1. Cancer Biology
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Flura-seq identifies organ-specific metabolic adaptations during early metastatic colonization

  1. Harihar Basnet
  2. Lin Tian
  3. Karuna Ganesh
  4. Yun-Han Huang
  5. Danilo G Macalinao
  6. Edi Brogi
  7. Lydia Finley
  8. Joan Massagué  Is a corresponding author
  1. Memorial Sloan-Kettering Cancer Center, United States
Research Article
  • Cited 12
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Cite this article as: eLife 2019;8:e43627 doi: 10.7554/eLife.43627

Abstract

Metastasis-initiating cells dynamically adapt to the distinct microenvironments of different organs, but these early adaptations are poorly understood due to the limited sensitivity of in situ transcriptomics. We developed fluorouracil-labeled RNA sequencing (Flura-seq) for in situ analysis with high sensitivity. Flura-seq utilizes cytosine deaminase (CD) to convert fluorocytosine to fluorouracil, metabolically labeling nascent RNA in rare cell populations in situ for purification and sequencing. Flura-seq revealed hundreds of unique, dynamic organ-specific gene signatures depending on the microenvironment in mouse xenograft breast cancer micrometastases. Specifically, the mitochondrial electron transport Complex I, oxidative stress and counteracting antioxidant programs were induced in pulmonary micrometastases, compared to mammary tumors or brain micrometastases. We confirmed lung metastasis-specific increase in oxidative stress and upregulation of antioxidants in clinical samples, thus validating Flura-seq's utility in identifying clinically actionable microenvironmental adaptations in early metastasis. The sensitivity, robustness and economy of Flura-seq are broadly applicable beyond cancer research.

Article and author information

Author details

  1. Harihar Basnet

    Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, United States
    Competing interests
    Harihar Basnet, Has filed for patent for Flura-seq method (PCT/US18/22092).
  2. Lin Tian

    Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, United States
    Competing interests
    No competing interests declared.
  3. Karuna Ganesh

    Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, United States
    Competing interests
    No competing interests declared.
  4. Yun-Han Huang

    Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, United States
    Competing interests
    No competing interests declared.
  5. Danilo G Macalinao

    Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, United States
    Competing interests
    No competing interests declared.
  6. Edi Brogi

    Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, United States
    Competing interests
    No competing interests declared.
  7. Lydia Finley

    Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, United States
    Competing interests
    No competing interests declared.
  8. Joan Massagué

    Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, United States
    For correspondence
    j-massague@ski.mskcc.org
    Competing interests
    Joan Massagué, Reviewing editor, eLife. Has filed for patent for Flura-seq method (PCT/US18/22092). Serves in the scientific advisory board and owns company stock in Scholar Rock.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9324-8408

Funding

National Institutes of Health (P01-CA094060)

  • Joan Massagué

Damon Runyon Cancer Research Foundation (DR-12998)

  • Harihar Basnet

Department of Defense (W81XWH-12-0074)

  • Joan Massagué

National Institutes of Health (T32-CA009207)

  • Karuna Ganesh

National Institutes of Health (T32-GM07739)

  • Yun-Han Huang

National Institutes of Health (K08-CA230213)

  • Karuna Ganesh

National Institutes of Health (F30-CA203238)

  • Yun-Han Huang

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Animal experimentation: Mouse experiments were performed following the protocols approved by the MSKCC Institutional Animal Care and Use Committee (IACUC) (#99-09-032).

Reviewing Editor

  1. Matthew G Vander Heiden, Massachusetts Institute of Technology, United States

Publication history

  1. Received: November 14, 2018
  2. Accepted: March 6, 2019
  3. Accepted Manuscript published: March 26, 2019 (version 1)
  4. Version of Record published: March 29, 2019 (version 2)

Copyright

© 2019, Basnet et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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