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Franco Nitta C, Pierce M, Hem S, Parker A, Bell J, Huang Y, Patel S, Gundimeda SK, Dings J, Shaw N, Dobrowolski M, Flanagan K, Stefanski J, Vasani D, Delany J, Hedrick C, Ratnani S, Karukappadath M, Cortez A, Parrish K, Claflin S, Battacharya S, Williamson C, Li P, Qiu J, Kuksin D, Lin B, Smith T, Chan LLY. Cellaca® PLX image cytometer as an alternative for immunophenotyping, GFP/RFP transfection efficiencies, and apoptosis analysis. Anal Biochem 2024; 685:115389. [PMID: 37951455 DOI: 10.1016/j.ab.2023.115389] [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: 10/03/2023] [Revised: 11/02/2023] [Accepted: 11/05/2023] [Indexed: 11/14/2023]
Abstract
Cell and gene therapy is a fast-growing field for cancer therapeutics requiring reliable instrumentation and technologies. Key parameters essential for satisfying Chemistry Manufacturing and Controls criteria standards are routinely performed using flow cytometry. Recently, image cytometry was developed for cell characterization and cell-based assays but had not yet demonstrated sufficient sensitivity for surface marker detection. We developed the Cellaca® PLX image cytometry system and the respective methodologies required for immunophenotyping, GFP and RFP transfection/transduction efficiencies, and cell health analyses for routine cell characterization. All samples tested were compared directly to results from the CytoFLEX flow cytometer. PBMCs were stained with T-cell surface markers for immunophenotyping, and results show highly comparable CD3, CD4, and CD8 populations (within 5 %). GFP- or RFP-expressing cell lines were analyzed for transfection/transduction efficiencies, and the percentage positive cells and respective viabilities were equivalent on both systems. Staurosporine-treated Jurkat cells were stained for apoptotic markers, where annexin V and caspase-3 positive cells were within 5 % comparing both instruments. The proposed system may provide a complementary tool for performing routine cell-based experiments with improved efficiency and sensitivity compared to prior image cytometers, which may be significantly valuable to the cell and gene therapy field.
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Affiliation(s)
| | | | - Sopaul Hem
- Department of Consumables and Reagent Development, USA
| | - Aiyana Parker
- Department of Consumables and Reagent Development, USA
| | | | | | | | | | | | | | - Marek Dobrowolski
- Department of Software Development, Revvity Health Sciences, Inc, 360 Merrimack St, Suite 200, Lawrence, MA, 01843, USA
| | - Kevin Flanagan
- Department of Software Development, Revvity Health Sciences, Inc, 360 Merrimack St, Suite 200, Lawrence, MA, 01843, USA
| | - John Stefanski
- Department of Software Development, Revvity Health Sciences, Inc, 360 Merrimack St, Suite 200, Lawrence, MA, 01843, USA
| | - Devang Vasani
- Department of Software Development, Revvity Health Sciences, Inc, 360 Merrimack St, Suite 200, Lawrence, MA, 01843, USA
| | - James Delany
- Department of Software Development, Revvity Health Sciences, Inc, 360 Merrimack St, Suite 200, Lawrence, MA, 01843, USA
| | - Chuck Hedrick
- Department of Software Development, Revvity Health Sciences, Inc, 360 Merrimack St, Suite 200, Lawrence, MA, 01843, USA
| | - Surbhi Ratnani
- Department of Software Development, Revvity Health Sciences, Inc, 360 Merrimack St, Suite 200, Lawrence, MA, 01843, USA
| | - Mili Karukappadath
- Department of Software Development, Revvity Health Sciences, Inc, 360 Merrimack St, Suite 200, Lawrence, MA, 01843, USA
| | - Alex Cortez
- Department of Software Development, Revvity Health Sciences, Inc, 360 Merrimack St, Suite 200, Lawrence, MA, 01843, USA
| | - Kevin Parrish
- Department of Software Development, Revvity Health Sciences, Inc, 360 Merrimack St, Suite 200, Lawrence, MA, 01843, USA
| | - Sam Claflin
- Department of Software Development, Revvity Health Sciences, Inc, 360 Merrimack St, Suite 200, Lawrence, MA, 01843, USA
| | | | | | - Peter Li
- Department of Consumables and Reagent Development, USA; Department of Advanced Technology R&D, USA; Department of Engineering, USA; Department of Software Development, Revvity Health Sciences, Inc, 360 Merrimack St, Suite 200, Lawrence, MA, 01843, USA
| | - Jean Qiu
- Department of Consumables and Reagent Development, USA; Department of Advanced Technology R&D, USA; Department of Engineering, USA; Department of Software Development, Revvity Health Sciences, Inc, 360 Merrimack St, Suite 200, Lawrence, MA, 01843, USA
| | - Dmitry Kuksin
- Department of Consumables and Reagent Development, USA; Department of Advanced Technology R&D, USA
| | - Bo Lin
- Department of Consumables and Reagent Development, USA; Department of Advanced Technology R&D, USA
| | - Timothy Smith
- Department of Engineering, USA; Department of Software Development, Revvity Health Sciences, Inc, 360 Merrimack St, Suite 200, Lawrence, MA, 01843, USA
| | - Leo Li-Ying Chan
- Department of Consumables and Reagent Development, USA; Department of Advanced Technology R&D, USA; Department of Engineering, USA
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Patel S, McDonald JI, Mohammed H, Parthasarathy V, Hernandez V, Stuckey T, Lin AH, Gundimeda SK, Lin B, Reading J, Chan LLY. Development of a high-throughput image cytometric screening method as a research tool for immunophenotypic characterization of patient samples from clinical studies. J Immunol Methods 2024; 524:113587. [PMID: 38040192 DOI: 10.1016/j.jim.2023.113587] [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: 07/12/2023] [Revised: 11/08/2023] [Accepted: 11/27/2023] [Indexed: 12/03/2023]
Abstract
Immunophenotyping has been the primary assay for characterization of immune cells from patients undergoing therapeutic treatments in clinical research, which is critical for understanding disease progression and treatment efficacy. Currently, flow cytometry has been the dominant methodology for characterizing surface marker expression for immunological research. Flow cytometry has been proven to be an effective and efficient method for immunophenotyping, however, it requires highly trained users and a large time commitment. Recently, a novel image cytometry system (Cellaca® PLX Image Cytometer, Revvity Health Sciences, Inc., Lawrence, MA) has been developed as a complementary method to flow cytometry for performing rapid and high-throughput immunophenotyping. In this work, we demonstrated an image cytometric screening method to characterize immune cell populations, streamlining the analysis of routine surface marker panels. The T cell, B cell, NK cell, and monocyte populations of 46 primary PBMC samples from subjects enrolled in autoimmune and oncological disease study cohorts were analyzed with two optimized immunophenotyping staining kits: Panel 1 (CD3, CD56, CD14) and Panel 2 (CD3, CD56, CD19). We validated the proposed image cytometry method by comparing the Cellaca® PLX and the AuroraTM flow cytometer (Cytek Biosciences, Fremont, CA). The image cytometry system was employed to generate bright field and fluorescent images, as well as scatter plots for multiple patient PBMC samples. In addition, the image cytometry method can directly determine cell concentrations for downstream assays. The results demonstrated comparable CD3, CD14, CD19, and CD56 cell populations from the primary PBMC samples, which showed an average of 5% differences between flow and image cytometry. The proposed image cytometry method provides a novel research tool to potentially streamline immunophenotyping workflow for characterizing patient samples in clinical studies.
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Affiliation(s)
- Samir Patel
- Department of Advanced Technology R&D, Revvity Health Sciences, Inc., Lawrence, MA 01843, USA
| | - James I McDonald
- Department of Advanced Technology R&D, Revvity Health Sciences, Inc., Lawrence, MA 01843, USA
| | - Hamza Mohammed
- Department of Advanced Technology R&D, Revvity Health Sciences, Inc., Lawrence, MA 01843, USA
| | | | - Veronica Hernandez
- Allen Institute for Immunology, 615 Westlake Avenue N, Seattle, WA 98109, USA
| | - Tyanna Stuckey
- Allen Institute for Immunology, 615 Westlake Avenue N, Seattle, WA 98109, USA
| | - Allen H Lin
- Department of Advanced Technology R&D, Revvity Health Sciences, Inc., Lawrence, MA 01843, USA
| | | | - Bo Lin
- Department of Advanced Technology R&D, Revvity Health Sciences, Inc., Lawrence, MA 01843, USA
| | - Julian Reading
- Allen Institute for Immunology, 615 Westlake Avenue N, Seattle, WA 98109, USA
| | - Leo Li-Ying Chan
- Department of Advanced Technology R&D, Revvity Health Sciences, Inc., Lawrence, MA 01843, USA.
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3
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Thomson Z, He Z, Swanson E, Henderson K, Phalen C, Zaim SR, Pebworth MP, Okada LY, Heubeck AT, Roll CR, Hernandez V, Weiss M, Genge PC, Reading J, Giles JR, Manne S, Dougherty J, Jasen CJ, Greenplate AR, Becker LA, Graybuck LT, Vasaikar SV, Szeto GL, Savage AK, Speake C, Buckner JH, Li XJ, Bumol TF, Wherry EJ, Torgerson TR, Vella LA, Henrickson SE, Skene PJ, Gustafson CE. Trimodal single-cell profiling reveals a novel pediatric CD8αα + T cell subset and broad age-related molecular reprogramming across the T cell compartment. Nat Immunol 2023; 24:1947-1959. [PMID: 37845489 PMCID: PMC10602854 DOI: 10.1038/s41590-023-01641-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 09/07/2023] [Indexed: 10/18/2023]
Abstract
Age-associated changes in the T cell compartment are well described. However, limitations of current single-modal or bimodal single-cell assays, including flow cytometry, RNA-seq (RNA sequencing) and CITE-seq (cellular indexing of transcriptomes and epitopes by sequencing), have restricted our ability to deconvolve more complex cellular and molecular changes. Here, we profile >300,000 single T cells from healthy children (aged 11-13 years) and older adults (aged 55-65 years) by using the trimodal assay TEA-seq (single-cell analysis of mRNA transcripts, surface protein epitopes and chromatin accessibility), which revealed that molecular programming of T cell subsets shifts toward a more activated basal state with age. Naive CD4+ T cells, considered relatively resistant to aging, exhibited pronounced transcriptional and epigenetic reprogramming. Moreover, we discovered a novel CD8αα+ T cell subset lost with age that is epigenetically poised for rapid effector responses and has distinct inhibitory, costimulatory and tissue-homing properties. Together, these data reveal new insights into age-associated changes in the T cell compartment that may contribute to differential immune responses.
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Affiliation(s)
| | - Ziyuan He
- Allen Institute for Immunology, Seattle, WA, USA
| | - Elliott Swanson
- Allen Institute for Immunology, Seattle, WA, USA
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Cole Phalen
- Allen Institute for Immunology, Seattle, WA, USA
| | | | | | | | | | - Charles R Roll
- Allen Institute for Immunology, Seattle, WA, USA
- Microbiology, Immunology and Cancer Biology (MICaB) Program, University of Minnesota, Minneapolis, Minneapolis, MN, USA
| | | | - Morgan Weiss
- Allen Institute for Immunology, Seattle, WA, USA
| | | | | | - Josephine R Giles
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Sasikanth Manne
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Jeanette Dougherty
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - C J Jasen
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Allison R Greenplate
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | | | - Suhas V Vasaikar
- Allen Institute for Immunology, Seattle, WA, USA
- Seagen, Bothell, WA, USA
| | - Gregory L Szeto
- Allen Institute for Immunology, Seattle, WA, USA
- Seagen, Bothell, WA, USA
| | | | - Cate Speake
- Center for Interventional Immunology, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - Jane H Buckner
- Center for Translational Immunology, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - Xiao-Jun Li
- Allen Institute for Immunology, Seattle, WA, USA
| | | | - E John Wherry
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | - Laura A Vella
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Pediatrics, Children's Hospital of Philadelphia and the University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sarah E Henrickson
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Pediatrics, Children's Hospital of Philadelphia and the University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
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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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5
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Wen G, Gu W. Circular RNAs in peripheral blood mononuclear cells are more stable than linear RNAs upon sample processing delay. J Cell Mol Med 2022; 26:5021-5032. [PMID: 36039821 PMCID: PMC9549506 DOI: 10.1111/jcmm.17525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 08/06/2022] [Accepted: 08/11/2022] [Indexed: 12/01/2022] Open
Abstract
Circular RNAs (circRNAs) are a novel class of RNAs with closed loop structure. Blood circRNAs are widely acknowledged to be more stable than linear mRNAs, which show promising prospect to be liquid biopsy biomarkers for clinical applications. However, accumulating studies have demonstrated that sample processing delays have profound effects on blood transcriptome expression profiles, wherein knowledge remains elusive about the impacts of prolonged sample processing on blood expression profiles of circRNAs. We collected whole blood samples from three donors and isolated peripheral blood mononuclear cells (PBMCs) at six different incubation time points. We measured total RNA expression profiles using RNA sequencing (RNA‐seq) and investigated the differentially expressed circRNAs, mRNAs and lncRNAs upon blood processing delay. Meanwhile, we explored the underlying inducement of aberrant expression of circRNAs against their corresponding mRNA transcripts. Finally, we utilized rMATS‐turbo and CIRI‐AS, respectively, to screen out differential alternative splicing (AS) events in linear mRNAs and circRNAs. Sample incubation at 4°C lasting to 48 hours (h) led to minimal effects to circRNAs' expression. However, it induced extensive alterations for mRNAs and lncRNAs when the incubation time was beyond 12 h. Additionally, only 2 h processing delays may result in profound impacts on AS events of linear mRNAs, while less impact on the equivalence of circRNAs. Our results suggested that PBMC circRNAs are stable upon sample processing delay, which are more suitable to be liquid biopsy biomarkers.
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Affiliation(s)
- Guoxia Wen
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, China
| | - Wanjun Gu
- Collaborative Innovation Center of Jiangsu Province of Cancer Prevention and Treatment of Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing, China.,School of Artificial Intelligence and Information Technology, Nanjing University of Chinese Medicine, Nanjing, China
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Swanson E, Reading J, Graybuck LT, Skene PJ. BarWare: efficient software tools for barcoded single-cell genomics. BMC Bioinformatics 2022; 23:106. [PMID: 35346022 PMCID: PMC8962164 DOI: 10.1186/s12859-022-04620-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 02/28/2022] [Indexed: 11/10/2022] Open
Abstract
Background Barcode-based multiplexing methods can be used to increase throughput and reduce batch effects in large single-cell genomics studies. Despite advantages in flexibility of sample collection and scale, there are additional complications in the data deconvolution steps required to assign each cell to their originating samples. Results To meet computational needs for efficient sample deconvolution, we developed the tools BarCounter and BarMixer that compute barcode counts and deconvolute mixed single-cell data into sample-specific files, respectively. Together, these tools are implemented as the BarWare pipeline to support demultiplexing from large sequencing projects with many wells of hashed 10x Genomics scRNA-seq data. Conclusions BarWare is a modular set of tools linked by shell scripting: BarCounter, a computationally efficient barcode sequence quantification tool implemented in C; and BarMixer, an R package for identification of barcoded populations, merging barcoded data from multiple wells, and quality-control reporting related to scRNA-seq data. These tools and a self-contained implementation of the pipeline are freely available for non-commercial use at https://github.com/AllenInstitute/BarWare-pipeline. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04620-2.
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