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

Ellen M Quardokus^#¹, Diane C Saunders^#^{2

3}, Elizabeth McDonough⁴, John W Hickey⁵, Christopher Werlein⁶, Christine Surrette⁴, Presha Rajbhandari⁷, Anna Martinez Casals^{5

8

9}, Hua Tian¹⁰, Lisa Lowery⁴, Elizabeth K Neumann^{11

12

13}, Frida Björklund⁸, Taruna V Neelakantan¹⁴, Josh Croteau¹⁵, Anne E Wiblin¹⁶, Jeremy Fisher¹⁷, April J Livengood¹⁸, Karen G Dowell¹⁹, Jonathan C Silverstein²⁰, Jeffrey M Spraggins^{11

12

21

22}, Gloria S Pryhuber²³, Gail Deutsch²⁴, Fiona Ginty⁴, Garry P Nolan⁵, Simon Melov²⁵, Danny Jonigk^{6

26

27}, Michael A Caldwell²⁸, Ioannis S Vlachos^{29

30

31}, Werner Muller^{32

33}, Nils Gehlenborg³⁴, Brent R Stockwell^{7

14}, Emma Lundberg^{5

8

9}, Michael P Snyder³⁵, Ronald N Germain³⁶, Jeannie M Camarillo^{28

37}, Neil L Kelleher^#²⁸, Katy Börner^#¹, Andrea J Radtke³⁸

Affiliations

¹ Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA.
² Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
³ Vanderbilt Diabetes Center, Vanderbilt University School of Medicine, Nashville, TN, USA.
⁴ GE Research, Niskayuna, NY, USA.
⁵ Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
⁶ Institute of Pathology, Hannover Medical School, Hannover, Germany.
⁷ Department of Biological Sciences, Columbia University, New York, NY, USA.
⁸ Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden.
⁹ Department of Bioengineering, Stanford University, Stanford, CA, USA.
¹⁰ Department of Chemistry, Pennsylvania State University, University Park, PA, USA.
¹¹ Department of Biochemistry, Vanderbilt University, Nashville, TN, USA.
¹² Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA.
¹³ Department of Chemistry, University of California Davis, Davis, CA, USA.
¹⁴ Department of Chemistry, Columbia University, New York, NY, USA.
¹⁵ Department of Business Development, BioLegend Inc., San Diego, CA, USA.
¹⁶ Department of Research and Development, Abcam PLC, Discovery Drive, Cambridge Biomedical Campus, Cambridge, UK.
¹⁷ Department of Research and Development, Cell Signaling Technology, Inc., Danvers, MA, USA.
¹⁸ Department of Protein and Cell Analysis, Thermo Fisher Scientific, Carlsbad, CA, USA.
¹⁹ Akoya Biosciences, Marlborough, MA, USA.
²⁰ Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
²¹ Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
²² Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA.
²³ Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA.
²⁴ Department of Pathology, University of Washington Medical Center, Seattle, WA, USA.
²⁵ Buck Institute for Research on Aging, Novato, CA, USA.
²⁶ German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany.
²⁷ Institute of Pathology, RWTH University of Aachen, Aachen, Germany.
²⁸ Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA.
²⁹ Spatial Technologies Unit, Harvard Medical School Initiative for RNA Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA.
³⁰ Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA.
³¹ Broad Institute of MIT and Harvard, Cambridge, MA, USA.
³² Miltenyi Biotec B.V. and Co. KG, Bergisch Gladbach, Germany.
³³ Division of Infection, Immunity and Respiratory Medicine, University of Manchester, Manchester, UK.
³⁴ Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
³⁵ Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
³⁶ Laboratory of Immune System Biology, Lymphocyte Biology Section and Center for Advanced Tissue Imaging, NIAID, NIH, Bethesda, MD, USA.
³⁷ Inotiv, Nashville, TN, USA.
³⁸ Laboratory of Immune System Biology, Lymphocyte Biology Section and Center for Advanced Tissue Imaging, NIAID, NIH, Bethesda, MD, USA. andrea.radtke@nih.gov.

^# Contributed equally.

PMID: 37468619
PMCID: PMC10406602
DOI: 10.1038/s41592-023-01846-7

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

Ellen M Quardokus et al. Nat Methods. 2023 Aug.

. 2023 Aug;20(8):1174-1178.

doi: 10.1038/s41592-023-01846-7. Epub 2023 Jul 19.

Authors

Affiliations

¹ Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA.
² Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
³ Vanderbilt Diabetes Center, Vanderbilt University School of Medicine, Nashville, TN, USA.
⁴ GE Research, Niskayuna, NY, USA.
⁵ Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
⁶ Institute of Pathology, Hannover Medical School, Hannover, Germany.
⁷ Department of Biological Sciences, Columbia University, New York, NY, USA.
⁸ Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden.
⁹ Department of Bioengineering, Stanford University, Stanford, CA, USA.
¹⁰ Department of Chemistry, Pennsylvania State University, University Park, PA, USA.
¹¹ Department of Biochemistry, Vanderbilt University, Nashville, TN, USA.
¹² Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA.
¹³ Department of Chemistry, University of California Davis, Davis, CA, USA.
¹⁴ Department of Chemistry, Columbia University, New York, NY, USA.
¹⁵ Department of Business Development, BioLegend Inc., San Diego, CA, USA.
¹⁶ Department of Research and Development, Abcam PLC, Discovery Drive, Cambridge Biomedical Campus, Cambridge, UK.
¹⁷ Department of Research and Development, Cell Signaling Technology, Inc., Danvers, MA, USA.
¹⁸ Department of Protein and Cell Analysis, Thermo Fisher Scientific, Carlsbad, CA, USA.
¹⁹ Akoya Biosciences, Marlborough, MA, USA.
²⁰ Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
²¹ Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
²² Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA.
²³ Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA.
²⁴ Department of Pathology, University of Washington Medical Center, Seattle, WA, USA.
²⁵ Buck Institute for Research on Aging, Novato, CA, USA.
²⁶ German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany.
²⁷ Institute of Pathology, RWTH University of Aachen, Aachen, Germany.
²⁸ Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA.
²⁹ Spatial Technologies Unit, Harvard Medical School Initiative for RNA Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA.
³⁰ Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA.
³¹ Broad Institute of MIT and Harvard, Cambridge, MA, USA.
³² Miltenyi Biotec B.V. and Co. KG, Bergisch Gladbach, Germany.
³³ Division of Infection, Immunity and Respiratory Medicine, University of Manchester, Manchester, UK.
³⁴ Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
³⁵ Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
³⁶ Laboratory of Immune System Biology, Lymphocyte Biology Section and Center for Advanced Tissue Imaging, NIAID, NIH, Bethesda, MD, USA.
³⁷ Inotiv, Nashville, TN, USA.
³⁸ Laboratory of Immune System Biology, Lymphocyte Biology Section and Center for Advanced Tissue Imaging, NIAID, NIH, Bethesda, MD, USA. andrea.radtke@nih.gov.

^# Contributed equally.

PMID: 37468619
PMCID: PMC10406602
DOI: 10.1038/s41592-023-01846-7

Abstract

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.

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Conflict of interest statement

A.E.W. is an employee and shareholder of Abcam PLC. J.F. is an employee of Cell Signaling Technology, Inc. J.C. is an employee and stakeholder of BioLegend. A.J.L. is an employee and shareholder of Thermo Fisher Scientific. E.M., L.L., C.S. and F.G. are employees of GE Research. B.R.S. is an inventor on patents and patent applications involving small molecule drug discovery, and the 3F3-FMA antibody, cofounded and serves as a consultant to Exarta Therapeutics and ProJenX Inc.; holds equity in Sonata Therapeutics, receives sponsored research from Sumitomo Pharma Oncology Inc and serves as a consultant to Weatherwax Biotechnologies Corporation and Akin Gump Strauss Hauer and Feld LLP. M.P.S. is cofounder and advisory board member of Personalis, Qbio, January AI, Mirvie, Filtricine, Fodsel, Lollo and Protos. G.P.N. has equity in and is a scientific advisory board member of Akoya Biosciences, Inc. I.S.V. consults for Guidepoint Global, Cowen, Mosaic and NextRNA. N.G. is a cofounder and equity owner of Datavisyn. W.M. is an employee of Miltenyi Biotec B.V. and Co. KG. E.L. serves as a consultant for 10x Genomics, Moleculent AB, Pixelgen Technologies and Nautilus Biotechnology. K.G.D. is an employee of Akoya Biosciences. The remaining authors declare no competing interests.

Figures

**Fig. 1. OMAPs enhance standardization, discovery and stewardship of resources used in the spatial mapping of tissues at single-cell resolution.**
a, Bar graph depicting the number of AS, CT and BP covered by each OMAP. Numbers were calculated by comparing with the relevant ASCT+B table and were reviewed by domain experts. b, Plot showing the cost to develop (filled circles) and use (unfilled circle) the OMAPs described here. Costs (in 2022 US dollars) are shown for antibodies and/or conjugation kits and exclude labor, amortization of purchased equipment such as microscopes, and consumables other than antibodies and conjugation kits. Cost to use is calculated for 100 tests. DNA (CODEX), Fluorophore (IBEX), Fluorophore* (Cell DIVE), Metal (SIMS). c, Schematic detailing the creation of a base OMAP panel. Gray antibodies indicate antibodies that do not pass the first quality control check for accurate immunolabeling. Colored antibodies outside of the filter reflect validated antibodies that are not suitable for the final OMAP, for example, need amplification or a different conjugate. d, Images of human lymph node depicting AS, CT and cell states identified using IBEX. GC, Tfr (follicular regulatory T cells), Treg (regulatory T cells), TBM (tingible body macrophages) and R1–R4 refer to different regions in the secondary follicle. 3⁺⁺ indicates CD69⁺⁺, ICOS⁺⁺ and PD-1⁺⁺; 1⁺ indicates CD69⁺ or ICOS+ or PD-1⁺. Large insets, 150 µm; small insets, 50 µm. Representative of a dataset of ten samples.

**Fig. 2. Process, required metadata, and future data integration plans for OMAP effort.**
a, Main milestones in constructing an OMAP, outlined via steps 1–5. Nephron and renal corpuscle illustrations were adapted from the HuBMAP CCF 2D Reference Object Library. b, Metadata table illustrates the common fields shared across HuBMAP entities (OMAP, AVR and ASCT+B) to enhance search capabilities and promote community adoption of controlled vocabularies. Visit the Human Reference Atlas Portal (https://humanatlas.io/) for more details. c, In the future, OMAPs will be linked directly to the AVR searchable database, such that users can easily query information about BProtein markers for a specific OMAP. The ARWG is also collaborating with the Vitessce software team to create a user interface with grouped image channels by BProtein and CT that additionally displays annotations by subject matter experts.

See this image and copyright information in PMC

References

1. Hickey JW, et al. Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging. Nat. Methods. 2022;19:284–295. doi: 10.1038/s41592-021-01316-y. - DOI - PMC - PubMed
1. Uhlen M, et al. A proposal for validation of antibodies. Nat. Methods. 2016;13:823–827. doi: 10.1038/nmeth.3995. - DOI - PMC - PubMed
1. Bordeaux J, et al. Antibody validation. Biotechniques. 2010;48:197–209. doi: 10.2144/000113382. - DOI - PMC - PubMed
1. Snyder MP, et al. The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. Nature. 2019;574:187–192. doi: 10.1038/s41586-019-1629-x. - DOI - PMC - PubMed
1. Roederer M, Tárnok A. OMIPs—orchestrating multiplexity in polychromatic science. Cytom. Part A. 2010;77A:811–812. doi: 10.1002/cyto.a.20959. - DOI - PubMed

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

Affiliations

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

Authors

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Abstract

Conflict of interest statement

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