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Hickey JW, Neumann EK, Radtke AJ, Camarillo JM, Beuschel RT, Albanese A, McDonough E, Hatler J, Wiblin AE, Fisher J, Croteau J, Small EC, Sood A, Caprioli RM, Angelo RM, Nolan GP, Chung K, Hewitt SM, Germain RN, Spraggins JM, Lundberg E, Snyder MP, Kelleher NL, Saka SK. Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging. Nat Methods 2022; 19:284-295. [PMID: 34811556 PMCID: PMC9264278 DOI: 10.1038/s41592-021-01316-y] [Citation(s) in RCA: 115] [Impact Index Per Article: 57.5] [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: 04/02/2021] [Accepted: 09/15/2021] [Indexed: 02/07/2023]
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.
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Affiliation(s)
- John W Hickey
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Elizabeth K Neumann
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
| | - Andrea J Radtke
- Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA.
| | - Jeannie M Camarillo
- Departments of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, USA
| | - Rebecca T Beuschel
- Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Alexandre Albanese
- Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Boston Children's Hospital, Division of Hematology/Oncology, Boston, MA, USA
| | | | - Julia Hatler
- Antibody Development Department, Bio-Techne, Minneapolis, MN, USA
| | - Anne E Wiblin
- Department of Research and Development, Abcam, Cambridge, UK
| | - Jeremy Fisher
- Department of Research and Development, Cell Signaling Technology, Danvers, MA, USA
| | - Josh Croteau
- Department of Applications Science, BioLegend, San Diego, CA, USA
| | | | | | - Richard M Caprioli
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - R Michael Angelo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kwanghun Chung
- Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Chemical Engineering, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea
- Yonsei-IBS Institute, Yonsei University, Seoul, Republic of Korea
| | - Stephen M Hewitt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ronald N Germain
- Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Jeffrey M Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Emma Lundberg
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Neil L Kelleher
- Departments of Chemistry, Molecular Biosciences and the National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, USA
| | - Sinem K Saka
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
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Tan E, Frew E, Cooper J, Humphrey J, Holden M, Mand AR, Li J, Anderson S, Bi M, Hatler J, Person A, Mortari F, Gould K, Barry S. Use of Lateral Flow Immunoassay to Characterize SARS-CoV-2 RBD-Specific Antibodies and Their Ability to React with the UK, SA and BR P.1 Variant RBDs. Diagnostics (Basel) 2021; 11:1190. [PMID: 34208912 PMCID: PMC8303872 DOI: 10.3390/diagnostics11071190] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/23/2021] [Accepted: 06/25/2021] [Indexed: 12/23/2022] Open
Abstract
Identifying anti-spike antibodies that exhibit strong neutralizing activity against current dominant circulating variants, and antibodies that are escaped by these variants, has important implications in the development of therapeutic and diagnostic solutions and in improving understanding of the humoral response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. We characterized seven anti-SARS-CoV-2 receptor binding domain (RBD) antibodies for binding activity, pairing capability, and neutralization activity to SARS-CoV-2 and three variant RBDs via lateral flow immunoassays. The results allowed us to group these antibodies into three distinct epitope bins. Our studies showed that two antibodies had broadly potent neutralizing activity against SARS-CoV-2 and these variant RBDs and that one antibody did not neutralize the South African (SA) and Brazilian P.1 (BR P.1) RBDs. The antibody escaped by the SA and BR P.1 RBDs retained binding activity to SA and BR P.1 RBDs but was unable to induce neutralization. We demonstrated that lateral flow immunoassay could be a rapid and effective tool for antibody characterization, including epitope classification and antibody neutralization kinetics. The potential contributions of the mutations (N501Y, E484K, and K417N/T) contained in these variants' RBDs to the antibody pairing capability, neutralization activity, and therapeutic antibody targeting strategy are discussed.
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Affiliation(s)
- Enqing Tan
- Diagnostic Reagents Division, Bio-Techne Corporation, Devens Site, Devens, MA 01434, USA; (E.T.); (E.F.); (M.H.); (A.R.M.)
| | - Erica Frew
- Diagnostic Reagents Division, Bio-Techne Corporation, Devens Site, Devens, MA 01434, USA; (E.T.); (E.F.); (M.H.); (A.R.M.)
| | - Jeff Cooper
- Reagent Solutions Division, Bio-Techne Corporation, Minneapolis Site, Minneapolis, MN 55413, USA; (J.C.); (J.H.); (J.L.); (S.A.); (M.B.); (J.H.); (A.P.)
| | - John Humphrey
- Reagent Solutions Division, Bio-Techne Corporation, Minneapolis Site, Minneapolis, MN 55413, USA; (J.C.); (J.H.); (J.L.); (S.A.); (M.B.); (J.H.); (A.P.)
| | - Matthew Holden
- Diagnostic Reagents Division, Bio-Techne Corporation, Devens Site, Devens, MA 01434, USA; (E.T.); (E.F.); (M.H.); (A.R.M.)
| | - Amanda Restell Mand
- Diagnostic Reagents Division, Bio-Techne Corporation, Devens Site, Devens, MA 01434, USA; (E.T.); (E.F.); (M.H.); (A.R.M.)
| | - Jun Li
- Reagent Solutions Division, Bio-Techne Corporation, Minneapolis Site, Minneapolis, MN 55413, USA; (J.C.); (J.H.); (J.L.); (S.A.); (M.B.); (J.H.); (A.P.)
| | - Shaya Anderson
- Reagent Solutions Division, Bio-Techne Corporation, Minneapolis Site, Minneapolis, MN 55413, USA; (J.C.); (J.H.); (J.L.); (S.A.); (M.B.); (J.H.); (A.P.)
| | - Ming Bi
- Reagent Solutions Division, Bio-Techne Corporation, Minneapolis Site, Minneapolis, MN 55413, USA; (J.C.); (J.H.); (J.L.); (S.A.); (M.B.); (J.H.); (A.P.)
| | - Julia Hatler
- Reagent Solutions Division, Bio-Techne Corporation, Minneapolis Site, Minneapolis, MN 55413, USA; (J.C.); (J.H.); (J.L.); (S.A.); (M.B.); (J.H.); (A.P.)
| | - Anthony Person
- Reagent Solutions Division, Bio-Techne Corporation, Minneapolis Site, Minneapolis, MN 55413, USA; (J.C.); (J.H.); (J.L.); (S.A.); (M.B.); (J.H.); (A.P.)
| | - Frank Mortari
- Corporate Development, Bio-Techne Corporation, Minneapolis Site, Minneapolis, MN 55413, USA;
| | - Kevin Gould
- Diagnostic Reagents Division, Bio-Techne Corporation, San Marcos Site, San Marcos, CA 92078, USA
| | - Shelly Barry
- Diagnostic Reagents Division, Bio-Techne Corporation, Devens Site, Devens, MA 01434, USA; (E.T.); (E.F.); (M.H.); (A.R.M.)
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Clark CR, Conboy C, Maile M, Janik C, Hatler J, Cormier R, Largaespada D, Starr TK. Abstract 3665: WAC: A candidate tumor suppressor gene in colorectal cancer. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-3665] [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
Our lab recently performed a DNA transposon forward genetic screen in mice that was designed to identify low-frequency mutations that contribute to colorectal cancer (CRC) initiation and progression. Results from this screen identified the WW domain-containing adaptor with coiled-coil (WAC) gene as a top DNA transposon insertion site. WAC has previously been implicated in several cellular processes including amino acid starvation-induced autophagy, golgi biogenesis, and transcription associated histone modification but has never before been linked to tumorigenesis. Transposon mutagenesis screens performed by others (Takeda et al. Nature Genetics 2015) have also identified Wac as a common insertion site, a result that further implicates WAC as a candidate CRC driver gene. Analyses of transposon insertion patterns within Wac predict loss of gene function and a role as a tumor suppressor. Soft agar colony formation assays reveal that shRNA mediated silencing of Wac cooperates with Apc mutations in mouse colorectal cells to promote cellular transformation. Additional colony formation assays using immortalized human colonic epithelial cells and the adenoma derived AAC1 cell line also shows that silencing WAC is protumorigenic. Using a zebrafish model we demonstrated that overexpression of wild type but not cancer-associated mutant forms of WAC induce expression of the cell cycle inhibitor p21, which suggests that loss of WAC may lead to uncontrolled cellular proliferation. Finally, using publicly available mutation data we determined that WAC is somatically mutated in both breast and lung cancers; a finding that indicates WAC may serve a critical tumor suppressive role in several tissues. Currently we are developing a conditional knockout mouse to further investigate the role of WAC in CRC tumor formation.
Citation Format: Christopher R. Clark, Caitlin Conboy, Makayla Maile, Callie Janik, Julia Hatler, Robert Cormier, David Largaespada, Timothy K. Starr. WAC: A candidate tumor suppressor gene in colorectal cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3665.
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