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A prostate cancer susceptibility allele at 6q22 increases RFX6 expression by modulating HOXB13 chromatin binding

Nature Genetics volume 46, pages 126–135 (2014)Cite this article

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Abstract

Genome-wide association studies have identified thousands of SNPs associated with predisposition to various diseases, including prostate cancer. However, the mechanistic roles of these SNPs remain poorly defined, particularly for noncoding polymorphisms. Here we find that the prostate cancer risk-associated SNP rs339331 at 6q22 lies within a functional HOXB13-binding site. The risk-associated T allele at rs339331 increases binding of HOXB13 to a transcriptional enhancer, conferring allele-specific upregulation of the rs339331-associated gene RFX6. Suppression of RFX6 diminishes prostate cancer cell proliferation, migration and invasion. Clinical data indicate that RFX6 upregulation in human prostate cancers correlates with tumor progression, metastasis and risk of biochemical relapse. Finally, we observe a significant association between the risk-associated T allele at rs339331 and increased RFX6 mRNA levels in human prostate tumors. Together, our results suggest that rs339331 affects prostate cancer risk by altering RFX6 expression through a functional interaction with the prostate cancer susceptibility gene HOXB13.

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Figure 1: The prostate cancer risk-associated SNP rs339331 alters a HOXB13-binding site, and the T risk allele of rs339331 enhances HOXB13 DNA-binding affinity.
Figure 2: Allele-specific differences in HOXB13 chromatin binding and rs339331 enhancer activity at the prostate cancer 6q22 risk locus.
Figure 3: rs339331 confers HOXB13-regulated allelic imbalance in RFX6 expression.
Figure 4: The rs339331-associated gene RFX6 is a potential prostate cancer susceptibility gene with effects on cellular phenotypes related to tumor-associated properties.
Figure 5: Associations between rs339331 genotype, RFX6 expression and prostate cancer risk and severity.

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Gene Expression Omnibus

Sequence Read Archive

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Acknowledgements

We thank P. Vuokila, S. Lähdesmäki, J. Träskelin and A. Viklund for technical service, M. Männikkö for DNA sequencing, M. Taipale and L. Hu for massively parallel sequencing, P. Karppinen for critically reading the manuscript and A. Juffer for providing the Linux High-Performance Computing server. We also thank the TCGA Research Network for generating the TCGA data sets for prostate adenocarcinoma. A.M. and K.Z. are funded by the Academy of Finland (135560 and 251314). J.X. is funded by Chinese National Key Basic Research Program Grant 973 (2012CB518301). This work was supported by Strategic Funds from Biocenter Oulu and the University of Oulu, Biocenter Finland, the Sigrid Jusélius Foundation, the Jane and Aatos Erkko Foundation and a China Scholarship Council fellowship, 201206300074, via Northwest Agriculture and Forestry University.

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  1. Qilai Huang and Thomas Whitington: These authors contributed equally to this work.

Authors and Affiliations

  1. Biocenter Oulu, University of Oulu, Oulu, Finland

    Qilai Huang, Ping Gao, Yuehong Yang, Kai Zhang, Ruizhu Lin, Aki Manninen & Gong-Hong Wei

  2. Department of Medical Biochemistry and Molecular Biology, Institute of Biomedicine, University of Oulu, Oulu, Finland

    Qilai Huang, Ping Gao, Yuehong Yang, Kai Zhang, Ruizhu Lin, Aki Manninen & Gong-Hong Wei

  3. Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden

    Thomas Whitington, Jian Yan, Arttu Jolma & Jussi Taipale

  4. Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden

    Thomas Whitington, Johan F Lindberg, Robert Szulkin & Fredrik Wiklund

  5. Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China

    Jielin Sun & Jianfeng Xu

  6. Department of Pathology, Oulu University Hospital, Oulu, Finland

    Marja-Riitta Väisänen & Markku H Vaarala

  7. Prostate Cancer Research Center, Institute of Biomedical Technology and BioMediTech, University of Tampere and Tampere University Hospital, Tampere, Finland

    Matti Annala, Matti Nykter & Tapio Visakorpi

  8. Department of Pathology and Cytology, Karolinska University Hospital, Stockholm, Sweden

    Lars A Egevad

  9. Genome-Scale Biology Program, University of Helsinki, Helsinki, Finland

    Arttu Jolma & Jussi Taipale

  10. Medical Research Center, University of Oulu, Oulu, Finland

    Markku H Vaarala

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Contributions

G.-H.W. and J.T. conceived the study. G.-H.W. designed research. Q.H., P.G., Y.Y., J.Y., R.L. and G.-H.W. performed experiments. T.W. performed computing and clinical outcome analysis. G.-H.W. performed clinical correlations. J.F.L. and L.A.E. recruited the Swedish cohort of prostate cancer cases and performed pathological evaluation. J.S. and J.X. performed genetic analysis. M.-R.V. and M.H.V. recruited the Finnish Oulu cohort of prostate cancer cases and performed pathological evaluation. R.S. and F.W. performed association analysis in the Swedish prostate cancer GWAS cohort. J.Y. and A.J. contributed to gene cloning. K.Z. and A.M. contributed to virus production. T.V. contributed the Finnish Tampere cohort of prostate cancer cases. M.A. and M.N. performed RNA sequencing. G.-H.W. wrote the manuscript with help from Q.H. and T.W., and all authors critically revised the manuscript, interpreted data and approved the final draft.

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Correspondence to Jussi Taipale or Gong-Hong Wei.

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Huang, Q., Whitington, T., Gao, P. et al. A prostate cancer susceptibility allele at 6q22 increases RFX6 expression by modulating HOXB13 chromatin binding. Nat Genet 46, 126–135 (2014). https://doi.org/10.1038/ng.2862

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