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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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Rong G, Zhang Y, Chen Y, Chen J, Jiang N, Merchuk JC. The prodigiosin change on the surface of Serratia marcescens detected by flow cytometry. Cytometry A 2021; 101:254-263. [PMID: 34448526 DOI: 10.1002/cyto.a.24497] [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: 02/06/2021] [Revised: 07/25/2021] [Accepted: 08/06/2021] [Indexed: 11/11/2022]
Abstract
The potential of flow cytometry for the study of changes in prodigiosin on the cell surface of Serratia marcescens is of academic and practical interest. This is because S. marcescens can produce prodigiosin, a secondary metabolite, with potential use as a cancer-cell inhibitor. In this study, three groups of bacterial cultures with different carbon sources were compared, and the effect of the addition of cAMP to the sucrose-based culture was studied. Both cellular morphology and DNA content were detected by flow cytometry, rendering a broad description of the bacterial behavior. It is the first use of flow cytometry to investigate the dynamics of prodigiosin on the surface of S. marcescens during growth in different media. The fluorescence intensity is related to the DNA content, the forward-scattered light is related to cell volume, and the side-scattered light is related to the surface morphology, especially the surface prodigiosin. These may contribute to the potential development of a bacterial metabolic monitoring strategy using both DNA content analysis and bacterial morphology based on flow cytometry technique.
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Affiliation(s)
- Guangjian Rong
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, China.,Key Laboratory for Green Chemical Process of Ministry of Education, Wuhan Institute of Technology, LiuFang Campus, Wuhan, China.,Key Laboratory of Novel Reactor and Green Chemical Technology of Hubei Province, Wuhan Institute of Technology, LiuFang Campus, Wuhan, China
| | - Youhong Zhang
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, China.,Key Laboratory for Green Chemical Process of Ministry of Education, Wuhan Institute of Technology, LiuFang Campus, Wuhan, China.,Key Laboratory of Novel Reactor and Green Chemical Technology of Hubei Province, Wuhan Institute of Technology, LiuFang Campus, Wuhan, China.,School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, China
| | - Yan Chen
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, China
| | - Jie Chen
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, China
| | - Nan Jiang
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, China
| | - Jose C Merchuk
- Department of Chemical Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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Pitoiset F, Barbié M, Monneret G, Braudeau C, Pochard P, Pellegrin I, Trauet J, Labalette M, Klatzmann D, Rosenzwajg M. A standardized flow cytometry procedure for the monitoring of regulatory T cells in clinical trials. CYTOMETRY PART B-CLINICAL CYTOMETRY 2018; 94:621-626. [PMID: 29316248 DOI: 10.1002/cyto.b.21622] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 12/21/2017] [Accepted: 01/03/2018] [Indexed: 01/01/2023]
Abstract
BACKGROUND Quantification of regulatory T cells (Tregs) is crucial in immunomonitoring in clinical trials as this cell population has been shown to be involved in a wide range of diseases, including cancers, autoimmune diseases, infections, and allergies. Human Tregs are defined as CD4+ CD25+ CD127low FoxP3+ cells, and the standardization of their staining by flow cytometry is a challenge, especially in multicenter clinical trials, notably because of the intracellular location of FoxP3. METHOD A flow cytometry staining procedure was settled and standardized to measure human Tregs in peripheral whole blood using precoated dried antibodies in ready-to-use tubes. It was compared with reference methods and implemented and validated to be suitable with different cytometer platforms. RESULTS The standardized protocol developed with dried antibodies and reduced volumes of whole blood allows an optimal identification of Tregs. Compared with classical staining procedure, it reduces the number of steps required, in a very fast and simple technique. The accuracy of the method was confirmed by a multicenter comparison with different cytometer brands. CONCLUSIONS Our results highlight the reliability of this high-standard protocol that could become a reference method for the monitoring of Tregs in clinical trials. © 2018 International Clinical Cytometry Society.
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Affiliation(s)
- Fabien Pitoiset
- Sorbonne Université, UPMC Univ Paris 06, INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (I3), Paris F-75005, France.,Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (I2B), AP-HP, Hôpital Pitié-Salpêtrière, Paris, F-75651, France
| | - Michèle Barbié
- Sorbonne Université, UPMC Univ Paris 06, INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (I3), Paris F-75005, France.,Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (I2B), AP-HP, Hôpital Pitié-Salpêtrière, Paris, F-75651, France
| | - Guillaume Monneret
- Hospices Civils de Lyon, Hôpital Edouard Herriot, Laboratoire d'Immunologie, Lyon F-69003, France
| | - Cécile Braudeau
- CIMNA, Laboratoire d'Immunologie, CHU Nantes, Nantes, France.,Centre de Recherche en Transplantation et Immunologie (UMR1064), INSERM Université de Nantes, Nantes, France
| | - Pierre Pochard
- INSERM ERI29, EA2216, Université de Brest, Labex IGO, CHRU Morvan, Brest, France
| | - Isabelle Pellegrin
- Service d'Immunologie-Immunogénétique, Pôle de Biologie et Pathologie, Groupe Hospitalier Pellegrin, CHU Bordeaux, Bordeaux, France
| | - Jacques Trauet
- University of Lille, U995 - LIRIC-Lille Inflammation Research International Center, Lille F-59000, France.,INSERM, U995, Lille F-59000, France.,CHU LILLE, Institut d'Immunologie, Lille F-59000, France
| | - Myriam Labalette
- University of Lille, U995 - LIRIC-Lille Inflammation Research International Center, Lille F-59000, France.,INSERM, U995, Lille F-59000, France.,CHU LILLE, Institut d'Immunologie, Lille F-59000, France
| | - David Klatzmann
- Sorbonne Université, UPMC Univ Paris 06, INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (I3), Paris F-75005, France.,Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (I2B), AP-HP, Hôpital Pitié-Salpêtrière, Paris, F-75651, France
| | - Michelle Rosenzwajg
- Sorbonne Université, UPMC Univ Paris 06, INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (I3), Paris F-75005, France.,Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (I2B), AP-HP, Hôpital Pitié-Salpêtrière, Paris, F-75651, France
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Murray HC, Dun MD, Verrills NM. Harnessing the power of proteomics for identification of oncogenic, druggable signalling pathways in cancer. Expert Opin Drug Discov 2017; 12:431-447. [PMID: 28286965 DOI: 10.1080/17460441.2017.1304377] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Genomic and transcriptomic profiling of tumours has revolutionised our understanding of cancer. However, the majority of tumours possess multiple mutations, and determining which oncogene, or even which pathway, to target is difficult. Proteomics is emerging as a powerful approach to identify the functionally important pathways driving these cancers, and how they can be targeted therapeutically. Areas covered: The authors provide a technical overview of mass spectrometry based approaches for proteomic profiling, and review the current and emerging strategies available for the identification of dysregulated networks, pathways, and drug targets in cancer cells, with a key focus on the ability to profile cancer kinomes. The potential applications of mass spectrometry in the clinic are also highlighted. Expert opinion: The addition of proteomic information to genomic platforms - 'proteogenomics' - is providing unparalleled insight in cancer cell biology. Application of improved mass spectrometry technology and methodology, in particular the ability to analyse post-translational modifications (the PTMome), is providing a more complete picture of the dysregulated networks in cancer, and uncovering novel therapeutic targets. While the application of proteomics to discovery research will continue to rise, improved workflow standardisation and reproducibility is required before mass spectrometry can enter routine clinical use.
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Affiliation(s)
- Heather C Murray
- a School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, Priority Research Centre for Cancer Research, Innovation and Translation , University of Newcastle , Callaghan , NSW , Australia.,b Cancer Research Program , Hunter Medical Research Institute , Newcastle , NSW , Australia
| | - Matthew D Dun
- a School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, Priority Research Centre for Cancer Research, Innovation and Translation , University of Newcastle , Callaghan , NSW , Australia.,b Cancer Research Program , Hunter Medical Research Institute , Newcastle , NSW , Australia
| | - Nicole M Verrills
- a School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, Priority Research Centre for Cancer Research, Innovation and Translation , University of Newcastle , Callaghan , NSW , Australia.,b Cancer Research Program , Hunter Medical Research Institute , Newcastle , NSW , Australia
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