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Walker CR, Angelo M. Insights and Opportunity Costs in Applying Spatial Biology to Study the Tumor Microenvironment. Cancer Discov 2024; 14:707-710. [PMID: 38587535 DOI: 10.1158/2159-8290.cd-24-0348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
SUMMARY The recent development of high-dimensional spatial omics tools has revealed the functional importance of the tumor microenvironment in driving tumor progression. Here, we discuss practical factors to consider when designing a spatial biology cohort and offer perspectives on the future of spatial biology research.
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Affiliation(s)
- Cameron R Walker
- Department of Pathology, Stanford University School of Medicine, Palo Alto, California
| | - Michael Angelo
- Department of Pathology, Stanford University School of Medicine, Palo Alto, California
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2
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Jain S, Pei L, Spraggins JM, Angelo M, Carson JP, Gehlenborg N, Ginty F, Gonçalves JP, Hagood JS, Hickey JW, Kelleher NL, Laurent LC, Lin S, Lin Y, Liu H, Naba A, Nakayasu ES, Qian WJ, Radtke A, Robson P, Stockwell BR, Van de Plas R, Vlachos IS, Zhou M, Börner K, Snyder MP. Author Correction: Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP). Nat Cell Biol 2024; 26:839. [PMID: 38429479 DOI: 10.1038/s41556-024-01384-0] [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: 03/03/2024]
Affiliation(s)
- Sanjay Jain
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA.
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
| | - Liming Pei
- Center for Mitochondrial and Epigenomic Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Jeffrey M Spraggins
- Department of Cell and Developmental Biology and the Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN, USA.
| | - Michael Angelo
- Department of Pathology, Stanford School of Medicine, Stanford, CA, USA
| | - James P Carson
- Texas Advanced Computing Center, University of Texas at Austin, Austin, TX, USA
| | - Nils Gehlenborg
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | | | - Joana P Gonçalves
- Department of Intelligent Systems, Delft University of Technology, Delft, Netherlands
| | - James S Hagood
- Department of Pediatrics (Pulmonology) and Program for Rare and Interstitial Lung Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - John W Hickey
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Neil L Kelleher
- Departments of Medicine, Chemistry and Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Louise C Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Shin Lin
- Division of Cardiology, University of Washington School of Medicine, Seattle, WA, USA
| | - Yiing Lin
- Department of Surgery, Washington University School of Medicine, St Louis, MO, USA
| | - Huiping Liu
- Departments of Pharmacology, Medicine (Hematology and Oncology), Lurie Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Alexandra Naba
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL, USA
| | - Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Andrea Radtke
- Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Paul Robson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Brent R Stockwell
- Department of Biological Sciences and Department of Chemistry, Columbia University, New York, NY, USA
| | - Raf Van de Plas
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
| | - Ioannis S Vlachos
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Spatial Technologies Unit, Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, and Harvard Medical School, Boston, MA, USA
| | - Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Katy Börner
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA.
| | - Michael P Snyder
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA.
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3
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Yeo YY, Qiu H, Bai Y, Zhu B, Chang Y, Yeung J, Michel HA, Wright K, Shaban M, Sadigh S, Nkosi D, Shanmugam V, Rock P, Tung Yiu SP, Cramer P, Paczkowska J, Stephan P, Liao G, Huang AY, Wang H, Chen H, Frauenfeld L, Mitra B, Gewurz BE, Schürch CM, Zhao B, Nolan GP, Zhang B, Shalek AK, Angelo M, Mahmood F, Ma Q, Burack WR, Shipp MA, Rodig SJ, Jiang S. Epstein-Barr Virus Orchestrates Spatial Reorganization and Immunomodulation within the Classic Hodgkin Lymphoma Tumor Microenvironment. bioRxiv 2024:2024.03.05.583586. [PMID: 38496566 PMCID: PMC10942289 DOI: 10.1101/2024.03.05.583586] [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: 03/19/2024]
Abstract
Classic Hodgkin Lymphoma (cHL) is a tumor composed of rare malignant Hodgkin and Reed-Sternberg (HRS) cells nested within a T-cell rich inflammatory immune infiltrate. cHL is associated with Epstein-Barr Virus (EBV) in 25% of cases. The specific contributions of EBV to the pathogenesis of cHL remain largely unknown, in part due to technical barriers in dissecting the tumor microenvironment (TME) in high detail. Herein, we applied multiplexed ion beam imaging (MIBI) spatial pro-teomics on 6 EBV-positive and 14 EBV-negative cHL samples. We identify key TME features that distinguish between EBV-positive and EBV-negative cHL, including the relative predominance of memory CD8 T cells and increased T-cell dysfunction as a function of spatial proximity to HRS cells. Building upon a larger multi-institutional cohort of 22 EBV-positive and 24 EBV-negative cHL samples, we orthogonally validated our findings through a spatial multi-omics approach, coupling whole transcriptome capture with antibody-defined cell types for tu-mor and T-cell populations within the cHL TME. We delineate contrasting transcriptomic immunological signatures between EBV-positive and EBV-negative cases that differently impact HRS cell proliferation, tumor-immune interactions, and mecha-nisms of T-cell dysregulation and dysfunction. Our multi-modal framework enabled a comprehensive dissection of EBV-linked reorganization and immune evasion within the cHL TME, and highlighted the need to elucidate the cellular and molecular fac-tors of virus-associated tumors, with potential for targeted therapeutic strategies.
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Bialy N, Alber F, Andrews B, Angelo M, Beliveau B, Bintu L, Boettiger A, Boehm U, Brown CM, Maina MB, Chambers JJ, Cimini BA, Eliceiri K, Errington R, Faklaris O, Gaudreault N, Germain RN, Goscinski W, Grunwald D, Halter M, Hanein D, Hickey JW, Lacoste J, Laude A, Lundberg E, Ma J, Malacrida L, Moore J, Nelson G, Neumann EK, Nitschke R, Onami S, Pimentel JA, Plant AL, Radtke AJ, Sabata B, Schapiro D, Schöneberg J, Spraggins JM, Sudar D, Adrien Maria Vierdag WM, Volkmann N, Wählby C, Wang SS, Yaniv Z, Strambio-De-Castillia C. Harmonizing the Generation and Pre-publication Stewardship of FAIR Image data. ArXiv 2024:arXiv:2401.13022v4. [PMID: 38351940 PMCID: PMC10862930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Abstract
Together with the molecular knowledge of genes and proteins, biological images promise to significantly enhance the scientific understanding of complex cellular systems and to advance predictive and personalized therapeutic products for human health. For this potential to be realized, quality-assured image data must be shared among labs at a global scale to be compared, pooled, and reanalyzed, thus unleashing untold potential beyond the original purpose for which the data was generated. There are two broad sets of requirements to enable image data sharing in the life sciences. One set of requirements is articulated in the companion White Paper entitled "Enabling Global Image Data Sharing in the Life Sciences," which is published in parallel and addresses the need to build the cyberinfrastructure for sharing the digital array data (arXiv:2401.13023 [q-bio.OT], https://doi.org/10.48550/arXiv.2401.13023). In this White Paper, we detail a broad set of requirements, which involves collecting, managing, presenting, and propagating contextual information essential to assess the quality, understand the content, interpret the scientific implications, and reuse image data in the context of the experimental details. We start by providing an overview of the main lessons learned to date through international community activities, which have recently made considerable progress toward generating community standard practices for imaging Quality Control (QC) and metadata. We then provide a clear set of recommendations for amplifying this work. The driving goal is to address remaining challenges, and democratize access to common practices and tools for a spectrum of biomedical researchers, regardless of their expertise, access to resources, and geographical location.
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Affiliation(s)
- Nikki Bialy
- Morgridge Institute for Research, Madison, USA
| | | | | | | | | | | | | | | | | | | | | | - Beth A Cimini
- Broad Institute of MIT and Harvard, Imaging Platform, Cambridge, USA
| | - Kevin Eliceiri
- Morgridge Institute for Research, Madison, USA
- University of Wisconsin-Madison, Madison, USA
| | | | | | | | - Ronald N Germain
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, USA
| | | | | | - Michael Halter
- National Institute of Standards and Technology, Gaithersburg, USA
| | | | | | | | - Alex Laude
- Newcastle University, Newcastle upon Tyne, UK
| | - Emma Lundberg
- Stanford University, Palo Alto, USA
- SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Jian Ma
- Carnegie Mellon University, Pittsburgh, USA
| | - Leonel Malacrida
- Institut Pasteur de Montevideo, & Universidad de la República, Montevideo, Uruguay
| | - Josh Moore
- German BioImaging-Gesellschaft für Mikroskopie und Bildanalyse e.V., Constance, Germany
| | - Glyn Nelson
- Newcastle University, Newcastle upon Tyne, UK
| | | | | | - Shuichi Onami
- RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | | | - Anne L Plant
- National Institute of Standards and Technology, Gaithersburg, USA
| | - Andrea J Radtke
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, USA
| | | | | | | | | | - Damir Sudar
- Quantitative Imaging Systems LLC, Portland, USA
| | | | | | | | | | - Ziv Yaniv
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, USA
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5
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Ferrian S, Cao A, McCaffrey EF, Saito T, Greenwald NF, Nicolls MR, Bruce T, Zamanian RT, Del Rosario P, Rabinovitch M, Angelo M. Single-Cell Imaging Maps Inflammatory Cell Subsets to Pulmonary Arterial Hypertension Vasculopathy. Am J Respir Crit Care Med 2024; 209:206-218. [PMID: 37934691 PMCID: PMC10806425 DOI: 10.1164/rccm.202209-1761oc] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 09/16/2022] [Accepted: 11/07/2023] [Indexed: 11/09/2023] Open
Abstract
Rationale: Unraveling immune-driven vascular pathology in pulmonary arterial hypertension (PAH) requires a comprehensive understanding of the immune cell landscape. Although patients with hereditary (H)PAH and bone morphogenetic protein receptor type 2 (BMPR2) mutations have more severe pulmonary vascular pathology, it is not known whether this is related to specific immune cell subsets. Objectives: This study aims to elucidate immune-driven vascular pathology by identifying immune cell subtypes linked to severity of pulmonary arterial lesions in PAH. Methods: We used cutting-edge multiplexed ion beam imaging by time of flight to compare pulmonary arteries (PAs) and adjacent tissue in PAH lungs (idiopathic [I]PAH and HPAH) with unused donor lungs, as controls. Measurements and Main Results: We quantified immune cells' proximity and abundance, focusing on those features linked to vascular pathology, and evaluated their impact on pulmonary arterial smooth muscle cells (SMCs) and endothelial cells. Distinct immune infiltration patterns emerged between PAH subtypes, with intramural involvement independently linked to PA occlusive changes. Notably, we identified monocyte-derived dendritic cells within PA subendothelial and adventitial regions, influencing vascular remodeling by promoting SMC proliferation and suppressing endothelial gene expression across PAH subtypes. In patients with HPAH, pronounced immune dysregulation encircled PA walls, characterized by heightened perivascular inflammation involving T cell immunoglobulin and mucin domain-3 (TIM-3)+ T cells. This correlated with an expanded DC subset expressing indoleamine 2,3-dioxygenase 1, TIM-3, and SAM and HD domain-containing deoxynucleoside triphosphate triphosphohydrolase 1, alongside increased neutrophils, SMCs, and alpha-smooth muscle actin (ACTA2)+ endothelial cells, reinforcing the heightened severity of pulmonary vascular lesions. Conclusions: This study presents the first architectural map of PAH lungs, connecting immune subsets not only with specific PA lesions but also with heightened severity in HPAH compared with IPAH. Our findings emphasize the therapeutic potential of targeting monocyte-derived dendritic cells, neutrophils, cellular interactions, and immune responses to alleviate severe vascular pathology in IPAH and HPAH.
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Affiliation(s)
- Selena Ferrian
- Department of Pathology
- Early Clinical Development Informatics, Genentech Inc., South San Francisco, California
| | - Aiqin Cao
- Department of Pediatrics
- Vera Moulton Wall Center for Pulmonary Vascular Disease
- Cardiovascular Institute, and
- Basic Science and Engineering (BASE) Initiative, Betty Irene Moore Children’s Heart Center, Stanford, California
| | | | | | | | - Mark R. Nicolls
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California
- Veterans Affairs Palo Alto Health Care System, Palo Alto, California
- Vera Moulton Wall Center for Pulmonary Vascular Disease
- Cardiovascular Institute, and
- Stanford Cardiovascular Institute, Stanford University, Palo Alto, California
| | | | - Roham T. Zamanian
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California
- Stanford Cardiovascular Institute, Stanford University, Palo Alto, California
| | - Patricia Del Rosario
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California
- Vera Moulton Wall Center for Pulmonary Vascular Disease
| | - Marlene Rabinovitch
- Department of Pediatrics
- Vera Moulton Wall Center for Pulmonary Vascular Disease
- Cardiovascular Institute, and
- Basic Science and Engineering (BASE) Initiative, Betty Irene Moore Children’s Heart Center, Stanford, California
- Stanford Cardiovascular Institute, Stanford University, Palo Alto, California
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6
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Ahmadian M, Rickert C, Minic A, Wrobel J, Bitler BG, Xing F, Angelo M, Hsieh EWY, Ghosh D, Jordan KR. A platform-independent framework for phenotyping of multiplex tissue imaging data. PLoS Comput Biol 2023; 19:e1011432. [PMID: 37733781 PMCID: PMC10547204 DOI: 10.1371/journal.pcbi.1011432] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 12/02/2022] [Revised: 10/03/2023] [Accepted: 08/14/2023] [Indexed: 09/23/2023] Open
Abstract
Multiplex imaging is a powerful tool to analyze the structural and functional states of cells in their morphological and pathological contexts. However, hypothesis testing with multiplex imaging data is a challenging task due to the extent and complexity of the information obtained. Various computational pipelines have been developed and validated to extract knowledge from specific imaging platforms. A common problem with customized pipelines is their reduced applicability across different imaging platforms: Every multiplex imaging technique exhibits platform-specific characteristics in terms of signal-to-noise ratio and acquisition artifacts that need to be accounted for to yield reliable and reproducible results. We propose a pixel classifier-based image preprocessing step that aims to minimize platform-dependency for all multiplex image analysis pipelines. Signal detection and noise reduction as well as artifact removal can be posed as a pixel classification problem in which all pixels in multiplex images can be assigned to two general classes of either I) signal of interest or II) artifacts and noise. The resulting feature representation maps contain pixel-scale representations of the input data, but exhibit significantly increased signal-to-noise ratios with normalized pixel values as output data. We demonstrate the validity of our proposed image preprocessing approach by comparing the results of two well-accepted and widely-used image analysis pipelines.
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Affiliation(s)
- Mansooreh Ahmadian
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Christian Rickert
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Angela Minic
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Julia Wrobel
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Benjamin G. Bitler
- Division of Reproductive Sciences, Department of OB/GYN, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Fuyong Xing
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Michael Angelo
- Department of Pathology, Stanford University, Stanford, California, United States of America
| | - Elena W. Y. Hsieh
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
- Pediatrics, Section of Allergy and Immunology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Debashis Ghosh
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Kimberly R. Jordan
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
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Jain S, Pei L, Spraggins JM, Angelo M, Carson JP, Gehlenborg N, Ginty F, Gonçalves JP, Hagood JS, Hickey JW, Kelleher NL, Laurent LC, Lin S, Lin Y, Liu H, Naba A, Nakayasu ES, Qian WJ, Radtke A, Robson P, Stockwell BR, Van de Plas R, Vlachos IS, Zhou M, Börner K, Snyder MP. Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP). Nat Cell Biol 2023; 25:1089-1100. [PMID: 37468756 PMCID: PMC10681365 DOI: 10.1038/s41556-023-01194-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/22/2023] [Indexed: 07/21/2023]
Abstract
The Human BioMolecular Atlas Program (HuBMAP) aims to create a multi-scale spatial atlas of the healthy human body at single-cell resolution by applying advanced technologies and disseminating resources to the community. As the HuBMAP moves past its first phase, creating ontologies, protocols and pipelines, this Perspective introduces the production phase: the generation of reference spatial maps of functional tissue units across many organs from diverse populations and the creation of mapping tools and infrastructure to advance biomedical research.
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Affiliation(s)
- Sanjay Jain
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA.
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
| | - Liming Pei
- Center for Mitochondrial and Epigenomic Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Jeffrey M Spraggins
- Department of Cell and Developmental Biology and the Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN, USA.
| | - Michael Angelo
- Department of Pathology, Stanford School of Medicine, Stanford, CA, USA
| | - James P Carson
- Texas Advanced Computing Center, University of Texas at Austin, Austin, TX, USA
| | - Nils Gehlenborg
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | | | - Joana P Gonçalves
- Department of Intelligent Systems, Delft University of Technology, Delft, Netherlands
| | - James S Hagood
- Department of Pediatrics (Pulmonology) and Program for Rare and Interstitial Lung Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - John W Hickey
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Neil L Kelleher
- Departments of Medicine, Chemistry and Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Louise C Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Shin Lin
- Division of Cardiology, University of Washington School of Medicine, Seattle, WA, USA
| | - Yiing Lin
- Department of Surgery, Washington University School of Medicine, St Louis, MO, USA
| | - Huiping Liu
- Departments of Pharmacology, Medicine (Hematology and Oncology), Lurie Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Alexandra Naba
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL, USA
| | - Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Andrea Radtke
- Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Paul Robson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Brent R Stockwell
- Department of Biological Sciences and Department of Chemistry, Columbia University, New York, NY, USA
| | - Raf Van de Plas
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
| | - Ioannis S Vlachos
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Spatial Technologies Unit, Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, and Harvard Medical School, Boston, MA, USA
| | - Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Katy Börner
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA.
| | - Michael P Snyder
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA.
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8
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Liu CC, Greenwald NF, Kong A, McCaffrey EF, Leow KX, Mrdjen D, Cannon BJ, Rumberger JL, Varra SR, Angelo M. Robust phenotyping of highly multiplexed tissue imaging data using pixel-level clustering. Nat Commun 2023; 14:4618. [PMID: 37528072 PMCID: PMC10393943 DOI: 10.1038/s41467-023-40068-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [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: 03/28/2023] [Accepted: 07/11/2023] [Indexed: 08/03/2023] Open
Abstract
While technologies for multiplexed imaging have provided an unprecedented understanding of tissue composition in health and disease, interpreting this data remains a significant computational challenge. To understand the spatial organization of tissue and how it relates to disease processes, imaging studies typically focus on cell-level phenotypes. However, images can capture biologically important objects that are outside of cells, such as the extracellular matrix. Here, we describe a pipeline, Pixie, that achieves robust and quantitative annotation of pixel-level features using unsupervised clustering and show its application across a variety of biological contexts and multiplexed imaging platforms. Furthermore, current cell phenotyping strategies that rely on unsupervised clustering can be labor intensive and require large amounts of manual cluster adjustments. We demonstrate how pixel clusters that lie within cells can be used to improve cell annotations. We comprehensively evaluate pre-processing steps and parameter choices to optimize clustering performance and quantify the reproducibility of our method. Importantly, Pixie is open source and easily customizable through a user-friendly interface.
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Affiliation(s)
- Candace C Liu
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Alex Kong
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Ke Xuan Leow
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Dunja Mrdjen
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Bryan J Cannon
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Josef Lorenz Rumberger
- Max-Delbrueck-Center for Molecular Medicine, Berlin, Germany
- Charité University Medicine, Berlin, Germany
| | | | - Michael Angelo
- Department of Pathology, Stanford University, Stanford, CA, 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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Greenbaum S, Averbukh I, Soon E, Rizzuto G, Baranski A, Greenwald NF, Kagel A, Bosse M, Jaswa EG, Khair Z, Kwok S, Warshawsky S, Piyadasa H, Goldston M, Spence A, Miller G, Schwartz M, Graf W, Van Valen D, Winn VD, Hollmann T, Keren L, van de Rijn M, Angelo M. A spatially resolved timeline of the human maternal-fetal interface. Nature 2023; 619:595-605. [PMID: 37468587 PMCID: PMC10356615 DOI: 10.1038/s41586-023-06298-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [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: 09/03/2021] [Accepted: 06/08/2023] [Indexed: 07/21/2023]
Abstract
Beginning in the first trimester, fetally derived extravillous trophoblasts (EVTs) invade the uterus and remodel its spiral arteries, transforming them into large, dilated blood vessels. Several mechanisms have been proposed to explain how EVTs coordinate with the maternal decidua to promote a tissue microenvironment conducive to spiral artery remodelling (SAR)1-3. However, it remains a matter of debate regarding which immune and stromal cells participate in these interactions and how this evolves with respect to gestational age. Here we used a multiomics approach, combining the strengths of spatial proteomics and transcriptomics, to construct a spatiotemporal atlas of the human maternal-fetal interface in the first half of pregnancy. We used multiplexed ion beam imaging by time-of-flight and a 37-plex antibody panel to analyse around 500,000 cells and 588 arteries within intact decidua from 66 individuals between 6 and 20 weeks of gestation, integrating this dataset with co-registered transcriptomics profiles. Gestational age substantially influenced the frequency of maternal immune and stromal cells, with tolerogenic subsets expressing CD206, CD163, TIM-3, galectin-9 and IDO-1 becoming increasingly enriched and colocalized at later time points. By contrast, SAR progression preferentially correlated with EVT invasion and was transcriptionally defined by 78 gene ontology pathways exhibiting distinct monotonic and biphasic trends. Last, we developed an integrated model of SAR whereby invasion is accompanied by the upregulation of pro-angiogenic, immunoregulatory EVT programmes that promote interactions with the vascular endothelium while avoiding the activation of maternal immune cells.
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Affiliation(s)
- Shirley Greenbaum
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Department of Obstetrics and Gynecology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel.
| | - Inna Averbukh
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Erin Soon
- Department of Pathology, Stanford University, Stanford, CA, USA
- Immunology Program, Stanford University, Stanford, CA, USA
| | - Gabrielle Rizzuto
- Department of Pathology, University of Californica San Francisco, San Francisco, CA, USA
| | - Alex Baranski
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Noah F Greenwald
- Department of Pathology, Stanford University, Stanford, CA, USA
- Cancer Biology Program, Stanford University, Stanford, CA, USA
| | - Adam Kagel
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Marc Bosse
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Eleni G Jaswa
- Department of Obstetrics Gynecology and Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Zumana Khair
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Shirley Kwok
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | | | - Mako Goldston
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Angie Spence
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Geneva Miller
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA, USA
| | - Morgan Schwartz
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA, USA
| | - Will Graf
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA, USA
| | - David Van Valen
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA, USA
| | - Virginia D Winn
- Department of Obstetrics and Gynecology, Stanford University, Stanford, CA, USA
| | - Travis Hollmann
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Leeat Keren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Michael Angelo
- Department of Pathology, Stanford University, Stanford, CA, USA.
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11
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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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12
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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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13
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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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14
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Houlahan KE, Khan A, Greenwald NF, West RB, Angelo M, Curtis C. Germline-mediated immunoediting sculpts breast cancer subtypes and metastatic proclivity. bioRxiv 2023:2023.03.15.532870. [PMID: 36993286 PMCID: PMC10055121 DOI: 10.1101/2023.03.15.532870] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Cancer represents a broad spectrum of molecularly and morphologically diverse diseases. Individuals with the same clinical diagnosis can have tumors with drastically different molecular profiles and clinical response to treatment. It remains unclear when these differences arise during disease course and why some tumors are addicted to one oncogenic pathway over another. Somatic genomic aberrations occur within the context of an individual's germline genome, which can vary across millions of polymorphic sites. An open question is whether germline differences influence somatic tumor evolution. Interrogating 3,855 breast cancer lesions, spanning pre-invasive to metastatic disease, we demonstrate that germline variants in highly expressed and amplified genes influence somatic evolution by modulating immunoediting at early stages of tumor development. Specifically, we show that the burden of germline-derived epitopes in recurrently amplified genes selects against somatic gene amplification in breast cancer. For example, individuals with a high burden of germline-derived epitopes in ERBB2, encoding human epidermal growth factor receptor 2 (HER2), are significantly less likely to develop HER2-positive breast cancer compared to other subtypes. The same holds true for recurrent amplicons that define four subgroups of ER-positive breast cancers at high risk of distant relapse. High epitope burden in these recurrently amplified regions is associated with decreased likelihood of developing high risk ER-positive cancer. Tumors that overcome such immune-mediated negative selection are more aggressive and demonstrate an "immune cold" phenotype. These data show the germline genome plays a previously unappreciated role in dictating somatic evolution. Exploiting germline-mediated immunoediting may inform the development of biomarkers that refine risk stratification within breast cancer subtypes.
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Affiliation(s)
- Kathleen E. Houlahan
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Aziz Khan
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Noah F Greenwald
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Robert B. West
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael Angelo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Christina Curtis
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine (Oncology), Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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15
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Rahim MK, Okholm TLH, Jones KB, McCarthy EE, Liu CC, Yee JL, Tamaki SJ, Marquez DM, Tenvooren I, Wai K, Cheung A, Davidson BR, Johri V, Samad B, O'Gorman WE, Krummel MF, van Zante A, Combes AJ, Angelo M, Fong L, Algazi AP, Ha P, Spitzer MH. Dynamic CD8 + T cell responses to cancer immunotherapy in human regional lymph nodes are disrupted in metastatic lymph nodes. Cell 2023; 186:1127-1143.e18. [PMID: 36931243 PMCID: PMC10348701 DOI: 10.1016/j.cell.2023.02.021] [Citation(s) in RCA: 59] [Impact Index Per Article: 59.0] [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: 09/01/2022] [Revised: 11/28/2022] [Accepted: 02/16/2023] [Indexed: 03/18/2023]
Abstract
CD8+ T cell responses are critical for anti-tumor immunity. While extensively profiled in the tumor microenvironment, recent studies in mice identified responses in lymph nodes (LNs) as essential; however, the role of LNs in human cancer patients remains unknown. We examined CD8+ T cells in human head and neck squamous cell carcinomas, regional LNs, and blood using mass cytometry, single-cell genomics, and multiplexed ion beam imaging. We identified progenitor exhausted CD8+ T cells (Tpex) that were abundant in uninvolved LN and clonally related to terminally exhausted cells in the tumor. After anti-PD-L1 immunotherapy, Tpex in uninvolved LNs reduced in frequency but localized near dendritic cells and proliferating intermediate-exhausted CD8+ T cells (Tex-int), consistent with activation and differentiation. LN responses coincided with increased circulating Tex-int. In metastatic LNs, these response hallmarks were impaired, with immunosuppressive cellular niches. Our results identify important roles for LNs in anti-tumor immune responses in humans.
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Affiliation(s)
- Maha K Rahim
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Trine Line H Okholm
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kyle B Jones
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA 94143, USA; Pharma Technical Cell and Gene Therapy, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Elizabeth E McCarthy
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Candace C Liu
- Department of Pathology, Stanford University, Stanford, CA 94304, USA
| | - Jacqueline L Yee
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Stanley J Tamaki
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Diana M Marquez
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Iliana Tenvooren
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Katherine Wai
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Alexander Cheung
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Brittany R Davidson
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Vrinda Johri
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Bushra Samad
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA
| | - William E O'Gorman
- Department of Translational Medicine, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Matthew F Krummel
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129, USA
| | - Annemieke van Zante
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Alexis J Combes
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Michael Angelo
- Department of Pathology, Stanford University, Stanford, CA 94304, USA
| | - Lawrence Fong
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129, USA
| | - Alain P Algazi
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Patrick Ha
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Matthew H Spitzer
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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16
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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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17
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Rovira-Clavé X, Drainas AP, Jiang S, Bai Y, Baron M, Zhu B, Dallas AE, Lee MC, Chu TP, Holzem A, Ayyagari R, Bhattacharya D, McCaffrey EF, Greenwald NF, Markovic M, Coles GL, Angelo M, Bassik MC, Sage J, Nolan GP. Spatial epitope barcoding reveals clonal tumor patch behaviors. Cancer Cell 2022; 40:1423-1439.e11. [PMID: 36240778 PMCID: PMC9673683 DOI: 10.1016/j.ccell.2022.09.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 07/22/2022] [Accepted: 09/21/2022] [Indexed: 01/09/2023]
Abstract
Intratumoral heterogeneity is a seminal feature of human tumors contributing to tumor progression and response to treatment. Current technologies are still largely unsuitable to accurately track phenotypes and clonal evolution within tumors, especially in response to genetic manipulations. Here, we developed epitopes for imaging using combinatorial tagging (EpicTags), which we coupled to multiplexed ion beam imaging (EpicMIBI) for in situ tracking of barcodes within tissue microenvironments. Using EpicMIBI, we dissected the spatial component of cell lineages and phenotypes in xenograft models of small cell lung cancer. We observed emergent properties from mixed clones leading to the preferential expansion of clonal patches for both neuroendocrine and non-neuroendocrine cancer cell states in these models. In a tumor model harboring a fraction of PTEN-deficient cancer cells, we observed a non-autonomous increase of clonal patch size in PTEN wild-type cancer cells. EpicMIBI facilitates in situ interrogation of cell-intrinsic and cell-extrinsic processes involved in intratumoral heterogeneity.
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Affiliation(s)
- Xavier Rovira-Clavé
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Alexandros P Drainas
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Sizun Jiang
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Yunhao Bai
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Maya Baron
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Bokai Zhu
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Alec E Dallas
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Myung Chang Lee
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Theresa P Chu
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Alessandra Holzem
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Ramya Ayyagari
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Debadrita Bhattacharya
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Erin F McCaffrey
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Noah F Greenwald
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Maxim Markovic
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Garry L Coles
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Michael Angelo
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Michael C Bassik
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Julien Sage
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA.
| | - Garry P Nolan
- Department of Pathology, Stanford University, Stanford, CA 94305, USA.
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18
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Jiang S, Chan CN, Rovira-Clavé X, Chen H, Bai Y, Zhu B, McCaffrey E, Greenwald NF, Liu C, Barlow GL, Weirather JL, Oliveria JP, Nakayama T, Lee IT, Matter MS, Carlisle AE, Philips D, Vazquez G, Mukherjee N, Busman-Sahay K, Nekorchuk M, Terry M, Younger S, Bosse M, Demeter J, Rodig SJ, Tzankov A, Goltsev Y, McIlwain DR, Angelo M, Estes JD, Nolan GP. Combined protein and nucleic acid imaging reveals virus-dependent B cell and macrophage immunosuppression of tissue microenvironments. Immunity 2022; 55:1118-1134.e8. [PMID: 35447093 PMCID: PMC9220319 DOI: 10.1016/j.immuni.2022.03.020] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [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: 05/18/2021] [Revised: 10/13/2021] [Accepted: 03/25/2022] [Indexed: 12/12/2022]
Abstract
Understanding the mechanisms of HIV tissue persistence necessitates the ability to visualize tissue microenvironments where infected cells reside; however, technological barriers limit our ability to dissect the cellular components of these HIV reservoirs. Here, we developed protein and nucleic acid in situ imaging (PANINI) to simultaneously quantify DNA, RNA, and protein levels within these tissue compartments. By coupling PANINI with multiplexed ion beam imaging (MIBI), we measured over 30 parameters simultaneously across archival lymphoid tissues from healthy or simian immunodeficiency virus (SIV)-infected nonhuman primates. PANINI enabled the spatial dissection of cellular phenotypes, functional markers, and viral events resulting from infection. SIV infection induced IL-10 expression in lymphoid B cells, which correlated with local macrophage M2 polarization. This highlights a potential viral mechanism for conditioning an immunosuppressive tissue environment for virion production. The spatial multimodal framework here can be extended to decipher tissue responses in other infectious diseases and tumor biology.
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Affiliation(s)
- Sizun Jiang
- Department of Pathology, Stanford University, Stanford, CA, USA; Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
| | - Chi Ngai Chan
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA
| | | | - Han Chen
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Yunhao Bai
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Bokai Zhu
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Erin McCaffrey
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Candace Liu
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Graham L Barlow
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Jason L Weirather
- Center of Immuno-Oncology, Dana-Faber Cancer Institute, Boston, MA, USA
| | - John Paul Oliveria
- Department of Pathology, Stanford University, Stanford, CA, USA; Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Tsuguhisa Nakayama
- Department of Pathology, Stanford University, Stanford, CA, USA; Department of Otorhinolaryngology, Jikei University School of Medicine, Tokyo, Japan
| | - Ivan T Lee
- Department of Pathology, Stanford University, Stanford, CA, USA; Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthias S Matter
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Anne E Carlisle
- Center of Immuno-Oncology, Dana-Faber Cancer Institute, Boston, MA, USA
| | - Darci Philips
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Gustavo Vazquez
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Kathleen Busman-Sahay
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA
| | - Michael Nekorchuk
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA
| | - Margaret Terry
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA
| | - Skyler Younger
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA
| | - Marc Bosse
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Janos Demeter
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Scott J Rodig
- Department of Pathology, Brigham & Women's Hospital, Boston, MA, USA
| | - Alexandar Tzankov
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Yury Goltsev
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Michael Angelo
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Jacob D Estes
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA; Division of Pathobiology & Immunology, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA.
| | - Garry P Nolan
- Department of Pathology, Stanford University, Stanford, CA, USA.
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19
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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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20
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Ghahremani P, Li Y, Kaufman A, Vanguri R, Greenwald N, Angelo M, Hollmann TJ, Nadeem S. Deep learning-inferred multiplex immunofluorescence for immunohistochemical image quantification. NAT MACH INTELL 2022; 4:401-412. [DOI: 10.1038/s42256-022-00471-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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21
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Schapiro D, Yapp C, Sokolov A, Reynolds SM, Chen YA, Sudar D, Xie Y, Muhlich J, Arias-Camison R, Arena S, Taylor AJ, Nikolov M, Tyler M, Lin JR, Burlingame EA, Chang YH, Farhi SL, Thorsson V, Venkatamohan N, Drewes JL, Pe'er D, Gutman DA, Herrmann MD, Gehlenborg N, Bankhead P, Roland JT, Herndon JM, Snyder MP, Angelo M, Nolan G, Swedlow JR, Schultz N, Merrick DT, Mazzili SA, Cerami E, Rodig SJ, Santagata S, Sorger PK. MITI minimum information guidelines for highly multiplexed tissue images. Nat Methods 2022; 19:262-267. [PMID: 35277708 PMCID: PMC9009186 DOI: 10.1038/s41592-022-01415-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The imminent release of tissue atlases combining multi-channel microscopy with single cell sequencing and other omics data from normal and diseased specimens creates an urgent need for data and metadata standards that guide data deposition, curation and release. We describe a Minimum Information about highly multiplexed Tissue Imaging (MITI) standard that applies best practices developed for genomics and other microscopy data to highly multiplexed tissue images and traditional histology.
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Affiliation(s)
- Denis Schapiro
- Laboratory of Systems Pharmacology, Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University Hospital and Heidelberg University, Heidelberg, Germany
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Clarence Yapp
- Laboratory of Systems Pharmacology, Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
- Image and Data Analysis Core, Harvard Medical School, Boston, MA, USA
| | - Artem Sokolov
- Laboratory of Systems Pharmacology, Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | | | - Yu-An Chen
- Laboratory of Systems Pharmacology, Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
| | - Damir Sudar
- Quantitative Imaging Systems LLC, Portland, OR, USA
| | - Yubin Xie
- Program in Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jeremy Muhlich
- Laboratory of Systems Pharmacology, Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
| | - Raquel Arias-Camison
- Laboratory of Systems Pharmacology, Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
| | - Sarah Arena
- Laboratory of Systems Pharmacology, Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
| | | | | | - Madison Tyler
- Laboratory of Systems Pharmacology, Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
| | - Jia-Ren Lin
- Laboratory of Systems Pharmacology, Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA
| | - Erik A Burlingame
- Oregon Health and Science University, Portland, OR, USA
- Indica Labs, Albuquerque, NM, USA
| | - Young H Chang
- Oregon Health and Science University, Portland, OR, USA
| | - Samouil L Farhi
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Julia L Drewes
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Dana Pe'er
- Program in Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Markus D Herrmann
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Nils Gehlenborg
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Peter Bankhead
- Edinburgh Pathology, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Joseph T Roland
- Vanderbilt University School of Medicine, Nashville, TN, USA
| | - John M Herndon
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Michael Angelo
- School of Medicine, Stanford University, Stanford, CA, USA
| | - Garry Nolan
- School of Medicine, Stanford University, Stanford, CA, USA
| | - Jason R Swedlow
- Division of Computational Biology and Centre for Gene Regulation and Expression, University of Dundee, Dundee, UK
| | - Nikolaus Schultz
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | | | - Scott J Rodig
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Sandro Santagata
- Laboratory of Systems Pharmacology, Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA.
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, MA, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
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22
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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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23
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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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24
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Averbukh I, Greenwald NF, Liu CC, Angelo M. Evaluation of Geuenich et al.: Targeting a crucial bottleneck for analyzing single-cell multiplexed imaging data. Cell Syst 2021; 12:1121-1123. [PMID: 34914901 DOI: 10.1016/j.cels.2021.11.003] [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: 11/28/2022]
Abstract
One snapshot of the peer review process for "Automated assignment of cell identity from single-cell multiplexed imaging and proteomic data" (Geuenich et al., 2021).
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Affiliation(s)
- Inna Averbukh
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Candace C Liu
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Michael Angelo
- Department of Pathology, Stanford University, Stanford, CA, USA.
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25
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Elhanani O, Keren L, Angelo M. High-Dimensional Tissue Profiling by Multiplexed Ion Beam Imaging. Methods Mol Biol 2021; 2386:147-156. [PMID: 34766270 DOI: 10.1007/978-1-0716-1771-7_10] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Multiplexed Ion Beam Imaging by Time of Flight (MIBI-TOF) enables high-dimensional imaging in situ of clinical specimens at single-cell resolution. In MIBI-TOF, tissue sections are stained with dozens of metal-labeled antibodies, whose abundance and location are read by secondary ionization mass spectrometry. The result is a multi-dimensional image, depicting sub-cellular expression and localization for dozens of distinct proteins in situ. Here, we describe the staining and imaging procedures of a MIBI-TOF experiment.
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Affiliation(s)
- Ofer Elhanani
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Leeat Keren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
| | - Michael Angelo
- Department of Pathology, Stanford University, Stanford, CA, USA.
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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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27
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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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28
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Patwa A, Yamashita R, Long J, Risom T, Angelo M, Keren L, Rubin DL. Multiplexed imaging analysis of the tumor-immune microenvironment reveals predictors of outcome in triple-negative breast cancer. Commun Biol 2021; 4:852. [PMID: 34244605 PMCID: PMC8271023 DOI: 10.1038/s42003-021-02361-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [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: 05/17/2021] [Accepted: 06/10/2021] [Indexed: 12/18/2022] Open
Abstract
Triple-negative breast cancer, the poorest-prognosis breast cancer subtype, lacks clinically approved biomarkers for patient risk stratification and treatment management. Prior literature has shown that interrogation of the tumor-immune microenvironment may be a promising approach to fill these gaps. Recently developed high-dimensional tissue imaging technology, such as multiplexed ion beam imaging, provide spatial context to protein expression in the microenvironment, allowing in-depth characterization of cellular processes. We demonstrate that profiling the functional proteins involved in cell-to-cell interactions in the microenvironment can predict recurrence and overall survival. We highlight the immunological relevance of the immunoregulatory proteins PD-1, PD-L1, IDO, and Lag3 by tying interactions involving them to recurrence and survival. Multivariate analysis reveals that our methods provide additional prognostic information compared to clinical variables. In this work, we present a computational pipeline for the examination of the tumor-immune microenvironment using multiplexed ion beam imaging that produces interpretable results, and is generalizable to other cancer types.
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Affiliation(s)
- Aalok Patwa
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Archbishop Mitty High School, San Jose, CA, USA
| | - Rikiya Yamashita
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Center for Artificial Intelligence in Medicine and Imaging, Stanford University, Stanford, CA, USA
| | - Jin Long
- Center for Artificial Intelligence in Medicine and Imaging, Stanford University, Stanford, CA, USA
| | - Tyler Risom
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Michael Angelo
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Leeat Keren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Daniel L Rubin
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
- Center for Artificial Intelligence in Medicine and Imaging, Stanford University, Stanford, CA, USA.
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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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30
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Baranski A, Milo I, Greenbaum S, Oliveria JP, Mrdjen D, Angelo M, Keren L. MAUI (MBI Analysis User Interface)-An image processing pipeline for Multiplexed Mass Based Imaging. PLoS Comput Biol 2021; 17:e1008887. [PMID: 33872301 PMCID: PMC8084329 DOI: 10.1371/journal.pcbi.1008887] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 04/29/2021] [Accepted: 03/17/2021] [Indexed: 11/19/2022] Open
Abstract
Mass Based Imaging (MBI) technologies such as Multiplexed Ion Beam Imaging by time of flight (MIBI-TOF) and Imaging Mass Cytometry (IMC) allow for the simultaneous measurement of the expression levels of 40 or more proteins in biological tissue, providing insight into cellular phenotypes and organization in situ. Imaging artifacts, resulting from the sample, assay or instrumentation complicate downstream analyses and require correction by domain experts. Here, we present MBI Analysis User Interface (MAUI), a series of graphical user interfaces that facilitate this data pre-processing, including the removal of channel crosstalk, noise and antibody aggregates. Our software streamlines these steps and accelerates processing by enabling real-time and interactive parameter tuning across multiple images. High-dimensional Imaging technologies allow to simultaneously measure the expression levels of dozens of proteins in biological tissue, providing insight into single-cell phenotypes and organization in situ. Imaging artifacts, resulting from the sample, assay or instrumentation complicate downstream analyses and require correction by domain experts. Here, we present MAUI, a series of graphical user interfaces that facilitate this data pre-processing, including the removal of channel crosstalk, noise and antibody aggregates. MAUI accelerates and automates these steps, such that reproducible, high-quality data will be the input for subsequent stages of analysis.
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Affiliation(s)
- Alex Baranski
- School of Medicine, Department of Pathology, Stanford University, Stanford, California, United States of America
| | - Idan Milo
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Shirley Greenbaum
- School of Medicine, Department of Pathology, Stanford University, Stanford, California, United States of America
| | - John-Paul Oliveria
- School of Medicine, Department of Pathology, Stanford University, Stanford, California, United States of America
- Department of Medicine, Division of Respirology, McMaster University, Hamilton, Ontario, Canada
| | - Dunja Mrdjen
- School of Medicine, Department of Pathology, Stanford University, Stanford, California, United States of America
| | - Michael Angelo
- School of Medicine, Department of Pathology, Stanford University, Stanford, California, United States of America
- * E-mail: (MA); (LK)
| | - Leeat Keren
- School of Medicine, Department of Pathology, Stanford University, Stanford, California, United States of America
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- * E-mail: (MA); (LK)
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31
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Angelo M. Abstract PD5-07: Mapping the tumor and microenvironmental evolution underlying DCIS progression throughmultiplexed ion beam imaging. Cancer Res 2021. [DOI: 10.1158/1538-7445.sabcs20-pd5-07] [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
Ductal Carcinoma in Situ (DCIS) is a pre-invasive lesion that accounts for nearly 20% of new breast cancer diagnoses. Of these cases, about half will progress to invasive breast cancer (IBC) within ten years. However, because diagnostic criteria for delineating low risk lesions from those likely to progress to IBC have not been identified, many patients are receiving unnecessary chemotherapy and surgery that can result in therapy-related morbidity and death. With this in mind, we used Multiplexed Ion Beam Imaging by time of flight (MIBI-TOF) and RNA-seq laser-capture microdissection (SMART-3SEQ) to construct a comprehensive spatial atlas describing the structure, function, and cellular composition of DCIS. MIBI-TOF and SMART-3SEQ were used to compare lesions from patients that later developed IBC with those from age- and history matched DCIS controls without recurrence. Using a 37-marker staining panel to interrogate 137 lesions, we identified 17 distinct cell populations of epithelial, stromal, and immune cells that were arranged in recurrent cellular microenvironments specific for DCIS or invasive disease. We observe a coordinated shift in the immune and stromal compartments as invasive disease arises, including a robust influx of lymphocytes and expansion reactive stromal phenotypes in synchronous DCIS + IBC, which was distinct from the macrophage-dominant, highly vascularized microenvironment of recurrent IBC. Further, single cell segmentation using a deep learning model was combined with pixel-level coexpression analysis to extensively evaluate how the thickness, continuity, and phenotype of ductal myoepithelium changes as tumors progress from a pre-invasive state. These data were incorporated into a comprehensive model which was subsequently used to identify a subset of features that correlate with disease-free survival following DCIS tumor resection. Taken together, these features represent important prognostic metrics that can be used to separate pre-invasive from indolent DCIS tumors, and allow for tailored therapy that improves patient outcomes and quality of life in this disease.
Citation Format: Michael Angelo. Mapping the tumor and microenvironmental evolution underlying DCIS progression throughmultiplexed ion beam imaging [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PD5-07.
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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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33
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Risom T, Rivero B, Liu C, Baranski A, Strand S, Greenwald N, McCaffrey E, Varma S, Keren L, Srivastava S, Zhu C, Vennam S, Hwang S, Colditz G, Bendall S, West R, Angelo M. Abstract PR05: Mapping the tumor and microenvironmental evolution underlying DCIS progression through multiplexed ion beam imaging. Cancer Res 2020. [DOI: 10.1158/1538-7445.tumhet2020-pr05] [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
Ductal Carcinoma in Situ (DCIS) is a pre-invasive lesion that accounts for nearly 20% of new breast cancer diagnoses. Of these cases, about half will progress to invasive breast cancer (IBC) within ten years. However, because diagnostic criteria for delineating low risk lesions from those likely to progress to IBC have not been identified, many patients are receiving unnecessary chemotherapy and surgery that can result in therapy-related morbidity and death. With this in mind, we used Multiplexed Ion Beam Imaging by time of flight (MIBI-TOF) and RNA-seq laser-capture microdissection (SMART-3SEQ) to construct a comprehensive spatial atlas describing the structure, function, and cellular composition of DCIS. MIBI-TOF and SMART-3SEQ were used to compare lesions from patients that later developed IBC with those from age- and history matched DCIS controls without recurrence. Using a 37-marker staining panel to interrogate 137 lesions, we identified 30 distinct cell populations of the epithelial, stromal, and immune lineages that were arranged in recurrent cellular microenvironments specific for DCIS or invasive disease. We observe a coordinated shift in the immune and stromal compartments as invasive disease arises, including an expansion of immune cell diversity and transition to reactive stromal phenotypes in synchronous DCIS + IBC, which was distinct from the macrophage-dominant microenvironment of recurrent IBC. Single-cell segmentation using a deep learning model was combined with pixel-level coexpression analysis to determine how thickness, continuity, and phenotype of ductal myoepithelium changes as tumors progress from a pre-invasive state. These data were incorporated into a comprehensive model which was subsequently used to identify a subset of features that correlate with disease-free survival following DCIS tumor resection. Taken together, these features represent important prognostic metrics that can be used to separate pre-invasive from indolent DCIS tumors, and allow for tailored therapy that improves patient outcomes and quality of life in this disease.
Citation Format: Tyler Risom, Belen Rivero, Candace Liu, Alex Baranski, Siri Strand, Noah Greenwald, Erin McCaffrey, Sushama Varma, Leeat Keren, Sucheta Srivastava, Chunfang Zhu, Sujay Vennam, Shelley Hwang, Graham Colditz, Sean Bendall, Robert West, Michael Angelo. Mapping the tumor and microenvironmental evolution underlying DCIS progression through multiplexed ion beam imaging [abstract]. In: Proceedings of the AACR Virtual Special Conference on Tumor Heterogeneity: From Single Cells to Clinical Impact; 2020 Sep 17-18. Philadelphia (PA): AACR; Cancer Res 2020;80(21 Suppl):Abstract nr PR05.
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34
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Taube JM, Akturk G, Angelo M, Engle EL, Gnjatic S, Greenbaum S, Greenwald NF, Hedvat CV, Hollmann TJ, Juco J, Parra ER, Rebelatto MC, Rimm DL, Rodriguez-Canales J, Schalper KA, Stack EC, Ferreira CS, Korski K, Lako A, Rodig SJ, Schenck E, Steele KE, Surace MJ, Tetzlaff MT, von Loga K, Wistuba II, Bifulco CB. The Society for Immunotherapy of Cancer statement on best practices for multiplex immunohistochemistry (IHC) and immunofluorescence (IF) staining and validation. J Immunother Cancer 2020; 8:e000155. [PMID: 32414858 PMCID: PMC7239569 DOI: 10.1136/jitc-2019-000155] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [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] [Accepted: 01/09/2020] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVES The interaction between the immune system and tumor cells is an important feature for the prognosis and treatment of cancer. Multiplex immunohistochemistry (mIHC) and multiplex immunofluorescence (mIF) analyses are emerging technologies that can be used to help quantify immune cell subsets, their functional state, and their spatial arrangement within the tumor microenvironment. METHODS The Society for Immunotherapy of Cancer (SITC) convened a task force of pathologists and laboratory leaders from academic centers as well as experts from pharmaceutical and diagnostic companies to develop best practice guidelines for the optimization and validation of mIHC/mIF assays across platforms. RESULTS Representative outputs and the advantages and disadvantages of mIHC/mIF approaches, such as multiplexed chromogenic IHC, multiplexed immunohistochemical consecutive staining on single slide, mIF (including multispectral approaches), tissue-based mass spectrometry, and digital spatial profiling are discussed. CONCLUSIONS mIHC/mIF technologies are becoming standard tools for biomarker studies and are likely to enter routine clinical practice in the near future. Careful assay optimization and validation will help ensure outputs are robust and comparable across laboratories as well as potentially across mIHC/mIF platforms. Quantitative image analysis of mIHC/mIF output and data management considerations will be addressed in a complementary manuscript from this task force.
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Affiliation(s)
- Janis M Taube
- Department of Dermatology, Johns Hopkins School of Medicine, Bloomberg~Kimmel Institute for Cancer Immunotherapy, Baltimore, Maryland, USA
| | - Guray Akturk
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York City, USA
| | - Michael Angelo
- Department of Pathology, Stanford University School of Medicine, Palo Alto, California, USA
| | - Elizabeth L Engle
- Department of Dermatology, Johns Hopkins School of Medicine, Bloomberg~Kimmel Institute for Cancer Immunotherapy, Baltimore, Maryland, USA
| | - Sacha Gnjatic
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York City, USA
| | - Shirley Greenbaum
- Department of Pathology, Stanford University School of Medicine, Palo Alto, California, USA
| | - Noah F Greenwald
- Department of Pathology, Stanford University School of Medicine, Palo Alto, California, USA
- Cancer Biology Program, Stanford University School of Medicine, Palo Alto, California, USA
| | | | - Travis J Hollmann
- Dermatopathology, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | | | - Edwin R Parra
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - David L Rimm
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | | | - Kurt A Schalper
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | | | - Cláudia S Ferreira
- Pharma Research and Early Development (pRED), Roche Innovation Center Munich, Penzberg, Germany
| | - Konstanty Korski
- Pharma Research and Early Development (pRED), Roche Innovation Center Munich, Penzberg, Germany
| | - Ana Lako
- Dana-Farber/Brigham and Women's Cancer Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Scott J Rodig
- Dana-Farber/Brigham and Women's Cancer Center, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | | | | | | | - Michael T Tetzlaff
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Katharina von Loga
- Biomedical Research Centre, Royal Marsden NHS Foundation Trust, London, UK
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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Affiliation(s)
- Leeat Keren
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Michael Angelo
- Department of Pathology, Stanford University, Stanford, CA, USA.
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St-Pierre J, Angelo M, Zhai Y. Focusing Research by Developing Performance Related Selection Criteria for PEMFC Contaminants. ACTA ACUST UNITED AC 2019. [DOI: 10.1149/1.3635561] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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37
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Keren L, Bosse M, Thompson S, Risom T, Vijayaragavan K, McCaffrey E, Marquez D, Angoshtari R, Greenwald NF, Fienberg H, Wang J, Kambham N, Kirkwood D, Nolan G, Montine TJ, Galli SJ, West R, Bendall SC, Angelo M. MIBI-TOF: A multiplexed imaging platform relates cellular phenotypes and tissue structure. Sci Adv 2019; 5:eaax5851. [PMID: 31633026 PMCID: PMC6785247 DOI: 10.1126/sciadv.aax5851] [Citation(s) in RCA: 192] [Impact Index Per Article: 38.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 09/14/2019] [Indexed: 05/13/2023]
Abstract
Understanding tissue structure and function requires tools that quantify the expression of multiple proteins while preserving spatial information. Here, we describe MIBI-TOF (multiplexed ion beam imaging by time of flight), an instrument that uses bright ion sources and orthogonal time-of-flight mass spectrometry to image metal-tagged antibodies at subcellular resolution in clinical tissue sections. We demonstrate quantitative, full periodic table coverage across a five-log dynamic range, imaging 36 labeled antibodies simultaneously with histochemical stains and endogenous elements. We image fields of view up to 800 μm × 800 μm at resolutions down to 260 nm with sensitivities approaching single-molecule detection. We leverage these properties to interrogate intrapatient heterogeneity in tumor organization in triple-negative breast cancer, revealing regional variability in tumor cell phenotypes in contrast to a structured immune response. Given its versatility and sample back-compatibility, MIBI-TOF is positioned to leverage existing annotated, archival tissue cohorts to explore emerging questions in cancer, immunology, and neurobiology.
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Affiliation(s)
- Leeat Keren
- Department of Pathology, Stanford University, Stanford, CA
| | - Marc Bosse
- Department of Pathology, Stanford University, Stanford, CA
| | - Steve Thompson
- Department of Pathology, Stanford University, Stanford, CA
| | - Tyler Risom
- Department of Pathology, Stanford University, Stanford, CA
| | | | - Erin McCaffrey
- Department of Pathology, Stanford University, Stanford, CA
- Immunology Program, Stanford University School of Medicine, Stanford, CA
| | - Diana Marquez
- Department of Pathology, Stanford University, Stanford, CA
| | | | - Noah F. Greenwald
- Department of Pathology, Stanford University, Stanford, CA
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA
| | | | - Jennifer Wang
- Department of Pathology, Stanford University, Stanford, CA
| | | | - David Kirkwood
- Department of Pathology, Stanford University, Stanford, CA
| | - Garry Nolan
- Department of Microbiology and Immunology, Stanford University, Stanford, CA
| | | | | | - Robert West
- Department of Pathology, Stanford University, Stanford, CA
| | | | - Michael Angelo
- Department of Pathology, Stanford University, Stanford, CA
- Corresponding.author.
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Yucel N, Wang YX, Mai T, Porpiglia E, Lund PJ, Markov G, Garcia BA, Bendall SC, Angelo M, Blau HM. Glucose Metabolism Drives Histone Acetylation Landscape Transitions that Dictate Muscle Stem Cell Function. Cell Rep 2019; 27:3939-3955.e6. [PMID: 31242425 PMCID: PMC6788807 DOI: 10.1016/j.celrep.2019.05.092] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [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: 04/11/2018] [Revised: 04/25/2019] [Accepted: 05/22/2019] [Indexed: 12/22/2022] Open
Abstract
The impact of glucose metabolism on muscle regeneration remains unresolved. We identify glucose metabolism as a crucial driver of histone acetylation and myogenic cell fate. We use single-cell mass cytometry (CyTOF) and flow cytometry to characterize the histone acetylation and metabolic states of quiescent, activated, and differentiating muscle stem cells (MuSCs). We find glucose is dispensable for mitochondrial respiration in proliferating MuSCs, so that glucose becomes available for maintaining high histone acetylation via acetyl-CoA. Conversely, quiescent and differentiating MuSCs increase glucose utilization for respiration and have consequently reduced acetylation. Pyruvate dehydrogenase (PDH) activity serves as a rheostat for histone acetylation and must be controlled for muscle regeneration. Increased PDH activity in proliferation increases histone acetylation and chromatin accessibility at genes that must be silenced for differentiation to proceed, and thus promotes self-renewal. These results highlight metabolism as a determinant of MuSC histone acetylation, fate, and function during muscle regeneration.
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Affiliation(s)
- Nora Yucel
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yu Xin Wang
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Thach Mai
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ermelinda Porpiglia
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peder J Lund
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Glenn Markov
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Benjamin A Garcia
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sean C Bendall
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Michael Angelo
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Helen M Blau
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
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Weiskopf D, Grifoni A, Angelo M, Moore E, Sidney J, Phillips EJ, Mallal SA, de Silva AD, Peters B, Sette A. Characterization of HLA-DP and DQ restricted dengue virus-specific CD4+T cell responses reveals lower magnitude responses associated with a differential pattern of immunodominance as compared to DR restricted responses. The Journal of Immunology 2019. [DOI: 10.4049/jimmunol.202.supp.140.14] [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] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Background
Assessment of adaptive immunity is an important element to understand immunopathology and to define the correlates of protection against dengue virus (DENV). While previous studies characterized responses restricted by the HLA DRB1 locus, the responses associated with the DP and DQ loci have not been characterized to date. Accordingly, here we mapped HLA DP and DQ restricted DENV-specific CD4 T cell epitopes in PBMCs from individuals previously exposed to DENV from the general population of the Sri Lanka.
Methods
We studied the DP (*0101, *0201, *0401, *0402) and DQ (*0501, *0602, *0301, *0302, *0201) allelic variants which provide a greater than 80% population coverage worldwide. CD4+ T cells purified by magnetic bead negative selection were cultured for two weeks with autologous APC and pools of HLA –specific predicted binders and tested for reactivity in a standard IFNγ ELISPOT assay.
Results
Magnitude of responses for both the DP and DQ loci were significantly lower than previously observed for the DRB1 locus. This was correlated with lower membrane expression of HLA- DP and DQ molecules on the PBMCs as compared to HLA DR. While responses against Capsid were dominant for the various DR and DP alleles this protein was hardly recognized by DQ alleles. Responses against NS3 were dominant in the case of DR and DQ but absent in the case of DP, and response to NS1 were prominent in the case of the DP alleles, but negligible in the case of the DR and DQ alleles tested.
Conclusion
The HLA DP and DQ loci mediate DENV-CD4 specific immune responses of lower magnitude as compared to HLA DRB1. The responses mediated by the DP and DQ loci are also associated with distinct and characteristic patterns of immunodominance.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Bjoern Peters
- 1La Jolla Institute for Immunology
- 4University of California San Diego
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40
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Gajera CR, Fernandez R, Postupna N, Montine KS, Fox EJ, Tebaykin D, Angelo M, Bendall SC, Keene CD, Montine TJ. Mass synaptometry: High-dimensional multi parametric assay for single synapses. J Neurosci Methods 2018; 312:73-83. [PMID: 30465796 DOI: 10.1016/j.jneumeth.2018.11.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [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: 08/24/2018] [Revised: 11/09/2018] [Accepted: 11/10/2018] [Indexed: 01/19/2023]
Abstract
BACKGROUND Synaptic alterations, especially presynaptic changes, are cardinal features of neurodegenerative diseases and strongly correlate with cognitive decline. NEW METHOD We report "Mass Synaptometry" for the high-dimensional analysis of individual human synaptosomes, enriched nerve terminals from brain. This method was adapted from cytometry by time-of-flight mass spectrometry (CyTOF), which is commonly used for single-cell analysis of immune and blood cells. RESULT Here we overcome challenges for single synapse analysis by optimizing synaptosome preparations, generating a 'SynTOF panel,' recalibrating acquisition settings, and applying computational analyses. Through the analysis of 390,000 individual synaptosomes, we also provide proof-of principle validation by characterizing changes in synaptic diversity in Lewy Body Disease (LBD), Alzheimer's disease and normal brain. COMPARISON WITH EXISTING METHOD(S) Current imaging methods to study synapses in humans are capable of analyzing a limited number of synapses, and conventional flow cytometric techniques are typically restricted to fewer than 6 parameters. Our method allows for the simultaneous detection of 34 parameters from tens of thousands of individual synapses. CONCLUSION We applied Mass Synaptometry to analyze 34 parameters simultaneously on more than 390,000 synaptosomes from 13 human brain samples. This new approach revealed regional and disease-specific changes in synaptic phenotypes, including validation of this method with the expected changes in the molecular composition of striatal dopaminergic synapses in Lewy body disease and Alzheimer's disease. Mass synaptometry enables highly parallel molecular profiling of individual synaptic terminals.
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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
| | - Edward J Fox
- Department of Pathology, Stanford University Medical Center, Stanford, CA, United States
| | - Dmitry Tebaykin
- Department of Pathology, Stanford University Medical Center, Stanford, CA, United States
| | - Michael Angelo
- Department of Pathology, Stanford University Medical Center, Stanford, CA, United States
| | - Sean C Bendall
- Department of Pathology, Stanford University Medical Center, Stanford, CA, United States
| | - C Dirk Keene
- Department of Pathology, University of Washington, Seattle, WA, United States
| | - Thomas J Montine
- Department of Pathology, Stanford University Medical Center, Stanford, CA, United States.
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41
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Moore E, Grifoni A, Weiskopf D, Schulten V, Arlehamn CSL, Angelo M, Pham J, Leary S, Sidney J, Broide D, Frazier A, Phillips E, Mallal S, Mack SJ, Sette A. Sequence-based HLA-A, B, C, DP, DQ, and DR typing of 496 adults from San Diego, California, USA. Hum Immunol 2018; 79:821-822. [PMID: 30278218 DOI: 10.1016/j.humimm.2018.09.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 09/21/2018] [Accepted: 09/27/2018] [Indexed: 11/26/2022]
Abstract
DNA sequence-based typing at the HLA-A, -B, -C, -DPB1, -DQA1, -DQB1, and -DRB1 loci was performed on 496 healthy adult donors from San Diego, California, to characterize allele frequencies in support of studies of T cell responses to common allergens. Deviations from Hardy Weinberg proportions were detected at each locus except A and C. Several alleles were found in more than 15% of individuals, including the class II alleles DPB1∗02:01, DPB1∗04:01, DQA1∗01:02, DQA1∗05:01, DQB1∗03:01, and the class I allele A∗02:01. Genotype data will be available in the Allele Frequencies Net Database (AFND 3562).
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Affiliation(s)
- Eugene Moore
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology, La Jolla, CA 92037, USA.
| | - Alba Grifoni
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology, La Jolla, CA 92037, USA
| | - Daniela Weiskopf
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology, La Jolla, CA 92037, USA
| | - Veronique Schulten
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology, La Jolla, CA 92037, USA
| | | | - Michael Angelo
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology, La Jolla, CA 92037, USA
| | - John Pham
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology, La Jolla, CA 92037, USA
| | - Shay Leary
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia 6150, Australia
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology, La Jolla, CA 92037, USA
| | - David Broide
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - April Frazier
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology, La Jolla, CA 92037, USA
| | - Elizabeth Phillips
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia 6150, Australia; Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Simon Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia 6150, Australia; Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Steven J Mack
- Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology, La Jolla, CA 92037, USA; Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
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42
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Keren L, Bosse M, Marquez D, Angoshtari R, Jain S, Varma S, Yang SR, Kurian A, Van Valen D, West R, Bendall SC, Angelo M. A Structured Tumor-Immune Microenvironment in Triple Negative Breast Cancer Revealed by Multiplexed Ion Beam Imaging. Cell 2018; 174:1373-1387.e19. [PMID: 30193111 PMCID: PMC6132072 DOI: 10.1016/j.cell.2018.08.039] [Citation(s) in RCA: 563] [Impact Index Per Article: 93.8] [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: 04/16/2018] [Revised: 06/13/2018] [Accepted: 08/17/2018] [Indexed: 12/12/2022]
Abstract
The immune system is critical in modulating cancer progression, but knowledge of immune composition, phenotype, and interactions with tumor is limited. We used multiplexed ion beam imaging by time-of-flight (MIBI-TOF) to simultaneously quantify in situ expression of 36 proteins covering identity, function, and immune regulation at sub-cellular resolution in 41 triple-negative breast cancer patients. Multi-step processing, including deep-learning-based segmentation, revealed variability in the composition of tumor-immune populations across individuals, reconciled by overall immune infiltration and enriched co-occurrence of immune subpopulations and checkpoint expression. Spatial enrichment analysis showed immune mixed and compartmentalized tumors, coinciding with expression of PD1, PD-L1, and IDO in a cell-type- and location-specific manner. Ordered immune structures along the tumor-immune border were associated with compartmentalization and linked to survival. These data demonstrate organization in the tumor-immune microenvironment that is structured in cellular composition, spatial arrangement, and regulatory-protein expression and provide a framework to apply multiplexed imaging to immune oncology.
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Affiliation(s)
- Leeat Keren
- Department of Pathology, Stanford University, Stanford CA, 94305, USA
| | - Marc Bosse
- Department of Pathology, Stanford University, Stanford CA, 94305, USA
| | - Diana Marquez
- Department of Pathology, Stanford University, Stanford CA, 94305, USA
| | - Roshan Angoshtari
- Department of Pathology, Stanford University, Stanford CA, 94305, USA
| | - Samir Jain
- Department of Pathology, Stanford University, Stanford CA, 94305, USA
| | - Sushama Varma
- Department of Pathology, Stanford University, Stanford CA, 94305, USA
| | - Soo-Ryum Yang
- Department of Pathology, Stanford University, Stanford CA, 94305, USA
| | - Allison Kurian
- Department of Pathology, Stanford University, Stanford CA, 94305, USA
| | - David Van Valen
- Department of Biology, Caltech, Pasadena, CA 91125, USA; Department of Bioengineering, Caltech, Pasadena, CA 91125, USA
| | - Robert West
- Department of Pathology, Stanford University, Stanford CA, 94305, USA
| | - Sean C Bendall
- Department of Pathology, Stanford University, Stanford CA, 94305, USA.
| | - Michael Angelo
- Department of Pathology, Stanford University, Stanford CA, 94305, USA.
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43
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Grifoni A, Weiskopf D, Lindestam Arlehamn CS, Angelo M, Leary S, Sidney J, Frazier A, Phillips E, Mallal S, Mack SJ, Tippalagama R, Goonewardana S, Premawansa S, Premawansa G, Wijewickrama A, De Silva AD, Sette A. Sequence-based HLA-A, B, C, DP, DQ, and DR typing of 714 adults from Colombo, Sri Lanka. Hum Immunol 2017; 79:87-88. [PMID: 29289740 DOI: 10.1016/j.humimm.2017.12.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 12/04/2017] [Revised: 12/15/2017] [Accepted: 12/15/2017] [Indexed: 10/18/2022]
Abstract
DNA sequence-based typing at the HLA-A, -B, -C, -DPB1, -DQA1, -DQB1, and -DRB1 loci was performed on 714 healthy adult blood bank donors from Colombo, Sri Lanka, to characterize allele frequencies in support of studies on T cell immunity against pathogens, including Dengue virus. Deviations from Hardy Weinberg proportions were not detected at any locus. Several alleles were found in >30% of individuals, including the class II alleles DPB1 * 04:01, DPB1 * 02:01, DQB1 * 06:01 and DRB1 * 07:01, and the class I alleles A * 33:03 and A * 24:02. Genotype data will be available in the Allele Frequencies Net Database.
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Affiliation(s)
- Alba Grifoni
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology, La Jolla, CA 92037, USA
| | - Daniela Weiskopf
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology, La Jolla, CA 92037, USA
| | | | - Michael Angelo
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology, La Jolla, CA 92037, USA
| | - Shay Leary
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia 6150, Australia
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology, La Jolla, CA 92037, USA
| | - April Frazier
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology, La Jolla, CA 92037, USA
| | - Elizabeth Phillips
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia 6150, Australia; Vanderbilt University School of Medicine, Nashville, TN 37235, USA
| | - Simon Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia 6150, Australia; Vanderbilt University School of Medicine, Nashville, TN 37235, USA
| | - Steven J Mack
- Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA
| | | | | | - Sunil Premawansa
- Department of Zoology and Environmental Science, Science Faculty, University of Colombo, Sri Lanka
| | | | | | - Aruna D De Silva
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology, La Jolla, CA 92037, USA; Genetech Research Institute, Colombo, Sri Lanka(1)
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology, La Jolla, CA 92037, USA; Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
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44
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Weiskopf D, Grifoni A, Arlehamn CSL, Angelo M, Leary S, Sidney J, Frazier A, Mack SJ, Phillips E, Mallal S, Cerpas C, Balmaseda A, Harris E, Sette A. Sequence-based HLA-A, B, C, DP, DQ, and DR typing of 339 adults from Managua, Nicaragua. Hum Immunol 2017; 79:1-2. [PMID: 29122684 DOI: 10.1016/j.humimm.2017.11.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [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: 09/29/2017] [Revised: 10/27/2017] [Accepted: 11/03/2017] [Indexed: 11/26/2022]
Abstract
DNA sequence-based typing at the HLA-A, -B, -C, -DPB1, -DQA1, -DQB1, and -DRB1 loci was performed on anonymized samples provided by 339 healthy adult blood bank donors in Managua, Nicaragua. The purpose of the study was to characterize allele frequencies in the local population to support studies of T cell immunity against pathogens, including Dengue virus. Deviations from Hardy Weinberg proportions were detected for all class II loci (HLA-DPB1, -DQA1, -DQB1 and -DRB1), and at the class I C locus, but not at the class I A and B loci. The genotype data will be available in the Allele Frequencies Net Database.
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Affiliation(s)
- Daniela Weiskopf
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology (LJI), La Jolla, CA 92037, USA
| | - Alba Grifoni
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology (LJI), La Jolla, CA 92037, USA
| | | | - Michael Angelo
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology (LJI), La Jolla, CA 92037, USA
| | - Shay Leary
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia 6150, Australia
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology (LJI), La Jolla, CA 92037, USA.
| | - April Frazier
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology (LJI), La Jolla, CA 92037, USA
| | - Steven J Mack
- Children's Hospital Oakland Research Institute, Oakland, CA, USA
| | - Elizabeth Phillips
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia 6150, Australia; Vanderbilt University School of Medicine, Nashville, TN 37235, USA
| | - Simon Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia 6150, Australia; Vanderbilt University School of Medicine, Nashville, TN 37235, USA
| | - Cristhiam Cerpas
- Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministerio de Salud, Managua, Nicaragua
| | - Angel Balmaseda
- Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministerio de Salud, Managua, Nicaragua
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA, USA
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy & Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
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45
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Grifoni A, Angelo M, Sidney J, Paul S, Peters B, de Silva AD, Phillips EJ, Mallal SA, Diehl SA, Botten J, Boyson JE, Kirkpatrick BD, Whitehead SS, Durbin A, Sette A, Weiskopf D. Cellular immunity patterns of rDEN2Δ30 (Tonga/74) support its suitability as a human DENV challenge strain. The Journal of Immunology 2017. [DOI: 10.4049/jimmunol.198.supp.199.12] [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] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
The need for human DENV challenge model to better evaluate DENV candidate vaccines has become of extreme importance in the past years after neutralizing antibody failure to be a good correlate of protection and the lack of valid alternatives. rDEN2Δ30, a variant of DENV2 Tonga/74 strain lacking 30 nucleotides from its 3′ untranslated region, has been established as DENV human challenge model. In this study, DENV cellular immune responses of rDEN2Δ30 strain have been compared with natural infection to derive correlates of protection for DENV vaccines based on cellular immunity. For this purpose, HLA class I and class II restricted peptides have been predicted and tested in an IFN-gamma ELISPOT assay, to assess CD8+ and CD4+ T cell responses in healthy donors infected with rDEN2Δ30. CD8 and CD4 responses were detected in approximately 80% and 90% of donors respectively. Strong CD8 responses are detected in rDEN2Δ30 recipients and when compared with natural infections similarity in terms of magnitude and numbers of recognized epitopes is observed. In particular, the immunodominance hierarchy of the DENV nonstructural proteins NS3, NS5 is maintained in both analyzed cohorts. On the contrary, CD4 responses were mainly focused on nonstructural proteins and less strong respect to natural infection. Large overlap is observed in the epitopes recognized by rDEN2Δ30 infection and natural infection both for CD8 (100%) and CD4 (85%) responses. Finally, when rDEN2Δ30 CD8 response is compared with the one induced by other attenuated DENV isolates, a stronger response is observed. In conclusion, T cell response of rDENV2D30 has very similar specificity to natural infection supporting its suitability as an appropriate human DENV challenge model.
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Affiliation(s)
| | | | | | - Sinu Paul
- 1La Jolla Inst. for Allergy and Immunology
| | | | - Aruna D de Silva
- 1La Jolla Inst. for Allergy and Immunology
- 2Genetech Research Institute, Sri Lanka
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Angelo M. Highly multiplexed IHC in clinical tissue biopsies using multiplexed ion beam imaging. J Histotechnol 2016. [DOI: 10.1080/01478885.2016.1233749] [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: 10/20/2022]
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Weiskopf D, Angelo M, Zapardiel J, Seumois G, de Silva A, de Silva AD, Vijay P, Peters B, Sette A. DENV-specific CD4 T-cells dominantly recognize capsid-derived epitopes and display a cytotoxic phenotype. The Journal of Immunology 2016. [DOI: 10.4049/jimmunol.196.supp.147.13] [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] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Abstract
While DENV-specific CD8+ T cell responses have been extensively studied, the breadth and specificity of CD4+ T cell responses remains to be defined. Here we map CD4 T cell responses in individuals previously exposed to dengue virus. To identify HLA class II candidates, we utilized a panel of algorithms for sixteen common HLA DR molecules representative of the main DR super types. These efforts led to the identification of 365 epitopes derived from all 10 DENV proteins. In contrast to CD8 T cell targets, the highest number of epitopes was associated with the structural capsid protein (C), followed by nonstructural NS3, NS2A, NS5 and envelope proteins (E). Phenotyping of the responding CD4+ T cell subset revealed a DENV specific T cell subset, specifically expanded in donors carrying an allele associated with protection from severe disease and which is absent in DENV negative donors. This subset of DENV specific CD4 T cells is associated with markers of cytotoxic T cells such as Granzyme B, Perforin, CD107a, T bet, Eomes and co-expression of CD8α. We are currently establishing specific gene expression signatures associated with these characteristic phenotypes, as a function of different HLA restricting alleles. Detailed knowledge of phenotype and function of DENV-specific T cells will aid in the establishment of correlates of protection against severe disease.
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Affiliation(s)
| | | | | | | | | | - Aruna D de Silva
- 1La Jolla Inst. for Allergy and Immunology
- 3Genentech, Inc., Sri Lanka
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Levenson RM, Borowsky AD, Angelo M. Immunohistochemistry and mass spectrometry for highly multiplexed cellular molecular imaging. J Transl Med 2015; 95:397-405. [PMID: 25730370 PMCID: PMC7062454 DOI: 10.1038/labinvest.2015.2] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 12/23/2014] [Accepted: 12/24/2014] [Indexed: 01/02/2023] Open
Abstract
The role of immunohistochemistry (IHC) in the management of cancer has expanded to provide improved diagnostic classification, as well as guidance on disease prognosis, therapy, and relapse. These new tasks require evaluation of an increasing number of protein targets; however, conventional multiplexing, usually achieved using serial tissue sections stained for a single analyte per slide, can exhaust small biopsy specimens, complicate slide-to-slide protein expression correlation, and leave insufficient material for additional molecular assays. A new approach, mass spectrometry immunohistochemistry (MSIHC), compatible with high levels of target multiplexing and suitable for use on formalin-fixed, paraffin-embedded samples can circumvent many of these issues. The strategy employs antibodies that are labeled with elemental mass tags, such as isotopically pure lanthanides not typically found in biological specimens, rather than with typical fluorophores or chromogens. The metal-labeled antibodies are then detected in tissue using lasers or ion beams to liberate the tags for subsequent mass spectrometry detection. Within a given multiplexed IHC panel, the metal labels are selected so that their respective masses do not overlap. More than 30 antibodies have been imaged simultaneously, and up to 100 antibodies could potentially be detected at once if the full available mass spectrum is deployed. MSIHC has a number of advantages over conventional IHC techniques. Background due to autofluorescence is absent and the dynamic range is 10(5), exceeding immunofluorescence and chromogenic IHC by 100-fold and 1000-fold, respectively. Detection of labeled primary antibodies improves assay linearity over both chromogenic and fluorescent IHC. Multiplexed mass-tagged antibodies incubated simultaneously with tissue do not appear to cross-interfere, and because the mass tags do not degrade, samples are stable indefinitely. The imaging resolution of multiplexed ion-beam imaging can be better than light microscopy. With appropriate instrumentation, MSIHC has the potential to transform research and clinical pathology practice.
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Affiliation(s)
- Richard M Levenson
- Department of Pathology and Laboratory Medicine, UC Davis Medical Center, Sacramento, CA, USA
| | - Alexander D Borowsky
- Department of Pathology and Laboratory Medicine, UC Davis Medical Center, Sacramento, CA, USA
| | - Michael Angelo
- Department of Pathology, Stanford University, Palo Alto, CA, USA
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Weiskopf D, Angelo M, Bangs D, Sidney J, de Silva A, Lindow J, Durbin A, Whitehead S, Kirkpatrick B, Sette A. HLA restricted CD8+ T cell responses following vaccination with monovalent and tetravalent dengue live attenuated vaccines (VAC7P.983). The Journal of Immunology 2014. [DOI: 10.4049/jimmunol.192.supp.141.28] [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] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
The frequency of infection with any of the four dengue viruses (DENV 1-4) has increased dramatically in the last few decades, and the lack of a vaccine has led to significant morbidity and mortality worldwide. Correlates of protection from severe dengue disease and vaccine efficacy have not yet been established. A recent comprehensive analysis of T cell response against dengue virus suggested an HLA-linked protective role for CD8+ T cells, predominantly targeting the non-structural (NS) proteins. Here, we characterize for the first time CD8+ T cell responses after experimental vaccination and compare it to responses observed in natural infection with dengue virus (DENV). We have collected full blood donations from study participants receiving a dose of the monovalent or tetravalent live attenuated DENV vaccine (DLAV) developed by the NIH. CD8+ T cell responses in vaccinees were readily detectable with magnitude and breadth similar to natural dengue infection. Interestingly, while broad responses to all proteins have been observed after monovalent vaccination we have observed a dramatic focus of the T cell responses to the highly conserved proteins NS3 and NS5. Epitopes from these proteins are highly represented in a vast variety of field isolates and are able to elicit multifunctional T cell responses. Detailed knowledge of the T cell response may contribute to identify robust correlates of protection in natural immunity and vaccination against DENV.
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Affiliation(s)
- Daniela Weiskopf
- 1Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA
| | - Michael Angelo
- 1Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA
| | - Derek Bangs
- 1Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA
| | - John Sidney
- 1Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA
| | - Aruna de Silva
- 2Genetech Research Institute, Colombo, Sri Lanka
- 1Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA
| | - Janet Lindow
- 3College of Medicine, University of Vermont, Burlington, VT
| | - Anna Durbin
- 4Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD
| | - Stephen Whitehead
- 5National Institute for Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | | | - Alessandro Sette
- 1Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA
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Angelo M, Bendall SC, Finck R, Hale MB, Hitzman C, Borowsky AD, Levenson RM, Lowe JB, Liu SD, Zhao S, Natkunam Y, Nolan GP. Multiplexed ion beam imaging of human breast tumors. Nat Med 2014; 20:436-42. [PMID: 24584119 DOI: 10.1038/nm.3488] [Citation(s) in RCA: 712] [Impact Index Per Article: 71.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 12/17/2013] [Indexed: 01/11/2023]
Abstract
Immunohistochemistry (IHC) is a tool for visualizing protein expression that is employed as part of the diagnostic workup for the majority of solid tissue malignancies. Existing IHC methods use antibodies tagged with fluorophores or enzyme reporters that generate colored pigments. Because these reporters exhibit spectral and spatial overlap when used simultaneously, multiplexed IHC is not routinely used in clinical settings. We have developed a method that uses secondary ion mass spectrometry to image antibodies tagged with isotopically pure elemental metal reporters. Multiplexed ion beam imaging (MIBI) is capable of analyzing up to 100 targets simultaneously over a five-log dynamic range. Here, we used MIBI to analyze formalin-fixed, paraffin-embedded human breast tumor tissue sections stained with ten labels simultaneously. The resulting data suggest that MIBI can provide new insights into disease pathogenesis that will be valuable for basic research, drug discovery and clinical diagnostics.
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Affiliation(s)
- Michael Angelo
- 1] Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, California, USA. [2] Department of Laboratory Medicine, University of California-San Francisco, San Francisco, California, USA
| | - Sean C Bendall
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, California, USA
| | - Rachel Finck
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, California, USA
| | - Matthew B Hale
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, California, USA
| | - Chuck Hitzman
- Department of Materials Science and Engineering, Stanford University, Stanford, California, USA
| | - Alexander D Borowsky
- Department of Pathology and Laboratory Medicine, University of California-Davis, Health System, Sacramento, California, USA
| | - Richard M Levenson
- Department of Pathology and Laboratory Medicine, University of California-Davis, Health System, Sacramento, California, USA
| | - John B Lowe
- Department of Pathology, Genentech, South San Francisco, California, USA
| | - Scot D Liu
- Department of Pathology, Genentech, South San Francisco, California, USA
| | - Shuchun Zhao
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Yasodha Natkunam
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Garry P Nolan
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, California, USA
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