1
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Patel AG, Ashenberg O, Collins NB, Segerstolpe Å, Jiang S, Slyper M, Huang X, Caraccio C, Jin H, Sheppard H, Xu K, Chang TC, Orr BA, Shirinifard A, Chapple RH, Shen A, Clay MR, Tatevossian RG, Reilly C, Patel J, Lupo M, Cline C, Dionne D, Porter CBM, Waldman J, Bai Y, Zhu B, Barrera I, Murray E, Vigneau S, Napolitano S, Wakiro I, Wu J, Grimaldi G, Dellostritto L, Helvie K, Rotem A, Lako A, Cullen N, Pfaff KL, Karlström Å, Jané-Valbuena J, Todres E, Thorner A, Geeleher P, Rodig SJ, Zhou X, Stewart E, Johnson BE, Wu G, Chen F, Yu J, Goltsev Y, Nolan GP, Rozenblatt-Rosen O, Regev A, Dyer MA. A spatial cell atlas of neuroblastoma reveals developmental, epigenetic and spatial axis of tumor heterogeneity. bioRxiv 2024:2024.01.07.574538. [PMID: 38260392 PMCID: PMC10802404 DOI: 10.1101/2024.01.07.574538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Neuroblastoma is a pediatric cancer arising from the developing sympathoadrenal lineage with complex inter- and intra-tumoral heterogeneity. To chart this complexity, we generated a comprehensive cell atlas of 55 neuroblastoma patient tumors, collected from two pediatric cancer institutions, spanning a range of clinical, genetic, and histologic features. Our atlas combines single-cell/nucleus RNA-seq (sc/scRNA-seq), bulk RNA-seq, whole exome sequencing, DNA methylation profiling, spatial transcriptomics, and two spatial proteomic methods. Sc/snRNA-seq revealed three malignant cell states with features of sympathoadrenal lineage development. All of the neuroblastomas had malignant cells that resembled sympathoblasts and the more differentiated adrenergic cells. A subset of tumors had malignant cells in a mesenchymal cell state with molecular features of Schwann cell precursors. DNA methylation profiles defined four groupings of patients, which differ in the degree of malignant cell heterogeneity and clinical outcomes. Using spatial proteomics, we found that neuroblastomas are spatially compartmentalized, with malignant tumor cells sequestered away from immune cells. Finally, we identify spatially restricted signaling patterns in immune cells from spatial transcriptomics. To facilitate the visualization and analysis of our atlas as a resource for further research in neuroblastoma, single cell, and spatial-omics, all data are shared through the Human Tumor Atlas Network Data Commons at www.humantumoratlas.org.
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Affiliation(s)
- Anand G Patel
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
- These authors contributed equally
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- These authors contributed equally
| | - Natalie B Collins
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA, USA
- These authors contributed equally
| | - Åsa Segerstolpe
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - 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
| | - Michal Slyper
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xin Huang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Chiara Caraccio
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Hongjian Jin
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Heather Sheppard
- Comparative Pathology Core, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ke Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ti-Cheng Chang
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Brent A Orr
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Abbas Shirinifard
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Richard H Chapple
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Amber Shen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael R Clay
- Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Ruth G Tatevossian
- Cancer Biomarkers Laboratory, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Colleen Reilly
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jaimin Patel
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Marybeth Lupo
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Cynthia Cline
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Danielle Dionne
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Caroline B M Porter
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Julia Waldman
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yunhao Bai
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Bokai Zhu
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Evan Murray
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sébastien Vigneau
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sara Napolitano
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Isaac Wakiro
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jingyi Wu
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Grace Grimaldi
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Laura Dellostritto
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Karla Helvie
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Asaf Rotem
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ana Lako
- Center for Immuno-Oncology (CIO), Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nicole Cullen
- Center for Immuno-Oncology (CIO), Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kathleen L Pfaff
- Center for Immuno-Oncology (CIO), Dana-Farber Cancer Institute, Boston, MA, USA
| | - Åsa Karlström
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Judit Jané-Valbuena
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ellen Todres
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aaron Thorner
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Paul Geeleher
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Scott J Rodig
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Xin Zhou
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Elizabeth Stewart
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Bruce E Johnson
- Center for Cancer Genomics, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gang Wu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Fei Chen
- Broad Institute of MIT and Harvard, Boston, MA, USA
| | - Jiyang Yu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yury Goltsev
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Current address: Research and Early Development, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Koch Institute of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Current address: Research and Early Development, Genentech Inc., South San Francisco, CA, 94080, USA
- Lead contacts
| | - Michael A Dyer
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Lead contacts
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2
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Hickey JW, Haist M, Horowitz N, Caraccio C, Tan Y, Rech AJ, Baertsch MA, Rovira-Clavé X, Zhu B, Vazquez G, Barlow G, Agmon E, Goltsev Y, Sunwoo JB, Covert M, Nolan GP. T cell-mediated curation and restructuring of tumor tissue coordinates an effective immune response. Cell Rep 2023; 42:113494. [PMID: 38085642 PMCID: PMC10765317 DOI: 10.1016/j.celrep.2023.113494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 09/06/2023] [Accepted: 11/10/2023] [Indexed: 12/30/2023] Open
Abstract
Antigen-specific T cells traffic to, are influenced by, and create unique cellular microenvironments. Here we characterize these microenvironments over time with multiplexed imaging in a melanoma model of adoptive T cell therapy and human patients with melanoma treated with checkpoint inhibitor therapy. Multicellular neighborhood analysis reveals dynamic immune cell infiltration and inflamed tumor cell neighborhoods associated with CD8+ T cells. T cell-focused analysis indicates T cells are found along a continuum of neighborhoods that reflect the progressive steps coordinating the anti-tumor immune response. More effective anti-tumor immune responses are characterized by inflamed tumor-T cell neighborhoods, flanked by dense immune infiltration neighborhoods. Conversely, ineffective T cell therapies express anti-inflammatory cytokines, resulting in regulatory neighborhoods, spatially disrupting productive T cell-immune and -tumor interactions. Our study provides in situ mechanistic insights into temporal tumor microenvironment changes, cell interactions critical for response, and spatial correlates of immunotherapy outcomes, informing cellular therapy evaluation and engineering.
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Affiliation(s)
- John W Hickey
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Maximillian Haist
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nina Horowitz
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Chiara Caraccio
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yuqi Tan
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andrew J Rech
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marc-Andrea Baertsch
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Xavier Rovira-Clavé
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Bokai Zhu
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Gustavo Vazquez
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Graham Barlow
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Eran Agmon
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Center for Cell Analysis and Modeling, University of Connecticut Health, Farmington, CT 06032, USA
| | - Yury Goltsev
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - John B Sunwoo
- Department of Otolaryngology, Head and Neck Surgery, Stanford Cancer Institute, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Markus Covert
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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3
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Affiliation(s)
- Yury Goltsev
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
| | - Garry Nolan
- Department of Pathology, Stanford University, Stanford, CA, USA.
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4
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Zhu B, Chen S, Bai Y, Chen H, Liao G, Mukherjee N, Vazquez G, McIlwain DR, Tzankov A, Lee IT, Matter MS, Goltsev Y, Ma Z, Nolan GP, Jiang S. Robust single-cell matching and multimodal analysis using shared and distinct features. Nat Methods 2023; 20:304-315. [PMID: 36624212 PMCID: PMC9911356 DOI: 10.1038/s41592-022-01709-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 10/31/2022] [Indexed: 01/10/2023]
Abstract
The ability to align individual cellular information from multiple experimental sources is fundamental for a systems-level understanding of biological processes. However, currently available tools are mainly designed for single-cell transcriptomics matching and integration, and generally rely on a large number of shared features across datasets for cell matching. This approach underperforms when applied to single-cell proteomic datasets due to the limited number of parameters simultaneously accessed and lack of shared markers across these experiments. Here, we introduce a cell-matching algorithm, matching with partial overlap (MARIO) that accounts for both shared and distinct features, while consisting of vital filtering steps to avoid suboptimal matching. MARIO accurately matches and integrates data from different single-cell proteomic and multimodal methods, including spatial techniques and has cross-species capabilities. MARIO robustly matched tissue macrophages identified from COVID-19 lung autopsies via codetection by indexing imaging to macrophages recovered from COVID-19 bronchoalveolar lavage fluid by cellular indexing of transcriptomes and epitopes by sequencing, revealing unique immune responses within the lung microenvironment of patients with COVID.
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Affiliation(s)
- Bokai Zhu
- grid.168010.e0000000419368956Department of Microbiology and Immunology, Stanford University, Stanford, CA USA ,grid.168010.e0000000419368956Department of Pathology, Stanford University, Stanford, CA USA
| | - Shuxiao Chen
- grid.25879.310000 0004 1936 8972Department of Statistics and Data Science, The Wharton School, University of Pennsylvania, PA, USA
| | - Yunhao Bai
- grid.168010.e0000000419368956Department of Pathology, Stanford University, Stanford, CA USA ,grid.168010.e0000000419368956Department of Chemistry, Stanford University, Stanford, CA USA
| | - Han Chen
- grid.168010.e0000000419368956Department of Pathology, Stanford University, Stanford, CA USA
| | - Guanrui Liao
- grid.239395.70000 0000 9011 8547Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA USA
| | - Nilanjan Mukherjee
- grid.168010.e0000000419368956Department of Pathology, Stanford University, Stanford, CA USA
| | - Gustavo Vazquez
- grid.168010.e0000000419368956Department of Pathology, Stanford University, Stanford, CA USA
| | - David R. McIlwain
- grid.168010.e0000000419368956Department of Pathology, Stanford University, Stanford, CA USA
| | - Alexandar Tzankov
- grid.6612.30000 0004 1937 0642Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Ivan T. Lee
- grid.168010.e0000000419368956Department of Pathology, Stanford University, Stanford, CA USA
| | - Matthias S. Matter
- grid.6612.30000 0004 1937 0642Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Yury Goltsev
- grid.168010.e0000000419368956Department of Pathology, Stanford University, Stanford, CA USA
| | - Zongming Ma
- Department of Statistics and Data Science, The Wharton School, University of Pennsylvania, PA, USA.
| | - Garry P. Nolan
- grid.168010.e0000000419368956Department of Pathology, Stanford University, Stanford, CA USA
| | - Sizun Jiang
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA. .,Department of Pathology, Dana Farber Cancer Institute, Boston, MA, USA. .,Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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5
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Lu G, Baertsch MA, Hickey JW, Goltsev Y, Rech AJ, Mani L, Forgó E, Kong C, Jiang S, Nolan GP, Rosenthal EL. A real-time GPU-accelerated parallelized image processor for large-scale multiplexed fluorescence microscopy data. Front Immunol 2022; 13:981825. [PMID: 36211386 PMCID: PMC9539451 DOI: 10.3389/fimmu.2022.981825] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/07/2022] [Indexed: 11/20/2022] Open
Abstract
Highly multiplexed, single-cell imaging has revolutionized our understanding of spatial cellular interactions associated with health and disease. With ever-increasing numbers of antigens, region sizes, and sample sizes, multiplexed fluorescence imaging experiments routinely produce terabytes of data. Fast and accurate processing of these large-scale, high-dimensional imaging data is essential to ensure reliable segmentation and identification of cell types and for characterization of cellular neighborhoods and inference of mechanistic insights. Here, we describe RAPID, a Real-time, GPU-Accelerated Parallelized Image processing software for large-scale multiplexed fluorescence microscopy Data. RAPID deconvolves large-scale, high-dimensional fluorescence imaging data, stitches and registers images with axial and lateral drift correction, and minimizes tissue autofluorescence such as that introduced by erythrocytes. Incorporation of an open source CUDA-driven, GPU-assisted deconvolution produced results similar to fee-based commercial software. RAPID reduces data processing time and artifacts and improves image contrast and signal-to-noise compared to our previous image processing pipeline, thus providing a useful tool for accurate and robust analysis of large-scale, multiplexed, fluorescence imaging data.
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Affiliation(s)
- Guolan Lu
- Department of Otolaryngology, Stanford University School of Medicine, Stanford, CA, United States
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, United States
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Marc A. Baertsch
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, United States
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
| | - John W. Hickey
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, United States
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Yury Goltsev
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, United States
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Andrew J. Rech
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, United States
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Lucas Mani
- Department of Otolaryngology, Stanford University School of Medicine, Stanford, CA, United States
| | - Erna Forgó
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Christina Kong
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Sizun Jiang
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Garry P. Nolan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, United States
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
- *Correspondence: Garry P. Nolan, ; Eben L. Rosenthal,
| | - Eben L. Rosenthal
- Department of Otolaryngology, Stanford University School of Medicine, Stanford, CA, United States
- Department of Otolaryngology, Vanderbilt University Medical Center, Nashville, CA, United States
- *Correspondence: Garry P. Nolan, ; Eben L. Rosenthal,
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6
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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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7
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Abravanel DL, Klughammer J, Blosser T, Goltsev Y, Jiang S, Bai Y, Murray E, Alon S, Cui Y, Goodwin DR, Sinha A, Cohen O, Slyper M, Ashenberg O, Dionne D, Jané-Valbuena J, Porter CBM, Segerstolpe A, Waldman J, Vigneau S, Helvie K, Frangieh A, DelloStritto L, Patel M, We J, Pfaff K, Cullen N, Lako A, Turner M, Wakiro I, Napolitano S, Kanodia A, Ortiz R, MacKichan C, Inga S, Chen J, Thorner AR, Rotem A, Rodig S, Chen F, Boyden ES, Nolan GP, Zhuang X, Rozenblatt-Rosen O, Johnson BE, Regev A, Wagle N. Abstract PD6-03: Spatio-molecular dissection of the breast cancer metastatic microenvironment. Cancer Res 2022. [DOI: 10.1158/1538-7445.sabcs21-pd6-03] [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
Metastatic breast cancer (MBC) remains incurable due to inevitable development of therapeutic resistance. Although tumor cell intrinsic mechanisms of resistance in MBC are beginning to be elucidated by bulk sequencing studies, the roles of the tumor microenvironment and intratumor heterogeneity in therapeutic resistance remain underexplored due to both technological barriers and limited availability of samples. To comprehensively capture these characteristics we have adapted a research biopsy protocol to collect tissue for an array of single-cell and spatio-molecular assays whose performance we have optimized for MBC, including single-cell and single-nucleus RNA sequencing, Slide-Seq, Multiplexed Error-Robust FISH (MERFISH), Expansion Sequencing (ExSEQ), Co-detection by Indexing (CODEX) and Multiplexed Ion Beam Imaging (MIBI). To date, we have successfully performed single-cell or single-nucleus RNAseq in 67 MBC biopsies and generated detailed accompanying clinical annotations for each. These samples provide a representation of the clinicopathological diversity of MBC including different breast cancer subtypes (44 HR+/HER2-, 3 HR-/HER2+, 3 HR+/HER2+, 16 TNBC, 1 unknown), common anatomic sites of metastasis (37 liver, 9 axilla, 7 breast, 5 bone, 3 chest wall, 3 neck, 1 brain, 1 lung, 1 skin), metastatic presentations (53 recurrent, 14 de novo) and histologic subtypes in the breast (45 IDC, 7 ILC, 6 mixed, 3 DCIS, 1 mucinous, 5 unknown/NA). Following optimization, both single-cell and single-nucleus RNA seq perform well in these MBC biopsies recovering all expected cell types including the malignant, stromal (e.g. fibroblasts, endothelial cells), myeloid (e.g. monocytes, macrophages) and lymphoid compartments (e.g. T cells, B cells, NK cells) as well as relevant oncogenic programs (e.g. cell cycle programs in all compartments; EMT-like and ER signaling programs in the malignant compartment, immune checkpoint programs in the lymphoid compartment; and fibroblast activation and vascular homeostasis programs in the stromal compartment). In addition to differences between the two techniques, these data demonstrate substantial intratumor heterogeneity in cell type composition. For example in liver biopsies the average number of cells per sample compartment by single nucleus RNA-seq was 6745 malignant (56%, SD 4216), 4637 stromal (41%, SD 3727), 1196 lymphoid (8%, SD 1617) and 874 myeloid (6%, SD 852); in breast biopsies the average number of cells per compartment by single nucleus RNA-seq was 6421 malignant (70%, SD 3497), 1628 stromal (24%, SD 117), 333 lymphoid (4%, SD 170) and 213 myeloid (3%, SD 117). Additionally, we find both inter- and intra-tumor heterogeneity in expression patterns and programs including, for example, expression of ER, PR and HER2 within clinical receptor subtypes (log normalized counts for ER expression in tumor cells by single cell RNA-seq: HR+/HER2- 0.921 (SD 0.714); HR+/HER2+ 0.768 (SD 0.624); HR-/HER2+ 0.018 (SD 0.122); and HR-/HER2- 0.005 (SD 0.066). For a subset of 13 biopsies we are also completing the spatiomolecular characterization methods on serial sections of a single adjacent biopsy. This unique experimental setup was designed to enable efficient comparison and integration of these assays. In spite of differences between experimental techniques and readouts, cell typing can be approached by annotation transfer from matching single cell or single nucleus RNAseq data, enabling exploratory analyses including evaluation of spatial phenotypes and cell type colocalization. Overall, these single cell and spatial data afford a comprehensive atlas including cell types, cell states/programs, cell interactions and spatial organization in MBC lesions. Future analyses will include serial biopsies over time and integration of clinicopathologic data including therapeutic response and resistance.
Citation Format: Daniel L Abravanel, Johanna Klughammer, Timothy Blosser, Yury Goltsev, Sizun Jiang, Yunjao Bai, Evan Murray, Shahar Alon, Yi Cui, Daniel R Goodwin, Anubhav Sinha, Ofir Cohen, Michal Slyper, Orr Ashenberg, Danielle Dionne, Judit Jané-Valbuena, Caroline BM Porter, Asa Segerstolpe, Julia Waldman, Sébastien Vigneau, Karla Helvie, Allison Frangieh, Laura DelloStritto, Miraj Patel, Jingyi We, Kathleen Pfaff, Nicole Cullen, Ana Lako, Madison Turner, Isaac Wakiro, Sara Napolitano, Abhay Kanodia, Rebecca Ortiz, Colin MacKichan, Stephanie Inga, Judy Chen, Aaron R Thorner, Asaf Rotem, Scott Rodig, Fei Chen, Edward S Boyden, Garry P Nolan, Xiaowei Zhuang, Orit Rozenblatt-Rosen, Bruce E Johnson, Aviv Regev, Nikhil Wagle. Spatio-molecular dissection of the breast cancer metastatic microenvironment [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr PD6-03.
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Affiliation(s)
| | | | | | | | | | | | - Evan Murray
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Shahar Alon
- Massachusetts Institute of Technology, Cambridge, MA
| | - Yi Cui
- Massachusetts Institute of Technology, Cambridge, MA
| | | | - Anubhav Sinha
- Massachusetts Institute of Technology, Cambridge, MA
| | - Ofir Cohen
- Broad Institute of MIT and Harvard, Cambridge, MA
| | | | | | | | | | | | | | | | | | | | | | | | | | - Jingyi We
- Dana-Farber Cancer Institute, Boston, MA
| | | | | | - Ana Lako
- Dana-Farber Cancer Institute, Boston, MA
| | | | | | | | | | | | | | | | - Judy Chen
- Dana-Farber Cancer Institute, Boston, MA
| | | | - Asaf Rotem
- Dana-Farber Cancer Institute, Boston, MA
| | | | - Fei Chen
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Edward S Boyden
- Massachusetts Institute of Technology, Howard Hughes Medical Institute, Cambridge, MA
| | | | - Xiaowei Zhuang
- Harvard University, Howard Hughes Medical Institute, Cambridge, MA
| | | | | | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA
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8
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Vizcarra JC, Burlingame EA, Hug CB, Goltsev Y, White BS, Tyson DR, Sokolov A. A community-based approach to image analysis of cells, tissues and tumors. Comput Med Imaging Graph 2022; 95:102013. [PMID: 34864359 PMCID: PMC8761177 DOI: 10.1016/j.compmedimag.2021.102013] [Citation(s) in RCA: 2] [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: 07/26/2021] [Revised: 11/09/2021] [Accepted: 11/09/2021] [Indexed: 01/03/2023]
Abstract
Emerging multiplexed imaging platforms provide an unprecedented view of an increasing number of molecular markers at subcellular resolution and the dynamic evolution of tumor cellular composition. As such, they are capable of elucidating cell-to-cell interactions within the tumor microenvironment that impact clinical outcome and therapeutic response. However, the rapid development of these platforms has far outpaced the computational methods for processing and analyzing the data they generate. While being technologically disparate, all imaging assays share many computational requirements for post-collection data processing. As such, our Image Analysis Working Group (IAWG), composed of researchers in the Cancer Systems Biology Consortium (CSBC) and the Physical Sciences - Oncology Network (PS-ON), convened a workshop on "Computational Challenges Shared by Diverse Imaging Platforms" to characterize these common issues and a follow-up hackathon to implement solutions for a selected subset of them. Here, we delineate these areas that reflect major axes of research within the field, including image registration, segmentation of cells and subcellular structures, and identification of cell types from their morphology. We further describe the logistical organization of these events, believing our lessons learned can aid others in uniting the imaging community around self-identified topics of mutual interest, in designing and implementing operational procedures to address those topics and in mitigating issues inherent in image analysis (e.g., sharing exemplar images of large datasets and disseminating baseline solutions to hackathon challenges through open-source code repositories).
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Affiliation(s)
- Juan Carlos Vizcarra
- Department of Biomedical Engineering, Georgia Institute of Technology & Emory University, Atlanta, GA, USA
| | - Erik A Burlingame
- Computational Biology Program, Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA
| | - Clemens B Hug
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Boston, MA, USA
| | - Yury Goltsev
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Brian S White
- Computational Oncology, Sage Bionetworks, Seattle, WA, USA
| | - Darren R Tyson
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Artem Sokolov
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Boston, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
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9
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Jiang S, Mukherjee N, Bennett RS, Chen H, Logue J, Dighero-Kemp B, Kurtz JR, Adams R, Phillips D, Schürch CM, Goltsev Y, Hickey JW, McCaffrey EF, Delmastro A, Chu P, Reader JR, Keesler RI, Galván JA, Zlobec I, Van Rompay KKA, Liu DX, Hensley LE, Nolan GP, McIlwain DR. Rhesus Macaque CODEX Multiplexed Immunohistochemistry Panel for Studying Immune Responses During Ebola Infection. Front Immunol 2021; 12:729845. [PMID: 34938283 PMCID: PMC8685521 DOI: 10.3389/fimmu.2021.729845] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 11/16/2021] [Indexed: 11/13/2022] Open
Abstract
Non-human primate (NHP) animal models are an integral part of the drug research and development process. For some biothreat pathogens, animal model challenge studies may offer the only possibility to evaluate medical countermeasure efficacy. A thorough understanding of host immune responses in such NHP models is therefore vital. However, applying antibody-based immune characterization techniques to NHP models requires extensive reagent development for species compatibility. In the case of studies involving high consequence pathogens, further optimization for use of inactivated samples may be required. Here, we describe the first optimized CO-Detection by indEXing (CODEX) multiplexed tissue imaging antibody panel for deep profiling of spatially resolved single-cell immune responses in rhesus macaques. This 21-marker panel is composed of a set of 18 antibodies that stratify major immune cell types along with a set three Ebola virus (EBOV)-specific antibodies. We validated these two sets of markers using immunohistochemistry and CODEX in fully inactivated Formalin-Fixed Paraffin-Embedded (FFPE) tissues from mock and EBOV challenged macaques respectively and provide an efficient framework for orthogonal validation of multiple antibody clones using CODEX multiplexed tissue imaging. We also provide the antibody clones and oligonucleotide tag sequences as a valuable resource for other researchers to recreate this reagent set for future studies of tissue immune responses to EBOV infection and other diseases.
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Affiliation(s)
- Sizun Jiang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, United States
| | - Nilanjan Mukherjee
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Richard S. Bennett
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, United States
| | - Han Chen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - James Logue
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, United States
| | - Bonnie Dighero-Kemp
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, United States
| | - Jonathan R. Kurtz
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, United States
| | - Ricky Adams
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, United States
| | - Darci Phillips
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Christian M. Schürch
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
- Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany
| | - Yury Goltsev
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - John W. Hickey
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Erin F. McCaffrey
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Alea Delmastro
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Pauline Chu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - J. Rachel Reader
- California National Primate Research Center, University of California, Davis, CA, United States
| | - Rebekah I. Keesler
- California National Primate Research Center, University of California, Davis, CA, United States
| | - José A. Galván
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - Inti Zlobec
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - Koen K. A. Van Rompay
- California National Primate Research Center, University of California, Davis, CA, United States
| | - David X. Liu
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, United States
| | - Lisa E. Hensley
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, United States
| | - Garry P. Nolan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - David R. McIlwain
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
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Nakayama T, Lee IT, Jiang S, Matter MS, Yan CH, Overdevest JB, Wu CT, Goltsev Y, Shih LC, Liao CK, Zhu B, Bai Y, Lidsky P, Xiao Y, Zarabanda D, Yang A, Easwaran M, Schürch CM, Chu P, Chen H, Stalder AK, McIlwain DR, Borchard NA, Gall PA, Dholakia SS, Le W, Xu L, Tai CJ, Yeh TH, Erickson-Direnzo E, Duran JM, Mertz KD, Hwang PH, Haslbauer JD, Jackson PK, Menter T, Andino R, Canoll PD, DeConde AS, Patel ZM, Tzankov A, Nolan GP, Nayak JV. Determinants of SARS-CoV-2 entry and replication in airway mucosal tissue and susceptibility in smokers. Cell Rep Med 2021; 2:100421. [PMID: 34604819 PMCID: PMC8479532 DOI: 10.1016/j.xcrm.2021.100421] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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] [Received: 02/05/2021] [Revised: 07/21/2021] [Accepted: 09/22/2021] [Indexed: 02/07/2023]
Abstract
Understanding viral tropism is an essential step toward reducing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission, decreasing mortality from coronavirus disease 2019 (COVID-19) and limiting opportunities for mutant strains to arise. Currently, little is known about the extent to which distinct tissue sites in the human head and neck region and proximal respiratory tract selectively permit SARS-CoV-2 infection and replication. In this translational study, we discover key variabilities in expression of angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2), essential SARS-CoV-2 entry factors, among the mucosal tissues of the human proximal airways. We show that SARS-CoV-2 infection is present in all examined head and neck tissues, with a notable tropism for the nasal cavity and tracheal mucosa. Finally, we uncover an association between smoking and higher SARS-CoV-2 viral infection in the human proximal airway, which may explain the increased susceptibility of smokers to developing severe COVID-19. This is at least partially explained by differences in interferon (IFN)-β1 levels between smokers and non-smokers.
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Affiliation(s)
- Tsuguhisa Nakayama
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
- Department of Otorhinolaryngology, Jikei University School of Medicine, Tokyo, Japan
| | - Ivan T. Lee
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
- Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Sizun Jiang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Matthias S. Matter
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Carol H. Yan
- Division of Otolaryngology – Head and Neck Surgery, Department of Surgery, University of California San Diego School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jonathan B. Overdevest
- Department of Otolaryngology–Head and Neck Surgery, Columbia University School of Medicine, New York, NY, USA
| | - Chien-Ting Wu
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yury Goltsev
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Liang-Chun Shih
- Department of Otorhinolaryngology, China Medical University Hospital, Taichung, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Terry Fox Cancer Research Laboratory, Translational Medicine Center, China Medical University Hospital, Taichung, Taiwan
| | - Chun-Kang Liao
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan
| | - Bokai Zhu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yunhao Bai
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Peter Lidsky
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Yinghong Xiao
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - David Zarabanda
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
| | - Angela Yang
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
| | - Meena Easwaran
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
| | - Christian M. Schürch
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Pauline Chu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Han Chen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Anna K. Stalder
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - David R. McIlwain
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Nicole A. Borchard
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
| | - Phillip A. Gall
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
| | - Sachi S. Dholakia
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
| | - Wei Le
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
| | - Le Xu
- Department of Pediatrics, University of California San Diego School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Chih-Jaan Tai
- Department of Otorhinolaryngology, China Medical University Hospital, Taichung, Taiwan
- School of Medicine, China Medical University, Taichung, Taiwan
| | - Te-Huei Yeh
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan
- Department of Otolaryngology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Elizabeth Erickson-Direnzo
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
| | - Jason M. Duran
- Division of Cardiovascular Medicine, Department of Medicine, University of California San Diego School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kirsten D. Mertz
- Institute of Pathology, Cantonal Hospital Baselland, Liestal, Switzerland
| | - Peter H. Hwang
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
| | - Jasmin D. Haslbauer
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Peter K. Jackson
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Thomas Menter
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Peter D. Canoll
- Department of Pathology and Cell Biology, Columbia University Medical Center, Irving Cancer Research Center, New York, NY, USA
| | - Adam S. DeConde
- Division of Otolaryngology – Head and Neck Surgery, Department of Surgery, University of California San Diego School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Zara M. Patel
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
| | - Alexandar Tzankov
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Garry P. Nolan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jayakar V. Nayak
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
- Department of Otolaryngology – Head and Neck Surgery, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA
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11
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Hickey JW, Tan Y, Nolan GP, Goltsev Y. Strategies for Accurate Cell Type Identification in CODEX Multiplexed Imaging Data. Front Immunol 2021; 12:727626. [PMID: 34484237 PMCID: PMC8415085 DOI: 10.3389/fimmu.2021.727626] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [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: 06/19/2021] [Accepted: 08/02/2021] [Indexed: 12/29/2022] Open
Abstract
Multiplexed imaging is a recently developed and powerful single-cell biology research tool. However, it presents new sources of technical noise that are distinct from other types of single-cell data, necessitating new practices for single-cell multiplexed imaging processing and analysis, particularly regarding cell-type identification. Here we created single-cell multiplexed imaging datasets by performing CODEX on four sections of the human colon (ascending, transverse, descending, and sigmoid) using a panel of 47 oligonucleotide-barcoded antibodies. After cell segmentation, we implemented five different normalization techniques crossed with four unsupervised clustering algorithms, resulting in 20 unique cell-type annotations for the same dataset. We generated two standard annotations: hand-gated cell types and cell types produced by over-clustering with spatial verification. We then compared these annotations at four levels of cell-type granularity. First, increasing cell-type granularity led to decreased labeling accuracy; therefore, subtle phenotype annotations should be avoided at the clustering step. Second, accuracy in cell-type identification varied more with normalization choice than with clustering algorithm. Third, unsupervised clustering better accounted for segmentation noise during cell-type annotation than hand-gating. Fourth, Z-score normalization was generally effective in mitigating the effects of noise from single-cell multiplexed imaging. Variation in cell-type identification will lead to significant differential spatial results such as cellular neighborhood analysis; consequently, we also make recommendations for accurately assigning cell-type labels to CODEX multiplexed imaging.
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Affiliation(s)
- John W. Hickey
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, United States
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Yuqi Tan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, United States
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Garry P. Nolan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, United States
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Yury Goltsev
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, United States
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
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12
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Wu CT, Lidsky PV, Xiao Y, Lee IT, Cheng R, Nakayama T, Jiang S, Demeter J, Bevacqua RJ, Chang CA, Whitener RL, Stalder AK, Zhu B, Chen H, Goltsev Y, Tzankov A, Nayak JV, Nolan GP, Matter MS, Andino R, Jackson PK. SARS-CoV-2 infects human pancreatic β cells and elicits β cell impairment. Cell Metab 2021; 33:1565-1576.e5. [PMID: 34081912 PMCID: PMC8130512 DOI: 10.1016/j.cmet.2021.05.013] [Citation(s) in RCA: 185] [Impact Index Per Article: 61.7] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 04/01/2021] [Accepted: 05/07/2021] [Indexed: 01/08/2023]
Abstract
Emerging evidence points toward an intricate relationship between the pandemic of coronavirus disease 2019 (COVID-19) and diabetes. While preexisting diabetes is associated with severe COVID-19, it is unclear whether COVID-19 severity is a cause or consequence of diabetes. To mechanistically link COVID-19 to diabetes, we tested whether insulin-producing pancreatic β cells can be infected by SARS-CoV-2 and cause β cell depletion. We found that the SARS-CoV-2 receptor, ACE2, and related entry factors (TMPRSS2, NRP1, and TRFC) are expressed in β cells, with selectively high expression of NRP1. We discovered that SARS-CoV-2 infects human pancreatic β cells in patients who succumbed to COVID-19 and selectively infects human islet β cells in vitro. We demonstrated that SARS-CoV-2 infection attenuates pancreatic insulin levels and secretion and induces β cell apoptosis, each rescued by NRP1 inhibition. Phosphoproteomic pathway analysis of infected islets indicates apoptotic β cell signaling, similar to that observed in type 1 diabetes (T1D). In summary, our study shows SARS-CoV-2 can directly induce β cell killing.
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Affiliation(s)
- Chien-Ting Wu
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peter V Lidsky
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yinghong Xiao
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ivan T Lee
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA; Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Ran Cheng
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA, USA
| | - Tsuguhisa Nakayama
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA; Department of Otorhinolaryngology, Jikei University School of Medicine, Tokyo, Japan
| | - Sizun Jiang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Janos Demeter
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Romina J Bevacqua
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Charles A Chang
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Robert L Whitener
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Anna K Stalder
- Institute of Pathology, University of Basel, Schönbeinstrasse 40, 4003 Basel, Switzerland
| | - Bokai Zhu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Han Chen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yury Goltsev
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alexandar Tzankov
- Institute of Pathology, University of Basel, Schönbeinstrasse 40, 4003 Basel, Switzerland
| | - Jayakar V Nayak
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matthias S Matter
- Institute of Pathology, University of Basel, Schönbeinstrasse 40, 4003 Basel, Switzerland.
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA.
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13
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Black S, Phillips D, Hickey JW, Kennedy-Darling J, Venkataraaman VG, Samusik N, Goltsev Y, Schürch CM, Nolan GP. CODEX multiplexed tissue imaging with DNA-conjugated antibodies. Nat Protoc 2021; 16:3802-3835. [PMID: 34215862 PMCID: PMC8647621 DOI: 10.1038/s41596-021-00556-8] [Citation(s) in RCA: 181] [Impact Index Per Article: 60.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 04/14/2021] [Indexed: 02/06/2023]
Abstract
Advances in multiplexed imaging technologies have drastically improved our ability to characterize healthy and diseased tissues at the single-cell level. Co-detection by indexing (CODEX) relies on DNA-conjugated antibodies and the cyclic addition and removal of complementary fluorescently labeled DNA probes and has been used so far to simultaneously visualize up to 60 markers in situ. CODEX enables a deep view into the single-cell spatial relationships in tissues and is intended to spur discovery in developmental biology, disease and therapeutic design. Herein, we provide optimized protocols for conjugating purified antibodies to DNA oligonucleotides, validating the conjugation by CODEX staining and executing the CODEX multicycle imaging procedure for both formalin-fixed, paraffin-embedded (FFPE) and fresh-frozen tissues. In addition, we describe basic image processing and data analysis procedures. We apply this approach to an FFPE human tonsil multicycle experiment. The hands-on experimental time for antibody conjugation is ~4.5 h, validation of DNA-conjugated antibodies with CODEX staining takes ~6.5 h and preparation for a CODEX multicycle experiment takes ~8 h. The multicycle imaging and data analysis time depends on the tissue size, number of markers in the panel and computational complexity.
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Affiliation(s)
- Sarah Black
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Darci Phillips
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - John W Hickey
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Julia Kennedy-Darling
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Akoya Biosciences, Menlo Park, CA, USA
| | - Vishal G Venkataraaman
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Nikolay Samusik
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Becton Dickinson, San Jose, CA, USA
| | - Yury Goltsev
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Christian M Schürch
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Pathology and Neuropathology, University Hospital and Comprehensive Cancer Center Tübingen, Tübingen, Germany.
| | - Garry P Nolan
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
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14
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Kennedy‐Darling J, Bhate SS, Hickey JW, Black S, Barlow GL, Vazquez G, Venkataraaman VG, Samusik N, Goltsev Y, Schürch CM, Nolan GP. Highly multiplexed tissue imaging using repeated oligonucleotide exchange reaction. Eur J Immunol 2021; 51:1262-1277. [PMID: 33548142 PMCID: PMC8251877 DOI: 10.1002/eji.202048891] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [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: 08/02/2020] [Revised: 11/21/2020] [Accepted: 02/04/2021] [Indexed: 01/04/2023]
Abstract
Multiparameter tissue imaging enables analysis of cell-cell interactions in situ, the cellular basis for tissue structure, and novel cell types that are spatially restricted, giving clues to biological mechanisms behind tissue homeostasis and disease. Here, we streamlined and simplified the multiplexed imaging method CO-Detection by indEXing (CODEX) by validating 58 unique oligonucleotide barcodes that can be conjugated to antibodies. We showed that barcoded antibodies retained their specificity for staining cognate targets in human tissue. Antibodies were visualized one at a time by adding a fluorescently labeled oligonucleotide complementary to oligonucleotide barcode, imaging, stripping, and repeating this cycle. With this we developed a panel of 46 antibodies that was used to stain five human lymphoid tissues: three tonsils, a spleen, and a LN. To analyze the data produced, an image processing and analysis pipeline was developed that enabled single-cell analysis on the data, including unsupervised clustering, that revealed 31 cell types across all tissues. We compared cell-type compositions within and directly surrounding follicles from the different lymphoid organs and evaluated cell-cell density correlations. This sequential oligonucleotide exchange technique enables a facile imaging of tissues that leverages pre-existing imaging infrastructure to decrease the barriers to broad use of multiplexed imaging.
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Affiliation(s)
- Julia Kennedy‐Darling
- Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCAUSA
- Akoya Biosciences1505 O'Brien DriveMenlo ParkCAUSA
| | - Salil S. Bhate
- Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCAUSA
- Department of PathologyStanford University School of MedicineStanfordCAUSA
- Department of BioengineeringStanford UniversityStanfordCAUSA
| | - John W. Hickey
- Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCAUSA
- Department of PathologyStanford University School of MedicineStanfordCAUSA
| | - Sarah Black
- Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCAUSA
- Department of PathologyStanford University School of MedicineStanfordCAUSA
| | - Graham L. Barlow
- Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCAUSA
- Department of PathologyStanford University School of MedicineStanfordCAUSA
| | - Gustavo Vazquez
- Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCAUSA
- Department of PathologyStanford University School of MedicineStanfordCAUSA
| | - Vishal G. Venkataraaman
- Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCAUSA
- Department of PathologyStanford University School of MedicineStanfordCAUSA
| | - Nikolay Samusik
- Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCAUSA
- Becton DickinsonSan JoseCAUSA
| | - Yury Goltsev
- Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCAUSA
- Department of PathologyStanford University School of MedicineStanfordCAUSA
| | - Christian M. Schürch
- Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCAUSA
- Department of PathologyStanford University School of MedicineStanfordCAUSA
- Department of Pathology and NeuropathologyUniversity Hospital and Comprehensive Cancer Center TübingenTübingenGermany
| | - Garry P. Nolan
- Department of Microbiology & ImmunologyStanford University School of MedicineStanfordCAUSA
- Department of PathologyStanford University School of MedicineStanfordCAUSA
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15
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Malkovskiy AV, Van Wassenhove LD, Goltsev Y, Osei-Sarfo K, Chen CH, Efron B, Gudas LJ, Mochly-Rosen D, Rajadas J. The Effect of Ethanol Consumption on Composition and Morphology of Femur Cortical Bone in Wild-Type and ALDH2*2-Homozygous Mice. Calcif Tissue Int 2021; 108:265-276. [PMID: 33068139 PMCID: PMC8092984 DOI: 10.1007/s00223-020-00769-1] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 10/05/2020] [Indexed: 11/28/2022]
Abstract
ALDH2 inactivating mutation (ALDH2*2) is the most abundant mutation leading to bone morphological aberration. Osteoporosis has long been associated with changes in bone biomaterial in elderly populations. Such changes can be exacerbated with elevated ethanol consumption and in subjects with impaired ethanol metabolism, such as carriers of aldehyde dehydrogenase 2 (ALDH2)-deficient gene, ALDH2*2. So far, little is known about bone compositional changes besides a decrease in mineralization. Raman spectroscopic imaging has been utilized to study the changes in overall composition of C57BL/6 female femur bone sections, as well as in compound spatial distribution. Raman maps of bone sections were analyzed using multilinear regression with these four isolated components, resulting in maps of their relative distribution. A 15-week treatment of both wild-type (WT) and ALDH2*2/*2 mice with 20% ethanol in the drinking water resulted in a significantly lower mineral content (p < 0.05) in the bones. There was no significant change in mineral and collagen content due to the mutation alone (p > 0.4). Highly localized islets of elongated adipose tissue were observed on most maps. Elevated fat content was found in ALDH2*2 knock-in mice consuming ethanol (p < 0.0001) and this effect appeared cumulative. This work conclusively demonstrates that that osteocytes in femurs of older female mice accumulate fat, as has been previously theorized, and that fat accumulation is likely modulated by levels of acetaldehyde, the ethanol metabolite.
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Affiliation(s)
- Andrey V Malkovskiy
- Biomaterials and Advanced Drug Delivery Laboratory, Stanford Medical School, Stanford, CA, 94305, USA.
- Department of Chemical and Systems Biology, Stanford Medical School, Stanford, CA, 94305, USA.
| | - Lauren D Van Wassenhove
- Department of Chemical and Systems Biology, Stanford Medical School, Stanford, CA, 94305, USA
| | - Yury Goltsev
- Department of Microbiology and Immunology, Baxter Laboratory in Stem Cell Biology, Stanford Medical School, Stanford, CA, 94305, USA
| | - Kwame Osei-Sarfo
- Department of Pharmacology, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Che-Hong Chen
- Department of Chemical and Systems Biology, Stanford Medical School, Stanford, CA, 94305, USA
| | - Bradley Efron
- Department of Biomedical Data Science, Stanford Medical School, Stanford, CA, 94305, USA
| | - Lorraine J Gudas
- Department of Pharmacology, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Daria Mochly-Rosen
- Department of Chemical and Systems Biology, Stanford Medical School, Stanford, CA, 94305, USA
| | - Jayakumar Rajadas
- Biomaterials and Advanced Drug Delivery Laboratory, Stanford Medical School, Stanford, CA, 94305, USA.
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16
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Lee I, Nakayama T, Jiang S, Goltsev Y, Schürch C, Zhu B, McIlwain D, Chu P, Chen H, Tzankov A, Matter M, Nayak J, Nolan G. SARS-CoV-2 entry factors are expressed in nasal, ocular, and oral tissues: implications for COVID-19 prophylaxes/therapeutics. J Allergy Clin Immunol 2021. [PMCID: PMC7849513 DOI: 10.1016/j.jaci.2020.12.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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17
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Schürch CM, Bhate SS, Barlow GL, Phillips DJ, Noti L, Zlobec I, Chu P, Black S, Demeter J, McIlwain DR, Kinoshita S, Samusik N, Goltsev Y, Nolan GP. Coordinated Cellular Neighborhoods Orchestrate Antitumoral Immunity at the Colorectal Cancer Invasive Front. Cell 2020; 183:838. [PMID: 33125896 PMCID: PMC7658307 DOI: 10.1016/j.cell.2020.10.021] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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18
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Lee IT, Nakayama T, Wu CT, Goltsev Y, Jiang S, Gall PA, Liao CK, Shih LC, Schürch CM, McIlwain DR, Chu P, Borchard NA, Zarabanda D, Dholakia SS, Yang A, Kim D, Chen H, Kanie T, Lin CD, Tsai MH, Phillips KM, Kim R, Overdevest JB, Tyler MA, Yan CH, Lin CF, Lin YT, Bau DT, Tsay GJ, Patel ZM, Tsou YA, Tzankov A, Matter MS, Tai CJ, Yeh TH, Hwang PH, Nolan GP, Nayak JV, Jackson PK. ACE2 localizes to the respiratory cilia and is not increased by ACE inhibitors or ARBs. Nat Commun 2020; 11:5453. [PMID: 33116139 PMCID: PMC7595232 DOI: 10.1038/s41467-020-19145-6] [Citation(s) in RCA: 155] [Impact Index Per Article: 38.8] [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: 05/18/2020] [Accepted: 09/30/2020] [Indexed: 12/26/2022] Open
Abstract
The coronavirus SARS-CoV-2 is the causative agent of the ongoing severe acute respiratory disease pandemic COVID-19. Tissue and cellular tropism is one key to understanding the pathogenesis of SARS-CoV-2. We investigate the expression and subcellular localization of the SARS-CoV-2 receptor, angiotensin-converting enzyme 2 (ACE2), within the upper (nasal) and lower (pulmonary) respiratory tracts of human donors using a diverse panel of banked tissues. Here, we report our discovery that the ACE2 receptor protein robustly localizes within the motile cilia of airway epithelial cells, which likely represents the initial or early subcellular site of SARS-CoV-2 viral entry during host respiratory transmission. We further determine whether ciliary ACE2 expression in the upper airway is influenced by patient demographics, clinical characteristics, comorbidities, or medication use, and show the first mechanistic evidence that the use of angiotensin-converting enzyme inhibitors (ACEI) or angiotensin II receptor blockers (ARBs) does not increase susceptibility to SARS-CoV-2 infection through enhancing the expression of ciliary ACE2 receptor. These findings are crucial to our understanding of the transmission of SARS-CoV-2 for prevention and control of this virulent pathogen.
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Affiliation(s)
- Ivan T Lee
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
- Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Tsuguhisa Nakayama
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
- Department of Otorhinolaryngology, Jikei University School of Medicine, Tokyo, Japan
| | - Chien-Ting Wu
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yury Goltsev
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Sizun Jiang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Phillip A Gall
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Chun-Kang Liao
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan
| | - Liang-Chun Shih
- Department of Otorhinolaryngology, China Medical University Hospital, Taichung, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Terry Fox Cancer Research Laboratory, Translational Medicine Center, China Medical University Hospital, Taichung, Taiwan
| | - Christian M Schürch
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - David R McIlwain
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Pauline Chu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Nicole A Borchard
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - David Zarabanda
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Sachi S Dholakia
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Angela Yang
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Dayoung Kim
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Han Chen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Tomoharu Kanie
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Chia-Der Lin
- Department of Otorhinolaryngology, China Medical University Hospital, Taichung, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- School of Medicine, China Medical University, Taichung, Taiwan
| | - Ming-Hsui Tsai
- Department of Otorhinolaryngology, China Medical University Hospital, Taichung, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- School of Medicine, China Medical University, Taichung, Taiwan
| | - Katie M Phillips
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Raymond Kim
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Jonathan B Overdevest
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
- Department of Otolaryngology-Head and Neck Surgery, Columbia University School of Medicine, New York City, NY, USA
| | - Matthew A Tyler
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
- Department of Otolaryngology-Head and Neck Surgery, University of Minnesota School of Medicine, Minneapolis, MN, USA
| | - Carol H Yan
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
- Department of Otolaryngology-Head and Neck Surgery, University of California San Diego School of Medicine, San Diego, CA, USA
| | - Chih-Feng Lin
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan
| | - Yi-Tsen Lin
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan
| | - Da-Tian Bau
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Terry Fox Cancer Research Laboratory, Translational Medicine Center, China Medical University Hospital, Taichung, Taiwan
| | - Gregory J Tsay
- School of Medicine, China Medical University, Taichung, Taiwan
- Division of Immunology and Rheumatology, Department of Internal Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Zara M Patel
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Yung-An Tsou
- Department of Otorhinolaryngology, China Medical University Hospital, Taichung, Taiwan
- School of Medicine, China Medical University, Taichung, Taiwan
| | - Alexandar Tzankov
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Matthias S Matter
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Chih-Jaan Tai
- Department of Otorhinolaryngology, China Medical University Hospital, Taichung, Taiwan
- School of Medicine, China Medical University, Taichung, Taiwan
| | - Te-Huei Yeh
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan
- Department of Otolaryngology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Peter H Hwang
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Jayakar V Nayak
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Peter K Jackson
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA
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19
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Schürch CM, Bhate SS, Barlow GL, Phillips DJ, Noti L, Zlobec I, Chu P, Black S, Demeter J, McIlwain DR, Kinoshita S, Samusik N, Goltsev Y, Nolan GP. Coordinated Cellular Neighborhoods Orchestrate Antitumoral Immunity at the Colorectal Cancer Invasive Front. Cell 2020; 182:1341-1359.e19. [PMID: 32763154 PMCID: PMC7479520 DOI: 10.1016/j.cell.2020.07.005] [Citation(s) in RCA: 324] [Impact Index Per Article: 81.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 04/22/2020] [Accepted: 07/08/2020] [Indexed: 12/21/2022]
Abstract
Antitumoral immunity requires organized, spatially nuanced interactions between components of the immune tumor microenvironment (iTME). Understanding this coordinated behavior in effective versus ineffective tumor control will advance immunotherapies. We re-engineered co-detection by indexing (CODEX) for paraffin-embedded tissue microarrays, enabling simultaneous profiling of 140 tissue regions from 35 advanced-stage colorectal cancer (CRC) patients with 56 protein markers. We identified nine conserved, distinct cellular neighborhoods (CNs)-a collection of components characteristic of the CRC iTME. Enrichment of PD-1+CD4+ T cells only within a granulocyte CN positively correlated with survival in a high-risk patient subset. Coupling of tumor and immune CNs, fragmentation of T cell and macrophage CNs, and disruption of inter-CN communication was associated with inferior outcomes. This study provides a framework for interrogating how complex biological processes, such as antitumoral immunity, occur through concerted actions of cells and spatial domains.
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Affiliation(s)
- Christian M Schürch
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Salil S Bhate
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Graham L Barlow
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Darci J Phillips
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Luca Noti
- Institute of Pathology, University of Bern, 3008 Bern, Switzerland
| | - Inti Zlobec
- Institute of Pathology, University of Bern, 3008 Bern, Switzerland
| | - Pauline Chu
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sarah Black
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Janos Demeter
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - David R McIlwain
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shigemi Kinoshita
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nikolay Samusik
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yury Goltsev
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Garry P Nolan
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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20
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Lee IT, Nakayama T, Wu CT, Goltsev Y, Jiang S, Gall PA, Liao CK, Shih LC, Schürch CM, McIlwain DR, Chu P, Borchard NA, Zarabanda D, Dholakia SS, Yang A, Kim D, Kanie T, Lin CD, Tsai MH, Phillips KM, Kim R, Overdevest JB, Tyler MA, Yan CH, Lin CF, Lin YT, Bau DT, Tsay GJ, Patel ZM, Tsou YA, Tai CJ, Yeh TH, Hwang PH, Nolan GP, Nayak JV, Jackson PK. Robust ACE2 protein expression localizes to the motile cilia of the respiratory tract epithelia and is not increased by ACE inhibitors or angiotensin receptor blockers. medRxiv 2020:2020.05.08.20092866. [PMID: 32511516 PMCID: PMC7273284 DOI: 10.1101/2020.05.08.20092866] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 12/26/2022]
Abstract
We investigated the expression and subcellular localization of the SARS-CoV-2 receptor, angiotensin-converting enzyme 2 (ACE2), within the upper (nasal) and lower (pulmonary) respiratory tracts of healthy human donors. We detected ACE2 protein expression within the cilia organelle of ciliated airway epithelial cells, which likely represents the initial or early subcellular site of SARS-CoV-2 viral entry during respiratory transmission. We further determined whether ACE2 expression in the cilia of upper respiratory cells was influenced by patient demographics, clinical characteristics, co-morbidities, or medication use, and found no evidence that the use of angiotensin-converting enzyme inhibitors (ACEI) or angiotensin II receptor blockers (ARBs) increases ACE2 protein expression.
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Affiliation(s)
- Ivan T. Lee
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
- Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- These authors contributed equally: Ivan T. Lee, Tsuguhisa Nakayama, Chien-Ting Wu, Yury Goltsev
| | - Tsuguhisa Nakayama
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
- These authors contributed equally: Ivan T. Lee, Tsuguhisa Nakayama, Chien-Ting Wu, Yury Goltsev
| | - Chien-Ting Wu
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, USA
- These authors contributed equally: Ivan T. Lee, Tsuguhisa Nakayama, Chien-Ting Wu, Yury Goltsev
| | - Yury Goltsev
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
- These authors contributed equally: Ivan T. Lee, Tsuguhisa Nakayama, Chien-Ting Wu, Yury Goltsev
| | - Sizun Jiang
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Phillip A. Gall
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
| | - Chun-Kang Liao
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan
| | - Liang-Chun Shih
- Department of Otorhinolaryngology, China Medical University Hospital, Taichung, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Terry Fox Cancer Research Laboratory, Translational Medicine Center, China Medical University Hospital, Taichung, Taiwan
| | - Christian M. Schürch
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - David R. McIlwain
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Pauline Chu
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Nicole A. Borchard
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
| | - David Zarabanda
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
| | - Sachi S. Dholakia
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
| | - Angela Yang
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
| | - Dayoung Kim
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
| | - Tomoharu Kanie
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Chia-Der Lin
- Department of Otorhinolaryngology, China Medical University Hospital, Taichung, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- School of Medicine, China Medical University, Taichung, Taiwan
| | - Ming-Hsui Tsai
- Department of Otorhinolaryngology, China Medical University Hospital, Taichung, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- School of Medicine, China Medical University, Taichung, Taiwan
| | - Katie M. Phillips
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
| | - Raymond Kim
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
| | - Jonathan B. Overdevest
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
- Department of Otolaryngology–Head and Neck Surgery, Columbia University School of Medicine, New York City, NY
| | - Matthew A. Tyler
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
- Department of Otolaryngology–Head and Neck Surgery, University of Minnesota School of Medicine, Minneapolis, MN
| | - Carol H. Yan
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
- Department of Otolaryngology–Head and Neck Surgery, University of California San Diego School of Medicine, San Diego, CA
| | - Chih-Feng Lin
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan
| | - Yi-Tsen Lin
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan
| | - Da-Tian Bau
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Terry Fox Cancer Research Laboratory, Translational Medicine Center, China Medical University Hospital, Taichung, Taiwan
| | - Gregory J. Tsay
- School of Medicine, China Medical University, Taichung, Taiwan
- Division of Immunology and Rheumatology, Department of Internal Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Zara M. Patel
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
| | - Yung-An Tsou
- Department of Otorhinolaryngology, China Medical University Hospital, Taichung, Taiwan
- School of Medicine, China Medical University, Taichung, Taiwan
| | - Chih-Jaan Tai
- Department of Otorhinolaryngology, China Medical University Hospital, Taichung, Taiwan
- School of Medicine, China Medical University, Taichung, Taiwan
| | - Te-Huei Yeh
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan
| | - Peter H. Hwang
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
| | - Garry P. Nolan
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
- These authors jointly supervised this work: Garry P. Nolan, Jayakar V. Nayak, Peter K. Jackson
| | - Jayakar V. Nayak
- Department of Otolaryngology–Head and Neck Surgery, Stanford University School of Medicine, 801 Welch Road, Stanford, CA, USA
- These authors jointly supervised this work: Garry P. Nolan, Jayakar V. Nayak, Peter K. Jackson
| | - Peter K. Jackson
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, USA
- These authors jointly supervised this work: Garry P. Nolan, Jayakar V. Nayak, Peter K. Jackson
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21
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Kagan J, Moritz RL, Mazurchuk R, Lee JH, Kharchenko PV, Rozenblatt-Rosen O, Ruppin E, Edfors F, Ginty F, Goltsev Y, Wells JA, LaCava J, Riesterer JL, Germain RN, Shi T, Chee MS, Budnik BA, Yates JR, Chait BT, Moffitt JR, Smith RD, Srivastava S. National Cancer Institute Think-Tank Meeting Report on Proteomic Cartography and Biomarkers at the Single-Cell Level: Interrogation of Premalignant Lesions. J Proteome Res 2020; 19:1900-1912. [PMID: 32163288 DOI: 10.1021/acs.jproteome.0c00021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A Think-Tank Meeting was convened by the National Cancer Institute (NCI) to solicit experts' opinion on the development and application of multiomic single-cell analyses, and especially single-cell proteomics, to improve the development of a new generation of biomarkers for cancer risk, early detection, diagnosis, and prognosis as well as to discuss the discovery of new targets for prevention and therapy. It is anticipated that such markers and targets will be based on cellular, subcellular, molecular, and functional aberrations within the lesion and within individual cells. Single-cell proteomic data will be essential for the establishment of new tools with searchable and scalable features that include spatial and temporal cartographies of premalignant and malignant lesions. Challenges and potential solutions that were discussed included (i) The best way/s to analyze single-cells from fresh and preserved tissue; (ii) Detection and analysis of secreted molecules and from single cells, especially from a tissue slice; (iii) Detection of new, previously undocumented cell type/s in the premalignant and early stage cancer tissue microenvironment; (iv) Multiomic integration of data to support and inform proteomic measurements; (v) Subcellular organelles-identifying abnormal structure, function, distribution, and location within individual premalignant and malignant cells; (vi) How to improve the dynamic range of single-cell proteomic measurements for discovery of differentially expressed proteins and their post-translational modifications (PTM); (vii) The depth of coverage measured concurrently using single-cell techniques; (viii) Quantitation - absolute or semiquantitative? (ix) Single methodology or multiplexed combinations? (x) Application of analytical methods for identification of biologically significant subsets; (xi) Data visualization of N-dimensional data sets; (xii) How to construct intercellular signaling networks in individual cells within premalignant tumor microenvironments (TME); (xiii) Associations between intrinsic cellular processes and extrinsic stimuli; (xiv) How to predict cellular responses to stress-inducing stimuli; (xv) Identification of new markers for prediction of progression from precursor, benign, and localized lesions to invasive cancer, based on spatial and temporal changes within individual cells; (xvi) Identification of new targets for immunoprevention or immunotherapy-identification of neoantigens and surfactome of individual cells within a lesion.
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Affiliation(s)
- Jacob Kagan
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland, United States
| | - Robert L Moritz
- Institute for Systems Biology, Seattle, Washington, United States
| | - Richard Mazurchuk
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland, United States
| | - Je Hyuk Lee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States
| | - Peter Vasili Kharchenko
- Blavatnik Institute for Biomedical Information, Harvard Medical School, Boston, Massachusetts, United States
| | | | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States
| | - Fredrik Edfors
- Science for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Fiona Ginty
- Life Sciences and Molecular Diagnostics Laboratory, GE Global Research Center, Niskayuna, New York, United States
| | - Yury Goltsev
- Department of Microbiology and Immunology, Baxter Laboratory in Stem Cell Biology, Stanford University, Stanford Medical School, Stanford, California, United States
| | - James A Wells
- Department of Pharmaceutical Sciences, University of California, San Francisco, California, United States
| | - John LaCava
- Laboratory of Cellular and Structural Biology, Rockefeller University, New York, New York, United States
| | - Jessica L Riesterer
- Center for Spatial Systems Biomedicine, Oregon Health and Science University, Portland, Oregon, United States
| | - Ronald N Germain
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, United States
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States
| | - Mark S Chee
- Encodia, Inc., San Diego, California, United States
| | - Bogdan A Budnik
- Faculty of Arts & Sciences, Division of Science. Harvard University, Boston, Massachusetts, United States
| | - John R Yates
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, California, United States
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York, United States
| | - Jeffery R Moffitt
- Boston Children's Hospital and Harvard University Medical School, Boston, Massachusetts, United States
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States
| | - Sudhir Srivastava
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland, United States
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22
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Goltsev Y, Samusik N, Kennedy-Darling J, Bhate S, Hale M, Vazquez G, Black S, Nolan GP. Deep Profiling of Mouse Splenic Architecture with CODEX Multiplexed Imaging. Cell 2018; 174:968-981.e15. [PMID: 30078711 PMCID: PMC6086938 DOI: 10.1016/j.cell.2018.07.010] [Citation(s) in RCA: 703] [Impact Index Per Article: 117.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 02/05/2018] [Accepted: 07/03/2018] [Indexed: 12/14/2022]
Abstract
A highly multiplexed cytometric imaging approach, termed co-detection by indexing (CODEX), is used here to create multiplexed datasets of normal and lupus (MRL/lpr) murine spleens. CODEX iteratively visualizes antibody binding events using DNA barcodes, fluorescent dNTP analogs, and an in situ polymerization-based indexing procedure. An algorithmic pipeline for single-cell antigen quantification in tightly packed tissues was developed and used to overlay well-known morphological features with de novo characterization of lymphoid tissue architecture at a single-cell and cellular neighborhood levels. We observed an unexpected, profound impact of the cellular neighborhood on the expression of protein receptors on immune cells. By comparing normal murine spleen to spleens from animals with systemic autoimmune disease (MRL/lpr), extensive and previously uncharacterized splenic cell-interaction dynamics in the healthy versus diseased state was observed. The fidelity of multiplexed spatial cytometry demonstrated here allows for quantitative systemic characterization of tissue architecture in normal and clinically aberrant samples. Autoimmunity analyzed by multiplexed DNA-tagged antibody staining (CODEX) CODEX data reveal pairwise interactions and niches changing with disease First tier of neighbors significantly impacts marker expression in the index cells Changes in splenic morphology correlate with shifts in cell frequencies
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Affiliation(s)
- Yury Goltsev
- Department of Microbiology and Immunology, Baxter Laboratory in Stem Cell Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Nikolay Samusik
- Department of Microbiology and Immunology, Baxter Laboratory in Stem Cell Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Julia Kennedy-Darling
- Department of Microbiology and Immunology, Baxter Laboratory in Stem Cell Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Salil Bhate
- Department of Microbiology and Immunology, Baxter Laboratory in Stem Cell Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew Hale
- Department of Microbiology and Immunology, Baxter Laboratory in Stem Cell Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Gustavo Vazquez
- Department of Microbiology and Immunology, Baxter Laboratory in Stem Cell Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Sarah Black
- Department of Microbiology and Immunology, Baxter Laboratory in Stem Cell Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Garry P Nolan
- Department of Microbiology and Immunology, Baxter Laboratory in Stem Cell Biology, Stanford University School of Medicine, Stanford, CA, USA.
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Bhate SS, Samusik N, Goltsev Y, Nolan GP. Abstract PR14: Automatic identification of cell niches and immune interactions important for clinical outcomes using multiparameter imaging and deep neural networks. Cancer Immunol Res 2016. [DOI: 10.1158/2326-6066.imm2016-pr14] [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
Multiparameter cytometry, for example with CyTOF, has enabled the interrogation of immune phenotypes in unprecedented detail in many clinical contexts. But cytometry is incapable of answering a question of critical importance to many tissue context studies, and especially understanding how local interactions between tumor cells and immune cells correlate to clinical outcomes. This becomes especially relevant to understanding the subtleties of how different immunotherapeutic approaches operate in vivo.
We recently developed a multiparameter immunofluorescence technique, termed CODEX, which allows the capture of spatial information for protein and RNA expression in tissue sections. This spatial information enables us to establish not only cell-types according to traditional phenotypic surface marker expression, but also to potentially surmise specific tissue states driving clinical responses. To make sense of the high-dimensional data afforded by CODEX, we apply here state-of-the-art deep neural networks (DNNs). These networks, which have achieved superhuman classification accuracy in many diverse domains, automatically identify cells, cell niches and regions (at multiple scales) that are capable of distinguishing healthy and diseased samples. This is done in an unbiased way, with only ‘healthy’ vs. ‘disease’ labels as additional input alongside the imaging data.
We first train DNNs to successfully classify multiparameter tissue images from independent replicates across conditions. Having achieved a high accuracy of classification, we set the network output to highlight cells and regions deemed to be most relevant to classify each condition. Applying this methodology to healthy and mrl (lupus) spleens stained for 30 markers, our neural network is able to successfully identify a not previously observed enrichment of cell confluences (niches) consisting of CD8 T-cells and conventional dendritic cells enriched in MRL samples, as well as other novel niches completely unpredicted by prior knowledge.
Our DNN enables the systematic and unbiased discovery of specific immune interactions in any tissue type. Applying our technique to the analysis of samples from immunotherapy recipients could enable the discovery of key factors in the tumor microenvironment that distinguish positive responders as well as the subsequent identification of targets for perturbation.
Citation Format: Salil S. Bhate, Nikolay Samusik, Yury Goltsev, Garry P. Nolan. Automatic identification of cell niches and immune interactions important for clinical outcomes using multiparameter imaging and deep neural networks [abstract]. In: Proceedings of the Second CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; 2016 Sept 25-28; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(11 Suppl):Abstract nr PR14.
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Kennedy-Darling J, Nolan GP, Goltsev Y, Samusik N. Abstract A089: Multiparametric immunofluorescence analysis of the tumor microenvironment using CODEX. Cancer Immunol Res 2016. [DOI: 10.1158/2326-6066.imm2016-a089] [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
The tumor microenvironment plays a critical role in cancer progression and has implications for the efficacy of various cancer immunotherapy treatment options. Immune infiltrates within the tumor microenvironment can correlate with both positive and negative outcomes, depending upon the both the type of cancer as well as infiltrating immune cell(s). These analyses are typically performed using standard immunofluorescence and immunohistochemistry assays where no more than four simultaneous parameters can be visualized on the same tissue. Unfortunately, these tools cannot fully characterize the complexity of the tumor microenvironment due to the inherent limitations of fluorophore spectral overlap. In order to identify each type of immune and tumor cell within a single tissue, at least 40 parameters need to be measured simultaneously. We have developed a multiparametric immunofluorescence technology, entitled CODEX (Co-Detection by IndEXing), which utilizes unique DNA tags as a means of iteratively measuring more than 40 parameters within the same tissue. More than 40 human antibodies have been validated using this approach, including numerous immune markers, checkpoint ligands, tumor markers and cellular activity markers. We are currently analyzing tissue sample from patients with lung cancer. By measuring nearly 50 simultaneous markers within the same tissue, CODEX has the potential to greatly enhance our knowledge of the tumor microenvironment and more accurately define immune infiltrates at the single-cell level.
Citation Format: Julia Kennedy-Darling, Garry P. Nolan, Yury Goltsev, Nikolay Samusik. Multiparametric immunofluorescence analysis of the tumor microenvironment using CODEX [abstract]. In: Proceedings of the Second CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; 2016 Sept 25-28; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(11 Suppl):Abstract nr A089.
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Affiliation(s)
| | | | - Yury Goltsev
- Stanford University School of Medicine, Stanford, CA
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Zunder ER, Lujan E, Goltsev Y, Wernig M, Nolan GP. A continuous molecular roadmap to iPSC reprogramming through progression analysis of single-cell mass cytometry. Cell Stem Cell 2016; 16:323-37. [PMID: 25748935 DOI: 10.1016/j.stem.2015.01.015] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 10/10/2014] [Accepted: 01/23/2015] [Indexed: 12/21/2022]
Abstract
To analyze cellular reprogramming at the single-cell level, mass cytometry was used to simultaneously measure markers of pluripotency, differentiation, cell-cycle status, and cellular signaling throughout the reprogramming process. Time-resolved progression analysis of the resulting data sets was used to construct a continuous molecular roadmap for three independent reprogramming systems. Although these systems varied substantially in Oct4, Sox2, Klf4, and c-Myc stoichiometry, they presented a common set of reprogramming landmarks. Early in the reprogramming process, Oct4(high)Klf4(high) cells transitioned to a CD73(high)CD104(high)CD54(low) partially reprogrammed state. Ki67(low) cells from this intermediate population reverted to a MEF-like phenotype, but Ki67(high) cells advanced through the M-E-T and then bifurcated into two distinct populations: an ESC-like Nanog(high)Sox2(high)CD54(high) population and a mesendoderm-like Nanog(low)Sox2(low)Lin28(high)CD24(high)PDGFR-α(high) population. The methods developed here for time-resolved, single-cell progression analysis may be used for the study of additional complex and dynamic systems, such as cancer progression and embryonic development.
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Affiliation(s)
- Eli R Zunder
- Department of Microbiology and Immunology, Baxter Laboratory for Stem Cell Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ernesto Lujan
- Department of Pathology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yury Goltsev
- Department of Microbiology and Immunology, Baxter Laboratory for Stem Cell Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marius Wernig
- Department of Pathology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Garry P Nolan
- Department of Microbiology and Immunology, Baxter Laboratory for Stem Cell Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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26
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Nishikii H, Umemoto T, Goltsev Y, Matsuzaki Y, Yamato M, Nolan G, Negrin R, Chiba S. Unipotent megakaryopoietic pathway bridging hematopoietic stem cells and mature megakaryocytes. Exp Hematol 2015. [DOI: 10.1016/j.exphem.2015.06.212] [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: 10/23/2022]
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27
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Nishikii H, Kanazawa Y, Umemoto T, Goltsev Y, Matsuzaki Y, Matsushita K, Yamato M, Nolan GP, Negrin R, Chiba S. Unipotent Megakaryopoietic Pathway Bridging Hematopoietic Stem Cells and Mature Megakaryocytes. Stem Cells 2015; 33:2196-207. [PMID: 25753067 DOI: 10.1002/stem.1985] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [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: 08/12/2014] [Revised: 01/07/2015] [Accepted: 02/06/2015] [Indexed: 12/24/2022]
Abstract
Recent identification of platelet/megakaryocyte-biased hematopoietic stem/repopulating cells requires revision of the intermediate pathway for megakaryopoiesis. Here, we show a unipotent megakaryopoietic pathway bypassing the bipotent megakaryocyte/erythroid progenitors (biEMPs). Cells purified from mouse bone marrow by CD42b (GPIbα) marking were demonstrated to be unipotent megakaryocytic progenitors (MKPs) by culture and transplantation. A subpopulation of freshly isolated CD41(+) cells in the lineage Sca1(+) cKit(+) (LSK) fraction (subCD41(+) LSK) differentiated only into MKP and mature megakaryocytes in culture. Although CD41(+) LSK cells as a whole were capable of differentiating into all myeloid and lymphoid cells in vivo, they produced unipotent MKP, mature megakaryocytes, and platelets in vitro and in vivo much more efficiently than Flt3(+) CD41(-) LSK cells, especially at the early phase after transplantation. In single cell polymerase chain reaction and thrombopoietin (TPO) signaling analyses, the MKP and a fraction of CD41(+) LSK, but not the biEMP, showed the similarities in mRNA expression profile and visible TPO-mediated phosphorylation. On increased demand of platelet production after 5-FU treatment, a part of CD41(+) LSK population expressed CD42b on the surface, and 90% of them showed unipotent megakaryopoietic capacity in single cell culture and predominantly produced platelets in vivo at the early phase after transplantation. These results suggest that the CD41(+) CD42b(+) LSK are straightforward progenies of megakaryocytes/platelet-biased stem/repopulating cells, but not progenies of biEMP. Consequently, we show a unipotent/highly biased megakaryopoietic pathway interconnecting stem/repopulating cells and mature megakaryocytes, the one that may play physiologic roles especially in emergency megakaryopoiesis.
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Affiliation(s)
- Hidekazu Nishikii
- Department of Hematology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan.,Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.,Division of Blood and Marrow Transplantation, Department of Medicine, Stanford University, Stanford, California, USA
| | - Yosuke Kanazawa
- Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Terumasa Umemoto
- Institute of Advanced Biomedical Engineering and Science, Tokyo Women's Medical University, Shinjuku-ku, Tokyo, Japan
| | - Yury Goltsev
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University of School of Medicine, Stanford, California, USA
| | - Yu Matsuzaki
- Institute of Advanced Biomedical Engineering and Science, Tokyo Women's Medical University, Shinjuku-ku, Tokyo, Japan
| | - Kenji Matsushita
- Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Masayuki Yamato
- Institute of Advanced Biomedical Engineering and Science, Tokyo Women's Medical University, Shinjuku-ku, Tokyo, Japan
| | - Garry P Nolan
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University of School of Medicine, Stanford, California, USA
| | - Robert Negrin
- Division of Blood and Marrow Transplantation, Department of Medicine, Stanford University, Stanford, California, USA
| | - Shigeru Chiba
- Department of Hematology, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan.,Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.,Life Science Center, Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba, Ibaraki, Japan
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28
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Lai C, Levinson S, Lin A, Pache J, Goltsev Y, Nolan G, Bers G, Nguyen Q. A robust and sensitive flow cytometric method for multiplex RNA in-situ hybridization analysis of blood cells using oligo probes and branched DNA based signal amplification (P3356). The Journal of Immunology 2013. [DOI: 10.4049/jimmunol.190.supp.135.4] [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
We present here a novel method for in-situ hybridization (ISH) detection of multiple RNA targets in single cells using standard flow cytometer. This method is based on the use of oligo pairs as probes and bDNA signal amplification for highly sensitive and specific ISH detection of RNA. The oligo pairs are designed to hybridize to specific target sequences and can be readily synthesized. The oligo probes/RNA target complex is detected after signal is generated by bDNA signal amplification. The method is compatible with immunostaining, so simultaneous staining of protein and RNA in single cells is feasible. We demonstrated the co-staining of RNA and surface marker proteins in PBMC, B cells, T cells and leukemic cell lines of U937, K562, Jurkat and M1. In addition, the flow cytometric analysis of cytokine gene induction by lipopolysaccharides/R848 in PBMC was shown by staining with antibody for CD14 protein and probes for RNAs encoding interleukin-1 beta, -6, -8 and tumor necrosis factor-alpha. Taken together, this novel RNA ISH flow cytometry assay offers an invaluable tool for studying immune response, stem cell biology and infectious diseases.
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Affiliation(s)
- Chunfai Lai
- 1R&D Department, Affymetrix, Inc., Santa Clara, CA
| | | | - Audrey Lin
- 1R&D Department, Affymetrix, Inc., Santa Clara, CA
| | - Jared Pache
- 1R&D Department, Affymetrix, Inc., Santa Clara, CA
| | - Yury Goltsev
- 2Department of Microbiology and Immunology, Stanford Univ. Sch. of Med., Palo Alto, CA
| | - Garry Nolan
- 2Department of Microbiology and Immunology, Stanford Univ. Sch. of Med., Palo Alto, CA
| | - George Bers
- 1R&D Department, Affymetrix, Inc., Santa Clara, CA
| | - Quan Nguyen
- 1R&D Department, Affymetrix, Inc., Santa Clara, CA
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29
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Gibbs KD, Jager A, Crespo O, Goltsev Y, Trejo A, Richard CE, Nolan GP. Decoupling of tumor-initiating activity from stable immunophenotype in HoxA9-Meis1-driven AML. Cell Stem Cell 2012; 10:210-7. [PMID: 22305570 DOI: 10.1016/j.stem.2012.01.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Revised: 10/26/2011] [Accepted: 01/06/2012] [Indexed: 01/28/2023]
Abstract
Increasing evidence suggests tumors are maintained by cancer stem cells; however, their nature remains controversial. In a HoxA9-Meis1 (H9M) model of acute myeloid leukemia (AML), we found that tumor-initiating activity existed in three, immunophenotypically distinct compartments, corresponding to disparate lineages on the normal hematopoietic hierarchy--stem/progenitor cells (Lin(-)kit(+)) and committed progenitors of the myeloid (Gr1(+)kit(+)) and lymphoid lineages (Lym(+)kit(+)). These distinct tumor-initiating cells (TICs) clonally recapitulated the immunophenotypic spectrum of the original tumor in vivo (including cells with a less-differentiated immunophenotype) and shared signaling networks, such that in vivo pharmacologic targeting of conserved TIC survival pathways (DNA methyltransferase and MEK phosphorylation) significantly increased survival. Collectively, H9M AML is organized as an atypical hierarchy that defies the strict lineage marker boundaries and unidirectional differentiation of normal hematopoiesis. Moreover, this suggests that in certain malignancies tumor-initiation activity (or "cancer stemness") can represent a cellular state that exists independently of distinct immunophenotypic definition.
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Affiliation(s)
- Kenneth D Gibbs
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
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Gibbs KD, Jager A, Crespo O, Goltsev Y, Tejo A, Richard C, Nolan G. Abstract 3307: Improved survival in AML by in vivo drug targeting of conserved regulatory pathways in phenotypically distinct tumor-initiating compartments. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-3307] [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
Increasing evidence suggests tumors are maintained by cancer stem cells, however their nature remains controversial. In a HoxA9-Meis1 (H9M) driven model of acute myeloid leukemia (AML), we found that tumor-initiating activity existed in three, immunophenotypically distinct compartments, corresponding to disparate lineages on the normal hematopoietic hierarchy–stem/progenitor cells (Lin−kit+), and committed progenitors of the myeloid (Gr1+kit+) and lymphoid lineages (Lym+kit+). Each compartment clonally recapitulated the original range of tumor cell immunophenotypes in vivo, including cells with a less-differentiated immunophenotype. These distinct populations largely shared signaling networks, and in vivo pharmacologic targeting of shared pathways (DNA methyltransferase and MEK phosphorylation) significantly increased survival. Collectively, these data show that H9M AML is organized as an atypical hierarchy that defies the strict lineage marker boundaries and unidirectional differentiation of normal hematopoiesis. Moreover, in some malignancies, tumor-initiation ability (or “cancer-stemness”) can represent a targetable, cellular state that can exithat exists independently of distinct immunophenotypic definition.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3307. doi:1538-7445.AM2012-3307
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Hsu F, Nolan GP, Chen T, Goltsev Y. Abstract LB-33: Identification of two unrecognized acute myeloid leukemia (AML) subtypes based on cell by cell analysis of leukemic blasts. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-lb-33] [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
Single cell multiparametric flow cytometry studies have previously shown that G-CSF-mediated intracellular signaling responsiveness of blast cell subsets stratified clinical outcomes of AML patients. 13 AML samples were stimulated with G-CSF, fixed, and permeabilized with a technique we developed that preserves mRNA integrity in a manner suitable for microarray-based expression analysis. From the microarray profiles we identified surface markers that could be prospectively used to separately enrich G-CSF Responsive Cells (GRCs) and non-G-CSF Responsive Cells (NGRCs) from each sample. The results demonstrate that two previously unrecognized subtypes of AML could be discerned, as portrayed by the proteomic and molecular characteristics of the GRC and NGRC subsets. First, GRC cells had a higher colony formation capacity as well as being more reactive to cytokines secreted by NGRCs In one discovered AML subtype, patients present with bone marrow that had higher percentages of GRCs (20-50%), with the remainder being NGRCs. The molecular signatures of both the GRCs and NGRCs in this subtype had a hematopoietic progenitors mRNA signature (HPMS). In the second subtype of AML there were lower percentages of GRCs (0.5-10%, which had the HPMS) but in these cases the NGRC mRNA signatures were distinct resembling those of a more differentiated myeloid phenotype. Therefore, in most AML patients tested, two blast cell populations inevitably appear, and each of these blasts represented a distinct level of hematopoietic maturity, or cytokine responsiveness. The common thread between the two subtypes is that the GRCs in each patient were more capable of colony formation, enabled by a potentially more “stem-like” phenotype. Critically, each population would be clinically termed “blast” cells and would therefore be considered malignant and a potential target for chemotherapy. These results lead to two important conclusions. The first is that the blast phenotype can exist independently of the apparent cell maturation stage. This raises the questions of whether each blast subtype is equally susceptible to standard chemotherapy, whether a strategy of defining the molecular players that drive the formation of each of these blast types should be pursued, and finally whether such information can be used to better combat these aspects of the leukemic disease spectrum.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-33. doi:1538-7445.AM2012-LB-33
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Affiliation(s)
- Faye Hsu
- 1Stanford University, Stanford, CA
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Gibbs K, Jager A, Crespo O, Goltsev Y, Trejo A, Richard C, Nolan G. Decoupling of Tumor-Initiating Activity from Stable Immunophenotype in HoxA9-Meis1-Driven AML. Cell Stem Cell 2012. [DOI: 10.1016/j.stem.2012.02.019] [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: 11/16/2022]
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Papatsenko D, Levine M, Goltsev Y. Clusters of temporal discordances reveal distinct embryonic patterning mechanisms in Drosophila and anopheles. PLoS Biol 2011; 9:e1000584. [PMID: 21283609 PMCID: PMC3026761 DOI: 10.1371/journal.pbio.1000584] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Accepted: 12/08/2010] [Indexed: 12/13/2022] Open
Abstract
Evolutionary innovations can be driven by spatial and temporal changes in gene expression. Several such differences have been documented in the embryos of lower and higher Diptera. One example is the reduction of the ancient extraembryonic envelope composed of amnion and serosa as seen in mosquitoes to the single amnioserosa of fruit flies. We used transcriptional datasets collected during the embryonic development of the fruit fly, Drosophila melanogaster, and the malaria mosquito, Anopheles gambiae, to search for whole-genome changes in gene expression underlying differences in their respective embryonic morphologies. We found that many orthologous gene pairs could be clustered based on the presence of coincident discordances in their temporal expression profiles. One such cluster contained genes expressed specifically in the mosquito serosa. As shown previously, this cluster is re-deployed later in development at the time of cuticle synthesis. In addition, there is a striking difference in the temporal expression of a subset of maternal genes. Specifically, maternal transcripts that exhibit a sharp reduction at the time of the maternal-zygotic transition in Drosophila display sustained expression in the Anopheles embryo. We propose that gene clustering by local temporal discordance can be used for the de novo identification of the gene batteries underlying morphological diversity.
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Affiliation(s)
- Dmitri Papatsenko
- Department of Molecular and Cell Biology, Division of Genetics Genomics and Development, Center for Integrative Genomics, University of California, Berkeley, California, United States of America
| | - Michael Levine
- Department of Molecular and Cell Biology, Division of Genetics Genomics and Development, Center for Integrative Genomics, University of California, Berkeley, California, United States of America
| | - Yury Goltsev
- Department of Molecular and Cell Biology, Division of Genetics Genomics and Development, Center for Integrative Genomics, University of California, Berkeley, California, United States of America
- * E-mail:
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Oh ST, Zahn JM, Simonds EF, Bell J, Natsoulis G, Buenstro J, Jones C, Hale MB, Goltsev Y, Gibbs KD, Merker JD, Zehnder JL, Davis RW, Nolan GP, Ji HP, Gotlib J. Abstract B6: Identification of novel mutations in the inhibitory adaptor protein LNK in patients with JAK2 V617F-negative and -positive chronic myeloproliferative neoplasms. Clin Cancer Res 2010. [DOI: 10.1158/1078-0432.tcmusa10-b6] [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
Dysregulated JAK-STAT signaling is a hallmark of myeloproliferative neoplasms (MPNs), as evidenced by the identification of activating mutations in JAK2, and the thrombopoietin (TPO) receptor MPL in a subset of MPN patients. Clinical trials with highly specific inhibitors of JAK2 are currently ongoing, and clinical responses have been observed in the majority of MPN patients, validating JAK2 as an important therapeutic target in these patients. In addition, responses have been observed in patients lacking known mutations in JAK2 or MPL, suggesting that other regulatory elements in this pathway are altered. However, the molecular basis for this observation is not well understood.
One regulator of JAK-STAT signaling is LNK (SH2B3), a member of a family of adaptor proteins that share several structural motifs, including a proline-rich N-terminal dimerization domain (Pro/DD), a pleckstrin homology (PH) domain, an SH2 domain, and a conserved C-terminal tyrosine residue. LNK binds to MPL via its SH2 domain and co-localizes to the plasma membrane via its PH domain. Upon cytokine stimulation with TPO, LNK binds strongly to JAK2 and inhibits downstream STAT activation, thereby providing critical negative feedback regulation. LNK-/- mice exhibit an MPN phenotype, including an expanded hematopoietic stem cell compartment, megakaryocyte hyperplasia, splenomegaly, leukocytosis, and thrombocytosis.
We sequenced LNK in a cohort of MPN patients, leading to the identification of novel mutations in 7/159 (4.4%) patients. One patient with JAK2 V617F-negative primary myelofibrosis (PMF) exhibited a 5 base-pair deletion and missense mutation (DEL) leading to a premature stop codon and loss of the PH and SH2 domains. Six additional patients were found to have point mutations affecting conserved residues in the PH domain. Interestingly, a point mutation leading to an E208Q substitution was found in one JAK2 V617F- negative patient with essential thrombocythemia (ET), as well as one JAK2 V617F-positive ET patient. Similarly, a P242S substitution was also found in both a JAK2 V617F-negative ET patient, as well as a JAK2 V617F-positive patient with post-polycythemic myelofibrosis.
These latter findings suggest that even in the presence of the JAK2 V617F mutation, abrogation of LNK function may be a cooperating pathogenetic mutation.
TPO-dependent BaF3-MPL cells transduced with the LNK DEL mutant exhibited augmented and sustained TPO-dependent growth and activation of JAK2-STAT3/5. The E208Q mutation resulted in partial loss of LNK function, suggesting that LNK mutations may confer a spectrum of phenotypes. Primary patient samples from MPN patients bearing the LNK DEL and E208Q mutations exhibited aberrant JAK-STAT activation, and cytokine-responsive CD34+ early progenitors were abnormally abundant. The STAT3/5 activation response was abrogated by JAK inhibition, suggesting that JAK2 inhibitors may be a feasible option for MPN patients bearing LNK mutations.
Our identification of mutations in LNK, the first reported in human disease, demonstrates that loss of JAK-STAT negative feedback control is a novel mechanism of MPN pathogenesis. As each of these LNK mutations localizes to the PH domain and appears to be heterozygous, mislocalized mutant LNK may exert a dominant negative effect by binding and sequestering wild-type LNK. These findings may also partly explain why some MPN patients lacking JAK2 or MPL mutations respond to treatment with JAK2 inhibitors, and highlight the importance of a more complete understanding of the role of inhibitory pathways in MPN pathogenesis.
Citation Information: Clin Cancer Res 2010;16(14 Suppl):B6.
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Affiliation(s)
- Stephen T. Oh
- 1Stanford University School of Medicine, Stanford, CA
| | - Jacob M. Zahn
- 1Stanford University School of Medicine, Stanford, CA
| | | | - John Bell
- 1Stanford University School of Medicine, Stanford, CA
| | | | | | - Carol Jones
- 1Stanford University School of Medicine, Stanford, CA
| | | | - Yury Goltsev
- 1Stanford University School of Medicine, Stanford, CA
| | | | | | | | | | | | - Hanlee P. Ji
- 1Stanford University School of Medicine, Stanford, CA
| | - Jason Gotlib
- 1Stanford University School of Medicine, Stanford, CA
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Goltsev Y, Papatsenko D. Time warping of evolutionary distant temporal gene expression data based on noise suppression. BMC Bioinformatics 2009; 10:353. [PMID: 19857268 PMCID: PMC2771023 DOI: 10.1186/1471-2105-10-353] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Accepted: 10/26/2009] [Indexed: 03/24/2023] Open
Abstract
Background Comparative analysis of genome wide temporal gene expression data has a broad potential area of application, including evolutionary biology, developmental biology, and medicine. However, at large evolutionary distances, the construction of global alignments and the consequent comparison of the time-series data are difficult. The main reason is the accumulation of variability in expression profiles of orthologous genes, in the course of evolution. Results We applied Pearson distance matrices, in combination with other noise-suppression techniques and data filtering to improve alignments. This novel framework enhanced the capacity to capture the similarities between the temporal gene expression datasets separated by large evolutionary distances. We aligned and compared the temporal gene expression data in budding (Saccharomyces cerevisiae) and fission (Schizosaccharomyces pombe) yeast, which are separated by more then ~400 myr of evolution. We found that the global alignment (time warping) properly matched the duration of cell cycle phases in these distant organisms, which was measured in prior studies. At the same time, when applied to individual ortholog pairs, this alignment procedure revealed groups of genes with distinct alignments, different from the global alignment. Conclusion Our alignment-based predictions of differences in the cell cycle phases between the two yeast species were in a good agreement with the existing data, thus supporting the computational strategy adopted in this study. We propose that the existence of the alternative alignments, specific to distinct groups of genes, suggests presence of different synchronization modes between the two organisms and possible functional decoupling of particular physiological gene networks in the course of evolution.
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Affiliation(s)
- Yury Goltsev
- Department of Molecular and Cell biology, University of California, Berkeley, USA.
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Abstract
Most cell-specific enhancers are thought to lack an inherent organization, with critical binding sites distributed in a more or less random fashion. However, there are examples of fixed arrangements of binding sites, such as helical phasing, that promote the formation of higher-order protein complexes on the enhancer DNA template. Here, we investigate the regulatory ‘grammar’ of nearly 100 characterized enhancers for developmental control genes active in the early Drosophila embryo. The conservation of grammar is examined in seven divergent Drosophila genomes. Linked binding sites are observed for particular combinations of binding motifs, including Bicoid–Bicoid, Hunchback–Hunchback, Bicoid–Dorsal, Bicoid–Caudal and Dorsal–Twist. Direct evidence is presented for the importance of Bicoid–Dorsal linkage in the integration of the anterior–posterior and dorsal–ventral patterning systems. Hunchback–Hunchback interactions help explain unresolved aspects of segmentation, including the differential regulation of the eve stripe 3 + 7 and stripe 4 + 6 enhancers. We also present evidence that there is an under-representation of nucleosome positioning sequences in many enhancers, raising the possibility for a subtle higher-order structure extending across certain enhancers. We conclude that grammar of gene control regions is pervasively used in the patterning of the Drosophila embryo.
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Affiliation(s)
- Dmitri Papatsenko
- Department of Molecular Cell Biology, Division of Genetics, Genomics & Development, Center for Integrative Genomics, University of California, Berkeley, CA 94720-200, USA.
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Goltsev Y, Rezende GL, Vranizan K, Lanzaro G, Valle D, Levine M. Developmental and evolutionary basis for drought tolerance of the Anopheles gambiae embryo. Dev Biol 2009; 330:462-70. [PMID: 19298808 DOI: 10.1016/j.ydbio.2009.02.038] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2008] [Revised: 02/19/2009] [Accepted: 02/23/2009] [Indexed: 10/21/2022]
Abstract
During the evolution of the Diptera there is a dramatic modification of the embryonic ectoderm, whereby mosquitoes contain separate amnion and serosa lineages while higher flies such as Drosophila melanogaster contain a single amnioserosa. Whole-genome transcriptome assays were performed with isolated serosa from Anopheles gambiae embryos. These assays identified a large number of genes implicated in the production of the larval cuticle. In D. melanogaster, these genes are activated just once during embryogenesis, during late stages where they are used for the production of the larval cuticle. Evidence is presented that the serosal cells secrete a dedicated serosal cuticle, which protects A. gambiae embryos from desiccation. Detailed temporal microarray assays of mosquito gene expression profiles revealed that the cuticular genes display biphasic expression during A. gambiae embryogenesis, first in the serosa of early embryos and then again during late stages as seen in D. melanogaster. We discuss how evolutionary modifications in the well-defined dorsal-ventral patterning network led to the wholesale deployment of the cuticle biosynthesis pathway in early embryos of A. gambiae.
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Affiliation(s)
- Yury Goltsev
- Department of Mol. Cell Biology, Division of Genetics Genomics and Development, Center for Integrative Genomics, University of California, Berkeley, CA 94720, USA
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Goltsev Y, Fuse N, Frasch M, Zinzen RP, Lanzaro G, Levine M. Evolution of the dorsal-ventral patterning network in the mosquito, Anopheles gambiae. Development 2007; 134:2415-24. [PMID: 17522157 DOI: 10.1242/dev.02863] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [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] [Indexed: 11/20/2022]
Abstract
The dorsal-ventral patterning of the Drosophila embryo is controlled by a well-defined gene regulation network. We wish to understand how changes in this network produce evolutionary diversity in insect gastrulation. The present study focuses on the dorsal ectoderm in two highly divergent dipterans, the fruitfly Drosophila melanogaster and the mosquito Anopheles gambiae. In D. melanogaster, the dorsal midline of the dorsal ectoderm forms a single extra-embryonic membrane, the amnioserosa. In A. gambiae, an expanded domain forms two distinct extra-embryonic tissues, the amnion and serosa. The analysis of approximately 20 different dorsal-ventral patterning genes suggests that the initial specification of the mesoderm and ventral neurogenic ectoderm is highly conserved in flies and mosquitoes. By contrast, there are numerous differences in the expression profiles of genes active in the dorsal ectoderm. Most notably, the subdivision of the extra-embryonic domain into separate amnion and serosa lineages in A. gambiae correlates with novel patterns of gene expression for several segmentation repressors. Moreover, the expanded amnion and serosa anlage correlates with a broader domain of Dpp signaling as compared with the D. melanogaster embryo. Evidence is presented that this expanded signaling is due to altered expression of the sog gene.
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Affiliation(s)
- Yury Goltsev
- Department MCB, Division of GGD, Center for Integrative Genomics, University of California, Berkeley, CA 94720, USA
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Goltsev Y, Hsiong W, Lanzaro G, Levine M. Different combinations of gap repressors for common stripes in Anopheles and Drosophila embryos. Dev Biol 2005; 275:435-46. [PMID: 15501229 DOI: 10.1016/j.ydbio.2004.08.021] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2004] [Revised: 08/17/2004] [Accepted: 08/17/2004] [Indexed: 11/20/2022]
Abstract
Drosophila segmentation is governed by a well-defined gene regulation network. The evolution of this network was investigated by examining the expression profiles of a complete set of segmentation genes in the early embryos of the mosquito, Anopheles gambiae. There are numerous differences in the expression profiles as compared with Drosophila. The germline determinant Oskar is expressed in both the anterior and posterior poles of Anopheles embryos but is strictly localized within the posterior plasm of Drosophila. The gap genes hunchback and giant display inverted patterns of expression in posterior regions of Anopheles embryos, while tailless exhibits an expanded pattern as compared with Drosophila. These observations suggest that the segmentation network has undergone considerable evolutionary change in the dipterans and that similar patterns of pair-rule gene expression can be obtained with different combinations of gap repressors. We discuss the evolution of separate stripe enhancers in the eve loci of different dipterans.
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Affiliation(s)
- Yury Goltsev
- Department of Molecular and Cellular Biology, Division of Genetics and Development, University of California, Berkeley, CA 94720, USA.
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Wallach D, Boldin M, Goncharov T, Goltsev Y, Mett I, Malinin N, Adar R, Kovalenko A, Varfolomeev E. Exploring cell death mechanisms by analyzing signaling cascades of the TNF/NGF receptor family. Behring Inst Mitt 1996:144-55. [PMID: 8950472] [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] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The ability of ligands of the tumor necrosis factor (TNF) family to induce death of cells independently of new protein synthesis provides a unique approach to molecular analysis of programmed cell death mechanisms. Sequential analysis of the protein-protein interactions by which these receptors signal, allows identification of specific molecules that participate in the cell death process and unequivocal definition of cause-effect relationships between them. Several receptors of this family, with structurally unrelated intracellular domains, have the ability to trigger cell death. some intracellular proteins that bind to the receptors and participate in the induction of their effects have been identified. Association of the Fas/APO1-interacting protein MORT1/FADD with the p55 TNF receptor-interacting protein TRADD, and the association of both MORT1/FADD and TRADD with a third protein, RIP, provide potential cross-talk mechanisms between Fas/APO1 and the p55 TNF receptor. TRAF2, a cytoplasmic protein that binds to the p75 TNF receptor, as well as to several other receptors of the TNF/NGF family, also binds to TRADD, thus further extending the range of receptors of this family that can share common signaling mechanisms. The N-terminal part of MORT1/FADD binds to a protease of the CED3/ICE family, MACH alpha. Activation of MACH alpha by the TNF/NGF receptors appears to be the most upstream enzymatic activity in the cascade of signaling for cell death.
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Affiliation(s)
- D Wallach
- Department of Membrane Research and Biophysics, Weizmann Institute of Science, Rehovot, Israel
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