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Gallaccio G, Wang M, Schlickeiser S, Kunkel D, Böttcher C, Fernández-Zapata C. Protocol to characterize immune cell subpopulations in cerebrospinal fluid of patients with neuroinflammatory diseases using mass cytometry. STAR Protoc 2024; 5:103038. [PMID: 38678568 PMCID: PMC11068925 DOI: 10.1016/j.xpro.2024.103038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/25/2024] [Accepted: 04/11/2024] [Indexed: 05/01/2024] Open
Abstract
Phenotypic and compositional changes of immune cells in cerebrospinal fluid (CSF) can be used as biomarkers to help diagnose and track disease activity for neuroinflammatory and neurodegenerative diseases. Here, we present a workflow to perform high-dimensional immune profiling at single-cell resolution using cytometry by time-of-flight (CyTOF) on cells isolated from the CSF of patients with neuroinflammation. We describe steps for sample collection and preparation, barcoding to allow for multiplexing, and downstream data analysis using R. For complete details on the use and execution of this protocol, please refer to Fernández-Zapata et al.1.
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Affiliation(s)
- Gerardina Gallaccio
- Experimental and Clinical Research Center, A Cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité-Universitätsmedizin Berlin, Berlin, Germany; Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany; Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt- Universität zu Berlin, Berlin, Germany
| | - Meng Wang
- Experimental and Clinical Research Center, A Cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité-Universitätsmedizin Berlin, Berlin, Germany; Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany; Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt- Universität zu Berlin, Berlin, Germany
| | - Stephan Schlickeiser
- Institute of Medical Immunology, BIH-Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, and Berlin Institute of Health Berlin, Berlin, Germany
| | - Desiree Kunkel
- Berlin Institute of Health at Charité - Universitiätsmedizin Berlin, Flow & Mass Cytometry Core Facility, Berlin, Germany
| | - Chotima Böttcher
- Experimental and Clinical Research Center, A Cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité-Universitätsmedizin Berlin, Berlin, Germany; Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany; Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt- Universität zu Berlin, Berlin, Germany.
| | - Camila Fernández-Zapata
- Experimental and Clinical Research Center, A Cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité-Universitätsmedizin Berlin, Berlin, Germany; Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany; Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt- Universität zu Berlin, Berlin, Germany.
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2
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Schüller SS, Barman S, Mendez-Giraldez R, Soni D, Daley J, Baden LR, Levy O, Dowling DJ. Immune profiling of age and adjuvant-specific activation of human blood mononuclear cells in vitro. Commun Biol 2024; 7:709. [PMID: 38851856 PMCID: PMC11162429 DOI: 10.1038/s42003-024-06390-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 05/27/2024] [Indexed: 06/10/2024] Open
Abstract
Vaccination reduces morbidity and mortality due to infections, but efficacy may be limited due to distinct immunogenicity at the extremes of age. This raises the possibility of employing adjuvants to enhance immunogenicity and protection. Early IFNγ production is a hallmark of effective vaccine immunogenicity in adults serving as a biomarker that may predict effective adjuvanticity. We utilized mass cytometry (CyTOF) to dissect the source of adjuvant-induced cytokine production in human blood mononuclear cells (BMCs) from newborns (~39-week-gestation), adults (~18-63 years old) and elders (>65 years of age) after stimulation with pattern recognition receptors agonist (PRRa) adjuvants. Dimensionality reduction analysis of CyTOF data mapped the BMC compartment, elucidated age-specific immune responses and profiled PRR-mediated activation of monocytes and DCs upon adjuvant stimulation. Furthermore, we demonstrated PRRa adjuvants mediated innate IFNγ induction and mapped NK cells as the key source of TLR7/8 agonist (TLR7/8a) specific innate IFNγ responses. Hierarchical clustering analysis revealed age and TLR7/8a-specific accumulation of innate IFNγ producing γδ T cells. Our study demonstrates the application of mass cytometry and cutting-edge computational approaches to characterize immune responses across immunologically distinct age groups and may inform identification of the bespoke adjuvantation systems tailored to enhance immunity in distinct vulnerable populations.
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Affiliation(s)
- Simone S Schüller
- Precision Vaccines Program, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Neonatal Directorate, Child and Adolescent Health Service, Perth, Australia
| | - Soumik Barman
- Precision Vaccines Program, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | - Dheeraj Soni
- Precision Vaccines Program, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Sanofi, Cambridge, MA, USA
| | - John Daley
- Dana Farber CyTOF Core Facility, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Lindsey R Baden
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Ofer Levy
- Precision Vaccines Program, Boston Children's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT & Harvard, Cambridge, MA, USA.
| | - David J Dowling
- Precision Vaccines Program, Boston Children's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
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3
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Spasic M, Ogayo ER, Parsons AM, Mittendorf EA, van Galen P, McAllister SS. Spectral Flow Cytometry Methods and Pipelines for Comprehensive Immunoprofiling of Human Peripheral Blood and Bone Marrow. CANCER RESEARCH COMMUNICATIONS 2024; 4:895-910. [PMID: 38466569 PMCID: PMC10962315 DOI: 10.1158/2767-9764.crc-23-0357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/20/2023] [Accepted: 03/05/2024] [Indexed: 03/13/2024]
Abstract
Profiling hematopoietic and immune cells provides important information about disease risk, disease status, and therapeutic responses. Spectral flow cytometry enables high-dimensional single-cell evaluation of large cohorts in a high-throughput manner. Here, we designed, optimized, and implemented new methods for deep immunophenotyping of human peripheral blood and bone marrow by spectral flow cytometry. Two blood antibody panels capture 48 cell-surface markers to assess more than 58 cell phenotypes, including subsets of T cells, B cells, monocytes, natural killer (NK) cells, and dendritic cells, and their respective markers of exhaustion, activation, and differentiation in less than 2 mL of blood. A bone marrow antibody panel captures 32 markers for 35 cell phenotypes, including stem/progenitor populations, T-cell subsets, dendritic cells, NK cells, and myeloid cells in a single tube. We adapted and developed innovative flow cytometric analysis algorithms, originally developed for single-cell genomics, to improve data integration and visualization. We also highlight technical considerations for users to ensure data fidelity. Our protocol and analysis pipeline accurately identifies rare cell types, discerns differences in cell abundance and phenotype across donors, and shows concordant immune landscape trends in patients with known hematologic malignancy. SIGNIFICANCE This study introduces optimized methods and analysis algorithms that enhance capabilities in comprehensive immunophenotyping of human blood and bone marrow using spectral flow cytometry. This approach facilitates detection of rare cell types, enables measurement of cell variations across donors, and provides proof-of-concept in identifying known hematologic malignancies. By unlocking complexities of hematopoietic and immune landscapes at the single-cell level, this advancement holds potential for understanding disease states and therapeutic responses.
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Affiliation(s)
- Milos Spasic
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Esther R. Ogayo
- Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, Massachusetts
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, Massachusetts
| | - Adrienne M. Parsons
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Elizabeth A. Mittendorf
- Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, Massachusetts
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, Massachusetts
| | - Peter van Galen
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
- Harvard Stem Cell Institute, Cambridge, Massachusetts
- Ludwig Center at Harvard, Harvard Medical School, Boston, Massachusetts
| | - Sandra S. McAllister
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
- Harvard Stem Cell Institute, Cambridge, Massachusetts
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4
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Hallisey M, Dennis J, Gabriel EP, Masciarelli A, Chen J, Abrecht C, Brainard M, Marcotte WM, Dong H, Hathaway E, Tarannum M, Vergara JA, Schork AN, Tyan K, Tarantino G, Liu D, Romee R, Rahma OE, Severgnini M, Hodi FS, Baginska J. Profiling of Natural Killer Interactions With Cancer Cells Using Mass Cytometry. J Transl Med 2023; 103:100174. [PMID: 37169083 DOI: 10.1016/j.labinv.2023.100174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 05/13/2023] Open
Abstract
We developed a comprehensive method for functional assessment of the changes in immune populations and killing activity of peripheral blood mononuclear cells after cocultures with cancer cells using mass cytometry. In this study, a 43-marker mass cytometry panel was applied to a coculture of immune cells from healthy donors' peripheral blood mononuclear cells with diverse cancer cell lines. DNA content combined with classical CD45 surface staining was used as gating parameters for cocultures of immune cells (CD45high/DNAlow) with hematological (CD45low/DNAhigh) and solid cancer cell lines (CD45neg/DNAhigh). This strategy allows for universal discrimination of cancer cells from immune populations without the need for a specific cancer cell marker and simultaneous assessment of phenotypical changes in both populations. The use of mass cytometry allows for simultaneous detection of changes in natural killer, natural killer T cell, and T cell phenotypes and degranulation of immune populations upon target recognition, analysis of target cells for cytotoxic protein granzyme B content, and cancer cell death. These findings have broad applicability in research and clinical settings with the aim to phenotype and assess functional changes following not only NK-cancer cell interactions but also the effect of those interactions on other immune populations.
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Affiliation(s)
- Margaret Hallisey
- Department of Medical Oncology, Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jenna Dennis
- Department of Medical Oncology, Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Elizabeth P Gabriel
- Department of Medical Oncology, Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Alyssa Masciarelli
- Department of Medical Oncology, Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jiajia Chen
- Department of Medical Oncology, Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts; Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Charlotte Abrecht
- Department of Medical Oncology, Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Martha Brainard
- Department of Medical Oncology, Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - William M Marcotte
- Department of Medical Oncology, Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Han Dong
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Emma Hathaway
- Department of Medical Oncology, Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Mubin Tarannum
- Division of Hematologic Malignancies, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Juliana A Vergara
- Division of Hematologic Malignancies, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Abigail N Schork
- Longwood Medical Area CyTOF Core, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kevin Tyan
- Department of Medical Oncology, Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts; Harvard Medical School, Boston, Massachusetts
| | - Giuseppe Tarantino
- Department of Medical Oncology, Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts; Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - David Liu
- Department of Medical Oncology, Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts; Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Rizwan Romee
- Division of Hematologic Malignancies, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Osama E Rahma
- Department of Medical Oncology, Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts; Harvard Medical School, Boston, Massachusetts
| | - Mariano Severgnini
- Department of Medical Oncology, Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - F Stephen Hodi
- Department of Medical Oncology, Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Joanna Baginska
- Department of Medical Oncology, Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
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5
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Shin SM, Hernandez A, Coyne E, Munjal K, Gross NE, Charmsaz S, Yuan X, Yang H, Ho WJ. CyTOF protocol for immune monitoring of solid tumors from mouse models. STAR Protoc 2023; 4:101949. [PMID: 36538397 PMCID: PMC9794973 DOI: 10.1016/j.xpro.2022.101949] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 10/19/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
Techniques for robust immune profiling of mouse tumor and blood are key to understanding immunological responses in mouse models of cancer. Here, we describe mass cytometry (cytometry by time-of-flight) procedures to facilitate high-parameter profiling of low-volume survival blood samples and end-of-study tumor samples. We employ live-cell barcoding systems to mark all cells from each tumor and blood to improve cost-effectiveness and minimize batch effects. For complete details on the use and execution of this protocol, please refer to Charmsaz et al. (2021).1.
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Affiliation(s)
- Sarah M Shin
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA
| | - Alexei Hernandez
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA
| | - Erin Coyne
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA
| | - Kabeer Munjal
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA
| | - Nicole E Gross
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA
| | - Soren Charmsaz
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA
| | - Xuan Yuan
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA; Mass Cytometry Facility at Johns Hopkins University, Baltimore, MD 21287, USA
| | - Hongqui Yang
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA; Mass Cytometry Facility at Johns Hopkins University, Baltimore, MD 21287, USA
| | - Won Jin Ho
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA; Mass Cytometry Facility at Johns Hopkins University, Baltimore, MD 21287, USA; Convergence Institute, Johns Hopkins University, Baltimore, MD 21287, USA.
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6
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Protocol for large scale whole blood immune monitoring by mass cytometry and Cyto Quality Pipeline. STAR Protoc 2022; 3:101697. [DOI: 10.1016/j.xpro.2022.101697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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7
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Gadalla R, Boukhaled GM, Brooks DG, Wang BX. Mass cytometry immunostaining protocol for multiplexing clinical samples. STAR Protoc 2022; 3:101643. [PMID: 36052346 PMCID: PMC9424627 DOI: 10.1016/j.xpro.2022.101643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
This is a cytometry by time-of-flight (CyTOF) staining protocol for hematopoietic-derived cells, that leverages live-cell barcoding using receptor-type tyrosine-protein phosphatase C (CD45) antibodies conjugated to metal isotopes in combination with DNA-based palladium barcoding to multiplex up to 40 samples. In this protocol, DNA-based barcoding is performed before surface and intracellular immunostaining, which reduces the batch effects that result from day-to-day variations in staining and instrument sensitivity. This protocol also reduces antibody consumption and eliminates the need for repeated instrument adjustment. Mass cytometry immunostaining for 40+ samples to reduce batch-to-batch variation Barcoding samples before immunostaining ensures consistency across all samples Reduction in antibody volume consumption and data acquisition time
Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
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8
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Urbiola-Salvador V, Miroszewska D, Jabłońska A, Qureshi T, Chen Z. Proteomics approaches to characterize the immune responses in cancer. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119266. [PMID: 35390423 DOI: 10.1016/j.bbamcr.2022.119266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 03/01/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Despite the dynamic development of cancer research, annually millions of people die of cancer. The human immune system is the major 'guard' against tumor development. Unfortunately, cancer cells have the ability to evade the immune system and continue to grow. The proper understanding of the intricate immune response in tumorigenesis remains the holy grail of cancer immunology and designing effective immunotherapy. To decode the immune responses in cancer, in recent years, proteomics studies have received considerable attention. Proteomics studies focus on the detection and quantification of proteins, which are the effectors of biological functions, and as such, are proven to reflect the cell state more accurately, in comparison to genomic or transcriptomic studies. In this review, we discuss the proteomics studies applied to characterize the immune responses in cancer and tumor immune microenvironment heterogeneity. Further, we describe emerging single-cell proteomics approaches that have the potential to be applied in cancer immunity studies.
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Affiliation(s)
- Víctor Urbiola-Salvador
- Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Poland.
| | - Dominika Miroszewska
- Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Poland.
| | - Agnieszka Jabłońska
- Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Poland.
| | - Talha Qureshi
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.
| | - Zhi Chen
- Intercollegiate Faculty of Biotechnology of University of Gdańsk and Medical University of Gdańsk, University of Gdańsk, Poland; Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.
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Delgado-Gonzalez A, Huang YW, Porpiglia E, Donoso K, Gonzalez VD, Fantl WJ. Measuring trogocytosis between ovarian tumor and natural killer cells. STAR Protoc 2022; 3:101425. [PMID: 35693208 PMCID: PMC9185020 DOI: 10.1016/j.xpro.2022.101425] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Trogocytosis is an active transport mechanism by which one cell extracts a plasma membrane fragment with embedded molecules from an adjacent cell in a contact-dependent process leading to the acquisition of a new function. Our protocol, which has general applicability, consolidates and optimizes existing protocols while highlighting key experimental variables to demonstrate that natural killer (NK) cells acquire the tetraspanin CD9 by trogocytosis from ovarian tumor cells. For complete details on the use and execution of this protocol, please refer to Gonzalez et al. (2021).
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Affiliation(s)
- Antonio Delgado-Gonzalez
- Deparment of Urology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ying-Wen Huang
- Deparment of Urology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ermelinda Porpiglia
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
| | - Kenyi Donoso
- Deparment of Urology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Veronica D. Gonzalez
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Wendy J. Fantl
- Deparment of Urology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA 94305, USA
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10
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Shapiro RM, Birch GC, Hu G, Vergara Cadavid J, Nikiforow S, Baginska J, Ali AK, Tarannum M, Sheffer M, Abdulhamid YZ, Rambaldi B, Arihara Y, Reynolds C, Halpern MS, Rodig SJ, Cullen N, Wolff JO, Pfaff KL, Lane AA, Lindsley RC, Cutler CS, Antin JH, Ho VT, Koreth J, Gooptu M, Kim HT, Malmberg KJ, Wu CJ, Chen J, Soiffer RJ, Ritz J, Romee R. Expansion, persistence, and efficacy of donor memory-like NK cells infused for posttransplant relapse. J Clin Invest 2022; 132:e154334. [PMID: 35349491 PMCID: PMC9151697 DOI: 10.1172/jci154334] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 03/23/2022] [Indexed: 11/17/2022] Open
Abstract
BackgroundResponses to conventional donor lymphocyte infusion for postallogeneic hematopoietic cell transplantation (HCT) relapse are typically poor. Natural killer (NK) cell-based therapy is a promising modality to treat post-HCT relapse.MethodsWe initiated this ongoing phase I trial of adoptively transferred cytokine-induced memory-like (CIML) NK cells in patients with myeloid malignancies who relapsed after haploidentical HCT. All patients received a donor-derived NK cell dose of 5 to 10 million cells/kg after lymphodepleting chemotherapy, followed by systemic IL-2 for 7 doses. High-resolution profiling with mass cytometry and single-cell RNA sequencing characterized the expanding and persistent NK cell subpopulations in a longitudinal manner after infusion.ResultsIn the first 6 enrolled patients on the trial, infusion of CIML NK cells led to a rapid 10- to 50-fold in vivo expansion that was sustained over months. The infusion was well tolerated, with fever and pancytopenia as the most common adverse events. Expansion of NK cells was distinct from IL-2 effects on endogenous post-HCT NK cells, and not dependent on CMV viremia. Immunophenotypic and transcriptional profiling revealed a dynamic evolution of the activated CIML NK cell phenotype, superimposed on the natural variation in donor NK cell repertoires.ConclusionGiven their rapid expansion and long-term persistence in an immune-compatible environment, CIML NK cells serve as a promising platform for the treatment of posttransplant relapse of myeloid disease. Further characterization of their unique in vivo biology and interaction with both T cells and tumor targets will lead to improvements in cell-based immunotherapies.Trial RegistrationClinicalTrials.gov NCT04024761.FundingDunkin' Donuts, NIH/National Cancer Institute, and the Leukemia and Lymphoma Society.
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Affiliation(s)
- Roman M. Shapiro
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Grace C. Birch
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Guangan Hu
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Juliana Vergara Cadavid
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Sarah Nikiforow
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Joanna Baginska
- Center for Immuno-oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Alaa K. Ali
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Mubin Tarannum
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Michal Sheffer
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Yasmin Z. Abdulhamid
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Benedetta Rambaldi
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- University of Milano-Bicocca, Monza, Italy
| | - Yohei Arihara
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Carol Reynolds
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Max S. Halpern
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | | | | | | | | | - Andrew A. Lane
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - R. Coleman Lindsley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Corey S. Cutler
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Joseph H. Antin
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Vincent T. Ho
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - John Koreth
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Mahasweta Gooptu
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Haesook T. Kim
- Department of Data Science, Dana-Farber Cancer Institute/Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Karl-Johan Malmberg
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Institute for Clinical Medicine, The University of Oslo, Oslo, Norway
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Solna, Sweden
| | - Catherine J. Wu
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Jianzhu Chen
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Robert J. Soiffer
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Jerome Ritz
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Rizwan Romee
- Division of Transplantation and Cellular Therapies, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
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11
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Functional analysis of human circulating immune cells based on high-dimensional mass cytometry. STAR Protoc 2022; 3:101310. [PMID: 35434658 PMCID: PMC9010797 DOI: 10.1016/j.xpro.2022.101310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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12
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Ioannidis LJ, Mitchell AJ, Zheng T, Hansen DS. CyTOF mass cytometry analysis of human memory CD4+ T cells and memory B cells. STAR Protoc 2022; 3:101269. [PMID: 35378884 PMCID: PMC8976126 DOI: 10.1016/j.xpro.2022.101269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
High-dimensional mass cytometry provides unparalleled insight into the cellular composition of the immune system. Here, we describe a mass-cytometry-based protocol to examine memory CD4+ T cell and memory B cell (MBC) responses in human peripheral blood. This approach allows for the identification of >50 distinct memory CD4+ T cell and MBC populations from a single clinical sample. This highly reproducible protocol has been successfully applied to multiple infectious disease settings to identify correlates of susceptibility or protection from infection. For complete details on the use and execution of this protocol, please refer to Ioannidis et al. (2021). CyTOF mass-cytometry-based protocol to analyze human peripheral blood mononuclear cells Optimized protocol for clinical samples Allows in-depth analysis of human memory CD4+ T cell and memory B cell responses Applicable to multiple disease settings
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13
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Hallisey M, Dennis J, Abrecht C, Pistofidis RS, Schork AN, Lightbody ED, Heilpern-Mallory D, Severgnini M, Ghobrial IM, Hodi FS, Baginska J. Mass cytometry staining for human bone marrow clinical samples. STAR Protoc 2022; 3:101163. [PMID: 35243367 PMCID: PMC8861824 DOI: 10.1016/j.xpro.2022.101163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
This protocol details a staining technique optimized for immunophenotyping of human bone marrow immune populations using mass cytometry. The protocol accounts for the limitations of working with human bone marrow, such as reduced viability, low cell counts, and fragile cell pellets, to successfully acquire single viable cells ready for downstream analysis. This assay can be used to characterize the activation, exhaustion, and cytotoxicity of immune populations and ensure comprehensive immunophenotyping of human bone marrow clinical samples.
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Affiliation(s)
- Margaret Hallisey
- Department of Medical Oncology, Center for Immuno-Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Jenna Dennis
- Department of Medical Oncology, Center for Immuno-Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Charlotte Abrecht
- Department of Medical Oncology, Center for Immuno-Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Romanos Sklavenitis Pistofidis
- Department of Medical Oncology, Center for Immuno-Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
- Center for Prevention of Progression of Blood Cancers, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Abigail N. Schork
- Longwood Medical Area CyTOF Core, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Elizabeth D. Lightbody
- Department of Medical Oncology, Center for Immuno-Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
- Center for Prevention of Progression of Blood Cancers, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Daniel Heilpern-Mallory
- Department of Medical Oncology, Center for Immuno-Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
- Center for Prevention of Progression of Blood Cancers, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Mariano Severgnini
- Department of Medical Oncology, Center for Immuno-Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Irene M. Ghobrial
- Department of Medical Oncology, Center for Immuno-Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
- Center for Prevention of Progression of Blood Cancers, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - F. Stephen Hodi
- Department of Medical Oncology, Center for Immuno-Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Joanna Baginska
- Department of Medical Oncology, Center for Immuno-Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
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14
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Schoeberl A, Gutmann M, Theiner S, Schaier M, Schweikert A, Berger W, Koellensperger G. Cisplatin Uptake in Macrophage Subtypes at the Single-Cell Level by LA-ICP-TOFMS Imaging. Anal Chem 2021; 93:16456-16465. [PMID: 34846133 PMCID: PMC8674877 DOI: 10.1021/acs.analchem.1c03442] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
A high-throughput
laser ablation–inductively coupled plasma–time-of-flight
mass spectrometry (LA-ICP-TOFMS) workflow was implemented for quantitative
single-cell analysis following cytospin preparation of cells. For
the first time, in vitro studies on cisplatin exposure addressed human
monocytes and monocyte-derived macrophages (undifferentiated THP-1
monocytic cells, differentiated M0 macrophages, as well as further
polarized M1 and M2 phenotypes) at the single-cell level. The models
are of particular interest as macrophages comprise the biggest part
of immune cells present in the tumor microenvironment and play an
important role in modulating tumor growth and progression. The introduced
bioimaging workflow proved to be universally applicable to adherent
and suspension cell cultures and fit-for-purpose for the quantitative
analysis of several hundreds of cells within minutes. Both, cross-validation
of the method with single-cell analysis in suspension for THP-1 cells
and with LA-ICP-TOFMS analysis of adherent M0 cells grown on chambered
glass coverslips, revealed agreeing platinum concentrations at the
single-cell level. A high incorporation of cisplatin was observed
in M2 macrophages compared to the M0 and M1 macrophage subtypes and
the monocyte model, THP-1. The combination with bright-field images
and monitoring of highly abundant endogenous elements such as phosphorus
and sodium at a high spatial resolution allowed assessing cell size
and important morphological cell parameters and thus straightforward
control over several cell conditions. This way, apoptotic cells and
cell debris as well as doublets or cell clusters could be easily excluded
prior to data evaluation without additional staining.
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Affiliation(s)
- Anna Schoeberl
- Institute of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Strasse 38, 1090 Vienna, Austria
| | - Michael Gutmann
- Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Borschkegasse 8A, 1090 Vienna, Austria
| | - Sarah Theiner
- Institute of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Strasse 38, 1090 Vienna, Austria
| | - Martin Schaier
- Institute of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Strasse 38, 1090 Vienna, Austria
| | - Andreas Schweikert
- Institute of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Strasse 38, 1090 Vienna, Austria.,Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Strasse 42, 1090 Vienna, Austria
| | - Walter Berger
- Institute of Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, Borschkegasse 8A, 1090 Vienna, Austria
| | - Gunda Koellensperger
- Institute of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Strasse 38, 1090 Vienna, Austria
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15
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Coevolving JAK2V617F+relapsed AML and donor T cells with PD-1 blockade after stem cell transplantation: an index case. Blood Adv 2021; 5:4701-4709. [PMID: 34432868 PMCID: PMC8759138 DOI: 10.1182/bloodadvances.2021004335] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/09/2021] [Indexed: 01/22/2023] Open
Abstract
Index case of nivolumab response associated with altered circulating T-cell composition and heterogeneous PD-L1 expression on AML blasts. Single-cell approaches provide complementary insight into cellular mechanisms of response and resistance to transplant/checkpoint blockade.
Relapse of myeloproliferative neoplasms (MPNs) after allogeneic hematopoietic stem cell transplantation (HSCT) is associated with poor outcomes, as therapeutic approaches to reinstate effective graft-versus-leukemia (GVL) responses remain suboptimal. Immune escape through overexpression of PD-L1 in JAK2V617F-mutated MPN provides a rationale for therapeutic PD-1 blockade, and indeed, clinical activity of nivolumab in relapsed MPN post-HSCT has been observed. Elucidation of the features of response following PD-1 blockade in such patients could inform novel therapeutic concepts that enhance GVL. Here, we report an integrated high-dimensional analysis using single-cell RNA sequencing, T-cell receptor sequencing, cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq), and assay for transposase-accessible chromatin using sequencing (scATAC-seq), together with mass cytometry, in peripheral blood mononuclear cells collected at 6 timepoints before, during, and after transient response to PD-1 blockade from an index case of relapsed MPN following HSCT. Before nivolumab infusion, acute myeloid leukemia (AML) blasts demonstrated high expression of chemokines, and T cells were characterized by expression of interferon-response genes. This baseline inflammatory signature disappeared after nivolumab infusion. Clinical response was characterized by transient expansion of a polyclonal CD4+ T-cell population and contraction of an AML subpopulation that exhibited megakaryocytic features and elevated PD-L1 expression. At relapse, the proportion of the AML subpopulation with progenitor-like features progressively increased, suggesting coevolution of AML blasts and donor-derived T cells. We thus demonstrate how single-cell technologies can provide complementary insight into cellular mechanisms underlying response to PD-1 blockade, motivating future longitudinal high-dimensional single-cell studies of GVL responses in relapsed myeloid disease.
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16
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Spurgeon BEJ, Michelson AD, Frelinger AL. Platelet Immunophenotyping by High-Dimensional Mass Cytometry. Curr Protoc 2021; 1:e112. [PMID: 33950581 DOI: 10.1002/cpz1.112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Platelets are small blood cells that contribute to hemostasis, immunity, and inflammation. Characterization of platelet surface markers allows for differentiation of activated platelets from resting platelets, diagnosis of platelet disorders, and investigation of platelet biology and pathology. In this article, we describe the use of mass cytometry or "CyTOF" (mass spectroscopy detection of metal-tagged antibodies on individual cells) to measure a large number of markers on each platelet and to identify platelet subsets based on the shared expression of multiple markers. This powerful new approach provides a vastly more detailed picture of platelet immunophenotypes than conventional flow cytometry and enables investigation of the roles of platelet subsets in health and disease. © 2021 Wiley Periodicals LLC. Basic Protocol: Platelet immunophenotyping by high-dimensional mass cytometry Support Protocol: Data preprocessing.
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Affiliation(s)
- Benjamin E J Spurgeon
- Center for Platelet Research Studies, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts
| | - Alan D Michelson
- Center for Platelet Research Studies, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts
| | - Andrew L Frelinger
- Center for Platelet Research Studies, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts
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17
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Penter L, Zhang Y, Savell A, Huang T, Cieri N, Thrash EM, Kim-Schulze S, Jhaveri A, Fu J, Ranasinghe S, Li S, Zhang W, Hathaway ES, Nazzaro M, Kim HT, Chen H, Thurin M, Rodig SJ, Severgnini M, Cibulskis C, Gabriel S, Livak KJ, Cutler C, Antin JH, Nikiforow S, Koreth J, Ho VT, Armand P, Ritz J, Streicher H, Neuberg D, Hodi FS, Gnjatic S, Soiffer RJ, Liu XS, Davids MS, Bachireddy P, Wu CJ. Molecular and cellular features of CTLA-4 blockade for relapsed myeloid malignancies after transplantation. Blood 2021; 137:3212-3217. [PMID: 33720354 PMCID: PMC8351891 DOI: 10.1182/blood.2021010867] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 02/23/2021] [Indexed: 02/07/2023] Open
Abstract
Relapsed myeloid disease after allogeneic stem cell transplantation (HSCT) remains largely incurable. We previously demonstrated the potent activity of immune checkpoint blockade in this clinical setting with ipilimumab or nivolumab. To define the molecular and cellular pathways by which CTLA-4 blockade with ipilimumab can reinvigorate an effective graft-versus-leukemia (GVL) response, we integrated transcriptomic analysis of leukemic biopsies with immunophenotypic profiling of matched peripheral blood samples collected from patients treated with ipilimumab following HSCT on the Experimental Therapeutics Clinical Trials Network 9204 trial. Response to ipilimumab was associated with transcriptomic evidence of increased local CD8+ T-cell infiltration and activation. Systemically, ipilimumab decreased naïve and increased memory T-cell populations and increased expression of markers of T-cell activation and costimulation such as PD-1, HLA-DR, and ICOS, irrespective of response. However, responding patients were characterized by higher turnover of T-cell receptor sequences in peripheral blood and showed increased expression of proinflammatory chemokines in plasma that was further amplified by ipilimumab. Altogether, these data highlight the compositional T-cell shifts and inflammatory pathways induced by ipilimumab both locally and systemically that associate with successful GVL outcomes. This trial was registered at www.clinicaltrials.gov as #NCT01822509.
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Affiliation(s)
- Livius Penter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA
- Harvard Medical School, Boston, MA
- Department of Hematology, Oncology, and Tumorimmunology, Campus Virchow Klinikum, Berlin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Yi Zhang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Alexandra Savell
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Teddy Huang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Translational Immunogenomics Laboratory and
| | - Nicoletta Cieri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA
- Harvard Medical School, Boston, MA
| | - Emily M Thrash
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Seunghee Kim-Schulze
- Human Immune Monitoring Center at the Icahn School of Medicine at Mount Sinai, New York, NY
| | - Aashna Jhaveri
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - Jingxin Fu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | | | - Shuqiang Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA
- Translational Immunogenomics Laboratory and
| | - Wandi Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Emma S Hathaway
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Matthew Nazzaro
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Haesook T Kim
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - Helen Chen
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD; and
| | - Magdalena Thurin
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD; and
| | | | | | - Carrie Cibulskis
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | - Stacey Gabriel
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | - Kenneth J Livak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Translational Immunogenomics Laboratory and
| | - Corey Cutler
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
| | - Joseph H Antin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
| | - Sarah Nikiforow
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
| | - John Koreth
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
| | - Vincent T Ho
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
| | - Philippe Armand
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
| | - Jerome Ritz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
| | - Howard Streicher
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD; and
| | - Donna Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - F Stephen Hodi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Sacha Gnjatic
- Human Immune Monitoring Center at the Icahn School of Medicine at Mount Sinai, New York, NY
| | - Robert J Soiffer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
| | - X Shirley Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Matthew S Davids
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
| | - Pavan Bachireddy
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA
- Harvard Medical School, Boston, MA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA
- Harvard Medical School, Boston, MA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
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18
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Rybakowska P, Van Gassen S, Quintelier K, Saeys Y, Alarcón-Riquelme ME, Marañón C. Data processing workflow for large-scale immune monitoring studies by mass cytometry. Comput Struct Biotechnol J 2021; 19:3160-3175. [PMID: 34141137 PMCID: PMC8188119 DOI: 10.1016/j.csbj.2021.05.032] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 05/14/2021] [Accepted: 05/20/2021] [Indexed: 12/27/2022] Open
Abstract
Mass cytometry is a powerful tool for deep immune monitoring studies. To ensure maximal data quality, a careful experimental and analytical design is required. However even in well-controlled experiments variability caused by either operator or instrument can introduce artifacts that need to be corrected or removed from the data. Here we present a data processing pipeline which ensures the minimization of experimental artifacts and batch effects, while improving data quality. Data preprocessing and quality controls are carried out using an R pipeline and packages like CATALYST for bead-normalization and debarcoding, flowAI and flowCut for signal anomaly cleaning, AOF for files quality control, flowClean and flowDensity for gating, CytoNorm for batch normalization and FlowSOM and UMAP for data exploration. As proper experimental design is key in obtaining good quality events, we also include the sample processing protocol used to generate the data. Both, analysis and experimental pipelines are easy to scale-up, thus the workflow presented here is particularly suitable for large-scale, multicenter, multibatch and retrospective studies.
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Affiliation(s)
- Paulina Rybakowska
- GENYO, Centre for Genomics and Oncological Research, Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Spain
| | - Sofie Van Gassen
- Department of Applied Mathematics, Computer Sciences and Statistics, Ghent University, Gent Belgium
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Gent, Belgium
| | - Katrien Quintelier
- Department of Applied Mathematics, Computer Sciences and Statistics, Ghent University, Gent Belgium
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Gent, Belgium
- Department of Pulmonary Diseases, Erasmus MC, Rotterdam, the Netherlands
| | - Yvan Saeys
- Department of Applied Mathematics, Computer Sciences and Statistics, Ghent University, Gent Belgium
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Gent, Belgium
| | - Marta E. Alarcón-Riquelme
- GENYO, Centre for Genomics and Oncological Research, Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Spain
- Institute for Environmental Medicine, Karolinska Institute, Stockholm, Sweden
| | - Concepción Marañón
- GENYO, Centre for Genomics and Oncological Research, Pfizer, University of Granada, Andalusian Regional Government, PTS Granada, Spain
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19
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Monjazeb AM, Giobbie-Hurder A, Lako A, Thrash EM, Brennick RC, Kao KZ, Manuszak C, Gentzler RD, Tesfaye A, Jabbour SK, Alese OB, Rahma OE, Cleary JM, Sharon E, Mamon HJ, Cho M, Streicher H, Chen HX, Ahmed MM, Mariño-Enríquez A, Kim-Schulze S, Gnjatic S, Maverakis E, Marusina AI, Merleev AA, Severgnini M, Pfaff KL, Lindsay J, Weirather JL, Ranasinghe S, Spektor A, Rodig SJ, Hodi SF, Schoenfeld JD. A Randomized Trial of Combined PD-L1 and CTLA-4 Inhibition with Targeted Low-Dose or Hypofractionated Radiation for Patients with Metastatic Colorectal Cancer. Clin Cancer Res 2021; 27:2470-2480. [PMID: 33568343 PMCID: PMC8102320 DOI: 10.1158/1078-0432.ccr-20-4632] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/14/2021] [Accepted: 02/05/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Prospective human data are lacking regarding safety, efficacy, and immunologic impacts of different radiation doses administered with combined PD-L1/CTLA-4 blockade. PATIENTS AND METHODS We performed a multicenter phase II study randomly assigning patients with metastatic microsatellite stable colorectal cancer to repeated low-dose fractionated radiation (LDFRT) or hypofractionated radiation (HFRT) with PD-L1/CTLA-4 inhibition. The primary endpoint was response outside the radiation field. Correlative samples were analyzed using multiplex immunofluorescence (IF), IHC, RNA/T-cell receptor (TCR) sequencing, cytometry by time-of-flight (CyTOF), and Olink. RESULTS Eighteen patients were evaluable for response. Median lines of prior therapy were four (range, 1-7). Sixteen patients demonstrated toxicity potentially related to treatment (84%), and 8 patients had grade 3-4 toxicity (42%). Best response was stable disease in 1 patient with out-of-field tumor shrinkage. Median overall survival was 3.8 months (90% confidence interval, 2.3-5.7 months). Correlative IF and RNA sequencing (RNA-seq) revealed increased infiltration of CD8+ and CD8+/PD-1+/Ki-67+ T cells in the radiation field after HFRT. LDFRT increased foci of micronuclei/primary nuclear rupture in two subjects. CyTOF and RNA-seq demonstrated significant declines in multiple circulating immune populations, particularly in patients receiving HFRT. TCR sequencing revealed treatment-associated changes in T-cell repertoire in the tumor and peripheral blood. CONCLUSIONS We demonstrate the feasibility and safety of adding LDFRT and HFRT to PD-L1/CTLA-4 blockade. Although the best response of stable disease does not support the use of concurrent PD-L1/CTLA-4 inhibition with HFRT or LDFRT in this population, biomarkers provide support that both LDFRT and HFRT impact the local immune microenvironment and systemic immunogenicity that can help guide future studies.
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Affiliation(s)
- Arta M Monjazeb
- Department of Radiation Oncology, University of California Davis, Comprehensive Cancer Center, Sacramento, California
| | | | - Ana Lako
- Brigham and Women's Hospital, Boston, Massachusetts
| | | | | | | | | | | | - Anteneh Tesfaye
- Karmanos Cancer Institute/Wayne State University, Detroit, Michigan
| | - Salma K Jabbour
- Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | | | - Osama E Rahma
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Brigham and Women's Hospital, Boston, Massachusetts
| | - James M Cleary
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Brigham and Women's Hospital, Boston, Massachusetts
| | - Elad Sharon
- Cancer Therapy Evaluation Program, NCI, Bethesda, Maryland
| | - Harvey J Mamon
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Brigham and Women's Hospital, Boston, Massachusetts
| | - May Cho
- Department of Radiation Oncology, University of California Davis, Comprehensive Cancer Center, Sacramento, California
| | | | - Helen X Chen
- Cancer Therapy Evaluation Program, NCI, Bethesda, Maryland
| | | | - Adrian Mariño-Enríquez
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Brigham and Women's Hospital, Boston, Massachusetts
| | | | | | - Emanual Maverakis
- Department of Dermatology, University of California Davis, School of Medicine, Sacramento, California
| | - Alina I Marusina
- Department of Dermatology, University of California Davis, School of Medicine, Sacramento, California
| | - Alexander A Merleev
- Department of Dermatology, University of California Davis, School of Medicine, Sacramento, California
| | | | | | | | | | | | - Alexander Spektor
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Brigham and Women's Hospital, Boston, Massachusetts
| | - Scott J Rodig
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Brigham and Women's Hospital, Boston, Massachusetts
| | - Stephen F Hodi
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Brigham and Women's Hospital, Boston, Massachusetts
| | - Jonathan D Schoenfeld
- Dana-Farber Cancer Institute, Boston, Massachusetts.
- Brigham and Women's Hospital, Boston, Massachusetts
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