Acevedo, V. D., Gangula, R. D., Freeman, K. W., Li, R. L., Zhang, Y. Y., Wang, F., Ayala, G. E., Peterson, L. E., Ittmann, M., and Spencer, D. M. (2007). Inducible FGFR-1 activation leads to irreversible prostate adenocarcinoma and an epithelial-to-mesenchymal transition. Cancer Cell 12, 559-571.
Alumkal, J. J., Sun, D. C., Lu, E., Beer, T. M., Thomas, G. V., Latour, E., Aggarwal, R., Cetnar, J., Ryan, C. J., Tabatabaei, S., et al. (2020). Transcriptional profiling identifies an androgen receptor activity-low, stemness program associated with enzalutamide resistance. P Natl Acad Sci USA 117, 12315-12323.
Aparicio, A. M., Shen, L., Tapia, E. L., Lu, J. F., Chen, H. C., Zhang, J., Wu, G., Wang, X., Troncoso, P., Corn, P., et al. (2016). Combined Tumor Suppressor Defects Characterize Clinically Defined Aggressive Variant Prostate Cancers. Clin Cancer Res 22, 1520-1530.
Arozarena, I., and Wellbrock, C. (2019). Phenotype plasticity as enabler of melanoma progression and therapy resistance. Nat Rev Cancer 19, 377-391.
Attard, G., Parker, C., Eeles, R. A., Schroder, F., Tomlins, S. A., Tannock, I., Drake, C. G., and de Bono, J. S. (2016). Prostate cancer. Lancet 387, 70-82.
Azare, J., Leslie, K., Al-Ahmadie, H., Gerald, W., Weinreb, P. H., Violette, S. M., and Bromberg, J. (2007). Constitutively activated Stat3 induces tumorigenesis and enhances cell motility of prostate epithelial cells through integrin beta 6. Mol Cell Biol 27, 4444-4453.
Bass, A. J., Watanabe, H., Mermel, C. H., Yu, S. Y., Perner, S., Verhaak, R. G., Kim, S. Y., Wardwell, L., Tamayo, P., Gat-Viks, I., et al. (2009). SOX2 is an amplified lineage-survival oncogene in lung and esophageal squamous cell carcinomas. Nat Genet 41, 1238-U1105.
Beltran, H., Rickman, D. S., Park, K., Chae, S. S., Sboner, A., MacDonald, T. Y., Wang, Y., Sheikh, K. L., Terry, S., Tagawa, S. T., et al. (2011). Molecular characterization of neuroendocrine prostate cancer and identification of new drug targets. Cancer Discov 1, 487-495.
Bierie, B., Pierce, S. E., Kroeger, C., Stover, D. G., Pattabiraman, D. R., Thiru, P., Liu Donaher, J., Reinhardt, F., Chaffer, C. L., Keckesova, Z., and Weinberg, R. A. (2017). Integrin-beta4 identifies cancer stem cell-enriched populations of partially mesenchymal carcinoma cells. Proc Natl Acad Sci U S A 114, E2337-E2346.
Blondel, V. D., Guillaume, J.-L., Lambiotte, R., and Lefebvre, E. (2008). Fast unfolding of communities in large networks. Journal of Statistical Mechanics: Theory and Experiment 2008, 10008.
Bluemn, E. G., Coleman, I. M., Lucas, J. M., Coleman, R. T., Hernandez-Lopez, S., Tharakan, R., Bianchi-Frias, D., Dumpit, R. F., Kaipainen, A., Corella, A. N., et al. (2017). Androgen Receptor Pathway-Independent Prostate Cancer Is Sustained through FGF Signaling. Cancer Cell 32, 474-+.
Bolger, A. M., Lohse, M., and Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114-2120.
Boroviak, T., Loos, R., Lombard, P., Okahara, J., Behr, R., Sasaki, E., Nichols, J., Smith, A., and Bertone, P. (2015). Lineage-Specific Profiling Delineates the Emergence and Progression of Naive Pluripotency in Mammalian Embryogenesis. Dev Cell 35, 366-382.
Boumahdi, S., and de Sauvage, F. J. (2020). The great escape: tumour cell plasticity in resistance to targeted therapy. Nat Rev Drug Discov 19, 39-56.
Boutros, P. C., Fraser, M., Harding, N. J., de Borja, R., Trudel, D., Lalonde, E., Meng, A., Hennings-Yeomans, P. H., McPherson, A., Sabelnykova, V. Y., et al. (2015). Spatial genomic heterogeneity within localized, multifocal prostate cancer. Nat Genet 47, 736-+.
Bracken, A. P., Dietrich, N., Pasini, D., Hansen, K. H., and Helin, K. (2006). Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitions. Genes Dev 20, 1123-1136.
Cai, Y. Y., Crowther, J., Pastor, T., Asbagh, L. A., Baietti, M. F., De Troyer, M., Vazquez, I., Talebi, A., Renzi, F., Dehairs, J., et al. (2016). Loss of Chromosome 8p Governs Tumor Progression and Drug Response by Altering Lipid Metabolism. Cancer Cell 29, 751-766.
Cancer Genome Atlas Research, N. (2015). The Molecular Taxonomy of Primary Prostate Cancer. Cell 163, 1011-1025.
Cao, J., Spielmann, M., Qiu, X., Huang, X., Ibrahim, D. M., Hill, A. J., Zhang, F., Mundlos, S., Christiansen, L., Steemers, F. J., et al. (2019). The single-cell transcriptional landscape of mammalian organogenesis. Nature 566, 496-502.
Chandarlapaty, S., Sawai, A., Scaltriti, M., Rodrik-Outmezguine, V., Grbovic-Huezo, O., Serra, V., Majumder, P. K., Baselga, J., and Rosen, N. (2011). AKT inhibition relieves feedback suppression of receptor tyrosine kinase expression and activity. Cancer Cell 19, 58-71.
Charafe-Jauffret, E., Ginestier, C., Monville, F., Finetti, P., Adelaide, J., Cervera, N., Fekairi, S., Xerri, L., Jacquemier, J., Birnbaum, D., and Bertucci, F. (2006). Gene expression profiling of breast cell lines identifies potential new basal markers. Oncogene 25, 2273-2284.
Chen, W. L., Qin, Y. Y., Wang, D., Zhou, L., Liu, Y., Chen, S., Yin, L., Xiao, Y. X., Yao, X. H., Yang, X. L., et al. (2018). CCL20 triggered by chemotherapy hinders the therapeutic efficacy of breast cancer. Plos Biol 16.
Chua, C. W., Shibata, M., Lei, M., Toivanen, R., Barlow, L. J., Bergren, S. K., Badani, K. K., Mc Kiernan, J. M., Benson, M. C., Hibshoosh, H., and Shen, M. M. (2014). Single luminal epithelial progenitors can generate prostate organoids in culture. Nat Cell Biol 16, 951-961.
de Bono, J. S., Logothetis, C. J., Molina, A., Fizazi, K., North, S., Chu, L., Chi, K. N., Jones, R. J., Goodman, O. B., Jr., Saad, F., et al. (2011). Abiraterone and increased survival in metastatic prostate cancer. N Engl J Med 364, 1995-2005.
Dhimolea, E., de Matos Simoes, R., Kansara, D., Al'Khafaji, A., Bouyssou, J., Weng, X., Sharma, S., Raja, J., Awate, P., Shirasaki, R., et al. (2021). An Embryonic Diapause-like Adaptation with Suppressed Myc Activity Enables Tumor Treatment Persistence. Cancer Cell 39, 240-256 e211.
Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., and Gingeras, T. R. (2013). STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15-21.
Domingo-Domenech, J., Vidal, S. J., Rodriguez-Bravo, V., Castillo-Martin, M., Quinn, S. A., Rodriguez-Barrueco, R., Bonal, D. M., Charytonowicz, E., Gladoun, N., de la Iglesia-Vicente, J., et al. (2012). Suppression of Acquired Docetaxel Resistance in Prostate Cancer through Depletion of Notch- and Hedgehog-Dependent Tumor-Initiating Cells. Cancer Cell 22, 373-388.
Dongre, A., and Weinberg, R. A. (2019). New insights into the mechanisms of epithelial-mesenchymal transition and implications for cancer. Nature Reviews Molecular Cell Biology 20, 69-84.
Efstathiou, E., Davis, J. W., Titus, M. A., Chapin, B. F., Zurita, A. J., Wen, S. J., Tapia, E. M. L. N., Hoang, A., Cornt, P. G., Wang, X. M., et al. (2016). Neoadjuvant enzalutamide (ENZA) and abiraterone acetate (AA) plus leuprolide acetate (LHRHa) versus AA plus LHRHa in localized high-risk prostate cancer (LHRPC). Journal of Clinical Oncology 34.
Epstein, J. I., Amin, M. B., Beltran, H., Lotan, T. L., Mosquera, J. M., Reuter, V. E., Robinson, B. D., Troncoso, P., and Rubin, M. A. (2014). Proposed Morphologic Classification of Prostate Cancer With Neuroendocrine Differentiation. Am J Surg Pathol 38, 756-767.
Fellmann, C., Hoffmann, T., Sridhar, V., Hopfgartner, B., Muhar, M., Roth, M., Lai, D. Y., Barbosa, I. A. M., Kwon, J. S., Guan, Y. Z., et al. (2013). An Optimized microRNA Backbone for Effective Single-Copy RNAi. Cell Reports 5, 1704-1713.
Feng, J., Liu, T., Qin, B., Zhang, Y., and Liu, X. S. (2012). Identifying ChIP-seq enrichment using MACS. Nat Protoc 7, 1728-1740.
Foulkes, W. D., Smith, I. E., and Reis-Filho, J. S. (2010). Triple-negative breast cancer. N Engl J Med 363, 1938-1948.
Fraser, M., Sabelnykova, V. Y., Yamaguchi, T. N., Heisler, L. E., Livingstone, J., Huang, V., Shiah, Y. J., Yousif, F., Lin, X., Masella, A. P., et al. (2017). Genomic hallmarks of localized, non-indolent prostate cancer. Nature 541, 359-364.
Gao, D., Vela, I., Sboner, A., Iaquinta, P. J., Karthaus, W. R., Gopalan, A., Dowling, C., Wanjala, J. N., Undvall, E. A., Arora, V. K., et al. (2014). Organoid Cultures Derived from Patients with Advanced Prostate Cancer. Cell 159, 176-187.
Gerhauser, C., Favero, F., Risch, T., Simon, R., Feuerbach, L., Assenov, Y., Heckmann, D., Sidiropoulos, N., Waszak, S. M., Hubschmann, D., et al. (2018). Molecular Evolution of Early-Onset Prostate Cancer Identifies Molecular Risk Markers and Clinical Trajectories. Cancer Cell 34, 996-1011 e1018.
Giancotti, F. G. (2013). Mechanisms Governing Metastatic Dormancy and Reactivation. Cell 155, 750-764.
Gotzmann, J., Fischer, A. N., Zojer, M., Mikula, M., Proell, V., Huber, H., Jechlinger, M., Waerner, T., Weith, A., Beug, H., and Mikulits, W. (2006). A crucial function of PDGF in TGF-beta-mediated cancer progression of hepatocytes. Oncogene 25, 3170-3185.
Gupta, P. B., Pastushenko, I., Skibinski, A., Blanpain, C., and Kuperwasser, C. (2019). Phenotypic Plasticity: Driver of Cancer Initiation, Progression, and Therapy Resistance. Cell Stem Cell 24, 65-78.
Hakem, R., delaPompa, J. L., Sirard, C., Mo, R., Woo, M., Hakem, A., Wakeham, A., Potter, J., Reitmair, A., Billia, F., et al. (1996). The tumor suppressor gene Brca1 is required for embryonic cellular proliferation in the mouse. Cell 85, 1009-1023.
Hangauer, M. J., Viswanathan, V. S., Ryan, M. J., Bole, D., Eaton, J. K., Matov, A., Galeas, J., Dhruv, H. D., Berens, M. E., Schreiber, S. L., et al. (2017). Drug-tolerant persister cancer cells are vulnerable to GPX4 inhibition. Nature 551, 247-250.
Hao, J., Ho, J. N., Lewis, J. A., Karim, K. A., Daniels, R. N., Gentry, P. R., Hopkins, C. R., Lindsley, C. W., and Hong, C. C. (2010). In Vivo Structure-Activity Relationship Study of Dorsomorphin Analogues Identifies Selective VEGF and BMP Inhibitors. Acs Chem Biol 5, 245-253.
Heinz, S., Benner, C., Spann, N., Bertolino, E., Lin, Y. C., Laslo, P., Cheng, J. X., Murre, C., Singh, H., and Glass, C. K. (2010). Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell 38, 576-589.
Henry, G. H., Malewska, A., Joseph, D. B., Malladi, V. S., Lee, J., Torrealba, J., Mauck, R. J., Gahan, J. C., Raj, G. V., Roehrborn, C. G., et al. (2018). A Cellular Anatomy of the Normal Adult Human Prostate and Prostatic Urethra. Cell Rep 25, 3530-3542 e3535.
Hugo, W., Zaretsky, J. M., Sun, L., Song, C., Moreno, B. H., Hu-Lieskovan, S., Berent-Maoz, B., Pang, J., Chmielowski, B., Cherry, G., et al. (2016). Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma. Cell 165, 35-44.
Izumi, K., Fang, L. Y., Mizokami, A., Namiki, M., Li, L., Lin, W. J., and Chang, C. (2013). Targeting the androgen receptor with siRNA promotes prostate cancer metastasis through enhanced macrophage recruitment via CCL2/CCR2-induced STAT3 activation. Embo Mol Med 5, 1383-1401.
Jechlinger, M., Grunert, S., Tamir, I. H., Janda, E., Ludemann, S., Waerner, T., Seither, P., Weith, A., Beug, H., and Kraut, N. (2003). Expression profiling of epithelial plasticity in tumor progression. Oncogene 22, 7155-7169.
Ji, Z., He, L. Z., Regev, A., and Struhl, K. (2019). Inflammatory regulatory network mediated by the joint action of NF-kB, STAT3, and AP-1 factors is involved in many human cancers. P Natl Acad Sci USA 116, 9453-9462.
Jiang, P., Gu, S. Q., Pan, D., Fu, J. X., Sahu, A., Hu, X. H., Li, Z. Y., Traugh, N., Bu, X., Li, B., et al. (2018). Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response. Nat Med 24, 1550-+.
Jiao, J., Wang, S. Y., Qiao, R., Vivanco, I., Watson, P. A., Sawyers, C. L., and Wu, H. (2007). Murine cell lines derived from Pten null prostate cancer show the critical role of PTEN in hormone refractory prostate cancer development. Cancer Research 67, 6083-6091.
Johnson, W. E., Li, C., and Rabinovic, A. (2007). Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 8, 118-127.
Justilien, V., Walsh, M. P., Ali, S. A., Thompson, E. A., Murray, N. R., and Fields, A. P. (2014). The PRKCI and SOX2 Oncogenes Are Coamplified and Cooperate to Activate Hedgehog Signaling in Lung Squamous Cell Carcinoma. Cancer Cell 25, 139-151.
Karthaus, W. R., Hofree, M., Choi, D., Linton, E. L., Turkekul, M., Bejnood, A., Carver, B., Gopalan, A., Abida, W., Laudone, V., et al. (2020). Regenerative potential of prostate luminal cells revealed by single-cell analysis. Science 368, 497-+.
Kastenhuber, E. R., and Lowe, S. W. (2017). Putting p53 in Context. Cell 170, 1062-1078.
Keenan, A. B., Torre, D., Lachmann, A., Leong, A. K., Wojciechowicz, M. L., Utti, V., Jagodnik, K. M., Kropiwnicki, E., Wang, Z. C., and Ma'ayan, A. (2019). ChEA3: transcription factor enrichment analysis by orthogonal omics integration. Nucleic Acids Res 47, W212-W224.
Kent, W. J., Sugnet, C. W., Furey, T. S., Roskin, K. M., Pringle, T. H., Zahler, A. M., and Haussler, D. (2002). The human genome browser at UCSC. Genome Res 12, 996-1006.
Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R., and Salzberg, S. L. (2013). TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14, R36.
Kishan, A. U., Romero, T., Alshalalfa, M., Liu, Y., Tran, P. T., Nickols, N. G., Ye, H. H., Sajed, D., Rettig, M. B., Reiter, R. E., et al. (2020). Transcriptomic Heterogeneity of Gleason Grade Group 5 Prostate Cancer. European Urology 78, 327-332.
Klemm, S. L., Shipony, Z., and Greenleaf, W. J. (2019). Chromatin accessibility and the regulatory epigenome. Nat Rev Genet 20, 207-220.
Kron, K. J., Murison, A., Zhou, S., Huang, V., Yamaguchi, T. N., Shiah, Y. J., Fraser, M., van der Kwast, T., Boutros, P. C., Bristow, R. G., and Lupien, M. (2017). TMPRSS2-ERG fusion co-opts master transcription factors and activates NOTCH signaling in primary prostate cancer. Nat Genet 49, 1336-+.
Ku, S. Y., Rosario, S., Wang, Y., Mu, P., Seshadri, M., Goodrich, Z. W., Goodrich, M. M., Labbe, D. P., Gomez, E. C., Wang, J., et al. (2017). Rb1 and Trp53 cooperate to suppress prostate cancer lineage plasticity, metastasis, and antiandrogen resistance. Science 355, 78-83.
Kumar, A., Coleman, I., Morrissey, C., Zhang, X. T., True, L. D., Gulati, R., Etzioni, R., Bolouri, H., Montgomery, B., White, T., et al. (2016). Substantial interindividual and limited intraindividual genomic diversity among tumors from men with metastatic prostate cancer. Nat Med 22, 369-+.
Kuruma, H., Matsumoto, H., Shiota, M., Bishop, J., Lamoureux, F., Thomas, C., Briere, D., Los, G., Gleave, M., Fanjul, A., and Zoubeidi, A. (2013). A Novel Antiandrogen, Compound 30, Suppresses Castration-Resistant and MDV3100-Resistant Prostate Cancer Growth In Vitro and In Vivo. Mol Cancer Ther 12, 567-576.
Labrecque, M. P., Coleman, I. M., Brown, L. G., True, L. D., Kollath, L., Lakely, B., Nguyen, H. M., Yang, Y. C., da Costa, R. M. G., Kaipainen, A., et al. (2019). Molecular profiling stratifies diverse phenotypes of treatment-refractory metastatic castration-resistant prostate cancer. Journal of Clinical Investigation 129, 4492-4505.
Langmead, B., and Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nat Methods 9, 357-359.
Lee, Y. C., Cheng, C. J., Bilen, M. A., Lu, J. F., Satcher, R. L., Yu-Lee, L. Y., Gallick, G. E., Maity, S. N., and Lin, S. H. (2011). BMP4 promotes prostate tumor growth in bone through osteogenesis. Cancer Res 71, 5194-5203.
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., and Genome Project Data Processing, S. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079.
Li, J., Yen, C., Liaw, D., Podsypanina, K., Bose, S., Wang, S. I., Puc, J., Miliaresis, C., Rodgers, L., McCombie, R., et al. (1997). PTEN, a putative protein tyrosine phosphatase gene mutated in human brain, breast, and prostate cancer. Science 275, 1943-1947.
Li, L. K., Karanika, S., Yang, G., Wang, J. X., Park, S., Broom, B. M., Manyam, G. C., Wu, W. H., Luo, Y., Basourakos, S., et al. (2017). Androgen receptor inhibitor-induced "BRCAness" and PARP inhibition are synthetically lethal for castration-resistant prostate cancer. Sci Signal 10.
Li, Z. G., Mathew, P., Yang, J., Starbuck, M. W., Zurita, A. J., Liu, J., Sikes, C., Multani, A. S., Efstathiou, E., Lopez, A., et al. (2008). Androgen receptor-negative human prostate cancer cells induce osteogenesis in mice through FGF9-mediated mechanisms. J Clin Invest 118, 2697-2710.
Liu, Y., Mo, J. Q., Hu, Q. D., Boivin, G., Levin, L., Lu, S., Yang, D., Dong, Z. Y., and Lu, S. (2009). Targeted overexpression of Vav3 oncogene in prostatic epithelium induces nonbacterial prostatitis and prostate cancer. Cancer Research 69.
Logothetis, C. J., Gallick, G. E., Maity, S. N., Kim, J., Aparicio, A., Efstathiou, E., and Lin, S. H. (2013). Molecular classification of prostate cancer progression: foundation for marker-driven treatment of prostate cancer. Cancer Discov 3, 849-861.
Lu, X., Horner, J. W., Paul, E., Shang, X. Y., Troncoso, P., Deng, P. N., Jiang, S., Chang, Q., Spring, D. J., Sharma, P., et al. (2017). Effective combinatorial immunotherapy for castration-resistant prostate cancer. Nature 543, 728-+.
Massague, J. (2004). G1 cell-cycle control and cancer. Nature 432, 298-306.
McInnes, L., Healy, J., and Melville, J. (2018). UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction. In, p. arXiv:1802.03426.
Mellinghoff, I. K., Vivanco, I., Kwon, A., Tran, C., Wongvipat, J., and Sawyers, C. L. (2004). HER2/neu kinase-dependent modulation of androgen receptor function through effects on DNA binding and stability. Cancer Cell 6, 517-527.
Mishina, Y., Suzuki, A., Ueno, N., and Behringer, R. R. (1995). Bmpr encodes a type I bone morphogenetic protein receptor that is essential for gastrulation during mouse embryogenesis. Gene Dev 9, 3027-3037.
Mootha, V. K., Lindgren, C. M., Eriksson, K. F., Subramanian, A., Sihag, S., Lehar, J., Puigserver, P., Carlsson, E., Ridderstrale, M., Laurila, E., et al. (2003). PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet 34, 267-273.
Mostaghel, E. A., Zhang, A. L., Hernandez, S., Marck, B. T., Zhang, X. T., Tamae, D., Biehl, H. E., Tretiakova, M., Bartlett, J., Burns, J., et al. (2019). Contribution of Adrenal Glands to Intratumor Androgens and Growth of Castration-Resistant Prostate Cancer. Clinical Cancer Research 25, 426-439.
Mou, H., Vinarsky, V., Tata, P. R., Brazauskas, K., Choi, S. H., Crooke, A. K., Zhang, B., Solomon, G. M., Turner, B., Bihler, H., et al. (2016). Dual SMAD Signaling Inhibition Enables Long-Term Expansion of Diverse Epithelial Basal Cells. Cell Stem Cell 19, 217-231.
Mu, P., Zhang, Z., Benelli, M., Karthaus, W. R., Hoover, E., Chen, C. C., Wongvipat, J., Ku, S. Y., Gao, D., Cao, Z., et al. (2017). SOX2 promotes lineage plasticity and antiandrogen resistance in TP53- and RB1-deficient prostate cancer. Science 355, 84-88.
Mullan, P. B., Quinn, J. E., and Harkin, D. P. (2006). The role of BRCA1 in transcriptional regulation and cell cycle control. Oncogene 25, 5854-5863.
Naik, S., Larsen, S. B., Cowley, C. J., and Fuchs, E. (2018). Two to Tango: Dialog between Immunity and Stem Cells in Health and Disease. Cell 175, 908-920.
Neftel, C., Laffy, J., Filbin, M. G., Hara, T., Shore, M. E., Rahme, G. J., Richman, A. R., Silverbush, D., Shaw, M. L., Hebert, C. M., et al. (2019). An Integrative Model of Cellular States, Plasticity, and Genetics for Glioblastoma. Cell 178, 835-849 e821.
Newman, A. M., Liu, C. L., Green, M. R., Gentles, A. J., Feng, W., Xu, Y., Hoang, C. D., Diehn, M., and Alizadeh, A. A. (2015). Robust enumeration of cell subsets from tissue expression profiles. Nat Methods 12, 453-457.
Nouri, M., Massah, S., Caradec, J., Lubik, A. A., Li, N., Truong, S., Lee, A. R., Fazli, L., Ramnarine, V. R., Lovnicki, J. M., et al. (2020). Transient Sox9 Expression Facilitates Resistance to Androgen-Targeted Therapy in Prostate Cancer. Clinical Cancer Research 26, 1678-1689.
Omori, A., Miyagawa, S., Ogino, Y., Harada, M., Ishii, K., Sugimura, Y., Ogino, H., Nakagata, N., and Yamada, G. (2014). Essential roles of epithelial bone morphogenetic protein signaling during prostatic development. Endocrinology 155, 2534-2544.
Orme, J. J., and Huang, H. J. (2020). Microenvironment-Mediated Resistance to Anti-Androgen Therapy. Cancer Cell 38, 155-157.
Palanisamy, N., Yang, J., Shepherd, P. D. A., Li-Ning-Tapia, E. M., Labanca, E., Manyam, G. C., Ravoori, M. K., Kundra, V., Araujo, J. C., Efstathiou, E., et al. (2020). The MD Anderson Prostate Cancer Patient-derived Xenograft Series (MDA PCa PDX) Captures the Molecular Landscape of Prostate Cancer and Facilitates Marker-driven Therapy Development. Clin Cancer Res.
Park, J. W., Lee, J. K., Sheu, K. M., Wang, L., Balanis, N. G., Nguyen, K., Smith, B. A., Cheng, C., Tsai, B. L., Cheng, D., et al. (2018). Reprogramming normal human epithelial tissues to a common, lethal neuroendocrine cancer lineage. Science 362, 91-95.
Pastushenko, I., Brisebarre, A., Sifrim, A., Fioramonti, M., Revenco, T., Boumahdi, S., Van Keymeulen, A., Brown, D., Moers, V., Lemaire, S., et al. (2018). Identification of the tumour transition states occurring during EMT. Nature 556, 463-+.
Pelossof, R., Fairchild, L., Huang, C. H., Widmer, C., Sreedharan, V. T., Sinha, N., Lai, D. Y., Guan, Y., Premsrirut, P. K., Tschaharganeh, D. F., et al. (2017). Prediction of potent shRNAs with a sequential classification algorithm. Nat Biotechnol 35, 350-353.
Perou, C. M., Sorlie, T., Eisen, M. B., van de Rijn, M., Jeffrey, S. S., Rees, C. A., Pollack, J. R., Ross, D. T., Johnsen, H., Akslen, L. A., et al. (2000). Molecular portraits of human breast tumours. Nature 406, 747-752.
Pomerantz, M. M., Li, F. G., Takeda, D. Y., Lenci, R., Chonkar, A., Chabot, M., Cejas, P., Vazquez, F., Cook, J., Shivdasani, R. A., et al. (2015). The androgen receptor cistrome is extensively reprogrammed in human prostate tumorigenesis. Nat Genet 47, 1346-+.
Pomerantz, M. M., Qiu, X. T., Zhu, Y. Y., Takeda, D. Y., Pan, W. T., Baca, S. C., Gusev, A., Korthauer, K. D., Severson, T. M., Ha, G., et al. (2020). Prostate cancer reactivates developmental epigenomic programs during metastatic progression. Nat Genet 52, 790-+.
Puram, S. V., Tirosh, I., Parikh, A. S., Patel, A. P., Yizhak, K., Gillespie, S., Rodman, C., Luo, C. L., Mroz, E. A., Emerick, K. S., et al. (2017). Single-Cell Transcriptomic Analysis of Primary and Metastatic Tumor Ecosystems in Head and Neck Cancer. Cell 171, 1611-+.
Qian, J., Hassanein, M., Hoeksema, M. D., Harris, B. K., Zou, Y., Chen, H. D., Lu, P. C., Eisenberg, R., Wang, J., Espinosa, A., et al. (2015). The RNA binding protein FXR1 is a new driver in the 3q26-29 amplicon and predicts poor prognosis in human cancers. P Natl Acad Sci USA 112, 3469-3474.
Qiu, X., Mao, Q., Tang, Y., Wang, L., Chawla, R., Pliner, H. A., and Trapnell, C. (2017). Reversed graph embedding resolves complex single-cell trajectories. Nat Methods 14, 979-982.
Quigley, D. A., Dang, H. X., Zhao, S. G., Lloyd, P., Aggarwal, R., Alumkal, J. J., Foye, A., Kothari, V., Perry, M. D., Bailey, A. M., et al. (2018). Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer (vol 174, pg 758, 2018). Cell 175, 889-889.
Quinlan, A. R., and Hall, I. M. (2010). BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842.
Quintanal-Villalonga, A., Chan, J. M., Yu, H. A., Pe'er, D., Sawyers, C. L., Sen, T., and Rudin, C. M. (2020). Lineage plasticity in cancer: a shared pathway of therapeutic resistance. Nat Rev Clin Oncol 17, 360-371.
Rees, M. G., Seashore-Ludlow, B., Cheah, J. H., Adams, D. J., Price, E. V., Gill, S., Javaid, S., Coletti, M. E., Jones, V. L., Bodycombe, N. E., et al. (2016). Correlating chemical sensitivity and basal gene expression reveals mechanism of action. Nat Chem Biol 12, 109-+.
Ritchie, M. E., Phipson, B., Wu, D., Hu, Y. F., Law, C. W., Shi, W., and Smyth, G. K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Research 43.
Robinson, D., Van Allen, E. M., Wu, Y. M., Schultz, N., Lonigro, R. J., Mosquera, J. M., Montgomery, B., Taplin, M. E., Pritchard, C. C., Attard, G., et al. (2015). Integrative Clinical Genomics of Advanced Prostate Cancer. Cell 162, 454.
Sackmann Sala, L., Boutillon, F., Menara, G., De Goyon-Pelard, A., Leprevost, M., Codzamanian, J., Lister, N., Pencik, J., Clark, A., Cagnard, N., et al. (2017). A rare castration-resistant progenitor cell population is highly enriched in Pten-null prostate tumours. J Pathol 243, 51-64.
Sarrio, D., Rodriguez-Pinilla, S. M., Hardisson, D., Cano, A., Moreno-Bueno, G., and Palacios, J. (2008). Epithelial-mesenchymal transition in breast cancer relates to the basal-like phenotype. Cancer Res 68, 989-997.
Scher, H. I., Fizazi, K., Saad, F., Taplin, M. E., Sternberg, C. N., Miller, K., de Wit, R., Mulders, P., Chi, K. N., Shore, N. D., et al. (2012). Increased survival with enzalutamide in prostate cancer after chemotherapy. N Engl J Med 367, 1187-1197.
Scognamiglio, R., Cabezas-Wallscheid, N., Thier, M. C., Altamura, S., Reyes, A., Prendergast, A. M., Baumgartner, D., Carnevalli, L. S., Atzberger, A., Haas, S., et al. (2016). Myc Depletion Induces a Pluripotent Dormant State Mimicking Diapause. Cell 164, 668-680.
Shaffer, S. M., Dunagin, M. C., Torborg, S. R., Torre, E. A., Emert, B., Krepler, C., Beqiri, M., Sproesser, K., Brafford, P. A., Xiao, M., et al. (2018). Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance (vol 546, pg 431, 2017). Nature 555, 274-274.
Shiota, M., Bishop, J. L., Takeuchi, A., Nip, K. M., Cordonnier, T., Beraldi, E., Kuruma, H., Gleave, M. E., and Zoubeidi, A. (2015). Inhibition of the HER2-YB1-AR axis with Lapatinib synergistically enhances Enzalutamide anti-tumor efficacy in castration resistant prostate cancer. Oncotarget 6, 9086-9098.
Silke, J., and Vucic, D. (2014). IAP Family of Cell Death and Signaling Regulators. Method Enzymol 545, 35-65.
Silver, D. P., and Livingston, D. M. (2012). Mechanisms of BRCA1 Tumor Suppression. Cancer Discovery 2, 679-684.
Sircar, K., Huang, H., Hu, L., Cogdell, D., Dhillon, J., Tzelepi, V., Efstathiou, E., Koumakpayi, I. H., Saad, F., Luo, D., et al. (2012). Integrative molecular profiling reveals asparagine synthetase is a target in castration-resistant prostate cancer. Am J Pathol 180, 895-903.
Smith, B. A., Sokolov, A., Uzunangelov, V., Baertsch, R., Newton, Y., Graim, K., Mathis, C., Cheng, D., Stuart, J. M., and Witte, O. N. (2015). A basal stem cell signature identifies aggressive prostate cancer phenotypes. Proc Natl Acad Sci U S A 112, E6544-6552.
Sorlie, T., Perou, C. M., Tibshirani, R., Aas, T., Geisler, S., Johnsen, H., Hastie, T., Eisen, M. B., van de Rijn, M., Jeffrey, S. S., et al. (2001). Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci U S A 98, 10869-10874.
Su, W. J., Han, H. H., Wang, Y., Zhang, B. Y., Zhou, B., Cheng, Y. M., Rumandla, A., Gurrapu, S., Chakraborty, G., Su, J., et al. (2019). The Polycomb Repressor Complex 1 Drives Double-Negative Prostate Cancer Metastasis by Coordinating Stemness and Immune Suppression. Cancer Cell 36, 139-+.
Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., and Mesirov, J. P. (2005). Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. P Natl Acad Sci USA 102, 15545-15550.
Sun, C., Wang, L. Q., Huang, S. D., Heynen, G. J. J. E., Prahallad, A., Robert, C., Haanen, J., Blank, C., Wesseling, J., Willems, S. M., et al. (2014). Reversible and adaptive resistance to BRAF(V600E) inhibition in melanoma. Nature 508, 118-+.
Taniguchi, K., and Karin, M. (2018). NF-kappaB, inflammation, immunity and cancer: coming of age. Nat Rev Immunol 18, 309-324.
Tran, C., Ouk, S., Clegg, N. J., Chen, Y., Watson, P. A., Arora, V., Wongvipat, J., Smith-Jones, P. M., Yoo, D., Kwon, A., et al. (2009). Development of a second-generation antiandrogen for treatment of advanced prostate cancer. Science 324, 787-790.
Trapnell, C., Cacchiarelli, D., Grimsby, J., Pokharel, P., Li, S., Morse, M., Lennon, N. J., Livak, K. J., Mikkelsen, T. S., and Rinn, J. L. (2014). The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat Biotechnol 32, 381-386.
Trapnell, C., Hendrickson, D. G., Sauvageau, M., Goff, L., Rinn, J. L., and Pachter, L. (2013). Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol 31, 46-53.
Turner, N. C., and Reis, J. S. (2006). Basal-like breast cancer and the BRCA1 phenotype. Oncogene 25, 5846-5853.
Tzelepi, V., Zhang, J., Lu, J. F., Kleb, B., Wu, G., Wan, X., Hoang, A., Efstathiou, E., Sircar, K., Navone, N. M., et al. (2012). Modeling a lethal prostate cancer variant with small-cell carcinoma features. Clin Cancer Res 18, 666-677.
van Bokhoven, A., Varella-Garcia, M., Korch, C., Johannes, W. U., Smith, E. E., Miller, H. L., Nordeen, S. K., Miller, G. J., and Lucia, M. S. (2003). Molecular characterization of human prostate carcinoma cell lines. Prostate 57, 205-225.
Verhaak, R. G., Hoadley, K. A., Purdom, E., Wang, V., Qi, Y., Wilkerson, M. D., Miller, C. R., Ding, L., Golub, T., Mesirov, J. P., et al. (2010). Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell 17, 98-110.
Wagner, J., Rapsomaniki, M. A., Chevrier, S., Anzeneder, T., Langwieder, C., Dykgers, A., Rees, M., Ramaswamy, A., Muenst, S., Soysal, S. D., et al. (2019). A Single-Cell Atlas of the Tumor and Immune Ecosystem of Human Breast Cancer. Cell 177, 1330-1345 e1318.
Wang, H., Bierie, B., Li, A. G., Pathania, S., Toomire, K., Dimitrov, S. D., Liu, B., Gelman, R., Giobbie-Hurder, A., Feunteun, J., et al. (2016). BRCA1/FANCD2/BRG1-Driven DNA Repair Stabilizes the Differentiation State of Human Mammary Epithelial Cells. Mol Cell 63, 277-292.
Wang, H., Xiang, D., Liu, B., He, A., Randle, H. J., Zhang, K. X., Dongre, A., Sachs, N., Clark, A. P., Tao, L., et al. (2019). Inadequate DNA Damage Repair Promotes Mammary Transdifferentiation, Leading to BRCA1 Breast Cancer. Cell 178, 135-151 e119.
Wang, Q., Hu, B., Hu, X., Kim, H., Squatrito, M., Scarpace, L., deCarvalho, A. C., Lyu, S., Li, P., Li, Y., et al. (2017). Tumor Evolution of Glioma-Intrinsic Gene Expression Subtypes Associates with Immunological Changes in the Microenvironment. Cancer Cell 32, 42-56 e46.
Wang, X., Kruithof-de Julio, M., Economides, K. D., Walker, D., Yu, H. L., Halili, M. V., Hu, Y. P., Price, S. M., Abate-Shen, C., and Shen, M. M. (2009). A luminal epithelial stem cell that is a cell of origin for prostate cancer. Nature 461, 495-U461.
Watson, P. A., Arora, V. K., and Sawyers, C. L. (2015). Emerging mechanisms of resistance to androgen receptor inhibitors in prostate cancer. Nat Rev Cancer 15, 701-711.
Xue, W., Kitzing, T., Roessler, S., Zuber, J., Krasnitz, A., Schultz, N., Revill, K., Weissmueller, S., Rappaport, A. R., Simon, J., et al. (2012). A cluster of cooperating tumor-suppressor gene candidates in chromosomal deletions. P Natl Acad Sci USA 109, 8212-8217.
Yarden, Y., and Pines, G. (2012). The ERBB network: at last, cancer therapy meets systems biology. Nature Reviews Cancer 12, 553-563.
Yoshioka, T., Otero, J., Chen, Y., Kim, Y. M., Koutcher, J. A., Satagopan, J., Reuter, V., Carver, B., de Stanchina, E., Enomoto, K., et al. (2013). beta4 Integrin signaling induces expansion of prostate tumor progenitors. J Clin Invest 123, 682-699.
You, S., Knudsen, B. S., Erho, N., Alshalalfa, M., Takhar, M., Al-Deen Ashab, H., Davicioni, E., Karnes, R. J., Klein, E. A., Den, R. B., et al. (2016). Integrated Classification of Prostate Cancer Reveals a Novel Luminal Subtype with Poor Outcome. Cancer Res 76, 4948-4958.
Zhang, Z. D., Karthaus, W. R., Lee, Y. S., Gao, V. R., Wu, C., Russo, J. W., Liu, M. H., Mota, J. M., Abida, W., Linton, E., et al. (2020). Tumor Microenvironment-Derived NRG1 Promotes Antiandrogen Resistance in Prostate Cancer. Cancer Cell 38, 279-+.
Zhao, S. G., Chang, S. L., Erho, N., Yu, M., Lehrer, J., Alshalalfa, M., Speers, C., Cooperberg, M. R., Kim, W., Ryan, C. J., et al. (2017). Associations of Luminal and Basal Subtyping of Prostate Cancer With Prognosis and Response to Androgen Deprivation Therapy. JAMA Oncol 3, 1663-1672.
Zou, M., Toivanen, R., Mitrofanova, A., Floch, N., Hayati, S., Sun, Y. P., Le Magnen, C., Chester, D., Mostaghel, E. A., Califano, A., et al. (2017). Transdifferentiation as a Mechanism of Treatment Resistance in a Mouse Model of Castration-Resistant Prostate Cancer. Cancer Discovery 7, 736-749.