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Yu T, Xu-Monette ZY, Lagoo A, Shuai W, Wang B, Neff J, Carrillo LF, Carlsen ED, Pina-Oviedo S, Young KH. Flow cytometry quantification of tumor-infiltrating lymphocytes to predict the survival of patients with diffuse large B-cell lymphoma. Front Immunol 2024; 15:1335689. [PMID: 38348048 PMCID: PMC10859492 DOI: 10.3389/fimmu.2024.1335689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 01/08/2024] [Indexed: 02/15/2024] Open
Abstract
Introduction Our previous studies have demonstrated that tumor-infiltrating lymphocytes (TILs), including normal B cells, T cells, and natural killer (NK) cells, in diffuse large B-cell lymphoma (DLBCL) have a significantly favorable impact on the clinical outcomes of patients treated with standard chemoimmunotherapy. In this study, to gain a full overview of the tumor immune microenvironment (TIME), we assembled a flow cytometry cohort of 102 patients diagnosed with DLBCL at the Duke University Medical Center. Methods We collected diagnostic flow cytometry data, including the proportion of T cells, abnormal B cells, normal B cells, plasma cells, NK cells, monocytes, and granulocytes in fresh biopsy tissues at clinical presentation, and analyzed the correlations with patient survival and between different cell populations. Results We found that low T cell percentages in all viable cells and low ratios of T cells to abnormal B cells correlated with significantly poorer survival, whereas higher percentages of normal B cells among total B cells (or high ratios of normal B cells to abnormal B cells) and high percentages of NK cells among all viable cells correlated with significantly better survival in patients with DLBCL. After excluding a small number of patients with low T cell percentages, the normal B cell percentage among all B cells, but not T cell percentage among all cells, continued to show a remarkable prognostic effect. Data showed significant positive correlations between T cells and normal B cells, and between granulocytes and monocytes. Furthermore, we constructed a prognostic model based on clinical and flow cytometry factors, which divided the DLBCL cohort into two equal groups with remarkable differences in patient survival and treatment response. Summary TILs, including normal B cells, T cells, and NK cells, are associated with favorable clinical outcomes in DLBCL, and flow cytometry capable of quantifying the TIME may have additional clinical utility for prognostication.
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Affiliation(s)
- Tiantian Yu
- Hematopathology Division and Department of Pathology, Duke University Medical Center, Durham, NC, United States
| | - Zijun Y. Xu-Monette
- Hematopathology Division and Department of Pathology, Duke University Medical Center, Durham, NC, United States
- Duke University Cancer Institute, Durham, NC, United States
| | - Anand Lagoo
- Hematopathology Division and Department of Pathology, Duke University Medical Center, Durham, NC, United States
| | - Wen Shuai
- Hematopathology Division and Department of Pathology, Duke University Medical Center, Durham, NC, United States
| | - Bangchen Wang
- Department of Pathology, Duke University Medical Center, Durham, NC, United States
| | - Jadee Neff
- Hematopathology Division and Department of Pathology, Duke University Medical Center, Durham, NC, United States
| | - Luis F. Carrillo
- Hematopathology Division and Department of Pathology, Duke University Medical Center, Durham, NC, United States
| | - Eric D. Carlsen
- Hematopathology Division and Department of Pathology, Duke University Medical Center, Durham, NC, United States
- Duke University Cancer Institute, Durham, NC, United States
| | - Sergio Pina-Oviedo
- Hematopathology Division and Department of Pathology, Duke University Medical Center, Durham, NC, United States
| | - Ken H. Young
- Hematopathology Division and Department of Pathology, Duke University Medical Center, Durham, NC, United States
- Duke University Cancer Institute, Durham, NC, United States
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2
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DePriest BP, Vieira N, Bidgoli A, Paczesny S. An overview of multiplexed analyses of CAR T-cell therapies: insights and potential. Expert Rev Proteomics 2021; 18:767-780. [PMID: 34628995 PMCID: PMC8626704 DOI: 10.1080/14789450.2021.1992276] [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: 01/05/2023]
Abstract
INTRODUCTION Cancer immunotherapy is a rapidly growing field with exponential advancement in engineered immune cell-based therapies. For instance, an engineered chimeric antigen receptor (CAR) can be introduced in T-cells or other immune cells and adoptively transferred to target and kill cancer cells in hematologic malignancies or solid tumors. The first CAR-T-cell (CAR-T) therapy has been developed against CD19, a B-cell marker expressed on lymphoma and lymphoblastic leukemia. To allow for personalized treatment, proteomics approaches could provide insights into biomarkers for CAR-T therapy efficacy and toxicity. AREAS COVERED We researched the most recent technology methods of biomarker evaluation used in the laboratory and clinical setting. Publications of CAR-T biomarkers were then systematically reviewed to provide a narrative of the most validated biomarkers of CAR-T efficacy and toxicity. Examples of biomarkers include CAR-T functionality and phenotype as well as interleukin-6 and other cytokines. EXPERT COMMENTARY Biomarkers of CAR-T efficacy and toxicity have been identified, but still need to be validated and standardized across institutions. Moreover, few are used in the clinical setting due to limitations in real-time technology. Expansion of biomarker research could provide better understanding of patient response and risk of life-threatening side effects with potential for improved precision medicine.
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Affiliation(s)
- Brittany Paige DePriest
- Department of Microbiology and Immunology and Pediatrics, Medical University of South Carolina, Charleston, SC, USA
| | - Noah Vieira
- Department of Microbiology and Immunology and Pediatrics, Medical University of South Carolina, Charleston, SC, USA
| | - Alan Bidgoli
- Department of Microbiology and Immunology and Pediatrics, Medical University of South Carolina, Charleston, SC, USA
| | - Sophie Paczesny
- Department of Microbiology and Immunology and Pediatrics, Medical University of South Carolina, Charleston, SC, USA
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Flores-Montero J, Kalina T, Corral-Mateos A, Sanoja-Flores L, Pérez-Andrés M, Martin-Ayuso M, Sedek L, Rejlova K, Mayado A, Fernández P, van der Velden V, Bottcher S, van Dongen JJM, Orfao A. Fluorochrome choices for multi-color flow cytometry. J Immunol Methods 2019; 475:112618. [PMID: 31181212 DOI: 10.1016/j.jim.2019.06.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 05/29/2019] [Accepted: 06/04/2019] [Indexed: 12/21/2022]
Abstract
Fluorochrome selection is a key step in designing multi-color antibody panels. The list of available fluorochromes is continuously growing, fitting current needs in clinical flow cytometry to simultaneously use more markers to better define multiple leukocyte subpopulations in a single tube. Several criteria guide fluorochrome selection: i) the fluorescence profiles (excitation and emission), ii) relative brightness, iii) fluorescence overlap, iv) fluorochrome stability, and v) reproducible conjugation to antibodies. Here we used 75 samples (45 bone marrow and 30 blood) to illustrate EuroFlow strategies for evaluation of compatible fluorochromes, and how the results obtained guide fluorochrome selection as a critical step in the antibody-panel building process. Our results allowed identification of optimal fluorescence profiles (e.g. higher fluorescence intensity and/or resolution with limited fluorescence overlap into neighbor channels) for brilliant violet (BV)421 and BV510 in the violet laser and allophycocyanin (APC) hilite 7 (H7) or APC C750 in the red laser vs. other candidate fluorochromes generally applied for the same detectors and here evaluated. Moreover, evaluation of the same characteristics for another group of fluorochromes (e.g. BV605, BV650, PE CF594, AF700 or APC AF700) guided selection of the most appropriate fluorochrome conjugates to be combined in a multi-color antibody panel. Albeit this is a demanding approach, it could be successfully applied for selection of fluorochrome combinations for the EuroFlow antibody panels for diagnosis, classification and monitoring of hematological malignancies and primary immunodeficiencies. Consequently, sets of 8-, 10- and 12-color fluorochrome combinations are proposed as frame of reference for initial antibody panel design.
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Affiliation(s)
- Juan Flores-Montero
- Cancer Research Center (IBMCC-CSIC/USAL-IBSAL), Cytometry Service (NUCLEUS) and Department of Medicine, University of Salamanca, Salamanca, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBER-ONC) CB16/12/00400, Instituto de Salud Carlos III, Madrid, Spain
| | - Tomas Kalina
- CLIP Cytometry, Department of Pediatric Hematology and Oncology, 2nd Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Alba Corral-Mateos
- Cancer Research Center (IBMCC-CSIC/USAL-IBSAL), Cytometry Service (NUCLEUS) and Department of Medicine, University of Salamanca, Salamanca, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBER-ONC) CB16/12/00400, Instituto de Salud Carlos III, Madrid, Spain
| | - Luzalba Sanoja-Flores
- Cancer Research Center (IBMCC-CSIC/USAL-IBSAL), Cytometry Service (NUCLEUS) and Department of Medicine, University of Salamanca, Salamanca, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBER-ONC) CB16/12/00400, Instituto de Salud Carlos III, Madrid, Spain
| | - Martin Pérez-Andrés
- Cancer Research Center (IBMCC-CSIC/USAL-IBSAL), Cytometry Service (NUCLEUS) and Department of Medicine, University of Salamanca, Salamanca, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBER-ONC) CB16/12/00400, Instituto de Salud Carlos III, Madrid, Spain
| | | | - Lukasz Sedek
- Department of Pediatric Hematology and Oncology, Medical University of Silesia in Katowice, Zabrze, Poland
| | - Katerina Rejlova
- CLIP Cytometry, Department of Pediatric Hematology and Oncology, 2nd Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Andrea Mayado
- Cancer Research Center (IBMCC-CSIC/USAL-IBSAL), Cytometry Service (NUCLEUS) and Department of Medicine, University of Salamanca, Salamanca, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBER-ONC) CB16/12/00400, Instituto de Salud Carlos III, Madrid, Spain
| | - Paula Fernández
- FACS/Stem cell Laboratory, Institute of Laboratory Medicine, Kantonsspital Aarau AG, Aarau, Switzerland
| | - Vincent van der Velden
- Department of Immunology, Erasmus MC, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Sebastian Bottcher
- Rostock University Medical Center, Division of Internal Medicine, Medical Clinic III, Hematology, Oncology and Palliative Medicine, Special Hematology Laboratory, Rostock, Germany
| | - Jaques J M van Dongen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands.
| | - Alberto Orfao
- Cancer Research Center (IBMCC-CSIC/USAL-IBSAL), Cytometry Service (NUCLEUS) and Department of Medicine, University of Salamanca, Salamanca, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBER-ONC) CB16/12/00400, Instituto de Salud Carlos III, Madrid, Spain..
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Tran DN, Smith SABC, Brown DA, Parker AJC, Joseph JE, Armstrong N, Sewell WA. Polychromatic flow cytometry is more sensitive than microscopy in detecting small monoclonal plasma cell populations. CYTOMETRY PART B-CLINICAL CYTOMETRY 2016; 92:136-144. [PMID: 27416483 DOI: 10.1002/cyto.b.21401] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Revised: 05/19/2016] [Accepted: 07/13/2016] [Indexed: 11/11/2022]
Abstract
BACKGROUND There is an emerging role for flow cytometry (FC) in the assessment of small populations of plasma cells (PC). However, FC's utility has been questioned due to consistent underestimation of the percentage of PC compared to microscopy. METHODS A retrospective study was performed on bone marrow samples analysed by 8-colour FC. Plasma cell populations were classified as polyclonal or monoclonal based on FC analysis. FC findings were compared with microscopy of aspirates, histology and immunohistochemistry of trephine biopsies, and immunofixation (IFX) of serum and/or urine. RESULTS FC underestimated PC compared to aspirate and trephine microscopy. The 10% diagnostic cutoff for MM on aspirate microscopy corresponded to a 3.5% cutoff on FC. Abnormal plasma cell morphology by aspirate microscopy and clonality by FC correlated in 229 of 294 cases (78%). However, in 50 cases, FC demonstrated a monoclonal population but microscopy reported no abnormality. In 15 cases, abnormalities were reported by microscopy but not by FC. Clonality assessment by trephine microscopy and FC agreed in 251/280 cases (90%), but all 29 discordant cases were monoclonal by FC and not monoclonal by microscopy. These cases had fewer PC and proportionally more polyclonal PC, and when IFX detected a paraprotein, it had the same light chain as in the PC determined by FC. CONCLUSIONS FC was more sensitive in detecting monoclonal populations that were small or accompanied by polyclonal PC. This study supports the inclusion of FC in the evaluation of PC, especially in the assessment of small populations. © 2016 International Clinical Cytometry Society.
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Affiliation(s)
- Daniel N Tran
- Immunology Department, SydPath, St Vincent's Hospital Sydney, New South Wales, Australia.,St Vincent's Clinical School, University of New South Wales, New South Wales, Australia.,Garvan Institute of Medical Research, New South Wales, Australia
| | - Sandy A B C Smith
- Immunology Department, SydPath, St Vincent's Hospital Sydney, New South Wales, Australia
| | - David A Brown
- Immunology Department, SydPath, St Vincent's Hospital Sydney, New South Wales, Australia.,St Vincent's Clinical School, University of New South Wales, New South Wales, Australia.,Applied Medical Research Centre, St Vincent's Hospital Sydney, New South Wales, Australia
| | - Andrew J C Parker
- Anatomical Pathology Department, SydPath, St Vincent's Hospital Sydney, New South Wales, Australia
| | - Joanne E Joseph
- St Vincent's Clinical School, University of New South Wales, New South Wales, Australia.,Applied Medical Research Centre, St Vincent's Hospital Sydney, New South Wales, Australia.,Haematology Department, SydPath, St Vincent's Hospital Sydney, New South Wales, Australia
| | - Nicola Armstrong
- Garvan Institute of Medical Research, New South Wales, Australia.,Mathematics and Statistics, Murdoch University, Western Australia, Australia
| | - William A Sewell
- Immunology Department, SydPath, St Vincent's Hospital Sydney, New South Wales, Australia.,St Vincent's Clinical School, University of New South Wales, New South Wales, Australia.,Garvan Institute of Medical Research, New South Wales, Australia
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Vir P, Arrigucci R, Lakehal K, Davidow AL, Pine R, Tyagi S, Bushkin Y, Lardizabal A, Gennaro ML. Single-Cell Cytokine Gene Expression in Peripheral Blood Cells Correlates with Latent Tuberculosis Status. PLoS One 2015; 10:e0144904. [PMID: 26658491 PMCID: PMC4681842 DOI: 10.1371/journal.pone.0144904] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 11/25/2015] [Indexed: 12/29/2022] Open
Abstract
RNA flow cytometry (FISH-Flow) achieves high-throughput measurement of single-cell gene expression by combining in-situ nucleic acid hybridization with flow cytometry. We tested whether antigen-specific T-cell responses detected by FISH-Flow correlated with latent tuberculosis infection (LTBI), a condition affecting one-third of the world population. Peripheral-blood mononuclear cells from donors, identified as positive or negative for LTBI by current medical practice, were stimulated ex vivo with mycobacterial antigen. IFNG and IL2 mRNA production was assayed by FISH-Flow. Concurrently, immunophenotypes of the cytokine mRNA-positive cells were characterized by conventional, antibody-based staining of cell-surface markers. An association was found between donor LTBI status and antigen-specific induction of IFNG and IL2 transcripts. Induction of these cytokine genes, which was detected by FISH-Flow in a quarter the time required to see release of the corresponding proteins by ELISA, occurred primarily in activated CD4+ T cells via T-cell receptor engagement. Moreover, NK cells contributed to IFNG gene induction. These results show that antigen-driven induction of T-cell cytokine mRNA is a measurable single-cell parameter of the host responses associated with latent tuberculosis. FISH-Flow read-outs contribute a multi-scale dimension to the immunophenotyping afforded by antibody-based flow cytometry. Multi-scale, single-cell analyses may satisfy the need to determine disease stage and therapy response for tuberculosis and other infectious pathologies.
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Affiliation(s)
- Pooja Vir
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, United States of America
| | - Riccardo Arrigucci
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, United States of America
| | - Karim Lakehal
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, United States of America
| | - Amy L. Davidow
- Department of Biostatistics, School of Public Health, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, United States of America
| | - Richard Pine
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, United States of America
| | - Sanjay Tyagi
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, United States of America
| | - Yuri Bushkin
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, United States of America
| | - Alfred Lardizabal
- Global Tuberculosis Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, United States of America
| | - Maria Laura Gennaro
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, United States of America
- * E-mail:
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6
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Caraway NP. Evolving role of FNA biopsy in diagnosing lymphoma: Past, present, and future. Cancer Cytopathol 2015; 123:389-93. [DOI: 10.1002/cncy.21551] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 04/06/2015] [Accepted: 04/07/2015] [Indexed: 01/09/2023]
Affiliation(s)
- Nancy P. Caraway
- Section of Cytopathology; Department of Pathology; The University of Texas MD Anderson Cancer Center; Houston Texas
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O’Connor JE, Herrera G, Martínez-Romero A, de Oyanguren FS, Díaz L, Gomes A, Balaguer S, Callaghan RC. Systems Biology and immune aging. Immunol Lett 2014; 162:334-45. [DOI: 10.1016/j.imlet.2014.09.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Accepted: 09/12/2014] [Indexed: 10/24/2022]
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O'Connor JE, Herrera G, Martínez-Romero A, Oyanguren FSD, Díaz L, Gomes A, Balaguer S, Callaghan RC. WITHDRAWN: Systems Biology and Immune Aging. Immunol Lett 2014:S0165-2478(14)00197-7. [PMID: 25251659 DOI: 10.1016/j.imlet.2014.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 09/12/2014] [Indexed: 10/24/2022]
Abstract
The Publisher regrets that this article is an accidental duplication of anarticle that has already been published, http://dx.doi.org/10.1016/j.imlet.2014.09.009. The duplicate article has therefore been withdrawn.
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Affiliation(s)
- José-Enrique O'Connor
- Laboratory of Translational Cytomics, Joint Research Unit, The University of Valencia and Principe Felipe Research Center, Valencia, Spain; Cytometry Laboratory, Incliva Foundation, Clinical University Hospital, The University of Valencia, Valencia, Spain.
| | - Guadalupe Herrera
- Laboratory of Translational Cytomics, Joint Research Unit, The University of Valencia and Principe Felipe Research Center, Valencia, Spain; Cytometry Laboratory, Incliva Foundation, Clinical University Hospital, The University of Valencia, Valencia, Spain
| | - Alicia Martínez-Romero
- Cytometry Technological Service, Principe Felipe Research Center, Valencia, Spain; Cytometry Laboratory, Incliva Foundation, Clinical University Hospital, The University of Valencia, Valencia, Spain
| | - Francisco Sala-de Oyanguren
- Laboratory of Translational Cytomics, Joint Research Unit, The University of Valencia and Principe Felipe Research Center, Valencia, Spain; Cytometry Laboratory, Incliva Foundation, Clinical University Hospital, The University of Valencia, Valencia, Spain
| | - Laura Díaz
- Laboratory of Translational Cytomics, Joint Research Unit, The University of Valencia and Principe Felipe Research Center, Valencia, Spain; Cytometry Laboratory, Incliva Foundation, Clinical University Hospital, The University of Valencia, Valencia, Spain
| | - Angela Gomes
- Laboratory of Translational Cytomics, Joint Research Unit, The University of Valencia and Principe Felipe Research Center, Valencia, Spain; Cytometry Laboratory, Incliva Foundation, Clinical University Hospital, The University of Valencia, Valencia, Spain
| | - Susana Balaguer
- Laboratory of Translational Cytomics, Joint Research Unit, The University of Valencia and Principe Felipe Research Center, Valencia, Spain; Cytometry Laboratory, Incliva Foundation, Clinical University Hospital, The University of Valencia, Valencia, Spain
| | - Robert C Callaghan
- Department of Pathology, Faculty of Medicine, The University of Valencia, Valencia, Spain; Cytometry Laboratory, Incliva Foundation, Clinical University Hospital, The University of Valencia, Valencia, Spain
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9
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Gedye CA, Hussain A, Paterson J, Smrke A, Saini H, Sirskyj D, Pereira K, Lobo N, Stewart J, Go C, Ho J, Medrano M, Hyatt E, Yuan J, Lauriault S, Meyer M, Kondratyev M, van den Beucken T, Jewett M, Dirks P, Guidos CJ, Danska J, Wang J, Wouters B, Neel B, Rottapel R, Ailles LE. Cell surface profiling using high-throughput flow cytometry: a platform for biomarker discovery and analysis of cellular heterogeneity. PLoS One 2014; 9:e105602. [PMID: 25170899 PMCID: PMC4149490 DOI: 10.1371/journal.pone.0105602] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 07/22/2014] [Indexed: 11/18/2022] Open
Abstract
Cell surface proteins have a wide range of biological functions, and are often used as lineage-specific markers. Antibodies that recognize cell surface antigens are widely used as research tools, diagnostic markers, and even therapeutic agents. The ability to obtain broad cell surface protein profiles would thus be of great value in a wide range of fields. There are however currently few available methods for high-throughput analysis of large numbers of cell surface proteins. We describe here a high-throughput flow cytometry (HT-FC) platform for rapid analysis of 363 cell surface antigens. Here we demonstrate that HT-FC provides reproducible results, and use the platform to identify cell surface antigens that are influenced by common cell preparation methods. We show that multiple populations within complex samples such as primary tumors can be simultaneously analyzed by co-staining of cells with lineage-specific antibodies, allowing unprecedented depth of analysis of heterogeneous cell populations. Furthermore, standard informatics methods can be used to visualize, cluster and downsample HT-FC data to reveal novel signatures and biomarkers. We show that the cell surface profile provides sufficient molecular information to classify samples from different cancers and tissue types into biologically relevant clusters using unsupervised hierarchical clustering. Finally, we describe the identification of a candidate lineage marker and its subsequent validation. In summary, HT-FC combines the advantages of a high-throughput screen with a detection method that is sensitive, quantitative, highly reproducible, and allows in-depth analysis of heterogeneous samples. The use of commercially available antibodies means that high quality reagents are immediately available for follow-up studies. HT-FC has a wide range of applications, including biomarker discovery, molecular classification of cancers, or identification of novel lineage specific or stem cell markers.
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Affiliation(s)
- Craig A Gedye
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Ali Hussain
- Dept. of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Joshua Paterson
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Alannah Smrke
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Harleen Saini
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Danylo Sirskyj
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Keira Pereira
- Dept. of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Nazleen Lobo
- Dept. of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Jocelyn Stewart
- Dept. of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Christopher Go
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Jenny Ho
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Mauricio Medrano
- Dept. of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Elzbieta Hyatt
- Hospital for Sick Children Research Institute, Toronto, ON, Canada
| | - Julie Yuan
- Hospital for Sick Children Research Institute, Toronto, ON, Canada
| | - Stevan Lauriault
- Hospital for Sick Children Research Institute, Toronto, ON, Canada
| | | | - Maria Kondratyev
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | | | - Michael Jewett
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Peter Dirks
- Hospital for Sick Children Research Institute, Toronto, ON, Canada
| | - Cynthia J Guidos
- Hospital for Sick Children Research Institute, Toronto, ON, Canada
| | - Jayne Danska
- Hospital for Sick Children Research Institute, Toronto, ON, Canada
| | - Jean Wang
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Bradly Wouters
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Dept. of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Benjamin Neel
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Dept. of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Robert Rottapel
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Laurie E Ailles
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Dept. of Medical Biophysics, University of Toronto, Toronto, ON, Canada
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Johansson U, Bloxham D, Couzens S, Jesson J, Morilla R, Erber W, Macey M. Guidelines on the use of multicolour flow cytometry in the diagnosis of haematological neoplasms. British Committee for Standards in Haematology. Br J Haematol 2014; 165:455-88. [PMID: 24620735 DOI: 10.1111/bjh.12789] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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11
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Flor A, Williams JH, Blaine KM, Duggan RC, Sperling AI, Schwartz DA, Kron SJ. DNA-directed assembly of antibody-fluorophore conjugates for quantitative multiparametric flow cytometry. Chembiochem 2014; 15:267-75. [PMID: 24375983 PMCID: PMC3925401 DOI: 10.1002/cbic.201300464] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Indexed: 02/07/2023]
Abstract
Multiparametric flow cytometry offers a powerful approach to single-cell analysis with broad applications in research and diagnostics. Despite advances in instrumentation, progress in methodology has lagged. Currently there is no simple and efficient method for antibody labeling or quantifying the number of antibodies bound per cell. Herein, we describe a DNA-directed assembly approach to fluorescent labeling that overcomes these barriers. Oligonucleotide-tagged antibodies and microparticles can be annealed to complementary oligonucleotides bearing fluorophores to create assay-specific labeling probes and controls, respectively. The ratio of the fluorescence intensity of labeled cells to the control particles allows direct conversion of qualitative data to quantitative units of antibody binding per cell. Importantly, a single antibody can be labeled with any fluorophore by using a simple mix-and-match labeling strategy. Thus, any antibody can provide a quantitative probe in any fluorescent channel, thus overcoming major barriers to the use of flow cytometry as a technique for systems biology and clinical diagnostics.
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Affiliation(s)
- Amy Flor
- University of Chicago, Chicago, Illinois 60637 (USA)
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12
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Pedreira CE, Costa ES, Lecrevisse Q, van Dongen JJ, Orfao A. Overview of clinical flow cytometry data analysis: recent advances and future challenges. Trends Biotechnol 2013; 31:415-25. [DOI: 10.1016/j.tibtech.2013.04.008] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 04/26/2013] [Accepted: 04/28/2013] [Indexed: 12/15/2022]
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Wasik MA, Jimenez GS, Weisenburger DD. Targeting CD30 in malignant tissues: challenges in detection and clinical applications. Pathobiology 2013; 80:252-8. [PMID: 23689361 DOI: 10.1159/000347192] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 01/17/2013] [Indexed: 11/19/2022] Open
Abstract
The CD30 transmembrane receptor from the tumor necrosis factor receptor family is expressed in a distinct, yet diverse set of lymphoproliferative disorders and a small subset of normal activated lymphocytes. Therefore, detection of CD30 expression when performed properly according to the standardized methods facilitates diagnosis of Hodgkin lymphoma, anaplastic large cell lymphoma, and other disorders expressing the receptor. More recently, CD30 has also become an attractive therapeutic target. The preliminary observations indicate that the methods currently used to detect CD30 expression, typically immunohistochemistry performed on formalin-fixed, paraffin-embedded tissues, may be suboptimal in regard to identifying CD30 as a therapeutic target since only a limited number of CD30 receptor molecules per cell may be sufficient to achieve therapeutic effect.
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Affiliation(s)
- Mariusz A Wasik
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pa., USA.
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Goldeck D, Low I, Shadan NB, Mustafah S, Pawelec G, Larbi A. Multi-parametric phospho-flow cytometry: a crucial tool for T lymphocyte signaling studies. Cytometry A 2013; 83:265-72. [PMID: 23359365 DOI: 10.1002/cyto.a.22252] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 12/16/2012] [Accepted: 12/18/2012] [Indexed: 11/09/2022]
Abstract
Tools such as protein immunoblotting have proven benefits for investigating T lymphocyte signaling but have several drawbacks such as the number of cells required and the difficulty of distinguishing subset-specific differences without expensive and invasive cell sorting. Recent advances in immunology and the identification of T lymphocyte sub-populations making up only a very small fraction of the total population highlight the importance of studying signaling in those small subsets in a feasible, cost-effective, high-throughput manner. To this end, we have developed a simplified protocol to study both intracellular phosphorylation patterns of important signal transduction molecules concomitantly with T cell surface marker expression. A multi-parametric analysis may allow the quantification of the phosphorylation of up to five signaling molecules in CD4 and CD8 T lymphocytes and their naïve, central memory, effector memory, and TEMRA subsets. This enables precise identification of subset-specific signaling and alterations of signaling pathways in physiological and pathological situations. The importance of such detailed analysis is discussed.
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Affiliation(s)
- David Goldeck
- Center for Medical Research ZMF, Tübingen Aging and Tumor Immunology group, Tübingen, Germany
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Satori CP, Kostal V, Arriaga EA. Review on recent advances in the analysis of isolated organelles. Anal Chim Acta 2012; 753:8-18. [PMID: 23107131 PMCID: PMC3484375 DOI: 10.1016/j.aca.2012.09.041] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 09/22/2012] [Accepted: 09/24/2012] [Indexed: 10/27/2022]
Abstract
The analysis of isolated organelles is one of the pillars of modern bioanalytical chemistry. This review describes recent developments on the isolation and characterization of isolated organelles both from living organisms and cell cultures. Salient reports on methods to release organelles focused on reproducibility and yield, membrane isolation, and integrated devices for organelle release. New developments on organelle fractionation after their isolation were on the topics of centrifugation, immunocapture, free flow electrophoresis, flow field-flow fractionation, fluorescence activated organelle sorting, laser capture microdissection, and dielectrophoresis. New concepts on characterization of isolated organelles included atomic force microscopy, optical tweezers combined with Raman spectroscopy, organelle sensors, flow cytometry, capillary electrophoresis, and microfluidic devices.
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Affiliation(s)
- Chad P Satori
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
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Abstract
Flow cytometry is increasingly recognized as an invaluable technology in biomarker research. Owing to its multiparametric nature it can provide highly detailed information on any single cell in a heterogeneous population. Its versatility means it can be conducted in both the preclinical and clinical setting, generating biomarker data that can drive decisions pertaining to dose selection in clinical trials, treatment options for cancer sufferers and even suitability of patients to receive transplants. Most tissue types can be utilized by the flow cytometrist, allowing the technology to be applied to many fields of research, yet consensus still needs to be reached on standardization, regulation and validation of multiparametric flow cytometry assays. In parallel, continual innovation in analysis software to manage the huge datasets that can be generated is also needed. Nevertheless, the flexibility of flow cytometry means that it remains at the forefront of both routine and exploratory biomarker studies.
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