The androgen receptor cistrome is extensively reprogrammed in human prostate tumorigenesis

Nature Genetics

Volumn 47, Issue 11, 2015, Pages 1346-1351

  Pomerantz, Mark M ^a   Li, Fugen ^b   Takeda, David Y ^a,c   Lenci, Romina ^a   Chonkar, Apurva ^a   Chabot, Matthew ^a   Cejas, Paloma ^a,b   Vazquez, Francisca ^c   Cook, Jennifer ^a   Shivdasani, Ramesh A ^a,b   Bowden, Michaela ^d   Lis, Rosina ^d   Hahn, William C ^a,c   Kantoff, Philip W ^a   Brown, Myles ^a,b   Loda, Massimo ^a,c,d   Long, Henry W ^a,b   Freedman, Matthew L ^a,b,c  

^a HARVARD MEDICAL SCHOOL   (United States)

^b DANA FARBER CANCER INSTITUTE   (United States)

^c BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^d BRIGHAM AND WOMEN S HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANDROGEN RECEPTOR; HEPATOCYTE NUCLEAR FACTOR 3ALPHA; HOXB13 PROTEIN; MESSENGER RNA; PROTEIN; UNCLASSIFIED DRUG; AR PROTEIN, HUMAN; FOXA1 PROTEIN, HUMAN; HOMEODOMAIN PROTEIN; HOXB13 PROTEIN, HUMAN; PROTEIN BINDING; TRANSCRIPTOME;

ARTICLE; CANCER CELL CULTURE; CARCINOGENESIS; CONTROLLED STUDY; DOWN REGULATION; HUMAN; HUMAN CELL; HUMAN TISSUE; MALE; PRIORITY JOURNAL; PROSTATE CANCER; PROSTATE CARCINOGENESIS; PROSTATE EPITHELIUM; PROTEIN BINDING; PROTEIN LOCALIZATION; BINDING SITE; CELL TRANSFORMATION; CHROMATIN IMMUNOPRECIPITATION; CLUSTER ANALYSIS; DNA SEQUENCE; GENETICS; GENOME-WIDE ASSOCIATION STUDY; IMMUNOBLOTTING; KAPLAN MEIER METHOD; METABOLISM; PATHOLOGY; PROCEDURES; PROSTATE; PROSTATE TUMOR; RNA INTERFERENCE; TUMOR CELL LINE;

BINDING SITES; CARCINOGENESIS; CELL LINE, TUMOR; CELL TRANSFORMATION, NEOPLASTIC; CHROMATIN IMMUNOPRECIPITATION; CLUSTER ANALYSIS; GENOME-WIDE ASSOCIATION STUDY; HEPATOCYTE NUCLEAR FACTOR 3-ALPHA; HOMEODOMAIN PROTEINS; HUMANS; IMMUNOBLOTTING; KAPLAN-MEIER ESTIMATE; MALE; PROSTATE; PROSTATIC NEOPLASMS; PROTEIN BINDING; RECEPTORS, ANDROGEN; RNA INTERFERENCE; SEQUENCE ANALYSIS, DNA; TRANSCRIPTOME;

EID: 84945487712     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.3419     Document Type: Article

References (36)

1. Whyte, W.A., et al. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell 153, 307-319 (2013).
2. ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).
3. Lupien, M., & Brown, M. Cistromics of hormone-dependent cancer. Endocr. Relat. Cancer 16, 381-389 (2009).
4. Thompson, I.M., et al. The influence of finasteride on the development of prostate cancer. N. Engl. J. Med. 349, 215-224 (2003).
5. Huggins, C. Endocrine-induced regression of cancers. Cancer Res. 27, 1925-1930 (1967).
6. Berger, M.F., et al. The genomic complexity of primary human prostate cancer. Nature 470, 214-220 (2011).
7. Barbieri, C.E., et al. Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer. Nat. Genet. 44, 685-689 (2012).
8. Augello, M.A., Den, R.B., & Knudsen, K.E. AR function in promoting metastatic prostate cancer. Cancer Metastasis Rev. 33, 399-411 (2014).
9. Mills, I.G. Maintaining and reprogramming genomic androgen receptor activity in prostate cancer. Nat. Rev. Cancer 14, 187-198 (2014).
10. Robinson, J.L., et al. Elevated levels of FOXA1 facilitate androgen receptor chromatin binding resulting in a CRPC-like phenotype. Oncogene 33, 5666-5674 (2014).
11. Chen, Y., et al. ETS factors reprogram the androgen receptor cistrome and prime prostate tumorigenesis in response to PTEN loss. Nat. Med. 19, 1023-1029 (2013).
12. Sampson, N., Neuwirt, H., Puhr, M., Klocker, H., & Eder, I.E. In vitro model systems to study androgen receptor signaling in prostate cancer. Endocr. Relat. Cancer 20, R49-R64 (2013).
13. Feng, J., Liu, T., Qin, B., Zhang, Y., & Liu, X.S. Identifying ChIP-seq enrichment using MACS. Nat. Protoc. 7, 1728-1740 (2012).
14. Langmead, B., Trapnell, C., Pop, M., & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
15. 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).
16. He, H.H., et al. Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics. Genome Res. 22, 1015-1025 (2012).
17. Massie, C.E., et al. The androgen receptor fuels prostate cancer by regulating central metabolism and biosynthesis. EMBO J. 30, 2719-2733 (2011).
18. 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).
19. Berger, R., et al. Androgen-induced differentiation and tumorigenicity of human prostate epithelial cells. Cancer Res. 64, 8867-8875 (2004).
20. Taylor, B.S., et al. Integrative genomic profiling of human prostate cancer. Cancer Cell 18, 11-22 (2010).
21. Glinsky, G.V., Glinskii, A.B., Stephenson, A.J., Hoffman, R.M., & Gerald, W.L. Gene expression profiling predicts clinical outcome of prostate cancer. J. Clin. Invest. 113, 913-923 (2004).
22. Wang, D., et al. Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. Nature 474, 390-394 (2011).
23. Jin, H.J., Zhao, J.C., Wu, L., Kim, J., & Yu, J. Cooperativity and equilibrium with FOXA1 define the androgen receptor transcriptional program. Nat. Commun. 5, 3972 (2014).
24. Wang, Q., et al. Androgen receptor regulates a distinct transcription program in androgen-independent prostate cancer. Cell 138, 245-256 (2009).
25. Economides, K.D., & Capecchi, M.R. Hoxb13 is required for normal differentiation and secretory function of the ventral prostate. Development 130, 2061-2069 (2003).
26. Ewing, C.M., et al. Germline mutations in HOXB13 and prostate-cancer risk. N. Engl. J. Med. 366, 141-149 (2012).
27. Xu, J., et al. HOXB13 is a susceptibility gene for prostate cancer: results from the International Consortium for Prostate Cancer Genetics (ICPCG). Hum. Genet. 132, 5-14 (2013).
28. Zhang, Y., et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).
29. Smyth, G.K. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3, Article3 (2004).
30. Liu, T., et al. Cistrome: an integrative platform for transcriptional regulation studies. Genome Biol. 12, R83 (2011).
31. Heinz, S., et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576-589 (2010).
32. Bolstad, B.M., Irizarry, R.A., Astrand, M., & Speed, T.P. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19, 185-193 (2003).
33. Huang, Q., et al. A prostate cancer susceptibility allele at 6q22 increases RFX6 expression by modulating HOXB13 chromatin binding. Nat. Genet. 46, 126-135 (2014).
34. Dobin, A., et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15-21 (2013).
35. Trapnell, C., et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protoc. 7, 562-578 (2012).
36. Shao, D.D., et al. ATARiS: computational quantification of gene suppression phenotypes from multisample RNAi screens. Genome Res. 23, 665-678 (2013).