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G. de Castro C, G. del Hierro A, H-Vázquez J, Cuesta-Sancho S, Bernardo D. State-of-the-art cytometry in the search of novel biomarkers in digestive cancers. Front Oncol 2024; 14:1407580. [PMID: 38868532 PMCID: PMC11167087 DOI: 10.3389/fonc.2024.1407580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 05/10/2024] [Indexed: 06/14/2024] Open
Abstract
Despite that colorectal and liver cancer are among the most prevalent tumours in the world, the identification of non-invasive biomarkers to aid on their diagnose and subsequent prognosis is a current unmet need that would diminish both their incidence and mortality rates. In this context, conventional flow cytometry has been widely used in the screening of biomarkers with clinical utility in other malignant processes like leukaemia or lymphoma. Therefore, in this review, we will focus on how advanced cytometry panels covering over 40 parameters can be applied on the study of the immune system from patients with colorectal and hepatocellular carcinoma and how that can be used on the search of novel biomarkers to aid or diagnose, prognosis, and even predict clinical response to different treatments. In addition, these multiparametric and unbiased approaches can also provide novel insights into the specific immunopathogenic mechanisms governing these malignant diseases, hence potentially unravelling novel targets to perform immunotherapy or identify novel mechanisms, rendering the development of novel treatments. As a consequence, computational cytometry approaches are an emerging methodology for the early detection and predicting therapies for gastrointestinal cancers.
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Affiliation(s)
- Carolina G. de Castro
- Mucosal Immunology Lab, Institute of Biomedicine and Molecular Genetics (IBGM), University of Valladolid and Consejo Superior de Investigaciones Científicas (CSIC), Valladolid, Spain
| | - Alejandro G. del Hierro
- Mucosal Immunology Lab, Institute of Biomedicine and Molecular Genetics (IBGM), University of Valladolid and Consejo Superior de Investigaciones Científicas (CSIC), Valladolid, Spain
| | - Juan H-Vázquez
- Mucosal Immunology Lab, Institute of Biomedicine and Molecular Genetics (IBGM), University of Valladolid and Consejo Superior de Investigaciones Científicas (CSIC), Valladolid, Spain
| | - Sara Cuesta-Sancho
- Mucosal Immunology Lab, Institute of Biomedicine and Molecular Genetics (IBGM), University of Valladolid and Consejo Superior de Investigaciones Científicas (CSIC), Valladolid, Spain
| | - David Bernardo
- Mucosal Immunology Lab, Institute of Biomedicine and Molecular Genetics (IBGM), University of Valladolid and Consejo Superior de Investigaciones Científicas (CSIC), Valladolid, Spain
- Centro de Investigaciones Biomedicas en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
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2
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Lemieux ME, Reveles XT, Rebeles J, Bederka LH, Araujo PR, Sanchez JR, Grayson M, Lai SC, DePalo LR, Habib SA, Hill DG, Lopez K, Patriquin L, Sussman R, Joyce RP, Rebel VI. Detection of early-stage lung cancer in sputum using automated flow cytometry and machine learning. Respir Res 2023; 24:23. [PMID: 36681813 PMCID: PMC9862555 DOI: 10.1186/s12931-023-02327-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 01/12/2023] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Low-dose spiral computed tomography (LDCT) may not lead to a clear treatment path when small to intermediate-sized lung nodules are identified. We have combined flow cytometry and machine learning to develop a sputum-based test (CyPath Lung) that can assist physicians in decision-making in such cases. METHODS Single cell suspensions prepared from induced sputum samples collected over three consecutive days were labeled with a viability dye to exclude dead cells, antibodies to distinguish cell types, and a porphyrin to label cancer-associated cells. The labeled cell suspension was run on a flow cytometer and the data collected. An analysis pipeline combining automated flow cytometry data processing with machine learning was developed to distinguish cancer from non-cancer samples from 150 patients at high risk of whom 28 had lung cancer. Flow data and patient features were evaluated to identify predictors of lung cancer. Random training and test sets were chosen to evaluate predictive variables iteratively until a robust model was identified. The final model was tested on a second, independent group of 32 samples, including six samples from patients diagnosed with lung cancer. RESULTS Automated analysis combined with machine learning resulted in a predictive model that achieved an area under the ROC curve (AUC) of 0.89 (95% CI 0.83-0.89). The sensitivity and specificity were 82% and 88%, respectively, and the negative and positive predictive values 96% and 61%, respectively. Importantly, the test was 92% sensitive and 87% specific in cases when nodules were < 20 mm (AUC of 0.94; 95% CI 0.89-0.99). Testing of the model on an independent second set of samples showed an AUC of 0.85 (95% CI 0.71-0.98) with an 83% sensitivity, 77% specificity, 95% negative predictive value and 45% positive predictive value. The model is robust to differences in sample processing and disease state. CONCLUSION CyPath Lung correctly classifies samples as cancer or non-cancer with high accuracy, including from participants at different disease stages and with nodules < 20 mm in diameter. This test is intended for use after lung cancer screening to improve early-stage lung cancer diagnosis. Trial registration ClinicalTrials.gov ID: NCT03457415; March 7, 2018.
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Affiliation(s)
| | - Xavier T. Reveles
- bioAffinity Technologies, 22211 W I-10, Suite 1206, San Antonio, TX 78257 USA
| | - Jennifer Rebeles
- bioAffinity Technologies, 22211 W I-10, Suite 1206, San Antonio, TX 78257 USA
| | - Lydia H. Bederka
- bioAffinity Technologies, 22211 W I-10, Suite 1206, San Antonio, TX 78257 USA
| | - Patricia R. Araujo
- bioAffinity Technologies, 22211 W I-10, Suite 1206, San Antonio, TX 78257 USA
| | - Jamila R. Sanchez
- bioAffinity Technologies, 22211 W I-10, Suite 1206, San Antonio, TX 78257 USA
| | - Marcia Grayson
- bioAffinity Technologies, 22211 W I-10, Suite 1206, San Antonio, TX 78257 USA
| | - Shao-Chiang Lai
- bioAffinity Technologies, 22211 W I-10, Suite 1206, San Antonio, TX 78257 USA
| | - Louis R. DePalo
- grid.59734.3c0000 0001 0670 2351Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Sheila A. Habib
- grid.414059.d0000 0004 0617 9080South Texas Veterans Health Care System (STVHCS), Audie L. Murphy Memorial Veterans Hospital, San Antonio, TX USA
| | - David G. Hill
- Waterbury Pulmonary Associates LLC, Waterbury, CT USA
| | - Kathleen Lopez
- grid.477754.2Radiology Associates of Albuquerque, Albuquerque, NM USA
| | - Lara Patriquin
- grid.477754.2Radiology Associates of Albuquerque, Albuquerque, NM USA ,Present Address: Zia Diagnostic Imaging, Albuquerque, NM USA
| | | | | | - Vivienne I. Rebel
- bioAffinity Technologies, 22211 W I-10, Suite 1206, San Antonio, TX 78257 USA
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3
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Yamazaki T, Gunderson AJ, Gilchrist M, Whiteford M, Kiely MX, Hayman A, O'Brien D, Ahmad R, Manchio JV, Fox N, McCarty K, Phillips M, Brosnan E, Vaccaro G, Li R, Simon M, Bernstein E, McCormick M, Yamasaki L, Wu Y, Drokin A, Carnahan T, To Y, Redmond WL, Lee B, Louie J, Hansen E, Solhjem MC, Cramer J, Urba WJ, Gough MJ, Crittenden MR, Young KH. Galunisertib plus neoadjuvant chemoradiotherapy in patients with locally advanced rectal cancer: a single-arm, phase 2 trial. Lancet Oncol 2022; 23:1189-1200. [DOI: 10.1016/s1470-2045(22)00446-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/17/2022] [Accepted: 06/28/2022] [Indexed: 02/08/2023]
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4
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Eskandari G, Subedi S, Christensen P, Olsen RJ, Zu Y, Long SW. Implementing flowDensity for Automated Analysis of Bone Marrow Lymphocyte Population. J Pathol Inform 2022; 12:49. [PMID: 35070478 PMCID: PMC8721865 DOI: 10.4103/jopi.jopi_12_21] [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: 02/02/2021] [Accepted: 09/27/2021] [Indexed: 11/04/2022] Open
Abstract
Introduction Manual gating of flow cytometry (FCM) data for marrow cell analysis is a standard approach in current practice, although it is time- and labor-consuming. Recent advances in cytometry technology have led to significant efforts in developing partially or fully automated analysis methods. Although multiple supervised and unsupervised FCM data analysis algorithms have been developed, they have not been widely adopted by the clinical and research laboratories. In this study, we evaluated flowDensity, an open source freely available algorithm, as an automated analysis tool for classification of lymphocyte subsets in the bone marrow biopsy specimens. Materials and Methods FlowDensity-based gating was applied to 102 normal bone marrow samples and compared with the manual analysis. Independent expression of each cell marker was assessed for comprehensive expression analysis and visualization. Results Our findings showed a correlation between the manual and flowDensity-based gating in the lymphocyte subsets. However, flowDensity-based gating in the populations with a small number of cells in each cluster showed a low degree of correlation. Comprehensive expression analysis successfully identified and visualized the lymphocyte subsets. Discussion Our study found that although flowDensity might be a promising method for FCM data analysis, more optimization is required before implementing this algorithm into day-to-day workflow.
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Affiliation(s)
- Ghazaleh Eskandari
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Sishir Subedi
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Paul Christensen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Randall J Olsen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Youli Zu
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
| | - Scott W Long
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, USA
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5
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Stensland ZC, Coleman BM, Rihanek M, Baxter RM, Gottlieb PA, Hsieh EW, Sarapura VD, Simmons KM, Cambier JC, Smith MJ. Peripheral immunophenotyping of AITD subjects reveals alterations in immune cells in pediatric vs adult-onset AITD. iScience 2022; 25:103626. [PMID: 35005561 PMCID: PMC8718984 DOI: 10.1016/j.isci.2021.103626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/28/2021] [Accepted: 12/09/2021] [Indexed: 11/21/2022] Open
Abstract
Autoimmune thyroid disease (AITD) is caused by aberrant activation of the immune system allowing autoreactive B and T cells to target the thyroid gland leading to disease. Although AITD is more frequently diagnosed in adults, children are also affected but rarely studied. Here, we performed phenotypic and functional characterization of peripheral blood immune cells from pediatric and adult-onset AITD patients and age-matched controls using mass cytometry. Major findings indicate that unlike adult-onset AITD patients, pediatric AITD patients exhibit a decrease in anergic B cells (BND) and DN2 B cells and an increase in immature B cells compared to age-matched controls. These results indicate alterations in peripheral blood immune cells seen in pediatric-onset AITD could lead to rapid progression of disease. Hence, this study demonstrates diversity of AITD by showing differences in immune cell phenotypes and function based on age of onset, and may inform future therapies. Penetrance of high-risk HLA-DR3 haplotype is higher in pediatric AITD patients Pediatric AITD patients display altered frequency of autoreactive B cell subsets Immune cell subset frequency and function is similar in adult AITD and controls
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Affiliation(s)
- Zachary C. Stensland
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Brianne M. Coleman
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Marynette Rihanek
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Ryan M. Baxter
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Peter A. Gottlieb
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Elena W.Y. Hsieh
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Department of Pediatrics, Section of Allergy and Immunology, Children's Hospital Colorado, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Virginia D. Sarapura
- Division of Endocrinology, Metabolism, and Diabetes, University of Colorado Health Sciences Center, Aurora, CO 80045, USA
| | - Kimber M. Simmons
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - John C. Cambier
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Mia J. Smith
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Corresponding author
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6
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Maurer-Granofszky M, Schumich A, Buldini B, Gaipa G, Kappelmayer J, Mejstrikova E, Karawajew L, Rossi J, Suzan AÇ, Agriello E, Anastasiou-Grenzelia T, Barcala V, Barna G, Batinić D, Bourquin JP, Brüggemann M, Bukowska-Strakova K, Burnusuzov H, Carelli D, Deniz G, Dubravčić K, Feuerstein T, Gaillard MI, Galeano A, Giordano H, Gonzalez A, Groeneveld-Krentz S, Hevessy Z, Hrusak O, Iarossi MB, Jáksó P, Kloboves Prevodnik V, Kohlscheen S, Kreminska E, Maglia O, Malusardi C, Marinov N, Martin BM, Möller C, Nikulshin S, Palazzi J, Paterakis G, Popov A, Ratei R, Rodríguez C, Sajaroff EO, Sala S, Samardzija G, Sartor M, Scarparo P, Sędek Ł, Slavkovic B, Solari L, Svec P, Szczepanski T, Taparkou A, Torrebadell M, Tzanoudaki M, Varotto E, Vernitsky H, Attarbaschi A, Schrappe M, Conter V, Biondi A, Felice M, Campbell M, Kiss C, Basso G, Dworzak MN. An Extensive Quality Control and Quality Assurance (QC/QA) Program Significantly Improves Inter-Laboratory Concordance Rates of Flow-Cytometric Minimal Residual Disease Assessment in Acute Lymphoblastic Leukemia: An I-BFM-FLOW-Network Report. Cancers (Basel) 2021; 13:cancers13236148. [PMID: 34885257 PMCID: PMC8656726 DOI: 10.3390/cancers13236148] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/25/2021] [Accepted: 11/30/2021] [Indexed: 11/30/2022] Open
Abstract
Simple Summary Standardization of flow-cytometric assessment of minimal residual disease in acute lymphoid leukemia (ALL) is necessary to allow concordant multicentric application of the methodology. This is a prerequisite for internationally collaborative trials, such as the AIEOP-BFM-ALL and the ALL IC-BFM trial. We developed and applied a comprehensive training and quality control program involving a large number of international laboratories within the I-BFM consortium to complement standardization of the methodology with an educational component as well as with persistent quality control measures to allow large ALL treatment trials which use multi-laboratory FCM-MRD assessments for risk stratification of pediatric patients with ALL. Abstract Monitoring of minimal residual disease (MRD) by flow cytometry (FCM) is a powerful prognostic tool for predicting outcomes in acute lymphoblastic leukemia (ALL). To apply FCM-MRD in large, collaborative trials, dedicated laboratory staff must be educated to concordantly high levels of expertise and their performance quality should be continuously monitored. We sought to install a unique and comprehensive training and quality control (QC) program involving a large number of reference laboratories within the international Berlin-Frankfurt-Münster (I-BFM) consortium, in order to complement the standardization of the methodology with an educational component and persistent quality control measures. Our QC and quality assurance (QA) program is based on four major cornerstones: (i) a twinning maturation program, (ii) obligatory participation in external QA programs (spiked sample send around, United Kingdom National External Quality Assessment Service (UK NEQAS)), (iii) regular participation in list-mode-data (LMD) file ring trials (FCM data file send arounds), and (iv) surveys of independent data derived from trial results. We demonstrate that the training of laboratories using experienced twinning partners, along with continuous educational feedback significantly improves the performance of laboratories in detecting and quantifying MRD in pediatric ALL patients. Overall, our extensive education and quality control program improved inter-laboratory concordance rates of FCM-MRD assessments and ultimately led to a very high conformity of risk estimates in independent patient cohorts.
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Affiliation(s)
| | - Angela Schumich
- Children’s Cancer Research Institute, Medical University of Vienna, 1090 Vienna, Austria; (M.M.-G.); (A.S.)
| | - Barbara Buldini
- Pediatric Hematology, Oncology and Stem Cell Transplant Division, Maternal and Child Health Department, University of Padova, 35122 Padova, Italy; (B.B.); (P.S.); (E.V.); (G.B.)
| | - Giuseppe Gaipa
- M. Tettamanti Foundation Research Center, Department of Pediatrics, University of Milano-Bicocca, 20900 Monza, Italy; (G.G.); (O.M.); (S.S.)
| | - Janos Kappelmayer
- Department of Laboratory Medicine, University of Debrecen, 4032 Debrecen, Hungary; (J.K.); (Z.H.)
| | - Ester Mejstrikova
- Department of Paediatric Haematology and Oncology, University Hospital Motol, 150 06 Prague, Czech Republic; (E.M.); (O.H.)
| | - Leonid Karawajew
- Department of Pediatric Oncology and Hematology, Charité Berlin, 10117 Berlin, Germany; (L.K.); (S.G.-K.)
| | - Jorge Rossi
- Cellular Immunology Laboratory, Hospital de Pediatria “Dr. Juan P. Garrahan”, Buenos Aires C1245, Argentina; (J.R.); (E.O.S.)
| | - Adın Çınar Suzan
- Department of Immunology, Aziz Sancar Institute of Experimental Medicine, Istanbul University, 34452 Istanbul, Turkey; (A.Ç.S.); (G.D.)
| | - Evangelina Agriello
- LEB Laboratorio, Servicio de Hematologia Hospital Penna, Bahia Blanca B8000, Argentina;
| | | | - Virna Barcala
- Laboratory—Flow Cytometry, Citomlab, Buenos Aires C1406AWK, Argentina;
| | - Gábor Barna
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, 1085 Budapest, Hungary;
| | - Drago Batinić
- Division of Laboratory Immunology, Department of Laboratory Diagnostics, University Hospital Centre Zagreb & School of Medicine, 10000 Zagreb, Croatia; (D.B.); (K.D.)
| | - Jean-Pierre Bourquin
- Department of Oncology and Children’s Cancer Research Center, University Children’s Hospital, 8032 Zurich, Switzerland; (J.-P.B.); (C.M.)
| | - Monika Brüggemann
- Department of Hematology, University Hospital Schleswig-Holstein, 24105 Kiel, Germany; (M.B.); (S.K.)
| | - Karolina Bukowska-Strakova
- Department of Clinical Immunology, Institute of Pediatrics, Jagiellonian University Medical College, 31-008 Krakow, Poland;
| | - Hasan Burnusuzov
- Center of Competence “PERIMED”, Department of Pediatrics, Department of Microbiology and Clinical Immunology, Medical University Plovdiv, 4002 Plovdiv, Bulgaria;
| | | | - Günnur Deniz
- Department of Immunology, Aziz Sancar Institute of Experimental Medicine, Istanbul University, 34452 Istanbul, Turkey; (A.Ç.S.); (G.D.)
| | - Klara Dubravčić
- Division of Laboratory Immunology, Department of Laboratory Diagnostics, University Hospital Centre Zagreb & School of Medicine, 10000 Zagreb, Croatia; (D.B.); (K.D.)
| | - Tamar Feuerstein
- The Rina Zaizov Division of Pediatric Hematology-Oncology, Schneider’s Children’s Medical Center, Petah Tikva 4920235, Israel;
| | - Marie Isabel Gaillard
- Bioquimica, Inmunologia, Hospital de Ninos Rocardo Gutierrez, Buenos Aires C1425EFD, Argentina;
| | - Adriana Galeano
- Flow Cytometry Laboratory, FUNDALEU, Buenos Aires C1114, Argentina;
| | - Hugo Giordano
- Fundación Pérez Scremini, Pediatric Hematology-Oncology Service, Pereira Rossell Hospital, Montevideo 11600, Uruguay;
| | | | - Stefanie Groeneveld-Krentz
- Department of Pediatric Oncology and Hematology, Charité Berlin, 10117 Berlin, Germany; (L.K.); (S.G.-K.)
| | - Zsuzsanna Hevessy
- Department of Laboratory Medicine, University of Debrecen, 4032 Debrecen, Hungary; (J.K.); (Z.H.)
| | - Ondrej Hrusak
- Department of Paediatric Haematology and Oncology, University Hospital Motol, 150 06 Prague, Czech Republic; (E.M.); (O.H.)
| | - Maria Belen Iarossi
- Flow Cytometry Laboratory, Provincial Histocompatibility Reference Centre, CUCAIBA, Buenos Aires C1114, Argentina;
| | - Pál Jáksó
- Flow Cytometry Laboratory, Department of Pathology, Clinical Centre, University of Pécs, 7622 Pécs, Hungary;
| | - Veronika Kloboves Prevodnik
- Department of Cytopathology, Institute of Oncology, 1000 Ljubljana, Slovenia;
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Saskia Kohlscheen
- Department of Hematology, University Hospital Schleswig-Holstein, 24105 Kiel, Germany; (M.B.); (S.K.)
| | - Elena Kreminska
- Clinical Laboratory Diagnostics and Metrology of NCSH “OHMATDYT”, Ministry of Heath of Ukraine, 01601 Kiev, Ukraine;
| | - Oscar Maglia
- M. Tettamanti Foundation Research Center, Department of Pediatrics, University of Milano-Bicocca, 20900 Monza, Italy; (G.G.); (O.M.); (S.S.)
| | - Cecilia Malusardi
- Hospital de Clinica Jose de San Martin, Buenos Aires C1120, Argentina;
| | - Neda Marinov
- PINDA, Chilean National Pediatric Oncology Group, Hospital Roberto del Rio, Universidad de Chile, Santiago 8380418, Chile; (N.M.); (M.C.)
| | | | - Claudia Möller
- Department of Oncology and Children’s Cancer Research Center, University Children’s Hospital, 8032 Zurich, Switzerland; (J.-P.B.); (C.M.)
| | - Sergey Nikulshin
- Hematopathology and Flow Cytometry Division, Children’s Clinical University Hospital, LV-1004 Riga, Latvia;
| | | | | | - Alexander Popov
- Laboratory of Leukemia Immunophenotyping, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia;
| | - Richard Ratei
- Clinic for Hematology and Tumor Immunology, HELIOS Klinikum Berlin-Buch, 13125 Berlin, Germany;
| | - Cecilia Rodríguez
- Hospital Nacional de Clínicas, Universidad Nacional de Córdoba, Cordoba X5000HUA, Argentina;
| | - Elisa Olga Sajaroff
- Cellular Immunology Laboratory, Hospital de Pediatria “Dr. Juan P. Garrahan”, Buenos Aires C1245, Argentina; (J.R.); (E.O.S.)
| | - Simona Sala
- M. Tettamanti Foundation Research Center, Department of Pediatrics, University of Milano-Bicocca, 20900 Monza, Italy; (G.G.); (O.M.); (S.S.)
| | - Gordana Samardzija
- Laboratory for Flow Cytometry and Immunology, Institute for Health and Protection of Mother and Child of Serbia, 11070 Belgrade, Serbia; (G.S.); (B.S.)
| | - Mary Sartor
- The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia;
| | - Pamela Scarparo
- Pediatric Hematology, Oncology and Stem Cell Transplant Division, Maternal and Child Health Department, University of Padova, 35122 Padova, Italy; (B.B.); (P.S.); (E.V.); (G.B.)
| | - Łukasz Sędek
- Department of Microbiology and Immunology, Medical University of Silesia, 40-055 Katowice, Poland;
| | - Bojana Slavkovic
- Laboratory for Flow Cytometry and Immunology, Institute for Health and Protection of Mother and Child of Serbia, 11070 Belgrade, Serbia; (G.S.); (B.S.)
| | - Liliana Solari
- Servicio de Bioquimica, Hospital Posadas, Buenos Aires B1684, Argentina;
| | - Peter Svec
- National Institute of Children’s Diseases, 831 01 Bratislava, Slovakia;
| | - Tomasz Szczepanski
- Department of Pediatric Hematology and Oncology, Zabrze, Medical University of Silesia, 40-055 Katowice, Poland;
| | - Anna Taparkou
- Department of Pediatric Oncology Hippokration General Hospital, 546 42 Thessaloniki, Greece;
| | | | - Marianna Tzanoudaki
- Department of Immunology & Histocompatibility, “Agia Sophia” Children’s Hospital, 115 27 Athens, Greece;
| | - Elena Varotto
- Pediatric Hematology, Oncology and Stem Cell Transplant Division, Maternal and Child Health Department, University of Padova, 35122 Padova, Italy; (B.B.); (P.S.); (E.V.); (G.B.)
| | - Helly Vernitsky
- Hematology Lab, Sheba Medical Center, Ramat Gan 52621, Israel;
| | - Andishe Attarbaschi
- St. Anna Children’s Hospital, Department of Pediatrics, Medical University of Vienna, 1090 Vienna, Austria;
| | - Martin Schrappe
- Department of Pediatrics, University Medical Center SchleswigHolstein, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany;
| | - Valentino Conter
- Clinica Pediatrica University degli Studi di Milano Biococca, Fondazione MBBM, 20900 Monza, Italy; (V.C.); (A.B.)
| | - Andrea Biondi
- Clinica Pediatrica University degli Studi di Milano Biococca, Fondazione MBBM, 20900 Monza, Italy; (V.C.); (A.B.)
| | - Marisa Felice
- Department of Hematology and Oncology, Hospital de Pediatria “Dr. Juan P. Garrahan”, Buenos Aires C1245, Argentina;
| | - Myriam Campbell
- PINDA, Chilean National Pediatric Oncology Group, Hospital Roberto del Rio, Universidad de Chile, Santiago 8380418, Chile; (N.M.); (M.C.)
| | - Csongor Kiss
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
| | - Giuseppe Basso
- Pediatric Hematology, Oncology and Stem Cell Transplant Division, Maternal and Child Health Department, University of Padova, 35122 Padova, Italy; (B.B.); (P.S.); (E.V.); (G.B.)
| | - Michael N. Dworzak
- Children’s Cancer Research Institute, Medical University of Vienna, 1090 Vienna, Austria; (M.M.-G.); (A.S.)
- St. Anna Children’s Hospital, Department of Pediatrics, Medical University of Vienna, 1090 Vienna, Austria;
- Correspondence: ; Tel.: +43-1-40470-4064
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7
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Sanjabi S, Lear S. New cytometry tools for immune monitoring during cancer immunotherapy. CYTOMETRY PART B-CLINICAL CYTOMETRY 2021; 100:10-18. [PMID: 33432667 DOI: 10.1002/cyto.b.21984] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/11/2020] [Accepted: 12/15/2020] [Indexed: 12/23/2022]
Abstract
The success of cancer immunotherapy (CIT) in the past decade has brought renewed excitement and the need to better understand how the human immune system functions during health and disease. Advances in single cell technologies have also inspired the creation of a Human Cell Atlas to identify and describe every cell in the human body with the intention of elucidating how to "fix" the ones that fail normal function. For example, treatment of cancer patients with immune checkpoint blockade (ICB) antibodies can reinvigorate their T cells and produce durable clinical benefit in a subset of patients, but a number of resistance mechanisms exist that prohibit full benefit to all treated patients. Early detection of biomarkers of response and mechanisms of resistance are needed to identify the patients who can benefit most from ICB. A noninvasive approach to predict treatment outcomes early after immunotherapies is a longitudinal analysis of peripheral blood immune cells using flow cytometry. Here we review some of the advances in our understanding of how ICB antibodies can re-invigorate tumor-specific T cells and also highlight the recent advances in high complexity flow cytometry, including spectral cytometers, that allow longitudinal sampling and deep immune phenotyping in clinical settings. We encourage the scientific community to utilize advanced cytometry platforms and analyses for immune monitoring in order to optimize CIT treatments for maximum clinical benefit.
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Affiliation(s)
- Shomyseh Sanjabi
- Department of Oncology Biomarker Development, Genentech Developmental Sciences, South San Francisco, California, USA
| | - Sean Lear
- Department of OMNI Biomarker Development, Genentech Developmental Sciences, South San Francisco, California, USA
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8
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Hu-Lieskovan S, Bhaumik S, Dhodapkar K, Grivel JCJB, Gupta S, Hanks BA, Janetzki S, Kleen TO, Koguchi Y, Lund AW, Maccalli C, Mahnke YD, Novosiadly RD, Selvan SR, Sims T, Zhao Y, Maecker HT. SITC cancer immunotherapy resource document: a compass in the land of biomarker discovery. J Immunother Cancer 2020; 8:e000705. [PMID: 33268350 PMCID: PMC7713206 DOI: 10.1136/jitc-2020-000705] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2020] [Indexed: 02/07/2023] Open
Abstract
Since the publication of the Society for Immunotherapy of Cancer's (SITC) original cancer immunotherapy biomarkers resource document, there have been remarkable breakthroughs in cancer immunotherapy, in particular the development and approval of immune checkpoint inhibitors, engineered cellular therapies, and tumor vaccines to unleash antitumor immune activity. The most notable feature of these breakthroughs is the achievement of durable clinical responses in some patients, enabling long-term survival. These durable responses have been noted in tumor types that were not previously considered immunotherapy-sensitive, suggesting that all patients with cancer may have the potential to benefit from immunotherapy. However, a persistent challenge in the field is the fact that only a minority of patients respond to immunotherapy, especially those therapies that rely on endogenous immune activation such as checkpoint inhibitors and vaccination due to the complex and heterogeneous immune escape mechanisms which can develop in each patient. Therefore, the development of robust biomarkers for each immunotherapy strategy, enabling rational patient selection and the design of precise combination therapies, is key for the continued success and improvement of immunotherapy. In this document, we summarize and update established biomarkers, guidelines, and regulatory considerations for clinical immune biomarker development, discuss well-known and novel technologies for biomarker discovery and validation, and provide tools and resources that can be used by the biomarker research community to facilitate the continued development of immuno-oncology and aid in the goal of durable responses in all patients.
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Affiliation(s)
- Siwen Hu-Lieskovan
- Huntsman Cancer Institute, Salt Lake City, UT, USA
- University of Utah School of Medicine, Salt Lake City, UT, USA
| | | | - Kavita Dhodapkar
- Department of Pediatrics, Emory University, Atlanta, Georgia, USA
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | | | - Sumati Gupta
- Huntsman Cancer Institute, Salt Lake City, Utah, USA
| | - Brent A Hanks
- Duke University Medical Center, Durham, North Carolina, USA
| | | | | | - Yoshinobu Koguchi
- Earle A Chiles Research Institute, Providence Cancer Institute, Portland, Oregon, USA
| | - Amanda W Lund
- Oregon Health and Science University, Portland, Oregon, USA
| | | | | | | | | | - Tasha Sims
- Regeneron Pharmaceuticals Inc, Tarrytown, New York, USA
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9
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Czechowska K, Lannigan J, Aghaeepour N, Back JB, Begum J, Behbehani G, Bispo C, Bitoun D, Fernández AB, Boova ST, Brinkman RR, Ciccolella CO, Cotleur B, Davies D, Dela Cruz GV, Del Rio-Guerra R, Des Lauriers-Cox AM, Douagi I, Dumrese C, Bonilla Escobar DL, Estevam J, Ewald C, Fossum A, Gaudillière B, Green C, Groves C, Hall C, Haque Y, Hedrick MN, Hogg K, Hsieh EWY, Irish J, Lederer J, Leipold M, Lewis-Tuffin LJ, Litwin V, Lopez P, Nasdala I, Nedbal J, Ohlsson-Wilhelm BM, Price KM, Rahman AH, Rayanki R, Rieger AM, Robinson JP, Shapiro H, Sun YS, Tang VA, Tesfa L, Telford WG, Walker R, Welsh JA, Wheeler P, Tárnok A. Cyt-Geist: Current and Future Challenges in Cytometry: Reports of the CYTO 2019 Conference Workshops. Cytometry A 2020; 95:1236-1274. [PMID: 31833655 DOI: 10.1002/cyto.a.23941] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
| | - Joanne Lannigan
- Flow Cytometry Support Services, LLC, Alexandria, Virginia.,Flow Cytometry Core, University of Virginia, School of Medicine, Charlottesville, Virginia
| | - Nima Aghaeepour
- Department of Anesthesiology, Department of Biomedical Data Sciences, Department of Pediatrics, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford University, Stanford, California
| | - Jessica B Back
- Department of Oncology, Wayne State University, Detroit, Michigan
| | - Julfa Begum
- Flow Cytometry Facility, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Greg Behbehani
- Wexner Medical Center, Ohio State University, Columbus, Ohio
| | - Cláudia Bispo
- Parnassus Flow Cytometry Core, University of California San Francisco, San Francisco, California.,ISAC SRL Emerging Leader, Arlington, Virginia
| | - Daniel Bitoun
- EMA Regional Marketing, BD Lifesciences, International Office, Belgium
| | - Alfonso Blanco Fernández
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland
| | - Samuel Tony Boova
- High Burden HIV Global Markets, Beckman Coulter, Inc., Miami, Florida
| | - Ryan Remy Brinkman
- Medical Genetics, University of British Columbia and British Columbia Cancer, Vancouver, British Columbia, Canada.,Cytapex Bioinformatics Inc., Vancouver, British Columbia, Canada
| | | | | | - Derek Davies
- Science Technology Platform Training Lead, Francis Crick Institute, London, UK
| | - Gelo Victoriano Dela Cruz
- Novo Nordisk Foundation Center for Stem Cell Biology - DanStem, Flow Cytometry Platform, Copenhagen, Denmark
| | - Roxana Del Rio-Guerra
- Flow Cytometry and Cell Sorting Facility, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | | | - Iyadh Douagi
- Flow Cytometry Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Claudia Dumrese
- Cytometry Facility, University of Zürich, Zürich, Switzerland
| | | | - Jose Estevam
- Center of Biomarker Innovation and Development, Takeda Pharmaceuticals, Cambridge, Massachusetts
| | - Christina Ewald
- Cytometry Facility Senior Scientist, University of Zürich, Zürich, Switzerland
| | - Anna Fossum
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Brice Gaudillière
- Anesthesiology Department, Stanford University, Stanford, California
| | - Cherie Green
- Flow Cytometry Biomarkers Development Sciences, Genentech, Inc., San Francisco, California
| | - Christopher Groves
- Cytometry/Dynamic Omics in R&D Antibody Discovery and Protein Engineering, Astra Zeneca, Gaithersburg, Maryland
| | - Christopher Hall
- ISAC SRL Emerging Leader, Arlington, Virginia.,Cytometry Core Facility, Wellcome Sanger Institute, Hinxton, UK
| | - Yasmin Haque
- Flow Cytometry Facility, Department of Immunobiology and Infectious Diseases, King's College London, London, UK
| | | | - Karen Hogg
- Imaging and Cytometry Laboratory, Bioscience Technology Facility, Department of Biology, University of York, York, UK
| | - Elena W Y Hsieh
- Department of Immunology and Microbiology, Department of Pediatrics, Division of Allergy and Immunology, School of Medicine, University of Colorado, Aurora, Colorado
| | - Jonathan Irish
- Cancer & Immunology Core and Mass Cytometry Center of Excellence, Vanderbilt University, Nashville, Tennessee
| | - James Lederer
- Department of Surgery (Immunology), Brigham and Women's Hospital/Harvard Medical School, Boston, Massachusetts
| | - Michael Leipold
- Human Immune Monitoring Center (HIMC), Stanford University, Stanford, California
| | - Laura J Lewis-Tuffin
- Microscopy and Flow Cytometry Shared Resource, Mayo Clinic, Jacksonville, Florida
| | - Virginia Litwin
- Caprion Biosciences, Inc., Immunology, Montreal, Quebec, Canada
| | - Peter Lopez
- Cytometry and Cell Sorting Laboratory, New York University School of Medicine, New York, New York
| | | | - Jakub Nedbal
- Physics Department, King's College London, London, UK.,ISAC Marylou Ingram Scholar, Arlington, Virginia
| | | | - Kylie M Price
- Hugh Green Cytometry Centre, Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Adeeb H Rahman
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, New York.,Dept. of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Radhika Rayanki
- Cytometry/Dynamic Omics in R&D Antibody Discovery and Protein Engineering, Astra Zeneca, Gaithersburg, Maryland
| | - Aja M Rieger
- ISAC SRL Emerging Leader, Arlington, Virginia.,University of Alberta, Flow Cytometry Facility, Faculty of Medicine and Dentistry, Alberta, Canada
| | - J Paul Robinson
- College of Veterinary Medicine and Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana
| | | | | | - Vera A Tang
- University of Ottawa, Flow Cytometry and Virometry Core Facility, Ottawa, Canada.,Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Lydia Tesfa
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York
| | - William G Telford
- Experimental Transplantation and Immunology Branch, Center for Cancer Research, National Cancer Center Institute, National Institutes of Health, Bethesda, Maryland
| | - Rachael Walker
- Flow Cytometry Core Facility, Babraham Institute, Cambridge, UK
| | - Joshua A Welsh
- ISAC Marylou Ingram Scholar, Arlington, Virginia.,Laboratory of Pathology, Translational Nanobiology Section, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Paul Wheeler
- Flow Cytometry, Luminex Corporation, Peterborough, UK
| | - Attila Tárnok
- Institute for Medical Informatics, Statistics and Epidemiology (IMISE), University of Leipzig, Leipzig, Germany.,Department Therapy Validation, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
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10
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Czechowska K, Lannigan J, Wang L, Arcidiacono J, Ashhurst TM, Barnard RM, Bauer S, Bispo C, Bonilla DL, Brinkman RR, Cabanski M, Chang HD, Chakrabarti L, Chojnowski G, Cotleur B, Degheidy H, Dela Cruz GV, Eck S, Elliott J, Errington R, Filby A, Gagnon D, Gardner R, Green C, Gregory M, Groves CJ, Hall C, Hammes F, Hedrick M, Hoffman R, Icha J, Ivaska J, Jenner DC, Jones D, Kerckhof FM, Kukat C, Lanham D, Leavesley S, Lee M, Lin-Gibson S, Litwin V, Liu Y, Molloy J, Moore JS, Müller S, Nedbal J, Niesner R, Nitta N, Ohlsson-Wilhelm B, Paul NE, Perfetto S, Portat Z, Props R, Radtke S, Rayanki R, Rieger A, Rogers S, Rubbens P, Salomon R, Schiemann M, Sharpe J, Sonder SU, Stewart JJ, Sun Y, Ulrich H, Van Isterdael G, Vitaliti A, van Vreden C, Weber M, Zimmermann J, Vacca G, Wallace P, Tárnok A. Cyt-Geist: Current and Future Challenges in Cytometry: Reports of the CYTO 2018 Conference Workshops. Cytometry A 2020; 95:598-644. [PMID: 31207046 DOI: 10.1002/cyto.a.23777] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
| | - Joanne Lannigan
- Flow Cytometry Core, University of Virginia, School of Medicine, 1300 Jefferson Park Ave., Charlottesville, Virginia
| | - Lili Wang
- Biosystems and Biomaterials Division, National Institute of Standards and Technology (NIST), 100 Bureau Drive, Stop 8312, Gaithersburg, Maryland
| | - Judith Arcidiacono
- Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland
| | - Thomas M Ashhurst
- Sydney Cytometry Facility, Discipline of Pathology, and Ramaciotti Facility for Human Systems Biology; Charles Perkins Centre, The University of Sydney and Centenary Institute, New South Wales, Australia
| | - Ruth M Barnard
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Herts SG1 2NY, UK
| | - Steven Bauer
- Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland
| | - Cláudia Bispo
- UCSF Parnassus Flow Cytometry Core Facility, 513 Parnassus Ave, San Francisco, California
| | - Diana L Bonilla
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ryan R Brinkman
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada.,Terry Fox Laboratory, BC Cancer, Vancouver, Canada
| | - Maciej Cabanski
- Novartis Pharma AG, Fabrikstrasse 10-4.27.02, CH-4056, Basel, Switzerland
| | - Hyun-Dong Chang
- Schwiete-Laboratory Microbiota and Inflammation, German Rheumatism Research Centre Berlin (DRFZ), a Leibniz Institute, Berlin, Germany
| | - Lina Chakrabarti
- Research and Development, MedImmune, an AstraZeneca Company, One Medimmune Way, Gaithersburg, Maryland
| | - Grace Chojnowski
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Queensland 4006, Australia
| | | | - Heba Degheidy
- Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, Maryland
| | - Gelo V Dela Cruz
- Flow Cytometry Platform, Novo Nordisk Center for Stem Cell Biology - Danstem, University of Copenhagen, 3B Blegdamsvej, DK-2200, Copenhagen, Denmark
| | - Steven Eck
- Research and Development, MedImmune, an AstraZeneca Company, One Medimmune Way, Gaithersburg, Maryland
| | - John Elliott
- Biosystems and Biomaterials Division, National Institute of Standards and Technology (NIST), 100 Bureau Drive, Stop 8312, Gaithersburg, Maryland
| | | | - Andy Filby
- Newcastle University, Flow Cytometry Core Facility, Newcastle upon Tyne, Tyne and Wear NE1 7RU, UK
| | | | - Rui Gardner
- Memorial Sloan Kettering Cancer Center, Flow Cytometry Core, New York, New York
| | | | - Michael Gregory
- Division of Advanced Research Technologies, New York University Langone Health, New York, New York
| | - Christopher J Groves
- Research and Development, MedImmune, an AstraZeneca Company, One Medimmune Way, Gaithersburg, Maryland
| | | | - Frederik Hammes
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | | | | | - Jaroslav Icha
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Johanna Ivaska
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland.,Department of Biochemistry, University of Turku, Turku, Finland
| | - Dominic C Jenner
- Defence Science and Technology Laboratory, Chemical Biological and Radiological Division, Porton Down, Salisbury, Wiltshire SP4 0JQ, UK
| | | | - Frederiek-Maarten Kerckhof
- Center for Microbial Ecology and Technology, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Christian Kukat
- FACS & Imaging Core Facility, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931, Köln, Germany
| | | | | | - Michael Lee
- The University California San Francisco, 505 Parnassus Ave, San Francisco, California
| | - Sheng Lin-Gibson
- Biosystems and Biomaterials Division, National Institute of Standards and Technology (NIST), 100 Bureau Drive, Stop 8312, Gaithersburg, Maryland
| | - Virginia Litwin
- Memorial Sloan Kettering Cancer Center, Flow Cytometry Core, New York, New York
| | | | - Jenny Molloy
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | | | - Susann Müller
- Working Group Flow Cytometry, Department of Environmental Microbiology, Helmholtz Center for Environmental Research (UFZ), Leipzig, Germany
| | - Jakub Nedbal
- Marylou Ingram ISAC Scholar, King's College London, UK
| | - Raluca Niesner
- Marylou Ingram ISAC Scholar, German Rheumatism Research Centre, Berlin, Germany
| | - Nao Nitta
- Department of Chemistry, The University of Tokyo
| | - Betsy Ohlsson-Wilhelm
- SciGro, North Central Office, Foster Plaza 5, Suite 300/PMB 20, 651 Holiday Drive, Pittsburgh, Pennsylvania
| | - Nicole E Paul
- LMA CyTOF Core, Dana-Faber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts
| | - Stephen Perfetto
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institute of Health (NIH), 40 Convent Drive, Bethesda, Maryland
| | - Ziv Portat
- Weizmann Institute of Science, Life Sciences Core Facilities, Flow Cytometry Unit, Rehovot, 7610001, Israel
| | - Ruben Props
- Center for Microbial Ecology and Technology, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Stefan Radtke
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, Washington
| | - Radhika Rayanki
- Research and Development, MedImmune, an AstraZeneca Company, One Medimmune Way, Gaithersburg, Maryland
| | - Aja Rieger
- Faculty of Medicine and Dentistry Flow Cytometry Facility, Department of Medical Microbiology & Immunology, University of Alberta, 6-020C Katz Group Centre for Pharmacy and Health Research, Canada
| | - Samson Rogers
- TTP plc, Melbourn Science Park, Melbourn, Hertfordshire SG8 6EE, UK
| | - Peter Rubbens
- KERMIT, Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Robert Salomon
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, New South Wales, Australia
| | - Matthias Schiemann
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, Munich, Germany
| | - John Sharpe
- Cytonome/ST LLC, 9 Oak Park Drive, Bedford, Massachusetts
| | | | - Jennifer J Stewart
- Flow Contract Site Laboratory, LLC 18323, Bothell, Everett Highway, Suite 110, Bothell, Washington
| | | | - Henning Ulrich
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Gert Van Isterdael
- VIB Flow Core, VIB Center for Inflammation Research, Technologiepark-Zwijnaarde 71, B-9052, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | | | - Caryn van Vreden
- Sydney Cytometry Facility and Ramaciotti Facility for Human Systems Biology, The University of Sydney and Centenary Institute, Camperdown, New South Wales 2050, Australia
| | - Michael Weber
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts
| | - Jacob Zimmermann
- Mucosal Immunology and Host-Microbial Mutualism laboratories, Department for BioMedical Research, University of Bern, Bern, Switzerland
| | | | - Paul Wallace
- Roswell Park Comprehensive Cancer Center, New York
| | - Attila Tárnok
- Institute for Medical Informatics, Statistics and Epidemiology (IMISE), University of Leipzig, Leipzig, Germany.,Department Therapy Validation, Fraunhofer Institute for Cell Therapy and Immunology IZI, Leipzig, Germany
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11
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Standardization procedure for flow cytometry data harmonization in prospective multicenter studies. Sci Rep 2020; 10:11567. [PMID: 32665668 PMCID: PMC7360585 DOI: 10.1038/s41598-020-68468-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 06/22/2020] [Indexed: 01/26/2023] Open
Abstract
One of the most challenging objective for clinical cytometry in prospective multicenter immunomonitoring trials is to compare frequencies, absolute numbers of leukocyte populations and further the mean fluorescence intensities of cell markers, especially when the data are generated from different instruments. Here, we describe an innovative standardization workflow to compare all data to carry out any large-scale, prospective multicentric flow cytometry analysis whatever the duration, the number or type of instruments required for the realization of such projects.
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12
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Lucchesi S, Furini S, Medaglini D, Ciabattini A. From Bivariate to Multivariate Analysis of Cytometric Data: Overview of Computational Methods and Their Application in Vaccination Studies. Vaccines (Basel) 2020; 8:E138. [PMID: 32244919 PMCID: PMC7157606 DOI: 10.3390/vaccines8010138] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/17/2020] [Accepted: 03/18/2020] [Indexed: 12/15/2022] Open
Abstract
Flow and mass cytometry are used to quantify the expression of multiple extracellular or intracellular molecules on single cells, allowing the phenotypic and functional characterization of complex cell populations. Multiparametric flow cytometry is particularly suitable for deep analysis of immune responses after vaccination, as it allows to measure the frequency, the phenotype, and the functional features of antigen-specific cells. When many parameters are investigated simultaneously, it is not feasible to analyze all the possible bi-dimensional combinations of marker expression with classical manual analysis and the adoption of advanced automated tools to process and analyze high-dimensional data sets becomes necessary. In recent years, the development of many tools for the automated analysis of multiparametric cytometry data has been reported, with an increasing record of publications starting from 2014. However, the use of these tools has been preferentially restricted to bioinformaticians, while few of them are routinely employed by the biomedical community. Filling the gap between algorithms developers and final users is fundamental for exploiting the advantages of computational tools in the analysis of cytometry data. The potentialities of automated analyses range from the improvement of the data quality in the pre-processing steps up to the unbiased, data-driven examination of complex datasets using a variety of algorithms based on different approaches. In this review, an overview of the automated analysis pipeline is provided, spanning from the pre-processing phase to the automated population analysis. Analysis based on computational tools might overcame both the subjectivity of manual gating and the operator-biased exploration of expected populations. Examples of applications of automated tools that have successfully improved the characterization of different cell populations in vaccination studies are also presented.
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Affiliation(s)
- Simone Lucchesi
- Laboratory of Molecular Microbiology and Biotechnology (LA.M.M.B.), Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (S.L.); (D.M.)
| | - Simone Furini
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy;
| | - Donata Medaglini
- Laboratory of Molecular Microbiology and Biotechnology (LA.M.M.B.), Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (S.L.); (D.M.)
| | - Annalisa Ciabattini
- Laboratory of Molecular Microbiology and Biotechnology (LA.M.M.B.), Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (S.L.); (D.M.)
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13
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Kalina T, Lundsten K, Engel P. Relevance of Antibody Validation for Flow Cytometry. Cytometry A 2019; 97:126-136. [DOI: 10.1002/cyto.a.23895] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 07/10/2019] [Accepted: 08/22/2019] [Indexed: 01/01/2023]
Affiliation(s)
- Tomas Kalina
- CLIP‐Childhood Leukemia Investigation Prague, Department of Pediatric Hematology and Oncology, 2nd Medical SchoolCharles University and University Hospital Motol Prague Czech Republic
| | | | - Pablo Engel
- Department of Biomedical SciencesFaculty of Medicine and Health Sciences, University of Barcelona Barcelona Spain
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14
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Brinkman RR. Improving the Rigor and Reproducibility of Flow Cytometry-Based Clinical Research and Trials Through Automated Data Analysis. Cytometry A 2019; 97:107-112. [PMID: 31515945 DOI: 10.1002/cyto.a.23883] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 06/13/2019] [Accepted: 08/08/2019] [Indexed: 01/17/2023]
Affiliation(s)
- Ryan R Brinkman
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada.,Cytapex Bioinformatics Inc., Vancouver, British Columbia, Canada
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15
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Montante S, Brinkman RR. Flow cytometry data analysis: Recent tools and algorithms. Int J Lab Hematol 2019; 41 Suppl 1:56-62. [PMID: 31069980 DOI: 10.1111/ijlh.13016] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 02/25/2019] [Accepted: 02/26/2019] [Indexed: 12/21/2022]
Abstract
Flow cytometry (FCM) allows scientists to rapidly quantify up to 50 parameters for millions of cells per sample. The bottleneck in the application of the technology is data analysis, and the high number of parameters measured by the current generation of instruments requires the use of advanced computational algorithms to make full use of their capabilities. This review summarizes the main steps of FCM data analysis, focusing on the use of the most recent bioinformatic tools developed for an R-based programming environment. In particular, for each stage of the data analysis, libraries and packages currently available are listed, and a brief description of their functioning is included.
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Affiliation(s)
| | - Ryan R Brinkman
- Terry Fox Laboratory, BC Cancer, Vancouver, British Columbia, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
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16
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Bonham CA, Hrusch CL, Blaine KM, Manns ST, Vij R, Oldham JM, Churpek MM, Strek ME, Noth I, Sperling AI. T cell Co-Stimulatory molecules ICOS and CD28 stratify idiopathic pulmonary fibrosis survival. RESPIRATORY MEDICINE: X 2019; 1. [PMID: 32455343 PMCID: PMC7243672 DOI: 10.1016/j.yrmex.2019.100002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a devastating disease that kills as many Americans as breast cancer each year. This study investigated whether lung function decline and survival associates with adaptive immunity in patients with IPF, specifically the expression of checkpoint molecules ICOS, CD28 and PD-1 on circulating CD4 T cells. Clinical data, blood samples and pulmonary function tests were collected prospectively and longitudinally from 59 patients with IPF over a study period of 5 years. Patients were followed until death, lung transplantation, or study end, and cell surface expression of CD45RO, CD28, ICOS, and PD-1 was measured on CD4 T cells via flow cytometry. Repeated measures of ICOS and CD28 on CD4 T cells revealed significant associations between declining ICOS and CD28 expression, and declining lung function parameters FVC and DLCO, independent of age, sex, race, smoking history, or immunosuppressant use. Strikingly, patients in the highest quintile of ICOS at study entry had markedly improved survival, while those with low CD28 fared poorly. No change in PD-1 expression was found. Analysis of ICOS and CD28 from the first blood draw identified three populations of IPF patients; those at high risk for early death, those with intermediate risk, and those at low risk. These results highlight the role of T cell mediated immunity in IPF survival, finding the assessment of two T cell stimulatory checkpoint molecules, CD28 and ICOS, was sufficient to discriminate three distinct survival trajectories over 5 years of patient follow up.
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Affiliation(s)
- Catherine A Bonham
- Pulmonary and Critical Care Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Cara L Hrusch
- Pulmonary and Critical Care Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Kelly M Blaine
- Pulmonary and Critical Care Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Stephenie T Manns
- Pulmonary and Critical Care Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Rekha Vij
- Pulmonary and Critical Care Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Justin M Oldham
- Pulmonary and Critical Care Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Matthew M Churpek
- Pulmonary and Critical Care Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Mary E Strek
- Pulmonary and Critical Care Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Imre Noth
- Pulmonary and Critical Care Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Anne I Sperling
- Pulmonary and Critical Care Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA.,Committee of Immunology, University of Chicago, Chicago, IL, USA
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17
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Buldini B, Maurer-Granofszky M, Varotto E, Dworzak MN. Flow-Cytometric Monitoring of Minimal Residual Disease in Pediatric Patients With Acute Myeloid Leukemia: Recent Advances and Future Strategies. Front Pediatr 2019; 7:412. [PMID: 31681710 PMCID: PMC6798174 DOI: 10.3389/fped.2019.00412] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 09/25/2019] [Indexed: 01/10/2023] Open
Abstract
Minimal residual disease (MRD) by multiparametric flow cytometry (MFC) has been recently shown as a strong and independent prognostic marker of relapse in pediatric AML (pedAML) when measured at specific time points during Induction and/or Consolidation therapy. Hence, MFC-MRD has the potential to refine the current strategies of pedAML risk stratification, traditionally based on the cytogenetic and molecular genetic aberrations at diagnosis. Consequently, it may guide the modulation of therapy intensity and clinical decision making. However, the use of non-standardized protocols, including different staining panels, analysis, and gating strategies, may hamper a broad implementation of MFC-MRD monitoring in clinical routine. Besides, the thresholds of MRD positivity still need to be validated in large, prospective and multi-center clinical studies, as well as optimal time points of MRD assessment during therapy, to better discriminate patients with different prognosis. In the present review, we summarize the most relevant findings on MFC-MRD testing in pedAML. We examine the clinical significance of MFC-MRD and the recent advances in its standardization, including innovative approaches with an automated analysis of MFC-MRD data. We also touch upon other technologies for MRD assessment in AML, such as quantitative genomic breakpoint PCR, current challenges and future strategies to enable full incorporation of MFC-MRD into clinical practice.
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Affiliation(s)
- Barbara Buldini
- Laboratory of Hematology-Oncology, Department of Woman's and Child's Health, University of Padova, Padova, Italy
| | | | - Elena Varotto
- Laboratory of Hematology-Oncology, Department of Woman's and Child's Health, University of Padova, Padova, Italy
| | - Michael N Dworzak
- Children's Cancer Research Institute (CCRI), St. Anna Kinderkrebsforschung, Vienna, Austria
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