Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging
Tissues and organs are composed of distinct cell types that must operate in concert to perform physiological functions. Efforts to create high-dimensional biomarker catalogs of these cells have been largely based on single-cell sequencing approaches, which lack the spatial context required to unders...
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| Published in: | Nature methods Vol. 19; no. 3; pp. 284 - 295 |
|---|---|
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , |
| Format: | Journal Article |
| Language: | English |
| Published: |
New York
Nature Publishing Group US
01.03.2022
Nature Publishing Group |
| Subjects: | |
| ISSN: | 1548-7091, 1548-7105, 1548-7105 |
| Online Access: | Get full text |
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| Abstract | Tissues and organs are composed of distinct cell types that must operate in concert to perform physiological functions. Efforts to create high-dimensional biomarker catalogs of these cells have been largely based on single-cell sequencing approaches, which lack the spatial context required to understand critical cellular communication and correlated structural organization. To probe in situ biology with sufficient depth, several multiplexed protein imaging methods have been recently developed. Though these technologies differ in strategy and mode of immunolabeling and detection tags, they commonly utilize antibodies directed against protein biomarkers to provide detailed spatial and functional maps of complex tissues. As these promising antibody-based multiplexing approaches become more widely adopted, new frameworks and considerations are critical for training future users, generating molecular tools, validating antibody panels, and harmonizing datasets. In this Perspective, we provide essential resources, key considerations for obtaining robust and reproducible imaging data, and specialized knowledge from domain experts and technology developers.
This Perspective offers guidance for robust and reproducible antibody-based highly multiplexed tissue imaging. |
|---|---|
| AbstractList | Tissues and organs are composed of distinct cell types that must operate in concert to perform physiological functions. Efforts to create high-dimensional biomarker catalogs of these cells have been largely based on single-cell sequencing approaches, which lack the spatial context required to understand critical cellular communication and correlated structural organization. To probe in situ biology with sufficient depth, several multiplexed protein imaging methods have been recently developed. Though these technologies differ in strategy and mode of immunolabeling and detection tags, they commonly utilize antibodies directed against protein biomarkers to provide detailed spatial and functional maps of complex tissues. As these promising antibody-based multiplexing approaches become more widely adopted, new frameworks and considerations are critical for training future users, generating molecular tools, validating antibody panels, and harmonizing datasets. In this Perspective, we provide essential resources, key considerations for obtaining robust and reproducible imaging data, and specialized knowledge from domain experts and technology developers.
This Perspective offers guidance for robust and reproducible antibody-based highly multiplexed tissue imaging. Tissues and organs are composed of distinct cell types that must operate in concert to perform physiological functions. Efforts to create high-dimensional biomarker catalogs of these cells have been largely based on single-cell sequencing approaches, which lack the spatial context required to understand critical cellular communication and correlated structural organization. To probe in situ biology with sufficient depth, several multiplexed protein imaging methods have been recently developed. Though these technologies differ in strategy and mode of immunolabeling and detection tags, they commonly utilize antibodies directed against protein biomarkers to provide detailed spatial and functional maps of complex tissues. As these promising antibody-based multiplexing approaches become more widely adopted, new frameworks and considerations are critical for training future users, generating molecular tools, validating antibody panels, and harmonizing datasets. In this Perspective, we provide essential resources, key considerations for obtaining robust and reproducible imaging data, and specialized knowledge from domain experts and technology developers. Tissues and organs are composed of distinct cell types that must operate in concert to perform physiological functions. Efforts to create high-dimensional biomarker catalogs of these cells have been largely based on single-cell sequencing approaches, which lack the spatial context required to understand critical cellular communication and correlated structural organization. To probe in situ biology with sufficient depth, several multiplexed protein imaging methods have been recently developed. Though these technologies differ in strategy and mode of immunolabeling and detection tags, they commonly utilize antibodies directed against protein biomarkers to provide detailed spatial and functional maps of complex tissues. As these promising antibody-based multiplexing approaches become more widely adopted, new frameworks and considerations are critical for training future users, generating molecular tools, validating antibody panels, and harmonizing datasets. In this Perspective, we provide essential resources, key considerations for obtaining robust and reproducible imaging data, and specialized knowledge from domain experts and technology developers.Tissues and organs are composed of distinct cell types that must operate in concert to perform physiological functions. Efforts to create high-dimensional biomarker catalogs of these cells have been largely based on single-cell sequencing approaches, which lack the spatial context required to understand critical cellular communication and correlated structural organization. To probe in situ biology with sufficient depth, several multiplexed protein imaging methods have been recently developed. Though these technologies differ in strategy and mode of immunolabeling and detection tags, they commonly utilize antibodies directed against protein biomarkers to provide detailed spatial and functional maps of complex tissues. As these promising antibody-based multiplexing approaches become more widely adopted, new frameworks and considerations are critical for training future users, generating molecular tools, validating antibody panels, and harmonizing datasets. In this Perspective, we provide essential resources, key considerations for obtaining robust and reproducible imaging data, and specialized knowledge from domain experts and technology developers. Tissues and organs are composed of distinct cell types that must operate in concert to perform physiological functions. Efforts to create high-dimensional biomarker catalogs of these cells have been largely based on single-cell sequencing approaches, which lack the spatial context required to understand critical cellular communication and correlated structural organization. To probe in situ biology with sufficient depth, several multiplexed protein imaging methods have been recently developed. Though these technologies differ in strategy and mode of immunolabeling and detection tags, they commonly utilize antibodies directed against protein biomarkers to provide detailed spatial and functional maps of complex tissues. As these promising antibody-based multiplexing approaches become more widely adopted, new frameworks and considerations are critical for training future users, generating molecular tools, validating antibody panels, and harmonizing datasets. In this Perspective, we provide essential resources, key considerations for obtaining robust and reproducible imaging data, and specialized knowledge from domain experts and technology developers.This Perspective offers guidance for robust and reproducible antibody-based highly multiplexed tissue imaging. |
| Author | McDonough, Elizabeth Fisher, Jeremy Chung, Kwanghun Camarillo, Jeannie M. Germain, Ronald N. Hatler, Julia Lundberg, Emma Nolan, Garry P. Small, Eliza C. Sood, Anup Snyder, Michael P. Beuschel, Rebecca T. Hickey, John W. Hewitt, Stephen M. Radtke, Andrea J. Croteau, Josh Albanese, Alexandre Neumann, Elizabeth K. Saka, Sinem K. Caprioli, Richard M. Angelo, R. Michael Kelleher, Neil L. Spraggins, Jeffrey M. Wiblin, Anne E. |
| AuthorAffiliation | 19 Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA 22 Department of Genetics, Stanford University School of Medicine, Stanford, California, USA 18 Yonsei-IBS Institute, Yonsei University, Seoul, Republic of Korea 3 Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA 8 GE Research, Niskayuna, NY, USA 11 Department of Research and Development, Cell Signaling Technology, Danvers, MA, USA 23 Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA 10 Department of Research and Development, Abcam, Cambridge, UK 25 Present address: Boston Children’s Hospital, Division of Hematology/Oncology, Boston, MA, USA 15 Department of Chemical Engineering, MIT, Cambridge, MA, USA 1 Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA 26 These authors contributed equally: John W. Hickey, Elizabeth K. Neumann, Andrea J. Radtke 16 Department of Brai |
| AuthorAffiliation_xml | – name: 5 Departments of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, USA – name: 19 Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA – name: 17 Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea – name: 11 Department of Research and Development, Cell Signaling Technology, Danvers, MA, USA – name: 22 Department of Genetics, Stanford University School of Medicine, Stanford, California, USA – name: 1 Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA – name: 3 Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA – name: 15 Department of Chemical Engineering, MIT, Cambridge, MA, USA – name: 26 These authors contributed equally: John W. Hickey, Elizabeth K. Neumann, Andrea J. Radtke – name: 6 Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA – name: 24 European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany – name: 8 GE Research, Niskayuna, NY, USA – name: 9 Antibody Development Department, Bio-Techne, Minneapolis, MN, USA – name: 7 Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA – name: 4 Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA – name: 25 Present address: Boston Children’s Hospital, Division of Hematology/Oncology, Boston, MA, USA – name: 21 Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH–Royal Institute of Technology, Stockholm, Sweden – name: 23 Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA – name: 18 Yonsei-IBS Institute, Yonsei University, Seoul, Republic of Korea – name: 13 Thermo Fisher Scientific, Rockford, IL, USA – name: 16 Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA – name: 12 Department of Applications Science, BioLegend, San Diego, CA, USA – name: 2 Department of Biochemistry, Vanderbilt University, Nashville, TN, USA – name: 10 Department of Research and Development, Abcam, Cambridge, UK – name: 14 Department of Chemistry, Vanderbilt University, Nashville, TN, USA – name: 20 Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA |
| Author_xml | – sequence: 1 givenname: John W. surname: Hickey fullname: Hickey, John W. organization: Department of Pathology, Stanford University School of Medicine – sequence: 2 givenname: Elizabeth K. orcidid: 0000-0002-6078-3321 surname: Neumann fullname: Neumann, Elizabeth K. organization: Department of Biochemistry, Vanderbilt University, Mass Spectrometry Research Center, Vanderbilt University – sequence: 3 givenname: Andrea J. orcidid: 0000-0003-4379-8967 surname: Radtke fullname: Radtke, Andrea J. email: andrea.radtke@nih.gov organization: Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH – sequence: 4 givenname: Jeannie M. surname: Camarillo fullname: Camarillo, Jeannie M. organization: Departments of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University – sequence: 5 givenname: Rebecca T. surname: Beuschel fullname: Beuschel, Rebecca T. organization: Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH – sequence: 6 givenname: Alexandre surname: Albanese fullname: Albanese, Alexandre organization: Institute for Medical Engineering and Science, MIT, Picower Institute for Learning and Memory, MIT, Boston Children’s Hospital, Division of Hematology/Oncology – sequence: 7 givenname: Elizabeth orcidid: 0000-0001-7524-8260 surname: McDonough fullname: McDonough, Elizabeth organization: GE Research – sequence: 8 givenname: Julia surname: Hatler fullname: Hatler, Julia organization: Antibody Development Department, Bio-Techne – sequence: 9 givenname: Anne E. surname: Wiblin fullname: Wiblin, Anne E. organization: Department of Research and Development, Abcam – sequence: 10 givenname: Jeremy surname: Fisher fullname: Fisher, Jeremy organization: Department of Research and Development, Cell Signaling Technology – sequence: 11 givenname: Josh orcidid: 0000-0002-8142-0482 surname: Croteau fullname: Croteau, Josh organization: Department of Applications Science, BioLegend – sequence: 12 givenname: Eliza C. surname: Small fullname: Small, Eliza C. organization: Thermo Fisher Scientific – sequence: 13 givenname: Anup surname: Sood fullname: Sood, Anup organization: GE Research – sequence: 14 givenname: Richard M. surname: Caprioli fullname: Caprioli, Richard M. organization: Department of Biochemistry, Vanderbilt University, Mass Spectrometry Research Center, Vanderbilt University, Department of Chemistry, Vanderbilt University – sequence: 15 givenname: R. Michael orcidid: 0000-0003-1531-5067 surname: Angelo fullname: Angelo, R. Michael organization: Department of Pathology, Stanford University School of Medicine – sequence: 16 givenname: Garry P. orcidid: 0000-0002-8862-9043 surname: Nolan fullname: Nolan, Garry P. organization: Department of Pathology, Stanford University School of Medicine – sequence: 17 givenname: Kwanghun orcidid: 0000-0002-8167-3340 surname: Chung fullname: Chung, Kwanghun organization: Institute for Medical Engineering and Science, MIT, Picower Institute for Learning and Memory, MIT, Department of Chemical Engineering, MIT, Department of Brain and Cognitive Sciences, MIT, Center for Nanomedicine, Institute for Basic Science (IBS), Yonsei-IBS Institute, Yonsei University – sequence: 18 givenname: Stephen M. orcidid: 0000-0001-8283-1788 surname: Hewitt fullname: Hewitt, Stephen M. organization: Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health – sequence: 19 givenname: Ronald N. orcidid: 0000-0003-1495-9143 surname: Germain fullname: Germain, Ronald N. organization: Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH – sequence: 20 givenname: Jeffrey M. orcidid: 0000-0001-9198-5498 surname: Spraggins fullname: Spraggins, Jeffrey M. organization: Mass Spectrometry Research Center, Vanderbilt University, Department of Chemistry, Vanderbilt University, Department of Cell and Developmental Biology, Vanderbilt University School of Medicine – sequence: 21 givenname: Emma orcidid: 0000-0001-7034-0850 surname: Lundberg fullname: Lundberg, Emma organization: Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH–Royal Institute of Technology – sequence: 22 givenname: Michael P. orcidid: 0000-0003-0784-7987 surname: Snyder fullname: Snyder, Michael P. organization: Department of Genetics, Stanford University School of Medicine – sequence: 23 givenname: Neil L. orcidid: 0000-0002-8815-3372 surname: Kelleher fullname: Kelleher, Neil L. organization: Departments of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University – sequence: 24 givenname: Sinem K. orcidid: 0000-0002-5017-379X surname: Saka fullname: Saka, Sinem K. email: sinem.saka@embl.de organization: Wyss Institute for Biologically Inspired Engineering at Harvard University, European Molecular Biology Laboratory (EMBL), Genome Biology Unit |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/34811556$$D View this record in MEDLINE/PubMed https://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-313200$$DView record from Swedish Publication Index (Kungliga Tekniska Högskolan) |
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| Title | Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging |
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