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The DNA methylation landscape of advanced prostate cancer


Although DNA methylation is a key regulator of gene expression, the comprehensive methylation landscape of metastatic cancer has never been defined. Through whole-genome bisulfite sequencing paired with deep whole-genome and transcriptome sequencing of 100 castration-resistant prostate metastases, we discovered alterations affecting driver genes that were detectable only with integrated whole-genome approaches. Notably, we observed that 22% of tumors exhibited a novel epigenomic subtype associated with hypermethylation and somatic mutations in TET2, DNMT3B, IDH1 and BRAF. We also identified intergenic regions where methylation is associated with RNA expression of the oncogenic driver genes AR, MYC and ERG. Finally, we showed that differential methylation during progression preferentially occurs at somatic mutational hotspots and putative regulatory regions. This study is a large integrated study of whole-genome, whole-methylome and whole-transcriptome sequencing in metastatic cancer that provides a comprehensive overview of the important regulatory role of methylation in metastatic castration-resistant prostate cancer.

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Fig. 1: CpG methylator phenotype.
Fig. 2: DNA methylation valleys.
Fig. 3: Methylation associated with prostate-cancer-specific genes.
Fig. 4: Methylation association with the androgen-response pathway.
Fig. 5: Methylation association with TMPRSS2-ERG and MYC.
Fig. 6: Genome-wide analysis of differential methylation.

Data availability

WGBS, WGS and RNA-seq data are available at dbGAP (phs001648). All figures use these raw data. Processed ChIP–seq and CHIA–PET data were obtained from the Gene Expression Omnibus: GSE114385; GSE96652; GSE120738; GSE28219; GSE70079; GSE14097; GSE54946.

Code availability

All code used in the manuscript is available at


  1. 1.

    Jones, P. A. & Baylin, S. B. The fundamental role of epigenetic events in cancer. Nat. Rev. Genet. 3, 415–428 (2002).

    CAS  PubMed  Google Scholar 

  2. 2.

    Feinberg, A. P., Koldobskiy, M. A. & Gondor, A. Epigenetic modulators, modifiers and mediators in cancer aetiology and progression. Nat. Rev. Genet. 17, 284–299 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  3. 3.

    Okano, M., Bell, D. W., Haber, D. A. & Li, E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99, 247–257 (1999).

    CAS  PubMed  Google Scholar 

  4. 4.

    Rechache, N. S. et al. DNA methylation profiling identifies global methylation differences and markers of adrenocortical tumors. J. Clin. Endocrinol. Metab. 97, E1004–E1013 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  5. 5.

    Skvortsova, K. et al. DNA hypermethylation encroachment at CpG island borders in cancer is predisposed by H3K4 monomethylation patterns. Cancer Cell 35, 297–314.e8 (2019).

    CAS  PubMed  Google Scholar 

  6. 6.

    Saghafinia, S., Mina, M., Riggi, N., Hanahan, D. & Ciriello, G. Pan-cancer landscape of aberrant DNA methylation across human tumors. Cell Rep. 25, 1066–1080.e8 (2018).

    CAS  PubMed  Google Scholar 

  7. 7.

    Kobayashi, Y. et al. DNA methylation profiling reveals novel biomarkers and important roles for DNA methyltransferases in prostate cancer. Genome Res. 21, 1017–1027 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  8. 8.

    Kim, J. H. et al. Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer. Genome Res. 21, 1028–1041 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  9. 9.

    Maruyama, R. et al. Aberrant promoter methylation profile of prostate cancers and its relationship to clinicopathological features. Clin. Cancer Res. 8, 514–519 (2002).

    CAS  PubMed  Google Scholar 

  10. 10.

    Bhasin, J. M. et al. Methylome-wide sequencing detects DNA hypermethylation distinguishing indolent from aggressive prostate Cancer. Cell Rep. 13, 2135–2146 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  11. 11.

    Yu, Y. P. et al. Whole-genome methylation sequencing reveals distinct impact of differential methylations on gene transcription in prostate cancer. Am. J. Pathol. 183, 1960–1970 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. 12.

    Cancer Genome Atlas Research Network The molecular taxonomy of primary prostate cancer. Cell 163, 1011–1025 (2015).

    Google Scholar 

  13. 13.

    Borno, S. T. et al. Genome-wide DNA methylation events in TMPRSS2–ERG fusion-negative prostate cancers implicate an EZH2-dependent mechanism with miR-26a hypermethylation. Cancer Discov. 2, 1024–1035 (2012).

    PubMed  Google Scholar 

  14. 14.

    Gerhauser, C. et al. Molecular evolution of early-onset prostate cancer identifies molecular risk markers and clinical trajectories. Cancer Cell 34, 996–1011.e8 (2018).

    CAS  PubMed  Google Scholar 

  15. 15.

    Yegnasubramanian, S. et al. Hypermethylation of CpG islands in primary and metastatic human prostate cancer. Cancer Res. 64, 1975–1986 (2004).

    CAS  PubMed  Google Scholar 

  16. 16.

    Robinson, D. et al. Integrative clinical genomics of advanced prostate cancer. Cell 161, 1215–1228 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  17. 17.

    Quigley, D. A. et al. Genomic hallmarks and structural variation in metastatic prostate. Cell 174, 758–769.e9 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  18. 18.

    Viswanathan, S. R. et al. Structural alterations driving castration-resistant prostate cancer revealed by linked-read genome sequencing. Cell 174, 433–447.e19 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  19. 19.

    Fraser, M. et al. Genomic hallmarks of localized, non-indolent prostate cancer. Nature 541, 359–364 (2017).

    CAS  PubMed  Google Scholar 

  20. 20.

    Beltran, H. et al. Divergent clonal evolution of castration-resistant neuroendocrine prostate cancer. Nat. Med. 22, 298–305 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  21. 21.

    Aryee, M. J. et al. DNA methylation alterations exhibit intraindividual stability and interindividual heterogeneity in prostate cancer metastases. Sci. Transl. Med. 5, 169ra10 (2013).

    PubMed  PubMed Central  Google Scholar 

  22. 22.

    Hama, N. et al. Epigenetic landscape influences the liver cancer genome architecture. Nat. Commun. 9, 1643 (2018).

    PubMed  PubMed Central  Google Scholar 

  23. 23.

    Kretzmer, H. et al. DNA methylome analysis in Burkitt and follicular lymphomas identifies differentially methylated regions linked to somatic mutation and transcriptional control. Nat. Genet. 47, 1316–1325 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  24. 24.

    Kulis, M. et al. Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia. Nat. Genet. 44, 1236–1242 (2012).

    CAS  PubMed  Google Scholar 

  25. 25.

    Berman, B. P. et al. Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains. Nat. Genet. 44, 40–46 (2011).

    PubMed  PubMed Central  Google Scholar 

  26. 26.

    Klughammer, J. et al. The DNA methylation landscape of glioblastoma disease progression shows extensive heterogeneity in time and space. Nat. Med. 24, 1611–1624 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  27. 27.

    Queiros, A. C. et al. Decoding the DNA methylome of mantle cell lymphoma in the light of the entire B cell lineage. Cancer Cell 30, 806–821 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  28. 28.

    Hovestadt, V. et al. Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing. Nature 510, 537–541 (2014).

    CAS  PubMed  Google Scholar 

  29. 29.

    McDonald, O. G. et al. Epigenomic reprogramming during pancreatic cancer progression links anabolic glucose metabolism to distant metastasis. Nat. Genet. 49, 367–376 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  30. 30.

    Chun, H. E. et al. Genome-wide profiles of extra-cranial malignant rhabdoid tumors reveal heterogeneity and dysregulated developmental pathways. Cancer Cell 29, 394–406 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  31. 31.

    Spencer, D. H. et al. CpG island hypermethylation mediated by DNMT3A is a consequence of AML progression. Cell 168, 801–816.e13 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  32. 32.

    Hughes, L. A. et al. The CpG island methylator phenotype: what’s in a name? Cancer Res. 73, 5858–5868 (2013).

    CAS  PubMed  Google Scholar 

  33. 33.

    Takeda, D. Y. et al. A somatically acquired enhancer of the androgen receptor is a noncoding driver in advanced prostate cancer. Cancer Cell 174, 422–432.e13 (2018).

    CAS  Google Scholar 

  34. 34.

    Kron, K. J. et al. TMPRSS2–ERG fusion co-opts master transcription factors and activates NOTCH signaling in primary prostate cancer. Nat. Genet. 49, 1336–1345 (2017).

    CAS  PubMed  Google Scholar 

  35. 35.

    Stelloo, S. et al. Integrative epigenetic taxonomy of primary prostate cancer. Nat. Commun. 9, 4900 (2018).

    PubMed  PubMed Central  Google Scholar 

  36. 36.

    Sharma, N. L. et al. The androgen receptor induces a distinct transcriptional program in castration-resistant prostate cancer in man. Cancer Cell 23, 35–47 (2013).

    CAS  PubMed  Google Scholar 

  37. 37.

    Pomerantz, M. M. et al. The androgen receptor cistrome is extensively reprogrammed in human prostate tumorigenesis. Nat. Genet. 47, 1346–1351 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  38. 38.

    Yu, J. et al. An integrated network of androgen receptor, polycomb, and TMPRSS2ERG gene fusions in prostate cancer progression. Cancer Cell 17, 443–454 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  39. 39.

    Zhang, Z. et al. An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells. Genome Res. 29, 223–235 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  40. 40.

    Sun, W. et al. The association between copy number aberration, DNA methylation and gene expression in tumor samples. Nucleic Acids Res. 46, 3009–3018 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  41. 41.

    Gardiner-Garden, M. & Frommer, M. CpG islands in vertebrate genomes. J. Mol. Biol. 196, 261–282 (1987).

    CAS  PubMed  Google Scholar 

  42. 42.

    Saxonov, S., Berg, P. & Brutlag, D. L. A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc. Natl Acad. Sci. USA 103, 1412–1417 (2006).

    CAS  PubMed  Google Scholar 

  43. 43.

    Ioshikhes, I. P. & Zhang, M. Q. Large-scale human promoter mapping using CpG islands. Nat. Genet. 26, 61–63 (2000).

    CAS  PubMed  Google Scholar 

  44. 44.

    Aggarwal, R. R. et al. Whole-genome and transcriptional analysis of treatment-emergent small-cell neuroendocrine prostate cancer demonstrates intraclass heterogeneity. Mol. Cancer Res. 17, 1235–1240 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  45. 45.

    Aggarwal, R. et al. Clinical and genomic characterization of treatment-emergent small-cell neuroendocrine prostate cancer: a multi-institutional prospective study. J. Clin. Oncol. 36, 2492–2503 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  46. 46.

    Hennig, C. Cluster-wise assessment of cluster stability. Comput. Stat. Data Anal. 52, 258–271 (2007).

    Google Scholar 

  47. 47.

    Weisenberger, D. J. et al. CpG island methylator phenotype underlies sporadic microsatellite instability and is tightly associated with BRAF mutation in colorectal cancer. Nat. Genet. 38, 787–793 (2006).

    CAS  PubMed  Google Scholar 

  48. 48.

    Figueroa, M. E. et al. Leukemic IDH1 and IDH2 mutations result in a hypermethylation phenotype, disrupt TET2 function, and impair hematopoietic differentiation. Cancer Cell 18, 553–567 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  49. 49.

    Buscarlet, M. et al. DNMT3A and TET2 dominate clonal hematopoiesis and demonstrate benign phenotypes and different genetic predispositions. Blood 130, 753–762 (2017).

    CAS  PubMed  Google Scholar 

  50. 50.

    Delhommeau, F. et al. Mutation in TET2 in myeloid cancers. N. Engl. J. Med 360, 2289–2301 (2009).

    PubMed  Google Scholar 

  51. 51.

    Langemeijer, S. M. et al. Acquired mutations in TET2 are common in myelodysplastic syndromes. Nat. Genet. 41, 838–842 (2009).

    CAS  PubMed  Google Scholar 

  52. 52.

    Dong, C. et al. Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies. Hum. Mol. Genet. 24, 2125–2137 (2015).

    CAS  PubMed  Google Scholar 

  53. 53.

    Wong, T. N. et al. Cellular stressors contribute to the expansion of hematopoietic clones of varying leukemic potential. Nat. Commun. 9, 455 (2018).

    PubMed  PubMed Central  Google Scholar 

  54. 54.

    Odejide, O. et al. A targeted mutational landscape of angioimmunoblastic T-cell lymphoma. Blood 123, 1293–1296 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  55. 55.

    Coolen, M. W. et al. Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity. Nat. Cell Biol. 12, 235–246 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  56. 56.

    Bert, S. A. et al. Regional activation of the cancer genome by long-range epigenetic remodeling. Cancer Cell 23, 9–22 (2013).

    CAS  PubMed  Google Scholar 

  57. 57.

    Zhou, W. et al. DNA methylation loss in late-replicating domains is linked to mitotic cell division. Nat. Genet. 50, 591–602 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  58. 58.

    Brinkman, A. B. et al. Partially methylated domains are hypervariable in breast cancer and fuel widespread CpG island hypermethylation. Nat. Commun. 10, 1749 (2019).

    PubMed  PubMed Central  Google Scholar 

  59. 59.

    Xie, W. et al. Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell 153, 1134–1148 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  60. 60.

    Jeong, M. et al. Large conserved domains of low DNA methylation maintained by Dnmt3a. Nat. Genet. 46, 17–23 (2014).

    CAS  PubMed  Google Scholar 

  61. 61.

    Li, Y. et al. Genome-wide analyses reveal a role of Polycomb in promoting hypomethylation of DNA methylation valleys. Genome Biol. 19, 18 (2018).

    PubMed  PubMed Central  Google Scholar 

  62. 62.

    Kumar, A. et al. Substantial interindividual and limited intraindividual genomic diversity among tumors from men with metastatic prostate cancer. Nat. Med. 22, 369–378 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  63. 63.

    Mu, P. et al. SOX2 promotes lineage plasticity and antiandrogen resistance in TP53- and RB1-deficient prostate cancer. Science 355, 84–88 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  64. 64.

    Beltran, H. et al. The role of lineage plasticity in prostate cancer therapy resistance. Clin. Cancer Res. 25, 6916–6924 (2019).

    PubMed  PubMed Central  Google Scholar 

  65. 65.

    Jones, P. A. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat. Rev. Genet. 13, 484–492 (2012).

    CAS  PubMed  Google Scholar 

  66. 66.

    Pacis, A. et al. Gene activation precedes DNA demethylation in response to infection in human dendritic cells. Proc. Natl Acad. Sci. USA 116, 6938–6943 (2019).

    CAS  PubMed  Google Scholar 

  67. 67.

    Teschendorff, A. E. et al. DNA methylation outliers in normal breast tissue identify field defects that are enriched in cancer. Nat. Commun. 7, 10478 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  68. 68.

    Yang, X. et al. Gene body methylation can alter gene expression and is a therapeutic target in cancer. Cancer Cell 26, 577–590 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  69. 69.

    Massie, C. E., Mills, I. G. & Lynch, A. G. The importance of DNA methylation in prostate cancer development. J. Steroid Biochem. Mol. Biol. 166, 1–15 (2017).

    CAS  PubMed  Google Scholar 

  70. 70.

    Gery, S., Sawyers, C. L., Agus, D. B., Said, J. W. & Koeffler, H. P. TMEFF2 is an androgen-regulated gene exhibiting antiproliferative effects in prostate cancer cells. Oncogene 21, 4739–4746 (2002).

    CAS  PubMed  Google Scholar 

  71. 71.

    Qian, X. et al. Spondin-2 (SPON2), a more prostate-cancer-specific diagnostic biomarker. PLoS One 7, e37225 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  72. 72.

    Boormans, J. L. et al. Identification of TDRD1 as a direct target gene of ERG in primary prostate cancer. Int. J. Cancer 133, 335–345 (2013).

    CAS  PubMed  Google Scholar 

  73. 73.

    Xu, J. et al. Identification and characterization of prostein, a novel prostate-specific protein. Cancer Res. 61, 1563–1568 (2001).

    CAS  PubMed  Google Scholar 

  74. 74.

    Prensner, J. R. et al. RNA biomarkers associated with metastatic progression in prostate cancer: a multi-institutional high-throughput analysis of SChLAP1. Lancet Oncol. 15, 1469–1480 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  75. 75.

    White, N. M. et al. Multi-institutional analysis shows that low PCAT-14 expression associates with poor outcomes in prostate cancer. Eur. Urol. 71, 257–266 (2017).

    CAS  PubMed  Google Scholar 

  76. 76.

    Eisenberg, E. & Levanon, E. Y. Human housekeeping genes, revisited. Trends Genet. 29, 569–574 (2013).

    CAS  PubMed  Google Scholar 

  77. 77.

    Liberzon, A. et al. The Molecular Signatures Database (MSigDB) hallmark gene set collection. Cell Syst. 1, 417–425 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  78. 78.

    Zhao, S. G. et al. The immune landscape of prostate cancer and nomination of PD-L2 as a potential therapeutic target. J. Natl. Cancer Inst. 111, 301–310 (2019).

    PubMed  Google Scholar 

  79. 79.

    Tomlins, S. A. et al. Role of the TMPRSS2ERG gene fusion in prostate cancer. Neoplasia 10, 177–188 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  80. 80.

    Domcke, S. et al. Competition between DNA methylation and transcription factors determines binding of NRF1. Nature 528, 575–579 (2015).

    CAS  PubMed  Google Scholar 

  81. 81.

    Feldmann, A. et al. Transcription factor occupancy can mediate active turnover of DNA methylation at regulatory regions. PLoS Genet. 9, e1003994 (2013).

    PubMed  PubMed Central  Google Scholar 

  82. 82.

    Yin, Y. et al. Impact of cytosine methylation on DNA binding specificities of human transcription factors.Science 356, eaaj2239 (2017).

    PubMed  Google Scholar 

  83. 83.

    Cho, S. W. et al. Promoter of lncRNA gene PVT1 is a tumor-suppressor DNA boundary element. Cell 173, 1398–1412.e22 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  84. 84.

    Bell, R. E. et al. Enhancer methylation dynamics contribute to cancer plasticity and patient mortality. Genome Res. 26, 601–611 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  85. 85.

    Yegnasubramanian, S. et al. DNA hypomethylation arises later in prostate cancer progression than CpG island hypermethylation and contributes to metastatic tumor heterogeneity. Cancer Res. 68, 8954–8967 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  86. 86.

    Kulis, M. & Esteller, M. DNA methylation and cancer. Adv. Genet. 70, 27–56 (2010).

    PubMed  Google Scholar 

  87. 87.

    Chen, R. Z., Pettersson, U., Beard, C., Jackson-Grusby, L. & Jaenisch, R. DNA hypomethylation leads to elevated mutation rates. Nature 395, 89–93 (1998).

    CAS  PubMed  Google Scholar 

  88. 88.

    Zhao, S. G. et al. Associations of luminal and basal subtyping of prostate cancer with prognosis and response to androgen deprivation therapy. JAMA Oncol. 3, 1663–1672 (2017).

    PubMed  PubMed Central  Google Scholar 

  89. 89.

    Yamazaki, J. et al. TET2 mutations affect non-CpG island DNA methylation at enhancers and transcription factor-binding sites in chronic myelomonocytic leukemia. Cancer Res. 75, 2833–2843 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  90. 90.

    Yamazaki, J. et al. Effects of TET2 mutations on DNA methylation in chronic myelomonocytic leukemia. Epigenetics 7, 201–207 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  91. 91.

    Ko, M. et al. Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2. Nature 468, 839–843 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  92. 92.

    Rasmussen, K. D. et al. Loss of TET2 in hematopoietic cells leads to DNA hypermethylation of active enhancers and induction of leukemogenesis. Genes Dev. 29, 910–922 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  93. 93.

    Liao, J. et al. Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells. Nat. Genet. 47, 469–478 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  94. 94.

    Duymich, C. E., Charlet, J., Yang, X., Jones, P. A. & Liang, G. DNMT3B isoforms without catalytic activity stimulate gene body methylation as accessory proteins in somatic cells. Nat. Commun. 7, 11453 (2016).

    PubMed  PubMed Central  Google Scholar 

  95. 95.

    Itzykson, R. et al. Impact of TET2 mutations on response rate to azacitidine in myelodysplastic syndromes and low blast count acute myeloid leukemias. Leukemia 25, 1147–1152 (2011).

    CAS  PubMed  Google Scholar 

  96. 96.

    Bejar, R. et al. TET2 mutations predict response to hypomethylating agents in myelodysplastic syndrome patients. Blood 124, 2705–2712 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  97. 97.

    Brocks, D. et al. Intratumor DNA methylation heterogeneity reflects clonal evolution in aggressive prostate cancer. Cell Rep. 8, 798–806 (2014).

    CAS  PubMed  Google Scholar 

  98. 98.

    Krueger, F. & Andrews, S. R. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27, 1571–1572 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  99. 99.

    Burger, L., Gaidatzis, D., Schubeler, D. & Stadler, M. B. Identification of active regulatory regions from DNA methylation data. Nucleic Acids Res. 41, e155 (2013).

    PubMed  PubMed Central  Google Scholar 

  100. 100.

    Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923–930 (2014).

    CAS  Google Scholar 

  101. 101.

    Roller, E., Ivakhno, S., Lee, S., Royce, T. & Tanner, S. Canvas: versatile and scalable detection of copy number variants. Bioinformatics 32, 2375–2377 (2016).

    CAS  PubMed  Google Scholar 

  102. 102.

    Yoshihara, K. et al. Inferring tumour purity and stromal and immune cell admixture from expression data. Nat. Commun. 4, 2612 (2013).

    PubMed  PubMed Central  Google Scholar 

  103. 103.

    Sanchez-Vega, F. et al. Oncogenic signaling pathways in The Cancer Genome Atlas. Cell 173, 321–337.e10 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  104. 104.

    Bailey, M. H. et al. Comprehensive characterization of cancer driver genes and mutations. Cell 173, 371–385.e18 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  105. 105.

    Goldman, M. et al. The UCSC Cancer Genomics Browser: update 2015. Nucleic Acids Res. 43, D812–D817 (2015).

    CAS  PubMed  Google Scholar 

  106. 106.

    Faraway, J. J Linear Models with R (Taylor & Francis, 2014).

  107. 107.

    Wu, H. et al. Detection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates. Nucleic Acids Res. 43, e141 (2015).

    PubMed  PubMed Central  Google Scholar 

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We thank the patients who selflessly contributed samples to this study and without whom this research would not have been possible. We would also like to acknowledge the assistance of Steven Kronenberg and Barbara Panning. This research was supported by a Stand Up To Cancer-Prostate Cancer Foundation Prostate Cancer Dream Team Award (SU2C-AACR-DT0812 to E.J.S.) and by the Movember Foundation. Stand Up To Cancer is a division of the Entertainment Industry Foundation. This research grant was administered by the American Association for Cancer Research, the scientific partner of SU2C. S.G.Z., D.A.Q., Hui Li, R.A., J.T.H., R.B. and R.Y. were funded by Prostate Cancer Foundation Young Investigator Awards. F.Y.F. was funded by Prostate Cancer Foundation Challenge Awards. Additional funding was provided by a UCSF Benioff Initiative for Prostate Cancer Research award. F.Y.F. and A.A. were supported by National Institutes of Health (NIH)/National Cancer Institute (NCI) 1R01CA230516-01. F.Y.F. and N.M. were supported by NIH/NCI 1R01CA227025 and Prostate Cancer Foundation (PCF) 17CHAL06. F.Y.F. and A.M.C. were supported by NIH P50CA186786. A.M.C. is supported by NIH R35CA231996 and U01CA214170. D.A.Q. was funded by a BRCA Foundation Young Investigator Award. M.S. was supported by the Swedish Research Council (Vetenskapsrådet) with grant number 2018–00382 and the Swedish Society of Medicine (Svenska Läkaresällskapet). L.A.G. was supported by K99/R00 CA204602 and DP2 CA239597, as well as the Goldberg-Benioff Endowed Professorship in Prostate Cancer Translational Biology. P.C.B. was supported by the NIH/NCI under award number P30CA016042 and by an operating grant from the National Cancer Institute Early Detection Research Network (1U01CA214194-01).

Author information




S.G.Z., W.S.C., E.J.S., D.A.Q. and F.Y.F. conceived and designed the study. S.G.Z., Haolong Li, A.F., R.A., D.P., J.J.A., R.D., T.J.B., A.M.B., E.C., T.M.B., G.T., K.N.C., M.G., A.Z., R.E.R., M.B.R., O.W., M.Y.K., P.N.L., C.P.E., P.F., S.B., J.H., J.F.C., J.L., A.W.W., K.F., E.J.S., D.A.Q. and F.Y.F. acquired the data. S.G.Z., W.S.C., Haolong Li, M.Z., M.S., R.A., A.L., R.D., J.C., J.T.H., M.P., H.X.D., R.Y., R.M.-B., L.Z., M.A., S.L.C., K.E.H., Y.J.S., M.Y.K., L.F., D.E.S., T.M.M., R.B., F.W.H., Hui Li, L.C., T.S., H.G., I.A.A., S.S., J.M.L., N.M., K.E.K., H.H.H., W.Z., S.A.T., A.W.W., S.M.D., A.A., L.A.G., P.C.B., A.M.C., C.A.M., E.J.S., D.A.Q. and F.Y.F. analysed and interpreted the data. All authors drafted the article or revised it critically for important intellectual content. All authors approved the final version of the manuscript.

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Correspondence to Felix Y. Feng.

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Competing interests

P.F., S.B., K.F. and A.L. are employees of Illumina Inc., which provided material support for this project. No other commercial entities contributed to or played a role in the writing of this article. J.M.L. holds equity in Salus Discovery, LLC. L.F. has funding from BMS, Abbvie, Janssen, Roche/Genentech and Merck. O.W. currently has consulting, equity and/or board relationships with Trethera Corporation, Kronos Biosciences, Sofie Biosciences, Breakthrough Properties, Vida Ventures, Nanmi Therapeutics and Allogene Therapeutics. The University of Michigan and Brigham and Women’s Hospital have been issued patents on ETS gene fusions in prostate cancer, on which S.A.T. is a co-inventor. The diagnostic field of use was licensed to Hologic/Gen-Probe Inc., which has sublicensed rights to Roche/Ventana Medical Systems. S.A.T. has served as a consultant for and received honoraria from Janssen, AbbVie, Sanofi, Almac Diagnostics and Astellas/Medivation. S.A.T. has sponsored research agreements with Astellas/Medivation and GenomeDX. S.A.T. is a cofounder, previous consultant for and current employee of Strata Oncology. T.M.B. has research funding from Alliance Foundation Trials, Boehringer Ingelheim, Concept Therapeutics, Endocyte Inc., Janssen R&D, Medivation Inc./Astellas, oncoGenex, Sotio and Theraclone Sciences/OncoResponse. T.M.B. has received consulting fees from AbbVie, AstraZeneca, Astellas Pharma, Bayer, Boehringer Ingelheim, Clovis Oncology, GlaxoSmithKline, Janssen Biotech, Janssen Japan, Merck and Pfizer. T.M.B. holds stock in Salarius Pharmaceuticals. M.R. reports consulting and Speakers’ Bureau for Johnson & Johnson, research funding from Novartis, research support from Merck and Astellas/Medivation, and a provisional patent with UCLA on the development of small-molecule inhibitors of the androgen receptor N-terminal domain. J.J.A. has consulted for or held advisory roles at Astellas Pharma, Bayer and Janssen Biotech Inc. He has received research funding from Aragon Pharmaceuticals Inc., Astellas Pharma, Novartis, Zenith Epigenetics Ltd. and Gilead Sciences Inc. A.A. is a co-founder of Tango Therapeutics, Azkarra Therapeutics and Ovibio Corporation; is a consultant for SPARC, Bluestar, ProLynx, Earli, Cura, GenVivo and GSK; is a member of the SAB of Genentech and GLAdiator; receives grant/research support from SPARC and AstraZeneca; and holds patents on the use of PARP inhibitors held jointly with AstraZeneca, from which he has benefitted financially (and may do so in the future). F.Y.F. has consulted for Astellas, Bayer, BlueEarth Diagnostics, Celgene, Clovis, EMD Serono, Genentech, Janssen, Myovant, Ryovant and Sanofi, and is a co-founder and has an ownership stake in PFS Genomics. S.L.C. is in a leadership role at PFS Genomics. S.G.Z., S.L.C. and F.Y.F. have patent applications with Decipher Biosciences on molecular signatures in prostate cancer unrelated to this work. S.G.Z. and F.Y.F. have a patent application for a molecular signature in breast cancer unrelated to this work and licensed to PFS Genomics. S.G.Z. and F.Y.F. have patent applications with Celgene unrelated to this work.

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Zhao, S.G., Chen, W.S., Li, H. et al. The DNA methylation landscape of advanced prostate cancer. Nat Genet 52, 778–789 (2020).

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