Risk SNP-Mediated Promoter-Enhancer Switching Drives Prostate Cancer through lncRNA PCAT19

Junjie Tony Hua¹, Musaddeque Ahmed², Haiyang Guo², Yuzhe Zhang³, Sujun Chen¹, Fraser Soares², Jennifer Lu⁴, Stanley Zhou¹, Miranda Wang², Hui Li⁵, Nicholas B Larson⁶, Shannon K McDonnell⁶, Parasvi S Patel¹, Yi Liang², Cindy Q Yao⁷, Theodorus van der Kwast⁸, Mathieu Lupien⁹, Felix Y Feng¹⁰, Amina Zoubeidi¹¹, Ming-Sound Tsao¹, Stephen N Thibodeau¹², Paul C Boutros¹³, Housheng Hansen He¹⁴

Affiliations

¹ Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada.
² Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 1L7, Canada.
³ Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 1L7, Canada; College of Life Sciences, Central China Normal University, Wuhan, Hubei, China; College of Basic Medical Sciences, Dali University, Dali, Yunnan, China.
⁴ Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A1, Canada.
⁵ Department of Radiation Oncology, University of California at San Francisco, San Francisco, CA, USA.
⁶ Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA.
⁷ Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada.
⁸ Department of Pathology and Laboratory Medicine, Toronto General Hospital/University Health Network, Toronto, ON, Canada.
⁹ Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada.
¹⁰ Department of Radiation Oncology, University of California at San Francisco, San Francisco, CA, USA; Department of Urology, University of California at San Francisco, San Francisco, CA, USA; Department of Medicine, University of California at San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, USA.
¹¹ Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada.
¹² Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
¹³ Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada.
¹⁴ Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada. Electronic address: hansenhe@uhnresearch.ca.

PMID: 30033362
DOI: 10.1016/j.cell.2018.06.014

Free article

Risk SNP-Mediated Promoter-Enhancer Switching Drives Prostate Cancer through lncRNA PCAT19

Junjie Tony Hua et al. Cell. 2018.

Free article

. 2018 Jul 26;174(3):564-575.e18.

doi: 10.1016/j.cell.2018.06.014. Epub 2018 Jul 19.

Authors

Affiliations

¹ Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada.
² Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 1L7, Canada.
³ Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 1L7, Canada; College of Life Sciences, Central China Normal University, Wuhan, Hubei, China; College of Basic Medical Sciences, Dali University, Dali, Yunnan, China.
⁴ Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A1, Canada.
⁵ Department of Radiation Oncology, University of California at San Francisco, San Francisco, CA, USA.
⁶ Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA.
⁷ Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada.
⁸ Department of Pathology and Laboratory Medicine, Toronto General Hospital/University Health Network, Toronto, ON, Canada.
⁹ Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada.
¹⁰ Department of Radiation Oncology, University of California at San Francisco, San Francisco, CA, USA; Department of Urology, University of California at San Francisco, San Francisco, CA, USA; Department of Medicine, University of California at San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, USA.
¹¹ Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada.
¹² Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
¹³ Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada.
¹⁴ Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada. Electronic address: hansenhe@uhnresearch.ca.

PMID: 30033362
DOI: 10.1016/j.cell.2018.06.014

Abstract

The prostate cancer (PCa) risk-associated SNP rs11672691 is positively associated with aggressive disease at diagnosis. We showed that rs11672691 maps to the promoter of a short isoform of long noncoding RNA PCAT19 (PCAT19-short), which is in the third intron of the long isoform (PCAT19-long). The risk variant is associated with decreased and increased levels of PCAT19-short and PCAT19-long, respectively. Mechanistically, the risk SNP region is bifunctional with both promoter and enhancer activity. The risk variants of rs11672691 and its LD SNP rs887391 decrease binding of transcription factors NKX3.1 and YY1 to the promoter of PCAT19-short, resulting in weaker promoter but stronger enhancer activity that subsequently activates PCAT19-long. PCAT19-long interacts with HNRNPAB to activate a subset of cell-cycle genes associated with PCa progression, thereby promoting PCa tumor growth and metastasis. Taken together, these findings reveal a risk SNP-mediated promoter-enhancer switching mechanism underlying both initiation and progression of aggressive PCa.

Keywords: HNRNPAB; NKX3.1; PCAT19; YY1; bifunctional regulatory element; lncRNA; promoter-enhancer switching; prostate cancer progression; risk SNP; rs11672691.

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Comment in

Changing the Guard at a Prostate Cancer SNP.
Bulger M. Bulger M. Cell. 2018 Jul 26;174(3):501-502. doi: 10.1016/j.cell.2018.07.014. Cell. 2018. PMID: 30053422
Mechanistic insights into a non-coding risk SNP.
Bradley CA. Bradley CA. Nat Rev Urol. 2018 Nov;15(11):655. doi: 10.1038/s41585-018-0079-9. Nat Rev Urol. 2018. PMID: 30135604 No abstract available.

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Risk SNP-Mediated Promoter-Enhancer Switching Drives Prostate Cancer through lncRNA PCAT19

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Risk SNP-Mediated Promoter-Enhancer Switching Drives Prostate Cancer through lncRNA PCAT19

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