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.
-
Organ-specific in situ transcriptomics of MDA231 cells identified by Flura-seqNCBI Gene Expression Omnibus, GSE118937.
-
Flura-seq of TGFB treated MDA231 cellsNCBI Gene Expression Omnibus, GSE93605.
-
Integrated RNA and DNA sequencing reveals early drivers of metastatic breast cancerNCBI Gene Expression Omnibus, GSE110590.
-
ubpopulations of MDA-MB-231 and Primary Breast CancersNCBI Gene Expression Omnibus, GSE2603.
-
Breast cancer relapse free survival and lung metastasis free survivalNCBI Gene Expression Omnibus, GSE5327.
-
Breast cancer relapse free survivalNCBI Gene Expression Omnibus, GSE2034.
-
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).
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.
Metrics
-
- 5,866
- views
-
- 833
- downloads
-
- 53
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Flura-seq identifies organ-specific metabolic adaptations during early metastatic colonization
eLife 8:e43627.
https://doi.org/10.7554/eLife.43627
Further reading
-
- Cancer Biology
- Cell Biology
TIPE (TNFAIP8) has been identified as an oncogene and participates in tumor biology. However, how its role in the metabolism of tumor cells during melanoma development remains unclear. Here, we demonstrated that TIPE promoted glycolysis by interacting with pyruvate kinase M2 (PKM2) in melanoma. We found that TIPE-induced PKM2 dimerization, thereby facilitating its translocation from the cytoplasm to the nucleus. TIPE-mediated PKM2 dimerization consequently promoted HIF-1α activation and glycolysis, which contributed to melanoma progression and increased its stemness features. Notably, TIPE specifically phosphorylated PKM2 at Ser 37 in an extracellular signal-regulated kinase (ERK)-dependent manner. Consistently, the expression of TIPE was positively correlated with the levels of PKM2 Ser37 phosphorylation and cancer stem cell (CSC) markers in melanoma tissues from clinical samples and tumor bearing mice. In summary, our findings indicate that the TIPE/PKM2/HIF-1α signaling pathway plays a pivotal role in promoting CSC properties by facilitating the glycolysis, which would provide a promising therapeutic target for melanoma intervention.
-
- Cancer Biology
- Chromosomes and Gene Expression
Telomeres are crucial for cancer progression. Immune signalling in the tumour microenvironment has been shown to be very important in cancer prognosis. However, the mechanisms by which telomeres might affect tumour immune response remain poorly understood. Here, we observed that interleukin-1 signalling is telomere-length dependent in cancer cells. Mechanistically, non-telomeric TRF2 (telomeric repeat binding factor 2) binding at the IL-1-receptor type-1 (IL1R1) promoter was found to be affected by telomere length. Enhanced TRF2 binding at the IL1R1 promoter in cells with short telomeres directly recruited the histone-acetyl-transferase (HAT) p300, and consequent H3K27 acetylation activated IL1R1. This altered NF-kappa B signalling and affected downstream cytokines like IL6, IL8, and TNF. Further, IL1R1 expression was telomere-sensitive in triple-negative breast cancer (TNBC) clinical samples. Infiltration of tumour-associated macrophages (TAM) was also sensitive to the length of tumour cell telomeres and highly correlated with IL1R1 expression. The use of both IL1 Receptor antagonist (IL1RA) and IL1R1 targeting ligands could abrogate M2 macrophage infiltration in TNBC tumour organoids. In summary, using TNBC cancer tissue (>90 patients), tumour-derived organoids, cancer cells, and xenograft tumours with either long or short telomeres, we uncovered a heretofore undeciphered function of telomeres in modulating IL1 signalling and tumour immunity.
