1
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Sun K, Roy A, Tobin JM. Artificial intelligence and machine learning: Definition of terms and current concepts in critical care research. J Crit Care 2024; 82:154792. [PMID: 38554543 DOI: 10.1016/j.jcrc.2024.154792] [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: 04/06/2023] [Revised: 07/05/2023] [Accepted: 07/17/2023] [Indexed: 04/01/2024]
Abstract
With increasing computing power, artificial intelligence (AI) and machine learning (ML) have prospered, which facilitate the analysis of large datasets, especially those found in critical care. It is important to define these terminologies, to inform a standardized approach to critical care research. This manuscript hopes to clarify these terms with examples from medical literature. Three major components that are required for a successful ML implementation: (i) reliable dataset, (ii) ML algorithm, and (iii) unbiased model evaluation, are discussed. A reliable dataset can be structured or unstructured with limited noise, outliers, and missing values. ML, a subset of AI, is typically focused on supervised or unsupervised learning tasks in which the output is based on inputs and derived from iterative pattern recognition algorithms, while AI is the overall ability of a machine to "think" or mimic human behavior; and to analyze data free from human influence. Even with successful implementation, advanced AI and ML algorithms have faced challenges in adoption into practice, mainly due to their lack of interpretability, which hinders trust, buy-in, and engagement from clinicians. Consequently, traditional algorithms, such as linear and logistic regression, that may have reduced predictive power but are highly interpretable, continue to be widely used.
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Affiliation(s)
- Kai Sun
- Department of Management Science and Statistics, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249, USA; Department of Anesthesiology, University of Texas Health Sciences Center San Antonio, 7703 Floyd Curl Dr, San Antonio, TX 78229, USA.
| | - Arkajyoti Roy
- Department of Management Science and Statistics, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249, USA.
| | - Joshua M Tobin
- Department of Anesthesiology, University of Texas Health Sciences Center San Antonio, 7703 Floyd Curl Dr, San Antonio, TX 78229, USA.
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2
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Zhao M, Cheng Y, Gao J, Zhou F. Single-cell mass cytometry in immunological skin diseases. Front Immunol 2024; 15:1401102. [PMID: 39081313 PMCID: PMC11286489 DOI: 10.3389/fimmu.2024.1401102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 07/01/2024] [Indexed: 08/02/2024] Open
Abstract
Immune-related skin diseases represent a collective of dermatological disorders intricately linked to dysfunctional immune system processes. These conditions are primarily characterized by an immoderate activation of the immune system or deviant immune responses, involving diverse immune components including immune cells, antibodies, and inflammatory mediators. However, the precise molecular dysregulation underlying numerous individual cases of these diseases and unique subsets respond under disease conditions remains elusive. Comprehending the mechanisms and determinants governing the homeostasis and functionality of diseases could offer potential therapeutic opportunities for intervention. Mass cytometry enables precise and high-throughput quantitative measurement of proteins within individual cells by utilizing antibodies labeled with rare heavy metal isotopes. Imaging mass cytometry employs mass spectrometry to obtain spatial information on cell-to-cell interactions within tissue sections, simultaneously utilizing more than 40 markers. The application of single-cell mass cytometry presents a unique opportunity to conduct highly multiplexed analysis at the single-cell level, thereby revolutionizing our understanding of cell population heterogeneity and hierarchy, cellular states, multiplexed signaling pathways, proteolysis products, and mRNA transcripts specifically in the context of many autoimmune diseases. This information holds the potential to offer novel approaches for the diagnosis, prognostic assessment, and monitoring responses to treatment, thereby enriching our strategies in managing the respective conditions. This review summarizes the present-day utilization of single-cell mass cytometry in studying immune-related skin diseases, highlighting its advantages and limitations. This technique will become increasingly prevalent in conducting extensive investigations into these disorders, ultimately yielding significant contributions to their accurate diagnosis and efficacious therapeutic interventions.
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Affiliation(s)
- Mingming Zhao
- Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, Anhui, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Yuqi Cheng
- Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, Anhui, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Jinping Gao
- Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, Anhui, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Fusheng Zhou
- Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, Anhui, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
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3
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Ng DP, Simonson PD, Tarnok A, Lucas F, Kern W, Rolf N, Bogdanoski G, Green C, Brinkman RR, Czechowska K. Recommendations for using artificial intelligence in clinical flow cytometry. CYTOMETRY. PART B, CLINICAL CYTOMETRY 2024; 106:228-238. [PMID: 38407537 DOI: 10.1002/cyto.b.22166] [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: 08/13/2023] [Revised: 01/16/2024] [Accepted: 02/06/2024] [Indexed: 02/27/2024]
Abstract
Flow cytometry is a key clinical tool in the diagnosis of many hematologic malignancies and traditionally requires close inspection of digital data by hematopathologists with expert domain knowledge. Advances in artificial intelligence (AI) are transferable to flow cytometry and have the potential to improve efficiency and prioritization of cases, reduce errors, and highlight fundamental, previously unrecognized associations with underlying biological processes. As a multidisciplinary group of stakeholders, we review a range of critical considerations for appropriately applying AI to clinical flow cytometry, including use case identification, low and high risk use cases, validation, revalidation, computational considerations, and the present regulatory frameworks surrounding AI in clinical medicine. In particular, we provide practical guidance for the development, implementation, and suggestions for potential regulation of AI-based methods in the clinical flow cytometry laboratory. We expect these recommendations to be a helpful initial framework of reference, which will also require additional updates as the field matures.
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Affiliation(s)
- David P Ng
- Department of Pathology, University of Utah, Salt Lake City, Utah, USA
| | - Paul D Simonson
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Attila Tarnok
- Department of Preclinical Development and Validation, Fraunhofer Institute for Cell Therapy and Immunology, IZI, Leipzig, Germany
| | - Fabienne Lucas
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Wolfgang Kern
- MLL Munich Leukemia Laboratory GmbH, Munich, Germany
| | - Nina Rolf
- BC Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Goce Bogdanoski
- Clinical Development & Operations Quality, R&D Quality, Bristol Myers Squibb, Princeton, New Jersey, USA
| | - Cherie Green
- Translational Science, Ozette Technologies, Seattle, Washington, USA
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Zhuang S, Semenec L, Nagy SS, Cain AK, Inglis DW. High-precision screening and sorting of double emulsion droplets. Cytometry A 2024; 105:547-554. [PMID: 38634684 DOI: 10.1002/cyto.a.24842] [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: 12/14/2023] [Revised: 03/25/2024] [Accepted: 04/04/2024] [Indexed: 04/19/2024]
Abstract
Mounting evidence suggests that cell populations are extremely heterogeneous, with individual cells fulfilling different roles within the population. Flow cytometry (FC) is a high-throughput tool for single-cell analysis that works at high optical resolution. Sub-populations with unique properties can be screened, isolated and sorted through fluorescence-activated cell sorting (FACS), using intracellular fluorescent products or surface-tagged fluorescent products of interest. However, traditional FC and FACS methods cannot identify or isolate cells that secrete extracellular products of interest. Double emulsion (DE) droplets are an innovative approach to retaining these extracellular products so cells producing them can be identified and isolated with FC and FACS. The water-in-oil-in-water structure makes DE droplets compatible with the sheath flow of flow cytometry. Single cells can be encapsulated with other reagents into DEs, which act as pico-reactors. These droplets allow biological activities to take place while allowing for cell cultivation monitoring, rare mutant identification, and cellular events characterization. However, using DEs in FACS presents technical challenges, including rupture of DEs, poor accuracy and low sorting efficiency. This study presents high-performance sorting using fluorescent beads (as simulants for cells). This study aims to guide researchers in the use of DE-based flow cytometry, offering insights into how to resolve the technical difficulties associated with DE-based screening and sorting using FC.
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Affiliation(s)
- Siyuan Zhuang
- School of Engineering, Macquarie University, Sydney, New South Wales, Australia
| | - Lucie Semenec
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Stephanie S Nagy
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Amy K Cain
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - David W Inglis
- School of Engineering, Macquarie University, Sydney, New South Wales, Australia
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5
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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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6
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G. de Castro C, G. del Hierro A, H-Vázquez J, Cuesta-Sancho S, Bernardo D. State-of-the-art cytometry in the search of novel biomarkers in digestive cancers. Front Oncol 2024; 14:1407580. [PMID: 38868532 PMCID: PMC11167087 DOI: 10.3389/fonc.2024.1407580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 05/10/2024] [Indexed: 06/14/2024] Open
Abstract
Despite that colorectal and liver cancer are among the most prevalent tumours in the world, the identification of non-invasive biomarkers to aid on their diagnose and subsequent prognosis is a current unmet need that would diminish both their incidence and mortality rates. In this context, conventional flow cytometry has been widely used in the screening of biomarkers with clinical utility in other malignant processes like leukaemia or lymphoma. Therefore, in this review, we will focus on how advanced cytometry panels covering over 40 parameters can be applied on the study of the immune system from patients with colorectal and hepatocellular carcinoma and how that can be used on the search of novel biomarkers to aid or diagnose, prognosis, and even predict clinical response to different treatments. In addition, these multiparametric and unbiased approaches can also provide novel insights into the specific immunopathogenic mechanisms governing these malignant diseases, hence potentially unravelling novel targets to perform immunotherapy or identify novel mechanisms, rendering the development of novel treatments. As a consequence, computational cytometry approaches are an emerging methodology for the early detection and predicting therapies for gastrointestinal cancers.
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Affiliation(s)
- Carolina G. de Castro
- Mucosal Immunology Lab, Institute of Biomedicine and Molecular Genetics (IBGM), University of Valladolid and Consejo Superior de Investigaciones Científicas (CSIC), Valladolid, Spain
| | - Alejandro G. del Hierro
- Mucosal Immunology Lab, Institute of Biomedicine and Molecular Genetics (IBGM), University of Valladolid and Consejo Superior de Investigaciones Científicas (CSIC), Valladolid, Spain
| | - Juan H-Vázquez
- Mucosal Immunology Lab, Institute of Biomedicine and Molecular Genetics (IBGM), University of Valladolid and Consejo Superior de Investigaciones Científicas (CSIC), Valladolid, Spain
| | - Sara Cuesta-Sancho
- Mucosal Immunology Lab, Institute of Biomedicine and Molecular Genetics (IBGM), University of Valladolid and Consejo Superior de Investigaciones Científicas (CSIC), Valladolid, Spain
| | - David Bernardo
- Mucosal Immunology Lab, Institute of Biomedicine and Molecular Genetics (IBGM), University of Valladolid and Consejo Superior de Investigaciones Científicas (CSIC), Valladolid, Spain
- Centro de Investigaciones Biomedicas en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
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7
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Reyes JGA, Ni D, Santner-Nanan B, Pinget GV, Kraftova L, Ashhurst TM, Marsh-Wakefield F, Wishart CL, Tan J, Hsu P, King NJC, Macia L, Nanan R. A unique human cord blood CD8 +CD45RA +CD27 +CD161 + T-cell subset identified by flow cytometric data analysis using Seurat. Immunology 2024. [PMID: 38798051 DOI: 10.1111/imm.13803] [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: 11/10/2023] [Accepted: 05/06/2024] [Indexed: 05/29/2024] Open
Abstract
Advances in single-cell level analytical techniques, especially cytometric approaches, have led to profound innovation in biomedical research, particularly in the field of clinical immunology. This has resulted in an expansion of high-dimensional data, posing great challenges for comprehensive and unbiased analysis. Conventional manual analysis is thus becoming untenable to handle these challenges. Furthermore, most newly developed computational methods lack flexibility and interoperability, hampering their accessibility and usability. Here, we adapted Seurat, an R package originally developed for single-cell RNA sequencing (scRNA-seq) analysis, for high-dimensional flow cytometric data analysis. Based on a 20-marker antibody panel and analyses of T-cell profiles in both adult blood and cord blood (CB), we showcased the robust capacity of Seurat in flow cytometric data analysis, which was further validated by Spectre, another high-dimensional cytometric data analysis package, and conventional manual analysis. Importantly, we identified a unique CD8+ T-cell population defined as CD8+CD45RA+CD27+CD161+ T cell that was predominantly present in CB. We characterised its IFN-γ-producing and potential cytotoxic properties using flow cytometry experiments and scRNA-seq analysis from a published dataset. Collectively, we identified a unique human CB CD8+CD45RA+CD27+CD161+ T-cell subset and demonstrated that Seurat, a widely used package for scRNA-seq analysis, possesses great potential to be repurposed for cytometric data analysis. This facilitates an unbiased and thorough interpretation of complicated high-dimensional data using a single analytical pipeline and opens a novel avenue for data-driven investigation in clinical immunology.
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Affiliation(s)
- Julen Gabirel Araneta Reyes
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- Nepean Hospital, Nepean Blue Mountains Local Health District, Penrith, New South Wales, Australia
- Nepean Clinical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Duan Ni
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- Nepean Hospital, Nepean Blue Mountains Local Health District, Penrith, New South Wales, Australia
- Nepean Clinical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Brigitte Santner-Nanan
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- Nepean Hospital, Nepean Blue Mountains Local Health District, Penrith, New South Wales, Australia
- Nepean Clinical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Gabriela Veronica Pinget
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- Nepean Clinical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Lucie Kraftova
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- Nepean Clinical School, The University of Sydney, Sydney, New South Wales, Australia
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic
| | - Thomas Myles Ashhurst
- Sydney Cytometry Core Research Facility, Charles Perkins Centre, The University of Sydney and Centenary Institute, Sydney, New South Wales, Australia
| | - Felix Marsh-Wakefield
- Liver Injury and Cancer Program, Centenary Institute, Sydney, New South Wales, Australia
- Human Cancer and Viral Immunology Laboratory, The University of Sydney, Sydney, New South Wales, Australia
| | - Claire Leana Wishart
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- Viral immunopathology Laboratory, Infection, Immunity and Inflammation Research Theme, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Ramaciotti Facility for Human System Biology, The University of Sydney and Centenary Institute, Sydney, New South Wales, Australia
| | - Jian Tan
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Peter Hsu
- Kids Research, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
- Discipline of Child and Adolescent Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Nicholas Jonathan Cole King
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- Sydney Cytometry Core Research Facility, Charles Perkins Centre, The University of Sydney and Centenary Institute, Sydney, New South Wales, Australia
- Viral immunopathology Laboratory, Infection, Immunity and Inflammation Research Theme, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Ramaciotti Facility for Human System Biology, The University of Sydney and Centenary Institute, Sydney, New South Wales, Australia
- The University of Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, New South Wales, Australia
- Sydney Nano, The University of Sydney, Sydney, New South Wales, Australia
| | - Laurence Macia
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- Sydney Cytometry Core Research Facility, Charles Perkins Centre, The University of Sydney and Centenary Institute, Sydney, New South Wales, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Ralph Nanan
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
- Nepean Hospital, Nepean Blue Mountains Local Health District, Penrith, New South Wales, Australia
- Nepean Clinical School, The University of Sydney, Sydney, New South Wales, Australia
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Hermansen JU, Yin Y, Rein ID, Skånland SS. Immunophenotyping with (phospho)protein profiling and fluorescent cell barcoding for single-cell signaling analysis and biomarker discovery. NPJ Precis Oncol 2024; 8:107. [PMID: 38769096 PMCID: PMC11106235 DOI: 10.1038/s41698-024-00604-y] [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: 11/03/2023] [Accepted: 05/08/2024] [Indexed: 05/22/2024] Open
Abstract
The microenvironment of hematologic cancers contributes to tumor cell survival and proliferation, as well as treatment resistance. Understanding tumor- and drug-induced changes to the immune cell composition and functionality is therefore critical for implementing optimal treatment strategies and for the development of novel cancer therapies. The liquid nature of peripheral blood makes this organ uniquely suited for single-cell studies by flow cytometry. (Phospho)protein profiles detected by flow cytometry analyses have been shown to correlate with ex vivo drug sensitivity and to predict treatment outcomes in hematologic cancers, demonstrating that this method is suitable for pre-clinical studies. Here, we present a flow cytometry protocol that combines multi-parameter immunophenotyping with single-cell (phospho)protein profiling. The protocol makes use of fluorescent cell barcoding, which means that multiple cell samples, either collected from different donors or exposed to different treatment conditions, can be combined and analyzed as one experiment. This reduces variability between samples, increases the throughput of the experiment, and lowers experimental costs. This protocol may serve as a guide for the use and further development of assays to study immunophenotype and cell signaling at single-cell resolution in normal and malignant cells. The read-outs may provide biological insight into cancer pathogenesis, identify novel drug targets, and ultimately serve as a biomarker to guide clinical decision-making.
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Affiliation(s)
- Johanne U Hermansen
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- K. G. Jebsen Centre for B Cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Yanping Yin
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- K. G. Jebsen Centre for B Cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Idun Dale Rein
- Department of Radiation Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Sigrid S Skånland
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.
- K. G. Jebsen Centre for B Cell Malignancies, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
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Astakhova EA, Morozov AA, Vavilova JD, Filatov AV. Antigenic Cartography of SARS-CoV-2. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:862-871. [PMID: 38880647 DOI: 10.1134/s0006297924050079] [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: 11/07/2023] [Revised: 01/14/2024] [Accepted: 01/17/2024] [Indexed: 06/18/2024]
Abstract
Antigenic cartography is a tool for interpreting and visualizing antigenic differences between virus variants based on virus neutralization data. This approach has been successfully used in the selection of influenza vaccine seed strains. With the emergence of SARS-CoV-2 variants escaping vaccine-induced antibody response, adjusting COVID-19 vaccines has become essential. This review provides information on the antigenic differences between SARS-CoV-2 variants revealed by antigenic cartography and explores a potential of antigenic cartography-based methods (e.g., building antibody landscapes and neutralization breadth gain plots) for the quantitative assessment of the breadth of the antibody response. Understanding the antigenic differences of SARS-CoV-2 and the possibilities of the formed humoral immunity aids in the prompt modification of preventative vaccines against COVID-19.
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Affiliation(s)
- Ekaterina A Astakhova
- National Research Center Institute of Immunology, Federal Medical Biological Agency of Russia, Moscow, 115522, Russia.
- Department of Immunology, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Alexey A Morozov
- National Research Center Institute of Immunology, Federal Medical Biological Agency of Russia, Moscow, 115522, Russia
- Department of Immunology, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Julia D Vavilova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Alexander V Filatov
- National Research Center Institute of Immunology, Federal Medical Biological Agency of Russia, Moscow, 115522, Russia
- Department of Immunology, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
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10
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Wang W, Yang L, Sun H, Peng X, Yuan J, Zhong W, Chen J, He X, Ye L, Zeng Y, Gao Z, Li Y, Qu X. Cellular nucleus image-based smarter microscope system for single cell analysis. Biosens Bioelectron 2024; 250:116052. [PMID: 38266616 DOI: 10.1016/j.bios.2024.116052] [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: 10/15/2023] [Revised: 12/31/2023] [Accepted: 01/18/2024] [Indexed: 01/26/2024]
Abstract
Cell imaging technology is undoubtedly a powerful tool for studying single-cell heterogeneity due to its non-invasive and visual advantages. It covers microscope hardware, software, and image analysis techniques, which are hindered by low throughput owing to abundant hands-on time and expertise. Herein, a cellular nucleus image-based smarter microscope system for single-cell analysis is reported to achieve high-throughput analysis and high-content detection of cells. By combining the hardware of an automatic fluorescence microscope and multi-object recognition/acquisition software, we have achieved more advanced process automation with the assistance of Robotic Process Automation (RPA), which realizes a high-throughput collection of single-cell images. Automated acquisition of single-cell images has benefits beyond ease and throughout and can lead to uniform standard and higher quality images. We further constructed a single-cell image database-based convolutional neural network (Efficient Convolutional Neural Network, E-CNN) exceeding 20618 single-cell nucleus images. Computational analysis of large and complex data sets enhances the content and efficiency of single-cell analysis with the assistance of Artificial Intelligence (AI), which breaks through the super-resolution microscope's hardware limitation, such as specialized light sources with specific wavelengths, advanced optical components, and high-performance graphics cards. Our system can identify single-cell nucleus images that cannot be artificially distinguished with an accuracy of 95.3%. Overall, we build an ordinary microscope into a high-throughput analysis and high-content smarter microscope system, making it a candidate tool for Imaging cytology.
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Affiliation(s)
- Wentao Wang
- Key Laboratory of Sensing Technology and Biomedical Instruments of Guangdong Province, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen, Guangdong Province, 518017, China
| | - Lin Yang
- Key Laboratory of Sensing Technology and Biomedical Instruments of Guangdong Province, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen, Guangdong Province, 518017, China
| | - Hang Sun
- Key Laboratory of Sensing Technology and Biomedical Instruments of Guangdong Province, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen, Guangdong Province, 518017, China
| | - Xiaohong Peng
- YueYang Central Hospital, YueYang, Hunan Province, 414000, China
| | - Junjie Yuan
- Key Laboratory of Sensing Technology and Biomedical Instruments of Guangdong Province, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen, Guangdong Province, 518017, China
| | - Wenhao Zhong
- Key Laboratory of Sensing Technology and Biomedical Instruments of Guangdong Province, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen, Guangdong Province, 518017, China
| | - Jinqi Chen
- Key Laboratory of Sensing Technology and Biomedical Instruments of Guangdong Province, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen, Guangdong Province, 518017, China
| | - Xin He
- Key Laboratory of Sensing Technology and Biomedical Instruments of Guangdong Province, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen, Guangdong Province, 518017, China
| | - Lingzhi Ye
- Key Laboratory of Sensing Technology and Biomedical Instruments of Guangdong Province, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen, Guangdong Province, 518017, China
| | - Yi Zeng
- College of Chemistry and Chemical Engineering, Huanggang Normal University, Huanggang, 438000, China
| | - Zhifan Gao
- Key Laboratory of Sensing Technology and Biomedical Instruments of Guangdong Province, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen, Guangdong Province, 518017, China.
| | - Yunhui Li
- Department of Laboratory Medical Center, General Hospital of Northern Theater Command, No.83, Wenhua Road, Shenhe District, Shenyang, Liaoning Province, 110016, China.
| | - Xiangmeng Qu
- Key Laboratory of Sensing Technology and Biomedical Instruments of Guangdong Province, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen, Guangdong Province, 518017, China.
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11
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Nollmann C, Moskorz W, Wimmenauer C, Jäger PS, Cadeddu RP, Timm J, Heinzel T, Haas R. Characterization of CD34 + Cells from Patients with Acute Myeloid Leukemia (AML) and Myelodysplastic Syndromes (MDS) Using a t-Distributed Stochastic Neighbor Embedding (t-SNE) Protocol. Cancers (Basel) 2024; 16:1320. [PMID: 38610998 PMCID: PMC11010974 DOI: 10.3390/cancers16071320] [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: 02/29/2024] [Revised: 03/26/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
Using multi-color flow cytometry analysis, we studied the immunophenotypical differences between leukemic cells from patients with AML/MDS and hematopoietic stem and progenitor cells (HSPCs) from patients in complete remission (CR) following their successful treatment. The panel of markers included CD34, CD38, CD45RA, CD123 as representatives for a hierarchical hematopoietic stem and progenitor cell (HSPC) classification as well as programmed death ligand 1 (PD-L1). Rather than restricting the evaluation on a 2- or 3-dimensional analysis, we applied a t-distributed stochastic neighbor embedding (t-SNE) approach to obtain deeper insight and segregation between leukemic cells and normal HPSCs. For that purpose, we created a t-SNE map, which resulted in the visualization of 27 cell clusters based on their similarity concerning the composition and intensity of antigen expression. Two of these clusters were "leukemia-related" containing a great proportion of CD34+/CD38- hematopoietic stem cells (HSCs) or CD34+ cells with a strong co-expression of CD45RA/CD123, respectively. CD34+ cells within the latter cluster were also highly positive for PD-L1 reflecting their immunosuppressive capacity. Beyond this proof of principle study, the inclusion of additional markers will be helpful to refine the differentiation between normal HSPCs and leukemic cells, particularly in the context of minimal disease detection and antigen-targeted therapeutic interventions. Furthermore, we suggest a protocol for the assignment of new cell ensembles in quantitative terms, via a numerical value, the Pearson coefficient, based on a similarity comparison of the t-SNE pattern with a reference.
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Affiliation(s)
- Cathrin Nollmann
- Condensed Matter Physics Laboratory, Heinrich-Heine-University, 40204 Düsseldorf, Germany; (C.N.)
| | - Wiebke Moskorz
- Institute of Virology, Heinrich-Heine-University, 40204 Düsseldorf, Germany (J.T.)
| | - Christian Wimmenauer
- Condensed Matter Physics Laboratory, Heinrich-Heine-University, 40204 Düsseldorf, Germany; (C.N.)
| | - Paul S. Jäger
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany; (P.S.J.)
| | - Ron P. Cadeddu
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany; (P.S.J.)
| | - Jörg Timm
- Institute of Virology, Heinrich-Heine-University, 40204 Düsseldorf, Germany (J.T.)
| | - Thomas Heinzel
- Condensed Matter Physics Laboratory, Heinrich-Heine-University, 40204 Düsseldorf, Germany; (C.N.)
| | - Rainer Haas
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany; (P.S.J.)
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12
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Peña FJ, Martín-Cano FE, Becerro-Rey L, Ortega-Ferrusola C, Gaitskell-Phillips G, da Silva-Álvarez E, Gil MC. The future of equine semen analysis. Reprod Fertil Dev 2024; 36:RD23212. [PMID: 38467450 DOI: 10.1071/rd23212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 02/15/2024] [Indexed: 03/13/2024] Open
Abstract
We are currently experiencing a period of rapid advancement in various areas of science and technology. The integration of high throughput 'omics' techniques with advanced biostatistics, and the help of artificial intelligence, is significantly impacting our understanding of sperm biology. These advances will have an appreciable impact on the practice of reproductive medicine in horses. This article provides a brief overview of recent advances in the field of spermatology and how they are changing assessment of sperm quality. This article is written from the authors' perspective, using the stallion as a model. We aim to portray a brief overview of the changes occurring in the assessment of sperm motility and kinematics, advances in flow cytometry, implementation of 'omics' technologies, and the use of artificial intelligence/self-learning in data analysis. We also briefly discuss how some of the advances can be readily available to the practitioner, through the implementation of 'on-farm' devices and telemedicine.
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Affiliation(s)
- Fernando J Peña
- Laboratory of Equine Reproduction and Equine Spermatology, Veterinary Teaching Hospital, University of Extremadura, Cáceres, Spain
| | - Francisco Eduardo Martín-Cano
- Laboratory of Equine Reproduction and Equine Spermatology, Veterinary Teaching Hospital, University of Extremadura, Cáceres, Spain
| | - Laura Becerro-Rey
- Laboratory of Equine Reproduction and Equine Spermatology, Veterinary Teaching Hospital, University of Extremadura, Cáceres, Spain
| | - Cristina Ortega-Ferrusola
- Laboratory of Equine Reproduction and Equine Spermatology, Veterinary Teaching Hospital, University of Extremadura, Cáceres, Spain
| | - Gemma Gaitskell-Phillips
- Laboratory of Equine Reproduction and Equine Spermatology, Veterinary Teaching Hospital, University of Extremadura, Cáceres, Spain
| | - Eva da Silva-Álvarez
- Laboratory of Equine Reproduction and Equine Spermatology, Veterinary Teaching Hospital, University of Extremadura, Cáceres, Spain
| | - María Cruz Gil
- Laboratory of Equine Reproduction and Equine Spermatology, Veterinary Teaching Hospital, University of Extremadura, Cáceres, Spain
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13
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Patel VJ, Joharapurkar A, Jain MR. The Perspective of Using Flow Cytometry for Unpuzzling Hypoxia-Inducible Factors Signalling. Drug Res (Stuttg) 2024; 74:113-122. [PMID: 38350634 DOI: 10.1055/a-2248-9180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
Hypoxia-inducible factors (HIFs) are transcription factors that are responsible for adapting to the changes in oxygen levels in the cellular environment. HIF activity determines the expression of cellular proteins that control the development and physiology of the cells and pathophysiology of a disease. Understanding the role of specific HIF (HIF-1-3) in cellular function is essential for development of the HIF-targeted therapies. In this review, we have discussed the use of flow cytometry in analysing HIF function in cells. Proper understanding of HIF-signalling will help to design pharmacological interventions HIF-mediated therapy. We have discussed the role of HIF-signalling in various diseases such as cancer, renal and liver diseases, ulcerative colitis, arthritis, diabetes and diabetic complications, psoriasis, and wound healing. We have also discussed protocols that help to decipher the role of HIFs in these diseases that would eventually help to design promising therapies.
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Affiliation(s)
- Vishal J Patel
- Department of Pharmacology and Toxicology, Zydus Research Centre, Zydus Lifesciences Limited, Moraiya, Ahmedabad, India
| | - Amit Joharapurkar
- Department of Pharmacology and Toxicology, Zydus Research Centre, Zydus Lifesciences Limited, Moraiya, Ahmedabad, India
| | - Mukul R Jain
- Department of Pharmacology and Toxicology, Zydus Research Centre, Zydus Lifesciences Limited, Moraiya, Ahmedabad, India
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14
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Tettero JM, Heidinga ME, Mocking TR, Fransen G, Kelder A, Scholten WJ, Snel AN, Ngai LL, Bachas C, van de Loosdrecht AA, Ossenkoppele GJ, de Leeuw DC, Cloos J, Janssen JJWM. Impact of hemodilution on flow cytometry based measurable residual disease assessment in acute myeloid leukemia. Leukemia 2024; 38:630-639. [PMID: 38272991 PMCID: PMC10912027 DOI: 10.1038/s41375-024-02158-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 01/08/2024] [Accepted: 01/12/2024] [Indexed: 01/27/2024]
Abstract
Measurable residual disease (MRD) measured in the bone marrow (BM) of acute myeloid leukemia (AML) patients after induction chemotherapy is an established prognostic factor. Hemodilution, stemming from peripheral blood (PB) mixing within BM during aspiration, can yield false-negative MRD results. We prospectively examined hemodilution by measuring MRD in BM aspirates obtained from three consecutive 2 mL pulls, along with PB samples. Our results demonstrated a significant decrease in MRD percentages between the first and second pulls (P = 0.025) and between the second and third pulls (P = 0.025), highlighting the impact of hemodilution. Initially, 39% of MRD levels (18/46 leukemia-associated immunophenotypes) exceeded the 0.1% cut-off, decreasing to 30% (14/46) in the third pull. Additionally, we assessed the performance of six published methods and parameters for distinguishing BM from PB samples, addressing or compensating for hemodilution. The most promising results relied on the percentages of CD16dim granulocytic population (scarce in BM) and CD117high mast cells (exclusive to BM). Our findings highlight the importance of estimating hemodilution in MRD assessment to qualify MRD results, particularly near the common 0.1% cut-off. To avoid false-negative results by hemodilution, it is essential to collect high-quality BM aspirations and preferably utilizing the initial pull for MRD testing.
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Affiliation(s)
- Jesse M Tettero
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Hematology, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Maaike E Heidinga
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Hematology, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Tim R Mocking
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Hematology, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Glenn Fransen
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Hematology, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Angèle Kelder
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Hematology, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Willemijn J Scholten
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Hematology, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Alexander N Snel
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Hematology, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Lok Lam Ngai
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Hematology, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Costa Bachas
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Hematology, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Arjan A van de Loosdrecht
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Hematology, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Gert J Ossenkoppele
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Hematology, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - David C de Leeuw
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Hematology, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Jacqueline Cloos
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Hematology, Amsterdam, The Netherlands.
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands.
| | - Jeroen J W M Janssen
- Department of Hematology, Radboud University Medical Center, Nijmegen, The Netherlands
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15
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Hauchamps P, Bayat B, Delandre S, Hamrouni M, Toussaint M, Temmerman S, Lin D, Gatto L. CytoPipeline and CytoPipelineGUI: a Bioconductor R package suite for building and visualizing automated pre-processing pipelines for flow cytometry data. BMC Bioinformatics 2024; 25:80. [PMID: 38378440 PMCID: PMC10877884 DOI: 10.1186/s12859-024-05691-z] [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: 11/10/2023] [Accepted: 02/02/2024] [Indexed: 02/22/2024] Open
Abstract
BACKGROUND With the increase of the dimensionality in flow cytometry data over the past years, there is a growing need to replace or complement traditional manual analysis (i.e. iterative 2D gating) with automated data analysis pipelines. A crucial part of these pipelines consists of pre-processing and applying quality control filtering to the raw data, in order to use high quality events in the downstream analyses. This part can in turn be split into a number of elementary steps: signal compensation or unmixing, scale transformation, debris, doublets and dead cells removal, batch effect correction, etc. However, assembling and assessing the pre-processing part can be challenging for a number of reasons. First, each of the involved elementary steps can be implemented using various methods and R packages. Second, the order of the steps can have an impact on the downstream analysis results. Finally, each method typically comes with its specific, non standardized diagnostic and visualizations, making objective comparison difficult for the end user. RESULTS Here, we present CytoPipeline and CytoPipelineGUI, two R packages to build, compare and assess pre-processing pipelines for flow cytometry data. To exemplify these new tools, we present the steps involved in designing a pre-processing pipeline on a real life dataset and demonstrate different visual assessment use cases. We also set up a benchmarking comparing two pre-processing pipelines differing by their quality control methods, and show how the package visualization utilities can provide crucial user insight into the obtained benchmark metrics. CONCLUSION CytoPipeline and CytoPipelineGUI are two Bioconductor R packages that help building, visualizing and assessing pre-processing pipelines for flow cytometry data. They increase productivity during pipeline development and testing, and complement benchmarking tools, by providing user intuitive insight into benchmarking results.
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Affiliation(s)
- Philippe Hauchamps
- Computational Biology and Bioinformatics, de duve Institute, UCLouvain, Brussels, Belgium
| | | | | | | | | | | | | | - Laurent Gatto
- Computational Biology and Bioinformatics, de duve Institute, UCLouvain, Brussels, Belgium.
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16
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Beckers L, Baeten P, Popescu V, Swinnen D, Cardilli A, Hamad I, Van Wijmeersch B, Tavernier SJ, Kleinewietfeld M, Broux B, Fraussen J, Somers V. Alterations in the innate and adaptive immune system in a real-world cohort of multiple sclerosis patients treated with ocrelizumab. Clin Immunol 2024; 259:109894. [PMID: 38185268 DOI: 10.1016/j.clim.2024.109894] [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: 10/18/2023] [Revised: 12/22/2023] [Accepted: 01/03/2024] [Indexed: 01/09/2024]
Abstract
B cell depletion by the anti-CD20 antibody ocrelizumab is effective in relapsing-remitting (RR) and primary progressive (PP) multiple sclerosis (MS). We investigated immunological changes in peripheral blood of a real-world MS cohort after 6 and 12 months of ocrelizumab. All RRMS and most PPMS patients (15/20) showed treatment response. Ocrelizumab not only reduced CD20+ B cells, but also numbers of CD20+ T cells. Absolute numbers of monocytes, dendritic cells and CD8+ T cells were increased, while CD56hi natural killer cells were reduced after ocrelizumab. The residual B cell population shifted towards transitional and activated, IgA+ switched memory B cells, double negative B cells, and antibody-secreting cells. Delaying the treatment interval by 2-3 months increased mean B cell frequencies and enhanced naive B cell repopulation. Ocrelizumab reduced plasma levels of interleukin(IL)-12p70 and interferon(IFN)-α2. These findings will contribute to understanding ineffective treatment responses, dealing with life-threatening infections and further unravelling MS pathogenesis.
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Affiliation(s)
- L Beckers
- University MS Center (UMSC), Hasselt-Pelt, Hasselt, Belgium; Department of Immunology and Infection, Biomedical Research Institute, Hasselt University, Hasselt, Belgium
| | - P Baeten
- University MS Center (UMSC), Hasselt-Pelt, Hasselt, Belgium; Department of Immunology and Infection, Biomedical Research Institute, Hasselt University, Hasselt, Belgium
| | - V Popescu
- University MS Center (UMSC), Hasselt-Pelt, Hasselt, Belgium; Department of Immunology and Infection, Biomedical Research Institute, Hasselt University, Hasselt, Belgium; Noorderhart, Rehabilitation and MS Center, Pelt, Belgium
| | - D Swinnen
- University MS Center (UMSC), Hasselt-Pelt, Hasselt, Belgium; Department of Immunology and Infection, Biomedical Research Institute, Hasselt University, Hasselt, Belgium; VIB Laboratory of Translational Immunomodulation, Center for Inflammation Research (IRC), Diepenbeek, Belgium
| | - A Cardilli
- University MS Center (UMSC), Hasselt-Pelt, Hasselt, Belgium; Department of Immunology and Infection, Biomedical Research Institute, Hasselt University, Hasselt, Belgium; VIB Laboratory of Translational Immunomodulation, Center for Inflammation Research (IRC), Diepenbeek, Belgium
| | - I Hamad
- University MS Center (UMSC), Hasselt-Pelt, Hasselt, Belgium; Department of Immunology and Infection, Biomedical Research Institute, Hasselt University, Hasselt, Belgium; VIB Laboratory of Translational Immunomodulation, Center for Inflammation Research (IRC), Diepenbeek, Belgium
| | - B Van Wijmeersch
- University MS Center (UMSC), Hasselt-Pelt, Hasselt, Belgium; Department of Immunology and Infection, Biomedical Research Institute, Hasselt University, Hasselt, Belgium; Noorderhart, Rehabilitation and MS Center, Pelt, Belgium
| | - S J Tavernier
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium; Unit of Molecular Signal Transduction in Inflammation, VIB-UGent Center for Inflammation Research (IRC), Ghent, Belgium
| | - M Kleinewietfeld
- University MS Center (UMSC), Hasselt-Pelt, Hasselt, Belgium; Department of Immunology and Infection, Biomedical Research Institute, Hasselt University, Hasselt, Belgium; VIB Laboratory of Translational Immunomodulation, Center for Inflammation Research (IRC), Diepenbeek, Belgium
| | - B Broux
- University MS Center (UMSC), Hasselt-Pelt, Hasselt, Belgium; Department of Immunology and Infection, Biomedical Research Institute, Hasselt University, Hasselt, Belgium
| | - J Fraussen
- University MS Center (UMSC), Hasselt-Pelt, Hasselt, Belgium; Department of Immunology and Infection, Biomedical Research Institute, Hasselt University, Hasselt, Belgium
| | - V Somers
- University MS Center (UMSC), Hasselt-Pelt, Hasselt, Belgium; Department of Immunology and Infection, Biomedical Research Institute, Hasselt University, Hasselt, Belgium.
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17
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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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18
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Reuschlé Q, Van Heddegem L, Bosteels V, Moncan M, Depauw S, Wadier N, Maréchal S, De Nolf C, Delgado V, Messai Y, Stolzenberg MC, Magérus A, Werck A, Olagne J, Li Q, Lefevre G, Korganow AS, Rieux-Laucat F, Janssens S, Soulas-Sprauel P. Loss of function of XBP1 splicing activity of IRE1α favors B cell tolerance breakdown. J Autoimmun 2024; 142:103152. [PMID: 38071801 DOI: 10.1016/j.jaut.2023.103152] [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: 07/06/2023] [Revised: 10/27/2023] [Accepted: 11/20/2023] [Indexed: 03/23/2024]
Abstract
Anti-nuclear antibodies are the hallmark of autoimmune diseases such as systemic lupus erythematosus (SLE) and scleroderma. However, the molecular mechanisms of B cell tolerance breakdown in these pathological contexts are poorly known. The study of rare familial forms of autoimmune diseases could therefore help to better describe common biological mechanisms leading to B cell tolerance breakdown. By Whole-Exome Sequencing, we identified a new heterozygous mutation (p.R594C) in ERN1 gene, encoding IRE1α (Inositol-Requiring Enzyme 1α), in a multiplex family with several members presenting autoantibody-mediated autoimmunity. Using human cell lines and a knock-in (KI) transgenic mouse model, we showed that this mutation led to a profound defect of IRE1α ribonuclease activity on X-Box Binding Protein 1 (XBP1) splicing. The KI mice developed a broad panel of autoantibodies, however in a subclinical manner. These results suggest that a decrease of spliced form of XBP1 (XBP1s) production could contribute to B cell tolerance breakdown and give new insights into the function of IRE1α which are important to consider for the development of IRE1α targeting strategies.
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Affiliation(s)
- Quentin Reuschlé
- Laboratoire d'ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, F-67000, Strasbourg, France; Strasbourg University, Faculty of Pharmacy and Faculty of Medicine, Strasbourg, France; Arthritis R&D, Neuilly sur Seine, France
| | - Laurien Van Heddegem
- Laboratory for ER Stress and Inflammation, VIB Center for Inflammation Research, Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Victor Bosteels
- Laboratory for ER Stress and Inflammation, VIB Center for Inflammation Research, Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Matthieu Moncan
- Université Paris Cité, Laboratoire d'immunogénétique des maladies auto-immunes pédiatriques, Institut Imagine, INSERM UMR_S1163, Paris, France
| | - Sabine Depauw
- Laboratoire d'ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, F-67000, Strasbourg, France; Strasbourg University, Faculty of Pharmacy and Faculty of Medicine, Strasbourg, France
| | - Nadège Wadier
- Laboratoire d'ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, F-67000, Strasbourg, France; Strasbourg University, Faculty of Pharmacy and Faculty of Medicine, Strasbourg, France
| | - Sandra Maréchal
- Laboratory for ER Stress and Inflammation, VIB Center for Inflammation Research, Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Clint De Nolf
- Laboratory for ER Stress and Inflammation, VIB Center for Inflammation Research, Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium; Barriers in Inflammation, VIB Center for Inflammation Research, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Virginia Delgado
- Laboratoire d'ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, F-67000, Strasbourg, France; Strasbourg University, Faculty of Pharmacy and Faculty of Medicine, Strasbourg, France
| | | | - Marie-Claude Stolzenberg
- Université Paris Cité, Laboratoire d'immunogénétique des maladies auto-immunes pédiatriques, Institut Imagine, INSERM UMR_S1163, Paris, France
| | - Aude Magérus
- Université Paris Cité, Laboratoire d'immunogénétique des maladies auto-immunes pédiatriques, Institut Imagine, INSERM UMR_S1163, Paris, France
| | - Angélique Werck
- Department of Pathology, University Hospital, Strasbourg, France
| | - Jérôme Olagne
- Department of Pathology, University Hospital, Strasbourg, France; Department of Adult Nephrology, University Hospital, Strasbourg, France
| | - Quan Li
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Guillaume Lefevre
- Inserm, U1286 - INFINITE - Institute for Translational Research in Inflammation, University of Lille, CHU Lille, Lille, France
| | - Anne-Sophie Korganow
- Laboratoire d'ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, F-67000, Strasbourg, France; Strasbourg University, Faculty of Pharmacy and Faculty of Medicine, Strasbourg, France; Department of Clinical Immunology and Internal Medicine, National Reference Center for Systemic Autoimmune Diseases (CNR RESO), Tertiary Center for Primary Immunodeficiency, Strasbourg University Hospital, F-67000, Strasbourg, France
| | - Frédéric Rieux-Laucat
- Université Paris Cité, Laboratoire d'immunogénétique des maladies auto-immunes pédiatriques, Institut Imagine, INSERM UMR_S1163, Paris, France
| | - Sophie Janssens
- Laboratory for ER Stress and Inflammation, VIB Center for Inflammation Research, Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Pauline Soulas-Sprauel
- Laboratoire d'ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, F-67000, Strasbourg, France; Strasbourg University, Faculty of Pharmacy and Faculty of Medicine, Strasbourg, France; Department of Clinical Immunology and Internal Medicine, National Reference Center for Systemic Autoimmune Diseases (CNR RESO), Tertiary Center for Primary Immunodeficiency, Strasbourg University Hospital, F-67000, Strasbourg, France.
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19
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Yang Y, Alves T, Miao M, Wu Y, Li G, Lou J, Hasturk H, Van Dyke T, Kantarci A, Wu D. Single-Cell Transcriptomic Analysis of Dental Pulp and Periodontal Ligament Stem Cells. J Dent Res 2024; 103:71-80. [PMID: 37982164 PMCID: PMC10850875 DOI: 10.1177/00220345231205283] [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: 11/21/2023] Open
Abstract
The regeneration of periodontal, periapical, and pulpal tissues is a complex process requiring the direct involvement of cells derived from pluripotent stem cells in the periodontal ligament and dental pulp. Dental pulp stem cells (DPSCs) and periodontal ligament stem cells (PDLSCs) are spatially distinct with the potential to differentiate into similar functional and phenotypic cells. We aimed to identify the cell heterogeneity of DPSCs and PDLSCs and explore the differentiation potentials of their specialized organ-specific functions using single-cell transcriptomic analysis. Our results revealed 7 distinct clusters, with cluster 3 showing the highest potential for differentiation. Clusters 0 to 2 displayed features similar to fibroblasts. The trajectory route of the cell state transition from cluster 3 to clusters 0, 1, and 2 indicated the distinct nature of cell differentiation. PDLSCs had a higher proportion of cells (78.6%) at the G1 phase, while DPSCs had a higher proportion of cells at the S and G2/M phases (36.1%), mirroring the lower cell proliferation capacity of PDLSCs than DPSCs. Our study suggested the heterogeneity of stemness across PDLSCs and DPSCs, the similarities of these 2 stem cell compartments to be potentially integrated for regenerative strategies, and the distinct features between them potentially particularized for organ-specific functions of the dental pulp and periodontal ligament for a targeted regenerative dental tissue repair and other regeneration therapies.
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Affiliation(s)
- Y. Yang
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - T. Alves
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - M.Z. Miao
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Thurston Arthritis Research Center, Division of Rheumatology, Allergy, and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Cell Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Y.C. Wu
- The Forsyth Institute, Cambridge, MA, USA
| | - G. Li
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- eScience Institute, University of Washington, Seattle, WA, USA
| | - J. Lou
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - H. Hasturk
- The Forsyth Institute, Cambridge, MA, USA
| | | | | | - D. Wu
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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20
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Önen S, Gizer M, Korkusuz P. Flow Cytometric and Immunohistochemical Follow-Up of Spermatogonial Lineage Commitment. Methods Mol Biol 2024; 2849:239-251. [PMID: 37801256 DOI: 10.1007/7651_2023_506] [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: 10/07/2023]
Abstract
Flow cytometry and immunohistochemistry techniques both determine the target protein by immunolabeling. Flow cytometric analysis quantifies total number of fluorescent labeled cells and qualify sup-populations according to size and granularity. Immunohistochemistry is able to map immune-labeled cells and extracellular matrix components under light and electron microscope by enzyme or fluorescent molecules. Real-time identification, in-time classification, and final plotting of spermatogonial lineage are of crucial importance for monitoring the fertility potential of spermatogonial stem cell microenvironment and predicting progress of spermatogenesis. Here we define the evaluation of mouse male germ cell microenvironment at single cell and whole tissue section levels by using flow cytometric and immunohistochemical approaches.
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Affiliation(s)
| | - Merve Gizer
- METU MEMS Center, Ankara, Turkey
- Department of Stem Cell Sciences, Graduate School of Health Sciences, Hacettepe University, Ankara, Turkey
| | - Petek Korkusuz
- METU MEMS Center, Ankara, Turkey.
- Department of Histology and Embryology, Faculty of Medicine, Hacettepe University, Ankara, Turkey.
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21
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Villegas-Valverde CA, Bencomo-Hernandez AA, Castillo-Aleman YM, Ventura-Carmenate Y, Casado-Hernandez I, Rivero-Jimenez RA. Application of mass cytometry to characterize hematopoietic stem cells in apheresis products of patients with hematological malignancies. Hematol Transfus Cell Ther 2023:S2531-1379(23)02600-7. [PMID: 38177056 DOI: 10.1016/j.htct.2023.10.008] [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: 05/04/2023] [Revised: 07/25/2023] [Accepted: 10/20/2023] [Indexed: 01/06/2024] Open
Abstract
INTRODUCTION Hematopoietic stem cell transplantation (HSCT) is a widely used therapy, but its success largely depends on the number and quality of stem cells collected. Current evidence shows the complexity of the hematopoietic system, which implies that, in the quality assurance of the apheresis product, the hematopoietic stem cells are adequately characterized and quantified, in which mass cytometry (MC) can provide its advantages in high-dimensional analysis. OBJECTIVE This research aimed to characterize and enumerate CD45dim/CD34+ stem cells using the MC in apheresis product yields from patients with chronic lymphoid malignant diseases undergoing autologous transplantation at the Abu Dhabi Stem Cells Center. METHODS An analytical and cross-sectional study was performed on 31 apheresis products from 15 patients diagnosed with multiple myeloma (n = 9) and non-Hodgkin lymphomas (n = 6) eligible for HSCT. The MC was employed using the MaxPar Kit for stem cell immunophenotyping. The analysis was performed manually in the Kaluza and unsupervised by machine learning in Cytobank Premium. RESULTS An excellent agreement was found between mass and flow cytometry for the relative and absolute counts of CD45dim/CD34+ cells (Bland-Altman bias: -0.029 and -64, respectively), seven subpopulations were phenotyped and no lineage bias was detected for any of the methods used in the pool of collected cells. A CD34+/CD38+/CD138+ population was seen in the analyses performed on four patients with multiple myeloma. CONCLUSIONS The MC helps to characterize subpopulations of stem cells in apheresis products. It also allows cell quantification by double platform. Unsupervised analysis allows results completion and validation of the manual strategy. The proposed methodology can be extended to apheresis products for purposes other than HSCT.
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22
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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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23
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Gravano DM, Rieger AM, Nettenstrom L, Hall C, Ferrer-Font L. Shared resource lab (SRL) strategies for supporting high-dimensional cytometry data analysis. Cytometry A 2023; 103:947-952. [PMID: 37800362 DOI: 10.1002/cyto.a.24800] [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: 05/09/2023] [Revised: 09/08/2023] [Accepted: 09/18/2023] [Indexed: 10/07/2023]
Abstract
With the increase in the number of parameters that can be detected at the single-cell level using flow and mass cytometry, there has been a paradigm shift when handling and analyzing data sets. Cytometry Shared Resource Laboratories (SRLs) already take on the responsibility of ensuring users have resources and training in experimental design and operation of instruments to promote high-quality data acquisition. However, the role of SRLs downstream, during data handling and analysis, is not as well defined and agreed upon. Best practices dictate a central role for SRLs in this process as they are in a pivotal position to support research in this context, but key considerations about how to effectively fill this role need to be addressed. Two surveys and one workshop at CYTO 2022 in Philadelphia, PA, were performed to gain insight into what strategies SRLs are successfully employing to support high-dimensional data analysis and where SRLs and their users see limitations and long-term challenges in this area. Recommendations for high-dimensional data analysis support provided by SRLs will be offered and discussed.
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Affiliation(s)
- David M Gravano
- Stem Cell Instrumentation Foundry, University of California Merced, Merced, California, USA
| | - Aja M Rieger
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | | | | | - Laura Ferrer-Font
- Medical and scientific affairs, BD Biosciences, La Jolla, California, USA
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24
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Shetab Boushehri S, Essig K, Chlis NK, Herter S, Bacac M, Theis FJ, Glasmacher E, Marr C, Schmich F. Explainable machine learning for profiling the immunological synapse and functional characterization of therapeutic antibodies. Nat Commun 2023; 14:7888. [PMID: 38036503 PMCID: PMC10689847 DOI: 10.1038/s41467-023-43429-2] [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: 11/08/2022] [Accepted: 11/09/2023] [Indexed: 12/02/2023] Open
Abstract
Therapeutic antibodies are widely used to treat severe diseases. Most of them alter immune cells and act within the immunological synapse; an essential cell-to-cell interaction to direct the humoral immune response. Although many antibody designs are generated and evaluated, a high-throughput tool for systematic antibody characterization and prediction of function is lacking. Here, we introduce the first comprehensive open-source framework, scifAI (single-cell imaging flow cytometry AI), for preprocessing, feature engineering, and explainable, predictive machine learning on imaging flow cytometry (IFC) data. Additionally, we generate the largest publicly available IFC dataset of the human immunological synapse containing over 2.8 million images. Using scifAI, we analyze class frequency and morphological changes under different immune stimulation. T cell cytokine production across multiple donors and therapeutic antibodies is quantitatively predicted in vitro, linking morphological features with function and demonstrating the potential to significantly impact antibody design. scifAI is universally applicable to IFC data. Given its modular architecture, it is straightforward to incorporate into existing workflows and analysis pipelines, e.g., for rapid antibody screening and functional characterization.
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Affiliation(s)
- Sayedali Shetab Boushehri
- Institute of AI for Health, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Technical University of Munich, Department of Mathematics, Munich, Germany
- Data & Analytics (D&A), Roche Pharma Research and Early Development (pRED), Roche Innovation Center Munich, Munich, Germany
| | - Katharina Essig
- Large Molecule Research (LMR), Roche Pharma Research and Early Development (pRED), Roche Innovation Center Munich, Munich, Germany
| | - Nikolaos-Kosmas Chlis
- Large Molecule Research (LMR), Roche Pharma Research and Early Development (pRED), Roche Innovation Center Munich, Munich, Germany
| | - Sylvia Herter
- Roche Innovation Center Zurich, Roche Pharma Research and Early Development (pRED), Zurich, Switzerland
| | - Marina Bacac
- Roche Innovation Center Zurich, Roche Pharma Research and Early Development (pRED), Zurich, Switzerland
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Technical University of Munich, Department of Mathematics, Munich, Germany
| | - Elke Glasmacher
- Research and Early Development (RED), Roche Diagnostics Solutions, Roche Innovation Center Munich, Munich, Germany.
| | - Carsten Marr
- Institute of AI for Health, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.
| | - Fabian Schmich
- Data & Analytics (D&A), Roche Pharma Research and Early Development (pRED), Roche Innovation Center Munich, Munich, Germany.
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25
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Na S, Choo Y, Yoon TH, Paek E. CyGate Provides a Robust Solution for Automatic Gating of Single Cell Cytometry Data. Anal Chem 2023; 95:16918-16926. [PMID: 37946317 PMCID: PMC10666088 DOI: 10.1021/acs.analchem.3c03006] [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: 07/10/2023] [Revised: 10/12/2023] [Accepted: 10/23/2023] [Indexed: 11/12/2023]
Abstract
To gain a better understanding of the complex human immune system, it is necessary to measure and interpret numerous cellular protein expressions at the single cell level. Mass cytometry is a relatively new technology that offers unprecedented information about the protein expression of a single cell. Conversely, the analysis of high-dimensional and multiparametric mass cytometric data sets presents a new computational challenge. For instance, conventional "manual gating" analysis was inefficient and unreliable for multiparametric phenotyping of the heterogeneous immune cellular system; consequently, automated methods have been developed to address the high dimensionality of mass cytometry data and enhance the reproducibility of the analysis. Here, we present CyGate, a semiautomated method for classifying single cells into their respective cell types. CyGate learns a gating strategy from a reference data set, trains a model for cell classification, and then automatically analyzes additional data sets using the trained model. CyGate also supports the machine learning framework for the classification of "ungated" cells, which are typically disregarded by automated methods. CyGate's utility was demonstrated by its high performance in cell type classification and the lowest generalization error on various public data sets when compared to the state-of-the-art semiautomated methods. Notably, CyGate had the shortest execution time, allowing it to scale with a growing number of samples. CyGate is available at https://github.com/seungjinna/cygate.
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Affiliation(s)
- Seungjin Na
- Institute
for Artificial Intelligence Research, Hanyang
University, Seoul 04763, Republic
of Korea
- Department
of Computer Science, Hanyang University, Seoul 04763, Republic of Korea
| | - Yujin Choo
- Department
of Artificial Intelligence, Hanyang University, Seoul 04763, Republic of Korea
| | - Tae Hyun Yoon
- Department
of Chemistry, College of Natural Sciences, Hanyang University, Seoul 04763, Republic
of Korea
- Institute
of Next Generation Material Design, Hanyang
University, Seoul 04763, Republic of Korea
- Yoon
Idea
Lab Co., Ltd., Seoul 04763, Republic of Korea
| | - Eunok Paek
- Institute
for Artificial Intelligence Research, Hanyang
University, Seoul 04763, Republic
of Korea
- Department
of Computer Science, Hanyang University, Seoul 04763, Republic of Korea
- Department
of Artificial Intelligence, Hanyang University, Seoul 04763, Republic of Korea
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26
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Tangherloni A, Riva SG, Myers B, Buffa FM, Cazzaniga P. MAGNETO: Cell type marker panel generator from single-cell transcriptomic data. J Biomed Inform 2023; 147:104510. [PMID: 37797704 DOI: 10.1016/j.jbi.2023.104510] [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: 02/28/2023] [Revised: 09/12/2023] [Accepted: 09/29/2023] [Indexed: 10/07/2023]
Abstract
Single-cell RNA sequencing experiments produce data useful to identify different cell types, including uncharacterized and rare ones. This enables us to study the specific functional roles of these cells in different microenvironments and contexts. After identifying a (novel) cell type of interest, it is essential to build succinct marker panels, composed of a few genes referring to cell surface proteins and clusters of differentiation molecules, able to discriminate the desired cells from the other cell populations. In this work, we propose a fully-automatic framework called MAGNETO, which can help construct optimal marker panels starting from a single-cell gene expression matrix and a cell type identity for each cell. MAGNETO builds effective marker panels solving a tailored bi-objective optimization problem, where the first objective regards the identification of the genes able to isolate a specific cell type, while the second conflicting objective concerns the minimization of the total number of genes included in the panel. Our results on three public datasets show that MAGNETO can identify marker panels that identify the cell populations of interest better than state-of-the-art approaches. Finally, by fine-tuning MAGNETO, our results demonstrate that it is possible to obtain marker panels with different specificity levels.
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Affiliation(s)
- Andrea Tangherloni
- Department of Computing Sciences, Bocconi University, Via Guglielmo Röntgen 1, Milan, 20136, Italy; Bocconi Institute for Data Science and Analytics, Bocconi University, Via Guglielmo Röntgen 1, Milan, 20136, Italy; Department of Human and Social Sciences, University of Bergamo, Piazzale S. Agostino 2, Bergamo, 24129, Italy.
| | - Simone G Riva
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, United Kingdom
| | - Brynelle Myers
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, United Kingdom
| | - Francesca M Buffa
- Department of Computing Sciences, Bocconi University, Via Guglielmo Röntgen 1, Milan, 20136, Italy; Bocconi Institute for Data Science and Analytics, Bocconi University, Via Guglielmo Röntgen 1, Milan, 20136, Italy; Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, United Kingdom
| | - Paolo Cazzaniga
- Department of Human and Social Sciences, University of Bergamo, Piazzale S. Agostino 2, Bergamo, 24129, Italy; Bicocca Bioinformatics, Biostatistics, and Bioimaging Centre - B4, Via Follereau 3, Vedano al Lambro, 20854, Italy
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27
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Liechti T, Van Gassen S, Beddall M, Ballard R, Iftikhar Y, Du R, Venkataraman T, Novak D, Mangino M, Perfetto S, Larman HB, Spector T, Saeys Y, Roederer M. A robust pipeline for high-content, high-throughput immunophenotyping reveals age- and genetics-dependent changes in blood leukocytes. CELL REPORTS METHODS 2023; 3:100619. [PMID: 37883924 PMCID: PMC10626267 DOI: 10.1016/j.crmeth.2023.100619] [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: 09/20/2022] [Revised: 05/29/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023]
Abstract
High-dimensional flow cytometry is the gold standard to study the human immune system in large cohorts. However, large sample sizes increase inter-experimental variation because of technical and experimental inaccuracies introduced by batch variability. Our high-throughput sample processing pipeline in combination with 28-color flow cytometry focuses on increased throughput (192 samples/experiment) and high reproducibility. We implemented quality control checkpoints to reduce technical and experimental variation. Finally, we integrated FlowSOM clustering to facilitate automated data analysis and demonstrate the reproducibility of our pipeline in a study with 3,357 samples. We reveal age-associated immune dynamics in 2,300 individuals, signified by decreasing T and B cell subsets with age. In addition, by combining genetic analyses, our approach revealed unique immune signatures associated with a single nucleotide polymorphism (SNP) that abrogates CD45 isoform splicing. In summary, we provide a versatile and reliable high-throughput, flow cytometry-based pipeline for immune discovery and exploration in large cohorts.
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Affiliation(s)
- Thomas Liechti
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA.
| | - Sofie Van Gassen
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium; Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Margaret Beddall
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA
| | - Reid Ballard
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA
| | - Yaser Iftikhar
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA
| | - Renguang Du
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA
| | - Thiagarajan Venkataraman
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - David Novak
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium; Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Massimo Mangino
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK; National Heart and Lung Institute, Cardiovascular Science Division, Imperial College London, London, UK
| | - Stephen Perfetto
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA
| | - H Benjamin Larman
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Tim Spector
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Yvan Saeys
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium; Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Mario Roederer
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA.
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28
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de Graaf JF, Arens R. Immunophenotyping beyond the limits of time. CELL REPORTS METHODS 2023; 3:100612. [PMID: 37883923 PMCID: PMC10626202 DOI: 10.1016/j.crmeth.2023.100612] [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: 09/14/2023] [Revised: 09/20/2023] [Accepted: 09/20/2023] [Indexed: 10/28/2023]
Abstract
Immunophenotyping is a powerful approach for deciphering responses of the immune system to drug screening and immunotherapy. In this issue of Cell Report Methods, Liechti et al. have advanced this approach by developing a pipeline, which allows high-throughput but still accurate single-cell immunophenotyping in time.
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Affiliation(s)
- J Fréderique de Graaf
- Department of Immunology, Leiden University Medical Center, 2333ZA Leiden, the Netherlands
| | - Ramon Arens
- Department of Immunology, Leiden University Medical Center, 2333ZA Leiden, the Netherlands.
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29
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Delgado AH, Fluxa R, Perez-Andres M, Diks AM, van Gaans-van den Brink JAM, Barkoff AM, Blanco E, Torres-Valle A, Berkowska MA, Grigore G, van Dongen J.J.M, Orfao A. Automated EuroFlow approach for standardized in-depth dissection of human circulating B-cells and plasma cells. Front Immunol 2023; 14:1268686. [PMID: 37915569 PMCID: PMC10616957 DOI: 10.3389/fimmu.2023.1268686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/29/2023] [Indexed: 11/03/2023] Open
Abstract
Background Multiparameter flow cytometry (FC) immunophenotyping is a key tool for detailed identification and characterization of human blood leucocytes, including B-lymphocytes and plasma cells (PC). However, currently used conventional data analysis strategies require extensive expertise, are time consuming, and show limited reproducibility. Objective Here, we designed, constructed and validated an automated database-guided gating and identification (AGI) approach for fast and standardized in-depth dissection of B-lymphocyte and PC populations in human blood. Methods For this purpose, 213 FC standard (FCS) datafiles corresponding to umbilical cord and peripheral blood samples from healthy and patient volunteers, stained with the 14-color 18-antibody EuroFlow BIgH-IMM panel, were used. Results The BIgH-IMM antibody panel allowed identification of 117 different B-lymphocyte and PC subsets. Samples from 36 healthy donors were stained and 14 of the datafiles that fulfilled strict inclusion criteria were analysed by an expert flow cytometrist to build the EuroFlow BIgH-IMM database. Data contained in the datafiles was then merged into a reference database that was uploaded in the Infinicyt software (Cytognos, Salamanca, Spain). Subsequently, we compared the results of manual gating (MG) with the performance of two classification algorithms -hierarchical algorithm vs two-step algorithm- for AGI of the cell populations present in 5 randomly selected FCS datafiles. The hierarchical AGI algorithm showed higher correlation values vs conventional MG (r2 of 0.94 vs. 0.88 for the two-step AGI algorithm) and was further validated in a set of 177 FCS datafiles against conventional expert-based MG. For virtually all identifiable cell populations a highly significant correlation was observed between the two approaches (r2>0.81 for 79% of all B-cell populations identified), with a significantly lower median time of analysis per sample (6 vs. 40 min, p=0.001) for the AGI tool vs. MG, respectively and both intra-sample (median CV of 1.7% vs. 10.4% by MG, p<0.001) and inter-expert (median CV of 3.9% vs. 17.3% by MG by 2 experts, p<0.001) variability. Conclusion Our results show that compared to conventional FC data analysis strategies, the here proposed AGI tool is a faster, more robust, reproducible, and standardized approach for in-depth analysis of B-lymphocyte and PC subsets circulating in human blood.
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Affiliation(s)
- Alejandro H. Delgado
- Cytognos SL, Salamanca, Spain
- Translational and Clinical Research Program, Centro de Investigación del Cáncer (CIC) and Instituto de Biología Molecular y Celular del Cancer (IBMCC), CSIC-University of Salamanca (USAL), Salamanca, Spain
| | | | - Martin Perez-Andres
- Translational and Clinical Research Program, Centro de Investigación del Cáncer (CIC) and Instituto de Biología Molecular y Celular del Cancer (IBMCC), CSIC-University of Salamanca (USAL), Salamanca, Spain
- Department of Medicine, University of Salamanca (USAL) and Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
- Biomedical Research Networking Centre Consortium of Oncology (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Annieck M. Diks
- Department of Immunology (IMMU), Leiden University Medical Center (LUMC), Leiden, Netherlands
| | | | | | - Elena Blanco
- Translational and Clinical Research Program, Centro de Investigación del Cáncer (CIC) and Instituto de Biología Molecular y Celular del Cancer (IBMCC), CSIC-University of Salamanca (USAL), Salamanca, Spain
- Department of Medicine, University of Salamanca (USAL) and Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Alba Torres-Valle
- Translational and Clinical Research Program, Centro de Investigación del Cáncer (CIC) and Instituto de Biología Molecular y Celular del Cancer (IBMCC), CSIC-University of Salamanca (USAL), Salamanca, Spain
- Department of Medicine, University of Salamanca (USAL) and Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Magdalena A. Berkowska
- Department of Immunology (IMMU), Leiden University Medical Center (LUMC), Leiden, Netherlands
| | | | - J .J .M. van Dongen
- Translational and Clinical Research Program, Centro de Investigación del Cáncer (CIC) and Instituto de Biología Molecular y Celular del Cancer (IBMCC), CSIC-University of Salamanca (USAL), Salamanca, Spain
- Department of Immunology (IMMU), Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Alberto Orfao
- Translational and Clinical Research Program, Centro de Investigación del Cáncer (CIC) and Instituto de Biología Molecular y Celular del Cancer (IBMCC), CSIC-University of Salamanca (USAL), Salamanca, Spain
- Department of Medicine, University of Salamanca (USAL) and Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
- Biomedical Research Networking Centre Consortium of Oncology (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
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30
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Robles EE, Jin Y, Smyth P, Scheuermann RH, Bui JD, Wang HY, Oak J, Qian Y. A cell-level discriminative neural network model for diagnosis of blood cancers. Bioinformatics 2023; 39:btad585. [PMID: 37756695 PMCID: PMC10563151 DOI: 10.1093/bioinformatics/btad585] [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: 02/06/2023] [Revised: 09/12/2023] [Accepted: 09/22/2023] [Indexed: 09/29/2023] Open
Abstract
MOTIVATION Precise identification of cancer cells in patient samples is essential for accurate diagnosis and clinical monitoring but has been a significant challenge in machine learning approaches for cancer precision medicine. In most scenarios, training data are only available with disease annotation at the subject or sample level. Traditional approaches separate the classification process into multiple steps that are optimized independently. Recent methods either focus on predicting sample-level diagnosis without identifying individual pathologic cells or are less effective for identifying heterogeneous cancer cell phenotypes. RESULTS We developed a generalized end-to-end differentiable model, the Cell Scoring Neural Network (CSNN), which takes sample-level training data and predicts the diagnosis of the testing samples and the identity of the diagnostic cells in the sample, simultaneously. The cell-level density differences between samples are linked to the sample diagnosis, which allows the probabilities of individual cells being diagnostic to be calculated using backpropagation. We applied CSNN to two independent clinical flow cytometry datasets for leukemia diagnosis. In both qualitative and quantitative assessments, CSNN outperformed preexisting neural network modeling approaches for both cancer diagnosis and cell-level classification. Post hoc decision trees and 2D dot plots were generated for interpretation of the identified cancer cells, showing that the identified cell phenotypes match the cancer endotypes observed clinically in patient cohorts. Independent data clustering analysis confirmed the identified cancer cell populations. AVAILABILITY AND IMPLEMENTATION The source code of CSNN and datasets used in the experiments are publicly available on GitHub (http://github.com/erobl/csnn). Raw FCS files can be downloaded from FlowRepository (ID: FR-FCM-Z6YK).
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Affiliation(s)
- Edgar E Robles
- Department of Computer Science, University of California, Irvine, CA 92697, United States
| | - Ye Jin
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, United States
| | - Padhraic Smyth
- Department of Computer Science, University of California, Irvine, CA 92697, United States
| | - Richard H Scheuermann
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA 92037, United States
- Department of Pathology, University of California, San Diego, CA 92093, United States
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, United States
| | - Jack D Bui
- Department of Pathology, University of California, San Diego, CA 92093, United States
| | - Huan-You Wang
- Department of Pathology, University of California, San Diego, CA 92093, United States
| | - Jean Oak
- Department of Pathology, Stanford University, Stanford, CA 94305, United States
| | - Yu Qian
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA 92037, United States
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31
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Wu J, Stewart WCL, Jayaprakash C, Das J. BioNetGMMFit: estimating parameters of a BioNetGen model from time-stamped snapshots of single cells. NPJ Syst Biol Appl 2023; 9:46. [PMID: 37736766 PMCID: PMC10516955 DOI: 10.1038/s41540-023-00299-0] [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: 01/28/2023] [Accepted: 07/31/2023] [Indexed: 09/23/2023] Open
Abstract
Mechanistic models are commonly employed to describe signaling and gene regulatory kinetics in single cells and cell populations. Recent advances in single-cell technologies have produced multidimensional datasets where snapshots of copy numbers (or abundances) of a large number of proteins and mRNA are measured across time in single cells. The availability of such datasets presents an attractive scenario where mechanistic models are validated against experiments, and estimated model parameters enable quantitative predictions of signaling or gene regulatory kinetics. To empower the systems biology community to easily estimate parameters accurately from multidimensional single-cell data, we have merged a widely used rule-based modeling software package BioNetGen, which provides a user-friendly way to code for mechanistic models describing biochemical reactions, and the recently introduced CyGMM, that uses cell-to-cell differences to improve parameter estimation for such networks, into a single software package: BioNetGMMFit. BioNetGMMFit provides parameter estimates of the model, supplied by the user in the BioNetGen markup language (BNGL), which yield the best fit for the observed single-cell, time-stamped data of cellular components. Furthermore, for more precise estimates, our software generates confidence intervals around each model parameter. BioNetGMMFit is capable of fitting datasets of increasing cell population sizes for any mechanistic model specified in the BioNetGen markup language. By streamlining the process of developing mechanistic models for large single-cell datasets, BioNetGMMFit provides an easily-accessible modeling framework designed for scale and the broader biochemical signaling community.
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Affiliation(s)
- John Wu
- Department of Computer Science, The Ohio State University, 281 W Lane Ave, Columbus, OH, 43210, USA.
- Steve and Cindy Rasmussen Institute for Genomics, The Abigail Wexner Research Institute, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH, 43205, USA.
| | | | - Ciriyam Jayaprakash
- Department of Physics, The Ohio State University, 191 W Woodruff Ave, Columbus, OH, 43210, USA
| | - Jayajit Das
- Steve and Cindy Rasmussen Institute for Genomics, The Abigail Wexner Research Institute, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH, 43205, USA.
- Departments of Pediatrics, Biomedical Informatics, Pelotonia Institute of Immuno-Oncology, College of Medicine, and Biophysics Program, The Ohio State University, 370 W 9th Ave, Columbus, OH, 43210, USA.
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32
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Velasco P, Bautista F, Rubio A, Aguilar Y, Rives S, Dapena JL, Pérez A, Ramirez M, Saiz-Ladera C, Izquierdo E, Escudero A, Camós M, Vega-García N, Ortega M, Hidalgo-Gómez G, Palacio C, Menéndez P, Bueno C, Montero J, Romecín PA, Zazo S, Alvarez F, Parras J, Ortega-Sabater C, Chulián S, Rosa M, Cirillo D, García E, García J, Manzano-Muñoz A, Minguela A, Fuster JL. The relapsed acute lymphoblastic leukemia network (ReALLNet): a multidisciplinary project from the spanish society of pediatric hematology and oncology (SEHOP). Front Pediatr 2023; 11:1269560. [PMID: 37800011 PMCID: PMC10547895 DOI: 10.3389/fped.2023.1269560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 09/06/2023] [Indexed: 10/07/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common pediatric cancer, with survival rates exceeding 85%. However, 15% of patients will relapse; consequently, their survival rates decrease to below 50%. Therefore, several research and innovation studies are focusing on pediatric relapsed or refractory ALL (R/R ALL). Driven by this context and following the European strategic plan to implement precision medicine equitably, the Relapsed ALL Network (ReALLNet) was launched under the umbrella of SEHOP in 2021, aiming to connect bedside patient care with expert groups in R/R ALL in an interdisciplinary and multicentric network. To achieve this objective, a board consisting of experts in diagnosis, management, preclinical research, and clinical trials has been established. The requirements of treatment centers have been evaluated, and the available oncogenomic and functional study resources have been assessed and organized. A shipping platform has been developed to process samples requiring study derivation, and an integrated diagnostic committee has been established to report results. These biological data, as well as patient outcomes, are collected in a national registry. Additionally, samples from all patients are stored in a biobank. This comprehensive repository of data and samples is expected to foster an environment where preclinical researchers and data scientists can seek to meet the complex needs of this challenging population. This proof of concept aims to demonstrate that a network-based organization, such as that embodied by ReALLNet, provides the ideal niche for the equitable and efficient implementation of "what's next" in the management of children with R/R ALL.
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Affiliation(s)
- Pablo Velasco
- Pediatric Oncology and Hematology Department, Vall d’Hebron Barcelona Hospital, Campus, Barcelona, Spain
| | - Francisco Bautista
- Trial and Data Centrum, Prinses Maxima Centrum, Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Alba Rubio
- Pediatric Oncology and Hematology Department, Hospital Infantil Universitario Niño Jesús, Madrid, Spain
| | - Yurena Aguilar
- Pediatric Oncology and Hematology Department, Hospital Miguel Servet Hospital, Zaragoza, Spain
| | - Susana Rives
- Leukemia and Lymphoma Unit, Pediatric Cancer Center Barcelona (PCCB), Hospital Sant Joan de Déu de Barcelona, Barcelona, Spain
- Pediatric Cancer Center Barcelona (PCCB), Institut de Recerca Sant Joan de Déu, Leukemia and Pediatric Hematology Disorders, Developmental Tumors Biology Group, Barcelona, Spain
| | - Jose L. Dapena
- Leukemia and Lymphoma Unit, Pediatric Cancer Center Barcelona (PCCB), Hospital Sant Joan de Déu de Barcelona, Barcelona, Spain
- Pediatric Cancer Center Barcelona (PCCB), Institut de Recerca Sant Joan de Déu, Leukemia and Pediatric Hematology Disorders, Developmental Tumors Biology Group, Barcelona, Spain
| | - Antonio Pérez
- Translational Research in Pediatric Oncology, Hematopoietic Transplantation and Cell Therapy Group, Hospital La Paz Institute for Health Research (IdiPAZ), La Paz University Hospital, Madrid, Spain
- Pediatric Hemato-Oncology Department, La Paz University Hospital, Madrid, Spain
- Pediatric Department, Universidad Autonoma de Madrid, Madrid, Spain
| | - Manuel Ramirez
- Hematology and Oncology Laboratory, Fundación Para La Investigación Biomédica Hospital Infantil Universitario Niño Jesús, Madrid, Spain
| | - Cristina Saiz-Ladera
- Hematology and Oncology Laboratory, Fundación Para La Investigación Biomédica Hospital Infantil Universitario Niño Jesús, Madrid, Spain
| | - Elisa Izquierdo
- Pediatric Hemato-Oncology Department, La Paz University Hospital, Madrid, Spain
- Department of Genetics, Institute of Medical and Molecular Genetics (INGEMM), La Paz University Hospital, Madrid, Spain
| | - Adela Escudero
- Pediatric Hemato-Oncology Department, La Paz University Hospital, Madrid, Spain
- Department of Genetics, Institute of Medical and Molecular Genetics (INGEMM), La Paz University Hospital, Madrid, Spain
| | - Mireia Camós
- Pediatric Cancer Center Barcelona (PCCB), Institut de Recerca Sant Joan de Déu, Leukemia and Pediatric Hematology Disorders, Developmental Tumors Biology Group, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Hematology Laboratory, Hospital Sant Joan de Déu Barcelona, Barcelona, Spain
| | - Nerea Vega-García
- Pediatric Cancer Center Barcelona (PCCB), Institut de Recerca Sant Joan de Déu, Leukemia and Pediatric Hematology Disorders, Developmental Tumors Biology Group, Barcelona, Spain
- Hematology Laboratory, Hospital Sant Joan de Déu Barcelona, Barcelona, Spain
| | - Margarita Ortega
- Hematology Service, Vall d’Hebron Barcelona Hospital, Campus, Barcelona, Spain
- Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Gloria Hidalgo-Gómez
- Hematology Service, Vall d’Hebron Barcelona Hospital, Campus, Barcelona, Spain
- Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Carlos Palacio
- Hematology Service, Vall d’Hebron Barcelona Hospital, Campus, Barcelona, Spain
- Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Pablo Menéndez
- Josep Carreras Leukemia Reserach Institute, Developmental Leukemia and Immunotherapy group, Barcelona, Spain
- Red Española de Terapias Avanzadas (TERAV)-Instituto de Salud Carlos III (ISCIII) (RICORS, RD21/0017/0029), Madrid, Spain
- CIBER-ONC, ISCIII, Barcelona, Spain
- Institució Catalana de Recerca I Estudis Avançats (ICREA), Barcelona, Spain
| | - Clara Bueno
- Josep Carreras Leukemia Reserach Institute, Developmental Leukemia and Immunotherapy group, Barcelona, Spain
- Red Española de Terapias Avanzadas (TERAV)-Instituto de Salud Carlos III (ISCIII) (RICORS, RD21/0017/0029), Madrid, Spain
- CIBER-ONC, ISCIII, Barcelona, Spain
- Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain
| | - Joan Montero
- Networking Biomedical Research Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universitat de Barcelona, Barcelona, Spain
| | - Paola A. Romecín
- Josep Carreras Leukemia Reserach Institute, Developmental Leukemia and Immunotherapy group, Barcelona, Spain
- Red Española de Terapias Avanzadas (TERAV)-Instituto de Salud Carlos III (ISCIII) (RICORS, RD21/0017/0029), Madrid, Spain
| | - Santiago Zazo
- Information Processing and Telecommunications Center, Universidad Politécnica de Madrid, Madrid, Spain
| | - Federico Alvarez
- Information Processing and Telecommunications Center, Universidad Politécnica de Madrid, Madrid, Spain
| | - Juan Parras
- Information Processing and Telecommunications Center, Universidad Politécnica de Madrid, Madrid, Spain
| | - Carmen Ortega-Sabater
- Mathematical Oncology Laboratory (MOLAB), University of Castilla-La Mancha, Ciudad Real, Spain
| | - Salvador Chulián
- Department of Mathematics, Universidad de Cádiz, Cádiz, Spain
- Biomedical Research and Innovation Institute of Cádiz (INiBICA), Hospital Universitario Puerta del Mar, Cádiz, Spain
| | - María Rosa
- Mathematical Oncology Laboratory (MOLAB), University of Castilla-La Mancha, Ciudad Real, Spain
- Department of Mathematics, Universidad de Cádiz, Cádiz, Spain
| | | | - Elena García
- Hematology and Oncology Laboratory, Fundación Para La Investigación Biomédica Hospital Infantil Universitario Niño Jesús, Madrid, Spain
| | - Jorge García
- Hematology and Oncology Laboratory, Fundación Para La Investigación Biomédica Hospital Infantil Universitario Niño Jesús, Madrid, Spain
| | - Albert Manzano-Muñoz
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universitat de Barcelona, Barcelona, Spain
- Nanobioengineering Group, Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Alfredo Minguela
- Immunology Department, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain
- Instituto Murciano de Investigación Biosanitaria (IMIB), Murcia, Spain
| | - Jose L. Fuster
- Instituto Murciano de Investigación Biosanitaria (IMIB), Murcia, Spain
- Paediatric Oncohematology Department. Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain
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Puccio S, Grillo G, Alvisi G, Scirgolea C, Galletti G, Mazza EMC, Consiglio A, De Simone G, Licciulli F, Lugli E. CRUSTY: a versatile web platform for the rapid analysis and visualization of high-dimensional flow cytometry data. Nat Commun 2023; 14:5102. [PMID: 37666818 PMCID: PMC10477295 DOI: 10.1038/s41467-023-40790-0] [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: 09/16/2022] [Accepted: 08/10/2023] [Indexed: 09/06/2023] Open
Abstract
Flow cytometry (FCM) can investigate dozens of parameters from millions of cells and hundreds of specimens in a short time and at a reasonable cost, but the amount of data that is generated is considerable. Computational approaches are useful to identify novel subpopulations and molecular biomarkers, but generally require deep expertize in bioinformatics and the use of different platforms. To overcome these limitations, we introduce CRUSTY, an interactive, user-friendly webtool incorporating the most popular algorithms for FCM data analysis, and capable of visualizing graphical and tabular results and automatically generating publication-quality figures within minutes. CRUSTY also hosts an interactive interface for the exploration of results in real time. Thus, CRUSTY enables a large number of users to mine complex datasets and reduce the time required for data exploration and interpretation. CRUSTY is accessible at https://crusty.humanitas.it/ .
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Affiliation(s)
- Simone Puccio
- Laboratory of Translational Immunology, IRCCS Humanitas Research Hospital, via Manzoni 56, 20089, Rozzano, Milan, Italy.
- Institute of Genetic and Biomedical Research, UoS Milan, National Research Council, via Manzoni 56, 20089, Rozzano, Milan, Italy.
| | - Giorgio Grillo
- Institute for Biomedical Technologies, National Research Council, via Amendola 122/D, 70126, Bari, Italy
| | - Giorgia Alvisi
- Laboratory of Translational Immunology, IRCCS Humanitas Research Hospital, via Manzoni 56, 20089, Rozzano, Milan, Italy
| | - Caterina Scirgolea
- Laboratory of Translational Immunology, IRCCS Humanitas Research Hospital, via Manzoni 56, 20089, Rozzano, Milan, Italy
| | - Giovanni Galletti
- Laboratory of Translational Immunology, IRCCS Humanitas Research Hospital, via Manzoni 56, 20089, Rozzano, Milan, Italy
- School of Biological Sciences, Department of Molecular Biology, University of California San Diego, San Diego, CA, USA
| | - Emilia Maria Cristina Mazza
- Laboratory of Translational Immunology, IRCCS Humanitas Research Hospital, via Manzoni 56, 20089, Rozzano, Milan, Italy
| | - Arianna Consiglio
- Institute for Biomedical Technologies, National Research Council, via Amendola 122/D, 70126, Bari, Italy
| | - Gabriele De Simone
- Flow Cytometry Core, IRCCS Humanitas Research Hospital, via Manzoni 56, 20089, Rozzano, Milan, Italy
| | - Flavio Licciulli
- Institute for Biomedical Technologies, National Research Council, via Amendola 122/D, 70126, Bari, Italy
| | - Enrico Lugli
- Laboratory of Translational Immunology, IRCCS Humanitas Research Hospital, via Manzoni 56, 20089, Rozzano, Milan, Italy.
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34
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Sadighi Akha AA, Csomós K, Ujházi B, Walter JE, Kumánovics A. Evolving Approach to Clinical Cytometry for Immunodeficiencies and Other Immune Disorders. Clin Lab Med 2023; 43:467-483. [PMID: 37481324 DOI: 10.1016/j.cll.2023.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
Abstract
Primary immunodeficiencies were initially identified on the basis of recurrent, severe or unusual infections. Subsequently, it was noted that these diseases can also manifest with autoimmunity, autoinflammation, allergy, lymphoproliferation and malignancy, hence a conceptual change and their renaming as inborn errors of immunity. Ongoing advances in flow cytometry provide the opportunity to expand or modify the utility and scope of existing laboratory tests in this field to mirror this conceptual change. Here we have used the B cell subset, variably known as CD21low B cells, age-associated B cells and T-bet+ B cells, as an example to demonstrate this possibility.
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Affiliation(s)
- Amir A Sadighi Akha
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Krisztián Csomós
- Division of Pediatric Allergy/Immunology, University of South Florida, Johns Hopkins All Children's Hospital, St. Petersburg, FL, USA
| | - Boglárka Ujházi
- Division of Pediatric Allergy/Immunology, University of South Florida, Johns Hopkins All Children's Hospital, St. Petersburg, FL, USA
| | - Jolán E Walter
- Division of Pediatric Allergy/Immunology, University of South Florida, Johns Hopkins All Children's Hospital, St. Petersburg, FL, USA
| | - Attila Kumánovics
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
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35
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Guldberg SM, Okholm TLH, McCarthy EE, Spitzer MH. Computational Methods for Single-Cell Proteomics. Annu Rev Biomed Data Sci 2023; 6:47-71. [PMID: 37040735 PMCID: PMC10621466 DOI: 10.1146/annurev-biodatasci-020422-050255] [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: 04/13/2023]
Abstract
Advances in single-cell proteomics technologies have resulted in high-dimensional datasets comprising millions of cells that are capable of answering key questions about biology and disease. The advent of these technologies has prompted the development of computational tools to process and visualize the complex data. In this review, we outline the steps of single-cell and spatial proteomics analysis pipelines. In addition to describing available methods, we highlight benchmarking studies that have identified advantages and pitfalls of the currently available computational toolkits. As these technologies continue to advance, robust analysis tools should be developed in tandem to take full advantage of the potential biological insights provided by these data.
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Affiliation(s)
- Sophia M Guldberg
- Department of Otolaryngology-Head and Neck Surgery and Department of Microbiology and Immunology, University of California, San Francisco, California, USA;
- Biomedical Sciences Graduate Program, University of California, San Francisco, California, USA
- Gladstone-UCSF Institute for Genomic Immunology, San Francisco, California, USA
| | - Trine Line Hauge Okholm
- Department of Otolaryngology-Head and Neck Surgery and Department of Microbiology and Immunology, University of California, San Francisco, California, USA;
- Gladstone-UCSF Institute for Genomic Immunology, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California, USA
| | - Elizabeth E McCarthy
- Department of Otolaryngology-Head and Neck Surgery and Department of Microbiology and Immunology, University of California, San Francisco, California, USA;
- Biomedical Sciences Graduate Program, University of California, San Francisco, California, USA
- Institute for Human Genetics; Division of Rheumatology, Department of Medicine; Medical Scientist Training Program; and Biological and Medical Informatics Graduate Program, University of California, San Francisco, California, USA
| | - Matthew H Spitzer
- Department of Otolaryngology-Head and Neck Surgery and Department of Microbiology and Immunology, University of California, San Francisco, California, USA;
- Gladstone-UCSF Institute for Genomic Immunology, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
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36
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Chulián S, Stolz BJ, Martínez-Rubio Á, Blázquez Goñi C, Rodríguez Gutiérrez JF, Caballero Velázquez T, Molinos Quintana Á, Ramírez Orellana M, Castillo Robleda A, Fuster Soler JL, Minguela Puras A, Martínez Sánchez MV, Rosa M, Pérez-García VM, Byrne HM. The shape of cancer relapse: Topological data analysis predicts recurrence in paediatric acute lymphoblastic leukaemia. PLoS Comput Biol 2023; 19:e1011329. [PMID: 37578973 PMCID: PMC10468039 DOI: 10.1371/journal.pcbi.1011329] [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: 09/29/2022] [Revised: 08/30/2023] [Accepted: 07/05/2023] [Indexed: 08/16/2023] Open
Abstract
Although children and adolescents with acute lymphoblastic leukaemia (ALL) have high survival rates, approximately 15-20% of patients relapse. Risk of relapse is routinely estimated at diagnosis by biological factors, including flow cytometry data. This high-dimensional data is typically manually assessed by projecting it onto a subset of biomarkers. Cell density and "empty spaces" in 2D projections of the data, i.e. regions devoid of cells, are then used for qualitative assessment. Here, we use topological data analysis (TDA), which quantifies shapes, including empty spaces, in data, to analyse pre-treatment ALL datasets with known patient outcomes. We combine these fully unsupervised analyses with Machine Learning (ML) to identify significant shape characteristics and demonstrate that they accurately predict risk of relapse, particularly for patients previously classified as 'low risk'. We independently confirm the predictive power of CD10, CD20, CD38, and CD45 as biomarkers for ALL diagnosis. Based on our analyses, we propose three increasingly detailed prognostic pipelines for analysing flow cytometry data from ALL patients depending on technical and technological availability: 1. Visual inspection of specific biological features in biparametric projections of the data; 2. Computation of quantitative topological descriptors of such projections; 3. A combined analysis, using TDA and ML, in the four-parameter space defined by CD10, CD20, CD38 and CD45. Our analyses readily extend to other haematological malignancies.
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Affiliation(s)
- Salvador Chulián
- Department of Mathematics, Universidad de Cádiz, Puerto Real (Cádiz), Spain
- Biomedical Research and Innovation Institute of Cádiz (INiBICA), Hospital Universitario Puerta del Mar, Cádiz, Spain
- Department of Mathematics, Mathematical Oncology Laboratory (MOLAB), Universidad de Castilla-La Mancha, Ciudad Real, Spain
| | - Bernadette J. Stolz
- Mathematical Institute, University of Oxford, Oxford, United Kingdom
- Laboratory for Topology and Neuroscience, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Álvaro Martínez-Rubio
- Department of Mathematics, Universidad de Cádiz, Puerto Real (Cádiz), Spain
- Biomedical Research and Innovation Institute of Cádiz (INiBICA), Hospital Universitario Puerta del Mar, Cádiz, Spain
- Department of Mathematics, Mathematical Oncology Laboratory (MOLAB), Universidad de Castilla-La Mancha, Ciudad Real, Spain
| | - Cristina Blázquez Goñi
- Biomedical Research and Innovation Institute of Cádiz (INiBICA), Hospital Universitario Puerta del Mar, Cádiz, Spain
- Department of Paediatric Haematology and Oncology, Hospital Universitario de Jerez, Jerez de la Frontera (Cádiz), Spain
- Department of Haematology, Hospital Universitario Vírgen del Rocío, Instituto de Biomedicina de Sevilla (IBIS), Sevilla, Spain
| | - Juan F. Rodríguez Gutiérrez
- Biomedical Research and Innovation Institute of Cádiz (INiBICA), Hospital Universitario Puerta del Mar, Cádiz, Spain
- Department of Paediatric Haematology and Oncology, Hospital Universitario de Jerez, Jerez de la Frontera (Cádiz), Spain
| | - Teresa Caballero Velázquez
- Department of Haematology, Hospital Universitario Vírgen del Rocío, Instituto de Biomedicina de Sevilla (IBIS), Sevilla, Spain
- CSIC, University of Sevilla, Sevilla, Spain
| | - Águeda Molinos Quintana
- Department of Haematology, Hospital Universitario Vírgen del Rocío, Instituto de Biomedicina de Sevilla (IBIS), Sevilla, Spain
- CSIC, University of Sevilla, Sevilla, Spain
| | - Manuel Ramírez Orellana
- Department of Paediatric Haematology and Oncology, Hospital Infantil Universitario Niño Jesús - Instituto Investigación Sanitaria La Princesa, Madrid, Spain
| | - Ana Castillo Robleda
- Department of Paediatric Haematology and Oncology, Hospital Infantil Universitario Niño Jesús - Instituto Investigación Sanitaria La Princesa, Madrid, Spain
| | - José Luis Fuster Soler
- Department of Paediatric Haematology and Oncology, Hospital Clínico Universitario Virgen de la Arrixaca - Instituto Murciano de Investigación Biosanitaria (IMIB), Murcia, Spain
| | - Alfredo Minguela Puras
- Immunology Service, Hospital Clínico Universitario Virgen de la Arrixaca - Instituto Murciano de Investigación Biosanitaria (IMIB), Murcia, Spain
| | - María V. Martínez Sánchez
- Immunology Service, Hospital Clínico Universitario Virgen de la Arrixaca - Instituto Murciano de Investigación Biosanitaria (IMIB), Murcia, Spain
| | - María Rosa
- Department of Mathematics, Universidad de Cádiz, Puerto Real (Cádiz), Spain
- Biomedical Research and Innovation Institute of Cádiz (INiBICA), Hospital Universitario Puerta del Mar, Cádiz, Spain
- Department of Mathematics, Mathematical Oncology Laboratory (MOLAB), Universidad de Castilla-La Mancha, Ciudad Real, Spain
| | - Víctor M. Pérez-García
- Department of Mathematics, Mathematical Oncology Laboratory (MOLAB), Universidad de Castilla-La Mancha, Ciudad Real, Spain
- Instituto de Matemática Aplicada a la Ciencia y la Ingeniería (IMACI), Universidad de Castilla-La Mancha, Ciudad Real, Spain
- ETSI Industriales, Universidad de Castilla-La Mancha, Ciudad Real, Spain
| | - Helen M. Byrne
- Mathematical Institute, University of Oxford, Oxford, United Kingdom
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37
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Nguyen PC, Nguyen V, Baldwin K, Kankanige Y, Blombery P, Came N, Westerman DA. Computational flow cytometry provides accurate assessment of measurable residual disease in chronic lymphocytic leukaemia. Br J Haematol 2023; 202:760-770. [PMID: 37052611 DOI: 10.1111/bjh.18802] [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: 12/06/2022] [Revised: 03/27/2023] [Accepted: 03/28/2023] [Indexed: 04/14/2023]
Abstract
Undetectable measurable residual disease (MRD) is associated with favourable clinical outcomes in chronic lymphocytic leukaemia (CLL). While assessment is commonly performed using multiparameter flow cytometry (MFC), this approach is associated with limitations including user bias and expertise that may not be widely available. Implementation of unsupervised clustering algorithms in the laboratory can address these limitations and have not been previously reported in a systematic quantitative manner. We developed a computational pipeline to assess CLL MRD using FlowSOM. In the training step, a self-organising map was generated with nodes representing the full breadth of normal immature and mature B cells along with disease immunophenotypes. This map was used to detect MRD in multiple validation cohorts containing a total of 456 samples. This included an evaluation of atypical CLL cases and samples collected from two different laboratories. Computational MRD showed high correlation with expert analysis (Pearson's r > 0.99 for typical CLL). Binary classification of typical CLL samples as either MRD positive or negative demonstrated high concordance (>98%). Interestingly, computational MRD detected disease in a small number of atypical CLL cases in which MRD was not detected by expert analysis. These results demonstrate the feasibility and value of automated MFC analysis in a diagnostic laboratory.
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Affiliation(s)
- Phillip C Nguyen
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Vuong Nguyen
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Kylie Baldwin
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Yamuna Kankanige
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Piers Blombery
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
- Department of Clinical Haematology, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Neil Came
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - David A Westerman
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
- Department of Clinical Haematology, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Victoria, Australia
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38
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Zhang J, Li J, Lin L. Statistical and machine learning methods for immunoprofiling based on single-cell data. Hum Vaccin Immunother 2023:2234792. [PMID: 37485833 PMCID: PMC10373621 DOI: 10.1080/21645515.2023.2234792] [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: 03/13/2023] [Revised: 06/30/2023] [Accepted: 07/04/2023] [Indexed: 07/25/2023] Open
Abstract
Immunoprofiling has become a crucial tool for understanding the complex interactions between the immune system and diseases or interventions, such as therapies and vaccinations. Immune response biomarkers are critical for understanding those relationships and potentially developing personalized intervention strategies. Single-cell data have emerged as a promising source for identifying immune response biomarkers. In this review, we discuss the current state-of-the-art methods for immunoprofiling, including those for reducing the dimensionality of high-dimensional single-cell data and methods for clustering, classification, and prediction. We also draw attention to recent developments in data integration.
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Affiliation(s)
- Jingxuan Zhang
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Jia Li
- Department of Statistics, Pennsylvania State University, University Park, PA, USA
| | - Lin Lin
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
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39
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Andronico LA, Jung SR, Fujimoto BS, Chiu DT. Improving Multicolor Colocalization in Single-Vesicle Flow Cytometry with Vesicle Transit Time. Anal Chem 2023; 95:10492-10497. [PMID: 37403691 PMCID: PMC10357400 DOI: 10.1021/acs.analchem.3c01197] [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: 03/18/2023] [Accepted: 06/21/2023] [Indexed: 07/06/2023]
Abstract
Immunophenotyping of vesicles, such as extracellular vesicles (EVs), is essential to understanding their origin and biological role. We previously described a custom-built flow analyzer that utilizes a gravity-driven flow, high numerical aperture objective, and micrometer-sized flow channels to reach the sensitivity needed for fast multidimensional analysis of the surface proteins of EVs, even down to the smallest EVs (e.g., ∼30-40 nm). It is difficult to flow focus small EVs, and thus, the transiting EVs exhibit a distribution in particle velocities due to the laminar flow. This distribution of vesicle velocities leads to potentially incorrect results when immunophenotyping nanometer-sized vesicles using cross-correlation analysis (Xcorr), as the order of appearance of the vesicles might not be the same at different spatially offset laser excitation regions. Here, we describe an alternative cross-correlation analysis strategy (Scorr), which uses information on particle transit time across the laser excitation beam width to improve multicolor colocalization in single-vesicle immunoprofiling. We tested the performance of the algorithm for colocalization analysis of multicolor nanobeads and EVs experimentally and via simulations and found that Scorr improved both the efficiency and accuracy of colocalization versus Xcorr. As shown from Monte Carlo simulations, Scorr provided an ∼1.2-4.7-fold increase in the number of colocalized peaks and ensured negligible colocalization of peaks. In silico results were in good agreement with experimental data, which showed an increase in colocalized peaks of ∼1.3-2.5-fold and ∼1.2-2-fold for multicolor beads and EVs, respectively.
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Affiliation(s)
- Luca A. Andronico
- Department
of Women’s and Children’s Health (KBH), Karolinska Institutet, Solna 17177, Sweden
| | - Seung-Ryoung Jung
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Bryant S. Fujimoto
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Daniel T. Chiu
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
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40
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Robinson JP, Ostafe R, Iyengar SN, Rajwa B, Fischer R. Flow Cytometry: The Next Revolution. Cells 2023; 12:1875. [PMID: 37508539 PMCID: PMC10378642 DOI: 10.3390/cells12141875] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/06/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Unmasking the subtleties of the immune system requires both a comprehensive knowledge base and the ability to interrogate that system with intimate sensitivity. That task, to a considerable extent, has been handled by an iterative expansion in flow cytometry methods, both in technological capability and also in accompanying advances in informatics. As the field of fluorescence-based cytomics matured, it reached a technological barrier at around 30 parameter analyses, which stalled the field until spectral flow cytometry created a fundamental transformation that will likely lead to the potential of 100 simultaneous parameter analyses within a few years. The simultaneous advance in informatics has now become a watershed moment for the field as it competes with mature systematic approaches such as genomics and proteomics, allowing cytomics to take a seat at the multi-omics table. In addition, recent technological advances try to combine the speed of flow systems with other detection methods, in addition to fluorescence alone, which will make flow-based instruments even more indispensable in any biological laboratory. This paper outlines current approaches in cell analysis and detection methods, discusses traditional and microfluidic sorting approaches as well as next-generation instruments, and provides an early look at future opportunities that are likely to arise.
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Affiliation(s)
- J Paul Robinson
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN 47907, USA
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Raluca Ostafe
- Molecular Evolution, Protein Engineering and Production Facility (PI4D), Purdue University, West Lafayette, IN 47907, USA
| | | | - Bartek Rajwa
- Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA
| | - Rainer Fischer
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute of Inflammation, Immunology and Infectious Diseases, Purdue University, West Lafayette, IN 47907, USA
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41
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Ferguson C, Zhang Y, Palego C, Cheng X. Recent Approaches to Design and Analysis of Electrical Impedance Systems for Single Cells Using Machine Learning. SENSORS (BASEL, SWITZERLAND) 2023; 23:5990. [PMID: 37447838 DOI: 10.3390/s23135990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/17/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023]
Abstract
Individual cells have many unique properties that can be quantified to develop a holistic understanding of a population. This can include understanding population characteristics, identifying subpopulations, or elucidating outlier characteristics that may be indicators of disease. Electrical impedance measurements are rapid and label-free for the monitoring of single cells and generate large datasets of many cells at single or multiple frequencies. To increase the accuracy and sensitivity of measurements and define the relationships between impedance and biological features, many electrical measurement systems have incorporated machine learning (ML) paradigms for control and analysis. Considering the difficulty capturing complex relationships using traditional modelling and statistical methods due to population heterogeneity, ML offers an exciting approach to the systemic collection and analysis of electrical properties in a data-driven way. In this work, we discuss incorporation of ML to improve the field of electrical single cell analysis by addressing the design challenges to manipulate single cells and sophisticated analysis of electrical properties that distinguish cellular changes. Looking forward, we emphasize the opportunity to build on integrated systems to address common challenges in data quality and generalizability to save time and resources at every step in electrical measurement of single cells.
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Affiliation(s)
- Caroline Ferguson
- Department of Bioengineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Yu Zhang
- Department of Bioengineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Cristiano Palego
- Department of Computer Science and Electronic Engineering, Bangor University, Bangor LL57 2DG, UK
| | - Xuanhong Cheng
- Department of Bioengineering, Lehigh University, Bethlehem, PA 18015, USA
- Department of Materials Science and Engineering, Lehigh University, Bethlehem, PA 18015, USA
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42
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Lajiness JD, Cook-Mills JM. Catching Our Breath: Updates on the Role of Dendritic Cell Subsets in Asthma. Adv Biol (Weinh) 2023; 7:e2200296. [PMID: 36755197 PMCID: PMC10293089 DOI: 10.1002/adbi.202200296] [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: 11/01/2022] [Revised: 01/04/2023] [Indexed: 02/10/2023]
Abstract
Dendritic cells (DCs), as potent antigen presenting cells, are known to play a central role in the pathophysiology of asthma. The understanding of DC biology has evolved over the years to include multiple subsets of DCs with distinct functions in the initiation and maintenance of asthma. Furthermore, asthma is increasingly recognized as a heterogeneous disease with potentially diverse underlying mechanisms. The goal of this review is to summarize the role of DCs and the various subsets therein in the pathophysiology of asthma and highlight some of the crucial animal models shaping the field today. Potential future avenues of investigation to address existing gaps in knowledge are discussed.
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Affiliation(s)
- Jacquelyn D Lajiness
- Department of Pediatrics, Division of Neonatology, Indiana University School of Medicine, 1030 West Michigan Street, Suite C 4600, Indianapolis, IN, 46202-5201, USA
| | - Joan M Cook-Mills
- Department of Pediatrics, Department of Microbiology and Immunology, Pediatric Pulmonary, Asthma, and Allergy Basic Research Program, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, 1044 W. Walnut Street, R4-202A, Indianapolis, IN, 46202, USA
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43
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Gao J, Luo Y, Li H, Zhao Y, Zhao J, Han X, Han J, Lin H, Qian F. Deep Immunophenotyping of Human Whole Blood by Standardized Multi-parametric Flow Cytometry Analyses. PHENOMICS (CHAM, SWITZERLAND) 2023; 3:309-328. [PMID: 37325713 PMCID: PMC10260734 DOI: 10.1007/s43657-022-00092-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 12/03/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
Immunophenotyping is proving crucial to understanding the role of the immune system in health and disease. High-throughput flow cytometry has been used extensively to reveal changes in immune cell composition and function at the single-cell level. Here, we describe six optimized 11-color flow cytometry panels for deep immunophenotyping of human whole blood. A total of 51 surface antibodies, which are readily available and validated, were selected to identify the key immune cell populations and evaluate their functional state in a single assay. The gating strategies for effective flow cytometry data analysis are included in the protocol. To ensure data reproducibility, we provide detailed procedures in three parts, including (1) instrument characterization and detector gain optimization, (2) antibody titration and sample staining, and (3) data acquisition and quality checks. This standardized approach has been applied to a variety of donors for a better understanding of the complexity of the human immune system. Supplementary Information The online version contains supplementary material available at 10.1007/s43657-022-00092-9.
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Affiliation(s)
- Jian Gao
- State Key Laboratory of Genetic Engineering, Shanghai Public Health Clinical Center, Human Phenome Institute, Zhangjiang Fudan International Innovation Center and School of Life Sciences, Fudan University, Shanghai, 200438 China
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Yali Luo
- State Key Laboratory of Genetic Engineering, Shanghai Public Health Clinical Center, Human Phenome Institute, Zhangjiang Fudan International Innovation Center and School of Life Sciences, Fudan University, Shanghai, 200438 China
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Helian Li
- State Key Laboratory of Genetic Engineering, Shanghai Public Health Clinical Center, Human Phenome Institute, Zhangjiang Fudan International Innovation Center and School of Life Sciences, Fudan University, Shanghai, 200438 China
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Yiran Zhao
- State Key Laboratory of Genetic Engineering, Shanghai Public Health Clinical Center, Human Phenome Institute, Zhangjiang Fudan International Innovation Center and School of Life Sciences, Fudan University, Shanghai, 200438 China
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Jialin Zhao
- State Key Laboratory of Genetic Engineering, Shanghai Public Health Clinical Center, Human Phenome Institute, Zhangjiang Fudan International Innovation Center and School of Life Sciences, Fudan University, Shanghai, 200438 China
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Xuling Han
- State Key Laboratory of Genetic Engineering, Shanghai Public Health Clinical Center, Human Phenome Institute, Zhangjiang Fudan International Innovation Center and School of Life Sciences, Fudan University, Shanghai, 200438 China
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Jingxuan Han
- State Key Laboratory of Genetic Engineering, Shanghai Public Health Clinical Center, Human Phenome Institute, Zhangjiang Fudan International Innovation Center and School of Life Sciences, Fudan University, Shanghai, 200438 China
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Huiqin Lin
- State Key Laboratory of Genetic Engineering, Shanghai Public Health Clinical Center, Human Phenome Institute, Zhangjiang Fudan International Innovation Center and School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Feng Qian
- State Key Laboratory of Genetic Engineering, Shanghai Public Health Clinical Center, Human Phenome Institute, Zhangjiang Fudan International Innovation Center and School of Life Sciences, Fudan University, Shanghai, 200438 China
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438 China
- Institute of Immunophenome, International Human Phenome Institutes (Shanghai), Shanghai, 200433 China
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44
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Wang G, Yao Y, Huang H, Zhou J, Ni C. Multiomics technologies for comprehensive tumor microenvironment analysis in triple-negative breast cancer under neoadjuvant chemotherapy. Front Oncol 2023; 13:1131259. [PMID: 37284197 PMCID: PMC10239824 DOI: 10.3389/fonc.2023.1131259] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 05/08/2023] [Indexed: 06/08/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is one of the most aggressive breast cancer subtypes and is characterized by abundant infiltrating immune cells within the microenvironment. As standard care, chemotherapy remains the fundamental neoadjuvant treatment in TNBC, and there is increasing evidence that supplementation with immune checkpoint inhibitors may potentiate the therapeutic efficiency of neoadjuvant chemotherapy (NAC). However, 20-60% of TNBC patients still have residual tumor burden after NAC and require additional chemotherapy; therefore, it is critical to understand the dynamic change in the tumor microenvironment (TME) during treatment to help improve the rate of complete pathological response and long-term prognosis. Traditional methods, including immunohistochemistry, bulk tumor sequencing, and flow cytometry, have been applied to elucidate the TME of breast cancer, but the low resolution and throughput may overlook key information. With the development of diverse high-throughput technologies, recent reports have provided new insights into TME alterations during NAC in four fields, including tissue imaging, cytometry, next-generation sequencing, and spatial omics. In this review, we discuss the traditional methods and the latest advances in high-throughput techniques to decipher the TME of TNBC and the prospect of translating these techniques to clinical practice.
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Affiliation(s)
- Gang Wang
- Department of Surgical Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China
| | - Yao Yao
- Department of Breast Surgery, Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, China
| | - Huanhuan Huang
- Department of Breast Surgery, Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, China
| | - Jun Zhou
- Department of Breast Surgery, Affiliated Hangzhou First People’s Hospital, Zhejiang University, Hangzhou, Zhejiang, China
| | - Chao Ni
- Department of Breast Surgery, Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, China
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45
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Yang J, Chen Y, Jing Y, Green MR, Han L. Advancing CAR T cell therapy through the use of multidimensional omics data. Nat Rev Clin Oncol 2023; 20:211-228. [PMID: 36721024 DOI: 10.1038/s41571-023-00729-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2023] [Indexed: 02/01/2023]
Abstract
Despite the notable success of chimeric antigen receptor (CAR) T cell therapies in the treatment of certain haematological malignancies, challenges remain in optimizing CAR designs and cell products, improving response rates, extending the durability of remissions, reducing toxicity and broadening the utility of this therapeutic modality to other cancer types. Data from multidimensional omics analyses, including genomics, epigenomics, transcriptomics, T cell receptor-repertoire profiling, proteomics, metabolomics and/or microbiomics, provide unique opportunities to dissect the complex and dynamic multifactorial phenotypes, processes and responses of CAR T cells as well as to discover novel tumour targets and pathways of resistance. In this Review, we summarize the multidimensional cellular and molecular profiling technologies that have been used to advance our mechanistic understanding of CAR T cell therapies. In addition, we discuss current applications and potential strategies leveraging multi-omics data to identify optimal target antigens and other molecular features that could be exploited to enhance the antitumour activity and minimize the toxicity of CAR T cell therapy. Indeed, fully utilizing multi-omics data will provide new insights into the biology of CAR T cell therapy, further accelerate the development of products with improved efficacy and safety profiles, and enable clinicians to better predict and monitor patient responses.
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Affiliation(s)
- Jingwen Yang
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Yamei Chen
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Ying Jing
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Michael R Green
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Leng Han
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA.
- Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX, USA.
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46
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Wang K, Yang Y, Wu F, Song B, Wang X, Wang T. Comparative analysis of dimension reduction methods for cytometry by time-of-flight data. Nat Commun 2023; 14:1836. [PMID: 37005472 PMCID: PMC10067013 DOI: 10.1038/s41467-023-37478-w] [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: 07/12/2022] [Accepted: 03/20/2023] [Indexed: 04/04/2023] Open
Abstract
While experimental and informatic techniques around single cell sequencing (scRNA-seq) are advanced, research around mass cytometry (CyTOF) data analysis has severely lagged behind. CyTOF data are notably different from scRNA-seq data in many aspects. This calls for the evaluation and development of computational methods specific for CyTOF data. Dimension reduction (DR) is one of the critical steps of single cell data analysis. Here, we benchmark the performances of 21 DR methods on 110 real and 425 synthetic CyTOF samples. We find that less well-known methods like SAUCIE, SQuaD-MDS, and scvis are the overall best performers. In particular, SAUCIE and scvis are well balanced, SQuaD-MDS excels at structure preservation, whereas UMAP has great downstream analysis performance. We also find that t-SNE (along with SQuad-MDS/t-SNE Hybrid) possesses the best local structure preservation. Nevertheless, there is a high level of complementarity between these tools, so the choice of method should depend on the underlying data structure and the analytical needs.
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Affiliation(s)
- Kaiwen Wang
- Department of Statistical Science, Southern Methodist University, Dallas, TX, 75275, USA
| | - Yuqiu Yang
- Department of Statistical Science, Southern Methodist University, Dallas, TX, 75275, USA
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Fangjiang Wu
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Bing Song
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Xinlei Wang
- Department of Statistical Science, Southern Methodist University, Dallas, TX, 75275, USA.
- Department of Mathematics, University of Texas at Arlington, Arlington, TX, 76019, USA.
- Center for Data Science Research and Education, College of Science, University of Texas at Arlington, Arlington, 76019, USA.
| | - Tao Wang
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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47
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Lu P, Oetjen KA, Bender DE, Ruzinova MB, Fisher DAC, Shim KG, Pachynski RK, Brennen WN, Oh ST, Link DC, Thorek DLJ. IMC-Denoise: a content aware denoising pipeline to enhance Imaging Mass Cytometry. Nat Commun 2023; 14:1601. [PMID: 36959190 PMCID: PMC10036333 DOI: 10.1038/s41467-023-37123-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 03/02/2023] [Indexed: 03/25/2023] Open
Abstract
Imaging Mass Cytometry (IMC) is an emerging multiplexed imaging technology for analyzing complex microenvironments using more than 40 molecularly-specific channels. However, this modality has unique data processing requirements, particularly for patient tissue specimens where signal-to-noise ratios for markers can be low, despite optimization, and pixel intensity artifacts can deteriorate image quality and downstream analysis. Here we demonstrate an automated content-aware pipeline, IMC-Denoise, to restore IMC images deploying a differential intensity map-based restoration (DIMR) algorithm for removing hot pixels and a self-supervised deep learning algorithm for shot noise image filtering (DeepSNiF). IMC-Denoise outperforms existing methods for adaptive hot pixel and background noise removal, with significant image quality improvement in modeled data and datasets from multiple pathologies. This includes in technically challenging human bone marrow; we achieve noise level reduction of 87% for a 5.6-fold higher contrast-to-noise ratio, and more accurate background noise removal with approximately 2 × improved F1 score. Our approach enhances manual gating and automated phenotyping with cell-scale downstream analyses. Verified by manual annotations, spatial and density analysis for targeted cell groups reveal subtle but significant differences of cell populations in diseased bone marrow. We anticipate that IMC-Denoise will provide similar benefits across mass cytometric applications to more deeply characterize complex tissue microenvironments.
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Affiliation(s)
- Peng Lu
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, USA
- Department of Radiology, Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, USA
- Program in Quantitative Molecular Therapeutics, Washington University School of Medicine, St. Louis, USA
| | - Karolyn A Oetjen
- Department of Medicine, Washington University School of Medicine, St. Louis, USA
| | - Diane E Bender
- The Bursky Center for Human Immunology and Immunotherapy Programs Immunomonitoring Laboratory, Washington University School of Medicine, St. Louis, USA
| | - Marianna B Ruzinova
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, USA
| | - Daniel A C Fisher
- Department of Medicine, Washington University School of Medicine, St. Louis, USA
| | - Kevin G Shim
- Department of Medicine, Washington University School of Medicine, St. Louis, USA
| | - Russell K Pachynski
- Department of Medicine, Washington University School of Medicine, St. Louis, USA
| | - W Nathaniel Brennen
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center (SKCCC), Johns Hopkins University, Baltimore, USA
- Department of Urology, James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Stephen T Oh
- Department of Medicine, Washington University School of Medicine, St. Louis, USA
- The Bursky Center for Human Immunology and Immunotherapy Programs Immunomonitoring Laboratory, Washington University School of Medicine, St. Louis, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, USA
| | - Daniel C Link
- Department of Medicine, Washington University School of Medicine, St. Louis, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, USA
| | - Daniel L J Thorek
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, USA.
- Department of Radiology, Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, USA.
- Program in Quantitative Molecular Therapeutics, Washington University School of Medicine, St. Louis, USA.
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, USA.
- Oncologic Imaging Program, Siteman Cancer Center, Washington University School of Medicine, St. Louis, USA.
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48
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Chen X, Cheng L, Pan Y, Chen P, Luo Y, Li S, Zou W, Wang K. Different immunological mechanisms between AQP4 antibody-positive and MOG antibody-positive optic neuritis based on RNA sequencing analysis of whole blood. Front Immunol 2023; 14:1095966. [PMID: 36969199 PMCID: PMC10036921 DOI: 10.3389/fimmu.2023.1095966] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/27/2023] [Indexed: 03/12/2023] Open
Abstract
Purpose To compare the different immunological mechanisms between aquaporin 4 antibody-associated optic neuritis (AQP4-ON) and myelin oligodendrocyte glycoprotein antibody-associated optic neuritis (MOG-ON) based on RNA sequencing (RNA-seq) of whole blood. Methods Whole blood was collected from seven healthy volunteers, 6 patients with AQP4-ON and 8 patients with MOG-ON, and used for RNA-seq analysis. An examination of immune cell infiltration was performed using the CIBERSORTx algorithm to identify infiltrated immune cells. Results RNA-seq analysis showed that the inflammatory signaling was mainly activated by TLR2, TLR5, TLR8 and TLR10 in AQP4-ON patients, while which was mainly activated by TLR1, TLR2, TLR4, TLR5 and TLR8 in MOG-ON patients. Biological function identification of differentially expressed genes (DEGs) based on Gene Ontology (GO) term and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis, as well as Disease Ontology (DO) analysis, showed that the inflammation in AQP4-ON was likely mediated by damage-associated molecular pattern (DAMP), while which in MOG-ON was likely mediated by pathogen-associated molecular pattern (PAMP). Analysis of immune cell infiltration showed that the proportion of immune cell infiltration was related to patients' vision. The infiltration ratios of monocytes (rs=0.69, P=0.006) and M0 macrophages (rs=0.66, P=0.01) were positively correlated with the BCVA (LogMAR), and the infiltration ratio of neutrophils was negatively correlated with the BCVA (LogMAR) (rs=0.65, P=0.01). Conclusion This study reveals different immunological mechanisms between AQP4-ON and MOG-ON based on transcriptomics analysis of patients' whole blood, which may expand the current knowledge regarding optic neuritis.
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Affiliation(s)
- Xuelian Chen
- Department of Ophthalmology, Affiliated Wuxi Clinical College of Nantong University, Wuxi, Jiangsu, China
- Department of Ophthalmology, Jiangnan University Medical Center (JUMC), Wuxi, Jiangsu, China
- Department of Ophthalmology, Wuxi No.2 People’s Hospital, Wuxi, Jiangsu, China
| | - Libo Cheng
- Department of Ophthalmology, Affiliated Wuxi Clinical College of Nantong University, Wuxi, Jiangsu, China
- Department of Ophthalmology, Jiangnan University Medical Center (JUMC), Wuxi, Jiangsu, China
- Department of Ophthalmology, Wuxi No.2 People’s Hospital, Wuxi, Jiangsu, China
- Department of Ophthalmology, The Affiliated Wuxi No.2 People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu, China
| | - Ying Pan
- Department of Ophthalmology, Affiliated Wuxi Clinical College of Nantong University, Wuxi, Jiangsu, China
- Department of Ophthalmology, Jiangnan University Medical Center (JUMC), Wuxi, Jiangsu, China
- Department of Ophthalmology, Wuxi No.2 People’s Hospital, Wuxi, Jiangsu, China
- Department of Ophthalmology, The Affiliated Wuxi No.2 People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu, China
| | - Peng Chen
- Department of Ophthalmology, Jiangnan University Medical Center (JUMC), Wuxi, Jiangsu, China
- Department of Ophthalmology, Wuxi No.2 People’s Hospital, Wuxi, Jiangsu, China
- Department of Ophthalmology, The Affiliated Wuxi No.2 People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu, China
| | - Yidan Luo
- Department of Ophthalmology, Affiliated Wuxi Clinical College of Nantong University, Wuxi, Jiangsu, China
- Department of Ophthalmology, Jiangnan University Medical Center (JUMC), Wuxi, Jiangsu, China
- Department of Ophthalmology, Wuxi No.2 People’s Hospital, Wuxi, Jiangsu, China
| | - Shiyi Li
- Department of Ophthalmology, Jiangnan University Medical Center (JUMC), Wuxi, Jiangsu, China
- Department of Ophthalmology, Wuxi No.2 People’s Hospital, Wuxi, Jiangsu, China
- Department of Ophthalmology, The Affiliated Wuxi No.2 People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu, China
| | - Wenjun Zou
- Department of Ophthalmology, Affiliated Wuxi Clinical College of Nantong University, Wuxi, Jiangsu, China
- Department of Ophthalmology, Jiangnan University Medical Center (JUMC), Wuxi, Jiangsu, China
- Department of Ophthalmology, Wuxi No.2 People’s Hospital, Wuxi, Jiangsu, China
- Department of Ophthalmology, The Affiliated Wuxi No.2 People’s Hospital of Nanjing Medical University, Wuxi, Jiangsu, China
| | - Ke Wang
- National Health Commission (NHC) Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu, China
- Department of Radiopharmaceuticals, School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, China
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Wu C, Wei X, Men X, Xu Y, Bai J, Wang Y, Zhou L, Yu YL, Xu ZR, Chen ML, Wang JH. Open flow cytometer with the combination of 3D hydrodynamic single cell focusing and confocal laser-induced fluorescence detection. Talanta 2023; 258:124424. [PMID: 36905790 DOI: 10.1016/j.talanta.2023.124424] [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: 01/28/2023] [Revised: 02/26/2023] [Accepted: 03/04/2023] [Indexed: 03/08/2023]
Abstract
Flow cytometry is among the most powerful tools for single-cell analysis, while the high cost and mechanical complexity of the commercial instrumentation limit the applications in personalized single-cell analysis. For this issue, we hereby construct an open and low-cost flow cytometer. It is highly compact to integrate the functions of (1) single cell aligning by a lab-made modularized 3D hydrodynamic focusing device, and (2) fluorescence detection of the single cells by a confocal laser-induced fluorescence (LIF) detector. The ceiling cost of the entire hardware for the LIF detection unit and 3D focusing device is $ 3200 and $ 400 respectively. A sheath flow velocity of 150 μL/min produces a focused sample stream of 17.6 μm × 14.6 μm at sample flow of 2 μL/min, based on the LIF response frequency and the laser beam spot diameter. The assay performance of the flow cytometer was evaluated by characterizing fluorescent microparticles and acridine orange (AO) stained HepG2 cells, producing throughputs of 40.5/s and 6.2/s respectively. Favorable assay precision and accuracy were demonstrated by the agreement of frequency histogram with imaging analysis, and good Gaussian-like distributions of fluorescent microparticles and AO-stained HepG2 cells. Practically, the flow cytometer was successfully applied for the evaluation of ROS generation in single HepG2 cells.
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Affiliation(s)
- Chengxin Wu
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang, 110819, China
| | - Xing Wei
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang, 110819, China
| | - Xue Men
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang, 110819, China
| | - Yulong Xu
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang, 110819, China
| | - Junjie Bai
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang, 110819, China
| | - Yu Wang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang, 110819, China
| | - Lei Zhou
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, 730000, China
| | - Yong-Liang Yu
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang, 110819, China
| | - Zhang-Run Xu
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang, 110819, China
| | - Ming-Li Chen
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang, 110819, China.
| | - Jian-Hua Wang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang, 110819, China.
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50
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Arifuzzman AKM, Asmare N, Ozkaya-Ahmadov T, Civelekoglu O, Wang N, Sarioglu AF. An autonomous microchip for real-time, label-free immune cell analysis. Biosens Bioelectron 2023; 222:114916. [PMID: 36462431 DOI: 10.1016/j.bios.2022.114916] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/05/2022] [Accepted: 11/13/2022] [Indexed: 11/21/2022]
Abstract
Characterization of cell populations and identification of distinct subtypes based on surface markers are needed in a variety of applications from basic research and clinical assays to cell manufacturing. Conventional immunophenotyping techniques such as flow cytometry or fluorescence microscopy require immunolabeling of cells, expensive and complex instrumentation, skilled operators, and are therefore incompatible with field deployment and automated cell manufacturing systems. In this work, we introduce an autonomous microchip that can electronically quantify the immunophenotypical composition of a cell suspension. Our microchip identifies different cell subtypes by capturing each in different microfluidic chambers functionalized against the markers of the target populations. All on-chip activity is electronically monitored by an integrated sensor network, which informs an algorithm determining subpopulation fractions from chip-wide immunocapture statistics in real time. Moreover, optimal operational conditions within the chip are enforced through a closed-loop feedback control on the sensor data and the cell flow speed, and hence, the antibody-antigen interaction time is maintained within its optimal range for selective immunocapture. We apply our microchip to analyze a mixture of unlabeled CD4+ and CD8+ T cell sub-populations and then validated the results against flow cytometry measurements. The demonstrated capability to quantitatively analyze immune cells with no labels has the potential to enable not only autonomous biochip-based immunoassays for remote testing but also cell manufacturing bioreactors with built-in, adaptive quality control.
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Affiliation(s)
- A K M Arifuzzman
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Norh Asmare
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Tevhide Ozkaya-Ahmadov
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Ozgun Civelekoglu
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Ningquan Wang
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - A Fatih Sarioglu
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA; Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA; Institute for Electronics and Nanotechnology, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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