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High-Dimensional Tissue Profiling by Multiplexed Ion Beam Imaging

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Single-Cell Protein Analysis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2386))

Abstract

Multiplexed Ion Beam Imaging by Time of Flight (MIBI-TOF) enables high-dimensional imaging in situ of clinical specimens at single-cell resolution. In MIBI-TOF, tissue sections are stained with dozens of metal-labeled antibodies, whose abundance and location are read by secondary ionization mass spectrometry. The result is a multi-dimensional image, depicting sub-cellular expression and localization for dozens of distinct proteins in situ. Here, we describe the staining and imaging procedures of a MIBI-TOF experiment.

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References

  1. de Matos LL, Trufelli DC, de Matos MGL, da Silva Pinhal MA (2010) Immunohistochemistry as an important tool in biomarkers detection and clinical practice. Biomark Insights 5:9–20

    Article  Google Scholar 

  2. Tirosh I, Izar B, Prakadan SM, Wadsworth MH, Treacy D, Trombetta JJ, Rotem A, Rodman C, Lian C, Murphy G, Fallahi-Sichani M, Dutton-Regester K, Lin J-R, Cohen O, Shah P, Lu D, Genshaft AS, Hughes TK, Ziegler CGK, Kazer SW, Gaillard A, Kolb KE, Villani A-C, Johannessen CM, Andreev AY, Van Allen EM, Bertagnolli M, Sorger PK, Sullivan RJ, Flaherty KT, Frederick DT, Jane-Valbuena J, Yoon CH, Rozenblatt-Rosen O, Shalek AK, Regev A, Garraway LA (2016) Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. Science 352:189–196. https://doi.org/10.1126/science.aad0501

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Giesen C, Wang HAO, Schapiro D, Zivanovic N, Jacobs A, Hattendorf B, Schüffler PJ, Grolimund D, Buhmann JM, Brandt S, Varga Z, Wild PJ, Günther D, Bodenmiller B (2014) Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry. Nat Methods 11:417–422. https://doi.org/10.1038/nmeth.2869

    Article  CAS  PubMed  Google Scholar 

  4. Chen KH, Boettiger AN, Moffitt JR, Wang S, Zhuang X (2015) Spatially resolved, highly multiplexed RNA profiling in single cells. Science 348:aaa6090. https://doi.org/10.1126/science.aaa6090

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Coskun AF, Cai L (2016) Dense transcript profiling in single cells by image correlation decoding. Nat Methods 13:657–660. https://doi.org/10.1038/nmeth.3895

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Huang W, Hennrick K, Drew S (2013) A colorful future of quantitative pathology: validation of Vectra technology using chromogenic multiplexed immunohistochemistry and prostate tissue microarrays. Hum Pathol 44:29–38. https://doi.org/10.1016/j.humpath.2012.05.009

    Article  CAS  PubMed  Google Scholar 

  7. Stack EC, Wang C, Roman KA, Hoyt CC (2014) Multiplexed immunohistochemistry, imaging, and quantitation: a review, with an assessment of Tyramide signal amplification, multispectral imaging and multiplex analysis. Methods 70:46–58. https://doi.org/10.1016/J.YMETH.2014.08.016

    Article  CAS  PubMed  Google Scholar 

  8. Lee JH, Daugharthy ER, Scheiman J, Kalhor R, Yang JL, Ferrante TC, Terry R, Jeanty SSF, Li C, Amamoto R, Peters DT, Turczyk BM, Marblestone AH, Inverso SA, Bernard A, Mali P, Rios X, Aach J, Church GM (2014) Highly multiplexed subcellular RNA sequencing in situ. Science 343:1360–1363. https://doi.org/10.1126/science.1250212

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Keren L, Angelo M (2020) Mapping cell phenotypes in breast cancer. Nat Cancer 1:156–157. https://doi.org/10.1038/s43018-020-0031-9

    Article  CAS  PubMed  Google Scholar 

  10. Angelo M, Bendall SC, Finck R, Hale MB, Hitzman C, Borowsky AD, Levenson RM, Lowe JB, Liu SD, Zhao S, Natkunam Y, Nolan GP (2014) Multiplexed ion beam imaging of human breast tumors. Nat Med 20:436–442. https://doi.org/10.1038/nm.3488

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Keren L, Bosse M, Thompson S, Risom T, Vijayaragavan K, McCaffrey E, Marquez D, Angoshtari R, Greenwald NF, Fienberg H, Wang J, Kambham N, Kirkwood D, Nolan G, Montine TJ, Galli SJ, West R, Bendall SC, Angelo M (2019) MIBI-TOF: A multiplexed imaging platform relates cellular phenotypes and tissue structure. Sci Adv 5:eaax5851. https://doi.org/10.1126/sciadv.aax5851

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Keren L, Bosse M, Marquez D, Angoshtari R, Jain S, Varma S, Yang S-R, Kurian A, Van Valen D, West R, Bendall SC, Angelo M (2018) A structured tumor-immune microenvironment in triple negative breast cancer revealed by multiplexed ion beam imaging. Cell 174:1373–1387.e19. https://doi.org/10.1016/J.CELL.2018.08.039

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Bendall SC, Simonds EF, Qiu P, Amir ED, Krutzik PO, Finck R, Bruggner RV, Melamed R, Trejo A, Ornatsky OI, Balderas RS, Plevritis SK, Sachs K, Pe’er D, Tanner SD, Nolan GP (2011) Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum. Science 332:687–696. https://doi.org/10.1126/science.1198704

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Author information

Authors and Affiliations

  1. Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel

    Ofer Elhanani & Leeat Keren

  2. Department of Pathology, Stanford University, Stanford, CA, USA

    Michael Angelo

Authors
  1. Ofer Elhanani
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  2. Leeat Keren
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  3. Michael Angelo
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Corresponding authors

Correspondence to Leeat Keren or Michael Angelo .

Editor information

Editors and Affiliations

  1. Mission Bio, Inc., South San Francisco, CA, USA

    Aik T. Ooi

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© 2022 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Elhanani, O., Keren, L., Angelo, M. (2022). High-Dimensional Tissue Profiling by Multiplexed Ion Beam Imaging. In: Ooi, A.T. (eds) Single-Cell Protein Analysis. Methods in Molecular Biology, vol 2386. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1771-7_10

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  • DOI: https://doi.org/10.1007/978-1-0716-1771-7_10

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1770-0

  • Online ISBN: 978-1-0716-1771-7

  • eBook Packages: Springer Protocols

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