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Visual barcodes for clonal-multiplexing of live microscopy-based assays

Author

Listed:
  • Tom Kaufman

    (Weizmann Institute of Science)

  • Erez Nitzan

    (Weizmann Institute of Science)

  • Nir Firestein

    (Weizmann Institute of Science)

  • Miriam Bracha Ginzberg

    (The Hospital for Sick Children)

  • Seshu Iyengar

    (University of Toronto)

  • Nish Patel

    (The Hospital for Sick Children)

  • Rotem Ben-Hamo

    (Weizmann Institute of Science)

  • Ziv Porat

    (Weizmann Institute of Science)

  • Jaryd Hunter

    (The Hospital for Sick Children
    University of Toronto)

  • Andreas Hilfinger

    (University of Toronto)

  • Varda Rotter

    (Weizmann Institute of Science)

  • Ran Kafri

    (The Hospital for Sick Children
    University of Toronto)

  • Ravid Straussman

    (Weizmann Institute of Science)

Abstract

While multiplexing samples using DNA barcoding revolutionized the pace of biomedical discovery, multiplexing of live imaging-based applications has been limited by the number of fluorescent proteins that can be deconvoluted using common microscopy equipment. To address this limitation, we develop visual barcodes that discriminate the clonal identity of single cells by different fluorescent proteins that are targeted to specific subcellular locations. We demonstrate that deconvolution of these barcodes is highly accurate and robust to many cellular perturbations. We then use visual barcodes to generate ‘Signalome’ cell-lines by mixing 12 clones of different live reporters into a single population, allowing simultaneous monitoring of the activity in 12 branches of signaling, at clonal resolution, over time. Using the ‘Signalome’ we identify two distinct clusters of signaling pathways that balance growth and proliferation, emphasizing the importance of growth homeostasis as a central organizing principle in cancer signaling. The ability to multiplex samples in live imaging applications, both in vitro and in vivo may allow better high-content characterization of complex biological systems.

Suggested Citation

  • Tom Kaufman & Erez Nitzan & Nir Firestein & Miriam Bracha Ginzberg & Seshu Iyengar & Nish Patel & Rotem Ben-Hamo & Ziv Porat & Jaryd Hunter & Andreas Hilfinger & Varda Rotter & Ran Kafri & Ravid Strau, 2022. "Visual barcodes for clonal-multiplexing of live microscopy-based assays," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-30008-0
    DOI: 10.1038/s41467-022-30008-0
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    References listed on IDEAS

    as
    1. Almut Schulze & Adrian L. Harris, 2012. "How cancer metabolism is tuned for proliferation and vulnerable to disruption," Nature, Nature, vol. 491(7424), pages 364-373, November.
    2. Cory M. Johannessen & Laura A. Johnson & Federica Piccioni & Aisha Townes & Dennie T. Frederick & Melanie K. Donahue & Rajiv Narayan & Keith T. Flaherty & Jennifer A. Wargo & David E. Root & Levi A. G, 2013. "A melanocyte lineage program confers resistance to MAP kinase pathway inhibition," Nature, Nature, vol. 504(7478), pages 138-142, December.
    3. Rotem Ben-Hamo & Adi Jacob Berger & Nancy Gavert & Mendy Miller & Guy Pines & Roni Oren & Eli Pikarsky & Cyril H. Benes & Tzahi Neuman & Yaara Zwang & Sol Efroni & Gad Getz & Ravid Straussman, 2020. "Predicting and affecting response to cancer therapy based on pathway-level biomarkers," Nature Communications, Nature, vol. 11(1), pages 1-16, December.
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