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Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression

Nature Biotechnology volume 29, pages 742–749 (2011)Cite this article

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Abstract

Noncoding RNAs (ncRNAs) are emerging as key molecules in human cancer, with the potential to serve as novel markers of disease and to reveal uncharacterized aspects of tumor biology. Here we discover 121 unannotated prostate cancer–associated ncRNA transcripts (PCATs) by ab initio assembly of high-throughput sequencing of polyA+ RNA (RNA-Seq) from a cohort of 102 prostate tissues and cells lines. We characterized one ncRNA, PCAT-1, as a prostate-specific regulator of cell proliferation and show that it is a target of the Polycomb Repressive Complex 2 (PRC2). We further found that patterns of PCAT-1 and PRC2 expression stratified patient tissues into molecular subtypes distinguished by expression signatures of PCAT-1–repressed target genes. Taken together, our findings suggest that PCAT-1 is a transcriptional repressor implicated in a subset of prostate cancer patients. These findings establish the utility of RNA-Seq to identify disease-associated ncRNAs that may improve the stratification of cancer subtypes.

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Figure 1: Analysis of transcriptome data for the detection of unannotated transcripts.
Figure 2: Prostate cancer transcriptome sequencing reveals dysregulation of unannotated transcripts.
Figure 3: Unannotated intergenic transcripts differentiate prostate cancer and benign prostate samples.
Figure 4: PCAT-1 is a marker of aggressive cancer and a PRC2-repressed ncRNA.
Figure 5: PCAT-1 promotes cell proliferation.
Figure 6: Prostate cancer tissues recapitulate PCAT-1 signaling.

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GenBank/EMBL/DDBJ

Gene Expression Omnibus

References

  1. Metzker, M.L. Sequencing technologies—the next generation. Nat. Rev. Genet. 11, 31–46 (2010).

    Article  CAS  PubMed  Google Scholar 

  2. Guttman, M. et al. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat. Biotechnol. 28, 503–510 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511–515 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Robertson, G. et al. De novo assembly and analysis of RNA-seq data. Nat. Methods 7, 909–912 (2010).

    Article  CAS  PubMed  Google Scholar 

  5. Zerbino, D.R. & Birney, E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821–829 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Huarte, M. et al. A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 142, 409–419 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Orom, U.A. et al. Long noncoding RNAs with enhancer-like function in human cells. Cell 143, 46–58 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Rinn, J.L. et al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129, 1311–1323 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Gupta, R.A. et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 464, 1071–1076 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Pasmant, E. et al. Characterization of a germ-line deletion, including the entire INK4/ARF locus, in a melanoma-neural system tumor family: identification of ANRIL, an antisense noncoding RNA whose expression coclusters with ARF. Cancer Res. 67, 3963–3969 (2007).

    Article  CAS  PubMed  Google Scholar 

  11. Yap, K.L. et al. Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a. Mol. Cell 38, 662–674 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Tsai, M.C. et al. Long noncoding RNA as modular scaffold of histone modification complexes. Science 329, 689–693 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Kotake, Y. et al. Long non-coding RNA ANRIL is required for the PRC2 recruitment to and silencing of p15(INK4B) tumor suppressor gene. Oncogene 30, 1956–1962 (2011).

    Article  CAS  PubMed  Google Scholar 

  14. de Kok, J.B. et al. DD3(PCA3), a very sensitive and specific marker to detect prostate tumors. Cancer Res. 62, 2695–2698 (2002).

    CAS  PubMed  Google Scholar 

  15. Li, J. et al. PTEN, a putative protein tyrosine phosphatase gene mutated in human brain, breast, and prostate cancer. Science 275, 1943–1947 (1997).

    Article  CAS  PubMed  Google Scholar 

  16. Prensner, J.R. & Chinnaiyan, A.M. Oncogenic gene fusions in epithelial carcinomas. Curr. Opin. Genet. Dev. 19, 82–91 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Tomlins, S.A. et al. Distinct classes of chromosomal rearrangements create oncogenic ETS gene fusions in prostate cancer. Nature 448, 595–599 (2007).

    Article  CAS  PubMed  Google Scholar 

  18. Tomlins, S.A. et al. Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 310, 644–648 (2005).

    Article  CAS  PubMed  Google Scholar 

  19. Trapnell, C., Pachter, L. & Salzberg, S.L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105–1111 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Thierry-Mieg, D. & Thierry-Mieg, J. AceView: a comprehensive cDNA-supported gene and transcripts annotation. Genome Biol. 7 (suppl. 1), S11–S14 (2006).

    Google Scholar 

  21. Birney, E. et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799–816 (2007).

    Article  CAS  PubMed  Google Scholar 

  22. The FANTOM Consortium. The transcriptional landscape of the mammalian genome. Science 309, 1559–1563 (2005).

  23. He, Y., Vogelstein, B., Velculescu, V.E., Papadopoulos, N. & Kinzler, K.W. The antisense transcriptomes of human cells. Science 322, 1855–1857 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Guttman, M. et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458, 223–227 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Yu, J. et al. An integrated network of androgen receptor, polycomb, and TMPRSS2-ERG gene fusions in prostate cancer progression. Cancer Cell 17, 443–454 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Day, D.S., Luquette, L.J., Park, P.J. & Kharchenko, P.V. Estimating enrichment of repetitive elements from high-throughput sequence data. Genome Biol. 11, R69 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Kim, T.K. et al. Widespread transcription at neuronal activity-regulated enhancers. Nature 465, 182–187 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Rubin, M.A. et al. Alpha-methylacyl coenzyme A racemase as a tissue biomarker for prostate cancer. J. Am. Med. Assoc. 287, 1662–1670 (2002).

    Article  CAS  Google Scholar 

  29. Dhanasekaran, S.M. et al. Delineation of prognostic biomarkers in prostate cancer. Nature 412, 822–826 (2001).

    Article  CAS  PubMed  Google Scholar 

  30. van Bakel, H., Nislow, C., Blencowe, B.J. & Hughes, T.R. Most “dark matter” transcripts are associated with known genes. PLoS Biol. 8, e1000371 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Tomlins, S.A. et al. The role of SPINK1 in ETS rearrangement-negative prostate cancers. Cancer Cell 13, 519–528 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Bjartell, A.S. et al. Association of cysteine-rich secretory protein 3 and beta-microseminoprotein with outcome after radical prostatectomy. Clin. Cancer Res. 13, 4130–4138 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Oosumi, T., Belknap, W.R. & Garlick, B. Mariner transposons in humans. Nature 378, 672 (1995).

    Article  CAS  PubMed  Google Scholar 

  34. Robertson, H.M., Zumpano, K.L., Lohe, A.R. & Hartl, D.L. Reconstructing the ancient mariners of humans. Nat. Genet. 12, 360–361 (1996).

    Article  CAS  PubMed  Google Scholar 

  35. Kleer, C.G. et al. EZH2 is a marker of aggressive breast cancer and promotes neoplastic transformation of breast epithelial cells. Proc. Natl. Acad. Sci. USA 100, 11606–11611 (2003).

    Article  CAS  PubMed  Google Scholar 

  36. Varambally, S. et al. The polycomb group protein EZH2 is involved in progression of prostate cancer. Nature 419, 624–629 (2002).

    Article  CAS  PubMed  Google Scholar 

  37. Ahmadiyeh, N. et al. 8q24 prostate, breast, and colon cancer risk loci show tissue-specific long-range interaction with MYC. Proc. Natl. Acad. Sci. USA 107, 9742–9746 (2010).

    Article  PubMed  Google Scholar 

  38. Al Olama, A.A. et al. Multiple loci on 8q24 associated with prostate cancer susceptibility. Nat. Genet. 41, 1058–1060 (2009).

    Article  CAS  PubMed  Google Scholar 

  39. Beroukhim, R. et al. The landscape of somatic copy-number alteration across human cancers. Nature 463, 899–905 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Gudmundsson, J. et al. Genome-wide association study identifies a second prostate cancer susceptibility variant at 8q24. Nat. Genet. 39, 631–637 (2007).

    Article  CAS  PubMed  Google Scholar 

  41. Sotelo, J. et al. Long-range enhancers on 8q24 regulate c-Myc. Proc. Natl. Acad. Sci. USA 107, 3001–3005 (2010).

    Article  PubMed  Google Scholar 

  42. Taylor, B.S. et al. Integrative genomic profiling of human prostate cancer. Cancer Cell 18, 11–22 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Huttenhower, C. et al. Exploring the human genome with functional maps. Genome Res. 19, 1093–1106 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Laxman, B. et al. A first-generation multiplex biomarker analysis of urine for the early detection of prostate cancer. Cancer Res. 68, 645–649 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Hessels, D. et al. DD3(PCA3)-based molecular urine analysis for the diagnosis of prostate cancer. Eur. Urol. 44, 8–16 (2003).

    Article  CAS  PubMed  Google Scholar 

  46. Maher, C.A. et al. Chimeric transcript discovery by paired-end transcriptome sequencing. Proc. Natl. Acad. Sci. USA 106, 12353–12358 (2009).

    Article  PubMed  Google Scholar 

  47. Tusher, V.G., Tibshirani, R. & Chu, G. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. USA 98, 5116–5121 (2001).

    Article  CAS  PubMed  Google Scholar 

  48. Dennis, G. Jr. et al. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol. 4, 3 (2003).

    Article  Google Scholar 

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Acknowledgements

We thank K. Ramnarayanan and R. Morey for technical assistance with next generation sequencing. We thank R.J. Lonigro, S. Kaylana-Sundaram, T. Barrette, and M. Quist for help with sequencing data analysis, and R. Mehra, B. Han and K. Suleman for prostate tissue specimens. We thank C. Trapnell and G. Pertea for assistance with computational analyses. We thank S. Tomlins, Y.-M. Wu, S. Roychowdhury and members of the Chinnaiyan laboratory for advice and discussions. We thank R. Beroukhim for guidance. This work was supported in part by the US National Institutes of Health (NIH) Prostate Specialized Program of Research Excellence grant P50CA69568, the Early Detection Research Network grant UO1 CA111275 (to A.M.C.), the NIH R01CA132874-01A1 (to A.M.C.), the Department of Defense grant W81XWH-10-0652 and W81XWH-11-1-0337 (to A.M.C.) and the National Center for Functional Genomics supported by the Department of Defense (to A.M.C.). A.M.C. is supported by the Doris Duke Charitable Foundation Clinical Scientist Award, a Burroughs Wellcome Foundation Award in Clinical Translational Research and the Prostate Cancer Foundation. A.M.C. is an American Cancer Society Research Professor. N.P. was supported by a University of Michigan Prostate SPORE Career Development Award. C.A.M. was supported by the American Association of Cancer Research Amgen Fellowship in Clinical/Translational Research, the Canary Foundation and American Cancer Society Early Detection Postdoctoral Fellowship, and a Prostate Cancer Foundation Young Investigator Award. Q.C. was supported by a Department of Defense Postdoctoral Fellowship grant PC094725. J.R.P. was supported by the NIH Cancer Biology Training grant CA009676-18 and the Department of Defense Predoctoral Fellowship W81XWH-10-1-0551. M.K.I. was supported by the Department of Defense Predoctoral Fellowship W81XWH-11-1-0136. J.R.P. and M.K.I. are Fellows of the University of Michigan Medical Scientist Training Program.

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  1. John R Prensner and Matthew K Iyer: These authors contributed equally to this work.

Authors and Affiliations

  1. Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA

    John R Prensner, Matthew K Iyer, O Alejandro Balbin, Saravana M Dhanasekaran, Qi Cao, J Chad Brenner, Irfan A Asangani, Catherine S Grasso, Hal D Kominsky, Xuhong Cao, Xiaojun Jing, Xiaoju Wang, Javed Siddiqui, Daniel Robinson, Nallasivam Palanisamy, Christopher A Maher & Arul M Chinnaiyan

  2. Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA

    Saravana M Dhanasekaran, Nallasivam Palanisamy, Christopher A Maher & Arul M Chinnaiyan

  3. Department of Medicine, University of Chicago, Chicago, Illinois, USA

    Bharathi Laxman

  4. Department of Urology, University of Michigan Medical School, Ann Arbor, Michigan, USA

    John T Wei & Arul M Chinnaiyan

  5. Department of Statistics, Colorado State University, Fort Collins, Colorado, USA

    Hari K Iyer

  6. Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan, USA

    Nallasivam Palanisamy & Arul M Chinnaiyan

  7. Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, Michigan, USA

    Arul M Chinnaiyan

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Contributions

M.K.I., J.R.P. and A.M.C. designed the project and directed experimental studies. M.K.I., O.A.B., C.S.G. and C.A.M. developed computational platforms and performed sequencing data analysis. M.K.I., O.A.B. and H.K.I. performed statistical analyses. J.R.P., S.M.D., J.C.B., Q.C., N.P., H.D.K., B.L., X.W., I.A.A., X.C., X.J. and D.R. performed experimental studies. J.S. and J.T.W. coordinated biospecimens. M.K.I., J.R.P. and A.M.C. interpreted data and wrote the manuscript.

Corresponding author

Correspondence to Arul M Chinnaiyan.

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Competing interests

The University of Michigan has filed for a patent on the detection of gene fusions in prostate cancer, on which A.M.C. is a co-inventor. The diagnostic field of use for ETS gene fusions has been licensed to GenProbe Inc. The University of Michigan has a sponsored research agreement with GenProbe, which is unrelated to this study. GenProbe has had no role in the design or experimentation of this study, nor has it participated in the writing of the manuscript.

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Prensner, J., Iyer, M., Balbin, O. et al. Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression. Nat Biotechnol 29, 742–749 (2011). https://doi.org/10.1038/nbt.1914

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