream single-cell multiomics. Using this streamlined workflow, we sorted natural killer cells and T cells efficiently using only ADT and dye-oligo reagents, avoiding the possibility of decreased marker resolution from co-staining cells with ADT and fluorescent antibodies. This novel workflow provides a viable option for improving ADT marker choice and cell sorting efficiency, allowing subsequent CITE-Seq.
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Affiliation(s)
- Xiaoshan Shi
- Applied Research & Technology, Medical Scientific Affairs, BD Biosciences, San Jose, California, USA
| | - Wei Fan
- Chemistry Development, BD Biosciences, San Jose, California, USA
| | - Majid Mehrpouyan
- Chemistry Development, BD Biosciences, San Jose, California, USA
| | - Yu Chen
- Chemistry Development, BD Biosciences, San Diego, California, USA
| | - Louise M D'Cruz
- Applied Research & Technology, Medical Scientific Affairs, BD Biosciences, San Diego, California, USA
| | - Stephanie J Widmann
- Applied Research & Technology, Medical Scientific Affairs, BD Biosciences, San Diego, California, USA
| | - Aaron J Tyznik
- Applied Research & Technology, Medical Scientific Affairs, BD Biosciences, San Diego, California, USA
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15
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Cook S, Tang VA, Lannigan J, Jones JC, Welsh JA. Quantitative flow cytometry enables end-to-end optimization of cross-platform extracellular vesicle studies. CELL REPORTS METHODS 2023; 3:100664. [PMID: 38113854 PMCID: PMC10753385 DOI: 10.1016/j.crmeth.2023.100664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/28/2023] [Accepted: 11/15/2023] [Indexed: 12/21/2023]
Abstract
Flow cytometry (FCM) is a common method for characterizing extracellular particles (EPs), including viruses and extracellular vesicles (EVs). Frameworks such as MIFlowCyt-EV exist to provide reporting guidelines for metadata, controls, and data reporting. However, tools to optimize FCM for EP analysis in a systematic and quantitative way are lacking. Here, we demonstrate a cohesive set of methods and software tools that optimize FCM settings and facilitate cross-platform comparisons for EP studies. We introduce an automated small-particle optimization (SPOT) pipeline to optimize FCM fluorescence and light scatter detector settings for EP analysis and leverage quantitative FCM (qFCM) as a tool to further enable FCM optimization of fluorophore panel selection, laser power, pulse statistics, and window extensions. Finally, we demonstrate the value of qFCM to facilitate standardized cross-platform comparisons, irrespective of instrument configuration, settings, and sensitivity, in a cross-platform standardization study utilizing a commercially available EV reference material.
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Affiliation(s)
- Sean Cook
- Laboratory of Pathology, Translational Nanobiology Section, Centre for Cancer Research, National Institute of Health, National Institutes of Health, Bethesda, MD, USA
| | - Vera A Tang
- Faculty of Medicine, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Flow Cytometry and Virometry Core Facility, Ottawa, ON K1H 8M5, Canada
| | | | - Jennifer C Jones
- Laboratory of Pathology, Translational Nanobiology Section, Centre for Cancer Research, National Institute of Health, National Institutes of Health, Bethesda, MD, USA
| | - Joshua A Welsh
- Laboratory of Pathology, Translational Nanobiology Section, Centre for Cancer Research, National Institute of Health, National Institutes of Health, Bethesda, MD, USA.
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16
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Konecny AJ, Mage P, Tyznik AJ, Prlic M, Mair F. 50-color phenotyping of the human immune system with in-depth assessment of T cells and dendritic cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.14.571745. [PMID: 38168221 PMCID: PMC10760076 DOI: 10.1101/2023.12.14.571745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
We report the development of an optimized 50-color spectral flow cytometry panel designed for the in-depth analysis of the immune system in human blood and tissues, with the goal of maximizing the amount of information that can be collected using currently available flow cytometry platforms. We established and tested this panel using peripheral blood mononuclear cells (PBMCs), but included CD45 to enable its use for the analysis of human tissue samples. The panel contains lineage markers for all major immune cell subsets, and an extensive set of phenotyping markers focused on the activation and differentiation status of the T cell and dendritic cell (DC) compartment. We outline the biological insight that can be gained from the simultaneous measurement of such a large number of proteins and propose that this approach provides a unique opportunity for the comprehensive exploration of the immune status in tissue biopsies and other human samples with a limited number of cells. Of note, we tested the panel to be compatible with cell sorting for further downstream applications. Furthermore, to facilitate the wide-spread implementation of such a panel across different cohorts and samples, we established a trimmed-down 45-color version which can be used with different spectral cytometry platforms. Finally, to generate this panel, we utilized not only existing panel design guidelines, but also developed new metrics to systematically identify the optimal combination of 50 fluorochromes and evaluate fluorochrome-specific resolution in the context of a 50-color unmixing matrix.
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Affiliation(s)
- Andrew J. Konecny
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle WA, 98107, USA
- Department of Immunology, University of Washington, Seattle, WA 98195, USA
| | - Peter Mage
- Advanced Technology Group, BD Biosciences, San Jose, CA 95131, USA
| | - Aaron J. Tyznik
- Applied Research & Technology, Medical and Scientific Affairs, BD Biosciences, San Diego, CA 92037, USA
| | - Martin Prlic
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle WA, 98107, USA
- Department of Immunology, University of Washington, Seattle, WA 98195, USA
| | - Florian Mair
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle WA, 98107, USA
- Flow Cytometry Core Facility, Institute of Molecular Health Sciences, ETH Zurich, 8093 Zurich, Switzerland
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17
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Bhowmick D, Lowe SK, Ratliff ML. Side-by-Side Comparison of Compensation Beads Used in Polychromatic Flow Cytometry. Immunohorizons 2023; 7:819-833. [PMID: 38055568 PMCID: PMC10759156 DOI: 10.4049/immunohorizons.2300066] [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: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 12/08/2023] Open
Abstract
Compensation or unmixing is essential in analyzing multiparameter flow cytometry data. Errors in data correction, either by compensation or unmixing, can completely change the outcome or mislead the researchers. Owing to limited cell numbers, researchers often use synthetic beads to generate the required single stains for the necessary calculation. In this study, the capacity of synthetic beads to influence data correction is evaluated. Corrected data for human peripheral blood cells were generated using cell-based compensation from the same cells or bead-based compensation to identify differences between the methods. These data suggest that correction with beads on full-spectrum and conventional cytometers does not always follow the basic flow compensation/unmixing expectations and alters the data. Overall, the best approach for bead-based correction for an experiment is to evaluate which beads and fluorochromes are most accurately compensated/unmixed.
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Affiliation(s)
- Debajit Bhowmick
- Flow Cytometry Facility, Brody School of Medicine, East Carolina University, Greenville, NC
| | - Sara K. Lowe
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC
| | - Michelle L. Ratliff
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC
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18
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Chang MY, Brune JE, Black M, Altemeier WA, Frevert CW. Multicompartmental analysis of the murine pulmonary immune response by spectral flow cytometry. Am J Physiol Lung Cell Mol Physiol 2023; 325:L518-L535. [PMID: 37581225 PMCID: PMC10639014 DOI: 10.1152/ajplung.00317.2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 07/12/2023] [Accepted: 07/24/2023] [Indexed: 08/16/2023] Open
Abstract
Studies of pulmonary inflammation require unique considerations due to the complex structure and composition of the lungs. The lungs have multiple compartments and diverse immune cell populations, with inherently high autofluorescence, and are involved in the host response to pulmonary pathogens. We describe a protocol that accounts for these factors through a novel combination of methodologies-in vivo compartmental analysis and spectral flow cytometry with a broad panel of antibodies. In vivo compartmental analysis enables the precise localization of immune cells within the marginated vasculature, lung interstitium, nonlavageable airways, and lavageable airways of the lungs, as well as the pulmonary lymph nodes. Spectral flow cytometry with a broad panel of antibodies supports an unbiased exploratory approach to investigating diverse immune cell populations during pulmonary inflammation. Most importantly, spectral flow uses cellular autofluorescence to aid in the resolution and identification of immune cell populations. This methodology enables the acquisition of high-quality data compatible with informed gating and dimensionality reduction algorithms. In addition, our protocol emphasizes considerations for compartmentalization of the inflammatory response, spectral flow panel design, and autofluorescence spectra analysis. These methodologies are critical for increasing the rigor of pulmonary research. We apply this protocol for the precise characterization and localization of leukocytes in the pulmonary host response to influenza A virus in C57BL/6J mice. In particular, we demonstrate that this protocol improves the quantification and localization of alveolar macrophages within the airways. The methodology is modifiable and expandable to allow for further characterization of leukocyte populations of special interest.NEW & NOTEWORTHY We describe a novel combination of methodologies that incorporates dual in vivo compartmental analysis using intravascular and intratracheal CD45 labeling, a broad panel of antibodies for identifying lymphoid and nonlymphoid cells, and spectral flow cytometry that uses cellular autofluorescence to aid in resolving and identifying immune cell populations. This methodology allows precise localization of immune cells in the lavageable airways, nonlavageable airways, interstitial lung tissue, and marginated in the lung vasculature.
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Affiliation(s)
- Mary Y Chang
- Department of Comparative Medicine, University of Washington, Seattle, Washington, United States
- Center for Lung Biology, University of Washington at South Lake Union, Seattle, Washington, United States
| | - Jourdan E Brune
- Department of Comparative Medicine, University of Washington, Seattle, Washington, United States
- Center for Lung Biology, University of Washington at South Lake Union, Seattle, Washington, United States
| | - Michele Black
- Department of Immunology, University of Washington, Seattle, Washington, United States
| | - William A Altemeier
- Center for Lung Biology, University of Washington at South Lake Union, Seattle, Washington, United States
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington, United States
| | - Charles W Frevert
- Department of Comparative Medicine, University of Washington, Seattle, Washington, United States
- Center for Lung Biology, University of Washington at South Lake Union, Seattle, Washington, United States
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington, United States
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19
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Paget V, Guipaud O, François A, Milliat F. Detection of radiation-induced senescence by the Debacq-Chainiaux protocol: Improvements and upgrade in the detection of positive events. Methods Cell Biol 2023; 181:161-180. [PMID: 38302237 DOI: 10.1016/bs.mcb.2022.10.015] [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: 02/03/2024]
Abstract
Senescent cells are blocked in the cell cycle but remain metabolically active. These cells, once engaged in the senescence process, fail to initiate DNA replication. Due to the shortening of telomeres, replicative senescence can be triggered by a DNA damage response. Moreover, cells can also be induced to senesce by DNA damage in response to elevated reactive oxygen species (ROS), activation of oncogenes, cell-cell fusion or after ionizing radiation. There are multiple experimental ways to detect senescent cells directly or indirectly. Senescence-associated cellular traits (SA β-Gal activity, increase in cell volume and lysosome content, appearance of γ-H2AX foci, increase of ROS and oxidative damage adducts, etc.) can be identified by numerous methods of detection (flow cytometry, confocal imaging, in situ staining, etc.). Here, we improved an existing flow cytometry protocol and further developed a new one specifically tailored to ionizing radiation-induced endothelial senescence. Thus, we have upgraded the Debacq-Chainiaux protocol and added improvements in this protocol (i) to better detect positive events (ii) to offer a compatibility to simultaneously analyze various intracellular molecules including phosphorylated signaling proteins and cytokines, whether related or not to senescence processes.
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Affiliation(s)
- V Paget
- Institute for Radiological Protection and Nuclear Safety (IRSN), PSE-SANTE/SERAMED/LRMed (Radiobiology of Medical Exposure Laboratory), Fontenay-aux-Roses, France.
| | - O Guipaud
- Institute for Radiological Protection and Nuclear Safety (IRSN), PSE-SANTE/SERAMED/LRMed (Radiobiology of Medical Exposure Laboratory), Fontenay-aux-Roses, France
| | - A François
- Institute for Radiological Protection and Nuclear Safety (IRSN), PSE-SANTE/SERAMED/LRMed (Radiobiology of Medical Exposure Laboratory), Fontenay-aux-Roses, France
| | - F Milliat
- Institute for Radiological Protection and Nuclear Safety (IRSN), PSE-SANTE/SERAMED/LRMed (Radiobiology of Medical Exposure Laboratory), Fontenay-aux-Roses, France
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20
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Qi H, Qin L, Li Y, Jin F, Kang Z, Hou J, Wang Y. A 16-color full spectrum flow cytometric analysis for comprehensive evaluation of T-cell reconstitution in SIV-infected rhesus macaques. J Immunol Methods 2023; 514:113404. [PMID: 36496008 DOI: 10.1016/j.jim.2022.113404] [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: 07/27/2022] [Revised: 11/01/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022]
Abstract
T-cell reconstitution is central in human immunodeficiency virus (HIV) infection/disease progression. Simian immunodeficiency virus (SIV)-infected rhesus macaques (Macaca mulatta) have been the most widely used animal model for HIV research so far. An effective flow cytometry panel is crucial for monitoring the T cell reconstitution in SIV infection progression. We developed this sixteen-color flow cytometry-based panel for a T cell subsets analysis by manual gating and, once successfully gated, to characterize T cells function in-depth in rhesus macaques. This panel included markers to characterize CD4+ T cells and CD8+ T cells, T regulatory cells (Tregs), and T cell differentiation status (CD45RA and CCR7). Additionally, we included antibodies that measure T cell activation and proliferation molecules (CD69, HLA-DR, CD38 and Ki67), antibodies that examine the expressions of key PD-1 pathway molecule (PD-1), SIV potential target (CD32) and the primary SIV co-receptor CCR5 (CD195). High-dimensional single cell analysis was also performed to identify CD3+ T cells immunophenotypes of SIV-infected rhesus macaques. We designed this panel to evaluate the responses of different T cell subsets to SIV in whole blood from SIV-infected rhesus macaques.
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Affiliation(s)
- Hemei Qi
- Guangzhou Jinan Biomedicine Research and Development Center, Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
| | - Li Qin
- CAS Lamvac (Guangzhou) Biomedical Technology CO.,Ltd., Guangzhou 510663, China
| | - Yuefeng Li
- Landao Biotech Co., Ltd, Guangzhou 510555, China
| | - Fujun Jin
- Guangzhou Jinan Biomedicine Research and Development Center, Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Zhongkui Kang
- CAS Lamvac (Guangzhou) Biomedical Technology CO.,Ltd., Guangzhou 510663, China
| | - Jianghou Hou
- Kunming City Matermal and Child Health Hospital, Kunming 650013, China.
| | - Yifei Wang
- Guangzhou Jinan Biomedicine Research and Development Center, Institute of Biomedicine, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
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21
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Ferrer-Font L, Kraker G, Hally KE, Price KM. Ensuring Full Spectrum Flow Cytometry Data Quality for High-Dimensional Data Analysis. Curr Protoc 2023; 3:e657. [PMID: 36744957 DOI: 10.1002/cpz1.657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Full spectrum flow cytometry (FSFC) allows for the analysis of more than 40 parameters at the single-cell level. Compared to the practice of manual gating, high-dimensional data analysis can be used to fully explore single-cell datasets and reduce analysis time. As panel size and complexity increases so too does the detail and time required to prepare and validate the quality of the resulting data for use in downstream high-dimensional data analyses. To ensure data analysis algorithms can be used efficiently and to avoid artifacts, some important steps should be considered. These include data cleaning (such as eliminating variable signal change over time, removing cell doublets, and antibody aggregates), proper unmixing of full spectrum data, ensuring correct scale transformation, and correcting for batch effects. We have developed a methodical step-by-step protocol to prepare full spectrum high-dimensional data for use with high-dimensional data analyses, with a focus on visualizing the impact of each step of data preparation using dimensionality reduction algorithms. Application of our workflow will aid FSFC users in their efforts to apply quality control methods to their datasets for use in high-dimensional analysis, and help them to obtain valid and reproducible results. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Data cleaning Basic Protocol 2: Validating the quality of unmixing Basic Protocol 3: Data scaling Basic Protocol 4: Batch-to-batch normalization.
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Affiliation(s)
- Laura Ferrer-Font
- Hugh Green Cytometry Centre, Malaghan Institute of Medical Research, Wellington, New Zealand
| | | | - Kathryn E Hally
- Department of Surgery and Anaesthesia, The University of Otago, Wellington, New Zealand
| | - Kylie M Price
- Hugh Green Cytometry Centre, Malaghan Institute of Medical Research, Wellington, New Zealand
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22
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Spurgeon BEJ, Frelinger AL. Platelet Phenotyping by Full Spectrum Flow Cytometry. Curr Protoc 2023; 3:e687. [PMID: 36779850 DOI: 10.1002/cpz1.687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
Platelets play key roles in hemostasis, immunity, and inflammation, and tests of platelet phenotype and function are useful in studies of disease biology and pathology. Full spectrum flow cytometry offers distinct advantages over standard tests and enables the sensitive and simultaneous detection of many biomarkers. A typical assay provides a wealth of information on platelet biology and allows the assessment of in vivo activation and in vitro reactivity, as well as the discovery of novel phenotypes. Here, we describe the analysis of platelets by full spectrum flow cytometry and discuss a range of controls and methods for interpreting results. © 2023 Wiley Periodicals LLC. Basic Protocol: Platelet phenotyping by full spectrum flow cytometry Support Protocol 1: Spectral unmixing Support Protocol 2: Data preprocessing.
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Affiliation(s)
- Benjamin E J Spurgeon
- Center for Platelet Research Studies, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts
| | - Andrew L Frelinger
- Center for Platelet Research Studies, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts
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23
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Santinon F, Young YK, Del Rincón SV, Mann KK. Analyzing the Tumor-Immune Microenvironment by Flow Cytometry. Methods Mol Biol 2023; 2614:17-36. [PMID: 36587116 DOI: 10.1007/978-1-0716-2914-7_2] [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: 01/02/2023]
Abstract
Flow cytometry is an essential tool for studying the tumor-immune microenvironment. It allows us to quickly quantify and identify multiple cell types in a heterogeneous sample. This chapter provides an overview of the flow cytometry instrumentation and a discussion of the appropriate considerations and steps in building a reproducible flow cytometry staining panel. We present an updated lymphoid tissue and solid tumor-infiltrating leucocyte flow cytometry staining protocol and an example of flow cytometry data analysis.
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Affiliation(s)
- François Santinon
- Lady Davis Institute for Medical Research, McGill University, Montreal, QC, Canada.
| | - Yoon Kow Young
- Lady Davis Institute for Medical Research, McGill University, Montreal, QC, Canada
| | - Sonia V Del Rincón
- Lady Davis Institute for Medical Research, McGill University, Montreal, QC, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada
| | - Koren K Mann
- Lady Davis Institute for Medical Research, McGill University, Montreal, QC, Canada.
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada.
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada.
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24
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Heubeck A, Savage A, Henderson K, Roll C, Hernandez V, Torgerson T, Bumol T, Reading J. Cross-platform immunophenotyping of human peripheral blood mononuclear cells with four high-dimensional flow cytometry panels. Cytometry A 2022. [PMID: 36571245 DOI: 10.1002/cyto.a.24715] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 12/13/2022] [Accepted: 12/20/2022] [Indexed: 12/27/2022]
Abstract
Immunophenotyping using high dimensional flow cytometry is a central component of human immune system multi-omic studies. We present four high parameter flow cytometry panels for deep immunophenotyping of human peripheral blood mononuclear cells (PBMC). This set of four 25+ color panels include 64 cell surface markers to resolve broad immune compartment populations, as well as activation and memory of specific T, B, natural killer (NK), and myeloid lineages. Common lineage bridging markers are integrated into each panel to allow for inter-panel quality control through major lineage frequency verification. These panels were developed using a five laser BD Symphony A5 conventional cytometer and successfully transferred to a five laser Cytek Aurora spectral cytometer capable of acquiring the panels. Nine representative PBMC samples were stained with the four phenotyping panels and acquired on both instruments to evaluate population frequency and visual staining patterns for gating between the systems. Both instruments produced comparable high quality flow cytometry data and supported our decision to acquire samples on the spectral cytometer moving forward. This modular set of panels and instrument performance metrics provide guidelines for designing flow cytometry experiments suitable for longitudinal or cross-sectional immune profiling.
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Affiliation(s)
| | - Adam Savage
- Allen Institute for Immunology, Seattle, Washington, USA
| | | | - Charles Roll
- Allen Institute for Immunology, Seattle, Washington, USA
| | | | - Troy Torgerson
- Allen Institute for Immunology, Seattle, Washington, USA
| | - Thomas Bumol
- Allen Institute for Immunology, Seattle, Washington, USA
| | - Julian Reading
- Allen Institute for Immunology, Seattle, Washington, USA
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25
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A roadmap for translational cancer glycoimmunology at single cell resolution. J Exp Clin Cancer Res 2022; 41:143. [PMID: 35428302 PMCID: PMC9013178 DOI: 10.1186/s13046-022-02335-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/17/2022] [Indexed: 11/11/2022] Open
Abstract
Cancer cells can evade immune responses by exploiting inhibitory immune checkpoints. Immune checkpoint inhibitor (ICI) therapies based on anti-CTLA-4 and anti-PD-1/PD-L1 antibodies have been extensively explored over the recent years to unleash otherwise compromised anti-cancer immune responses. However, it is also well established that immune suppression is a multifactorial process involving an intricate crosstalk between cancer cells and the immune systems. The cancer glycome is emerging as a relevant source of immune checkpoints governing immunosuppressive behaviour in immune cells, paving an avenue for novel immunotherapeutic options. This review addresses the current state-of-the-art concerning the role played by glycans controlling innate and adaptive immune responses, while shedding light on available experimental models for glycoimmunology. We also emphasize the tremendous progress observed in the development of humanized models for immunology, the paramount contribution of advances in high-throughput single-cell analysis in this context, and the importance of including predictive machine learning algorithms in translational research. This may constitute an important roadmap for glycoimmunology, supporting careful adoption of models foreseeing clinical translation of fundamental glycobiology knowledge towards next generation immunotherapies.
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26
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Crawford LB. Human Embryonic Stem Cells as a Model for Hematopoietic Stem Cell Differentiation and Viral Infection. Curr Protoc 2022; 2:e622. [PMID: 36521018 PMCID: PMC9885899 DOI: 10.1002/cpz1.622] [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] [Indexed: 12/23/2022]
Abstract
Pluripotent human embryonic stem cell (hESC) lines are a valuable in vitro tool to differentiate specific cell lineages, including cells from all three germ layers, i.e., neuronal cells, myocytes, and hematopoietic cells, including progenitors (described here), lymphoid cells, and myeloid cells. However, dramatically different cell subtypes and functional properties of specific cells can arise depending on the differentiation technique used. We previously optimized hematopoietic stem cell differentiation from two different NIH-approved hESC lines to generate CD34+ hematopoietic progenitor cells (HPCs). Infection of these HPCs with a common herpesvirus (human cytomegalovirus) results in maintenance of viral latency, capability of viral reactivation, recapitulation of viral mutant phenotypes, and virus-induced myelosuppression of hematopoietic differentiation. However, different HPC subpopulations support different viral latency and reactivation phenotypes, and different hESC-to-HPC differentiation methods alter the ratio of stem cell subsets. In addition, differences in differentiation methods are dependent on both protocol/reagents and user techniques. Here, we report a simplified and optimized method to generate large numbers of CD34+ HPCs with consistent phenotypes and demonstrate a comparison of several common methods that can be used to control the ratio of available HPC subpopulations. A key aspect of this approach is that we achieve consistency in differentiation across users in different laboratories and, importantly, among newly trained individuals. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Maintenance of human embryonic stem cells (hESCs) Basic Protocol 2: Differentiation of hESCs to hematopoietic progenitor cells (HPCs) Basic Protocol 3: Downstream functional differentiation of hESC-derived HPCs to mature lineages Support Protocol 1: Freezing and testing frozen batches of hESCs Support Protocol 2: Counting hESCs Support Protocol 3: Phenotyping by flow cytometry.
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Affiliation(s)
- Lindsey B. Crawford
- Department of Biochemistry, Nebraska Center for Virology, Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, Nebraska
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27
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Jensen HA, Kim J. iCoreDrop: A robust immune monitoring spectral cytometry assay with six open channels for biomarker flexibility. Cytometry A 2022; 103:405-418. [PMID: 36458334 DOI: 10.1002/cyto.a.24708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/27/2022] [Accepted: 11/28/2022] [Indexed: 12/04/2022]
Abstract
Recent advances in spectral cytometry have extended our ability to monitor immune cell subsets and activation status while simultaneously improving rare population detection. However, technical challenges in reference control selection and autofluorescence extraction serve as barriers to broad application of spectral flow cytometry. Furthermore, the complexity of spectral cytometry panel development limits the adaptation of established assays. Here, we describe the development of a spectral immunophenotyping assay with robust drop-in capability to enable biomarker interrogation flexibility. The immune monitoring core (iCore), which can be used in part or total, captures broad and granular immune subsets across T cells, B cells, NK cells, monocytes, dendritic cells, and granulocytes in peripheral whole blood. Additional user-selected biomarkers can be dropped in (Drop) using channels BV421, Alexa Fluor 488, PE, PE-Cy7, APC, and APC-Cy7. A comprehensive assessment of reagent and panel performance was conducted, including reference control comparison and optimal autofluorescence (AF) extraction on the 5-laser Cytek Aurora system for healthy donor blood. Assay precision and stability analyses revealed robust intra-assay precision, with 95% of 83 distinct population gates having <20% CV. In the presence of additional drop-in markers in two different settings, a T cell module and a myeloid/B cell module, the drop-in channels themselves achieved <20% CV across 12 out of 13 additionally queried population gates. Overall, establishment of optimal unmixing practices will enable widespread adoption of spectral cytometry assays.
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Affiliation(s)
- Holly A Jensen
- Translational Research, Tumor Microenvironment Thematic Research Center, Bristol Myers Squibb, Redwood City, California, USA
| | - Jeong Kim
- Translational Research, Tumor Microenvironment Thematic Research Center, Bristol Myers Squibb, Redwood City, California, USA
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28
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Whyte CE, Tumes DJ, Liston A, Burton OT. Do more with Less: Improving High Parameter Cytometry Through Overnight Staining. Curr Protoc 2022; 2:e589. [PMID: 36373983 PMCID: PMC9827877 DOI: 10.1002/cpz1.589] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Recent advances in flow cytometry have allowed high-dimensional characterization of biological phenomena, enabling breakthroughs in a multitude of fields. Despite the appreciation of the unique properties of antigens and fluorophores in high-parameter panel design, staining conditions are often standardized for short surface stains, regardless of antibody affinity or antigen accessibility. Here, we demonstrate how increasing antibody incubation times can lead to substantial improvements in sensitivity, maintaining specificity, and reducing background, while also significantly reducing the costs of high-parameter cytometry panels. Furthermore, overnight staining reduces the influence of interexperimental variability, assisting accurate pooling over experiments over extended time courses. We provide guidance on how to optimize staining conditions for diverse antigens, including how different fixation strategies can affect epitope accessibility. Overnight staining can thus substantially improve the resolution, repeatability, and cost-effectiveness of high-parameter cytometry. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC.
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Affiliation(s)
- Carly E. Whyte
- Centre for Cancer BiologySA Pathology and University of South AustraliaAdelaideAustralia
| | - Damon J. Tumes
- Centre for Cancer BiologySA Pathology and University of South AustraliaAdelaideAustralia
| | - Adrian Liston
- Immunology ProgrammeBabraham InstituteCambridgeUnited Kingdom
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29
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Jaimes MC, Leipold M, Kraker G, Amir E, Maecker H, Lannigan J. Full spectrum flow cytometry and mass cytometry: A 32-marker panel comparison. Cytometry A 2022; 101:942-959. [PMID: 35593221 PMCID: PMC9790709 DOI: 10.1002/cyto.a.24565] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 02/23/2022] [Accepted: 04/25/2022] [Indexed: 01/27/2023]
Abstract
High-dimensional single-cell data has become an important tool in unraveling the complexity of the immune system and its involvement in homeostasis and a large array of pathologies. As technological tools are developed, researchers are adopting them to answer increasingly complex biological questions. Up until recently, mass cytometry (MC) has been the main technology employed in cytometric assays requiring more than 29 markers. Recently, however, with the introduction of full spectrum flow cytometry (FSFC), it has become possible to break the fluorescence barrier and go beyond 29 fluorescent parameters. In this study, in collaboration with the Stanford Human Immune Monitoring Center (HIMC), we compared five patient samples using an established immune panel developed by the HIMC using their MC platform. Using split samples and the same antibody panel, we were able to demonstrate highly comparable results between the two technologies using multiple data analysis approaches. We report here a direct comparison of two technology platforms (MC and FSFC) using a 32-marker flow cytometric immune monitoring panel that can identify all the previously described and anticipated immune subpopulations defined by this panel.
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Affiliation(s)
| | - Michael Leipold
- Department of Microbiology/ImmunologyStanford UniversityStanfordCaliforniaUSA
| | - Geoffrey Kraker
- Technical Applications SupportCytek Biosciences Inc.FremontCaliforniaUSA
| | - El‐ad Amir
- Astrolabe DiagnosticsFort LeeNew JerseyUSA
| | - Holden Maecker
- Department of Microbiology/ImmunologyStanford UniversityStanfordCaliforniaUSA
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30
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Novo D. A comparison of spectral unmixing to conventional compensation for the calculation of fluorochrome abundances from flow cytometric data. Cytometry A 2022; 101:885-891. [PMID: 35841160 DOI: 10.1002/cyto.a.24669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 06/28/2022] [Accepted: 07/04/2022] [Indexed: 01/27/2023]
Abstract
Traditionally, flow cytometers acquired data using the same number of detectors as fluorochromes being measured in the experiment. More recently, spectral flow cytometers utilize a larger number of detectors than fluorochromes. This seemingly small difference opens the door to a wide variety of mathematical tools for the calculation of the true fluorochrome abundances from the raw detector values as compared with traditional compensation. This review will provide a brief overview of the mathematics and theory underlying traditional compensation and unmixing focusing on the differences between them and the additional information provided by unmixing approaches.
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Affiliation(s)
- David Novo
- De Novo Software, Pasadena, California, USA
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31
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Jameson VJ, Luke T, Yan Y, Hind A, Evrard M, Man K, Mackay LK, Kallies A, Villadangos JA, McWilliam HEG, Perez‐Gonzalez A. Unlocking autofluorescence in the era of full spectrum analysis: Implications for immunophenotype discovery projects. Cytometry A 2022; 101:922-941. [PMID: 35349225 PMCID: PMC9519814 DOI: 10.1002/cyto.a.24555] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 02/22/2022] [Accepted: 03/24/2022] [Indexed: 01/27/2023]
Abstract
Understanding the complex elements affecting signal resolution in cytometry is key for quality experimental design and data. In this study, we incorporate autofluorescence as a contributing factor to our understanding of resolution in cytometry and corroborate its impact in fluorescence signal detection through mathematical predictions supported by empirical evidence. Our findings illustrate the critical importance of autofluorescence extraction via full spectrum unmixing in unmasking dim signals and delineating the expression and subset distribution of low abundance markers in discovery projects. We apply our findings to the precise definition of the tissue and cellular distribution of a weakly expressed fluorescent protein that reports on a low-abundance immunological gene. Exploiting the full spectrum coverage enabled by Aurora 5L, we describe a novel approach to the isolation of pure cell subset-specific autofluorescence profiles based on high dimensionality reduction algorithms. This method can also be used to unveil differences in the autofluorescent fingerprints of tissues in homeostasis and after immunological challenges.
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Affiliation(s)
- Vanta J. Jameson
- Department of Anatomy and PhysiologyThe University of MelbourneParkvilleVictoriaAustralia,Department of Microbiology and ImmunologyThe University of Melbourne, at The Peter Doherty Institute of Infection and ImmunityParkvilleVictoriaAustralia,Melbourne Cytometry PlatformThe University of MelbourneParkvilleVictoriaAustralia
| | - Tina Luke
- Department of Microbiology and ImmunologyThe University of Melbourne, at The Peter Doherty Institute of Infection and ImmunityParkvilleVictoriaAustralia,Melbourne Cytometry PlatformThe University of MelbourneParkvilleVictoriaAustralia
| | - Yuting Yan
- Department of Microbiology and ImmunologyThe University of Melbourne, at The Peter Doherty Institute of Infection and ImmunityParkvilleVictoriaAustralia,School of MedicineTsinghua UniversityBeijingChina
| | - Angela Hind
- Department of Microbiology and ImmunologyThe University of Melbourne, at The Peter Doherty Institute of Infection and ImmunityParkvilleVictoriaAustralia,Melbourne Cytometry PlatformThe University of MelbourneParkvilleVictoriaAustralia
| | - Maximilien Evrard
- Department of Microbiology and ImmunologyThe University of Melbourne, at The Peter Doherty Institute of Infection and ImmunityParkvilleVictoriaAustralia
| | - Kevin Man
- Department of Microbiology and ImmunologyThe University of Melbourne, at The Peter Doherty Institute of Infection and ImmunityParkvilleVictoriaAustralia
| | - Laura K. Mackay
- Department of Microbiology and ImmunologyThe University of Melbourne, at The Peter Doherty Institute of Infection and ImmunityParkvilleVictoriaAustralia
| | - Axel Kallies
- Department of Microbiology and ImmunologyThe University of Melbourne, at The Peter Doherty Institute of Infection and ImmunityParkvilleVictoriaAustralia
| | - Jose A. Villadangos
- Department of Microbiology and ImmunologyThe University of Melbourne, at The Peter Doherty Institute of Infection and ImmunityParkvilleVictoriaAustralia,Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology InstituteThe University of MelbourneParkvilleVictoriaAustralia
| | - Hamish E. G. McWilliam
- Department of Microbiology and ImmunologyThe University of Melbourne, at The Peter Doherty Institute of Infection and ImmunityParkvilleVictoriaAustralia,Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology InstituteThe University of MelbourneParkvilleVictoriaAustralia
| | - Alexis Perez‐Gonzalez
- Department of Microbiology and ImmunologyThe University of Melbourne, at The Peter Doherty Institute of Infection and ImmunityParkvilleVictoriaAustralia,Melbourne Cytometry PlatformThe University of MelbourneParkvilleVictoriaAustralia
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32
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Lannigan J. Flow cytometry has seen the light: All of it. Cytometry A 2022; 101:809-811. [PMID: 36203398 DOI: 10.1002/cyto.a.24694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2022] [Indexed: 01/27/2023]
Affiliation(s)
- Joanne Lannigan
- Flow Cytometry Support Services, LLC, Alexandria, Virginia, USA
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33
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Farrand K, Holz LE, Ferrer-Font L, Wilson MD, Ganley M, Minnell JJ, Tang CW, Painter GF, Heath WR, Hermans IF, Burn OK. Using Full-Spectrum Flow Cytometry to Phenotype Memory T and NKT Cell Subsets with Optimized Tissue-Specific Preparation Protocols. Curr Protoc 2022; 2:e482. [PMID: 35819836 DOI: 10.1002/cpz1.482] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Full-spectrum flow cytometry is now routinely used in many laboratories internationally, and the demand for this technology is rapidly increasing. With capacity to use larger and more complex staining panels, standardized protocols are required for optimal panel design and analysis. Importantly, for ex vivo analysis, tissue preparation methods also need to be optimized to ensure samples are truly representative of tissues in situ. This is particularly relevant given the recent interest in adaptive immune cells that form residency in specific organs. Here we provide optimized protocols for tissue processing and phenotyping of memory T cells and natural killer T (NKT) cell subsets from liver, lung, spleen, and lymph node using full-spectrum flow cytometry. We provide a 21-color antibody panel for identification of different memory subsets, including tissue-resident memory T (TRM ) cells, which are increasingly regarded as important effectors in adaptive immunity. We show that processing procedures can affect outcomes, with liver TRM cells particularly sensitive to heat, such that accurate evaluation requires fast processing at defined temperatures. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Processing mouse liver for flow cytometric analysis of memory T and NKT cell subsets Basic Protocol 2: Processing mouse spleen for flow cytometric analysis of memory T and NKT cell subsets Basic Protocol 3: Processing mouse lungs for flow cytometric analysis of memory T and NKT cell subsets Basic Protocol 4: Processing mouse lymph nodes for flow cytometric analysis of memory T and NKT cell subsets Basic Protocol 5: Staining and flow cytometric analysis of samples for memory T and NKT cell subsets Support Protocol: Obtaining cell counts from flow cytometry data.
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Affiliation(s)
- Kathryn Farrand
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Lauren E Holz
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Victoria, Australia
| | - Laura Ferrer-Font
- Malaghan Institute of Medical Research, Wellington, New Zealand
- Maurice Wilkins Centre, Auckland, New Zealand
| | | | - Mitch Ganley
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand
| | | | - Ching-Wen Tang
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Gavin F Painter
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand
| | - William R Heath
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Victoria, Australia
| | - Ian F Hermans
- Malaghan Institute of Medical Research, Wellington, New Zealand
- Maurice Wilkins Centre, Auckland, New Zealand
| | - Olivia K Burn
- Malaghan Institute of Medical Research, Wellington, New Zealand
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34
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Prasit KK, Ferrer-Font L, Burn OK, Anderson RJ, Compton BJ, Schmidt AJ, Mayer JU, Chen CJJ, Dasyam N, Ritchie DS, Godfrey DI, Mattarollo SR, Dundar PR, Painter GF, Hermans IF. Intratumoural administration of an NKT cell agonist with CpG promotes NKT cell infiltration associated with an enhanced antitumour response and abscopal effect. Oncoimmunology 2022; 11:2081009. [PMID: 35712122 PMCID: PMC9196710 DOI: 10.1080/2162402x.2022.2081009] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Intratumoural administration of unmethylated cytosine-phosphate-guanine motifs (CpG) to stimulate toll-like receptor (TLR)-9 has been shown to induce tumour regression in preclinical studies and some efficacy in the clinic. Because activated natural killer T (NKT) cells can cooperate with pattern-recognition via TLRs to improve adaptive immune responses, we assessed the impact of combining a repeated dosing regimen of intratumoural CpG with a single intratumoural dose of the NKT cell agonist α-galactosylceramide (α-GalCer). The combination was superior to CpG alone at inducing regression of established tumours in several murine tumour models, primarily mediated by CD8+ T cells. An antitumour effect on distant untreated tumours (abscopal effect) was reliant on sustained activity of NKT cells and was associated with infiltration of KLRG1+ NKT cells in tumours and draining lymph nodes at both injected and untreated distant sites. Cytometric analysis pointed to increased exposure to type I interferon (IFN) affecting many immune cell types in the tumour and lymphoid organs. Accordingly, antitumour activity was lost in animals in which dendritic cells (DCs) were incapable of signaling through the type I IFN receptor. Studies in conditional ablation models showed that conventional type 1 DCs and plasmacytoid DCs were required for the response. In tumour models where the combined treatment was less effective, the addition of tumour-antigen derived peptide, preferably conjugated to α-GalCer, significantly enhanced the antitumour response. The combination of TLR ligation, NKT cell agonism, and peptide delivery could therefore be adapted to induce responses to both known and unknown antigens.
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Affiliation(s)
- Kef K Prasit
- Malaghan Institute of Medical Research, Wellington, New Zealand.,Maurice Wilkins Centre, Auckland, New Zealand
| | - Laura Ferrer-Font
- Maurice Wilkins Centre, Auckland, New Zealand.,Hugh Green Cytometry Centre, Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Olivia K Burn
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Regan J Anderson
- Ferrier Research Institute, Victoria University of Wellington, Lower Hutt, New Zealand
| | - Benjamin J Compton
- Ferrier Research Institute, Victoria University of Wellington, Lower Hutt, New Zealand
| | - Alfonso J Schmidt
- Hugh Green Cytometry Centre, Malaghan Institute of Medical Research, Wellington, New Zealand
| | | | - Chun-Jen J Chen
- Maurice Wilkins Centre, Auckland, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | | | - David S Ritchie
- Clinical Haematology, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Australia.,University of Melbourne, Melbourne, Australia
| | - Dale I Godfrey
- Department of Microbiology & Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Australia
| | - Stephen R Mattarollo
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, Australia
| | - P Rod Dundar
- Maurice Wilkins Centre, Auckland, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Gavin F Painter
- Ferrier Research Institute, Victoria University of Wellington, Lower Hutt, New Zealand
| | - Ian F Hermans
- Malaghan Institute of Medical Research, Wellington, New Zealand.,Maurice Wilkins Centre, Auckland, New Zealand
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35
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Woodruff MC, Nguyen DC, Faliti CE, Saini AS, Lee FEH, Sanz I. Response under pressure: deploying emerging technologies to understand B-cell-mediated immunity in COVID-19. Nat Methods 2022; 19:387-391. [PMID: 35396475 PMCID: PMC9703369 DOI: 10.1038/s41592-022-01450-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Matthew C Woodruff
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA
- Emory Autoimmunity Center of Excellence, Emory University, Atlanta, GA, USA
| | - Doan C Nguyen
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Emory University, Atlanta, GA, USA
| | - Caterina E Faliti
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA
- Emory Autoimmunity Center of Excellence, Emory University, Atlanta, GA, USA
| | - Ankur Singh Saini
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA
- Emory Autoimmunity Center of Excellence, Emory University, Atlanta, GA, USA
| | - F Eun-Hyung Lee
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Emory University, Atlanta, GA, USA
| | - Ignacio Sanz
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA.
- Emory Autoimmunity Center of Excellence, Emory University, Atlanta, GA, USA.
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Staggered starts in the race to T cell activation. Trends Immunol 2021; 42:994-1008. [PMID: 34649777 PMCID: PMC7612485 DOI: 10.1016/j.it.2021.09.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/12/2021] [Accepted: 09/13/2021] [Indexed: 02/07/2023]
Abstract
How T lymphocytes tune their responses to different strengths of stimulation is a fundamental question in immunology. Recent work using new optogenetic, single-cell genomic, and live-imaging approaches has revealed that stimulation strength controls the rate of individual cell responses within a population. Moreover, these responses have been found to use shared molecular programs, regardless of stimulation strength. However, additional data indicate that stimulation duration or cytokine feedback can impact later gene expression phenotypes of activated cells. In-depth molecular studies have suggested mechanisms by which stimulation strength might modulate the probability of T cell activation. This emerging model allows activating T cells to achieve a wide range of population responses through probabilistic control within individual cells.
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