Organ Mapping Antibody Panels: a community resource for standardized multiplexed tissue imaging.

Humans Reproducibility of Results Community Resources Antibodies Diagnostic Imaging

Journal

Nature methods
ISSN: 1548-7105
Titre abrégé: Nat Methods
Pays: United States
ID NLM: 101215604

Informations de publication

Date de publication:
08 2023
Historique:
received: 12 07 2022
accepted: 14 03 2023
medline: 9 8 2023
pubmed: 20 7 2023
entrez: 19 7 2023
Statut: ppublish

Résumé

Multiplexed antibody-based imaging enables the detailed characterization of molecular and cellular organization in tissues. Advances in the field now allow high-parameter data collection (>60 targets); however, considerable expertise and capital are needed to construct the antibody panels employed by these methods. Organ mapping antibody panels are community-validated resources that save time and money, increase reproducibility, accelerate discovery and support the construction of a Human Reference Atlas.

Identifiants

DOI: 10.1038/s41592-023-01846-7 PMID: 37468619 PMC: PMC10406602
pubmed: 37468619
doi: 10.1038/s41592-023-01846-7
pii: 10.1038/s41592-023-01846-7
pmc: PMC10406602
doi:

Substances chimiques

Antibodies 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Research Support, N.I.H., Extramural Research Support, N.I.H., Intramural

Langues

eng

Sous-ensembles de citation

IM

Pagination

1174-1178

Subventions

Organisme : NCI NIH HHS
ID : UH3 CA246635
Pays : United States
Organisme : NCI NIH HHS
ID : UH3 CA256962
Pays : United States
Organisme : NIDDK NIH HHS
ID : U54 DK134302
Pays : United States
Organisme : NCI NIH HHS
ID : R35 CA209896
Pays : United States
Organisme : NIA NIH HHS
ID : R01 AG078803
Pays : United States
Organisme : NHLBI NIH HHS
ID : UG3 HL145600
Pays : United States
Organisme : NIH HHS
ID : OT2 OD026671
Pays : United States
Organisme : NHGRI NIH HHS
ID : U54 HG010426
Pays : United States
Organisme : NIA NIH HHS
ID : U54 AG075932
Pays : United States
Organisme : NIEHS NIH HHS
ID : T32 ES007028
Pays : United States
Organisme : NIDDK NIH HHS
ID : P30 DK020593
Pays : United States
Organisme : NCI NIH HHS
ID : T32 CA196585
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA268108
Pays : United States
Organisme : NIDDK NIH HHS
ID : U01 DK120447
Pays : United States
Organisme : NHLBI NIH HHS
ID : U01 HL148861
Pays : United States
Organisme : NIH HHS
ID : OT2 OD026675
Pays : United States
Organisme : NIGMS NIH HHS
ID : P41 GM108569
Pays : United States
Organisme : NIAMS NIH HHS
ID : U54 AR081775
Pays : United States
Organisme : NCI NIH HHS
ID : UG3 CA268105
Pays : United States
Organisme : NHLBI NIH HHS
ID : U54 HL145608
Pays : United States
Organisme : NIDDK NIH HHS
ID : F32 DK128887
Pays : United States
Organisme : NEI NIH HHS
ID : U54 EY032442
Pays : United States
Organisme : NCI NIH HHS
ID : UG3 CA256962
Pays : United States
Organisme : NIH HHS
ID : OT2 OD033758
Pays : United States
Organisme : NCI NIH HHS
ID : UH3 CA246594
Pays : United States
Organisme : NIDDK NIH HHS
ID : U01 DK133766
Pays : United States

Informations de copyright

© 2023. The Author(s), under exclusive licence to Springer Nature America, Inc.

Références

Hickey, J. W. et al. Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging. Nat. Methods 19, 284–295 (2022).
doi: 10.1038/s41592-021-01316-y pubmed: 34811556
Uhlen, M. et al. A proposal for validation of antibodies. Nat. Methods 13, 823–827 (2016).
doi: 10.1038/nmeth.3995 pubmed: 27595404 pmcid: 10335836
Bordeaux, J. et al. Antibody validation. Biotechniques 48, 197–209 (2010).
doi: 10.2144/000113382 pubmed: 20359301 pmcid: 3891910
Snyder, M. P. et al. The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. Nature 574, 187–192 (2019).
doi: 10.1038/s41586-019-1629-x
Roederer, M. & Tárnok, A. OMIPs—orchestrating multiplexity in polychromatic science. Cytom. Part A 77A, 811–812 (2010).
doi: 10.1002/cyto.a.20959
Börner, K. et al. Anatomical structures, cell types and biomarkers of the Human Reference Atlas. Nat. Cell Biol. 23, 1117–1128 (2021).
doi: 10.1038/s41556-021-00788-6 pubmed: 34750582 pmcid: 10079270
Weber, G. M., Ju, Y. & Börner, K. Considerations for using the vasculature as a coordinate system to map all the cells in the human body. Front. Cardiovasc. Med. 7, 29 (2020).
doi: 10.3389/fcvm.2020.00029 pubmed: 32232057 pmcid: 7082726
Radtke, A. J. et al. The centuries long pursuit to map the human lymphatic system. Nat. Med. 28, 1518–1520 (2022).
doi: 10.1038/s41591-022-01865-5 pubmed: 35681105
Goltsev, Y. et al. Deep profiling of mouse splenic architecture with CODEX multiplexed imaging. Cell 174, 968–981 e915 (2018).
doi: 10.1016/j.cell.2018.07.010 pubmed: 30078711 pmcid: 6086938
Radtke, A. J. et al. IBEX: a versatile multiplex optical imaging approach for deep phenotyping and spatial analysis of cells in complex tissues. Proc. Natl Acad. Sci. USA 117, 33455–33465 (2020).
doi: 10.1073/pnas.2018488117 pubmed: 33376221 pmcid: 7776876
Gerdes, M. J. et al. Highly multiplexed single-cell analysis of formalin-fixed, paraffin-embedded cancer tissue. Proc. Natl Acad. Sci. USA 110, 11982–11987 (2013).
doi: 10.1073/pnas.1300136110 pubmed: 23818604 pmcid: 3718135
Gamble, L. J. & Anderton, C. R. Secondary ion mass spectrometry imaging of tissues, cells, and microbial systems. Microsc. Today 24, 24–31 (2016).
doi: 10.1017/S1551929516000018
Povey, S. et al. The HUGO Gene Nomenclature Committee (HGNC). Hum. Genet. 109, 678–680 (2001).
doi: 10.1007/s00439-001-0615-0 pubmed: 11810281
UniProt Consortium The universal protein resource (UniProt). Nucleic Acids Res. 36, D190–D195 (2008).
doi: 10.1093/nar/gkm895
Bandrowski, A. et al. The resource identification initiative: a cultural shift in publishing. Brain Behav. 6, e00417 (2016).
doi: 10.1002/brb3.417 pubmed: 27110440
Du, Z. et al. Qualifying antibodies for image-based immune profiling and multiplexed tissue imaging. Nat. Protoc. 14, 2900–2930 (2019).
doi: 10.1038/s41596-019-0206-y pubmed: 31534232 pmcid: 6959005
Lin, J. R. et al. Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes. eLife 7, e31657 (2018).
doi: 10.7554/eLife.31657 pubmed: 29993362 pmcid: 6075866
Osumi-Sutherland, D. et al. Cell type ontologies of the Human Cell Atlas. Nat. Cell Biol. 23, 1129–1135 (2021).
doi: 10.1038/s41556-021-00787-7 pubmed: 34750578
Keller, M.S. et al. Vitessce: a framework for integrative visualization of multi-modal and spatially-resolved single-cell data. Preprint at OSF https://doi.org/10.31219/osf.io/y8thv (2021).
Schapiro, D. et al. MITI minimum information guidelines for highly multiplexed tissue images. Nat. Methods 19, 262–267 (2022).
doi: 10.1038/s41592-022-01415-4 pubmed: 35277708 pmcid: 9009186
Bajema, K. et al. HuBMAP CCF 2D Reference Object Library https://humanatlas.io/2d-ftu-illustrations (2022).
Radtke, A. J. et al. SOP: construction of organ mapping antibody panels for multiplexed antibody-based imaging of human tissues. zenodo https://doi.org/10.5281/zenodo.5749882 (2022).
Galis, Z. S. Editorial: where is Waldo: contextualizing the endothelial cell in the era of precision biology. Front. Cardiovasc. Med. 7, 127 (2020).
doi: 10.3389/fcvm.2020.00127 pubmed: 32850985 pmcid: 7412703
Boppana, A. et al. Anatomical structures, cell types, and biomarkers of the healthy human blood vasculature. Preprint at bioRxiv https://doi.org/10.1101/2022.02.28.482302 (2022).
Black, S. et al. CODEX multiplexed tissue imaging with DNA-conjugated antibodies. Nat. Protoc. 16, 3802–3835 (2021).
doi: 10.1038/s41596-021-00556-8 pubmed: 34215862 pmcid: 8647621
Radtke, A. J. IBEX: an iterative immunolabeling and chemical bleaching method for high-content imaging of diverse tissues. Nat. Protocols 17, 378–401 (2022).
doi: 10.1038/s41596-021-00644-9 pubmed: 35022622

Auteurs

Ellen M Quardokus (EM)

Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA.
ORCID: 0000-0001-7655-4833

Diane C Saunders (DC)

Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
Vanderbilt Diabetes Center, Vanderbilt University School of Medicine, Nashville, TN, USA.
ORCID: 0000-0002-8849-6746

Elizabeth McDonough (E)

GE Research, Niskayuna, NY, USA.
ORCID: 0000-0001-7524-8260

John W Hickey (JW)

Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
ORCID: 0000-0001-9961-7673

Christopher Werlein (C)

Institute of Pathology, Hannover Medical School, Hannover, Germany.
ORCID: 0000-0002-7694-4257

Christine Surrette (C)

GE Research, Niskayuna, NY, USA.

Presha Rajbhandari (P)

Department of Biological Sciences, Columbia University, New York, NY, USA.

Anna Martinez Casals (AM)

Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden.
Department of Bioengineering, Stanford University, Stanford, CA, USA.

Hua Tian (H)

Department of Chemistry, Pennsylvania State University, University Park, PA, USA.
ORCID: 0000-0002-3598-0219

Lisa Lowery (L)

GE Research, Niskayuna, NY, USA.

Elizabeth K Neumann (EK)

Department of Biochemistry, Vanderbilt University, Nashville, TN, USA.
Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA.
Department of Chemistry, University of California Davis, Davis, CA, USA.

Frida Björklund (F)

Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden.

Taruna V Neelakantan (TV)

Department of Chemistry, Columbia University, New York, NY, USA.

Josh Croteau (J)

Department of Business Development, BioLegend Inc., San Diego, CA, USA.
ORCID: 0000-0002-8142-0482

Anne E Wiblin (AE)

Department of Research and Development, Abcam PLC, Discovery Drive, Cambridge Biomedical Campus, Cambridge, UK.
ORCID: 0000-0002-6087-5701

Jeremy Fisher (J)

Department of Research and Development, Cell Signaling Technology, Inc., Danvers, MA, USA.
ORCID: 0000-0002-7296-586X

April J Livengood (AJ)

Department of Protein and Cell Analysis, Thermo Fisher Scientific, Carlsbad, CA, USA.

Karen G Dowell (KG)

Akoya Biosciences, Marlborough, MA, USA.

Jonathan C Silverstein (JC)

Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
ORCID: 0000-0002-9252-6039

Jeffrey M Spraggins (JM)

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.
Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA.
ORCID: 0000-0001-9198-5498

Gloria S Pryhuber (GS)

Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA.
ORCID: 0000-0002-9185-3994

Gail Deutsch (G)

Department of Pathology, University of Washington Medical Center, Seattle, WA, USA.

Fiona Ginty (F)

GE Research, Niskayuna, NY, USA.

Garry P Nolan (GP)

Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.

Simon Melov (S)

Buck Institute for Research on Aging, Novato, CA, USA.
ORCID: 0000-0001-8554-2834

Danny Jonigk (D)

Institute of Pathology, Hannover Medical School, Hannover, Germany.
German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany.
Institute of Pathology, RWTH University of Aachen, Aachen, Germany.
ORCID: 0000-0002-5251-2281

Michael A Caldwell (MA)

Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA.

Ioannis S Vlachos (IS)

Spatial Technologies Unit, Harvard Medical School Initiative for RNA Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA.
Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA.
Broad Institute of MIT and Harvard, Cambridge, MA, USA.
ORCID: 0000-0002-8849-808X

Werner Muller (W)

Miltenyi Biotec B.V. and Co. KG, Bergisch Gladbach, Germany.
Division of Infection, Immunity and Respiratory Medicine, University of Manchester, Manchester, UK.
ORCID: 0000-0002-1297-9725

Nils Gehlenborg (N)

Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
ORCID: 0000-0003-0327-8297

Brent R Stockwell (BR)

Department of Biological Sciences, Columbia University, New York, NY, USA.
Department of Chemistry, Columbia University, New York, NY, USA.
ORCID: 0000-0002-3532-3868

Emma Lundberg (E)

Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden.
Department of Bioengineering, Stanford University, Stanford, CA, USA.
ORCID: 0000-0001-7034-0850

Michael P Snyder (MP)

Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
ORCID: 0000-0003-0784-7987

Ronald N Germain (RN)

Laboratory of Immune System Biology, Lymphocyte Biology Section and Center for Advanced Tissue Imaging, NIAID, NIH, Bethesda, MD, USA.
ORCID: 0000-0003-1495-9143

Jeannie M Camarillo (JM)

Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA.
Inotiv, Nashville, TN, USA.

Neil L Kelleher (NL)

Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA.
ORCID: 0000-0002-8815-3372

Katy Börner (K)

Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA.
ORCID: 0000-0002-3321-6137

Andrea J Radtke (AJ)

Laboratory of Immune System Biology, Lymphocyte Biology Section and Center for Advanced Tissue Imaging, NIAID, NIH, Bethesda, MD, USA. andrea.radtke@nih.gov.
ORCID: 0000-0003-4379-8967

Articles similaires

[Redispensing of expensive oral anticancer medicines: a practical application].

Lisanne N van Merendonk, Kübra Akgöl, Bastiaan Nuijen
1.00
Humans Antineoplastic Agents Administration, Oral Drug Costs Counterfeit Drugs

Smoking Cessation and Incident Cardiovascular Disease.

Jun Hwan Cho, Seung Yong Shin, Hoseob Kim et al.
1.00
Humans Male Smoking Cessation Cardiovascular Diseases Female

Evaluation of Low-Value Services Across Major Medicare Advantage Insurers and Traditional Medicare.

Ciara Duggan, Adam L Beckman, Ishani Ganguli et al.
1.00
Humans United States Aged Cross-Sectional Studies Medicare Part C

Effectiveness of Virtual Yoga for Chronic Low Back Pain: A Randomized Clinical Trial.

Hallie Tankha, Devyn Gaskins, Amanda Shallcross et al.
1.00
Humans Yoga Low Back Pain Female Male

Classifications MeSH

questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Organ Mapping Antibody Panels: a community...
questionsmedicales.fr › Environnement et santé publique › Santé publique › Méthodes épidémiologiques › Méthodologie en recherche épidémiologique › Reproductibilité des résultats › Organ Mapping Antibody Panels: a community...
questionsmedicales.fr › Organisations et économie des soins de santé › Ressources communautaires › Organ Mapping Antibody Panels: a community...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Globulines › Sérum-globulines › Immunoglobulines › Anticorps › Organ Mapping Antibody Panels: a community...
questionsmedicales.fr › Diagnostic › Techniques et procédures diagnostiques › Imagerie diagnostique › Organ Mapping Antibody Panels: a community...