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Reis LR, Costa-Rocha IA, Abdala-Torres T, Campi-Azevedo AC, Peruhype-Magalhães V, Araújo MSS, Spezialli E, do Valle Antonelli LR, da Silva-Pereira RA, Almeida GG, Fernandes EG, Fantinato FFST, Domingues CMAS, Lemos MCF, Chieppe A, Lemos JAC, Coelho-Dos-Reis JG, de Lima SMB, de Souza Azevedo A, Schwarcz WD, Camacho LAB, de Lourdes de Sousa Maia M, de Noronha TG, Duault C, Rosenberg-Hasson Y, Teixeira-Carvalho A, Maecker HT, Martins-Filho OA. Comprehensive landscape of neutralizing antibody and cell-mediated response elicited by the 1/5 fractional dose of 17DD-YF primary vaccination in adults. Sci Rep 2024; 14:7709. [PMID: 38565882 PMCID: PMC10987530 DOI: 10.1038/s41598-024-57645-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 03/20/2024] [Indexed: 04/04/2024] Open
Abstract
The present study aimed at evaluating the YF-specific neutralizing antibody profile besides a multiparametric analysis of phenotypic/functional features of cell-mediated response elicited by the 1/5 fractional dose of 17DD-YF vaccine, administered as a single subcutaneous injection. The immunological parameters of each volunteer was monitored at two time points, referred as: before (Day 0) [Non-Vaccinated, NV(D0)] and after vaccination (Day 30-45) [Primary Vaccinees, PV(D30-45)]. Data demonstrated high levels of neutralizing antibodies for PV(D30-45) leading to a seropositivity rate of 93%. A broad increase of systemic soluble mediators with a mixed profile was also observed for PV(D30-45), with IFN-γ and TNF-α presenting the highest baseline fold changes. Integrative network mapping of soluble mediators showed increased correlation numbers in PV(D30-45) as compared to NV(D0) (532vs398). Moreover, PV(D30-45) exhibited increased levels of Terminal Effector (CD45RA+CCR7-) CD4+ and CD8+ T-cells and Non-Classical memory B-cells (IgD+CD27+). Dimensionality reduction of Mass Cytometry data further support these findings. A polyfunctional cytokine profile (TNF-α/IFN-γ/IL-10/IL-17/IL-2) of T and B-cells was observed upon in vitro antigen recall. Mapping and kinetics timeline of soluble mediator signatures for PV(D30-45) further confirmed the polyfunctional profile upon long-term in vitro culture, mediated by increased levels of IFN-γ and TNF-α along with decreased production of IL-10. These findings suggest novel insights of correlates of protection elicited by the 1/5 fractional dose of 17DD-YF vaccine.
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Affiliation(s)
- Laise Rodrigues Reis
- Instituto René Rachou, Fundação Oswaldo Cruz - FIOCRUZ-Minas, Belo Horizonte, MG, Brazil
| | | | - Thais Abdala-Torres
- Instituto René Rachou, Fundação Oswaldo Cruz - FIOCRUZ-Minas, Belo Horizonte, MG, Brazil
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | | | | | | | - Elaine Spezialli
- Instituto René Rachou, Fundação Oswaldo Cruz - FIOCRUZ-Minas, Belo Horizonte, MG, Brazil
| | | | | | | | | | | | | | | | - Alexandre Chieppe
- Superintendência de Vigilância em Saúde, Secretaria Municipal de Saúde do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | | | - Jordana Grazziela Coelho-Dos-Reis
- Laboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas da Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, MG, Brazil
| | - Sheila Maria Barbosa de Lima
- Departamento de Desenvolvimento Experimental e Pré-Clínico, Instituto de Tecnologia em Imunobiológicos Bio-Manguinhos - FIOCRUZ, Rio de Janeiro, RJ, Brazil
| | - Adriana de Souza Azevedo
- Laboratório de Análise Imunomolecular, Instituto de Tecnologia em Imunobiológicos Bio-Manguinhos - FIOCRUZ, Rio de Janeiro, RJ, Brazil
| | - Waleska Dias Schwarcz
- Laboratório de Análise Imunomolecular, Instituto de Tecnologia em Imunobiológicos Bio-Manguinhos - FIOCRUZ, Rio de Janeiro, RJ, Brazil
| | | | | | - Tatiana Guimarães de Noronha
- Assessoria Clínica, Instituto de Tecnologia em Imunobiológicos Bio-Manguinhos - FIOCRUZ, Rio de Janeiro, RJ, Brazil
| | - Caroline Duault
- Human Immune Monitoring Center, Stanford University, Stanford, CA, USA
| | | | | | - Holden Terry Maecker
- Human Immune Monitoring Center, Stanford University, Stanford, CA, USA.
- Department of Microbiology and Immunology, Stanford University, Stanford, USA.
| | - Olindo Assis Martins-Filho
- Instituto René Rachou, Fundação Oswaldo Cruz - FIOCRUZ-Minas, Belo Horizonte, MG, Brazil.
- Grupo Integrado de Pesquisas em Biomarcadores, Instituto René Rachou, Fundação Oswaldo Cruz - FIOCRUZ-Minas, Belo Horizonte, MG, Brazil.
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2
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Lin D, Maecker HT. CyTOF Intracellular Cytokine Assays for Antigen-Specific T Cells. Methods Mol Biol 2024; 2779:395-405. [PMID: 38526796 DOI: 10.1007/978-1-0716-3738-8_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
T cells specific for a single antigen tend to be rare, even after expansion of memory cells. They are commonly detected by in vitro stimulation with peptides or protein, followed by staining for intracellular cytokines. In this protocol, CyTOF® mass cytometry is used to collect single-cell data on a large number of cytokines/chemokines, as well as cell-surface proteins that characterize T cells and other immune cells. A method for magnetic bead enrichment of antigen-stimulated T cells, based on their expression of CD154 and CD69, is also included. Coupling magnetic enrichment with highly multiparameter mass cytometry, this method enables the ability to dissect the frequency, phenotype, and function of antigen-specific T cells in greater detail than previously possible. Rare cell subsets can be examined, while minimizing run times on the CyTOF.
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Affiliation(s)
| | - Holden T Maecker
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA.
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3
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Kumar A, Taghi Khani A, Duault C, Aramburo S, Sanchez Ortiz A, Lee SJ, Chan A, McDonald T, Huang M, Lacayo NJ, Sakamoto KM, Yu J, Hurtz C, Carroll M, Tasian SK, Ghoda L, Marcucci G, Gu Z, Rosen ST, Armenian S, Izraeli S, Chen CW, Caligiuri MA, Forman SJ, Maecker HT, Swaminathan S. Intrinsic suppression of type I interferon production underlies the therapeutic efficacy of IL-15-producing natural killer cells in B-cell acute lymphoblastic leukemia. J Immunother Cancer 2023; 11:jitc-2022-006649. [PMID: 37217248 DOI: 10.1136/jitc-2022-006649] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2023] [Indexed: 05/24/2023] Open
Abstract
BACKGROUND Type I interferons (IFN-Is), secreted by hematopoietic cells, drive immune surveillance of solid tumors. However, the mechanisms of suppression of IFN-I-driven immune responses in hematopoietic malignancies including B-cell acute lymphoblastic leukemia (B-ALL) are unknown. METHODS Using high-dimensional cytometry, we delineate the defects in IFN-I production and IFN-I-driven immune responses in high-grade primary human and mouse B-ALLs. We develop natural killer (NK) cells as therapies to counter the intrinsic suppression of IFN-I production in B-ALL. RESULTS We find that high expression of IFN-I signaling genes predicts favorable clinical outcome in patients with B-ALL, underscoring the importance of the IFN-I pathway in this malignancy. We show that human and mouse B-ALL microenvironments harbor an intrinsic defect in paracrine (plasmacytoid dendritic cell) and/or autocrine (B-cell) IFN-I production and IFN-I-driven immune responses. Reduced IFN-I production is sufficient for suppressing the immune system and promoting leukemia development in mice prone to MYC-driven B-ALL. Among anti-leukemia immune subsets, suppression of IFN-I production most markedly lowers the transcription of IL-15 and reduces NK-cell number and effector maturation in B-ALL microenvironments. Adoptive transfer of healthy NK cells significantly prolongs survival of overt ALL-bearing transgenic mice. Administration of IFN-Is to B-ALL-prone mice reduces leukemia progression and increases the frequencies of total NK and NK-cell effectors in circulation. Ex vivo treatment of malignant and non-malignant immune cells in primary mouse B-ALL microenvironments with IFN-Is fully restores proximal IFN-I signaling and partially restores IL-15 production. In B-ALL patients, the suppression of IL-15 is the most severe in difficult-to-treat subtypes with MYC overexpression. MYC overexpression promotes sensitivity of B-ALL to NK cell-mediated killing. To counter the suppressed IFN-I-induced IL-15 production in MYChigh human B-ALL, we CRISPRa-engineered a novel human NK-cell line that secretes IL-15. CRISPRa IL-15-secreting human NK cells kill high-grade human B-ALL in vitro and block leukemia progression in vivo more effectively than NK cells that do not produce IL-15. CONCLUSION We find that restoration of the intrinsically suppressed IFN-I production in B-ALL underlies the therapeutic efficacy of IL-15-producing NK cells and that such NK cells represent an attractive therapeutic solution for the problem of drugging MYC in high-grade B-ALL.
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Affiliation(s)
- Anil Kumar
- Department of Systems Biology, City of Hope Beckman Research Institute, Monrovia, California, USA
| | - Adeleh Taghi Khani
- Department of Systems Biology, City of Hope Beckman Research Institute, Monrovia, California, USA
| | - Caroline Duault
- The Human Immune Monitoring Center (HIMC), Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California, USA
| | - Soraya Aramburo
- Department of Systems Biology, City of Hope Beckman Research Institute, Monrovia, California, USA
| | - Ashly Sanchez Ortiz
- Department of Systems Biology, City of Hope Beckman Research Institute, Monrovia, California, USA
| | - Sung June Lee
- Department of Systems Biology, City of Hope Beckman Research Institute, Monrovia, California, USA
| | - Anthony Chan
- Department of Systems Biology, City of Hope Beckman Research Institute, Monrovia, California, USA
| | - Tinisha McDonald
- The Hematopoietic Tissue Biorepository/Research Pathology Shared Resources, City of Hope, Duarte, California, USA
| | - Min Huang
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Norman J Lacayo
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Kathleen M Sakamoto
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Jianhua Yu
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, California, USA
| | - Christian Hurtz
- Department of Cancer and Cellular Biology, Fels Cancer Institute for Personalized Medicine Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania, USA
| | - Martin Carroll
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Sarah K Tasian
- Department of Pediatrics, Division of Oncology, The Children's Hospital, Philadelphia, Pennsylvania, USA
| | - Lucy Ghoda
- Hematological Malignancies Translational Science, City of Hope, Duarte, California, USA
| | - Guido Marcucci
- The Hematopoietic Tissue Biorepository/Research Pathology Shared Resources, City of Hope, Duarte, California, USA
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, California, USA
- Hematological Malignancies Translational Science, City of Hope, Duarte, California, USA
| | - Zhaohui Gu
- Department of Systems Biology, City of Hope Beckman Research Institute, Monrovia, California, USA
| | - Steven T Rosen
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, California, USA
| | - Saro Armenian
- Department of Pediatrics, City of Hope, Duarte, California, USA
| | - Shai Izraeli
- Department of Systems Biology, City of Hope Beckman Research Institute, Monrovia, California, USA
- Hematology-Oncology Department, Tel Aviv University, Tel Aviv, Israel
| | - Chun-Wei Chen
- Department of Systems Biology, City of Hope Beckman Research Institute, Monrovia, California, USA
| | - Michael A Caligiuri
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, California, USA
| | - Stephen J Forman
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Duarte, California, USA
| | - Holden T Maecker
- The Human Immune Monitoring Center (HIMC), Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California, USA
| | - Srividya Swaminathan
- Department of Systems Biology, City of Hope Beckman Research Institute, Monrovia, California, USA
- Department of Pediatrics, City of Hope, Duarte, California, USA
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Paracatu LC, Monlish DA, Greenberg ZJ, Fisher DAC, Walter MJ, Oh ST, Schuettpelz LG. Toll-like receptor and cytokine expression throughout the bone marrow differs between patients with low- and high-risk myelodysplastic syndromes. Exp Hematol 2022; 110:47-59. [PMID: 35367529 PMCID: PMC9590644 DOI: 10.1016/j.exphem.2022.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/14/2022] [Accepted: 03/20/2022] [Indexed: 11/20/2022]
Abstract
Myelodysplastic syndromes (MDS) are hematopoietic stem cell disorders, the pathogenesis of which involves enhanced immune signaling that promotes or selects for mutant hematopoietic stem and progenitor cells (HSPCs). In particular, toll-like receptor (TLR) expression and signaling are enhanced in MDS, and their inhibition is an attractive therapeutic strategy. Although prior studies have reported increased expression of TLR2 and its binding partners TLR1 and TLR6 in the CD34+ cells of patients with MDS (especially those with low-risk disease), TLR expression in other cell types throughout the bone marrow is largely unknown. To address this, we used mass cytometry to assess the expression of TLR1, TLR2, and TLR6 and cytokines in the bone marrow hematopoietic cells of six low/intermediate-risk and six high-risk unmatched MDS bone marrow samples, as well as healthy controls, both at baseline and in response to TLR agonists. We observed several consistent differences between the groups. Most notably, TLR expression was upregulated in multiple cell populations in the low/intermediate-risk, but not high-risk, patients. In addition, many cytokines, including interleukin-6, interleukin-8, tumor necrosis factor α, transforming growth factor β, macrophage inflammatory protein 1β, and granzyme B, were highly expressed from various cell types in low/intermediate-risk patients. However, these same cytokines, with the exception of transforming growth factor β, were expressed at lower levels in high-risk MDS. Together, these findings highlight the differential role of inflammation, and specifically TLR expression, in low/intermediate- versus high-risk MDS, and suggest that elevated TLR expression and cytokine production in multiple cell types likely influences the pathogenesis of MDS in lower-risk patients.
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Affiliation(s)
- Luana Chiquetto Paracatu
- Department of Pediatrics, Division of Hematology/Oncology, Washington University School of Medicine, St. Louis, MO
| | - Darlene A Monlish
- Department of Pediatrics, Division of Hematology/Oncology, Washington University School of Medicine, St. Louis, MO
| | - Zev J Greenberg
- Department of Pediatrics, Division of Hematology/Oncology, Washington University School of Medicine, St. Louis, MO
| | - Daniel A C Fisher
- Department of Medicine, Division of Hematology, Washington University School of Medicine, St. Louis, MO
| | - Matthew J Walter
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, MO
| | - Stephen T Oh
- Department of Medicine, Division of Hematology, Washington University School of Medicine, St. Louis, MO
| | - Laura G Schuettpelz
- Department of Pediatrics, Division of Hematology/Oncology, Washington University School of Medicine, St. Louis, MO.
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5
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Abstract
Mass cytometry has revolutionized immunophenotyping, particularly in exploratory settings where simultaneous breadth and depth of characterization of immune populations is needed with limited samples such as in preclinical and clinical tumor immunotherapy. Mass cytometry is also a powerful tool for single-cell immunological assays, especially for complex and simultaneous characterization of diverse intratumoral immune subsets or immunotherapeutic cell populations. Through the elimination of spectral overlap seen in optical flow cytometry by replacement of fluorescent labels with metal isotopes, mass cytometry allows, on average, robust analysis of 60 individual parameters simultaneously. This is, however, associated with significantly increased complexity in the design, execution, and interpretation of mass cytometry experiments. To address the key pitfalls associated with the fragmentation, complexity, and analysis of data in mass cytometry for immunologists who are novices to these techniques, we have developed a comprehensive resource guide. Included in this review are experiment and panel design, antibody conjugations, sample staining, sample acquisition, and data pre-processing and analysis. Where feasible multiple resources for the same process are compared, allowing researchers experienced in flow cytometry but with minimal mass cytometry expertise to develop a data-driven and streamlined project workflow. It is our hope that this manuscript will prove a useful resource for both beginning and advanced users of mass cytometry.
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Affiliation(s)
- Akshay Iyer
- Department of Pediatrics, University of Miami Miller School of Medicine, Miami, FL, United States
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Anouk A. J. Hamers
- Department of Pediatrics, University of Miami Miller School of Medicine, Miami, FL, United States
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL, United States
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Asha B. Pillai
- Department of Pediatrics, University of Miami Miller School of Medicine, Miami, FL, United States
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL, United States
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, United States
- Sheila and David Fuente Program in Cancer Biology, University of Miami Miller School of Medicine, Miami, FL, United States
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6
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Kong T, Laranjeira AB, Collins TB, De Togni ES, Wong AJ, Fulbright MC, Ruzinova M, Celik H, Challen GA, Fisher DA, Oh ST. Pevonedistat targets malignant cells in myeloproliferative neoplasms in vitro and in vivo via NFκB pathway inhibition. Blood Adv 2022; 6:611-623. [PMID: 34644371 PMCID: PMC8791597 DOI: 10.1182/bloodadvances.2020002804] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/19/2021] [Indexed: 11/20/2022] Open
Abstract
Targeted inhibitors of JAK2 (eg ruxolitinib) often provide symptomatic relief for myeloproliferative neoplasm (MPN) patients, but the malignant clone persists and remains susceptible to disease transformation. These observations suggest that targeting alternative dysregulated signaling pathways may provide therapeutic benefit. Previous studies identified NFκB pathway hyperactivation in myelofibrosis (MF) and secondary acute myeloid leukemia (sAML) that was insensitive to JAK2 inhibition. Here, we provide evidence that NFκB pathway inhibition via pevonedistat targets malignant cells in MPN patient samples as well as in MPN and patient-derived xenograft mouse models that are nonredundant with ruxolitinib. Colony forming assays revealed preferential inhibition of MF colony growth compared with normal colony formation. In mass cytometry studies, pevonedistat blunted canonical TNFα responses in MF and sAML patient CD34+ cells. Pevonedistat also inhibited hyperproduction of inflammatory cytokines more effectively than ruxolitinib. Upon pevonedistat treatment alone or in combination with ruxolitinib, MPN mouse models exhibited reduced disease burden and improved survival. These studies demonstrating efficacy of pevonedistat in MPN cells in vitro as well as in vivo provide a rationale for therapeutic inhibition of NFκB signaling for MF treatment. Based on these findings, a Phase 1 clinical trial combining pevonedistat with ruxolitinib has been initiated.
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Affiliation(s)
- Tim Kong
- Division of Hematology, Department of Medicine
| | | | | | | | | | | | | | - Hamza Celik
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO; and
| | - Grant A. Challen
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO; and
| | | | - Stephen T. Oh
- Division of Hematology, Department of Medicine
- Department of Pathology and Immunology, and
- Immunomonitoring Laboratory, Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO
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7
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Duault C, Kumar A, Taghi Khani A, Lee SJ, Yang L, Huang M, Hurtz C, Manning B, Ghoda L, McDonald T, Lacayo NJ, Sakamoto KM, Carroll M, Tasian SK, Marcucci G, Yu J, Caligiuri MA, Maecker HT, Swaminathan S. Activated natural killer cells predict poor clinical prognosis in high-risk B- and T-cell acute lymphoblastic leukemia. Blood 2021; 138:1465-1480. [PMID: 34077953 PMCID: PMC8532198 DOI: 10.1182/blood.2020009871] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 05/05/2021] [Indexed: 11/21/2022] Open
Abstract
B- and T-cell acute lymphoblastic leukemia (B/T-ALL) may be refractory or recur after therapy by suppressing host anticancer immune surveillance mediated specifically by natural killer (NK) cells. We delineated the phenotypic and functional defects in NK cells from high-risk patients with B/T-ALL using mass cytometry, flow cytometry, and in silico cytometry, with the goal of further elucidating the role of NK cells in sustaining acute lymphoblastic leukemia (ALL) regression. We found that, compared with their normal counterparts, NK cells from patients with B/T-ALL are less cytotoxic but exhibit an activated signature that is characterized by high CD56, high CD69, production of activated NK cell-origin cytokines, and calcium (Ca2+) signaling. We demonstrated that defective maturation of NK cells into cytotoxic effectors prevents NK cells from ALL from lysing NK cell-sensitive targets as efficiently as do normal NK cells. Additionally, we showed that NK cells in ALL are exhausted, which is likely caused by their chronic activation. We found that increased frequencies of activated cytokine-producing NK cells are associated with increased disease severity and independently predict poor clinical outcome in patients with ALL. Our studies highlight the benefits of developing NK cell profiling as a diagnostic tool to predict clinical outcome in patients with ALL and underscore the clinical potential of allogeneic NK cell infusions to prevent ALL recurrence.
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Affiliation(s)
- Caroline Duault
- The Human Immune Monitoring Center, Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA
| | - Anil Kumar
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA
| | - Adeleh Taghi Khani
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA
| | - Sung June Lee
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA
| | - Lu Yang
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA
| | - Min Huang
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Christian Hurtz
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Bryan Manning
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Lucy Ghoda
- Department of Hematological Malignancies and Translational Science, Beckman Research Institute of City of Hope, Duarte, CA
| | - Tinisha McDonald
- Department of Hematological Malignancies and Translational Science, Beckman Research Institute of City of Hope, Duarte, CA
| | - Norman J Lacayo
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Kathleen M Sakamoto
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Martin Carroll
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Sarah K Tasian
- Division of Oncology and Center for Childhood Cancer Research, Department of Pediatrics, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA; and
| | - Guido Marcucci
- Department of Hematological Malignancies and Translational Science, Beckman Research Institute of City of Hope, Duarte, CA
| | - Jianhua Yu
- Department of Hematology and Hematopoietic Stem Cell Transplantation, Beckman Research Institute of City of Hope, Duarte, CA
| | - Michael A Caligiuri
- Department of Hematology and Hematopoietic Stem Cell Transplantation, Beckman Research Institute of City of Hope, Duarte, CA
| | - Holden T Maecker
- The Human Immune Monitoring Center, Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA
| | - Srividya Swaminathan
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA
- Department of Hematological Malignancies and Translational Science, Beckman Research Institute of City of Hope, Duarte, CA
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8
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Manohar M, Dunham D, Gupta S, Yan Z, Zhang W, Minnicozzi S, Kirkey M, Bunning B, Chowdhury RR, Galli SJ, Boyd SD, Kost LE, Chinthrajah RS, Desai M, Oettgen HC, Maecker HT, Yu W, DeKruyff RH, Andorf S, Nadeau KC. Immune changes beyond Th2 pathways during rapid multifood immunotherapy enabled with omalizumab. Allergy 2021; 76:2809-2826. [PMID: 33782956 PMCID: PMC8609920 DOI: 10.1111/all.14833] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 02/03/2021] [Accepted: 02/15/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND Multifood oral immunotherapy (mOIT) with adjunctive anti-IgE (omalizumab, XOLAIR® ) treatment affords safe, effective, and rapid desensitization to multiple foods, although the specific immune mechanisms mediating this desensitization remain to be fully elucidated. METHODS Participants in our phase 2 mOIT trial (NCT02643862) received omalizumab from baseline to week 16 and mOIT from week 8 to week 36. We compared the immune profile of PBMCs and plasma taken at baseline, week 8, and week 36 using high-dimensional mass cytometry, component-resolved diagnostics, the indirect basophil activation test, and Luminex. RESULTS We found (i) decreased frequency of IL-4+ peanut-reactive CD4+ T cells and a marked downregulation of GPR15 expression and CXCR3 frequency among γδ and CD8+ T-cell subsets at week 8 during the initial, omalizumab-alone induction phase; (ii) significant upregulation of the skin-homing receptor CCR4 in peanut-reactive CD4+ T and Th2 effector memory (EM) cells and of cutaneous lymphocyte-associated antigen (CLA) in peanut-reactive CD8+ T and CD8+ EM cells; (iii) downregulation of CD86 expression among antigen-presenting cell subsets; and (iv) reduction in pro-inflammatory cytokines, notably IL-17, at week 36 post-OIT. We also observed significant attenuation of the Th2 phenotype post-OIT, defined by downregulation of IL-4 peanut-reactive T cells and OX40 in Th2EM cells, increased allergen component-specific IgG4/IgE ratio, and decreased allergen-driven activation of indirectly sensitized basophils. CONCLUSIONS This exploratory study provides novel comprehensive insight into the immune underpinnings of desensitization through omalizumab-facilitated mOIT. Moreover, this study provides encouraging results to support the complex immune changes that can be induced by OIT.
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Affiliation(s)
- Monali Manohar
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA
| | - Diane Dunham
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA
| | - Sheena Gupta
- Human Immune Monitoring Center, Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA
| | - Zheng Yan
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA
| | - Wenming Zhang
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA
| | - Samantha Minnicozzi
- Division of Immunology, Department of Pediatrics, Boston Children’s Hospital, Boston, MA; Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Matthew Kirkey
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA
| | - Bryan Bunning
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA
| | | | - Stephen J. Galli
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA
- Department of Microbiology and Immunology, Stanford, CA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Scott D. Boyd
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | | | | | - Manisha Desai
- Department of Biomedical and Data Science, Stanford University, Stanford, CA
| | - Hans C. Oettgen
- Division of Immunology, Department of Pediatrics, Boston Children’s Hospital, Boston, MA; Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Holden T. Maecker
- Human Immune Monitoring Center, Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA
- Department of Microbiology and Immunology, Stanford, CA
| | - Wong Yu
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA
| | | | - Sandra Andorf
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, Divisions of Biomedical Informatics and Allergy & Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Kari C. Nadeau
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA
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9
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Grandi FC, Bhutani N. Preparation of Human Chondrocytes for Profiling Using Cytometry by Time-of-flight (cyTOF). Bio Protoc 2021; 11:e4086. [PMID: 34395725 PMCID: PMC8329458 DOI: 10.21769/bioprotoc.4086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 04/01/2021] [Accepted: 04/19/2021] [Indexed: 02/04/2023] Open
Abstract
Single-cell technologies have allowed high-resolution profiling of tissues and thus a deeper understanding of tissue homeostasis and disease heterogeneity. Understanding this heterogeneity can be especially important for tailoring treatments in a patient-specific manner. Here, we detail methods for preparing human cartilage tissue for profiling via cytometry by time-of-flight (cyTOF). We have previously utilized this method to characterize several rare cell populations in cartilage, including cartilage-progenitor cells, inflammation-amplifying cells (Inf-A), and inflammation-dampening cells (Inf-D). Previous bio-protocols have focused on cyTOF staining of PBMCs. Therefore, here we detail the steps unique to the processing of human cartilage and chondrocytes. Briefly, cartilage tissue is digested to release individual chondrocytes, which can be expanded and manipulated in culture. These cells are then collected and fixed in preparation for cyTOF, followed by standard staining and analysis protocols.
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Affiliation(s)
- Fiorella Carla Grandi
- Department of Orthopedic Surgery, School of Medicine, Stanford University, Stanford, CA 94303, USA
| | - Nidhi Bhutani
- Department of Orthopedic Surgery, School of Medicine, Stanford University, Stanford, CA 94303, USA
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10
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Extended live-cell barcoding approach for multiplexed mass cytometry. Sci Rep 2021; 11:12388. [PMID: 34117319 PMCID: PMC8196040 DOI: 10.1038/s41598-021-91816-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 05/20/2021] [Indexed: 01/04/2023] Open
Abstract
Sample barcoding is essential in mass cytometry analysis, since it can eliminate potential procedural variations, enhance throughput, and allow simultaneous sample processing and acquisition. Sample pooling after prior surface staining termed live-cell barcoding is more desirable than intracellular barcoding, where samples are pooled after fixation and permeabilization, since it does not depend on fixation-sensitive antigenic epitopes. In live-cell barcoding, the general approach uses two tags per sample out of a pool of antibodies paired with five palladium (Pd) isotopes in order to preserve appreciable signal-to-noise ratios and achieve higher yields after sample deconvolution. The number of samples that can be pooled in an experiment using live-cell barcoding is limited, due to weak signal intensities associated with Pd isotopes and the relatively low number of available tags. Here, we describe a novel barcoding technique utilizing 10 different tags, seven cadmium (Cd) tags and three Pd tags, with superior signal intensities that do not impinge on lanthanide detection, which enables enhanced pooling of samples with multiple experimental conditions and markedly enhances sample throughput.
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11
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Co-evolution of tumor and immune cells during progression of multiple myeloma. Nat Commun 2021; 12:2559. [PMID: 33963182 PMCID: PMC8105337 DOI: 10.1038/s41467-021-22804-x] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 03/10/2021] [Indexed: 12/17/2022] Open
Abstract
Multiple myeloma (MM) is characterized by the uncontrolled proliferation of plasma cells. Despite recent treatment advances, it is still incurable as disease progression is not fully understood. To investigate MM and its immune environment, we apply single cell RNA and linked-read whole genome sequencing to profile 29 longitudinal samples at different disease stages from 14 patients. Here, we collect 17,267 plasma cells and 57,719 immune cells, discovering patient-specific plasma cell profiles and immune cell expression changes. Patients with the same genetic alterations tend to have both plasma cells and immune cells clustered together. By integrating bulk genomics and single cell mapping, we track plasma cell subpopulations across disease stages and find three patterns: stability (from precancer to diagnosis), and gain or loss (from diagnosis to relapse). In multiple patients, we detect “B cell-featured” plasma cell subpopulations that cluster closely with B cells, implicating their cell of origin. We validate AP-1 complex differential expression (JUN and FOS) in plasma cell subpopulations using CyTOF-based protein assays, and integrated analysis of single-cell RNA and CyTOF data reveals AP-1 downstream targets (IL6 and IL1B) potentially leading to inflammation regulation. Our work represents a longitudinal investigation for tumor and microenvironment during MM progression and paves the way for expanding treatment options. Clonal evolution in multiple myeloma (MM) needs to be understood in both the tumor and its microenvironment. Here the authors perform single-cell multi-omics profiling of samples from MM patients at different stages, finding transitions in the immune cell composition throughout progression.
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12
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Arjunan V, Hansen A, Deutzmann A, Sze DY, Dhanasekaran R. Spontaneous Regression of Hepatocellular Carcinoma: When the Immune System Stands Up to Cancer. Hepatology 2021; 73:1611-1614. [PMID: 32740961 PMCID: PMC8130562 DOI: 10.1002/hep.31489] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 07/03/2020] [Accepted: 07/19/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Vinodhini Arjunan
- Division of Gastroenterology and Hepatology, Stanford University, Stanford, CA
| | - Aida Hansen
- Division of Oncology, Stanford University, Stanford, CA
| | | | - Daniel Y. Sze
- Division of Interventional Radiology, Stanford University, Stanford, CA
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13
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Bucheli OTM, Sigvaldadóttir I, Eyer K. Measuring single-cell protein secretion in immunology: Technologies, advances, and applications. Eur J Immunol 2021; 51:1334-1347. [PMID: 33734428 PMCID: PMC8252417 DOI: 10.1002/eji.202048976] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 01/12/2021] [Accepted: 03/15/2021] [Indexed: 12/19/2022]
Abstract
The dynamics, nature, strength, and ultimately protective capabilities of an active immune response are determined by the extracellular constitution and concentration of various soluble factors. Generated effector cells secrete such mediators, including antibodies, chemo‐ and cytokines to achieve functionality. These secreted factors organize the individual immune cells into functional tissues, initiate, orchestrate, and regulate the immune response. Therefore, a single‐cell resolved analysis of protein secretion is a valuable tool for studying the heterogeneity and functionality of immune cells. This review aims to provide a comparative overview of various methods to characterize immune reactions by measuring single‐cell protein secretion. Spot‐based and cytometry‐based assays, such as ELISpot and flow cytometry, respectively, are well‐established methods applied in basic research and clinical settings. Emerging novel technologies, such as microfluidic platforms, offer new ways to measure and exploit protein secretion in immune reactions. Further technological advances will allow the deciphering of protein secretion in immunological responses with unprecedented detail, linking secretion to functionality. Here, we summarize the development and recent advances of tools that allow the analysis of protein secretion at the single‐cell level, and discuss and contrast their applications within immunology.
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Affiliation(s)
- Olivia T M Bucheli
- ETH Laboratory for Functional Immune Repertoire Analysis, Institute of Pharmaceutical Sciences, D-CHAB, ETH Zürich, Zürich, Switzerland
| | - Ingibjörg Sigvaldadóttir
- ETH Laboratory for Functional Immune Repertoire Analysis, Institute of Pharmaceutical Sciences, D-CHAB, ETH Zürich, Zürich, Switzerland
| | - Klaus Eyer
- ETH Laboratory for Functional Immune Repertoire Analysis, Institute of Pharmaceutical Sciences, D-CHAB, ETH Zürich, Zürich, Switzerland
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14
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Effects of processing conditions on stability of immune analytes in human blood. Sci Rep 2020; 10:17328. [PMID: 33060628 PMCID: PMC7566484 DOI: 10.1038/s41598-020-74274-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 09/09/2020] [Indexed: 11/30/2022] Open
Abstract
Minimizing variability in collection and processing of human blood samples for research remains a challenge. Delaying plasma or serum isolation after phlebotomy (processing delay) can cause perturbations of numerous analytes. Thus, a comprehensive understanding of how processing delay affects major endpoints used in human immunology research is necessary. Therefore, we studied how processing delay affects commonly measured cytokines and immune cell populations. We hypothesized that short-term time delays inherent to human research in serum and plasma processing impact commonly studied immunological analytes. Blood from healthy donors was subjected to processing delays commonly encountered in sample collection, and then assayed by 62-plex Luminex panel, 40-parameter mass cytometry panel, and 540,000 transcript expression microarray. Variance for immunological analytes was estimated using each individual’s baseline as a control. In general, short-term processing delay led to small changes in plasma and serum cytokines (range − 10.8 to 43.5%), markers and frequencies of peripheral blood mononuclear cell phenotypes (range 0.19 to 3.54 fold), and whole blood gene expression (stable for > 20 K genes)—with several exceptions described herein. Importantly, we built an open-access web application allowing investigators to estimate the degree of variance expected from processing delay for measurements of interest based on the data reported here.
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15
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Ho WJ, Yarchoan M, Charmsaz S, Munday RM, Danilova L, Sztein MB, Fertig EJ, Jaffee EM. Multipanel mass cytometry reveals anti-PD-1 therapy-mediated B and T cell compartment remodeling in tumor-draining lymph nodes. JCI Insight 2020; 5:132286. [PMID: 31855578 DOI: 10.1172/jci.insight.132286] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 12/12/2019] [Indexed: 12/16/2022] Open
Abstract
Anti-programmed cell death protein 1 (anti-PD-1) therapy has become an immunotherapeutic backbone for treating many cancer types. Although many studies have aimed to characterize the immune response to anti-PD-1 therapy in the tumor and in the peripheral blood, relatively less is known about the changes in the tumor-draining lymph nodes (TDLNs). TDLNs are primary sites of tumor antigen exposure that are critical to both regulation and cross-priming of the antitumor immune response. We used multipanel mass cytometry to obtain a high-parameter proteomic (39 total unique markers) immune profile of the TDLNs in a well-studied PD-1-responsive, immunocompetent mouse model. Based on combined hierarchal gating and unsupervised clustering analyses, we found that anti-PD-1 therapy enhances remodeling of both B and T cell compartments toward memory phenotypes. Functionally, expression of checkpoint markers was increased in conjunction with production of IFN-γ, TNF-α, or IL-2 in key cell types, including B and T cell subtypes, and rarer subsets, such as Tregs and NKT cells. A deeper profiling of the immunologic changes that occur in the TDLN milieu during effective anti-PD-1 therapy may lead to the discovery of novel biomarkers for monitoring response and provide key insights toward developing combination immunotherapeutic strategies.
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Affiliation(s)
- Won Jin Ho
- Sidney Kimmel Comprehensive Cancer Center.,Bloomberg-Kimmel Institute for Cancer Immunotherapy
| | - Mark Yarchoan
- Sidney Kimmel Comprehensive Cancer Center.,Bloomberg-Kimmel Institute for Cancer Immunotherapy
| | - Soren Charmsaz
- Sidney Kimmel Comprehensive Cancer Center.,Bloomberg-Kimmel Institute for Cancer Immunotherapy
| | | | - Ludmila Danilova
- Sidney Kimmel Comprehensive Cancer Center.,Bloomberg-Kimmel Institute for Cancer Immunotherapy.,Division of Biostatistics and Bioinformatics, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Marcelo B Sztein
- Center for Vaccine Development and Global Health.,Graduate Program in Molecular Microbiology and Immunology, Graduate Program in Life Sciences.,Department of Pediatrics, and.,Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Elana J Fertig
- Sidney Kimmel Comprehensive Cancer Center.,Bloomberg-Kimmel Institute for Cancer Immunotherapy.,McKusick-Nathans Institute for Genetic Medicine, and.,Division of Biostatistics and Bioinformatics, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Biomedical Engineering and.,Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Elizabeth M Jaffee
- Sidney Kimmel Comprehensive Cancer Center.,Bloomberg-Kimmel Institute for Cancer Immunotherapy.,Department of Pediatrics, and.,Pancreatic Cancer Precision Medicine Program and.,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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16
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Kowli S, Maecker H. Immunophenotyping and Intracellular Staining of Fixed Whole Blood for Mass Cytometry (CyTOF). Bio Protoc 2020. [DOI: 10.21769/bioprotoc.5004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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17
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Kowli S, Maecker H. Immunophenotyping and Intracellular Staining of Fixed Whole Blood for Mass Cytometry (CyTOF). Bio Protoc 2020. [DOI: 10.21769/bioprotoc.3750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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18
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Fisher DAC, Miner CA, Engle EK, Hu H, Collins TB, Zhou A, Allen MJ, Malkova ON, Oh ST. Cytokine production in myelofibrosis exhibits differential responsiveness to JAK-STAT, MAP kinase, and NFκB signaling. Leukemia 2019; 33:1978-1995. [PMID: 30718771 PMCID: PMC6813809 DOI: 10.1038/s41375-019-0379-y] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 12/13/2018] [Accepted: 12/19/2018] [Indexed: 12/31/2022]
Abstract
The distinct clinical features of myelofibrosis (MF) have been attributed in part to dysregulated inflammatory cytokine production. Circulating cytokine levels are elevated in MF patients; a subset of which have been shown to be poor prognostic indicators. In this study, cytokine overproduction was examined in MF patient plasma and in MF blood cells ex vivo using mass cytometry. Plasma cytokines measured following treatment with ruxolitinib remained markedly abnormal, indicating that aberrant cytokine production persists despite therapeutic JAK2 inhibition. In MF patient samples, 14/15 cytokines measured by mass cytometry were found to be constitutively overproduced, with the principal cellular source for most cytokines being monocytes, implicating a non-cell-autonomous role for monocyte-derived cytokines impacting disease-propagating stem/progenitor cells in MF. The majority of cytokines elevated in MF exhibited ex vivo hypersensitivity to thrombopoietin (TPO), toll-like receptor (TLR) ligands, and/or tumor necrosis factor (TNF). A subset of this group (including TNF, IL-6, IL-8, IL-10) was minimally sensitive to ruxolitinib. All TPO/TLR/TNF-sensitive cytokines, however, were sensitive to pharmacologic inhibition of NFκB and/or MAP kinase signaling. These results indicate that NFκB and MAP kinase signaling maintain cytokine overproduction in MF, and that inhibition of these pathways may provide optimal control of inflammatory pathophysiology in MF.
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Affiliation(s)
- Daniel A C Fisher
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Cathrine A Miner
- Immunomonitoring Laboratory, Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - Elizabeth K Engle
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Hengrui Hu
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Program in Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Taylor B Collins
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Amy Zhou
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Maggie J Allen
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Olga N Malkova
- Immunomonitoring Laboratory, Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
| | - Stephen T Oh
- Division of Hematology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Immunomonitoring Laboratory, Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA.
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19
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Holmes TH, Subrahmanyam PB, Wang W, Maecker HT. Penalized Supervised Star Plots: Example Application in Influenza-Specific CD4+ T Cells. Viral Immunol 2019; 32:102-109. [PMID: 30698511 DOI: 10.1089/vim.2018.0046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
An immune cell's phenotype expresses through its high-dimensional marker signature. Cluster analyses of data from high-throughput mass and flow cytometry marker panels permit discovery of previously undescribed immune cell phenotypes. Impactful reporting of new phenotypes demands low-dimensional visualization tools that preserve with integrity phenotypes' original high-dimensional structure. For this purpose, we introduce penalized supervised star plots. As designed and as we demonstrate, penalized supervised star plots are two-dimensional projections that tend to preserve separation of clusters as well as information on the relative contributions of various markers in differentiating phenotypes. The new method is robust to markers that do not differentiate phenotypes at all, as shown in a challenge data set. Results include comparison with other popular procedures. Penalized supervised star plots incorporate cross-validation to permit portability of estimated optimal projections to new samples. Supervised star plots are further illustrated with a featured influenza-specific T cell data set as well as a peripheral blood mononuclear cell phenotyping data set.
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Affiliation(s)
- Tyson H Holmes
- 1 Department of Medicine, Stanford University School of Medicine, Stanford, California.,2 Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, California
| | - Priyanka B Subrahmanyam
- 2 Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, California.,3 Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California
| | - Weiqi Wang
- 2 Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, California.,3 Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California
| | - Holden T Maecker
- 2 Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, California.,3 Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California
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20
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Olsen LR, Leipold MD, Pedersen CB, Maecker HT. The anatomy of single cell mass cytometry data. Cytometry A 2018; 95:156-172. [DOI: 10.1002/cyto.a.23621] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 08/28/2018] [Accepted: 09/05/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Lars R. Olsen
- Department of Bio and Health InformaticsTechnical University of Denmark Copenhagen Denmark
- Center for Genomic MedicineCopenhagen University Hospital Copenhagen Denmark
| | - Michael D. Leipold
- Institute for Immunity, Transplantation, and InfectionStanford University School of Medicine Stanford CA
| | - Christina B. Pedersen
- Department of Bio and Health InformaticsTechnical University of Denmark Copenhagen Denmark
- Center for Genomic MedicineCopenhagen University Hospital Copenhagen Denmark
| | - Holden Terry Maecker
- Institute for Immunity, Transplantation, and InfectionStanford University School of Medicine Stanford CA
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21
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Subrahmanyam PB, Dong Z, Gusenleitner D, Giobbie-Hurder A, Severgnini M, Zhou J, Manos M, Eastman LM, Maecker HT, Hodi FS. Distinct predictive biomarker candidates for response to anti-CTLA-4 and anti-PD-1 immunotherapy in melanoma patients. J Immunother Cancer 2018; 6:18. [PMID: 29510697 PMCID: PMC5840795 DOI: 10.1186/s40425-018-0328-8] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 02/16/2018] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND While immune checkpoint blockade has greatly improved clinical outcomes in diseases such as melanoma, there remains a need for predictive biomarkers to determine who will likely benefit most from which therapy. To date, most biomarkers of response have been identified in the tumors themselves. Biomarkers that could be assessed from peripheral blood would be even more desirable, because of ease of access and reproducibility of sampling. METHODS We used mass cytometry (CyTOF) to comprehensively profile peripheral blood of melanoma patients, in order to find predictive biomarkers of response to anti-CTLA-4 or anti-PD-1 therapy. Using a panel of ~ 40 surface and intracellular markers, we performed in-depth phenotypic and functional immune profiling to identify potential predictive biomarker candidates. RESULTS Immune profiling of baseline peripheral blood samples using CyTOF revealed that anti-CTLA-4 and anti-PD-1 therapies have distinct sets of candidate biomarkers. The distribution of CD4+ and CD8+ memory/non-memory cells and other memory subsets was different between responders and non-responders to anti-CTLA-4 therapy. In anti-PD-1 (but not anti-CTLA-4) treated patients, we discovered differences in CD69 and MIP-1β expressing NK cells between responders and non-responders. Finally, multivariate analysis was used to develop a model for the prediction of response. CONCLUSIONS Our results indicate that anti-CTLA-4 and anti-PD-1 have distinct predictive biomarker candidates. CD4+ and CD8+ memory T cell subsets play an important role in response to anti-CTLA-4, and are potential biomarker candidates. For anti-PD-1 therapy, NK cell subsets (but not memory T cell subsets) correlated with clinical response to therapy. These functionally active NK cell subsets likely play a critical role in the anti-tumor response triggered by anti-PD-1.
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Affiliation(s)
- Priyanka B Subrahmanyam
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Zhiwan Dong
- Center for Immuno-oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Daniel Gusenleitner
- Center for Immuno-oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Anita Giobbie-Hurder
- Center for Immuno-oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mariano Severgnini
- Center for Immuno-oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Jun Zhou
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Michael Manos
- Center for Immuno-oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Lauren M Eastman
- Center for Immuno-oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Holden T Maecker
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - F Stephen Hodi
- Center for Immuno-oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.
- Melanoma Disease Center, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA.
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22
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Abstract
T Cells specific for a single antigen tend to be rare, even after expansion of memory cells. They are commonly detected by in vitro stimulation with peptides or protein, followed by staining for intracellular cytokines. In this protocol, we use CyTOF® mass cytometry to collect single-cell data on a large number of cytokines/chemokines, as well as cell-surface proteins that characterize T cells and other immune cells. We also include a method for magnetic bead enrichment of antigen-stimulated T cells, based on their expression of CD154 and CD69. Coupling magnetic enrichment with highly multi-parameter mass cytometry, this method enables the ability to dissect the frequency, phenotype, and function of antigen-specific T cells in greater detail than previously possible. Rare cell subsets can be examined, while minimizing run times on the CyTOF.
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Affiliation(s)
- Dongxia Lin
- Fluidigm Corporation, South San Francisco, CA, 94080, USA
| | - Holden T Maecker
- Human Immune Monitoring Center, Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Fairchild Science Building, 299 Campus Drive, Stanford, CA, 94305-5124, USA.
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23
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Subrahmanyam PB, Maecker HT. CyTOF Measurement of Immunocompetence Across Major Immune Cell Types. ACTA ACUST UNITED AC 2017; 82:9.54.1-9.54.12. [PMID: 28967988 DOI: 10.1002/cpcy.27] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The central role of the immune system is becoming appreciated in a wide variety of diseases. Cancer immunotherapy is one area that has yielded much recent success, although not all patients benefit equally. At the same time, recent studies have highlighted the heterogeneity of the human immune system. Despite this heterogeneity, we do not routinely measure immune competence in clinical practice, and there are no consensus assays of healthy immune function. Using mass cytometry (CyTOF), we can simultaneously detect ∼40 markers to identify various cell subsets and determine their function by the expression of cytokines, cytotoxicity, and activation markers. This can help assess 'immunocompetence' and facilitate better implementation of immunotherapies, both in specific disease settings and perhaps eventually as a prognostic tool in healthy subjects. Here we introduce the concepts behind this assay and provide a protocol that we have successfully implemented to identify possible predictive biomarkers of immunotherapy outcome. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Priyanka B Subrahmanyam
- Post-doctoral Research Fellow, Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California
| | - Holden T Maecker
- Professor, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, California
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24
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Karnell FG, Lin D, Motley S, Duhen T, Lim N, Campbell DJ, Turka LA, Maecker HT, Harris KM. Reconstitution of immune cell populations in multiple sclerosis patients after autologous stem cell transplantation. Clin Exp Immunol 2017; 189:268-278. [PMID: 28498568 DOI: 10.1111/cei.12985] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2017] [Indexed: 12/13/2022] Open
Abstract
Multiple sclerosis is an inflammatory T cell-mediated autoimmune disease. In a Phase II clinical trial, high-dose immunosuppressive therapy combined with autologous CD34+ haematopoietic stem cell transplant resulted in 69·2% of subjects remaining disease-free without evidence of relapse, loss of neurological function or new magnetic resonance imaging (MRI) lesions to year 5 post-treatment. A combination of CyTOF mass cytometry and multi-parameter flow cytometry was used to explore the reconstitution kinetics of immune cell subsets in the periphery post-haematopoietic cell transplant (HSCT) and the impact of treatment on the phenotype of circulating T cells in this study population. Repopulation of immune cell subsets progressed similarly for all patients studied 2 years post-therapy, regardless of clinical outcome. At month 2, monocytes and natural killer (NK) cells were proportionally more abundant, while CD4 T cells and B cells were reduced, relative to baseline. In contrast to the changes observed at earlier time-points in the T cell compartment, B cells were proportionally more abundant and expansion in the proportion of naive B cells was observed 1 and 2 years post-therapy. Within the T cell compartment, the proportion of effector memory and late effector subsets of CD4 and CD8 T cells was increased, together with transient increases in proportions of CD45RA-regulatory T cells (Tregs ) and T helper type 1 (Th1 cells) and a decrease in Th17·1 cells. While none of the treatment effects studied correlated with clinical outcome, patients who remained healthy throughout the 5-year study had significantly higher absolute numbers of memory CD4 and CD8 T cells in the periphery prior to stem cell transplantation.
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Affiliation(s)
| | - D Lin
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - S Motley
- Benaroya Research Institute, Seattle, WA, USA.,Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA
| | - T Duhen
- Benaroya Research Institute, Seattle, WA, USA.,Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA
| | - N Lim
- Immune Tolerance Network, Bethesda, MD, USA
| | - D J Campbell
- Benaroya Research Institute, Seattle, WA, USA.,Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA
| | - L A Turka
- Immune Tolerance Network, Bethesda, MD, USA.,Massachusetts General Hospital, Center for Transplantation Sciences, Boston, MA, USA
| | - H T Maecker
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - K M Harris
- Immune Tolerance Network, Bethesda, MD, USA
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