Flura-seq identifies organ-specific metabolic adaptations during early metastatic colonization
- Memorial Sloan-Kettering Cancer Center, United States
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.
Data availability
Sequencing data have been deposited in GEO under accession codes GSE93605 and GSE118937.
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Organ-specific in situ transcriptomics of MDA231 cells identified by Flura-seqNCBI Gene Expression Omnibus, GSE118937.
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Flura-seq of TGFB treated MDA231 cellsNCBI Gene Expression Omnibus, GSE93605.
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Integrated RNA and DNA sequencing reveals early drivers of metastatic breast cancerNCBI Gene Expression Omnibus, GSE110590.
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ubpopulations of MDA-MB-231 and Primary Breast CancersNCBI Gene Expression Omnibus, GSE2603.
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Breast cancer relapse free survival and lung metastasis free survivalNCBI Gene Expression Omnibus, GSE5327.
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Breast cancer relapse free survivalNCBI Gene Expression Omnibus, GSE2034.
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Expression data from primary breast tumorsNCBI Gene Expression Omnibus, GSE12276.
Article and author information
Author details
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
- Matthew G Vander Heiden, Massachusetts Institute of Technology, United States
Publication history
- Received: November 14, 2018
- Accepted: March 6, 2019
- Accepted Manuscript published: March 26, 2019 (version 1)
- 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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Flura-seq identifies organ-specific metabolic adaptations during early metastatic colonization
eLife 8:e43627.
https://doi.org/10.7554/eLife.43627
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