Flura-seq identifies organ-specific metabolic adaptations during early metastatic colonization
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.
Document Details
- Document Type
- Pub Defense Publication
- Publication Date
- Mar 26, 2019
- Source ID
- 10.7554/elife.43627
Entities
People
- Danilo G. Macalinao
- Edi Brogi
- Harihar Basnet
- Joan Massagué Solé
- Karuna Ganesh
- Lin Tian
- Lydia Ws Finley
- Yun-han Huang
Organizations
- Damon Runyon Cancer Research Foundation
- Memorial Sloan Kettering Cancer Center
- National Institutes of Health
- United States Department of Defense
- Weill Cornell Medicine