1
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Fisch L, Heming M, Schulte-Mecklenbeck A, Gross CC, Zumdick S, Barkhau C, Emden D, Ernsting J, Leenings R, Sarink K, Winter NR, Dannlowski U, Wiendl H, Hörste GMZ, Hahn T. GateNet: A novel neural network architecture for automated flow cytometry gating. Comput Biol Med 2024; 179:108820. [PMID: 39002319 DOI: 10.1016/j.compbiomed.2024.108820] [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: 01/19/2024] [Revised: 06/12/2024] [Accepted: 06/25/2024] [Indexed: 07/15/2024]
Abstract
BACKGROUND AND OBJECTIVE Flow cytometry is a widely used technique for identifying cell populations in patient-derived fluids, such as peripheral blood (PB) or cerebrospinal fluid (CSF). Despite its ubiquity in research and clinical practice, the process of gating, i.e., manually identifying cell types, is labor-intensive and error-prone. The objective of this study is to address this challenge by introducing GateNet, a neural network architecture designed for fully end-to-end automated gating without the need for correcting batch effects. METHODS For this study a unique dataset is used which comprises over 8,000,000 events from N = 127 PB and CSF samples which were manually labeled independently by four experts. Applying cross-validation, the classification performance of GateNet is compared to the human experts performance. Additionally, GateNet is applied to a publicly available dataset to evaluate generalization. The classification performance is measured using the F1 score. RESULTS GateNet achieves F1 scores ranging from 0.910 to 0.997 demonstrating human-level performance on samples unseen during training. In the publicly available dataset, GateNet confirms its generalization capabilities with an F1 score of 0.936. Importantly, we also show that GateNet only requires ≈10 samples to reach human-level performance. Finally, gating with GateNet only takes 15 microseconds per event utilizing graphics processing units (GPU). CONCLUSIONS GateNet enables fully end-to-end automated gating in flow cytometry, overcoming the labor-intensive and error-prone nature of manual adjustments. The neural network achieves human-level performance on unseen samples and generalizes well to diverse datasets. Notably, its data efficiency, requiring only ∼10 samples to reach human-level performance, positions GateNet as a widely applicable tool across various domains of flow cytometry.
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Affiliation(s)
- Lukas Fisch
- University of Münster, Institute for Translational Psychiatry, Münster, Germany.
| | - Michael Heming
- Department of Neurology with Institute of Translational Neurology, University and University Hospital Münster, Münster, Germany
| | - Andreas Schulte-Mecklenbeck
- Department of Neurology with Institute of Translational Neurology, University and University Hospital Münster, Münster, Germany
| | - Catharina C Gross
- Department of Neurology with Institute of Translational Neurology, University and University Hospital Münster, Münster, Germany
| | - Stefan Zumdick
- University of Münster, Institute for Translational Psychiatry, Münster, Germany
| | - Carlotta Barkhau
- University of Münster, Institute for Translational Psychiatry, Münster, Germany
| | - Daniel Emden
- University of Münster, Institute for Translational Psychiatry, Münster, Germany
| | - Jan Ernsting
- University of Münster, Institute for Translational Psychiatry, Münster, Germany; Institute for Geoinformatics, University of Münster, Germany; Faculty of Mathematics and Computer Science, University of Münster, Germany
| | - Ramona Leenings
- University of Münster, Institute for Translational Psychiatry, Münster, Germany
| | - Kelvin Sarink
- University of Münster, Institute for Translational Psychiatry, Münster, Germany
| | - Nils R Winter
- University of Münster, Institute for Translational Psychiatry, Münster, Germany
| | - Udo Dannlowski
- University of Münster, Institute for Translational Psychiatry, Münster, Germany
| | - Heinz Wiendl
- Department of Neurology with Institute of Translational Neurology, University and University Hospital Münster, Münster, Germany
| | - Gerd Meyer Zu Hörste
- Department of Neurology with Institute of Translational Neurology, University and University Hospital Münster, Münster, Germany
| | - Tim Hahn
- University of Münster, Institute for Translational Psychiatry, Münster, Germany
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Seheult JN, Weybright MJ, Jevremovic D, Shi M, Olteanu H, Horna P. Computational Flow Cytometry Accurately Identifies Sezary Cells Based on Simplified Aberrancy and Clonality Features. J Invest Dermatol 2024; 144:1590-1599.e3. [PMID: 38237727 DOI: 10.1016/j.jid.2023.12.020] [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: 10/11/2023] [Revised: 12/21/2023] [Accepted: 12/24/2023] [Indexed: 03/09/2024]
Abstract
Flow cytometric identification of circulating neoplastic cells (Sezary cells) in patients with mycosis fungoides and Sezary syndrome is essential for diagnosis, staging, and prognosis. Although recent advances have improved the performance of this laboratory assay, the complex immunophenotype of Sezary cells and overlap with reactive T cells demand a high level of analytic expertise. We utilized machine learning to simplify this analysis using only 2 predefined Sezary cell-gating plots. We studied 114 samples from 59 patients with Sezary syndrome/mycosis fungoides and 66 samples from unique patients with inflammatory dermatoses. A single dimensionality reduction plot highlighted all TCR constant β chain-restricted (clonal) CD3+/CD4+ T cells detected by expert analysis. On receiver operator curve analysis, an aberrancy scale feature computed by comparison with controls (area under the curve = 0.98) outperformed loss of CD2 (0.76), CD3 (0.83), CD7 (0.77), and CD26 (0.82) in discriminating Sezary cells from reactive CD4+ T cells. Our results closely mirrored those obtained by exhaustive expert analysis for event classification (positive percentage agreement = 100%, negative percentage agreement = 99%) and Sezary cell quantitation (regression slope = 1.003, R squared = 0.9996). We demonstrate the potential of machine learning to simplify the accurate identification of Sezary cells.
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Affiliation(s)
- Jansen N Seheult
- Division of Hematopathology, Mayo Clinic, Rochester, Minnesota, USA
| | | | | | - Min Shi
- Division of Hematopathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Horatiu Olteanu
- Division of Hematopathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Pedro Horna
- Division of Hematopathology, Mayo Clinic, Rochester, Minnesota, USA.
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3
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Sun X, Teng X, Liu C, Tian W, Cheng J, Hao S, Jin Y, Hong L, Zheng Y, Dai X, Wu L, Liu L, Teng X, Shi Y, Zhao P, Fang W, Shi Y, Bao X. A Pathologically Friendly Strategy for Determining the Organ-specific Spatial Tumor Microenvironment Topology in Lung Adenocarcinoma Through the Integration of snRandom-seq and Imaging Mass Cytometry. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308892. [PMID: 38682485 PMCID: PMC11234426 DOI: 10.1002/advs.202308892] [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: 11/19/2023] [Revised: 03/24/2024] [Indexed: 05/01/2024]
Abstract
Heterogeneous organ-specific responses to immunotherapy exist in lung cancer. Dissecting tumor microenvironment (TME) can provide new insights into the mechanisms of divergent responses, the process of which remains poor, partly due to the challenges associated with single-cell profiling using formalin-fixed paraffin-embedded (FFPE) materials. In this study, single-cell nuclei RNA sequencing and imaging mass cytometry (IMC) are used to dissect organ-specific cellular and spatial TME based on FFPE samples from paired primary lung adenocarcinoma (LUAD) and metastases. Single-cell analyses of 84 294 cells from sequencing and 250 600 cells from IMC reveal divergent organ-specific immune niches. For sites of LUAD responding well to immunotherapy, including primary LUAD and adrenal gland metastases, a significant enrichment of B, plasma, and T cells is detected. Spatially resolved maps reveal cellular neighborhoods recapitulating functional units of the tumor ecosystem and the spatial proximity of B and CD4+ T cells at immunogenic sites. Various organ-specific densities of tertiary lymphoid structures are observed. Immunosuppressive sites, including brain and liver metastases, are deposited with collagen I, and T cells at these sites highly express TIM-3. This study originally deciphers the single-cell landscape of the organ-specific TME at both cellular and spatial levels for LUAD, indicating the necessity for organ-specific treatment approaches.
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Affiliation(s)
- Xuqi Sun
- Department of Medical OncologyThe First Affiliated HospitalZhejiang University School of MedicineHangzhou310003China
| | - Xiao Teng
- Department of Thoracic SurgeryThe First Affiliated HospitalZhejiang University School of MedicineHangzhou310003China
| | - Chuan Liu
- Department of Medical OncologyThe First Affiliated HospitalZhejiang University School of MedicineHangzhou310003China
| | - Weihong Tian
- Changzhou Third People's HospitalChangzhou Medical CenterNanjing Medical University140 Hanzhong Rd, GulouNanjingJiangsu210029China
| | - Jinlin Cheng
- State Key Laboratory for Diagnosis and Treatment of Infectious DiseasesThe First Affiliated HospitalZhejiang University School of MedicineHangzhou310003China
| | - Shuqiang Hao
- Department of Medical OncologyThe First Affiliated HospitalZhejiang University School of MedicineHangzhou310003China
| | - Yuzhi Jin
- Department of Medical OncologyThe First Affiliated HospitalZhejiang University School of MedicineHangzhou310003China
| | - Libing Hong
- Department of Medical OncologyThe First Affiliated HospitalZhejiang University School of MedicineHangzhou310003China
| | - Yongqiang Zheng
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhou510060China
| | - Xiaomeng Dai
- Department of Medical OncologyThe First Affiliated HospitalZhejiang University School of MedicineHangzhou310003China
| | - Linying Wu
- Department of Respiratory DiseaseThe First Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhou310003China
| | - Lulu Liu
- Department of Medical OncologyThe First Affiliated HospitalZhejiang University School of MedicineHangzhou310003China
| | - Xiaodong Teng
- Department of PathologyThe First Affiliated HospitalZhejiang University School of MedicineHangzhou310003China
| | - Yi Shi
- Bio‐X InstitutesKey Laboratory for the Genetics of Developmental and Neuropsychiatric DisordersShanghai Jiao Tong University1954 Huashan RoadShanghai200030China
| | - Peng Zhao
- Department of Medical OncologyThe First Affiliated HospitalZhejiang University School of MedicineHangzhou310003China
| | - Weijia Fang
- Department of Medical OncologyThe First Affiliated HospitalZhejiang University School of MedicineHangzhou310003China
| | - Yu Shi
- State Key Laboratory for Diagnosis and Treatment of Infectious DiseasesThe First Affiliated HospitalZhejiang University School of MedicineHangzhou310003China
| | - Xuanwen Bao
- Department of Medical OncologyThe First Affiliated HospitalZhejiang University School of MedicineHangzhou310003China
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4
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Zhang M, Zhang Y, Zhang J, Zhang J, Gao S, Li Z, Tao K, Liang X, Pan J, Zhu M. An automatic analysis and quality assurance method for lymphocyte subset identification. Clin Chem Lab Med 2024; 62:1411-1420. [PMID: 38217085 DOI: 10.1515/cclm-2023-1141] [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: 10/12/2023] [Accepted: 12/20/2023] [Indexed: 01/15/2024]
Abstract
OBJECTIVES Lymphocyte subsets are the predictors of disease diagnosis, treatment, and prognosis. Determination of lymphocyte subsets is usually carried out by flow cytometry. Despite recent advances in flow cytometry analysis, most flow cytometry data can be challenging with manual gating, which is labor-intensive, time-consuming, and error-prone. This study aimed to develop an automated method to identify lymphocyte subsets. METHODS We propose a knowledge-driven combined with data-driven method which can gate automatically to achieve subset identification. To improve accuracy and stability, we have implemented a Loop Adjustment Gating to optimize the gating result of the lymphocyte population. Furthermore, we have incorporated an anomaly detection mechanism to issue warnings for samples that might not have been successfully analyzed, ensuring the quality of the results. RESULTS The evaluation showed a 99.2 % correlation between our method results and manual analysis with a dataset of 2,000 individual cases from lymphocyte subset assays. Our proposed method attained 97.7 % accuracy for all cases and 100 % for the high-confidence cases. With our automated method, 99.1 % of manual labor can be saved when reviewing only the low-confidence cases, while the average turnaround time required is only 29 s, reducing by 83.7 %. CONCLUSIONS Our proposed method can achieve high accuracy in flow cytometry data from lymphocyte subset assays. Additionally, it can save manual labor and reduce the turnaround time, making it have the potential for application in the laboratory.
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Affiliation(s)
- MinYang Zhang
- Department of Digital Management Center, Guangzhou KingMed Diagnostics Group Co., Ltd., Guangzhou Kingmed Center for Clinical Laboratory Co., Ltd., Guangzhou, Guandong, P.R. China
| | - YaLi Zhang
- Department of Digital Management Center, Guangzhou KingMed Diagnostics Group Co., Ltd., Guangzhou Kingmed Center for Clinical Laboratory Co., Ltd., Guangzhou, Guandong, P.R. China
| | - JingWen Zhang
- Department of Clinical Hematology and Flow Cytometry Lab, Guangzhou Kingmed Center for Clinical Laboratory Co., Ltd., Guangzhou, Guandong, P.R. China
| | - JiaLi Zhang
- Department of Clinical Hematology and Flow Cytometry Lab, Guangzhou Kingmed Center for Clinical Laboratory Co., Ltd., Guangzhou, Guandong, P.R. China
| | - SiYuan Gao
- Department of Digital Management Center, Guangzhou KingMed Diagnostics Group Co., Ltd., Guangzhou Kingmed Center for Clinical Laboratory Co., Ltd., Guangzhou, Guandong, P.R. China
| | - ZeChao Li
- Department of Digital Management Center, Guangzhou KingMed Diagnostics Group Co., Ltd., Guangzhou Kingmed Center for Clinical Laboratory Co., Ltd., Guangzhou, Guandong, P.R. China
| | - KangPei Tao
- Department of Digital Management Center, Guangzhou KingMed Diagnostics Group Co., Ltd., Guangzhou Kingmed Center for Clinical Laboratory Co., Ltd., Guangzhou, Guandong, P.R. China
| | - XiaoDan Liang
- Department of Digital Management Center, Guangzhou KingMed Diagnostics Group Co., Ltd., Guangzhou Kingmed Center for Clinical Laboratory Co., Ltd., Guangzhou, Guandong, P.R. China
| | - JianHua Pan
- Department of Clinical Hematology and Flow Cytometry Lab, Guangzhou Kingmed Center for Clinical Laboratory Co., Ltd., Guangzhou, Guandong, P.R. China
| | - Min Zhu
- Department of Digital Management Center, Guangzhou KingMed Diagnostics Group Co., Ltd., Guangzhou Kingmed Center for Clinical Laboratory Co., Ltd., Guangzhou, Guandong, P.R. China
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5
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Hou H, Zhang R, Li J. Artificial intelligence in the clinical laboratory. Clin Chim Acta 2024; 559:119724. [PMID: 38734225 DOI: 10.1016/j.cca.2024.119724] [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: 04/17/2024] [Revised: 05/07/2024] [Accepted: 05/08/2024] [Indexed: 05/13/2024]
Abstract
Laboratory medicine has become a highly automated medical discipline. Nowadays, artificial intelligence (AI) applied to laboratory medicine is also gaining more and more attention, which can optimize the entire laboratory workflow and even revolutionize laboratory medicine in the future. However, only a few commercially available AI models are currently approved for use in clinical laboratories and have drawbacks such as high cost, lack of accuracy, and the need for manual review of model results. Furthermore, there are a limited number of literature reviews that comprehensively address the research status, challenges, and future opportunities of AI applications in laboratory medicine. Our article begins with a brief introduction to AI and some of its subsets, then reviews some AI models that are currently being used in clinical laboratories or that have been described in emerging studies, and explains the existing challenges associated with their application and possible solutions, finally provides insights into the future opportunities of the field. We highlight the current status of implementation and potential applications of AI models in different stages of the clinical testing process.
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Affiliation(s)
- Hanjing Hou
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, PR China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Rui Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, PR China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China.
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, PR China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China.
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6
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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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7
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Jyoti TP, Chandel S, Singh R. Flow cytometry: Aspects and application in plant and biological science. JOURNAL OF BIOPHOTONICS 2024; 17:e202300423. [PMID: 38010848 DOI: 10.1002/jbio.202300423] [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: 10/10/2023] [Accepted: 10/28/2023] [Indexed: 11/29/2023]
Abstract
Flow cytometry is a potent method that enables the quick and concurrent investigation of several characteristics of single cells in solution. Photodiodes or photomultiplier tubes are employed to detect the dispersed and fluorescent light signals that are produced by the laser beam as it passes through the cells. Photodetectors transform the light signals produced by the laser into electrical impulses. A computer then analyses these electrical impulses to identify and measure the various cell populations depending on their fluorescence or light scattering characteristics. Based on their fluorescence or light scattering properties, cell populations can be examined and/or isolated. This review covers the basic principle, components, working and specific biological applications of flow cytometry, including studies on plant, cell and molecular biology and methods employed for data processing and interpretation as well as the potential future relevance of this methodology in light of retrospective analysis and recent advancements in flow cytometry.
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Affiliation(s)
- Thakur Prava Jyoti
- Department of Pharmacognosy, ISF College of Pharmacy, Moga, Punjab, India
| | - Shivani Chandel
- Department of Pharmacognosy, ISF College of Pharmacy, Moga, Punjab, India
| | - Rajveer Singh
- Department of Pharmacognosy, ISF College of Pharmacy, Moga, Punjab, India
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8
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Dott T, Culina S, Chemali R, Mansour CA, Dubois F, Jagla B, Doisne JM, Rogge L, Huetz F, Jönsson F, Commere PH, Di Santo J, Terrier B, Quintana-Murci L, Duffy D, Hasan M. Standardized high-dimensional spectral cytometry protocol and panels for whole blood immune phenotyping in clinical and translational studies. Cytometry A 2024; 105:124-138. [PMID: 37751141 DOI: 10.1002/cyto.a.24801] [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: 07/18/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 09/27/2023]
Abstract
Flow cytometry is the method of choice for immunophenotyping in the context of clinical, translational, and systems immunology studies. Among the latter, the Milieu Intérieur (MI) project aims at defining the boundaries of a healthy immune response to identify determinants of immune response variation. MI used immunophenotyping of a 1000 healthy donor cohort by flow cytometry as a principal outcome for immune variance at steady state. New generation spectral cytometers now enable high-dimensional immune cell characterization from small sample volumes. Therefore, for the MI 10-year follow up study, we have developed two high-dimensional spectral flow cytometry panels for deep characterization of innate and adaptive whole blood immune cells (35 and 34 fluorescent markers, respectively). We have standardized the protocol for sample handling, staining, acquisition, and data analysis. This approach enables the reproducible quantification of over 182 immune cell phenotypes at a single site. We have applied the protocol to discern minor differences between healthy and patient samples and validated its value for application in immunomonitoring studies. Our protocol is currently used for characterization of the impact of age and environmental factors on peripheral blood immune phenotypes of >400 donors from the initial MI cohort.
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Affiliation(s)
- Tom Dott
- Cytometry and Biomarkers UTechS, Institut Pasteur, Université Paris Cité, Paris, France
- Translational Immunology Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - Slobodan Culina
- Cytometry and Biomarkers UTechS, Institut Pasteur, Université Paris Cité, Paris, France
| | - Rene Chemali
- Cytometry and Biomarkers UTechS, Institut Pasteur, Université Paris Cité, Paris, France
| | | | - Florian Dubois
- Cytometry and Biomarkers UTechS, Institut Pasteur, Université Paris Cité, Paris, France
- Translational Immunology Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - Bernd Jagla
- Cytometry and Biomarkers UTechS, Institut Pasteur, Université Paris Cité, Paris, France
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université Paris Cité, Paris, France
| | - Jean Marc Doisne
- Innate Immunity Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - Lars Rogge
- Immunoregulation Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - François Huetz
- Unit of Antibodies in Therapy and Pathology, INSERM UMR1222, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Friederike Jönsson
- Unit of Antibodies in Therapy and Pathology, INSERM UMR1222, Institut Pasteur, Université de Paris Cité, Paris, France
- CNRS, Paris, France
| | - Pierre-Henri Commere
- Cytometry and Biomarkers UTechS, Institut Pasteur, Université Paris Cité, Paris, France
| | - James Di Santo
- Innate Immunity Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | | | - Lluis Quintana-Murci
- Human Evolutionary Genetics Unit, CNRS, Institut Pasteur, Université Paris Cité, UMR2000, Paris, France
| | - Darragh Duffy
- Cytometry and Biomarkers UTechS, Institut Pasteur, Université Paris Cité, Paris, France
- Translational Immunology Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - Milena Hasan
- Cytometry and Biomarkers UTechS, Institut Pasteur, Université Paris Cité, Paris, France
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9
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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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10
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Ask EH, Tschan-Plessl A, Hoel HJ, Kolstad A, Holte H, Malmberg KJ. MetaGate: Interactive Analysis of High-Dimensional Cytometry Data with Meta Data Integration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.27.564454. [PMID: 37961421 PMCID: PMC10634916 DOI: 10.1101/2023.10.27.564454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Flow cytometry is a powerful technology for high-throughput protein quantification at the single-cell level, widely used in basic research and routine clinical diagnostics. Traditionally, data analysis is carried out using manual gating, in which cut-offs are defined manually for each marker. Recent technical advances, including the introduction of mass cytometry, have increased the number of proteins that can be simultaneously assessed in each cell. To tackle the resulting escalation in data complexity, numerous new analysis algorithms have been developed. However, many of these show limitations in terms of providing statistical testing, data sharing, cross-experiment comparability integration with clinical data. We developed MetaGate as a platform for interactive statistical analysis and visualization of manually gated high-dimensional cytometry data with integration of clinical meta data. MetaGate allows manual gating to take place in traditional cytometry analysis software, while providing a combinatorial gating system for simple and transparent definition of biologically relevant cell populations. We demonstrate the utility of MetaGate through a comprehensive analysis of peripheral blood immune cells from 28 patients with diffuse large B-cell lymphoma (DLBCL) along with 17 age- and sex-matched healthy controls using two mass cytometry panels made of a total of 55 phenotypic markers. In a two-step process, raw data from 143 FCS files is first condensed through a data reduction algorithm and combined with information from manual gates, user-defined cellular populations and clinical meta data. This results in one single small project file containing all relevant information to allow rapid statistical calculation and visualization of any desired comparison, including box plots, heatmaps and volcano plots. Our detailed characterization of the peripheral blood immune cell repertoire in patients with DLBCL corroborate previous reports showing expansion of monocytic myeloid-derived suppressor cells, as well as an inverse correlation between NK cell numbers and disease progression.
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Affiliation(s)
- Eivind Heggernes Ask
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- The Precision Immunotherapy Alliance, University of Oslo, Oslo, Norway
| | - Astrid Tschan-Plessl
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Division of Hematology, University Hospital Basel, Basel, Switzerland
| | - Hanna Julie Hoel
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Arne Kolstad
- Department of Oncology, Innlandet Hospital Trust Division Gjøvik, Lillehammer, Norway
| | - Harald Holte
- Department of Oncology, Oslo University Hospital, Oslo, Norway
- K.G. Jebsen Centre for B cell malignancies, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Karl-Johan Malmberg
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- The Precision Immunotherapy Alliance, University of Oslo, Oslo, Norway
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
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11
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Montante S, Chen Y, Brinkman RR. flowSim: Near duplicate detection for flow cytometry data. Cytometry A 2023; 103:889-901. [PMID: 37530476 PMCID: PMC10834853 DOI: 10.1002/cyto.a.24776] [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: 04/21/2023] [Revised: 06/22/2023] [Accepted: 07/11/2023] [Indexed: 08/03/2023]
Abstract
The analysis of large amounts of data is important for the development of machine learning (ML) models. flowSim is the first algorithm designed to visualize, detect and remove highly redundant information in flow cytometry (FCM) training sets to decrease the computational time for training and increase the performance of ML algorithms by reducing overfitting. flowSim performs near duplicate image detection by combining community detection algorithms with the density analysis of the marker expression values. flowSim clustering compared to consensus manual clustering on a dataset composed of 160 images of bivariate FCM data had a mean Adjusted Rand Index of 0.90, demonstrating its efficiency in identifying similar patterns. flowSim selectively discarded near duplicate files in datasets constructed with known redundancy, and removed 92.6% of FCM images in a dataset of over 500,000 drawn from public repositories.
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Affiliation(s)
- Sebastiano Montante
- Terry Fox Laboratory, BC Cancer Research, Vancouver, British Columbia, Canada
| | - Yixuan Chen
- Terry Fox Laboratory, BC Cancer Research, Vancouver, British Columbia, Canada
| | - Ryan R. Brinkman
- Terry Fox Laboratory, BC Cancer Research, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada, 675 West 10th Avenue
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12
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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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13
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Räuber S, Nelke C, Schroeter CB, Barman S, Pawlitzki M, Ingwersen J, Akgün K, Günther R, Garza AP, Marggraf M, Dunay IR, Schreiber S, Vielhaber S, Ziemssen T, Melzer N, Ruck T, Meuth SG, Herty M. Classifying flow cytometry data using Bayesian analysis helps to distinguish ALS patients from healthy controls. Front Immunol 2023; 14:1198860. [PMID: 37600819 PMCID: PMC10434536 DOI: 10.3389/fimmu.2023.1198860] [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: 04/02/2023] [Accepted: 07/13/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction Given its wide availability and cost-effectiveness, multidimensional flow cytometry (mFC) became a core method in the field of immunology allowing for the analysis of a broad range of individual cells providing insights into cell subset composition, cellular behavior, and cell-to-cell interactions. Formerly, the analysis of mFC data solely relied on manual gating strategies. With the advent of novel computational approaches, (semi-)automated gating strategies and analysis tools complemented manual approaches. Methods Using Bayesian network analysis, we developed a mathematical model for the dependencies of different obtained mFC markers. The algorithm creates a Bayesian network that is a HC tree when including raw, ungated mFC data of a randomly selected healthy control cohort (HC). The HC tree is used to classify whether the observed marker distribution (either patients with amyotrophic lateral sclerosis (ALS) or HC) is predicted. The relative number of cells where the probability q is equal to zero is calculated reflecting the similarity in the marker distribution between a randomly chosen mFC file (ALS or HC) and the HC tree. Results Including peripheral blood mFC data from 68 ALS and 35 HC, the algorithm could correctly identify 64/68 ALS cases. Tuning of parameters revealed that the combination of 7 markers, 200 bins, and 20 patients achieved the highest AUC on a significance level of p < 0.0001. The markers CD4 and CD38 showed the highest zero probability. We successfully validated our approach by including a second, independent ALS and HC cohort (55 ALS and 30 HC). In this case, all ALS were correctly identified and side scatter and CD20 yielded the highest zero probability. Finally, both datasets were analyzed by the commercially available algorithm 'Citrus', which indicated superior ability of Bayesian network analysis when including raw, ungated mFC data. Discussion Bayesian network analysis might present a novel approach for classifying mFC data, which does not rely on reduction techniques, thus, allowing to retain information on the entire dataset. Future studies will have to assess the performance when discriminating clinically relevant differential diagnoses to evaluate the complementary diagnostic benefit of Bayesian network analysis to the clinical routine workup.
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Affiliation(s)
- Saskia Räuber
- Department of Neurology, Medical Faculty, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
| | - Christopher Nelke
- Department of Neurology, Medical Faculty, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
| | - Christina B. Schroeter
- Department of Neurology, Medical Faculty, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
| | - Sumanta Barman
- Department of Neurology, Medical Faculty, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
| | - Marc Pawlitzki
- Department of Neurology, Medical Faculty, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
| | - Jens Ingwersen
- Department of Neurology, Medical Faculty, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
| | - Katja Akgün
- Department of Neurology, Center of Clinical Neuroscience, University Hospital Carl Gustav Carus, Dresden University of Technology, Dresden, Germany
| | - Rene Günther
- Department of Neurology, Center of Clinical Neuroscience, University Hospital Carl Gustav Carus, Dresden University of Technology, Dresden, Germany
| | - Alejandra P. Garza
- Institute of Inflammation and Neurodegeneration, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Michaela Marggraf
- Department of Neurology, Center of Clinical Neuroscience, University Hospital Carl Gustav Carus, Dresden University of Technology, Dresden, Germany
| | - Ildiko Rita Dunay
- Institute of Inflammation and Neurodegeneration, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Stefanie Schreiber
- Department of Neurology, Otto von Guericke University, Magdeburg, Germany
| | - Stefan Vielhaber
- Department of Neurology, Otto von Guericke University, Magdeburg, Germany
| | - Tjalf Ziemssen
- Department of Neurology, Center of Clinical Neuroscience, University Hospital Carl Gustav Carus, Dresden University of Technology, Dresden, Germany
| | - Nico Melzer
- Department of Neurology, Medical Faculty, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
| | - Tobias Ruck
- Department of Neurology, Medical Faculty, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
| | - Sven G. Meuth
- Department of Neurology, Medical Faculty, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
| | - Michael Herty
- Department of Mathematics, Institute of Geometry and Applied Mathematics, RWTH Aachen University, Aachen, Germany
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14
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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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15
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Baldzhieva A, Burnusuzov HA, Murdjeva MA, Dimcheva TD, Taskov HB. A concise review of flow cytometric methods for minimal residual disease assessment in childhood B-cell precursor acute lymphoblastic leukemia. Folia Med (Plovdiv) 2023; 65:355-361. [PMID: 38351809 DOI: 10.3897/folmed.65.e96440] [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: 10/17/2022] [Accepted: 01/04/2023] [Indexed: 02/16/2024] Open
Abstract
Minimal residual disease refers to a leukemia cell population that is resistant to chemotherapy or radiotherapy and leads to disease relapse. The assessment of MRD is crucial for making an accurate prognosis of the disease and for the choice of optimal treatment strategy. Here, we review the advantages and disadvantages of the available genetic and phenotypic methods and focus on the multiparametric flow cytometry as a promising method with greater sensitivity, speed, and standardization options. In addition, we discuss how the application of automated data analysis outweighs the use of complex combinations of windows and gates in classical analysis, thus eliminating subjective evaluation.
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16
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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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17
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Li Y, Nguyen J, Anastasiu DC, Arriaga EA. CosTaL: an accurate and scalable graph-based clustering algorithm for high-dimensional single-cell data analysis. Brief Bioinform 2023; 24:bbad157. [PMID: 37150778 PMCID: PMC10199777 DOI: 10.1093/bib/bbad157] [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: 11/10/2022] [Revised: 03/28/2023] [Accepted: 04/02/2023] [Indexed: 05/09/2023] Open
Abstract
With the aim of analyzing large-sized multidimensional single-cell datasets, we are describing a method for Cosine-based Tanimoto similarity-refined graph for community detection using Leiden's algorithm (CosTaL). As a graph-based clustering method, CosTaL transforms the cells with high-dimensional features into a weighted k-nearest-neighbor (kNN) graph. The cells are represented by the vertices of the graph, while an edge between two vertices in the graph represents the close relatedness between the two cells. Specifically, CosTaL builds an exact kNN graph using cosine similarity and uses the Tanimoto coefficient as the refining strategy to re-weight the edges in order to improve the effectiveness of clustering. We demonstrate that CosTaL generally achieves equivalent or higher effectiveness scores on seven benchmark cytometry datasets and six single-cell RNA-sequencing datasets using six different evaluation metrics, compared with other state-of-the-art graph-based clustering methods, including PhenoGraph, Scanpy and PARC. As indicated by the combined evaluation metrics, Costal has high efficiency with small datasets and acceptable scalability for large datasets, which is beneficial for large-scale analysis.
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Affiliation(s)
- Yijia Li
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 420 Washington Ave. S.E., Minneapolis, 55455, Minnesota, USA
| | - Jonathan Nguyen
- Department of Computer Science and Engineering, Santa Clara University, 500 El Camino Real, Santa Clara, 95053, California, USA
| | - David C Anastasiu
- Department of Computer Science and Engineering, Santa Clara University, 500 El Camino Real, Santa Clara, 95053, California, USA
| | - Edgar A Arriaga
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 420 Washington Ave. S.E., Minneapolis, 55455, Minnesota, USA
- Department of Chemistry, University of Minnesota, Smith Hall, 139 Smith Hall, Pleasant St SE, Minneapolis, 55455, Minnesota, USA
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18
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Fuda F, Chen M, Chen W, Cox A. Artificial intelligence in clinical multiparameter flow cytometry and mass cytometry-key tools and progress. Semin Diagn Pathol 2023; 40:120-128. [PMID: 36894355 DOI: 10.1053/j.semdp.2023.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/07/2023]
Abstract
There are many research studies and emerging tools using artificial intelligence (AI) and machine learning to augment flow and mass cytometry workflows. Emerging AI tools can quickly identify common cell populations with continuous improvement of accuracy, uncover patterns in high-dimensional cytometric data that are undetectable by human analysis, facilitate the discovery of cell subpopulations, perform semi-automated immune cell profiling, and demonstrate potential to automate aspects of clinical multiparameter flow cytometric (MFC) diagnostic workflow. Utilizing AI in the analysis of cytometry samples can reduce subjective variability and assist in breakthroughs in understanding diseases. Here we review the diverse types of AI that are being applied to clinical cytometry data and how AI is driving advances in data analysis to improve diagnostic sensitivity and accuracy. We review supervised and unsupervised clustering algorithms for cell population identification, various dimensionality reduction techniques, and their utilities in visualization and machine learning pipelines, and supervised learning approaches for classifying entire cytometry samples.Understanding the AI landscape will enable pathologists to better utilize open source and commercially available tools, plan exploratory research projects to characterize diseases, and work with machine learning and data scientists to implement clinical data analysis pipelines.
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Affiliation(s)
- Franklin Fuda
- Department of Pathology and Laboratory Medicine, University of Texas, Southwestern Medical Center, Dallas, Texas, USA
| | - Mingyi Chen
- Department of Pathology and Laboratory Medicine, University of Texas, Southwestern Medical Center, Dallas, Texas, USA
| | - Weina Chen
- Department of Pathology and Laboratory Medicine, University of Texas, Southwestern Medical Center, Dallas, Texas, USA
| | - Andrew Cox
- Lyda Hill Department of Bioinformatics, University of Texas, Southwestern Medical Center, Dallas, Texas, USA; Department of Cell and Molecular Biology, University of Texas, Southwestern Medical Center, Dallas, Texas, USA.
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19
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Spurgeon BEJ, Frelinger AL. Platelet Phenotyping by Full Spectrum Flow Cytometry. Curr Protoc 2023; 3:e687. [PMID: 36779850 DOI: 10.1002/cpz1.687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
Platelets play key roles in hemostasis, immunity, and inflammation, and tests of platelet phenotype and function are useful in studies of disease biology and pathology. Full spectrum flow cytometry offers distinct advantages over standard tests and enables the sensitive and simultaneous detection of many biomarkers. A typical assay provides a wealth of information on platelet biology and allows the assessment of in vivo activation and in vitro reactivity, as well as the discovery of novel phenotypes. Here, we describe the analysis of platelets by full spectrum flow cytometry and discuss a range of controls and methods for interpreting results. © 2023 Wiley Periodicals LLC. Basic Protocol: Platelet phenotyping by full spectrum flow cytometry Support Protocol 1: Spectral unmixing Support Protocol 2: Data preprocessing.
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Affiliation(s)
- Benjamin E J Spurgeon
- Center for Platelet Research Studies, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts
| | - Andrew L Frelinger
- Center for Platelet Research Studies, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts
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20
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Roca CP, Burton OT, Neumann J, Tareen S, Whyte CE, Gergelits V, Veiga RV, Humblet-Baron S, Liston A. A cross entropy test allows quantitative statistical comparison of t-SNE and UMAP representations. CELL REPORTS METHODS 2023; 3:100390. [PMID: 36814837 PMCID: PMC9939422 DOI: 10.1016/j.crmeth.2022.100390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 10/29/2022] [Accepted: 12/20/2022] [Indexed: 01/15/2023]
Abstract
The advent of high-dimensional single-cell data has necessitated the development of dimensionality-reduction tools. t-Distributed stochastic neighbor embedding (t-SNE) and uniform manifold approximation and projection (UMAP) are the two most frequently used approaches, allowing clear visualization of complex single-cell datasets. Despite the need for quantitative comparison, t-SNE and UMAP have largely remained visualization tools due to the lack of robust statistical approaches. Here, we have derived a statistical test for evaluating the difference between dimensionality-reduced datasets using the Kolmogorov-Smirnov test on the distributions of cross entropy of single cells within each dataset. As the approach uses the inter-relationship of single cells for comparison, the resulting statistic is robust and capable of identifying true biological variation. Further, the test provides a valid distance between single-cell datasets, allowing the organization of multiple samples into a dendrogram for quantitative comparison of complex datasets. These results demonstrate the largely untapped potential of dimensionality-reduction tools for biomedical data analysis beyond visualization.
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Affiliation(s)
- Carlos P. Roca
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Oliver T. Burton
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Julika Neumann
- VIB Center for Brain and Disease Research, 3000 Leuven, Belgium
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, 3000 Leuven, Belgium
| | - Samar Tareen
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Carly E. Whyte
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Vaclav Gergelits
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Rafael V. Veiga
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | | | - Adrian Liston
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
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21
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Obstfeld AE. Hematology and Machine Learning. J Appl Lab Med 2023; 8:129-144. [PMID: 36610431 DOI: 10.1093/jalm/jfac108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/18/2022] [Indexed: 01/09/2023]
Abstract
BACKGROUND Substantial improvements in computational power and machine learning (ML) algorithm development have vastly increased the limits of what autonomous machines are capable of. Since its beginnings in the 19th century, laboratory hematology has absorbed waves of progress yielding improvements in both of accuracy and efficiency. The next wave of change in laboratory hematology will be the result of the ML revolution that has already touched many corners of healthcare and society at large. CONTENT This review will describe the manifestations of ML and artificial intelligence (AI) already utilized in the clinical hematology laboratory. This will be followed by a topical summary of the innovative and investigational applications of this technology in each of the major subdomains within laboratory hematology. SUMMARY Application of this technology to laboratory hematology will increase standardization and efficiency by reducing laboratory staff involvement in automatable activities. This will unleash time and resources for focus on more meaningful activities such as the complexities of patient care, research and development, and process improvement.
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Affiliation(s)
- Amrom E Obstfeld
- Department of Pathology & Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
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22
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Burton RJ, Cuff SM, Morgan MP, Artemiou A, Eberl M. GeoWaVe: geometric median clustering with weighted voting for ensemble clustering of cytometry data. Bioinformatics 2023; 39:6839973. [PMID: 36413065 PMCID: PMC9805571 DOI: 10.1093/bioinformatics/btac751] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 11/08/2022] [Accepted: 11/21/2022] [Indexed: 11/23/2022] Open
Abstract
MOTIVATION Clustering is an unsupervised method for identifying structure in unlabelled data. In the context of cytometry, it is typically used to categorize cells into subpopulations of similar phenotypes. However, clustering is greatly dependent on hyperparameters and the data to which it is applied as each algorithm makes different assumptions and generates a different 'view' of the dataset. As such, the choice of clustering algorithm can significantly influence results, and there is often not one preferred method but different insights to be obtained from different methods. To overcome these limitations, consensus approaches are needed that directly address the effect of competing algorithms. To the best of our knowledge, consensus clustering algorithms designed specifically for the analysis of cytometry data are lacking. RESULTS We present a novel ensemble clustering methodology based on geometric median clustering with weighted voting (GeoWaVe). Compared to graph ensemble clustering methods that have gained popularity in single-cell RNA sequencing analysis, GeoWaVe performed favourably on different sets of high-dimensional mass and flow cytometry data. Our findings provide proof of concept for the power of consensus methods to make the analysis, visualization and interpretation of cytometry data more robust and reproducible. The wide availability of ensemble clustering methods is likely to have a profound impact on our understanding of cellular responses, clinical conditions and therapeutic and diagnostic options. AVAILABILITY AND IMPLEMENTATION GeoWaVe is available as part of the CytoCluster package https://github.com/burtonrj/CytoCluster and published on the Python Package Index https://pypi.org/project/cytocluster. Benchmarking data described are available from https://doi.org/10.5281/zenodo.7134723. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Simone M Cuff
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Matt P Morgan
- Adult Critical Care, University Hospital of Wales, Cardiff and Vale University Health Board, Cardiff CF14 4XW, UK
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23
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Heubeck A, Savage A, Henderson K, Roll C, Hernandez V, Torgerson T, Bumol T, Reading J. Cross-platform immunophenotyping of human peripheral blood mononuclear cells with four high-dimensional flow cytometry panels. Cytometry A 2022. [PMID: 36571245 DOI: 10.1002/cyto.a.24715] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 12/13/2022] [Accepted: 12/20/2022] [Indexed: 12/27/2022]
Abstract
Immunophenotyping using high dimensional flow cytometry is a central component of human immune system multi-omic studies. We present four high parameter flow cytometry panels for deep immunophenotyping of human peripheral blood mononuclear cells (PBMC). This set of four 25+ color panels include 64 cell surface markers to resolve broad immune compartment populations, as well as activation and memory of specific T, B, natural killer (NK), and myeloid lineages. Common lineage bridging markers are integrated into each panel to allow for inter-panel quality control through major lineage frequency verification. These panels were developed using a five laser BD Symphony A5 conventional cytometer and successfully transferred to a five laser Cytek Aurora spectral cytometer capable of acquiring the panels. Nine representative PBMC samples were stained with the four phenotyping panels and acquired on both instruments to evaluate population frequency and visual staining patterns for gating between the systems. Both instruments produced comparable high quality flow cytometry data and supported our decision to acquire samples on the spectral cytometer moving forward. This modular set of panels and instrument performance metrics provide guidelines for designing flow cytometry experiments suitable for longitudinal or cross-sectional immune profiling.
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Affiliation(s)
| | - Adam Savage
- Allen Institute for Immunology, Seattle, Washington, USA
| | | | - Charles Roll
- Allen Institute for Immunology, Seattle, Washington, USA
| | | | - Troy Torgerson
- Allen Institute for Immunology, Seattle, Washington, USA
| | - Thomas Bumol
- Allen Institute for Immunology, Seattle, Washington, USA
| | - Julian Reading
- Allen Institute for Immunology, Seattle, Washington, USA
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24
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Free T. Investigating myeloid cells? Go with the flow. Biotechniques 2022; 73:163-165. [PMID: 36205120 DOI: 10.2144/btn-2022-0099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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25
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Couckuyt A, Seurinck R, Emmaneel A, Quintelier K, Novak D, Van Gassen S, Saeys Y. Challenges in translational machine learning. Hum Genet 2022; 141:1451-1466. [PMID: 35246744 PMCID: PMC8896412 DOI: 10.1007/s00439-022-02439-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 02/08/2022] [Indexed: 11/25/2022]
Abstract
Machine learning (ML) algorithms are increasingly being used to help implement clinical decision support systems. In this new field, we define as "translational machine learning", joint efforts and strong communication between data scientists and clinicians help to span the gap between ML and its adoption in the clinic. These collaborations also improve interpretability and trust in translational ML methods and ultimately aim to result in generalizable and reproducible models. To help clinicians and bioinformaticians refine their translational ML pipelines, we review the steps from model building to the use of ML in the clinic. We discuss experimental setup, computational analysis, interpretability and reproducibility, and emphasize the challenges involved. We highly advise collaboration and data sharing between consortia and institutes to build multi-centric cohorts that facilitate ML methodologies that generalize across centers. In the end, we hope that this review provides a way to streamline translational ML and helps to tackle the challenges that come with it.
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Affiliation(s)
- Artuur Couckuyt
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Gent, Belgium
- Data Mining and Modeling for Biomedicine, VIB-UGent Center for Inflammation Research, Gent, Belgium
| | - Ruth Seurinck
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Gent, Belgium
- Data Mining and Modeling for Biomedicine, VIB-UGent Center for Inflammation Research, Gent, Belgium
| | - Annelies Emmaneel
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Gent, Belgium
- Data Mining and Modeling for Biomedicine, VIB-UGent Center for Inflammation Research, Gent, Belgium
| | - Katrien Quintelier
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Gent, Belgium
- Data Mining and Modeling for Biomedicine, VIB-UGent Center for Inflammation Research, Gent, Belgium
- Department of Pulmonary Diseases, Erasmus MC, Rotterdam, The Netherlands
| | - David Novak
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Gent, Belgium
- Data Mining and Modeling for Biomedicine, VIB-UGent Center for Inflammation Research, Gent, Belgium
| | - Sofie Van Gassen
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Gent, Belgium
- Data Mining and Modeling for Biomedicine, VIB-UGent Center for Inflammation Research, Gent, Belgium
| | - Yvan Saeys
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Gent, Belgium.
- Data Mining and Modeling for Biomedicine, VIB-UGent Center for Inflammation Research, Gent, Belgium.
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26
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DiSalvo M, Patrone PN, Kearsley AJ, Cooksey GA. Serial flow cytometry in an inertial focusing optofluidic microchip for direct assessment of measurement variations. LAB ON A CHIP 2022; 22:3217-3228. [PMID: 35856829 DOI: 10.1039/d1lc01169c] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Flow cytometry is an invaluable technology in biomedical research, but confidence in single-cell measurements remains limited due to a lack of appropriate techniques for uncertainty quantification (UQ). It is particularly challenging to evaluate the potential for different instrumentation designs or operating parameters to influence the measurement physics in ways that change measurement repeatability. Here, we report a direct experimental approach to UQ using a serial flow cytometer that measured each particle more than once along a flow path. The instrument was automated for real-time characterization of measurement precision and operated with particle velocities exceeding 1 m s-1, throughputs above 100 s-1, and analysis yields better than 99.9%. These achievements were enabled by a novel hybrid inertial and hydrodynamic particle focuser to tightly control particle positions and velocities. The cytometer identified ideal flow conditions with fluorescence area measurement precision on the order of 1% and characterized tradeoffs between precision, throughput, and analysis yield. The serial cytometer is anticipated to improve single-cell measurements through estimation (and subsequent control) of uncertainty contributions from various other instrument parameters leading to overall improvements in the ability to better classify sample composition and to find rare events.
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Affiliation(s)
- Matthew DiSalvo
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21287, USA
- Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA.
| | - Paul N Patrone
- Applied and Computational Mathematics Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Anthony J Kearsley
- Applied and Computational Mathematics Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Gregory A Cooksey
- Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA.
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27
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Bonilha CS. BCyto: A shiny app for flow cytometry data analysis. Mol Cell Probes 2022; 65:101848. [PMID: 35933055 DOI: 10.1016/j.mcp.2022.101848] [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: 05/25/2022] [Revised: 07/30/2022] [Accepted: 07/31/2022] [Indexed: 11/15/2022]
Abstract
Flow cytometry (FCM) is a widely used technique to simultaneously measure various characteristics of a cell or particle. Most of reliable software for FCM data analysis are commercially available at high costs. A few R packages are available; however, programming skills are required. In addition, currently, no package offers an interactive user interface (UI) with efficient tools for conventional FCM data analysis. BCyto is an open-source R package/shiny app that allows cell biologists with no coding skills to reliably analyse FCM data in R. BCyto provides intuitive axis transformation for better data visualization, easy visualization of compensation plots and modification of compensation matrices, fast generation of backgating and overlay plots, as well as built-in proliferation and dimensionality reduction tools. BCyto will not only improve accessibility to FCM data analysis but might also serve as an environment for the development of further R-based computational FCM algorithms.
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Affiliation(s)
- Caio Santos Bonilha
- Center for Research in Inflammatory Diseases, University of Sao Paulo, Ribeirao Preto, 14049-900, Brazil; Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK.
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28
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Paramithiotis E, Sugden S, Papp E, Bonhomme M, Chermak T, Crawford SY, Demetriades SZ, Galdos G, Lambert BL, Mattison J, McDade T, Pillet S, Murphy R. Cellular Immunity Is Critical for Assessing COVID-19 Vaccine Effectiveness in Immunocompromised Individuals. Front Immunol 2022; 13:880784. [PMID: 35693815 PMCID: PMC9179228 DOI: 10.3389/fimmu.2022.880784] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 04/12/2022] [Indexed: 12/28/2022] Open
Abstract
COVID-19 vaccine clinical development was conducted with unprecedented speed. Immunity measurements were concentrated on the antibody response which left significant gaps in our understanding how robust and long-lasting immune protection develops. Better understanding the cellular immune response will fill those gaps, especially in the elderly and immunocompromised populations which not only have the highest risk for severe infection, but also frequently have inadequate antibody responses. Although cellular immunity measurements are more logistically complex to conduct for clinical trials compared to antibody measurements, the feasibility and benefit of doing them in clinical trials has been demonstrated and so should be more widely adopted. Adding significant cellular response metrics will provide a deeper understanding of the overall immune response to COVID-19 vaccination, which will significantly inform vaccination strategies for the most vulnerable populations. Better monitoring of overall immunity will also substantially benefit other vaccine development efforts, and indeed any therapies that involve the immune system as part of the therapeutic strategy.
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Affiliation(s)
| | - Scott Sugden
- Scientific Team, CellCarta, Montreal, QC, Canada
| | - Eszter Papp
- Global Research and Development, CellCarta, Montreal, QC, Canada
| | - Marie Bonhomme
- Vaccine Sciences Division, Pharmaceutical Product Development (PPD) Inc., Wilmington, NC, United States
| | - Todd Chermak
- Regulatory and Government Affairs, CellCarta, Montreal, QC, Canada
| | - Stephanie Y. Crawford
- Department of Pharmacy Systems, Outcomes and Policy, University of Illinois Chicago, Chicago, IL, United States
| | | | - Gerson Galdos
- Robert J. Havey, MD Institute for Global Health, Northwestern University, Chicago, IL, United States
| | - Bruce L. Lambert
- Center for Communication and Health, Northwestern University, Evanston, IL, United States
| | - John Mattison
- Health Information, Kaiser Permanente, Pasadena, CA, United States
- Health Technology Advisory Board, Arsenal Capital, New York, NY, United States
| | - Thomas McDade
- Department of Anthropology, Northwestern University, Evanston, IL, United States
| | | | - Robert Murphy
- Robert J. Havey, MD Institute for Global Health, Northwestern University, Chicago, IL, United States
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29
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Li JL, Lin YC, Wang YF, Monaghan SA, Ko BS, Lee CC. A Chunking-for-Pooling Strategy for Cytometric Representation Learning for Automatic Hematologic Malignancy Classification. IEEE J Biomed Health Inform 2022; 26:4773-4784. [PMID: 35588419 DOI: 10.1109/jbhi.2022.3175514] [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: 11/07/2022]
Abstract
Differentiating types of hematologic malignancies is vital to determine therapeutic strategies for the newly diagnosed patients. Flow cytometry (FC) can be used as diagnostic indicator by measuring the multi-parameter fluorescent markers on thousands of antibody-bound cells, but the manual interpretation of large scale flow cytometry data has long been a time-consuming and complicated task for hematologists and laboratory professionals. Past studies have led to the development of representation learning algorithms to perform sample-level automatic classification. In this work, we propose a chunking-for-pooling strategy to include large-scale FC data into a supervised deep representation learning procedure for automatic hematologic malignancy classification. The use of discriminatively-trained representation learning strategy and the fixed-size chunking and pooling design are key components of this framework. It improves the discriminative power of the FC sample-level embedding and simultaneously addresses the robustness issue due to an inevitable use of down-sampling in conventional distribution based approaches for deriving FC representation. We evaluated our framework on two datasets. Our framework outperformed other baseline methods and achieved 92.3% unweighted average recall (UAR) for four-class recognition on the UPMC dataset and 85.0% UAR for five-class recognition on the hema.to dataset. We further compared the robustness of our proposed framework with that of the traditional downsampling approach. Analysis of the effects of the chunk size and the error cases revealed further insights about different hematologic malignancy characteristics in the FC data.
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30
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2021 White Paper on Recent Issues in Bioanalysis: ISR for Biomarkers, Liquid Biopsies, Spectral Cytometry, Inhalation/Oral & Multispecific Biotherapeutics, Accuracy/LLOQ for Flow Cytometry ( Part 2 - Recommendations on Biomarkers/CDx Assays Development & Validation, Cytometry Validation & Innovation, Biotherapeutics PK LBA Regulated Bioanalysis, Critical Reagents & Positive Controls Generation). Bioanalysis 2022; 14:627-692. [PMID: 35578974 DOI: 10.4155/bio-2022-0080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The 15th edition of the Workshop on Recent Issues in Bioanalysis (15th WRIB) was held on 27 September to 1 October 2021. Even with a last-minute move from in-person to virtual, an overwhelmingly high number of nearly 900 professionals representing pharma and biotech companies, contract research organizations (CROs), and multiple regulatory agencies still eagerly convened to actively discuss the most current topics of interest in bioanalysis. The 15th WRIB included three Main Workshops and seven Specialized Workshops that together spanned 1 week in order to allow exhaustive and thorough coverage of all major issues in bioanalysis, biomarkers, immunogenicity, gene therapy, cell therapy and vaccines. Moreover, in-depth workshops on biomarker assay development and validation (BAV) (focused on clarifying the confusion created by the increased use of the term "context of use" [COU]); mass spectrometry of proteins (therapeutic, biomarker and transgene); state-of-the-art cytometry innovation and validation; and critical reagent and positive control generation were the special features of the 15th edition. This 2021 White Paper encompasses recommendations emerging from the extensive discussions held during the workshop, and is aimed to provide the bioanalytical community with key information and practical solutions on topics and issues addressed, in an effort to enable advances in scientific excellence, improved quality and better regulatory compliance. Due to its length, the 2021 edition of this comprehensive White Paper has been divided into three parts for editorial reasons. This publication (Part 2) covers the recommendations on ISR for Biomarkers, Liquid Biopsies, Spectral Cytometry, Inhalation/Oral & Multispecific Biotherapeutics, Accuracy/LLOQ for Flow Cytometry. Part 1A (Endogenous Compounds, Small Molecules, Complex Methods, Regulated Mass Spec of Large Molecules, Small Molecule, PoC), Part 1B (Regulatory Agencies' Inputs on Bioanalysis, Biomarkers, Immunogenicity, Gene & Cell Therapy and Vaccine) and Part 3 (TAb/NAb, Viral Vector CDx, Shedding Assays; CRISPR/Cas9 & CAR-T Immunogenicity; PCR & Vaccine Assay Performance; ADA Assay Comparability & Cut Point Appropriateness) are published in volume 14 of Bioanalysis, issues 9 and 11 (2022), respectively.
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31
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Brando B. Issue Highlights-May 2022. CYTOMETRY. PART B, CLINICAL CYTOMETRY 2022; 102:185-188. [PMID: 35567410 DOI: 10.1002/cyto.b.22072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Affiliation(s)
- Bruno Brando
- Hematology Laboratory and Transfusion Center Western Milan Area Hospital Consortium 20025 Legnano (Milano), Italy
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32
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Cheung M, Campbell JJ, Thomas RJ, Braybrook J, Petzing J. Assessment of Automated Flow Cytometry Data Analysis Tools within Cell and Gene Therapy Manufacturing. Int J Mol Sci 2022; 23:ijms23063224. [PMID: 35328645 PMCID: PMC8955358 DOI: 10.3390/ijms23063224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/03/2022] [Accepted: 03/11/2022] [Indexed: 12/21/2022] Open
Abstract
Flow cytometry is widely used within the manufacturing of cell and gene therapies to measure and characterise cells. Conventional manual data analysis relies heavily on operator judgement, presenting a major source of variation that can adversely impact the quality and predictive potential of therapies given to patients. Computational tools have the capacity to minimise operator variation and bias in flow cytometry data analysis; however, in many cases, confidence in these technologies has yet to be fully established mirrored by aspects of regulatory concern. Here, we employed synthetic flow cytometry datasets containing controlled population characteristics of separation, and normal/skew distributions to investigate the accuracy and reproducibility of six cell population identification tools, each of which implement different unsupervised clustering algorithms: Flock2, flowMeans, FlowSOM, PhenoGraph, SPADE3 and SWIFT (density-based, k-means, self-organising map, k-nearest neighbour, deterministic k-means, and model-based clustering, respectively). We found that outputs from software analysing the same reference synthetic dataset vary considerably and accuracy deteriorates as the cluster separation index falls below zero. Consequently, as clusters begin to merge, the flowMeans and Flock2 software platforms struggle to identify target clusters more than other platforms. Moreover, the presence of skewed cell populations resulted in poor performance from SWIFT, though FlowSOM, PhenoGraph and SPADE3 were relatively unaffected in comparison. These findings illustrate how novel flow cytometry synthetic datasets can be utilised to validate a range of automated cell identification methods, leading to enhanced confidence in the data quality of automated cell characterisations and enumerations.
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Affiliation(s)
- Melissa Cheung
- Centre for Biological Engineering, Loughborough University, Loughborough LE11 3TU, Leicestershire, UK; (R.J.T.); (J.P.)
- Correspondence:
| | - Jonathan J. Campbell
- National Measurement Laboratory, LGC, Queens Road, Teddington TW11 0LY, Middlesex, UK; (J.J.C.); (J.B.)
| | - Robert J. Thomas
- Centre for Biological Engineering, Loughborough University, Loughborough LE11 3TU, Leicestershire, UK; (R.J.T.); (J.P.)
| | - Julian Braybrook
- National Measurement Laboratory, LGC, Queens Road, Teddington TW11 0LY, Middlesex, UK; (J.J.C.); (J.B.)
| | - Jon Petzing
- Centre for Biological Engineering, Loughborough University, Loughborough LE11 3TU, Leicestershire, UK; (R.J.T.); (J.P.)
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33
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UMAP Based Anomaly Detection for Minimal Residual Disease Quantification within Acute Myeloid Leukemia. Cancers (Basel) 2022; 14:cancers14040898. [PMID: 35205645 PMCID: PMC8870142 DOI: 10.3390/cancers14040898] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/28/2022] [Accepted: 02/02/2022] [Indexed: 11/22/2022] Open
Abstract
Simple Summary Acute myeloid leukemia (AML) is the second most frequent leukemia entity in children and adolescents, and definitely the most aggressive variant. Multiparameter flow-cytometry is one of the methodologies most useful to monitor the number of remaining leukemic cells in bone marrow (minimal residual disease, MRD) in AML patients, because it is widely available and applicable to most patients. However, AML flow cytometry data show very complex patterns and identifying leukemic cells in the data is subjective, time-consuming and requires experienced operators who are not available world-wide. In this paper, we approach automatic assessment of AML flow cytometry samples with a novel semi-supervised machine learning model, leveraging implicit expert knowledge stored in a collection of manually assessed samples. Because AML data exhibit a high degree of variability in the patterns of blast cell populations that is difficult to model, the model detects anomalies starting from the appearance of normal cell populations. Abstract Leukemia is the most frequent malignancy in children and adolescents, with acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML) as the most common subtypes. Minimal residual disease (MRD) measured by flow cytometry (FCM) has proven to be a strong prognostic factor in ALL as well as in AML. Machine learning techniques have been emerging in the field of automated MRD quantification with the objective of superseding subjective and time-consuming manual analysis of FCM-MRD data. In contrast to ALL, where supervised multi-class classification methods have been successfully deployed for MRD detection, AML poses new challenges: AML is rarer (with fewer available training data) than ALL and much more heterogeneous in its immunophenotypic appearance, where one-class classification (anomaly detection) methods seem more suitable. In this work, a new semi-supervised approach based on the UMAP algorithm for MRD detection utilizing only labels of blast free FCM samples is presented. The method is tested on a newly gathered set of AML FCM samples and results are compared to state-of-the-art methods. We reach a median F1-score of 0.794, while providing a transparent classification pipeline with explainable results that facilitates inter-disciplinary work between medical and technical experts. This work shows that despite several issues yet to overcome, the merits of automated MRD quantification can be fully exploited also in AML.
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34
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Varon E, Blumrosen G, Shefi O. A predictive model for personalization of nanotechnology-based phototherapy in cancer treatment. Front Oncol 2022; 12:1037419. [PMID: 36911792 PMCID: PMC9999042 DOI: 10.3389/fonc.2022.1037419] [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: 09/11/2022] [Accepted: 11/21/2022] [Indexed: 01/06/2023] Open
Abstract
A major challenge in radiation oncology is the prediction and optimization of clinical responses in a personalized manner. Recently, nanotechnology-based cancer treatments are being combined with photodynamic therapy (PDT) and photothermal therapy (PTT). Predictive models based on machine learning techniques can be used to optimize the clinical setup configuration, including such parameters as laser radiation intensity, treatment duration, and nanoparticle features. In this article we demonstrate a methodology that can be used to identify the optimal treatment parameters for PDT and PTT by collecting data from in vitro cytotoxicity assay of PDT/PTT-induced cell death using a single nanocomplex. We construct three machine learning prediction models, employing regression, interpolation, and low- degree analytical function fitting, to predict the laser radiation intensity and duration settings that maximize the treatment efficiency. To examine the accuracy of these prediction models, we construct a dedicated dataset for PDT, PTT, and a combined treatment; this dataset is based on cell death measurements after light radiation treatment and is divided into training and test sets. The preliminary results show that the performance of all three models is sufficient, with death rate errors of 0.09, 0.15, and 0.12 for the regression, interpolation, and analytical function fitting approaches, respectively. Nevertheless, due to its simple form, the analytical function method has an advantage in clinical application and can be used for further analysis of the sensitivity of performance to the treatment parameters. Overall, the results of this study form a baseline for a future personalized prediction model based on machine learning in the domain of combined nanotechnology- and phototherapy-based cancer treatment.
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Affiliation(s)
- Eli Varon
- Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel.,Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Gaddi Blumrosen
- Department of Digital Medical Technologies, Holon Institute of Technology, Holon, Israel.,Department of Computer Science, Holon Institute of Technology, Holon, Israel
| | - Orit Shefi
- Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel.,Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel.,Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat Gan, Israel
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Ru B, Jiang P. Discover immunotherapy biomarkers from single-cell cytometry data. PATTERNS (NEW YORK, N.Y.) 2021; 2:100384. [PMID: 34950905 PMCID: PMC8672134 DOI: 10.1016/j.patter.2021.100384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Currently, identifying novel biomarkers remains a crucial need for cancer immunotherapy. By leveraging single-cell cytometry data, Greene et al. developed an interpretable machine learning method, FAUST, to discover cell populations associated with clinical outcomes.
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Affiliation(s)
- Beibei Ru
- Cancer Data Science Lab, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Peng Jiang
- Cancer Data Science Lab, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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36
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Cossarizza A, Chang HD, Radbruch A, Abrignani S, Addo R, Akdis M, Andrä I, Andreata F, Annunziato F, Arranz E, Bacher P, Bari S, Barnaba V, Barros-Martins J, Baumjohann D, Beccaria CG, Bernardo D, Boardman DA, Borger J, Böttcher C, Brockmann L, Burns M, Busch DH, Cameron G, Cammarata I, Cassotta A, Chang Y, Chirdo FG, Christakou E, Čičin-Šain L, Cook L, Corbett AJ, Cornelis R, Cosmi L, Davey MS, De Biasi S, De Simone G, del Zotto G, Delacher M, Di Rosa F, Di Santo J, Diefenbach A, Dong J, Dörner T, Dress RJ, Dutertre CA, Eckle SBG, Eede P, Evrard M, Falk CS, Feuerer M, Fillatreau S, Fiz-Lopez A, Follo M, Foulds GA, Fröbel J, Gagliani N, Galletti G, Gangaev A, Garbi N, Garrote JA, Geginat J, Gherardin NA, Gibellini L, Ginhoux F, Godfrey DI, Gruarin P, Haftmann C, Hansmann L, Harpur CM, Hayday AC, Heine G, Hernández DC, Herrmann M, Hoelsken O, Huang Q, Huber S, Huber JE, Huehn J, Hundemer M, Hwang WYK, Iannacone M, Ivison SM, Jäck HM, Jani PK, Keller B, Kessler N, Ketelaars S, Knop L, Knopf J, Koay HF, Kobow K, Kriegsmann K, Kristyanto H, Krueger A, Kuehne JF, Kunze-Schumacher H, Kvistborg P, Kwok I, Latorre D, Lenz D, Levings MK, Lino AC, Liotta F, Long HM, Lugli E, MacDonald KN, Maggi L, Maini MK, Mair F, Manta C, Manz RA, Mashreghi MF, Mazzoni A, McCluskey J, Mei HE, Melchers F, Melzer S, Mielenz D, Monin L, Moretta L, Multhoff G, Muñoz LE, Muñoz-Ruiz M, Muscate F, Natalini A, Neumann K, Ng LG, Niedobitek A, Niemz J, Almeida LN, Notarbartolo S, Ostendorf L, Pallett LJ, Patel AA, Percin GI, Peruzzi G, Pinti M, Pockley AG, Pracht K, Prinz I, Pujol-Autonell I, Pulvirenti N, Quatrini L, Quinn KM, Radbruch H, Rhys H, Rodrigo MB, Romagnani C, Saggau C, Sakaguchi S, Sallusto F, Sanderink L, Sandrock I, Schauer C, Scheffold A, Scherer HU, Schiemann M, Schildberg FA, Schober K, Schoen J, Schuh W, Schüler T, Schulz AR, Schulz S, Schulze J, Simonetti S, Singh J, Sitnik KM, Stark R, Starossom S, Stehle C, Szelinski F, Tan L, Tarnok A, Tornack J, Tree TIM, van Beek JJP, van de Veen W, van Gisbergen K, Vasco C, Verheyden NA, von Borstel A, Ward-Hartstonge KA, Warnatz K, Waskow C, Wiedemann A, Wilharm A, Wing J, Wirz O, Wittner J, Yang JHM, Yang J. Guidelines for the use of flow cytometry and cell sorting in immunological studies (third edition). Eur J Immunol 2021; 51:2708-3145. [PMID: 34910301 PMCID: PMC11115438 DOI: 10.1002/eji.202170126] [Citation(s) in RCA: 185] [Impact Index Per Article: 61.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The third edition of Flow Cytometry Guidelines provides the key aspects to consider when performing flow cytometry experiments and includes comprehensive sections describing phenotypes and functional assays of all major human and murine immune cell subsets. Notably, the Guidelines contain helpful tables highlighting phenotypes and key differences between human and murine cells. Another useful feature of this edition is the flow cytometry analysis of clinical samples with examples of flow cytometry applications in the context of autoimmune diseases, cancers as well as acute and chronic infectious diseases. Furthermore, there are sections detailing tips, tricks and pitfalls to avoid. All sections are written and peer-reviewed by leading flow cytometry experts and immunologists, making this edition an essential and state-of-the-art handbook for basic and clinical researchers.
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Affiliation(s)
- Andrea Cossarizza
- Department of Medical and Surgical Sciences for Children & Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Hyun-Dong Chang
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
- Institute for Biotechnology, Technische Universität, Berlin, Germany
| | - Andreas Radbruch
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Sergio Abrignani
- Istituto Nazionale di Genetica Molecolare Romeo ed Enrica Invernizzi (INGM), Milan, Italy
- Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Richard Addo
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Mübeccel Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Immanuel Andrä
- Institut für Medizinische Mikrobiologie, Immunologie und Hygiene, Technische Universität München, Munich, Germany
| | - Francesco Andreata
- Division of Immunology, Transplantation and Infectious Diseases, IRCSS San Raffaele Scientific Institute, Milan, Italy
| | - Francesco Annunziato
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Eduardo Arranz
- Mucosal Immunology Lab, Unidad de Excelencia Instituto de Biomedicina y Genética Molecular de Valladolid (IBGM, Universidad de Valladolid-CSIC), Valladolid, Spain
| | - Petra Bacher
- Institute of Immunology, Christian-Albrechts Universität zu Kiel & Universitätsklinik Schleswig-Holstein, Kiel, Germany
- Institute of Clinical Molecular Biology Christian-Albrechts Universität zu Kiel, Kiel, Germany
| | - Sudipto Bari
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore
- Cancer & Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Vincenzo Barnaba
- Dipartimento di Medicina Interna e Specialità Mediche, Sapienza Università di Roma, Rome, Italy
- Center for Life Nano & Neuro Science@Sapienza, Istituto Italiano di Tecnologia (IIT), Rome, Italy
- Istituto Pasteur - Fondazione Cenci Bolognetti, Rome, Italy
| | | | - Dirk Baumjohann
- Medical Clinic III for Oncology, Hematology, Immuno-Oncology and Rheumatology, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Cristian G. Beccaria
- Division of Immunology, Transplantation and Infectious Diseases, IRCSS San Raffaele Scientific Institute, Milan, Italy
| | - David Bernardo
- Mucosal Immunology Lab, Unidad de Excelencia Instituto de Biomedicina y Genética Molecular de Valladolid (IBGM, Universidad de Valladolid-CSIC), Valladolid, Spain
- Centro de Investigaciones Biomédicas en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - Dominic A. Boardman
- Department of Surgery, The University of British Columbia, Vancouver, Canada
- BC Children’s Hospital Research Institute, Vancouver, Canada
| | - Jessica Borger
- Department of Immunology and Pathology, Monash University, Melbourne, Victoria, Australia
| | - Chotima Böttcher
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Leonie Brockmann
- Department of Microbiology & Immunology, Columbia University, New York City, USA
| | - Marie Burns
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Dirk H. Busch
- Institut für Medizinische Mikrobiologie, Immunologie und Hygiene, Technische Universität München, Munich, Germany
- German Center for Infection Research (DZIF), Munich, Germany
| | - Garth Cameron
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria, Australia
| | - Ilenia Cammarata
- Dipartimento di Medicina Interna e Specialità Mediche, Sapienza Università di Roma, Rome, Italy
| | - Antonino Cassotta
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Yinshui Chang
- Medical Clinic III for Oncology, Hematology, Immuno-Oncology and Rheumatology, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Fernando Gabriel Chirdo
- Instituto de Estudios Inmunológicos y Fisiopatológicos - IIFP (UNLP-CONICET), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Eleni Christakou
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King’s College London, UK
- National Institute for Health Research (NIHR) Biomedical Research Center (BRC), Guy’s and St Thomas’ NHS Foundation Trust and King’s College London, London, UK
| | - Luka Čičin-Šain
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Laura Cook
- BC Children’s Hospital Research Institute, Vancouver, Canada
- Department of Medicine, The University of British Columbia, Vancouver, Canada
| | - Alexandra J. Corbett
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Rebecca Cornelis
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Lorenzo Cosmi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Martin S. Davey
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Sara De Biasi
- Department of Medical and Surgical Sciences for Children & Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Gabriele De Simone
- Laboratory of Translational Immunology, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | | | - Michael Delacher
- Institute for Immunology, University Medical Center Mainz, Mainz, Germany
- Research Centre for Immunotherapy, University Medical Center Mainz, Mainz, Germany
| | - Francesca Di Rosa
- Institute of Molecular Biology and Pathology, National Research Council of Italy (CNR), Rome, Italy
- Immunosurveillance Laboratory, The Francis Crick Institute, London, UK
| | - James Di Santo
- Innate Immunity Unit, Department of Immunology, Institut Pasteur, Paris, France
- Inserm U1223, Paris, France
| | - Andreas Diefenbach
- Laboratory of Innate Immunity, Department of Microbiology, Infectious Diseases and Immunology, Charité – Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, Germany
- Mucosal and Developmental Immunology, German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Jun Dong
- Cell Biology, German Rheumatism Research Center Berlin (DRFZ), An Institute of the Leibniz Association, Berlin, Germany
| | - Thomas Dörner
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
- Department of Medicine/Rheumatology and Clinical Immunology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Regine J. Dress
- Institute of Systems Immunology, Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Charles-Antoine Dutertre
- Institut National de la Sante Et de la Recherce Medicale (INSERM) U1015, Equipe Labellisee-Ligue Nationale contre le Cancer, Villejuif, France
| | - Sidonia B. G. Eckle
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Pascale Eede
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Maximilien Evrard
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
| | - Christine S. Falk
- Institute of Transplant Immunology, Hannover Medical School, Hannover, Germany
| | - Markus Feuerer
- Regensburg Center for Interventional Immunology (RCI), Regensburg, Germany
- Chair for Immunology, University Regensburg, Regensburg, Germany
| | - Simon Fillatreau
- Institut Necker Enfants Malades, INSERM U1151-CNRS, UMR8253, Paris, France
- Université de Paris, Paris Descartes, Faculté de Médecine, Paris, France
- AP-HP, Hôpital Necker Enfants Malades, Paris, France
| | - Aida Fiz-Lopez
- Mucosal Immunology Lab, Unidad de Excelencia Instituto de Biomedicina y Genética Molecular de Valladolid (IBGM, Universidad de Valladolid-CSIC), Valladolid, Spain
| | - Marie Follo
- Department of Medicine I, Lighthouse Core Facility, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Gemma A. Foulds
- John van Geest Cancer Research Centre, School of Science and Technology, Nottingham Trent University, Nottingham, UK
- Centre for Health, Ageing and Understanding Disease (CHAUD), School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Julia Fröbel
- Immunology of Aging, Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
| | - Nicola Gagliani
- Department of Medicine, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Germany
| | - Giovanni Galletti
- Laboratory of Translational Immunology, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Anastasia Gangaev
- Division of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Natalio Garbi
- Institute of Molecular Medicine and Experimental Immunology, Faculty of Medicine, University of Bonn, Germany
| | - José Antonio Garrote
- Mucosal Immunology Lab, Unidad de Excelencia Instituto de Biomedicina y Genética Molecular de Valladolid (IBGM, Universidad de Valladolid-CSIC), Valladolid, Spain
- Laboratory of Molecular Genetics, Servicio de Análisis Clínicos, Hospital Universitario Río Hortega, Gerencia Regional de Salud de Castilla y León (SACYL), Valladolid, Spain
| | - Jens Geginat
- Istituto Nazionale di Genetica Molecolare Romeo ed Enrica Invernizzi (INGM), Milan, Italy
- Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Nicholas A. Gherardin
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria, Australia
| | - Lara Gibellini
- Department of Medical and Surgical Sciences for Children & Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Dale I. Godfrey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria, Australia
| | - Paola Gruarin
- Istituto Nazionale di Genetica Molecolare Romeo ed Enrica Invernizzi (INGM), Milan, Italy
| | - Claudia Haftmann
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Leo Hansmann
- Department of Hematology, Oncology, and Tumor Immunology, Charité - Universitätsmedizin Berlin (CVK), Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, Germany
| | - Christopher M. Harpur
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, Victoria, Australia
| | - Adrian C. Hayday
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King’s College London, UK
- National Institute for Health Research (NIHR) Biomedical Research Center (BRC), Guy’s and St Thomas’ NHS Foundation Trust and King’s College London, London, UK
- Immunosurveillance Laboratory, The Francis Crick Institute, London, UK
| | - Guido Heine
- Division of Allergy, Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Daniela Carolina Hernández
- Innate Immunity, German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Gastroenterology, Infectious Diseases, Rheumatology, Berlin, Germany
| | - Martin Herrmann
- Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Department of Medicine 3 – Rheumatology and Immunology and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie, Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Oliver Hoelsken
- Laboratory of Innate Immunity, Department of Microbiology, Infectious Diseases and Immunology, Charité – Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, Germany
- Mucosal and Developmental Immunology, German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Qing Huang
- Department of Surgery, The University of British Columbia, Vancouver, Canada
- BC Children’s Hospital Research Institute, Vancouver, Canada
| | - Samuel Huber
- Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Johanna E. Huber
- Institute for Immunology, Biomedical Center, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany
| | - Jochen Huehn
- Experimental Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Michael Hundemer
- Department of Hematology, Oncology and Rheumatology, University Heidelberg, Heidelberg, Germany
| | - William Y. K. Hwang
- Cancer & Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
- Department of Hematology, Singapore General Hospital, Singapore, Singapore
- Executive Offices, National Cancer Centre Singapore, Singapore
| | - Matteo Iannacone
- Division of Immunology, Transplantation and Infectious Diseases, IRCSS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
- Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Sabine M. Ivison
- Department of Surgery, The University of British Columbia, Vancouver, Canada
- BC Children’s Hospital Research Institute, Vancouver, Canada
| | - Hans-Martin Jäck
- Division of Molecular Immunology, Nikolaus-Fiebiger-Center, Department of Internal Medicine III, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Peter K. Jani
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Baerbel Keller
- Department of Rheumatology and Clinical Immunology, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Nina Kessler
- Institute of Molecular Medicine and Experimental Immunology, Faculty of Medicine, University of Bonn, Germany
| | - Steven Ketelaars
- Division of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Laura Knop
- Institute of Molecular and Clinical Immunology, Otto-von-Guericke University, Magdeburg, Germany
| | - Jasmin Knopf
- Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Department of Medicine 3 – Rheumatology and Immunology and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie, Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Hui-Fern Koay
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria, Australia
| | - Katja Kobow
- Department of Neuropathology, Universitätsklinikum Erlangen, Germany
| | - Katharina Kriegsmann
- Department of Hematology, Oncology and Rheumatology, University Heidelberg, Heidelberg, Germany
| | - H. Kristyanto
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Andreas Krueger
- Institute for Molecular Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Jenny F. Kuehne
- Institute of Transplant Immunology, Hannover Medical School, Hannover, Germany
| | - Heike Kunze-Schumacher
- Institute for Molecular Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Pia Kvistborg
- Division of Molecular Oncology and Immunology, the Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Immanuel Kwok
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
| | | | - Daniel Lenz
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Megan K. Levings
- Department of Surgery, The University of British Columbia, Vancouver, Canada
- BC Children’s Hospital Research Institute, Vancouver, Canada
- School of Biomedical Engineering, The University of British Columbia, Vancouver, Canada
| | - Andreia C. Lino
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Francesco Liotta
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Heather M. Long
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Enrico Lugli
- Laboratory of Translational Immunology, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Katherine N. MacDonald
- BC Children’s Hospital Research Institute, Vancouver, Canada
- School of Biomedical Engineering, The University of British Columbia, Vancouver, Canada
- Michael Smith Laboratories, The University of British Columbia, Vancouver, Canada
| | - Laura Maggi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Mala K. Maini
- Division of Infection & Immunity, Institute of Immunity & Transplantation, University College London, London, UK
| | - Florian Mair
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Calin Manta
- Department of Hematology, Oncology and Rheumatology, University Heidelberg, Heidelberg, Germany
| | - Rudolf Armin Manz
- Institute for Systemic Inflammation Research, University of Luebeck, Luebeck, Germany
| | | | - Alessio Mazzoni
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - James McCluskey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Henrik E. Mei
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Fritz Melchers
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Susanne Melzer
- Clinical Trial Center Leipzig, Leipzig University, Härtelstr.16, −18, Leipzig, 04107, Germany
| | - Dirk Mielenz
- Division of Molecular Immunology, Nikolaus-Fiebiger-Center, Department of Internal Medicine III, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Leticia Monin
- Immunosurveillance Laboratory, The Francis Crick Institute, London, UK
| | - Lorenzo Moretta
- Department of Immunology, IRCCS Bambino Gesù Children’s Hospital, Rome, Italy
| | - Gabriele Multhoff
- Radiation Immuno-Oncology Group, Center for Translational Cancer Research (TranslaTUM), Technical University of Munich (TUM), Klinikum rechts der Isar, Munich, Germany
- Department of Radiation Oncology, Technical University of Munich (TUM), Klinikum rechts der Isar, Munich, Germany
| | - Luis Enrique Muñoz
- Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Department of Medicine 3 – Rheumatology and Immunology and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie, Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Miguel Muñoz-Ruiz
- Immunosurveillance Laboratory, The Francis Crick Institute, London, UK
| | - Franziska Muscate
- Department of Medicine, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ambra Natalini
- Institute of Molecular Biology and Pathology, National Research Council of Italy (CNR), Rome, Italy
| | - Katrin Neumann
- Institute of Experimental Immunology and Hepatology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lai Guan Ng
- Division of Medical Sciences, National Cancer Centre Singapore, Singapore
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
- Department of Microbiology & Immunology, Immunology Programme, Life Science Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | | | - Jana Niemz
- Experimental Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Samuele Notarbartolo
- Istituto Nazionale di Genetica Molecolare Romeo ed Enrica Invernizzi (INGM), Milan, Italy
| | - Lennard Ostendorf
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Laura J. Pallett
- Division of Infection & Immunity, Institute of Immunity & Transplantation, University College London, London, UK
| | - Amit A. Patel
- Institut National de la Sante Et de la Recherce Medicale (INSERM) U1015, Equipe Labellisee-Ligue Nationale contre le Cancer, Villejuif, France
| | - Gulce Itir Percin
- Immunology of Aging, Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
| | - Giovanna Peruzzi
- Center for Life Nano & Neuro Science@Sapienza, Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Marcello Pinti
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - A. Graham Pockley
- John van Geest Cancer Research Centre, School of Science and Technology, Nottingham Trent University, Nottingham, UK
- Centre for Health, Ageing and Understanding Disease (CHAUD), School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Katharina Pracht
- Division of Molecular Immunology, Nikolaus-Fiebiger-Center, Department of Internal Medicine III, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Immo Prinz
- Institute of Immunology, Hannover Medical School, Hannover, Germany
- Institute of Systems Immunology, Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Irma Pujol-Autonell
- National Institute for Health Research (NIHR) Biomedical Research Center (BRC), Guy’s and St Thomas’ NHS Foundation Trust and King’s College London, London, UK
- Peter Gorer Department of Immunobiology, King’s College London, London, UK
| | - Nadia Pulvirenti
- Istituto Nazionale di Genetica Molecolare Romeo ed Enrica Invernizzi (INGM), Milan, Italy
| | - Linda Quatrini
- Department of Immunology, IRCCS Bambino Gesù Children’s Hospital, Rome, Italy
| | - Kylie M. Quinn
- School of Biomedical and Health Sciences, RMIT University, Bundorra, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Helena Radbruch
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Hefin Rhys
- Flow Cytometry Science Technology Platform, The Francis Crick Institute, London, UK
| | - Maria B. Rodrigo
- Institute of Molecular Medicine and Experimental Immunology, Faculty of Medicine, University of Bonn, Germany
| | - Chiara Romagnani
- Innate Immunity, German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Gastroenterology, Infectious Diseases, Rheumatology, Berlin, Germany
| | - Carina Saggau
- Institute of Immunology, Christian-Albrechts Universität zu Kiel & Universitätsklinik Schleswig-Holstein, Kiel, Germany
| | | | - Federica Sallusto
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Lieke Sanderink
- Regensburg Center for Interventional Immunology (RCI), Regensburg, Germany
- Chair for Immunology, University Regensburg, Regensburg, Germany
| | - Inga Sandrock
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | - Christine Schauer
- Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Department of Medicine 3 – Rheumatology and Immunology and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie, Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Alexander Scheffold
- Institute of Immunology, Christian-Albrechts Universität zu Kiel & Universitätsklinik Schleswig-Holstein, Kiel, Germany
| | - Hans U. Scherer
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Matthias Schiemann
- Institut für Medizinische Mikrobiologie, Immunologie und Hygiene, Technische Universität München, Munich, Germany
| | - Frank A. Schildberg
- Clinic for Orthopedics and Trauma Surgery, University Hospital Bonn, Bonn, Germany
| | - Kilian Schober
- Institut für Medizinische Mikrobiologie, Immunologie und Hygiene, Technische Universität München, Munich, Germany
- Mikrobiologisches Institut – Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Germany
| | - Janina Schoen
- Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Department of Medicine 3 – Rheumatology and Immunology and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie, Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Wolfgang Schuh
- Division of Molecular Immunology, Nikolaus-Fiebiger-Center, Department of Internal Medicine III, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Thomas Schüler
- Institute of Molecular and Clinical Immunology, Otto-von-Guericke University, Magdeburg, Germany
| | - Axel R. Schulz
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Sebastian Schulz
- Division of Molecular Immunology, Nikolaus-Fiebiger-Center, Department of Internal Medicine III, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Julia Schulze
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Sonia Simonetti
- Institute of Molecular Biology and Pathology, National Research Council of Italy (CNR), Rome, Italy
| | - Jeeshan Singh
- Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Department of Medicine 3 – Rheumatology and Immunology and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum für Immuntherapie, Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Katarzyna M. Sitnik
- Department of Viral Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Regina Stark
- Charité Universitätsmedizin Berlin – BIH Center for Regenerative Therapies, Berlin, Germany
- Sanquin Research – Adaptive Immunity, Amsterdam, The Netherlands
| | - Sarah Starossom
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Christina Stehle
- Innate Immunity, German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Gastroenterology, Infectious Diseases, Rheumatology, Berlin, Germany
| | - Franziska Szelinski
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
- Department of Medicine/Rheumatology and Clinical Immunology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Leonard Tan
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
- Department of Microbiology & Immunology, Immunology Programme, Life Science Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Attila Tarnok
- Institute for Medical Informatics, Statistics and Epidemiology (IMISE), University of Leipzig, Leipzig, Germany
- Department of Precision Instrument, Tsinghua University, Beijing, China
- Department of Preclinical Development and Validation, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
| | - Julia Tornack
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
| | - Timothy I. M. Tree
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King’s College London, UK
- National Institute for Health Research (NIHR) Biomedical Research Center (BRC), Guy’s and St Thomas’ NHS Foundation Trust and King’s College London, London, UK
| | - Jasper J. P. van Beek
- Laboratory of Translational Immunology, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Willem van de Veen
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | | | - Chiara Vasco
- Istituto Nazionale di Genetica Molecolare Romeo ed Enrica Invernizzi (INGM), Milan, Italy
| | - Nikita A. Verheyden
- Institute for Molecular Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Anouk von Borstel
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Kirsten A. Ward-Hartstonge
- Department of Surgery, The University of British Columbia, Vancouver, Canada
- BC Children’s Hospital Research Institute, Vancouver, Canada
| | - Klaus Warnatz
- Department of Rheumatology and Clinical Immunology, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Claudia Waskow
- Immunology of Aging, Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
- Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich-Schiller-University Jena, Jena, Germany
- Department of Medicine III, Technical University Dresden, Dresden, Germany
| | - Annika Wiedemann
- German Rheumatism Research Center Berlin (DRFZ), Berlin, Germany
- Department of Medicine/Rheumatology and Clinical Immunology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Anneke Wilharm
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | - James Wing
- Immunology Frontier Research Center, Osaka University, Japan
| | - Oliver Wirz
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jens Wittner
- Division of Molecular Immunology, Nikolaus-Fiebiger-Center, Department of Internal Medicine III, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Jennie H. M. Yang
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King’s College London, UK
- National Institute for Health Research (NIHR) Biomedical Research Center (BRC), Guy’s and St Thomas’ NHS Foundation Trust and King’s College London, London, UK
| | - Juhao Yang
- Experimental Immunology, Helmholtz Centre for Infection Research, Braunschweig, Germany
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With great power comes great responsibility: high-dimensional spectral flow cytometry to support clinical trials. Bioanalysis 2021; 13:1597-1616. [PMID: 34708658 DOI: 10.4155/bio-2021-0201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Flow cytometry is a powerful technology used in research, drug development and clinical sample analysis for cell identification and characterization, allowing for the simultaneous interrogation of multiple targets on various cell subsets from limited samples. Recent advancements in instrumentation and fluorochrome availability have resulted in significant increases in the complexity and dimensionality of flow cytometry panels. Though this increase in panel size allows for detection of a broader range of markers and sub-populations, even in restricted biological samples, it also comes with many challenges in panel design, optimization, and downstream data analysis and interpretation. In the current paper we describe the practices we established for development of high-dimensional panels on the Aurora spectral flow cytometer to aid clinical sample analysis.
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38
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The Plasmacytoid Dendritic Cell CD123+ Compartment in Acute Leukemia with or without RUNX1 Mutation: High Inter-Patient Variability Disclosed by Immunophenotypic Unsupervised Analysis and Clustering. HEMATO 2021. [DOI: 10.3390/hemato2030036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Plasmacytoid dendritic cells (PDC) constitute a small subset of normal bone marrow (BM) cells but have also been shown to be present, sometimes in large numbers, in several hematological malignancies such as acute myeloid leukemia with RUNX1 mutation, chronic myelomonocytic leukemia or, obviously, blastic plasmacytoid dendritic cell neoplasms. These cells have been reported to display somewhat variable immunophenotypic features in different conditions. However, little is known of their plasticity within individual patients. Using an unsupervised clustering tool (FlowSOM) to re-visit flow cytometry results of seven previously analyzed cases of hematological malignancies (6 acute myeloid leukemia and one chronic myelomonocytic leukemia) with a PDC contingent, we report here on the unexpectedly high variability of PDC subsets. Although five of the studied patients harbored a RUNX1 mutation, no consistent feature of PDCs could be disclosed as associated with this variant. Moreover, the one normal single-node small subset of PDC detected in the merged file of six normal BM could be retrieved in the remission BM samples of three successfully treated patients. This study highlights the capacity of unsupervised flow cytometry analysis to delineate cell subsets not detectable with classical supervised tools.
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Taranto D, Ramirez CFA, Vegna S, de Groot MHP, de Wit N, Van Baalen M, Klarenbeek S, Akkari L. Multiparametric Analyses of Hepatocellular Carcinoma Somatic Mouse Models and Their Associated Tumor Microenvironment. Curr Protoc 2021; 1:e147. [PMID: 34101385 DOI: 10.1002/cpz1.147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The rising incidence and increasing mortality of hepatocellular carcinoma (HCC), combined with its high tumor heterogeneity, lack of druggable targets, and tendency to develop resistance to chemotherapeutics, make the development of better models for this cancer an urgent challenge. To better mimic the high diversity within the HCC genetic landscape, versatile somatic murine models have recently been developed using the hydrodynamic tail vein injection (HDTVi) system. These represent novel in vivo tools to interrogate HCC phenotype and response to therapy, and importantly, allow further analyses of the associated tumor microenvironment (TME) shaped by distinct genetic backgrounds. Here, we describe several optimized protocols to generate, collect, and experimentally utilize various samples obtained from HCC somatic mouse models generated by HDTVi. More specifically, we focus on techniques relevant to ex vivo analyses of the complex liver TME using multiparameter flow cytometric analyses of over 21 markers, immunohistochemistry, immunofluorescence, and histochemistry. We describe the transcriptional assessment of whole tissue, or of isolated immune subsets by flow-cytometry-based cell sorting, and other protein-oriented analyses. Together, these streamlined protocols allow the optimal use of each HCC murine model of interest and will assist researchers in deciphering the relations between cancer cell genetics and systemic and local changes in immune cell landscapes in the context of HCC progression. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Generation of HCC mouse models by hydrodynamic tail vein injection Basic Protocol 2: Assessment of HCC tumor progression by magnetic resonance imaging Basic Protocol 3: Mouse sacrifice and sample collection in HCC mouse models Support Protocol 1: Preparation of serum or plasma from blood Basic Protocol 4: Single-cell preparation and HCC immune landscape phenotyping by flow cytometry Alternate Protocol 1: Flow cytometric analysis of circulating immune cells Support Protocol 2: Generation, maintenance, and characterization of HCC cell lines Support Protocol 3: Fluorescence-activated cell sorting of liver single-cell preparation Basic Protocol 5: Preparation and immunohistochemical analysis of tumor tissues from HCC-bearing liver Alternate Protocol 2: Preparation and analyses for immunofluorescence staining of HCC-bearing liver Support Protocol 4: Liver-specific phenotypic analyses of liver sections Support Protocol 5: Immunohistochemical quantification in liver sections Basic Protocol 6: Preparation of snap-frozen tumor tissue from extracted liver and transcriptional analyses of bulk tumor or sorted cells Alternate Protocol 3: Protein analyses from HCC samples and serum or plasma.
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Affiliation(s)
- Daniel Taranto
- Division of Tumour Biology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Christel F A Ramirez
- Division of Tumour Biology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Serena Vegna
- Division of Tumour Biology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marnix H P de Groot
- Division of Tumour Biology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Niels de Wit
- Mouse Clinic for Cancer and Aging (MCCA), Imaging Unit, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Martijn Van Baalen
- Flow Cytometry Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Sjoerd Klarenbeek
- Experimental Animal Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Leila Akkari
- Division of Tumour Biology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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40
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Rolf N, Liu LYT, Tsang A, Lange PF, Lim CJ, Maxwell CA, Vercauteren SM, Reid GSD. A cross-standardized flow cytometry platform to assess phenotypic stability in precursor B-cell acute lymphoblastic leukemia (B-ALL) xenografts. Cytometry A 2021; 101:57-71. [PMID: 34128309 PMCID: PMC9292200 DOI: 10.1002/cyto.a.24473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/07/2021] [Accepted: 06/10/2021] [Indexed: 11/17/2022]
Abstract
With the continued poor outcome of relapsed acute lymphoblastic leukemia (ALL), new patient‐specific approaches for disease progression monitoring and therapeutic intervention are urgently needed. Patient‐derived xenografts (PDX) of primary ALL in immune‐deficient mice have become a powerful tool for studying leukemia biology and therapy response. In PDX mice, the immunophenotype of the patient's leukemia is commonly believed to be stably propagated. In patients, however, the surface marker expression profile of the leukemic population often displays poorly understood immunophenotypic shifts during chemotherapy and ALL progression. We therefore developed a translational flow cytometry platform to study whether the patient‐specific immunophenotype is faithfully recapitulated in PDX mice. To enable valid assessment of immunophenotypic stability and subpopulation complexity of the patient's leukemia after xenotransplantation, we comprehensively immunophenotyped diagnostic B‐ALL from children and their matched PDX using identical, clinically standardized flow protocols and instrument settings. This cross‐standardized approach ensured longitudinal stability and cross‐platform comparability of marker expression intensity at high phenotyping depth. This analysis revealed readily detectable changes to the patient leukemia‐associated immunophenotype (LAIP) after xenotransplantation. To further investigate the mechanism underlying these complex immunophenotypic shifts, we applied an integrated analytical approach that combined clinical phenotyping depth and high analytical sensitivity with unbiased high‐dimensional algorithm‐based analysis. This high‐resolution analysis revealed that xenotransplantation achieves patient‐specific propagation of phenotypically stable B‐ALL subpopulations and that the immunophenotypic shifts observed at the level of bulk leukemia were consistent with changes in underlying subpopulation abundance. By incorporating the immunophenotypic complexity of leukemic populations, this novel cross‐standardized analytical platform could greatly expand the utility of PDX for investigating ALL progression biology and assessing therapies directed at eliminating relapse‐driving leukemic subpopulations.
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Affiliation(s)
- Nina Rolf
- Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lorraine Y T Liu
- Clinical Immunology Lab, Division of Hematopathology, BC Children's Hospital, Vancouver, British Columbia, Canada
| | - Angela Tsang
- Clinical Immunology Lab, Division of Hematopathology, BC Children's Hospital, Vancouver, British Columbia, Canada
| | - Philipp F Lange
- Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Chinten James Lim
- Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Christopher A Maxwell
- Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Suzanne M Vercauteren
- Clinical Immunology Lab, Division of Hematopathology, BC Children's Hospital, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gregor S D Reid
- Michael Cuccione Childhood Cancer Research Program, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
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41
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Grant R, Coopman K, Silva-Gomes S, Campbell JJ, Kara B, Braybrook J, Petzing J. Assessment of Protocol Impact on Subjectivity Uncertainty When Analyzing Peripheral Blood Mononuclear Cell Flow Cytometry Data Files. Methods Protoc 2021; 4:24. [PMID: 33808088 PMCID: PMC8103269 DOI: 10.3390/mps4020024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/26/2021] [Accepted: 03/28/2021] [Indexed: 12/21/2022] Open
Abstract
Measured variability of product within Cell and Gene Therapy (CGT) manufacturing arises from numerous sources across pre-analytical to post-analytical phases of testing. Operators are a function of the manufacturing process and are an important source of variability as a result of personal differences impacted by numerous factors. This research uses measurement uncertainty in comparison to Coefficient of Variation to quantify variation of participants when they complete Flow Cytometry data analysis through a 5-step gating sequence. Two study stages captured participants applying gates using their own judgement, and then following a diagrammatical protocol, respectively. Measurement uncertainty was quantified for each participant (and analysis phase) by following Guide to the Expression of Uncertainty in Measurement protocols, combining their standard deviations in quadrature from each gating step in the respective protocols. When participants followed a diagrammatical protocol, variation between participants reduced by 57%, increasing confidence in a more uniform reported cell count percentage. Measurement uncertainty provided greater resolution to the analysis processes, identifying that most variability contributed in the Flow Cytometry gating process is from the very first gate, where isolating target cells from dead or dying cells is required. This work has demonstrated the potential for greater usage of measurement uncertainty within CGT manufacturing scenarios, due to the resolution it provides for root cause analysis and continuous improvement.
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Affiliation(s)
- Rebecca Grant
- Wolfson School of Mechanical, Electrical and Manufacturing Engineering, Loughborough University, Loughborough, Leicestershire LE11 3TU, UK;
| | - Karen Coopman
- Department of Aeronautical, Automotive, Chemical and Materials Engineering, Loughborough University, Loughborough, Leicestershire LE11 3TU, UK;
| | - Sandro Silva-Gomes
- GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK; (S.S.-G.); (B.K.)
| | | | - Bo Kara
- GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK; (S.S.-G.); (B.K.)
| | - Julian Braybrook
- LGC Group, Queen’s Road, Teddington, Middlesex TW11 0LY, UK; (J.J.C.); (J.B.)
| | - Jon Petzing
- Wolfson School of Mechanical, Electrical and Manufacturing Engineering, Loughborough University, Loughborough, Leicestershire LE11 3TU, UK;
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