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Epigenetic expansion of VHL-HIF signal output drives multiorgan metastasis in renal cancer

Abstract

Inactivation of the von Hippel-Lindau tumor suppressor gene, VHL, is an archetypical tumor-initiating event in clear cell renal carcinoma (ccRCC) that leads to the activation of hypoxia-inducible transcription factors (HIFs). However, VHL mutation status in ccRCC is not correlated with clinical outcome. Here we show that during ccRCC progression, cancer cells exploit diverse epigenetic alterations to empower a branch of the VHL-HIF pathway for metastasis, and the strength of this activation is associated with poor clinical outcome. By analyzing metastatic subpopulations of VHL-deficient ccRCC cells, we discovered an epigenetically altered VHL-HIF response that is specific to metastatic ccRCC. Focusing on the two most prominent pro-metastatic VHL-HIF target genes, we show that loss of Polycomb repressive complex 2 (PRC2)-dependent histone H3 Lys27 trimethylation (H3K27me3) activates HIF-driven chemokine (C-X-C motif) receptor 4 (CXCR4) expression in support of chemotactic cell invasion, whereas loss of DNA methylation enables HIF-driven cytohesin 1 interacting protein (CYTIP) expression to protect cancer cells from death cytokine signals. Thus, metastasis in ccRCC is based on an epigenetically expanded output of the tumor-initiating pathway.

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Figure 1: Experimental model system and gene expression signature for ccRCC metastasis.
Figure 2: VHL-HIF signal output modulation is associated with ccRCC progression.
Figure 3: VHL-HIF pathway modulation activates functional mediators of ccRCC metastasis.
Figure 4: DNA demethylation activates CYTIP expression in metastatic ccRCC.
Figure 5: Histone modification patterns linked to ccRCC progression.
Figure 6: Loss of PRC2-dependent repression activates CXCR4 expression in metastatic ccRCC.

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Acknowledgements

We thank members of the Massagué lab for discussion, J. Brooks (Stanford University, California) for clinical annotations, W. Krek (ETH, Swiss Federal Institute of Technology, Zurich, Switzerland) for CXCR4 promoter constructs and C. David and S. Malladi for critical review of the manuscript. Gene expression profiling and high-throughput sequencing were done at the Memorial Sloan-Kettering Cancer Center (MSKCC) Genomics Core Facility, immunohistochemical staining was done at the MSKCC Molecular Cytology Core Facility, and DNA methylation analysis, RNA analysis of clinical samples and Sanger sequencing were done at the MSKCC Geoffrey Beene Translational Oncology Core Facility. The GSE2109 dataset was provided by the International Genomics Consortium and Expression Project for Oncology. S.V. received postdoctoral support from the Maud Kuistila Memorial Foundation, the Emil Aaltonen Foundation, the Paulo Foundation, the Orion-Farmos Research Foundation, the Instrumentarium Science Foundation, The Finnish Medical Foundation and the Academy of Finland. J.M. is an investigator of the Howard Hughes Medical Institute.

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S.V. and J.M. designed experiments. S.V. performed experiments and bioinformatic analysis. W.S. assisted with experiments. F.B. performed STAMP experiments. A.H. supervised Epityper analysis and genomic sequencing. V.E.R. and J.J.-D.H. provided clinical ccRCC specimens. A.A.H. analyzed CXCR4 expression in clinical specimens. A.V. supervised high-throughput sequencing. J.M.S. and S.V. analyzed high-throughput sequencing data. S.V. and J.M. wrote the paper.

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Correspondence to Joan Massagué.

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Vanharanta, S., Shu, W., Brenet, F. et al. Epigenetic expansion of VHL-HIF signal output drives multiorgan metastasis in renal cancer. Nat Med 19, 50–56 (2013). https://doi.org/10.1038/nm.3029

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