1
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Dellorusso PV, Proven MA, Calero-Nieto FJ, Wang X, Mitchell CA, Hartmann F, Amouzgar M, Favaro P, DeVilbiss A, Swann JW, Ho TT, Zhao Z, Bendall SC, Morrison S, Göttgens B, Passegué E. Autophagy counters inflammation-driven glycolytic impairment in aging hematopoietic stem cells. Cell Stem Cell 2024:S1934-5909(24)00174-7. [PMID: 38754428 DOI: 10.1016/j.stem.2024.04.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 03/14/2024] [Accepted: 04/24/2024] [Indexed: 05/18/2024]
Abstract
Autophagy is central to the benefits of longevity signaling programs and to hematopoietic stem cell (HSC) response to nutrient stress. With age, a subset of HSCs increases autophagy flux and preserves regenerative capacity, but the signals triggering autophagy and maintaining the functionality of autophagy-activated old HSCs (oHSCs) remain unknown. Here, we demonstrate that autophagy is an adaptive cytoprotective response to chronic inflammation in the aging murine bone marrow (BM) niche. We find that inflammation impairs glucose uptake and suppresses glycolysis in oHSCs through Socs3-mediated inhibition of AKT/FoxO-dependent signaling, with inflammation-mediated autophagy engagement preserving functional quiescence by enabling metabolic adaptation to glycolytic impairment. Moreover, we show that transient autophagy induction via a short-term fasting/refeeding paradigm normalizes glycolytic flux and significantly boosts oHSC regenerative potential. Our results identify inflammation-driven glucose hypometabolism as a key driver of HSC dysfunction with age and establish autophagy as a targetable node to reset oHSC regenerative capacity.
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Affiliation(s)
- Paul V Dellorusso
- Columbia Stem Cell Initiative, Department of Genetics & Development, Columbia University, New York, NY 10032, USA
| | - Melissa A Proven
- Columbia Stem Cell Initiative, Department of Genetics & Development, Columbia University, New York, NY 10032, USA
| | - Fernando J Calero-Nieto
- Welcome and MRC Cambridge Stem Cell Institute, Department of Haematology, Cambridge University, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Xiaonan Wang
- Welcome and MRC Cambridge Stem Cell Institute, Department of Haematology, Cambridge University, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Carl A Mitchell
- Columbia Stem Cell Initiative, Department of Genetics & Development, Columbia University, New York, NY 10032, USA
| | - Felix Hartmann
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Meelad Amouzgar
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Patricia Favaro
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Andrew DeVilbiss
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - James W Swann
- Columbia Stem Cell Initiative, Department of Genetics & Development, Columbia University, New York, NY 10032, USA
| | - Theodore T Ho
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Department of Medicine, Hematology/Oncology Division, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Zhiyu Zhao
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sean C Bendall
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Sean Morrison
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Berthold Göttgens
- Welcome and MRC Cambridge Stem Cell Institute, Department of Haematology, Cambridge University, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Emmanuelle Passegué
- Columbia Stem Cell Initiative, Department of Genetics & Development, Columbia University, New York, NY 10032, USA.
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2
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Yakabi K, Berson E, Montine KS, Bendall SC, MacCoss MJ, Poston KL, Montine TJ. Human cerebrospinal fluid single exosomes in Parkinson's and Alzheimer's diseases. bioRxiv 2023:2023.12.22.573124. [PMID: 38187636 PMCID: PMC10769431 DOI: 10.1101/2023.12.22.573124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Exosomes are proposed to be important in the pathogenesis of prevalent neurodegenerative diseases. We report the first application of solid-state technology to perform multiplex analysis of single exosomes in human cerebrospinal fluid (CSF) obtained from the lumbar sac of people diagnosed with Alzheimer's disease dementia (ADD, n=30) or Parkinson's disease dementia (PDD, n=30), as well as age-matched health controls (HCN, n=30). Single events were captured with mouse monoclonal antibodies to one of three different tetraspanins (CD9, CD63, or CD81) or with mouse (M) IgG control, and then probed with fluorescently labeled antibodies to prion protein (PrP) or CD47 to mark neuronal or presynaptic origin, as well as ADD- and PDD-related proteins: amyloid beta (Aβ), tau, α-synuclein, and Apolipoprotein (Apo) E. Data were collected only from captured events that were within the size range of 50 to 200 nm. Exosomes were present at approximately 100 billion per mL human CSF and were similarly abundant for CD9+ and CD81+ events, but CD63+ were only 22% to 25% of CD9+ (P<0.0001) or CD81+ (P<0.0001) events. Approximately 24% of CSF exosomes were PrP+, while only 2% were CD47+. The vast majority of exosomes were surface ApoE+, and the number of PrP-ApoE+ (P<0.001) and PrP+ApoE+ (P<0.01) exosomes were significantly reduced in ADD vs. HCN for CD9+ events only. Aβ, tau, and α-synuclein were not detected on the exosome surface or in permeabilized cargo. These data provide new insights into single exosome molecular features and highlight reduction in the CSF concentration of ApoE+ exosomes in patients with ADD.
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3
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Karacosta LG, Pancirer D, Preiss JS, Benson JA, Trope W, Shrager JB, Sung AW, Neal JW, Bendall SC, Wakelee H, Plevritis SK. Phenotyping EMT and MET cellular states in lung cancer patient liquid biopsies at a personalized level using mass cytometry. Sci Rep 2023; 13:21781. [PMID: 38065965 PMCID: PMC10709404 DOI: 10.1038/s41598-023-46458-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/01/2023] [Indexed: 12/18/2023] Open
Abstract
Malignant pleural effusions (MPEs) can be utilized as liquid biopsy for phenotyping malignant cells and for precision immunotherapy, yet MPEs are inadequately studied at the single-cell proteomic level. Here we leverage mass cytometry to interrogate immune and epithelial cellular profiles of primary tumors and pleural effusions (PEs) from early and late-stage non-small cell lung cancer (NSCLC) patients, with the goal of assessing epithelial-mesenchymal transition (EMT) and mesenchymal-epithelial transition (MET) states in patient specimens. By using the EMT-MET reference map PHENOSTAMP, we observe a variety of EMT states in cytokeratin positive (CK+) cells, and report for the first time MET-enriched CK+ cells in MPEs. We show that these states may be relevant to disease stage and therapy response. Furthermore, we found that the fraction of CD33+ myeloid cells in PEs was positively correlated to the fraction of CK+ cells. Longitudinal analysis of MPEs drawn 2 months apart from a patient undergoing therapy, revealed that CK+ cells acquired heterogeneous EMT features during treatment. We present this work as a feasibility study that justifies deeper characterization of EMT and MET states in malignant cells found in PEs as a promising clinical platform to better evaluate disease progression and treatment response at a personalized level.
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Affiliation(s)
- Loukia G Karacosta
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, 77054, USA
| | - Danny Pancirer
- Stanford Cancer Institute - Clinical Trials Office, Stanford University, Stanford, CA, 94305, USA
| | - Jordan S Preiss
- Stanford Cancer Institute - Clinical Trials Office, Stanford University, Stanford, CA, 94305, USA
| | - Jalen A Benson
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, 94305, USA
| | - Winston Trope
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, 94305, USA
| | - Joseph B Shrager
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, 94305, USA
- Palo Alto VA Health Care System, Palo Alto, USA
| | - Arthur Wai Sung
- Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Joel W Neal
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Sean C Bendall
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA
| | - Heather Wakelee
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Sylvia K Plevritis
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA.
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA.
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4
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Adamik J, Munson PV, Maurer DM, Hartmann FJ, Bendall SC, Argüello RJ, Butterfield LH. Immuno-metabolic dendritic cell vaccine signatures associate with overall survival in vaccinated melanoma patients. Nat Commun 2023; 14:7211. [PMID: 37938561 PMCID: PMC10632482 DOI: 10.1038/s41467-023-42881-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 10/24/2023] [Indexed: 11/09/2023] Open
Abstract
Efficacy of cancer vaccines remains low and mechanistic understanding of antigen presenting cell function in cancer may improve vaccine design and outcomes. Here, we analyze the transcriptomic and immune-metabolic profiles of Dendritic Cells (DCs) from 35 subjects enrolled in a trial of DC vaccines in late-stage melanoma (NCT01622933). Multiple platforms identify metabolism as an important biomarker of DC function and patient overall survival (OS). We demonstrate multiple immune and metabolic gene expression pathway alterations, a functional decrease in OCR/OXPHOS and increase in ECAR/glycolysis in patient vaccines. To dissect molecular mechanisms, we utilize single cell SCENITH functional profiling and show patient clinical outcomes (OS) correlate with DC metabolic profile, and that metabolism is linked to immune phenotype. With single cell metabolic regulome profiling, we show that MCT1 (monocarboxylate transporter-1), a lactate transporter, is increased in patient DCs, as is glucose uptake and lactate secretion. Importantly, pre-vaccination circulating myeloid cells in patients used as precursors for DC vaccine generation are significantly skewed metabolically as are several DC subsets. Together, we demonstrate that the metabolic profile of DC is tightly associated with the immunostimulatory potential of DC vaccines from cancer patients. We link phenotypic and functional metabolic changes to immune signatures that correspond to suppressed DC differentiation.
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Affiliation(s)
- Juraj Adamik
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, 94129, USA
| | - Paul V Munson
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, 94129, USA
| | - Deena M Maurer
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, 94129, USA
| | - Felix J Hartmann
- Systems Immunology and Single-Cell Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sean C Bendall
- Department of Pathology, Stanford University, Palo Alto, CA, 94304, USA
| | - Rafael J Argüello
- Aix Marseille Univ, CNRS, INSERM, CIML, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Lisa H Butterfield
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, 94129, USA.
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA.
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5
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Favaro P, Glass DR, Borges L, Baskar R, Reynolds W, Ho D, Bruce T, Tebaykin D, Scanlon VM, Shestopalov I, Bendall SC. Unravelling human hematopoietic progenitor cell diversity through association with intrinsic regulatory factors. bioRxiv 2023:2023.08.30.555623. [PMID: 37693547 PMCID: PMC10491219 DOI: 10.1101/2023.08.30.555623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Hematopoietic stem and progenitor cell (HSPC) transplantation is an essential therapy for hematological conditions, but finer definitions of human HSPC subsets with associated function could enable better tuning of grafts and more routine, lower-risk application. To deeply phenotype HSPCs, following a screen of 328 antigens, we quantified 41 surface proteins and functional regulators on millions of CD34+ and CD34- cells, spanning four primary human hematopoietic tissues: bone marrow, mobilized peripheral blood, cord blood, and fetal liver. We propose more granular definitions of HSPC subsets and provide new, detailed differentiation trajectories of erythroid and myeloid lineages. These aspects of our revised human hematopoietic model were validated with corresponding epigenetic analysis and in vitro clonal differentiation assays. Overall, we demonstrate the utility of using molecular regulators as surrogates for cellular identity and functional potential, providing a framework for description, prospective isolation, and cross-tissue comparison of HSPCs in humans.
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Affiliation(s)
- Patricia Favaro
- Department of Pathology, Stanford University
- These authors contributed equally
| | - David R. Glass
- Department of Pathology, Stanford University
- Immunology Graduate Program, Stanford University
- Present address: Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- These authors contributed equally
| | - Luciene Borges
- Department of Pathology, Stanford University
- Present address: Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT, USA
- These authors contributed equally
| | - Reema Baskar
- Department of Pathology, Stanford University
- Present address: Genome Institute of Singapore
| | | | - Daniel Ho
- Department of Pathology, Stanford University
| | | | | | - Vanessa M. Scanlon
- Department of Laboratory Medicine, Yale School of Medicine
- Present address: Center for Regenerative Medicine and Skeletal Biology, University of Connecticut Health
| | | | - Sean C. Bendall
- Department of Pathology, Stanford University
- Immunology Graduate Program, Stanford University
- Lead author
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6
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Berson E, Gajera CR, Phongpreecha T, Perna A, Bukhari SA, Becker M, Chang AL, De Francesco D, Espinosa C, Ravindra NG, Postupna N, Latimer CS, Shively CA, Register TC, Craft S, Montine KS, Fox EJ, Keene CD, Bendall SC, Aghaeepour N, Montine TJ. Cross-species comparative analysis of single presynapses. Sci Rep 2023; 13:13849. [PMID: 37620363 PMCID: PMC10449792 DOI: 10.1038/s41598-023-40683-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 08/16/2023] [Indexed: 08/26/2023] Open
Abstract
Comparing brain structure across species and regions enables key functional insights. Leveraging publicly available data from a novel mass cytometry-based method, synaptometry by time of flight (SynTOF), we applied an unsupervised machine learning approach to conduct a comparative study of presynapse molecular abundance across three species and three brain regions. We used neural networks and their attractive properties to model complex relationships among high dimensional data to develop a unified, unsupervised framework for comparing the profile of more than 4.5 million single presynapses among normal human, macaque, and mouse samples. An extensive validation showed the feasibility of performing cross-species comparison using SynTOF profiling. Integrative analysis of the abundance of 20 presynaptic proteins revealed near-complete separation between primates and mice involving synaptic pruning, cellular energy, lipid metabolism, and neurotransmission. In addition, our analysis revealed a strong overlap between the presynaptic composition of human and macaque in the cerebral cortex and neostriatum. Our unique approach illuminates species- and region-specific variation in presynapse molecular composition.
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Affiliation(s)
- Eloïse Berson
- Department of Pathology, Stanford University, 300 Pasteur Dr., Stanford, CA, 94304, USA
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
| | - Chandresh R Gajera
- Department of Pathology, Stanford University, 300 Pasteur Dr., Stanford, CA, 94304, USA
| | - Thanaphong Phongpreecha
- Department of Pathology, Stanford University, 300 Pasteur Dr., Stanford, CA, 94304, USA
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
| | - Amalia Perna
- Department of Pathology, Stanford University, 300 Pasteur Dr., Stanford, CA, 94304, USA
| | - Syed A Bukhari
- Department of Pathology, Stanford University, 300 Pasteur Dr., Stanford, CA, 94304, USA
| | - Martin Becker
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
| | - Alan L Chang
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
| | - Davide De Francesco
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
| | - Camilo Espinosa
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
| | - Neal G Ravindra
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
| | - Nadia Postupna
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA, USA
| | - Caitlin S Latimer
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA, USA
| | - Carol A Shively
- Department of Pathology/Comparative Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Thomas C Register
- Department of Pathology/Comparative Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Suzanne Craft
- Department of Internal Medicine-Geriatrics, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Kathleen S Montine
- Department of Pathology, Stanford University, 300 Pasteur Dr., Stanford, CA, 94304, USA
| | - Edward J Fox
- Department of Pathology, Stanford University, 300 Pasteur Dr., Stanford, CA, 94304, USA
| | - C Dirk Keene
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA, USA
| | - Sean C Bendall
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
| | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Thomas J Montine
- Department of Pathology, Stanford University, 300 Pasteur Dr., Stanford, CA, 94304, USA.
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7
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Dellorusso PV, Proven MA, Calero-Nieto FJ, Wang X, Mitchell CA, Hartmann F, Amouzgar M, Favaro P, DeVilbiss A, Swann JW, Ho TT, Zhao Z, Bendall SC, Morrison S, Göttgens B, Passegué E. Autophagy counters inflammation-driven glycolytic impairment in aging hematopoietic stem cells. bioRxiv 2023:2023.08.17.553736. [PMID: 37645930 PMCID: PMC10462159 DOI: 10.1101/2023.08.17.553736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Aging of the hematopoietic system promotes various blood, immune and systemic disorders and is largely driven by hematopoietic stem cell (HSC) dysfunction ( 1 ). Autophagy is central for the benefits associated with activation of longevity signaling programs ( 2 ), and for HSC function and response to nutrient stress ( 3,4 ). With age, a subset of HSCs increases autophagy flux and preserves some regenerative capacity, while the rest fail to engage autophagy and become metabolically overactivated and dysfunctional ( 4 ). However, the signals that promote autophagy in old HSCs and the mechanisms responsible for the increased regenerative potential of autophagy-activated old HSCs remain unknown. Here, we demonstrate that autophagy activation is an adaptive survival response to chronic inflammation in the aging bone marrow (BM) niche ( 5 ). We find that inflammation impairs glucose metabolism and suppresses glycolysis in aged HSCs through Socs3-mediated impairment of AKT/FoxO-dependent signaling. In this context, we show that inflammation-mediated autophagy engagement preserves functional quiescence by enabling metabolic adaptation to glycolytic impairment. Moreover, we demonstrate that transient autophagy induction via a short-term fasting/refeeding paradigm normalizes glucose uptake and glycolytic flux and significantly improves old HSC regenerative potential. Our results identify inflammation-driven glucose hypometabolism as a key driver of HSC dysfunction with age and establish autophagy as a targetable node to reset old HSC glycolytic and regenerative capacity. One-Sentence Summary Autophagy compensates for chronic inflammation-induced metabolic deregulation in old HSCs, and its transient modulation can reset old HSC glycolytic and regenerative capacity.
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8
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Rao M, Amouzgar M, Harden JT, Lapasaran MG, Trickey A, Armstrong B, Odim J, Debnam T, Esquivel CO, Bendall SC, Martinez OM, Krams SM. High-dimensional profiling of pediatric immune responses to solid organ transplantation. Cell Rep Med 2023; 4:101147. [PMID: 37552988 PMCID: PMC10439249 DOI: 10.1016/j.xcrm.2023.101147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 05/05/2023] [Accepted: 07/13/2023] [Indexed: 08/10/2023]
Abstract
Solid organ transplant remains a life-saving therapy for children with end-stage heart, lung, liver, or kidney disease; however, ∼33% of allograft recipients experience acute rejection within the first year after transplant. Our ability to detect early rejection is hampered by an incomplete understanding of the immune changes associated with allograft health, particularly in the pediatric population. We performed detailed, multilineage, single-cell analysis of the peripheral blood immune composition in pediatric solid organ transplant recipients, with high-dimensional mass cytometry. Supervised and unsupervised analysis methods to study cell-type proportions indicate that the allograft type strongly influences the post-transplant immune profile. Further, when organ-specific differences are considered, graft health is associated with changes in the proportion of distinct T cell subpopulations. Together, these data form the basis for mechanistic studies into the pathobiology of rejection and allow for the development of new immunosuppressive agents with greater specificity.
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Affiliation(s)
- Mahil Rao
- Department of Pediatrics, Division of Pediatric Critical Care Medicine, Stanford University School of Medicine, Palo Alto, CA 94304, USA; Transplant Immunology Lab, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Meelad Amouzgar
- Immunology Graduate Program, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - James T Harden
- Transplant Immunology Lab, Stanford University School of Medicine, Palo Alto, CA 94304, USA; Immunology Graduate Program, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - M Gay Lapasaran
- Transplant Immunology Lab, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Amber Trickey
- Department of Surgery, Division of Abdominal Transplant Surgery, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | | | - Jonah Odim
- National Institutes of Health, Bethesda, MD, USA
| | | | - Carlos O Esquivel
- Transplant Immunology Lab, Stanford University School of Medicine, Palo Alto, CA 94304, USA; Department of Surgery, Division of Abdominal Transplant Surgery, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Sean C Bendall
- Program in Immunology, Stanford University School of Medicine, Palo Alto, CA 94304, USA; Department of Pathology, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Olivia M Martinez
- Transplant Immunology Lab, Stanford University School of Medicine, Palo Alto, CA 94304, USA; Department of Surgery, Division of Abdominal Transplant Surgery, Stanford University School of Medicine, Palo Alto, CA 94304, USA; Program in Immunology, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Sheri M Krams
- Transplant Immunology Lab, Stanford University School of Medicine, Palo Alto, CA 94304, USA; Department of Surgery, Division of Abdominal Transplant Surgery, Stanford University School of Medicine, Palo Alto, CA 94304, USA; Program in Immunology, Stanford University School of Medicine, Palo Alto, CA 94304, USA.
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9
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Bai Y, Zhu B, Oliveria JP, Cannon BJ, Feyaerts D, Bosse M, Vijayaragavan K, Greenwald NF, Phillips D, Schürch CM, Naik SM, Ganio EA, Gaudilliere B, Rodig SJ, Miller MB, Angelo M, Bendall SC, Rovira-Clavé X, Nolan GP, Jiang S. Expanded vacuum-stable gels for multiplexed high-resolution spatial histopathology. Nat Commun 2023; 14:4013. [PMID: 37419873 PMCID: PMC10329015 DOI: 10.1038/s41467-023-39616-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/16/2023] [Indexed: 07/09/2023] Open
Abstract
Cellular organization and functions encompass multiple scales in vivo. Emerging high-plex imaging technologies are limited in resolving subcellular biomolecular features. Expansion Microscopy (ExM) and related techniques physically expand samples for enhanced spatial resolution, but are challenging to be combined with high-plex imaging technologies to enable integrative multiscaled tissue biology insights. Here, we introduce Expand and comPRESS hydrOgels (ExPRESSO), an ExM framework that allows high-plex protein staining, physical expansion, and removal of water, while retaining the lateral tissue expansion. We demonstrate ExPRESSO imaging of archival clinical tissue samples on Multiplexed Ion Beam Imaging and Imaging Mass Cytometry platforms, with detection capabilities of > 40 markers. Application of ExPRESSO on archival human lymphoid and brain tissues resolved tissue architecture at the subcellular level, particularly that of the blood-brain barrier. ExPRESSO hence provides a platform for extending the analysis compatibility of hydrogel-expanded biospecimens to mass spectrometry, with minimal modifications to protocols and instrumentation.
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Affiliation(s)
- Yunhao Bai
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Bokai Zhu
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - John-Paul Oliveria
- Department of Translational Medicine, Genentech, Inc., South San Francisco, CA, USA
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Bryan J Cannon
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Dorien Feyaerts
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA, USA
| | - Marc Bosse
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | | | - Darci Phillips
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Christian M Schürch
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany
| | - Samuel M Naik
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Edward A Ganio
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA, USA
| | - Brice Gaudilliere
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA, USA
| | - Scott J Rodig
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael B Miller
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael Angelo
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Sean C Bendall
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Xavier Rovira-Clavé
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
| | - Garry P Nolan
- Department of Pathology, Stanford University, Stanford, CA, USA.
| | - Sizun Jiang
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA.
- Department of Pathology, Dana Farber Cancer Institute, Boston, MA, USA.
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10
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Kumar R, Liu CC, Bendall SC, Angelo M. Synthesis, Characterization, and Applications of a Superior Dendrimer-Based Polymer for Multiplexed Ion Beam Imaging Time-of-Flight Analysis. Biomacromolecules 2023. [PMID: 37352475 DOI: 10.1021/acs.biomac.3c00174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2023]
Abstract
High-dimensional single-cell mass spectrometric imaging techniques such as multiplexed ion beam imaging by time-of-flight mass spectrometry (MIBI-TOF), imaging mass cytometry (IMC), and flow cytometry-based CyTOF utilize antibodies conjugated to linear metal-chelating polymers. Here, we report on the synthesis and characterization of a dendrimer-based polymer and its utilization in tissue imaging using MIBI-TOF. We compared the staining performance in FFPE tissue of antibodies for lineage-specific immune proteins (CD20, CD3, CD45, FoxP3) that were conjugated with dendrimer or linear polymer. Staining of serial tissue sections with dendron-conjugated and linear-polymer-conjugated antibodies revealed comparable avidities of dendrons and linear polymers with log2 (ratio of mean positive pixel intensity of staining for linear polymers to dendrons) within the range ±0.25. Interestingly, dendron-conjugated antibodies were observed to have some advantages over linear polymer-conjugated antibodies. For example, tissue staining of a nuclear protein, FoxP3 with dendron-conjugated antibodies showed notably less background staining than that of linear-polymer-conjugated antibodies. Additionally, dendron-conjugated antibodies did not exhibit off-target cytosolic binding in neural tissue typically observed when using linear polymer conjugates. Taken together, this work provides a versatile framework for using third-generation dendron-conjugated antibodies with improved staining over conventional linear polymers.
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Affiliation(s)
- Rashmi Kumar
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305-5119, United States
| | - Candace C Liu
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305-5119, United States
| | - Sean C Bendall
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305-5119, United States
| | - Michael Angelo
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305-5119, United States
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11
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Mrdjen D, Amouzgar M, Cannon B, Liu C, Spence A, McCaffrey E, Bharadwaj A, Tebaykin D, Bukhari S, Hartmann FJ, Kagel A, Vijayaragavan K, Oliveria JP, Yakabi K, Serrano GE, Corrada MM, Kawas CH, Camacho C, Bosse M, Tibshirani R, Beach TG, Angelo M, Montine T, Bendall SC. Spatial proteomics reveals human microglial states shaped by anatomy and neuropathology. Res Sq 2023:rs.3.rs-2987263. [PMID: 37398389 PMCID: PMC10312937 DOI: 10.21203/rs.3.rs-2987263/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Microglia are implicated in aging, neurodegeneration, and Alzheimer's disease (AD). Traditional, low-plex, imaging methods fall short of capturing in situ cellular states and interactions in the human brain. We utilized Multiplexed Ion Beam Imaging (MIBI) and data-driven analysis to spatially map proteomic cellular states and niches in healthy human brain, identifying a spectrum of microglial profiles, called the microglial state continuum (MSC). The MSC ranged from senescent-like to active proteomic states that were skewed across large brain regions and compartmentalized locally according to their immediate microenvironment. While more active microglial states were proximal to amyloid plaques, globally, microglia significantly shifted towards a, presumably, dysfunctional low MSC in the AD hippocampus, as confirmed in an independent cohort (n=26). This provides an in situ single cell framework for mapping human microglial states along a continuous, shifting existence that is differentially enriched between healthy brain regions and disease, reinforcing differential microglial functions overall.
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Affiliation(s)
- Dunja Mrdjen
- Department of Pathology, Stanford University, School of Medicine, Palo Alto 94304, CA, USA
| | - Meelad Amouzgar
- Department of Pathology, Stanford University, School of Medicine, Palo Alto 94304, CA, USA
| | - Bryan Cannon
- Department of Pathology, Stanford University, School of Medicine, Palo Alto 94304, CA, USA
| | - Candace Liu
- Department of Pathology, Stanford University, School of Medicine, Palo Alto 94304, CA, USA
| | - Angie Spence
- Department of Pathology, Stanford University, School of Medicine, Palo Alto 94304, CA, USA
| | - Erin McCaffrey
- Department of Pathology, Stanford University, School of Medicine, Palo Alto 94304, CA, USA
| | - Anusha Bharadwaj
- Department of Pathology, Stanford University, School of Medicine, Palo Alto 94304, CA, USA
| | - Dmitry Tebaykin
- Department of Pathology, Stanford University, School of Medicine, Palo Alto 94304, CA, USA
| | - Syed Bukhari
- Department of Pathology, Stanford University, School of Medicine, Palo Alto 94304, CA, USA
| | - Felix J. Hartmann
- Department of Pathology, Stanford University, School of Medicine, Palo Alto 94304, CA, USA
- Systems Immunology and Single-Cell Biology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Adam Kagel
- Department of Pathology, Stanford University, School of Medicine, Palo Alto 94304, CA, USA
| | - Kausalia Vijayaragavan
- Department of Pathology, Stanford University, School of Medicine, Palo Alto 94304, CA, USA
| | - John Paul Oliveria
- Department of Pathology, Stanford University, School of Medicine, Palo Alto 94304, CA, USA
| | - Koya Yakabi
- Department of Pathology, Stanford University, School of Medicine, Palo Alto 94304, CA, USA
| | | | - Maria M. Corrada
- Department of Neurology, University of California, Irvine, 9269, CA, USA
| | - Claudia H. Kawas
- Department of Neurology, University of California, Irvine, 9269, CA, USA
| | - Christine Camacho
- Department of Pathology, Stanford University, School of Medicine, Palo Alto 94304, CA, USA
| | - Marc Bosse
- Department of Pathology, Stanford University, School of Medicine, Palo Alto 94304, CA, USA
| | - Robert Tibshirani
- Department of Pathology, Stanford University, School of Medicine, Palo Alto 94304, CA, USA
| | - Thomas G. Beach
- Banner Sun Health Research Institute, Sun City, 85351, AZ, USA
| | - Michael Angelo
- Department of Pathology, Stanford University, School of Medicine, Palo Alto 94304, CA, USA
| | - Thomas Montine
- Department of Pathology, Stanford University, School of Medicine, Palo Alto 94304, CA, USA
| | - Sean C. Bendall
- Department of Pathology, Stanford University, School of Medicine, Palo Alto 94304, CA, USA
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12
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Sarno J, Domizi P, Liu Y, Merchant M, Pedersen CB, Jedoui D, Jager A, Nolan GP, Gaipa G, Bendall SC, Bava FA, Davis KL. Dasatinib overcomes glucocorticoid resistance in B-cell acute lymphoblastic leukemia. Nat Commun 2023; 14:2935. [PMID: 37217509 DOI: 10.1038/s41467-023-38456-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 04/28/2023] [Indexed: 05/24/2023] Open
Abstract
Resistance to glucocorticoids (GC) is associated with an increased risk of relapse in B-cell progenitor acute lymphoblastic leukemia (BCP-ALL). Performing transcriptomic and single-cell proteomic studies in healthy B-cell progenitors, we herein identify coordination between the glucocorticoid receptor pathway with B-cell developmental pathways. Healthy pro-B cells most highly express the glucocorticoid receptor, and this developmental expression is conserved in primary BCP-ALL cells from patients at diagnosis and relapse. In-vitro and in vivo glucocorticoid treatment of primary BCP-ALL cells demonstrate that the interplay between B-cell development and the glucocorticoid pathways is crucial for GC resistance in leukemic cells. Gene set enrichment analysis in BCP-ALL cell lines surviving GC treatment show enrichment of B cell receptor signaling pathways. In addition, primary BCP-ALL cells surviving GC treatment in vitro and in vivo demonstrate a late pre-B cell phenotype with activation of PI3K/mTOR and CREB signaling. Dasatinib, a multi-kinase inhibitor, most effectively targets this active signaling in GC-resistant cells, and when combined with glucocorticoids, results in increased cell death in vitro and decreased leukemic burden and prolonged survival in an in vivo xenograft model. Targeting the active signaling through the addition of dasatinib may represent a therapeutic approach to overcome GC resistance in BCP-ALL.
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Affiliation(s)
- Jolanda Sarno
- Hematology, Oncology, Stem Cell Transplant, and Regenerative Medicine, Department of Pediatrics, Stanford University, Stanford, CA, USA.
| | - Pablo Domizi
- Hematology, Oncology, Stem Cell Transplant, and Regenerative Medicine, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Yuxuan Liu
- Hematology, Oncology, Stem Cell Transplant, and Regenerative Medicine, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Milton Merchant
- Hematology, Oncology, Stem Cell Transplant, and Regenerative Medicine, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Christina Bligaard Pedersen
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Dorra Jedoui
- Hematology, Oncology, Stem Cell Transplant, and Regenerative Medicine, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Astraea Jager
- Hematology, Oncology, Stem Cell Transplant, and Regenerative Medicine, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Giuseppe Gaipa
- M. Tettamanti Research Center, Fondazione IRCCS San Gerardo dei Tintori, Monza, (MB), Italy
| | - Sean C Bendall
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Felice-Alessio Bava
- Baxter Laboratory, Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
- Institut national de la santé et de la recherche médicale (INSERM), Paris, France
| | - Kara L Davis
- Hematology, Oncology, Stem Cell Transplant, and Regenerative Medicine, Department of Pediatrics, Stanford University, Stanford, CA, USA.
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13
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Kim Y, Greenleaf WJ, Bendall SC. Systems biology approaches to unravel lymphocyte subsets and function. Curr Opin Immunol 2023; 82:102323. [PMID: 37028221 DOI: 10.1016/j.coi.2023.102323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/11/2023] [Accepted: 03/13/2023] [Indexed: 04/09/2023]
Abstract
Single-cell technologies have revealed the extensive heterogeneity and complexity of the immune system. Systems biology approaches in immunology have taken advantage of the high-parameter, high-throughput data and analyzed immune cell types in a 'bottom-up' data-driven method. This approach has discovered previously unrecognized cell types and functions. Especially for human immunology, in which experimental manipulations are challenging, systems approach has become a successful means to investigate physiologically relevant contexts. This review focuses on the recent findings in lymphocyte biology, from their development, differentiation into subsets, and heterogeneity in their functions, enabled by these systems approaches. Furthermore, we review examples of the application of findings from systems approach studies and discuss how now to leave the rich dataset in the curse of high dimensionality.
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Affiliation(s)
- YeEun Kim
- Immunology Graduate Program, Stanford University, Stanford, CA, USA; Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Sean C Bendall
- Department of Pathology, Stanford University, Stanford, CA, USA.
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14
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Chowdhury RR, Valainis JR, Dubey M, von Boehmer L, Sola E, Wilhelmy J, Guo J, Kask O, Ohanyan M, Sun M, Huang H, Huang X, Nguyen PK, Scriba TJ, Davis MM, Bendall SC, Chien YH. NK-like CD8 + γδ T cells are expanded in persistent Mycobacterium tuberculosis infection. Sci Immunol 2023; 8:eade3525. [PMID: 37000856 PMCID: PMC10408713 DOI: 10.1126/sciimmunol.ade3525] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 03/09/2023] [Indexed: 04/03/2023]
Abstract
The response of gamma delta (γδ) T cells in the acute versus chronic phases of the same infection is unclear. How γδ T cells function in acute Mycobacterium tuberculosis (Mtb) infection is well characterized, but their response during persistent Mtb infection is not well understood, even though most infections with Mtb manifest as a chronic, clinically asymptomatic state. Here, we analyze peripheral blood γδ T cells from a South African adolescent cohort and show that a unique CD8+ γδ T cell subset with features of "memory inflation" expands in chronic Mtb infection. These cells are hyporesponsive to T cell receptor (TCR)-mediated signaling but, like NK cells, can mount robust CD16-mediated cytotoxic responses. These CD8+ γδ T cells comprise a highly focused TCR repertoire, with clonotypes that are Mycobacterium specific but not phosphoantigen reactive. Using multiparametric single-cell pseudo-time trajectory analysis, we identified the differentiation paths that these CD8+ γδ T cells follow to develop into effectors in this infection state. Last, we found that circulating CD8+ γδ T cells also expand in other chronic inflammatory conditions, including cardiovascular disease and cancer, suggesting that persistent antigenic exposure may drive similar γδ T cell effector programs and differentiation fates.
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Affiliation(s)
- Roshni Roy Chowdhury
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
- Program in Immunology, Stanford University, Stanford, CA, USA
- Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
| | | | - Megha Dubey
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Lotta von Boehmer
- Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, CA, USA
| | - Elsa Sola
- Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, CA, USA
| | - Julie Wilhelmy
- Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, CA, USA
| | - Jing Guo
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Oliver Kask
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Mane Ohanyan
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Meng Sun
- Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, CA, USA
| | - Huang Huang
- Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, CA, USA
| | - Xianxi Huang
- Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA
- The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Patricia K. Nguyen
- Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA
| | - Thomas J. Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Mark M. Davis
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
- Program in Immunology, Stanford University, Stanford, CA, USA
- Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, CA, USA
- The Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Sean C. Bendall
- Program in Immunology, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Yueh-hsiu Chien
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
- Program in Immunology, Stanford University, Stanford, CA, USA
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15
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Robinson ML, Glass DR, Duran V, Agudelo Rojas OL, Sanz AM, Consuegra M, Sahoo MK, Hartmann FJ, Bosse M, Gelvez RM, Bueno N, Pinsky BA, Montoya JG, Maecker H, Estupiñan Cardenas MI, Villar Centeno LA, Garrido EMR, Rosso F, Bendall SC, Einav S. Magnitude and kinetics of the human immune cell response associated with severe dengue progression by single-cell proteomics. Sci Adv 2023; 9:eade7702. [PMID: 36961888 PMCID: PMC10038348 DOI: 10.1126/sciadv.ade7702] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 02/21/2023] [Indexed: 06/17/2023]
Abstract
Approximately 5 million dengue virus-infected patients progress to a potentially life-threatening severe dengue (SD) infection annually. To identify the immune features and temporal dynamics underlying SD progression, we performed deep immune profiling by mass cytometry of PBMCs collected longitudinally from SD progressors (SDp) and uncomplicated dengue (D) patients. While D is characterized by early activation of innate immune responses, in SDp there is rapid expansion and activation of IgG-secreting plasma cells and memory and regulatory T cells. Concurrently, SDp, particularly children, demonstrate increased proinflammatory NK cells, inadequate expansion of CD16+ monocytes, and high expression of the FcγR CD64 on myeloid cells, yet a signature of diminished antigen presentation. Syndrome-specific determinants include suppressed dendritic cell abundance in shock/hemorrhage versus enriched plasma cell expansion in organ impairment. This study reveals uncoordinated immune responses in SDp and provides insights into SD pathogenesis in humans with potential implications for prediction and treatment.
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Affiliation(s)
- Makeda L. Robinson
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - David R. Glass
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Veronica Duran
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, 499 Illinois St., 4th Floor, San Francisco, CA 94158, USA
| | | | - Ana Maria Sanz
- Clinical Research Center, Fundación Valle del Lili, Cali, Colombia
| | - Monika Consuegra
- Centro de Atención y Diagnóstico de Enfermedades Infecciosas (CDI), Fundación INFOVIDA, Bucaramanga, Colombia
| | - Malaya Kumar Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Felix J. Hartmann
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Marc Bosse
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Rosa Margarita Gelvez
- Centro de Atención y Diagnóstico de Enfermedades Infecciosas (CDI), Fundación INFOVIDA, Bucaramanga, Colombia
| | - Nathalia Bueno
- Centro de Atención y Diagnóstico de Enfermedades Infecciosas (CDI), Fundación INFOVIDA, Bucaramanga, Colombia
| | - Benjamin A. Pinsky
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jose G. Montoya
- Palo Alto Medical Foundation, Dr. Jack S. Remington Laboratory for Specialty Diagnostics, Palo Alto, CA, USA
| | - Holden Maecker
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Luis Angel Villar Centeno
- Centro de Atención y Diagnóstico de Enfermedades Infecciosas (CDI), Fundación INFOVIDA, Bucaramanga, Colombia
| | - Elsa Marina Rojas Garrido
- Centro de Atención y Diagnóstico de Enfermedades Infecciosas (CDI), Fundación INFOVIDA, Bucaramanga, Colombia
| | - Fernando Rosso
- Clinical Research Center, Fundación Valle del Lili, Cali, Colombia
- Department of Internal Medicine, Division of Infectious Diseases, Fundación Valle del Lili, Cali, Colombia
| | - Sean C. Bendall
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Shirit Einav
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, 499 Illinois St., 4th Floor, San Francisco, CA 94158, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
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16
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Piyadasa H, Angelo M, Bendall SC. Spatial proteomics of tumor microenvironments reveal why location matters. Nat Immunol 2023; 24:565-566. [PMID: 36959293 DOI: 10.1038/s41590-023-01471-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Affiliation(s)
- Hadeesha Piyadasa
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Michael Angelo
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA.
| | - Sean C Bendall
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA.
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17
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Munson PV, Adamik J, Hartmann FJ, Favaro PMB, Ho D, Bendall SC, Combes AJ, Krummel MF, Zhang K, Kelley RK, Butterfield LH. Polyunsaturated fatty acid-bound alpha-fetoprotein promotes immune suppression by altering human dendritic cell metabolism. Cancer Res 2023; 83:1543-1557. [PMID: 36847613 PMCID: PMC10152238 DOI: 10.1158/0008-5472.can-22-3551] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 01/04/2023] [Accepted: 02/21/2023] [Indexed: 03/01/2023]
Abstract
Alpha-fetoprotein (AFP) is expressed by stem-like and poor outcome hepatocellular cancer tumors and is a clinical tumor biomarker. AFP has been demonstrated to inhibit dendritic cell differentiation and maturation and to block oxidative phosphorylation. To identify the critical metabolic pathways leading to human dendritic cell functional suppression, here we utilized two recently described single cell profiling methods, scMEP (single-cell metabolic profiling) and SCENITH (single-cell energetic metabolism by profiling translation inhibition). Glycolytic capacity and glucose dependence of dendritic cells was significantly increased by tumor-derived, but not normal cord blood-derived, AFP, leading to increased glucose uptake and lactate secretion. Key molecules in the electron transport chain in particular were regulated by tumor-derived AFP. These metabolic changes occurred at mRNA and protein levels, with negative impact on dendritic cell stimulatory capacity. Tumor-derived AFP bound significantly more polyunsaturated fatty acids than cord blood-derived AFP. Polyunsaturated fatty acids bound to AFP increased metabolic skewing and promoted dendritic cell functional suppression. Polyunsaturated fatty acids inhibited dendritic cell differentiation in vitro, and ω-6 polyunsaturated fatty acids conferred potent immunoregulation when bound to tumor-derived AFP. Together, these findings provide mechanistic insights into how AFP antagonizes the innate immune response to limit anti-tumor immunity.
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Affiliation(s)
- Paul V Munson
- University of California San Francisco Medical Center, San Francisco, CA, United States
| | - Juraj Adamik
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, United States
| | | | | | - Daniel Ho
- Stanford University, Stanford, CA, United States
| | | | | | - Matthew F Krummel
- University of California, San Francisco, San Francisco, CA, United States
| | - Karen Zhang
- University of California, San Francisco, San Francisco, CA, United States
| | - Robin K Kelley
- University of California, San Francisco, San Francisco, CA, United States
| | - Lisa H Butterfield
- University of California San Francisco Medical Center, San Francisco, CA, United States
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18
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Moore AR, Vivanco Gonzalez N, Plummer KA, Mitchel OR, Kaur H, Rivera M, Collica B, Goldston M, Filiz F, Angelo M, Palmer TD, Bendall SC. Gestationally dependent immune organization at the maternal-fetal interface. Cell Rep 2022; 41:111651. [PMID: 36384130 PMCID: PMC9681661 DOI: 10.1016/j.celrep.2022.111651] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 04/13/2022] [Accepted: 10/20/2022] [Indexed: 11/17/2022] Open
Abstract
The immune system and placenta have a dynamic relationship across gestation to accommodate fetal growth and development. High-resolution characterization of this maternal-fetal interface is necessary to better understand the immunology of pregnancy and its complications. We developed a single-cell framework to simultaneously immuno-phenotype circulating, endovascular, and tissue-resident cells at the maternal-fetal interface throughout gestation, discriminating maternal and fetal contributions. Our data reveal distinct immune profiles across the endovascular and tissue compartments with tractable dynamics throughout gestation that respond to a systemic immune challenge in a gestationally dependent manner. We uncover a significant role for the innate immune system where phagocytes and neutrophils drive temporal organization of the placenta through remarkably diverse populations, including PD-L1+ subsets having compartmental and early gestational bias. Our approach and accompanying datasets provide a resource for additional investigations into gestational immunology and evoke a more significant role for the innate immune system in establishing the microenvironment of early pregnancy.
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Affiliation(s)
- Amber R Moore
- Immunology Graduate Program, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA; Department of Neurosurgery, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Nora Vivanco Gonzalez
- Immunology Graduate Program, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA; Department of Neurosurgery, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Katherine A Plummer
- Department of Neurosurgery, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Olivia R Mitchel
- Department of Neurosurgery, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Harleen Kaur
- Department of Neurosurgery, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Moises Rivera
- Department of Neurosurgery, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Brian Collica
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Mako Goldston
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Ferda Filiz
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Michael Angelo
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Theo D Palmer
- Department of Neurosurgery, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA.
| | - Sean C Bendall
- Immunology Graduate Program, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA.
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19
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Vijayaragavan K, Cannon BJ, Tebaykin D, Bossé M, Baranski A, Oliveria JP, Bukhari SA, Mrdjen D, Corces MR, McCaffrey EF, Greenwald NF, Sigal Y, Marquez D, Khair Z, Bruce T, Goldston M, Bharadwaj A, Montine KS, Angelo RM, Montine TJ, Bendall SC. Single-cell spatial proteomic imaging for human neuropathology. Acta Neuropathol Commun 2022; 10:158. [PMID: 36333818 PMCID: PMC9636771 DOI: 10.1186/s40478-022-01465-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
Neurodegenerative disorders are characterized by phenotypic changes and hallmark proteopathies. Quantifying these in archival human brain tissues remains indispensable for validating animal models and understanding disease mechanisms. We present a framework for nanometer-scale, spatial proteomics with multiplex ion beam imaging (MIBI) for capturing neuropathological features. MIBI facilitated simultaneous, quantitative imaging of 36 proteins on archival human hippocampus from individuals spanning cognitively normal to dementia. Customized analysis strategies identified cell types and proteopathies in the hippocampus across stages of Alzheimer's disease (AD) neuropathologic change. We show microglia-pathologic tau interactions in hippocampal CA1 subfield in AD dementia. Data driven, sample independent creation of spatial proteomic regions identified persistent neurons in pathologic tau neighborhoods expressing mitochondrial protein MFN2, regardless of cognitive status, suggesting a survival advantage. Our study revealed unique insights from multiplexed imaging and data-driven approaches for neuropathologic analysis and serves broadly as a methodology for spatial proteomic analysis of archival human neuropathology. TEASER: Multiplex Ion beam Imaging enables deep spatial phenotyping of human neuropathology-associated cellular and disease features.
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Affiliation(s)
| | - Bryan J Cannon
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Dmitry Tebaykin
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Marc Bossé
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Alex Baranski
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - J P Oliveria
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Syed A Bukhari
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Dunja Mrdjen
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | | | - Erin F McCaffrey
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Noah F Greenwald
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | | | - Diana Marquez
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Zumana Khair
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Trevor Bruce
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Mako Goldston
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Anusha Bharadwaj
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Kathleen S Montine
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - R Michael Angelo
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Thomas J Montine
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Sean C Bendall
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA.
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20
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Good Z, Spiegel JY, Sahaf B, Malipatlolla MB, Ehlinger ZJ, Kurra S, Desai MH, Reynolds WD, Wong Lin A, Vandris P, Wu F, Prabhu S, Hamilton MP, Tamaresis JS, Hanson PJ, Patel S, Feldman SA, Frank MJ, Baird JH, Muffly L, Claire GK, Craig J, Kong KA, Wagh D, Coller J, Bendall SC, Tibshirani RJ, Plevritis SK, Miklos DB, Mackall CL. Post-infusion CAR T Reg cells identify patients resistant to CD19-CAR therapy. Nat Med 2022; 28:1860-1871. [PMID: 36097223 PMCID: PMC10917089 DOI: 10.1038/s41591-022-01960-7] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/19/2022] [Indexed: 12/28/2022]
Abstract
Approximately 60% of patients with large B cell lymphoma treated with chimeric antigen receptor (CAR) T cell therapies targeting CD19 experience disease progression, and neurotoxicity remains a challenge. Biomarkers associated with resistance and toxicity are limited. In this study, single-cell proteomic profiling of circulating CAR T cells in 32 patients treated with CD19-CAR identified that CD4+Helios+ CAR T cells on day 7 after infusion are associated with progressive disease and less severe neurotoxicity. Deep profiling demonstrated that this population is non-clonal and manifests hallmark features of T regulatory (TReg) cells. Validation cohort analysis upheld the link between higher CAR TReg cells with clinical progression and less severe neurotoxicity. A model combining expansion of this subset with lactate dehydrogenase levels, as a surrogate for tumor burden, was superior for predicting durable clinical response compared to models relying on each feature alone. These data credential CAR TReg cell expansion as a novel biomarker of response and toxicity after CAR T cell therapy and raise the prospect that this subset may regulate CAR T cell responses in humans.
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Affiliation(s)
- Zinaida Good
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
- Parker Institute for Cancer Immunotherapy, Stanford University School of Medicine, Stanford, CA, USA
| | - Jay Y Spiegel
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Blood and Marrow Transplantation and Cellular Therapy, Stanford University School of Medicine, Stanford, CA, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Bita Sahaf
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Meena B Malipatlolla
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Zach J Ehlinger
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Sreevidya Kurra
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Homer Stryker M.D. School of Medicine, Western Michigan University, Kalamazoo, MI, USA
| | - Moksha H Desai
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Warren D Reynolds
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Anita Wong Lin
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Cancer Research Lab, Flow Cytometry Core Facility, University of California, Berkeley, Berkeley, CA, USA
| | - Panayiotis Vandris
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Fang Wu
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Snehit Prabhu
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Mark P Hamilton
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Blood and Marrow Transplantation and Cellular Therapy, Stanford University School of Medicine, Stanford, CA, USA
| | - John S Tamaresis
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Paul J Hanson
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Blood and Marrow Transplantation and Cellular Therapy, Stanford University School of Medicine, Stanford, CA, USA
| | - Shabnum Patel
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Laboratory for Cell and Gene Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Syncopation Life Sciences, San Mateo, CA, USA
| | - Steven A Feldman
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Laboratory for Cell and Gene Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew J Frank
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Blood and Marrow Transplantation and Cellular Therapy, Stanford University School of Medicine, Stanford, CA, USA
| | - John H Baird
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Blood and Marrow Transplantation and Cellular Therapy, Stanford University School of Medicine, Stanford, CA, USA
- Department of Hematology and Hematopoietic Cell Transplantation, Division of Lymphoma, City of Hope National Medical Center, Duarte, CA, USA
| | - Lori Muffly
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Blood and Marrow Transplantation and Cellular Therapy, Stanford University School of Medicine, Stanford, CA, USA
| | - Gursharan K Claire
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Blood and Marrow Transplantation and Cellular Therapy, Stanford University School of Medicine, Stanford, CA, USA
| | - Juliana Craig
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Blood and Marrow Transplantation and Cellular Therapy, Stanford University School of Medicine, Stanford, CA, USA
- School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
| | - Katherine A Kong
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Dhananjay Wagh
- Stanford Genomics Facility, Stanford University School of Medicine, Stanford, CA, USA
| | - John Coller
- Stanford Genomics Facility, Stanford University School of Medicine, Stanford, CA, USA
| | - Sean C Bendall
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Parker Institute for Cancer Immunotherapy, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Robert J Tibshirani
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
- Department of Statistics, Stanford University, Stanford, CA, USA
| | - Sylvia K Plevritis
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
- Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
| | - David B Miklos
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Medicine, Division of Blood and Marrow Transplantation and Cellular Therapy, Stanford University School of Medicine, Stanford, CA, USA.
| | - Crystal L Mackall
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.
- Parker Institute for Cancer Immunotherapy, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Medicine, Division of Blood and Marrow Transplantation and Cellular Therapy, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
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21
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Ulicna L, Kimmey SC, Weber CM, Allard GM, Wang A, Bui NQ, Bendall SC, Crabtree GR, Bean GR, Van Rechem C. The Interaction of SWI/SNF with the Ribosome Regulates Translation and Confers Sensitivity to Translation Pathway Inhibitors in Cancers with Complex Perturbations. Cancer Res 2022; 82:2829-2837. [PMID: 35749589 PMCID: PMC9379364 DOI: 10.1158/0008-5472.can-21-1360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 01/10/2022] [Accepted: 06/15/2022] [Indexed: 01/09/2023]
Abstract
Subunits from the chromatin remodelers mammalian SWItch/Sucrose Non-Fermentable (mSWI/SNF) are mutated, deleted, or amplified in more than 40% of cancers. Understanding their functions in normal cells and the consequences of cancerous alterations will provide insight into developing new targeted therapies. Here we examined whether mSWI/SNF mutations increase cellular sensitivity to specific drugs. Taking advantage of the DepMap studies, we demonstrate that cancer cells harboring mutations of specific mSWI/SNF subunits exhibit a genetic dependency on translation factors and are sensitive to translation pathway inhibitors. Furthermore, mSWI/SNF subunits were present in the cytoplasm and interacted with the translation initiation machinery, and short-term inhibition and depletion of specific subunits decreased global translation, implicating a direct role for these factors in translation. Depletion of specific mSWI/SNF subunits also increased sensitivity to mTOR-PI3K inhibitors. In patient-derived breast cancer samples, mSWI/SNF subunits expression in both the nucleus and the cytoplasm was substantially altered. In conclusion, an unexpected cytoplasmic role for mSWI/SNF complexes in translation suggests potential new therapeutic opportunities for patients afflicted by cancers demonstrating alterations in their subunits. SIGNIFICANCE This work establishes direct functions for mSWI/SNF in translation and demonstrates that alterations in mSWI/SNF confer a therapeutic vulnerability to translation pathway inhibitors in cancer cells.
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Affiliation(s)
- Livia Ulicna
- Department of Pathology, Stanford University, Stanford, California
| | - Samuel C. Kimmey
- Department of Pathology, Stanford University, Stanford, California.,Department of Medicine/Oncology, Stanford University, Stanford, California
| | | | - Grace M. Allard
- Department of Pathology, Stanford University, Stanford, California
| | - Aihui Wang
- Department of Pathology, Stanford University, Stanford, California
| | - Nam Q. Bui
- Department of Medicine/Oncology, Stanford University, Stanford, California
| | - Sean C. Bendall
- Department of Pathology, Stanford University, Stanford, California
| | - Gerald R. Crabtree
- Department of Pathology, Stanford University, Stanford, California.,Department of Developmental Biology, Stanford University, Stanford, California
| | - Gregory R. Bean
- Department of Pathology, Stanford University, Stanford, California
| | - Capucine Van Rechem
- Department of Pathology, Stanford University, Stanford, California.,Corresponding Author: Capucine Van Rechem, Ph.D. Stanford Medicine Department of Pathology, 269 Campus Drive, CCSR-3245C, Stanford, CA 94305-5176. Phone: 650-723-7698; E-mail:
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22
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Ramakrishna S, Kaczanowska S, Murty T, Contreras CF, Merchant M, Glod J, Gutierrez N, Alimadadi A, Stroncek D, Highfill S, Duault C, Subrahmanyam PB, Holmes T, Reynolds W, Baskar R, Barge A, Lyon H, Moravec R, Ranasinghe S, Yu J, Biswas R, Pollack S, Van Nostrand S, Lindsay J, Pichavant M, Sahaf B, Bendall SC, Gentles AJ, Maecker H, Hedrick CC, Mackall C, Kaplan R. Abstract CT142: GD2.Ox40.CD28.z CAR T cell trial in neuroblastoma and osteosarcoma. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-ct142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Chimeric antigen receptor T cells (CARTs) hold promising therapeutic potential for refractory tumors. GD2 is a tumor antigen expressed on neuroblastoma and osteosarcoma. In initial studies, T cells expressing 1st generation GD2-CARTs were shown to be safe and mediated modest antitumor activity in some patients with refractory neuroblastoma.
Methods: We developed a 3rd generation GD2-CART (GD2-CAR.OX40.28.z.ICD9) and conducted a phase I trial (NCT02107963) to determine the feasibility of producing and safety of administering escalating doses of GD2-CARTs in children and young adults with GD2+ solid tumors, including neuroblastoma and osteosarcoma, following cyclophosphamide-based lymphodepletion. Patient samples were evaluated for cytokine profile kinetics, immune phenotype analysis with mass cytometry (CyTOF), transcriptomic evaluation with RNA-sequencing (RNA-seq), epigenetic determination with Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq), and functional studies with flow cytometry.
Results: 15 patients aged 8-28 years were enrolled on four dose levels, of which 13 patients were infused. No dose-limiting toxicities were observed and administration of up to 1x107 GD2-CART/kg was feasible and safe for children and young adults with neuroblastoma and osteosarcoma. 15.4% (2/13) of patients experienced grade-1 cytokine release syndrome (CRS) and no neurological toxicity was observed. We measured the expansion and persistence of adoptively transferred GD2-CARTs in the peripheral blood. GD2-CARTs expanded in all patients receiving treatment, half of whom had expansion similar to that seen in clinically active CD19 and CD22 CARTs, but the GD2-CARTs had limited persistence. At Day 28 following GD2-CART infusion, 23.1% (3/13) of evaluable patients had progressive disease and 76.9% (10/13) had stable disease (SD). 3/10 SD patients remained stable at 60 days post-GD2-CART, but all patients eventually progressed. Since a major barrier to CART efficacy is inadequate CART expansion, we comprehensively evaluated for phenotypic, transcriptomic, and epigenetic immune profiles of patient apheresis, CART product, and post-treatment peripheral blood samples to identify determinants of CART expansion. GD2-CART expansion is significantly correlated with several T cell markers, and a larger baseline naïve and central memory T cell pool. Unique myeloid populations are associated with CART expansion. ATACseq identifies epigenetic differences in pre-treatment apheresis that may predict good CAR expansion in patients.
Conclusions: GD2-CART therapy following cyclophosphamide conditioning was well tolerated at all four dose levels in pediatric and young adult patients with neuroblastoma and osteosarcoma. Subsequent multi-dimensional analyses suggest key mechanisms underlying CART biology and function and highlight the potential of defining and applying molecular signatures in apheresis and CART product as biomarkers and prognostic indicators of CART expansion, with promise for advancing immunotherapies for solid tumor patients in the future.
Citation Format: Sneha Ramakrishna, Sabina Kaczanowska, Tara Murty, Cristina F. Contreras, Melinda Merchant, John Glod, Norma Gutierrez, Ahmad Alimadadi, David Stroncek, Steven Highfill, Caroline Duault, Priyanka B. Subrahmanyam, Tyson Holmes, Warren Reynolds, Reema Baskar, Antoine Barge, Hayley Lyon, Radim Moravec, Srinika Ranasinghe, Joyce Yu, Roshni Biswas, Samuel Pollack, Stephen Van Nostrand, James Lindsay, Mina Pichavant, Bita Sahaf, Sean C. Bendall, Andrew J. Gentles, Holden Maecker, Catherine C. Hedrick, Crystal Mackall, Rosandra Kaplan. GD2.Ox40.CD28.z CAR T cell trial in neuroblastoma and osteosarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr CT142.
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Affiliation(s)
- Sneha Ramakrishna
- 1Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | - Sabina Kaczanowska
- 2Pediatric Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD
| | - Tara Murty
- 1Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | | | | | - John Glod
- 2Pediatric Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD
| | | | | | - David Stroncek
- 5Center for Cellular Engineering, Department of Transfusion Medicine, NIH Clinical Center, Bethesda, MD
| | - Steven Highfill
- 5Center for Cellular Engineering, Department of Transfusion Medicine, NIH Clinical Center, Bethesda, MD
| | - Caroline Duault
- 6Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA
| | - Priyanka B. Subrahmanyam
- 6Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA
| | - Tyson Holmes
- 7Stanford Human Immune Monitoring Center, Stanford University School of Medicine, Stanford, CA
| | - Warren Reynolds
- 8Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Palo Alto, CA
| | - Reema Baskar
- 9Stanford University School of Medicine, Stanford, CA
| | - Antoine Barge
- 10Department of Medicine (Biomedical Informatics/Quantitative Sciences unit), Stanford University School of Medicine, Stanford, CA
| | | | | | | | - Joyce Yu
- 13Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | | | | | - Bita Sahaf
- 1Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | - Sean C. Bendall
- 14Department of Pathology, Stanford University, Stanford, CA
| | - Andrew J. Gentles
- 10Department of Medicine (Biomedical Informatics/Quantitative Sciences unit), Stanford University School of Medicine, Stanford, CA
| | - Holden Maecker
- 6Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA
| | | | - Crystal Mackall
- 1Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | - Rosandra Kaplan
- 2Pediatric Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD
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23
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Vivanco Gonzalez N, Oliveria JP, Tebaykin D, Ivison GT, Mukai K, Tsai MM, Borges L, Nadeau KC, Galli SJ, Tsai AG, Bendall SC. An optimized protocol for phenotyping human granulocytes by mass cytometry. STAR Protoc 2022; 3:101280. [PMID: 35434655 PMCID: PMC9010787 DOI: 10.1016/j.xpro.2022.101280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Nora Vivanco Gonzalez
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, United States
- Corresponding author
| | - John-Paul Oliveria
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, United States
- Department of Medicine, Division of Respirology, McMaster University, Hamilton, ON, L8S4K1, Canada
| | - Dmitry Tebaykin
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, United States
| | - Geoffrey T. Ivison
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, United States
| | - Kaori Mukai
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, United States
- Sean N. Parker Center for Allergy Research, School of Medicine, Stanford University, Stanford, CA, United States
| | - Mindy M. Tsai
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, United States
- Sean N. Parker Center for Allergy Research, School of Medicine, Stanford University, Stanford, CA, United States
| | - Luciene Borges
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, United States
| | - Kari C. Nadeau
- Sean N. Parker Center for Allergy Research, School of Medicine, Stanford University, Stanford, CA, United States
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, School of Medicine, Stanford University, Stanford, CA, United States
| | - Stephen J. Galli
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, United States
- Sean N. Parker Center for Allergy Research, School of Medicine, Stanford University, Stanford, CA, United States
- Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA, United States
| | - Albert G. Tsai
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, United States
| | - Sean C. Bendall
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, United States
- Corresponding author
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24
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McCaffrey EF, Donato M, Keren L, Chen Z, Delmastro A, Fitzpatrick MB, Gupta S, Greenwald NF, Baranski A, Graf W, Kumar R, Bosse M, Fullaway CC, Ramdial PK, Forgó E, Jojic V, Van Valen D, Mehra S, Khader SA, Bendall SC, van de Rijn M, Kalman D, Kaushal D, Hunter RL, Banaei N, Steyn AJC, Khatri P, Angelo M. Author Correction: The immunoregulatory landscape of human tuberculosis granulomas. Nat Immunol 2022; 23:814. [PMID: 35277696 PMCID: PMC9098386 DOI: 10.1038/s41590-022-01178-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Erin F McCaffrey
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michele Donato
- Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Leeat Keren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Zhenghao Chen
- Calico Life Sciences LLC, South San Francisco, CA, USA
| | - Alea Delmastro
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Sanjana Gupta
- Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Noah F Greenwald
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Alex Baranski
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - William Graf
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA, USA
| | - Rashmi Kumar
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Marc Bosse
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Pratista K Ramdial
- Africa Health Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Erna Forgó
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - David Van Valen
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA, USA
| | - Smriti Mehra
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Shabaana A Khader
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Sean C Bendall
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Matt van de Rijn
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel Kalman
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Deepak Kaushal
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Robert L Hunter
- Department of Pathology and Laboratory Medicine, University of Texas Health Sciences Center at Houston, Houston, TX, USA
| | - Niaz Banaei
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Division of Infectious Diseases & Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Adrie J C Steyn
- Africa Health Research Institute, University of KwaZulu-Natal, Durban, South Africa
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Purvesh Khatri
- Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael Angelo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
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25
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Glass MC, Glass DR, Oliveria JP, Mbiribindi B, Esquivel CO, Krams SM, Bendall SC, Martinez OM. Human IL-10-producing B cells have diverse states that are induced from multiple B cell subsets. Cell Rep 2022; 39:110728. [PMID: 35443184 PMCID: PMC9107325 DOI: 10.1016/j.celrep.2022.110728] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 02/13/2022] [Accepted: 03/31/2022] [Indexed: 02/04/2023] Open
Abstract
Regulatory B cells (Bregs) suppress immune responses through the secretion of interleukin-10 (IL-10). This immunomodulatory capacity holds therapeutic potential, yet a definitional immunophenotype for enumeration and prospective isolation of B cells capable of IL-10 production remains elusive. Here, we simultaneously quantify cytokine production and immunophenotype in human peripheral B cells across a range of stimulatory conditions and time points using mass cytometry. Our analysis shows that multiple functional B cell subsets produce IL-10 and that no phenotype uniquely identifies IL-10+ B cells. Further, a significant portion of IL-10+ B cells co-express the pro-inflammatory cytokines IL-6 and tumor necrosis factor alpha (TNFα). Despite this heterogeneity, operationally tolerant liver transplant recipients have a unique enrichment of IL-10+, but not TNFα+ or IL-6+, B cells compared with transplant recipients receiving immunosuppression. Thus, human IL-10-producing B cells constitute an induced, transient state arising from a diversity of B cell subsets that may contribute to maintenance of immune homeostasis.
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Affiliation(s)
- Marla C Glass
- Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA; Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - David R Glass
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Immunology Graduate Program, Stanford University, Stanford, CA, USA
| | - John-Paul Oliveria
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Department of Medicine, Division of Respirology, McMaster University, Hamilton, ON, Canada
| | - Berenice Mbiribindi
- Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA; Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Carlos O Esquivel
- Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Sheri M Krams
- Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA; Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Sean C Bendall
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Olivia M Martinez
- Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA; Immunology, Stanford University School of Medicine, Stanford, CA, USA.
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26
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Fragiadakis GK, Bjornson-Hooper ZB, Madhireddy D, Sachs K, Chen H, McIlwain DR, Spitzer MH, Bendall SC, Nolan GP. Variation of Immune Cell Responses in Humans Reveals Sex-Specific Coordinated Signaling Across Cell Types. Front Immunol 2022; 13:867016. [PMID: 35419006 PMCID: PMC8995898 DOI: 10.3389/fimmu.2022.867016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 02/28/2022] [Indexed: 12/28/2022] Open
Abstract
Assessing the health and competence of the immune system is central to evaluating vaccination responses, autoimmune conditions, cancer prognosis, and treatment. With an increasing number of studies examining immune dysregulation, there is a growing need for a curated reference of variation in immune parameters in healthy individuals. We used mass cytometry (CyTOF) to profile blood from 86 humans in response to 15 ex vivo immune stimuli. We present reference ranges for cell-specific immune markers and highlight differences that appear across sex and age. We identified modules of immune features that suggest there exists an underlying structure to the immune system based on signaling pathway responses across cell types. We observed increased MAPK signaling in inflammatory pathways in innate immune cells and greater overall coordination of immune cell responses in females. In contrast, males exhibited stronger pSTAT1 and pTBK1 responses. These reference data are publicly available as a resource for immune profiling studies.
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Affiliation(s)
- Gabriela K Fragiadakis
- Department of Microbiology & Immunology, Stanford University, Stanford, CA, United States.,Department of Medicine, Division of Rheumatology, University of California San Francisco, San Francisco, CA, United States.,CoLabs, University of California San Francisco, San Francisco, CA, United States.,Bakar ImmunoX Initiative, University of California San Francisco, San Francisco, CA, United States
| | | | - Deepthi Madhireddy
- Department of Microbiology & Immunology, Stanford University, Stanford, CA, United States
| | - Karen Sachs
- Department of Microbiology & Immunology, Stanford University, Stanford, CA, United States
| | - Han Chen
- Department of Microbiology & Immunology, Stanford University, Stanford, CA, United States
| | - David R McIlwain
- Department of Microbiology & Immunology, Stanford University, Stanford, CA, United States
| | - Matthew H Spitzer
- Immunology Program, Stanford University, Stanford, CA, United States.,Department of Otolaryngology - Head and Neck Surgery, University of California, San Francisco, San Francisco, CA, United States.,Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, United States.,Parker Institute for Cancer Immunotherapy, San Francisco, CA, United States.,Chan Zuckerberg Biohub, San Francisco, CA, United States
| | - Sean C Bendall
- Department of Pathology, Stanford University, Stanford, CA, United States
| | - Garry P Nolan
- Department of Microbiology & Immunology, Stanford University, Stanford, CA, United States.,Department of Pathology, Stanford University, Stanford, CA, United States
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27
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Baskar R, Chen AF, Favaro P, Reynolds W, Mueller F, Borges L, Jiang S, Park HS, Kool ET, Greenleaf WJ, Bendall SC. Integrating transcription-factor abundance with chromatin accessibility in human erythroid lineage commitment. Cell Rep Methods 2022; 2:100188. [PMID: 35463156 PMCID: PMC9017139 DOI: 10.1016/j.crmeth.2022.100188] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 01/20/2022] [Accepted: 03/01/2022] [Indexed: 01/01/2023]
Abstract
Master transcription factors (TFs) directly regulate present and future cell states by binding DNA regulatory elements and driving gene-expression programs. Their abundance influences epigenetic priming to different cell fates at the chromatin level, especially in the context of differentiation. In order to link TF protein abundance to changes in TF motif accessibility and open chromatin, we developed InTAC-seq, a method for simultaneous quantification of genome-wide chromatin accessibility and intracellular protein abundance in fixed cells. Our method produces high-quality data and is a cost-effective alternative to single-cell techniques. We showcase our method by purifying bone marrow (BM) progenitor cells based on GATA-1 protein levels and establish high GATA-1-expressing BM cells as both epigenetically and functionally similar to erythroid-committed progenitors.
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Affiliation(s)
- Reema Baskar
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
- Cancer Biology Program, Stanford University, Stanford, CA 94305, USA
| | - Amy F. Chen
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Patricia Favaro
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Warren Reynolds
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Fabian Mueller
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Luciene Borges
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Sizun Jiang
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Hyun Shin Park
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Eric T. Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
- ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - William J. Greenleaf
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Sean C. Bendall
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
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28
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Lo YC, Keyes TJ, Jager A, Sarno J, Domizi P, Majeti R, Sakamoto KM, Lacayo N, Mullighan CG, Waters J, Sahaf B, Bendall SC, Davis KL. CytofIn enables integrated analysis of public mass cytometry datasets using generalized anchors. Nat Commun 2022; 13:934. [PMID: 35177627 PMCID: PMC8854441 DOI: 10.1038/s41467-022-28484-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 01/27/2022] [Indexed: 11/09/2022] Open
Abstract
The increasing use of mass cytometry for analyzing clinical samples offers the possibility to perform comparative analyses across public datasets. However, challenges in batch normalization and data integration limit the comparison of datasets not intended to be analyzed together. Here, we present a data integration strategy, CytofIn, using generalized anchors to integrate mass cytometry datasets from the public domain. We show that low-variance controls, such as healthy samples and stable channels, are inherently homogeneous, robust against stimulation, and can serve as generalized anchors for batch correction. Single-cell quantification comparing mass cytometry data from 989 leukemia files pre- and post normalization with CytofIn demonstrates effective batch correction while recapitulating the gold-standard bead normalization. CytofIn integration of public cancer datasets enabled the comparison of immune features across histologies and treatments. We demonstrate the ability to integrate public datasets without necessitating identical control samples or bead standards for fast and robust analysis using CytofIn. Challenges in batch normalization and data integration limit the comparison of existing mass cytometry datasets. Here, the authors report CytofIn that can integrate mass cytometry datasets from the public domain and reveal cellular features associated with immune oncology by analyzing five public cancer datasets.
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Affiliation(s)
- Yu-Chen Lo
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Timothy J Keyes
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.,Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Astraea Jager
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Jolanda Sarno
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Pablo Domizi
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ravindra Majeti
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Kathleen M Sakamoto
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Norman Lacayo
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jeffrey Waters
- Center for Cancer Cellular Therapy, Cancer Correlative Sciences Unit, Stanford University School of Medicine, Stanford, CA, USA
| | - Bita Sahaf
- Center for Cancer Cellular Therapy, Cancer Correlative Sciences Unit, Stanford University School of Medicine, Stanford, CA, USA
| | - Sean C Bendall
- Center for Cancer Cellular Therapy, Cancer Correlative Sciences Unit, Stanford University School of Medicine, Stanford, CA, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kara L Davis
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA. .,Center for Cancer Cellular Therapy, Cancer Correlative Sciences Unit, Stanford University School of Medicine, Stanford, CA, USA.
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29
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Baskar R, Kimmey SC, Bendall SC. Revealing new biology from multiplexed, metal-isotope-tagged, single-cell readouts. Trends Cell Biol 2022; 32:501-512. [PMID: 35181197 DOI: 10.1016/j.tcb.2022.01.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 11/26/2022]
Abstract
Mass cytometry (MC) is a recent technology that pairs plasma-based ionization of cells in suspension with time-of-flight (TOF) mass spectrometry to sensitively quantify the single-cell abundance of metal-isotope-tagged affinity reagents to key proteins, RNA, and peptides. Given the ability to multiplex readouts (~50 per cell) and capture millions of cells per experiment, MC offers a robust way to assay rare, transitional cell states that are pertinent to human development and disease. Here, we review MC approaches that let us probe the dynamics of cellular regulation across multiple conditions and sample types in a single experiment. Additionally, we discuss current limitations and future extensions of MC as well as computational tools commonly used to extract biological insight from single-cell proteomic datasets.
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Affiliation(s)
- Reema Baskar
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Sam C Kimmey
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Sean C Bendall
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA.
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30
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Risom T, Glass DR, Averbukh I, Liu CC, Baranski A, Kagel A, McCaffrey EF, Greenwald NF, Rivero-Gutiérrez B, Strand SH, Varma S, Kong A, Keren L, Srivastava S, Zhu C, Khair Z, Veis DJ, Deschryver K, Vennam S, Maley C, Hwang ES, Marks JR, Bendall SC, Colditz GA, West RB, Angelo M. Transition to invasive breast cancer is associated with progressive changes in the structure and composition of tumor stroma. Cell 2022; 185:299-310.e18. [PMID: 35063072 PMCID: PMC8792442 DOI: 10.1016/j.cell.2021.12.023] [Citation(s) in RCA: 126] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 08/05/2021] [Accepted: 12/16/2021] [Indexed: 01/16/2023]
Abstract
Ductal carcinoma in situ (DCIS) is a pre-invasive lesion that is thought to be a precursor to invasive breast cancer (IBC). To understand the changes in the tumor microenvironment (TME) accompanying transition to IBC, we used multiplexed ion beam imaging by time of flight (MIBI-TOF) and a 37-plex antibody staining panel to interrogate 79 clinically annotated surgical resections using machine learning tools for cell segmentation, pixel-based clustering, and object morphometrics. Comparison of normal breast with patient-matched DCIS and IBC revealed coordinated transitions between four TME states that were delineated based on the location and function of myoepithelium, fibroblasts, and immune cells. Surprisingly, myoepithelial disruption was more advanced in DCIS patients that did not develop IBC, suggesting this process could be protective against recurrence. Taken together, this HTAN Breast PreCancer Atlas study offers insight into drivers of IBC relapse and emphasizes the importance of the TME in regulating these processes.
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Affiliation(s)
- Tyler Risom
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Department of Research Pathology, Genentech, South San Francisco, CA, USA
| | - David R Glass
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Inna Averbukh
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Candace C Liu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Alex Baranski
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Adam Kagel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Erin F McCaffrey
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Noah F Greenwald
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Siri H Strand
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Sushama Varma
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Alex Kong
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Leeat Keren
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Sucheta Srivastava
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Chunfang Zhu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Zumana Khair
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Deborah J Veis
- Departments of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Katherine Deschryver
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Sujay Vennam
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Carlo Maley
- Biodesign institute, Arizona State University, Tempe, AZ, USA
| | | | | | - Sean C Bendall
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Graham A Colditz
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Robert B West
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
| | - Michael Angelo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Departments of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA.
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31
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Gajera CR, Fernandez R, Postupna N, Montine KS, Keene CD, Bendall SC, Montine TJ. Mass Synaptometry: Applying Mass Cytometry to Single Synapse Analysis. Methods Mol Biol 2022; 2417:69-88. [PMID: 35099792 PMCID: PMC8820390 DOI: 10.1007/978-1-0716-1916-2_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Synaptic degeneration is one of the earliest and phenotypically most significant features associated with numerous neurodegenerative conditions, including Alzheimer's and Parkinson's diseases. Synaptic changes are also known to be important in neurocognitive disorders such as schizophrenia and autism spectrum disorders. Several labs, including ours, have demonstrated that conventional (fluorescence-based) flow cytometry of individual synaptosomes is a robust and reproducible method. However, the repertoire of probes needed to assess comprehensively the type of synapse, pathologic proteins (including protein products of risk genes discovered in GWAS), and markers of stress and injury far exceeds what is achievable with conventional flow cytometry. We recently developed a method that applies CyTOF (Cytometry by Time-Of-Flight mass spectrometry) to high-dimensional analysis of individual human synaptosomes, overcoming many of the multiplexing limitations of conventional flow cytometry. We call this new method Mass Synaptometry. Here we describe the preparation of synaptosomes from human and mouse brain, the generation and quality control of the "SynTOF" (Synapse by Time-Of-Flight mass spectrometry) antibody panel, the staining protocol, and CyTOF parameter setup for acquisition, post-acquisition processing, and analysis.
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Affiliation(s)
- Chandresh R. Gajera
- Department of Pathology, Stanford University Medical Center, Stanford, CA, United States
| | - Rosemary Fernandez
- Department of Pathology, Stanford University Medical Center, Stanford, CA, United States
| | - Nadia Postupna
- Department of Pathology, University of Washington, Seattle, WA, United States
| | - Kathleen S. Montine
- Department of Pathology, Stanford University Medical Center, Stanford, CA, United States
| | - C. Dirk Keene
- Department of Pathology, University of Washington, Seattle, WA, United States
| | - Sean C. Bendall
- Department of Pathology, Stanford University Medical Center, Stanford, CA, United States
| | - Thomas J. Montine
- Department of Pathology, Stanford University Medical Center, Stanford, CA, United States
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32
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Ivison GT, Vendrame E, Martínez-Colón GJ, Ranganath T, Vergara R, Zhao NQ, Martin MP, Bendall SC, Carrington M, Cyktor JC, McMahon DK, Eron J, Jones RB, Mellors JW, Bosch RJ, Gandhi RT, Holmes S, Blish CA. Natural Killer Cell Receptors and Ligands Are Associated With Markers of HIV-1 Persistence in Chronically Infected ART Suppressed Patients. Front Cell Infect Microbiol 2022; 12:757846. [PMID: 35223535 PMCID: PMC8866573 DOI: 10.3389/fcimb.2022.757846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 01/21/2022] [Indexed: 11/13/2022] Open
Abstract
The latent HIV-1 reservoir represents a major barrier to achieving a long-term antiretroviral therapy (ART)-free remission or cure for HIV-1. Natural Killer (NK) cells are innate immune cells that play a critical role in controlling viral infections and have been shown to be involved in preventing HIV-1 infection and, in those who are infected, delaying time to progression to AIDS. However, their role in limiting HIV-1 persistence on long term ART is still uncharacterized. To identify associations between markers of HIV-1 persistence and the NK cell receptor-ligand repertoire, we used twin mass cytometry panels to characterize the peripheral blood NK receptor-ligand repertoire in individuals with long-term antiretroviral suppression enrolled in the AIDS Clinical Trial Group A5321 study. At the time of testing, participants had been on ART for a median of 7 years, with virological suppression <50 copies/mL since at most 48 weeks on ART. We found that the NK cell receptor and ligand repertoires did not change across three longitudinal samples over one year-a median of 25 weeks and 50 weeks after the initial sampling. To determine the features of the receptor-ligand repertoire that associate with markers of HIV-1 persistence, we performed a LASSO normalized regression. This analysis revealed that the NK cell ligands CD58, HLA-B, and CRACC, as well as the killer cell immunoglobulin-like receptors (KIRs) KIR2DL1, KIR2DL3, and KIR2DS4 were robustly predictive of markers of HIV-1 persistence, as measured by total HIV-1 cell-associated DNA, HIV-1 cell-associated RNA, and single copy HIV-RNA assays. To characterize the roles of cell populations defined by multiple markers, we augmented the LASSO analysis with FlowSOM clustering. This analysis found that a less mature NK cell phenotype (CD16+CD56dimCD57-LILRB1-NKG2C-) was associated with lower HIV-1 cell associated DNA. Finally, we found that surface expression of HLA-Bw6 measured by CyTOF was associated with lower HIV-1 persistence. Genetic analysis revealed that this was driven by lower HIV-1 persistence in HLA-Bw4/6 heterozygotes. These findings suggest that there may be a role for NK cells in controlling HIV-1 persistence in individuals on long-term ART, which must be corroborated by future studies.
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Affiliation(s)
- Geoffrey T Ivison
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, United States.,Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States.,Program in Immunology, Stanford University School of Medicine, Stanford, CA, United States
| | - Elena Vendrame
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Giovanny J Martínez-Colón
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Thanmayi Ranganath
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Rosemary Vergara
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Nancy Q Zhao
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, United States.,Program in Immunology, Stanford University School of Medicine, Stanford, CA, United States
| | - Maureen P Martin
- Basic Science Program, Frederick National Laboratory for Cancer Research, National, Cancer Institute, Frederick, MD, United States.,Laboratory of Integrative Cancer, Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
| | - Sean C Bendall
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National, Cancer Institute, Frederick, MD, United States.,Laboratory of Integrative Cancer, Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States.,Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Boston, MA, United States
| | - Joshua C Cyktor
- Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, PA, United States
| | - Deborah K McMahon
- Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, PA, United States.,Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, United States
| | - Joseph Eron
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, NC, United States
| | - R Brad Jones
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - John W Mellors
- Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, PA, United States
| | - Ronald J Bosch
- Center for Biostatistics in AIDS Research, Harvard TH Chan School of Public Health, Boston, MA, United States
| | - Rajesh T Gandhi
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States.,Center for AIDS Research, Harvard University, Boston, MA, United States
| | - Susan Holmes
- Department of Statistics, School of Humanities and Sciences, Stanford University, Stanford, CA, United States
| | - Catherine A Blish
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, United States.,Chan Zuckerberg Biohub, San Francisco, CA, United States
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33
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Phongpreecha T, Gajera CR, Liu CC, Vijayaragavan K, Chang AL, Becker M, Fallahzadeh R, Fernandez R, Postupna N, Sherfield E, Tebaykin D, Latimer C, Shively CA, Register TC, Craft S, Montine KS, Fox EJ, Poston KL, Keene CD, Angelo M, Bendall SC, Aghaeepour N, Montine TJ. Single-synapse analyses of Alzheimer's disease implicate pathologic tau, DJ1, CD47, and ApoE. Sci Adv 2021; 7:eabk0473. [PMID: 34910503 PMCID: PMC8673771 DOI: 10.1126/sciadv.abk0473] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Synaptic molecular characterization is limited for Alzheimer’s disease (AD). Our newly invented mass cytometry–based method, synaptometry by time of flight (SynTOF), was used to measure 38 antibody probes in approximately 17 million single-synapse events from human brains without pathologic change or with pure AD or Lewy body disease (LBD), nonhuman primates (NHPs), and PS/APP mice. Synaptic molecular integrity in humans and NHP was similar. Although not detected in human synapses, Aβ was in PS/APP mice single-synapse events. Clustering and pattern identification of human synapses showed expected disease-specific differences, like increased hippocampal pathologic tau in AD and reduced caudate dopamine transporter in LBD, and revealed previously unidentified findings including increased hippocampal CD47 and lowered DJ1 in AD and higher ApoE in AD with dementia. Our results were independently supported by multiplex ion beam imaging of intact tissue. This highlights the higher depth and breadth of insight on neurodegenerative diseases obtainable through SynTOF.
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Affiliation(s)
- Thanaphong Phongpreecha
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | | | - Candace C. Liu
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Alan L. Chang
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Martin Becker
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Ramin Fallahzadeh
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | | | - Nadia Postupna
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Emily Sherfield
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Dmitry Tebaykin
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Caitlin Latimer
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Carol A. Shively
- Department of Pathology/Comparative Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Thomas C. Register
- Department of Pathology/Comparative Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Suzanne Craft
- Department of Internal Medicine–Geriatrics, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | | | - Edward J. Fox
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Kathleen L. Poston
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- Department of Neurosurgery, Stanford University, Stanford, CA, USA
| | - C. Dirk Keene
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Michael Angelo
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Sean C. Bendall
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Thomas J. Montine
- Department of Pathology, Stanford University, Stanford, CA, USA
- Corresponding author.
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Geeraerts X, Fernández-Garcia J, Hartmann FJ, de Goede KE, Martens L, Elkrim Y, Debraekeleer A, Stijlemans B, Vandekeere A, Rinaldi G, De Rycke R, Planque M, Broekaert D, Meinster E, Clappaert E, Bardet P, Murgaski A, Gysemans C, Nana FA, Saeys Y, Bendall SC, Laoui D, Van den Bossche J, Fendt SM, Van Ginderachter JA. Macrophages are metabolically heterogeneous within the tumor microenvironment. Cell Rep 2021; 37:110171. [DOI: 10.1016/j.celrep.2021.110171] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 08/26/2021] [Accepted: 12/03/2021] [Indexed: 12/13/2022] Open
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Liu CC, McCaffrey EF, Greenwald NF, Soon E, Risom T, Vijayaragavan K, Oliveria JP, Mrdjen D, Bosse M, Tebaykin D, Bendall SC, Angelo M. Multiplexed Ion Beam Imaging: Insights into Pathobiology. Annu Rev Pathol 2021; 17:403-423. [PMID: 34752710 DOI: 10.1146/annurev-pathmechdis-030321-091459] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Next-generation tools for multiplexed imaging have driven a new wave of innovation in understanding how single-cell function and tissue structure are interrelated. In previous work, we developed multiplexed ion beam imaging by time of flight, a highly multiplexed platform that uses secondary ion mass spectrometry to image dozens of antibodies tagged with metal reporters. As instrument throughput has increased, the breadth and depth of imaging data have increased as well. To extract meaningful information from these data, we have developed tools for cell identification, cell classification, and spatial analysis. In this review, we discuss these tools and provide examples of their application in various contexts, including ductal carcinoma in situ, tuberculosis, and Alzheimer's disease. We hope the synergy between multiplexed imaging and automated image analysis will drive a new era in anatomic pathology and personalized medicine wherein quantitative spatial signatures are used routinely for more accurate diagnosis, prognosis, and therapeutic selection. Expected final online publication date for the Annual Review of Pathology: Mechanisms of Disease, Volume 17 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Candace C Liu
- Department of Pathology, Stanford University, Stanford, California 94304 USA; , , , , , , , , , , ,
| | - Erin F McCaffrey
- Department of Pathology, Stanford University, Stanford, California 94304 USA; , , , , , , , , , , ,
| | - Noah F Greenwald
- Department of Pathology, Stanford University, Stanford, California 94304 USA; , , , , , , , , , , ,
| | - Erin Soon
- Department of Pathology, Stanford University, Stanford, California 94304 USA; , , , , , , , , , , ,
| | - Tyler Risom
- Department of Pathology, Stanford University, Stanford, California 94304 USA; , , , , , , , , , , , .,Current affiliation: Genentech, South San Francisco, California 94080; USA
| | - Kausalia Vijayaragavan
- Department of Pathology, Stanford University, Stanford, California 94304 USA; , , , , , , , , , , ,
| | - John-Paul Oliveria
- Department of Pathology, Stanford University, Stanford, California 94304 USA; , , , , , , , , , , , .,Current affiliation: Genentech, South San Francisco, California 94080; USA
| | - Dunja Mrdjen
- Department of Pathology, Stanford University, Stanford, California 94304 USA; , , , , , , , , , , ,
| | - Marc Bosse
- Department of Pathology, Stanford University, Stanford, California 94304 USA; , , , , , , , , , , ,
| | - Dmitry Tebaykin
- Department of Pathology, Stanford University, Stanford, California 94304 USA; , , , , , , , , , , ,
| | - Sean C Bendall
- Department of Pathology, Stanford University, Stanford, California 94304 USA; , , , , , , , , , , ,
| | - Michael Angelo
- Department of Pathology, Stanford University, Stanford, California 94304 USA; , , , , , , , , , , ,
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36
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Ferrian S, Liu CC, McCaffrey EF, Kumar R, Nowicki TS, Dawson DW, Baranski A, Glaspy JA, Ribas A, Bendall SC, Angelo M. Multiplexed imaging reveals an IFN-γ-driven inflammatory state in nivolumab-associated gastritis. Cell Rep Med 2021; 2:100419. [PMID: 34755133 PMCID: PMC8561237 DOI: 10.1016/j.xcrm.2021.100419] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 06/21/2021] [Accepted: 09/22/2021] [Indexed: 02/07/2023]
Abstract
Immune checkpoint blockade using PD-1 inhibition is an effective approach for treating a wide variety of cancer subtypes. While lower gastrointestinal (GI) side effects are more common, upper gastrointestinal adverse events are rarely reported. Here, we present a case of nivolumab-associated autoimmune gastritis. To elucidate the immunology underlying this condition, we leverage multiplexed ion beam imaging by time-of-flight (MIBI-TOF) to identify the presence and proportion of infiltrating immune cells from a single section of biopsy specimen. Using MIBI-TOF, we analyze formalin-fixed, paraffin-embedded human gastric tissue with 28 labels simultaneously. Our analyses reveal a gastritis characterized by severe mucosal injury, interferon gamma (IFN-γ)-producing gastric epithelial cells, and mixed inflammation that includes CD8 and CD4 T cell infiltrates with reduced expression of granzyme B and FOXP3, respectively. Here, we provide a comprehensive multiplexed histopathological mapping of gastric tissue, which identifies IFN-γ-producing epithelial cells as possible contributors to the nivolumab-associated gastritis.
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Affiliation(s)
- Selena Ferrian
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Candace C. Liu
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Erin F. McCaffrey
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Rashmi Kumar
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Theodore S. Nowicki
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - David W. Dawson
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at the University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Alex Baranski
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - John A. Glaspy
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at the University of California, Los Angeles, Los Angeles, CA 90095, USA
- Division of Hematology-Oncology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | - Antoni Ribas
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
- Division of Hematology-Oncology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90024, USA
- Division of Surgical-Oncology, Department of Surgery, University of California, Los Angeles, Los Angeles, CA 90024, USA
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129, USA
| | - Sean C. Bendall
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129, USA
| | - Michael Angelo
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
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Chen HX, Song M, Maecker HT, Gnjatic S, Patton D, Lee JJ, Adam SJ, Moravec R, Liu XS, Cerami E, Lindsay J, Tang M, Hodi FS, Wu CJ, Wistuba II, Al-Atrash G, Bernatchez C, Bendall SC, Hewitt SM, Sharon E, Streicher H, Enos RA, Bowman MD, Tatard-Leitman VM, Sanchez-Espiridion B, Ranasinghe S, Pichavant M, Del Valle DM, Yu J, Janssens S, Peterson-Klaus J, Rowe C, Bongers G, Jenq RR, Chang CC, Abrams JS, Mooney M, Doroshow JH, Harris LN, Thurin M. Network for Biomarker Immunoprofiling for Cancer Immunotherapy: Cancer Immune Monitoring and Analysis Centers and Cancer Immunologic Data Commons (CIMAC-CIDC). Clin Cancer Res 2021; 27:5038-5048. [PMID: 33419780 PMCID: PMC8491462 DOI: 10.1158/1078-0432.ccr-20-3241] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 11/09/2020] [Accepted: 12/23/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Immunoprofiling to identify biomarkers and integration with clinical trial outcomes are critical to improving immunotherapy approaches for patients with cancer. However, the translational potential of individual studies is often limited by small sample size of trials and the complexity of immuno-oncology biomarkers. Variability in assay performance further limits comparison and interpretation of data across studies and laboratories. EXPERIMENTAL DESIGN To enable a systematic approach to biomarker identification and correlation with clinical outcome across trials, the Cancer Immune Monitoring and Analysis Centers and Cancer Immunologic Data Commons (CIMAC-CIDC) Network was established through support of the Cancer MoonshotSM Initiative of the National Cancer Institute (NCI) and the Partnership for Accelerating Cancer Therapies (PACT) with industry partners via the Foundation for the NIH. RESULTS The CIMAC-CIDC Network is composed of four academic centers with multidisciplinary expertise in cancer immunotherapy that perform validated and harmonized assays for immunoprofiling and conduct correlative analyses. A data coordinating center (CIDC) provides the computational expertise and informatics platforms for the storage, integration, and analysis of biomarker and clinical data. CONCLUSIONS This overview highlights strategies for assay harmonization to enable cross-trial and cross-site data analysis and describes key elements for establishing a network to enhance immuno-oncology biomarker development. These include an operational infrastructure, validation and harmonization of core immunoprofiling assays, platforms for data ingestion and integration, and access to specimens from clinical trials. Published in the same volume are reports of harmonization for core analyses: whole-exome sequencing, RNA sequencing, cytometry by time of flight, and IHC/immunofluorescence.
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Affiliation(s)
- Helen X Chen
- Cancer Therapy Evaluation Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute (NCI), Bethesda, Maryland.
| | - Minkyung Song
- Cancer Therapy Evaluation Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute (NCI), Bethesda, Maryland
| | - Holden T Maecker
- The Human Immune Monitoring Center (HIMC), Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California
| | - Sacha Gnjatic
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - David Patton
- Center for Biomedical Informatics and Information Technology, NCI, Bethesda, Maryland
| | - J Jack Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Stacey J Adam
- Foundation for the National Institutes of Health, North Bethesda, Maryland
| | - Radim Moravec
- Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, NCI, Bethesda, Maryland
- Kelly Services, Rockville, Maryland
| | - Xiaole Shirley Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ethan Cerami
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - James Lindsay
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ming Tang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - F Stephen Hodi
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gheath Al-Atrash
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chantale Bernatchez
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sean C Bendall
- Department of Pathology, School of Medicine, Stanford University, Stanford, California
| | - Stephen M Hewitt
- Laboratory of Pathology, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Elad Sharon
- Cancer Therapy Evaluation Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute (NCI), Bethesda, Maryland
| | - Howard Streicher
- Cancer Therapy Evaluation Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute (NCI), Bethesda, Maryland
| | | | | | | | - Beatriz Sanchez-Espiridion
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Srinika Ranasinghe
- Center for Immuno-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Mina Pichavant
- The Human Immune Monitoring Center (HIMC), Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California
| | - Diane M Del Valle
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Joyce Yu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | | | - Cathy Rowe
- Center for Biomedical Informatics and Information Technology, NCI, Bethesda, Maryland
- Essex Management, Rockville, Maryland
| | - Gerold Bongers
- Microbiome Translational Center, Precision Immunology Institute, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Robert R Jenq
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chia-Chi Chang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jeffrey S Abrams
- Cancer Therapy Evaluation Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute (NCI), Bethesda, Maryland
| | - Margaret Mooney
- Cancer Therapy Evaluation Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute (NCI), Bethesda, Maryland
| | - James H Doroshow
- Division of Cancer Treatment and Diagnosis, NCI, Bethesda, Maryland
| | - Lyndsay N Harris
- Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, NCI, Bethesda, Maryland
| | - Magdalena Thurin
- Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, NCI, Bethesda, Maryland.
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38
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Sahaf B, Pichavant M, Lee BH, Duault C, Thrash EM, Davila M, Fernandez N, Millerchip K, Bentebibel SE, Haymaker C, Sigal N, Del Valle DM, Ranasinghe S, Fayle S, Sanchez-Espiridion B, Zhang J, Bernatchez C, Wu CJ, Wistuba II, Kim-Schulze S, Gnjatic S, Bendall SC, Song M, Thurin M, Lee JJ, Maecker HT, Rahman A. Immune Profiling Mass Cytometry Assay Harmonization: Multicenter Experience from CIMAC-CIDC. Clin Cancer Res 2021; 27:5062-5071. [PMID: 34266889 PMCID: PMC8448982 DOI: 10.1158/1078-0432.ccr-21-2052] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/10/2021] [Accepted: 07/12/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE The Cancer Immune Monitoring and Analysis Centers - Cancer Immunologic Data Commons (CIMAC-CIDC) Network is supported by the NCI to identify biomarkers of response to cancer immunotherapies across clinical trials using state-of-the-art assays. A primary platform for CIMAC-CIDC studies is cytometry by time of flight (CyTOF), performed at all CIMAC laboratories. To ensure the ability to generate comparable CyTOF data across labs, a multistep cross-site harmonization effort was undertaken. EXPERIMENTAL DESIGN We first harmonized standard operating procedures (SOPs) across the CIMAC sites. Because of a new acquisition protocol comparing original narrow- or new wide-bore injector introduced by the vendor (Fluidigm), we also tested this protocol across sites before finalizing the harmonized SOP. We then performed cross-site assay harmonization experiments using five shared cryopreserved and one lyophilized internal control peripheral blood mononuclear cell (PBMC) with a shared lyophilized antibody cocktail consisting of 14 isotype-tagged antibodies previously validated, plus additional liquid antibodies. These reagents and samples were distributed to the CIMAC sites and the data were centrally analyzed by manual gating and automated methods (Astrolabe). RESULTS Average coefficients of variation (CV) across sites for each cell population were reported and compared with a previous multisite CyTOF study. We reached an intersite CV of under 20% for most cell subsets, very similar to a previously published study. CONCLUSIONS These results establish the ability to reproduce CyTOF data across sites in multicenter clinical trials, and also highlight the importance of quality control procedures, such as the use of spike-in control samples, for tracking variability in this assay.
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Affiliation(s)
- Bita Sahaf
- Stanford Cancer Institute, Stanford Medicine, Stanford University, California.
| | - Mina Pichavant
- Stanford Institute for Immunity, Transplantation and Infection, Stanford Medicine, Stanford university, California
| | - Brian H Lee
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Caroline Duault
- Stanford Institute for Immunity, Transplantation and Infection, Stanford Medicine, Stanford university, California
| | - Emily M Thrash
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Melanie Davila
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Nicolas Fernandez
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Karen Millerchip
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Salah-Eddine Bentebibel
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Cara Haymaker
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Natalia Sigal
- Stanford Institute for Immunity, Transplantation and Infection, Stanford Medicine, Stanford university, California
| | - Diane M Del Valle
- Human Immune Monitoring Center, Tisch Cancer Institute and the Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Srinika Ranasinghe
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Sarah Fayle
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Beatriz Sanchez-Espiridion
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jiexin Zhang
- Department of Bioinformatics & Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chantale Bernatchez
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Harvard University, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Seunghee Kim-Schulze
- Human Immune Monitoring Center, Tisch Cancer Institute and the Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Sacha Gnjatic
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Sean C Bendall
- Department of Pathology, Stanford Medicine, Stanford University, Stanford, California
| | - Minkyung Song
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland
| | - Magdalena Thurin
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland
| | - J Jack Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Holden T Maecker
- Stanford Institute for Immunity, Transplantation and Infection, Stanford Medicine, Stanford university, California
| | - Adeeb Rahman
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, New York
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
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Gajera CR, Fernandez R, Montine KS, Fox EJ, Mrdjen D, Postupna NO, Keene CD, Bendall SC, Montine TJ. Mass-tag barcoding for multiplexed analysis of human synaptosomes and other anuclear events. Cytometry A 2021; 99:939-945. [PMID: 33818911 PMCID: PMC8590852 DOI: 10.1002/cyto.a.24340] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/27/2021] [Accepted: 03/17/2021] [Indexed: 12/17/2022]
Abstract
Mass-tag cell barcoding has increased the throughput, multiplexing, and robustness of multiple cytometry approaches. Previously, we adapted mass cytometry for cells to analyze synaptosome preparations (mass synaptometry or SynTOF), extending mass cytometry to these smaller, anuclear particles. To improve throughput and individual event resolution, we report here the application of palladium-based barcoding in human synaptosomes. Up to 20 individual samples, each with a unique combinatorial barcode, were pooled for labeling with an antibody cocktail. Our synaptosome protocol used six palladium-based barcoding reagents, and in combination with sequential gating increased the identification of presynaptic events approximately fourfold. These same parameters also efficiently resolved two other anuclear particles: human red blood cells and platelets. The addition of palladium-based mass-tag barcoding to our approach improves mass cytometry of synaptic particles.
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Affiliation(s)
| | - Rosemary Fernandez
- Department of Pathology, Stanford University, Stanford, CA, United States
| | | | - Edward J. Fox
- Department of Pathology, Stanford University, Stanford, CA, United States
| | - Dunja Mrdjen
- Department of Pathology, Stanford University, Stanford, CA, United States
| | - Nadia O. Postupna
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States
| | - C. Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States
| | - Sean C. Bendall
- Department of Pathology, Stanford University, Stanford, CA, United States
| | - Thomas J. Montine
- Department of Pathology, Stanford University, Stanford, CA, United States
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Abstract
Improvements in single-cell protein analysis are required to study the cell-to-cell variation inherent to diseases, including cancer. Single-cell immunoblotting (scIB) offers proteoform detection specificity, but often relies on fluorescence-based readout and is therefore limited in multiplexing capability. Among rising multiplexed imaging methods is multiplexed ion beam imaging by time-of-flight (MIBI-TOF), a mass spectrometry imaging technology. MIBI-TOF employs metal-tagged antibodies that do not suffer from spectral overlap to the same degree as fluorophore-tagged antibodies. We report for the first-time MIBI-TOF of single-cell immunoblotting (scIB-MIBI-TOF). The scIB assay subjects single-cell lysate to protein immunoblotting on a microscale device consisting of a 50- to 75-μm thick hydrated polyacrylamide (PA) gel matrix for protein immobilization prior to in-gel immunoprobing. We confirm antibody-protein binding in the PA gel with indirect fluorescence readout of metal-tagged antibodies. Since MIBI-TOF is a layer-by-layer imaging technique, and our protein target is immobilized within a 3D PA gel layer, we characterize the protein distribution throughout the PA gel depth by fluorescence confocal microscopy and confirm that the highest signal-to-noise ratio is achieved by imaging the entirety of the PA gel depth. Accordingly, we report the required MIBI-TOF ion dose strength needed to image varying PA gel depths. Lastly, by imaging ∼42% of PA gel depth with MIBI-TOF, we detect two isoelectrically separated TurboGFP (tGFP) proteoforms from individual glioblastoma cells, demonstrating that highly multiplexed mass spectrometry-based readout is compatible with scIB.
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Affiliation(s)
| | - Marc Bosse
- Department of Pathology, Stanford University, Stanford, California 94025, United States
| | - Sean C Bendall
- Department of Pathology, Stanford University, Stanford, California 94025, United States
| | - Michael Angelo
- Department of Pathology, Stanford University, Stanford, California 94025, United States
| | - Amy E Herr
- Chan Zuckerberg Biohub, San Francisco, California 94158, United States
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41
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Glass DR, Tsai AG, Oliveria JP, Hartmann FJ, Kimmey SC, Calderon AA, Borges L, Glass MC, Wagar LE, Davis MM, Bendall SC. An Integrated Multi-omic Single-Cell Atlas of Human B Cell Identity. Immunity 2021; 53:217-232.e5. [PMID: 32668225 PMCID: PMC7369630 DOI: 10.1016/j.immuni.2020.06.013] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 04/03/2020] [Accepted: 06/16/2020] [Indexed: 12/13/2022]
Abstract
B cells are capable of a wide range of effector functions including antibody secretion, antigen presentation, cytokine production, and generation of immunological memory. A consistent strategy for classifying human B cells by using surface molecules is essential to harness this functional diversity for clinical translation. We developed a highly multiplexed screen to quantify the co-expression of 351 surface molecules on millions of human B cells. We identified differentially expressed molecules and aligned their variance with isotype usage, VDJ sequence, metabolic profile, biosynthesis activity, and signaling response. Based on these analyses, we propose a classification scheme to segregate B cells from four lymphoid tissues into twelve unique subsets, including a CD45RB+CD27− early memory population, a class-switched CD39+ tonsil-resident population, and a CD19hiCD11c+ memory population that potently responds to immune activation. This classification framework and underlying datasets provide a resource for further investigations of human B cell identity and function. A mass cytometry screen reveals 98 surface molecules expressed by human B cells High-dimensional analysis identifies twelve B cell subsets across four tissues CD45RB, CD11c, CD39, CD73, and CD95 define subsets of antigen-experienced B cells Isotype usage, signaling, and metabolism vary in accordance with cell surface phenotype
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Affiliation(s)
- David R Glass
- Immunology Graduate Program, Stanford University, Stanford, CA, 94305, USA; Department of Pathology, Stanford University, Stanford, CA, 94305, USA
| | - Albert G Tsai
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA
| | - John Paul Oliveria
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA; Department of Medicine, Division of Respirology, McMaster University, Hamilton, ON, L8S4K1, Canada
| | - Felix J Hartmann
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA
| | - Samuel C Kimmey
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA; Department of Developmental Biology, Stanford University, Stanford CA, 94305, USA
| | - Ariel A Calderon
- Immunology Graduate Program, Stanford University, Stanford, CA, 94305, USA; Department of Pathology, Stanford University, Stanford, CA, 94305, USA
| | - Luciene Borges
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA
| | - Marla C Glass
- Department of Surgery, Stanford University, Stanford CA, 94305, USA
| | - Lisa E Wagar
- Department of Microbiology and Immunology, Stanford University, Stanford CA, 94305, USA
| | - Mark M Davis
- Department of Microbiology and Immunology, Stanford University, Stanford CA, 94305, USA
| | - Sean C Bendall
- Immunology Graduate Program, Stanford University, Stanford, CA, 94305, USA; Department of Pathology, Stanford University, Stanford, CA, 94305, USA.
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Hartmann FJ, Mrdjen D, McCaffrey E, Glass DR, Greenwald NF, Bharadwaj A, Khair Z, Verberk SGS, Baranski A, Baskar R, Graf W, Van Valen D, Van den Bossche J, Angelo M, Bendall SC. Single-cell metabolic profiling of human cytotoxic T cells. Nat Biotechnol 2021; 39:186-197. [PMID: 32868913 PMCID: PMC7878201 DOI: 10.1038/s41587-020-0651-8] [Citation(s) in RCA: 151] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 07/23/2020] [Indexed: 12/12/2022]
Abstract
Cellular metabolism regulates immune cell activation, differentiation and effector functions, but current metabolic approaches lack single-cell resolution and simultaneous characterization of cellular phenotype. In this study, we developed an approach to characterize the metabolic regulome of single cells together with their phenotypic identity. The method, termed single-cell metabolic regulome profiling (scMEP), quantifies proteins that regulate metabolic pathway activity using high-dimensional antibody-based technologies. We employed mass cytometry (cytometry by time of flight, CyTOF) to benchmark scMEP against bulk metabolic assays by reconstructing the metabolic remodeling of in vitro-activated naive and memory CD8+ T cells. We applied the approach to clinical samples and identified tissue-restricted, metabolically repressed cytotoxic T cells in human colorectal carcinoma. Combining our method with multiplexed ion beam imaging by time of flight (MIBI-TOF), we uncovered the spatial organization of metabolic programs in human tissues, which indicated exclusion of metabolically repressed immune cells from the tumor-immune boundary. Overall, our approach enables robust approximation of metabolic and functional states in individual cells.
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Affiliation(s)
- Felix J Hartmann
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Dunja Mrdjen
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Erin McCaffrey
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA
- Immunology Graduate Program, Stanford University, Palo Alto, CA, USA
| | - David R Glass
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA
- Immunology Graduate Program, Stanford University, Palo Alto, CA, USA
| | - Noah F Greenwald
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Anusha Bharadwaj
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Zumana Khair
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Sanne G S Verberk
- Department of Molecular Cell Biology and Immunology, Amsterdam Cardiovascular Sciences, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Alex Baranski
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Reema Baskar
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - William Graf
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - David Van Valen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jan Van den Bossche
- Department of Molecular Cell Biology and Immunology, Amsterdam Cardiovascular Sciences, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Michael Angelo
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Sean C Bendall
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA.
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43
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Ackerman SE, Pearson CI, Gregorio JD, Gonzalez JC, Kenkel JA, Hartmann FJ, Luo A, Ho PY, LeBlanc H, Blum LK, Kimmey SC, Luo A, Nguyen ML, Paik JC, Sheu LY, Ackerman B, Lee A, Li H, Melrose J, Laura RP, Ramani VC, Henning KA, Jackson DY, Safina BS, Yonehiro G, Devens BH, Carmi Y, Chapin SJ, Bendall SC, Kowanetz M, Dornan D, Engleman EG, Alonso MN. Immune-stimulating antibody conjugates elicit robust myeloid activation and durable antitumor immunity. Nat Cancer 2021; 2:18-33. [PMID: 35121890 PMCID: PMC9012298 DOI: 10.1038/s43018-020-00136-x] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 09/30/2020] [Indexed: 02/07/2023]
Abstract
Innate pattern recognition receptor agonists, including Toll-like receptors (TLRs), alter the tumor microenvironment and prime adaptive antitumor immunity. However, TLR agonists present toxicities associated with widespread immune activation after systemic administration. To design a TLR-based therapeutic suitable for systemic delivery and capable of safely eliciting tumor-targeted responses, we developed immune-stimulating antibody conjugates (ISACs) comprising a TLR7/8 dual agonist conjugated to tumor-targeting antibodies. Systemically administered human epidermal growth factor receptor 2 (HER2)-targeted ISACs were well tolerated and triggered a localized immune response in the tumor microenvironment that resulted in tumor clearance and immunological memory. Mechanistically, ISACs required tumor antigen recognition, Fcγ-receptor-dependent phagocytosis and TLR-mediated activation to drive tumor killing by myeloid cells and subsequent T-cell-mediated antitumor immunity. ISAC-mediated immunological memory was not limited to the HER2 ISAC target antigen since ISAC-treated mice were protected from rechallenge with the HER2- parental tumor. These results provide a strong rationale for the clinical development of ISACs.
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Affiliation(s)
- Shelley E Ackerman
- Department of Bioengineering, Stanford University Schools of Medicine and Engineering, Stanford, CA, USA
- Bolt Biotherapeutics, Inc., Redwood City, CA, USA
| | | | | | | | - Justin A Kenkel
- Bolt Biotherapeutics, Inc., Redwood City, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Felix J Hartmann
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Angela Luo
- Bolt Biotherapeutics, Inc., Redwood City, CA, USA
| | - Po Y Ho
- Bolt Biotherapeutics, Inc., Redwood City, CA, USA
| | | | - Lisa K Blum
- Bolt Biotherapeutics, Inc., Redwood City, CA, USA
| | - Samuel C Kimmey
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Andrew Luo
- Bolt Biotherapeutics, Inc., Redwood City, CA, USA
| | | | - Jason C Paik
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lauren Y Sheu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Benjamin Ackerman
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Arthur Lee
- Bolt Biotherapeutics, Inc., Redwood City, CA, USA
| | - Hai Li
- Bolt Biotherapeutics, Inc., Redwood City, CA, USA
| | | | | | | | | | | | | | | | | | - Yaron Carmi
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Sackler School of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | | | - Sean C Bendall
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - David Dornan
- Bolt Biotherapeutics, Inc., Redwood City, CA, USA
| | - Edgar G Engleman
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael N Alonso
- Bolt Biotherapeutics, Inc., Redwood City, CA, USA.
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
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44
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Vivanco Gonzalez N, Oliveria JP, Tebaykin D, Ivison GT, Mukai K, Tsai MM, Borges L, Nadeau KC, Galli SJ, Tsai AG, Bendall SC. Mass Cytometry Phenotyping of Human Granulocytes Reveals Novel Basophil Functional Heterogeneity. iScience 2020; 23:101724. [PMID: 33205028 PMCID: PMC7653073 DOI: 10.1016/j.isci.2020.101724] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 08/18/2020] [Accepted: 10/20/2020] [Indexed: 02/06/2023] Open
Abstract
Basophils, the rarest granulocyte, play critical roles in parasite- and allergen-induced inflammation. We applied mass cytometry (CyTOF) to simultaneously asses 44 proteins to phenotype and functionally characterize neutrophils, eosinophils, and basophils from 19 healthy donors. There was minimal heterogeneity seen in eosinophils and neutrophils, but data-driven analyses revealed four unique subpopulations within phenotypically basophilic granulocytes (PBG; CD45+HLA-DR−CD123+). Through CyTOF and fluorescence-activated cell sorting (FACS), we classified these four PBG subpopulations as (I) CD16lowFcεRIhighCD244high (88.5 ± 1.2%), (II) CD16highFcεRIhighCD244high (9.1 ± 0.4%), (III) CD16lowFcεRIlowCD244low (2.3 ± 1.3), and (IV) CD16highFcεRIlowCD244low (0.4 ± 0.1%). Prospective isolation confirmed basophilic-morphology of PBG I–III, but neutrophilic-morphology of PBG IV. Functional interrogation via IgE-crosslinking or IL-3 stimulation demonstrated that PBG I–II had significant increases in CD203c expression, whereas PBG III–IV remained unchanged compared with media-alone conditions. Thus, PBG III–IV could serve roles in non-IgE-mediated immunity. Our findings offer new perspectives in human basophil heterogeneity and the varying functional potential of these new subsets in health and disease. Unsupervised clustering revealed 4 basophil populations, driven by CD16, CD244, and FcεRI The rarest basophil subpopulation IV was morphologically neutrophils Anti-IgE and IL-3 stimulation did not induce functional responses in III and IV Basophil subpopulation heterogeneity was observed in healthy and CML samples
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Affiliation(s)
- Nora Vivanco Gonzalez
- Department of Pathology, School of Medicine, Stanford University, Stanford Blood Center, 3373 Hillview Avenue Room 230A, Palo Alto, CA 94305, USA
| | - John-Paul Oliveria
- Department of Pathology, School of Medicine, Stanford University, Stanford Blood Center, 3373 Hillview Avenue Room 230A, Palo Alto, CA 94305, USA
- Department of Medicine, Division of Respirology, McMaster University, Hamilton, ON, L8S4K1, Canada
| | - Dmitry Tebaykin
- Department of Pathology, School of Medicine, Stanford University, Stanford Blood Center, 3373 Hillview Avenue Room 230A, Palo Alto, CA 94305, USA
| | - Geoffrey T. Ivison
- Department of Pathology, School of Medicine, Stanford University, Stanford Blood Center, 3373 Hillview Avenue Room 230A, Palo Alto, CA 94305, USA
| | - Kaori Mukai
- Department of Pathology, School of Medicine, Stanford University, Stanford Blood Center, 3373 Hillview Avenue Room 230A, Palo Alto, CA 94305, USA
- Sean N. Parker Center for Allergy Research, School of Medicine, Stanford University, Palo Alto, CA 94305, USA
| | - Mindy M. Tsai
- Department of Pathology, School of Medicine, Stanford University, Stanford Blood Center, 3373 Hillview Avenue Room 230A, Palo Alto, CA 94305, USA
- Sean N. Parker Center for Allergy Research, School of Medicine, Stanford University, Palo Alto, CA 94305, USA
| | - Luciene Borges
- Department of Pathology, School of Medicine, Stanford University, Stanford Blood Center, 3373 Hillview Avenue Room 230A, Palo Alto, CA 94305, USA
| | - Kari C. Nadeau
- Sean N. Parker Center for Allergy Research, School of Medicine, Stanford University, Palo Alto, CA 94305, USA
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, School of Medicine, Stanford University, Palo Alto, CA 94305, USA
| | - Stephen J. Galli
- Department of Pathology, School of Medicine, Stanford University, Stanford Blood Center, 3373 Hillview Avenue Room 230A, Palo Alto, CA 94305, USA
- Sean N. Parker Center for Allergy Research, School of Medicine, Stanford University, Palo Alto, CA 94305, USA
- Department of Microbiology and Immunology, School of Medicine, Stanford University, Palo Alto, CA 94305, USA
| | - Albert G. Tsai
- Department of Pathology, School of Medicine, Stanford University, Stanford Blood Center, 3373 Hillview Avenue Room 230A, Palo Alto, CA 94305, USA
| | - Sean C. Bendall
- Department of Pathology, School of Medicine, Stanford University, Stanford Blood Center, 3373 Hillview Avenue Room 230A, Palo Alto, CA 94305, USA
- Corresponding author
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45
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Affiliation(s)
- Sean C Bendall
- Department of Pathology, Stanford University, Stanford, CA, USA.
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46
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Hartmann FJ, Babdor J, Gherardini PF, Amir EAD, Jones K, Sahaf B, Marquez DM, Krutzik P, O'Donnell E, Sigal N, Maecker HT, Meyer E, Spitzer MH, Bendall SC. Comprehensive Immune Monitoring of Clinical Trials to Advance Human Immunotherapy. Cell Rep 2020; 28:819-831.e4. [PMID: 31315057 PMCID: PMC6656694 DOI: 10.1016/j.celrep.2019.06.049] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 05/06/2019] [Accepted: 06/12/2019] [Indexed: 12/21/2022] Open
Abstract
The success of immunotherapy has led to a myriad of clinical trials accompanied by efforts to gain mechanistic insight and identify predictive signatures for personalization. However, many immune monitoring technologies face investigator bias, missing unanticipated cellular responses in limited clinical material. We present here a mass cytometry (CyTOF) workflow for standardized, systems-level biomarker discovery in immunotherapy trials. To broadly enumerate immune cell identity and activity, we established and extensively assessed a reference panel of 33 antibodies to cover major cell subsets, simultaneously quantifying activation and immune checkpoint molecules in a single assay. This assay enumerates ≥98% of peripheral immune cells with ≥4 positively identifying antigens. Robustness and reproducibility are demonstrated on multiple samples types, across two research centers and by orthogonal measurements. Using automated analysis, we identify stratifying immune signatures in bone marrow transplantation-associated graft-versus-host disease. Together, this validated workflow ensures comprehensive immunophenotypic analysis and data comparability and will accelerate biomarker discovery. Single assay to identify and characterize all major human immune cell lineages Readily available and extensively validated antibody panel Additional (>10) targets can be added to meet specific hypotheses Allows identification of disease-associated immune signatures and biomarkers
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Affiliation(s)
- Felix J Hartmann
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA 94305, USA
| | - Joel Babdor
- Departments of Otolaryngology-Head and Neck Surgery and Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - El-Ad D Amir
- Astrolabe Diagnostics, Inc., Fort Lee, NJ 07024, USA
| | - Kyle Jones
- Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Bita Sahaf
- Cancer Correlative Science Unit, Cancer Institute, School of Medicine, Stanford University, Palo Alto, CA 94305, USA
| | - Diana M Marquez
- Departments of Otolaryngology-Head and Neck Surgery and Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | | | - Natalia Sigal
- Department of Microbiology and Immunology, Stanford University, Palo Alto, CA 94305, USA
| | - Holden T Maecker
- Department of Microbiology and Immunology, Stanford University, Palo Alto, CA 94305, USA
| | - Everett Meyer
- Cellular Therapy Facility, Blood and Marrow Transplantation, School of Medicine, Stanford University, Palo Alto, CA 94305, USA
| | - Matthew H Spitzer
- Departments of Otolaryngology-Head and Neck Surgery and Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA 94125, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
| | - Sean C Bendall
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA 94305, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA 94125, USA.
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47
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Tsai AG, Glass DR, Juntilla M, Hartmann FJ, Oak JS, Fernandez-Pol S, Ohgami RS, Bendall SC. Multiplexed single-cell morphometry for hematopathology diagnostics. Nat Med 2020; 26:408-417. [PMID: 32161403 PMCID: PMC7301910 DOI: 10.1038/s41591-020-0783-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 01/30/2020] [Indexed: 01/13/2023]
Abstract
The diagnosis of lymphomas and leukemias requires hematopathologists to integrate microscopically visible cellular morphology with antibody-identified cell surface molecule expression. To merge these into one high-throughput, highly multiplexed, single-cell assay, we quantify cell morphological features by their underlying, antibody-measurable molecular components, which empowers mass cytometers to 'see' like pathologists. When applied to 71 diverse clinical samples, single-cell morphometric profiling reveals robust and distinct patterns of 'morphometric' markers for each major cell type. Individually, lamin B1 highlights acute leukemias, lamin A/C helps distinguish normal from neoplastic mature T cells, and VAMP-7 recapitulates light-cytometric side scatter. Combined with machine learning, morphometric markers form intuitive visualizations of normal and neoplastic cellular distribution and differentiation. When recalibrated for myelomonocytic blast enumeration, this approach is superior to flow cytometry and comparable to expert microscopy, bypassing years of specialized training. The contextualization of traditional surface markers on independent morphometric frameworks permits more sensitive and automated diagnosis of complex hematopoietic diseases.
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Affiliation(s)
- Albert G Tsai
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - David R Glass
- Department of Pathology, Stanford University, Stanford, CA, USA
- Immunology Graduate Program, Stanford University, Stanford, CA, USA
| | - Marisa Juntilla
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Jean S Oak
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Robert S Ohgami
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Sean C Bendall
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Immunology Graduate Program, Stanford University, Stanford, CA, USA.
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48
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Abstract
The cellular complexity and functional diversity of the human immune system necessitate the use of high-dimensional single-cell tools to uncover its role in multifaceted diseases such as rheumatic diseases, as well as other autoimmune and inflammatory disorders. Proteomic technologies that use elemental (heavy metal) reporter ions, such as mass cytometry (also known as CyTOF) and analogous high-dimensional imaging approaches (including multiplexed ion beam imaging (MIBI) and imaging mass cytometry (IMC)), have been developed from their low-dimensional counterparts, flow cytometry and immunohistochemistry, to meet this need. A growing number of studies have been published that use these technologies to identify functional biomarkers and therapeutic targets in rheumatic diseases, but the full potential of their application to rheumatic disease research has yet to be fulfilled. This Review introduces the underlying technologies for high-dimensional immune monitoring and discusses aspects necessary for their successful implementation, including study design principles, analytical tools and future developments for the field of rheumatology.
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Affiliation(s)
- Felix J Hartmann
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA
| | - Sean C Bendall
- Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA.
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49
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Greenbaum S, Bosse M, Baranski A, Khair Z, Bruce T, Tebaykin D, Oliveria JP, Bendall SC, Winn VD, Angelo M. 225: In-depth characterization of immune cells in preeclampsia using Multiplexed Ion Beam Imaging by Time-of-Flight (MIBI-TOF). Am J Obstet Gynecol 2020. [DOI: 10.1016/j.ajog.2019.11.241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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50
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Baskar R, Fienberg HG, Khair Z, Favaro P, Kimmey S, Green DR, Nolan GP, Plevritis S, Bendall SC. TRAIL-induced variation of cell signaling states provides nonheritable resistance to apoptosis. Life Sci Alliance 2019; 2:e201900554. [PMID: 31704709 PMCID: PMC6848270 DOI: 10.26508/lsa.201900554] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/24/2019] [Accepted: 10/25/2019] [Indexed: 02/06/2023] Open
Abstract
TNFα-related apoptosis-inducing ligand (TRAIL), specifically initiates programmed cell death, but often fails to eradicate all cells, making it an ineffective therapy for cancer. This fractional killing is linked to cellular variation that bulk assays cannot capture. Here, we quantify the diversity in cellular signaling responses to TRAIL, linking it to apoptotic frequency across numerous cell systems with single-cell mass cytometry (CyTOF). Although all cells respond to TRAIL, a variable fraction persists without apoptotic progression. This cell-specific behavior is nonheritable where both the TRAIL-induced signaling responses and frequency of apoptotic resistance remain unaffected by prior exposure. The diversity of signaling states upon exposure is correlated to TRAIL resistance. Concomitantly, constricting the variation in signaling response with kinase inhibitors proportionally decreases TRAIL resistance. Simultaneously, TRAIL-induced de novo translation in resistant cells, when blocked by cycloheximide, abrogated all TRAIL resistance. This work highlights how cell signaling diversity, and subsequent translation response, relates to nonheritable fractional escape from TRAIL-induced apoptosis. This refined view of TRAIL resistance provides new avenues to study death ligands in general.
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Affiliation(s)
- Reema Baskar
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Harris G Fienberg
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Immunology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Zumana Khair
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Patricia Favaro
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Sam Kimmey
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Developmental Biology Program, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Garry P Nolan
- Baxter Laboratory, Stanford University School of Medicine, Stanford, CA, USA
| | - Sylvia Plevritis
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Sean C Bendall
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Immunology Program, Stanford University School of Medicine, Stanford, CA, USA
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