Structural Alterations Driving Castration-Resistant Prostate Cancer Revealed by Linked-Read Genome Sequencing
Open accessAbstract
Nearly all prostate cancer deaths are from metastatic castration-resistant prostate cancer (mCRPC), but there have been few whole-genome sequencing (WGS) studies of this disease state. We performed linked-read WGS on 23 mCRPC biopsy specimens and analyzed cell-free DNA sequencing data from 86 patients with mCRPC. In addition to frequent rearrangements affecting known prostate cancer genes, we observed complex rearrangements of the AR locus in most cases. Unexpectedly, these rearrangements include highly recurrent tandem duplications involving an upstream enhancer of AR in 70%-87% of cases compared with <2% of primary prostate cancers. A subset of cases displayed AR or MYC enhancer duplication in the context of a genome-wide tandem duplicator phenotype associated with CDK12 inactivation. Our findings highlight the complex genomic structure of mCRPC, nominate alterations that may inform prostate cancer treatment, and suggest that additional recurrent events in the non-coding mCRPC genome remain to be discovered.
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Tumor alterations that reactivate AR signaling during treatment with an ARSI have been identified.
“We and other groups have identified tumor alterations that reactivate AR signaling during treatment with an ARSI2,22–29.”
From Genome-scale CRISPR screens identify PTGES3 as a direct modulator of androgen receptor function in advanced prostate cancer (2025) · cites this paper as [25]
Mechanisms of ARSI resistance include AR gene amplification, AR enhancer amplification, AR mutation, AR genomic structural rearrangements, AR splice variants and polymorphisms in androgen metabolism genes.
“These mechanisms of resistance include AR gene amplification22,23, AR enhancer amplification2,24,25, AR mutation26, AR genomic structural rearrangements27, AR splice variants28 and polymorphisms in androgen metabolism genes29.”
From Genome-scale CRISPR screens identify PTGES3 as a direct modulator of androgen receptor function in advanced prostate cancer (2025) · cites this paper as [25]
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Therapeutic Targeting of CDK12/CDK13 in Triple-Negative Breast Cancer
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Targeting SWI/SNF ATPases in enhancer-addicted prostate cancer
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“The expressions of AR , MYC and FOXA1 genes themselves are frequently amplified in advanced prostate cancer by copy amplification and/or enhancer duplication 15,26,27 .”
BackgroundTakeda, D. Y., Spisák, S., Seo, J.-H., Bell, C., O’Connor, E., Korthauer, K., Ribli, D., Csabai, I., Solymosi, N., Szállási, Z., et al. (2018) · Cell · doi:10.1016/j.cell.2018.05.037 · Cited by 317 · see citing works
“By contrast, the AR enhancer region does not appear to create de novo TFBS as there are no recurrent single nucleotide variants or indels (Viswanathan et al., 2018).”
Netto, G. J., Amin, M. B., Berney, D. M., Compérat, É., Gill, A. J., Hartmann, A., Menon, S. G., Raspollini, M. R., Rubin, M. A., Srigley, J. R., et al. (2022) · European Urology · doi:10.1016/j.eururo.2022.07.002 · Cited by 316 · see citing works
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Self-citationTranscription-Associated Cyclin-Dependent Kinases as Targets and Biomarkers for Cancer Therapy
Chou, J., Quigley, D. A., Robinson, T. M., Feng, F. Y.-C., & Ashworth, A. (2020) · Cancer Discovery · doi:10.1158/2159-8290.cd-19-0528 · Cited by 292 · see citing works
“BRCA1, BRCA2, and CDK12 mutations are mutually exclusive (84–86), but despite the mounting evidence that CDK12 regulates the expression of HR genes, the genomic signature of CDK12-mutated tumors is unique from those with BRCA1 or BRCA2 mutations (87, 88).”
BackgroundUtility of ctDNA to support patient selection for early phase clinical trials: the TARGET study
Rothwell, D. G., Ayub, M., Cook, N., Thistlethwaite, F. C., Carter, L., Dean, E. J., Smith, N., Villa, S., Dransfield, J., Clipson, A., et al. (2019) · Nature Medicine · doi:10.1038/s41591-019-0380-z · Cited by 290 · see citing works
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“CNV patterns or clusters have been associated with high Gleason prostate cancer (Gleason 8 + compared to Gleason 6–7 [Williams et al., 2014]) and recurrent disease (compared to primary [Visakorpi et al., 1995; Cancer Genome Atlas Research Network, 2015; Viswanathan et al., 2018]).”
BackgroundProstate cancer reactivates developmental epigenomic programs during metastatic progression
Pomerantz, M. M., Qiu, X., Zhu, Y., Takeda, D. Y., Pan, W., Baca, S. C., Gusev, A., Korthauer, K. D., Severson, T., Ha, G., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-0664-8 · Cited by 266 · see citing works
Self-citationTumor Microenvironment-Derived NRG1 Promotes Antiandrogen Resistance in Prostate Cancer
Zhang, Z., Karthaus, W. R., Lee, Y. S., Gao, V. R., Wu, C., Russo, J. W., Liu, M., Mota, J. M., Abida, W. M., Linton, E. L., et al. (2020) · Cancer Cell · doi:10.1016/j.ccell.2020.06.005 · Cited by 259 · see citing works
“, 2015), as well as tandem duplication events involving the AR enhancer (Quigley et al., 2018; Takeda et al., 2018; Viswanathan et al., 2018).”
BackgroundSelf-citationResolving the full spectrum of human genome variation using Linked-ReadsPreprint
Marks, P., Garcia, S., Barrio, Á. M., Belhocine, K., Bernate, J., Bharadwaj, R., Bjornson, K. P., Catalanotti, C., Delaney, J., Fehr, A. N., et al. (2019) · Genome Research · doi:10.1101/gr.234443.118 · Cited by 252 · see citing works
“…power of Linked-Reads to resolve complex variants in both germline and cancer samples (Collins et al. 2017; Greer et al. 2017; Nordlund et al. 2018; Viswanathan et al. 2018) and demonstrates that Linked-Reads out-performs the switch accuracy and phasing completeness of other haplotyping methods…”
Towards precision oncology in advanced prostate cancer
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“This study and others (25, 34, 36, 37) support continued evolution of AR gene alterations during disease progression.”
ResultDeep whole-genome ctDNA chronology of treatment-resistant prostate cancer
Herberts, C., Annala, M., Sipola, J., Ng, S. W. S., Chen, X. E., Nurminen, A., Korhonen, O. V., Munzur, A. D., Beja, K., Schönlau, E., et al. (2022) · Nature · doi:10.1038/s41586-022-04975-9 · Cited by 186 · see citing works
Targeting the Androgen Signaling Axis in Prostate Cancer
Dai, C. S., Dehm, S. M., & Sharifi, N. (2023) · Journal of Clinical Oncology · doi:10.1200/jco.23.00433 · Cited by 172 · see citing works
Self-citationProspective Comprehensive Genomic Profiling of Primary and Metastatic Prostate Tumors
Chung, J., Dewal, N., Sokol, E. S., Mathew, P. F., Whitehead, R. P., Millis, S. Z., Frampton, G. M., Bratslavsky, G., Pal, S. K., Lee, R. J., et al. (2019) · JCO Precision Oncology · doi:10.1200/po.18.00283 · Cited by 161 · see citing works
“CDK12 is a candidate biomarker for PARP inhibition(4) on the basis of preclinical studies(19,20); however, gLOH-H was significantly less frequent for CDK12-altered cases; this finding is consistent with recent studies suggesting that CDK12 GAs are associated with a focal tandem duplication phenotype that is distinct f…”
ResultThe main sources of circulating cell-free DNA: Apoptosis, necrosis and active secretion
Hu, Z., Chen, H., Long, Y., Li, P., & Gu, Y. (2020) · Critical Reviews in Oncology/Hematology · doi:10.1016/j.critrevonc.2020.103166 · Cited by 154 · see citing works
Cellular and Molecular Mechanisms Underlying Prostate Cancer Development: Therapeutic Implications
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“This enhancer region was found to be amplified in 87% of cancer metastatic samples, in association with an amplified copy of AR gene [164]; importantly, this enhancer region was found to be amplified in only 2% of primary tumors [164].”
BackgroundInfluentialThe MYC Enhancer-ome: Long-Range Transcriptional Regulation of MYC in Cancer
Lancho, O., & Herranz, D. (2018) · Trends in cancer · doi:10.1016/j.trecan.2018.10.003 · Cited by 137 · see citing works
Rubin, M. A., Bristow, R. G., Thienger, P., Dive, C., & Imielinski, M. B. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.10.033 · Cited by 136 · see citing works
Tumor fraction in cell-free DNA as a biomarker in prostate cancer
Choudhury, A. D., Werner, L. L., Francini, E., Wei, X. X., Ha, G., Freeman, S. S., Rhoades, J., Reed, S. C., Gydush, G., Rotem, D., et al. (2018) · JCI Insight · doi:10.1172/jci.insight.122109 · Cited by 139 · see citing works
Self-citationAndrogen receptor (AR) heterogeneity in prostate cancer and therapy resistance
Jamroze, A., Chatta, G. S., & Tang, D. G. (2021) · Cancer Letters · doi:10.1016/j.canlet.2021.06.006 · Cited by 136 · see citing works
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A framework for clinical cancer subtyping from nucleosome profiling of cell-free DNA
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Self-citationNSD2 is a conserved driver of metastatic prostate cancer progression
Aytés, À., Giacobbe, A., Mitrofanova, A., Ruggero, K., Cyrta, J., Arriaga, J. M., Palomero, L., Farran-Matas, S., Rubin, M. A., Shen, M. M., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-07511-4 · Cited by 119 · see citing works
CDK12 drives breast tumor initiation and trastuzumab resistance via WNT and IRS1‐ErbB‐PI3K signaling
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CDK7 Inhibition Suppresses Castration-Resistant Prostate Cancer through MED1 Inactivation
Rasool, R. U., Natesan, R., Deng, Q., Aras, S., Lal, P., Effron, S. S., Mitchell-Velasquez, E., Posimo, J. M., Carskadon, S. L., Baca, S. C., et al. (2019) · Cancer Discovery · doi:10.1158/2159-8290.cd-19-0189 · Cited by 116 · see citing works
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“CDK12-Bi inactivation in prostate cancer was associated with a higher prevalence of small-fragment copy-number alterations and a higher number of breakpoints across the genome, consistent with the previously described tandem duplicator phenotype [9,25], as tandem duplications are difficult to characterize directly usi…”
BackgroundA new era of long-read sequencing for cancer genomics
Sakamoto, Y., Sereewattanawoot, S., & Suzuki, A. (2019) · Journal of Human Genetics · doi:10.1038/s10038-019-0658-5 · Cited by 115 · see citing works
Clinical Outcomes in Cyclin-dependent Kinase 12 Mutant Advanced Prostate Cancer
Reimers, M. A., Yip, S., Zhang, L., Cieslik, M. P., Dhawan, M., Montgomery, B., Wyatt, A. W., Chi, K. N., Small, E. J., Chinnaiyan, A. M., et al. (2019) · European Urology · doi:10.1016/j.eururo.2019.09.036 · Cited by 113 · see citing works
Structural variations in cancer and the 3D genome
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“For example, the AR is often activated by amplifications of its enhancer that do not include the gene itself 146,156 .”
BackgroundSelf-citationZhu, Y., Dalrymple, S. L., Coleman, I. M., Zheng, S. L., Xu, J., Hooper, J. E., Antonarakis, E. S., Marzo, A. M. D., Meeker, A. K., Nelson, P. S., et al. (2020) · Oncogene · doi:10.1038/s41388-020-01479-6 · Cited by 104 · see citing works
Self-citationTargeting CDK12 for Cancer Therapy: Function, Mechanism, and Drug Discovery
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Annala, M., Taavitsainen, S., Khalaf, D. J., Vandekerkhove, G. R., Beja, K., Sipola, J., Warner, E. W., Herberts, C., Wong, A., Fu, S. Y. F., et al. (2021) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-21-1625 · Cited by 95 · see citing works
“An enhancer region 640 kb upstream ofARwas recently reported to contribute to increased AR expression through focal tandem duplications in patients with mCRPC (32, 33).”
BackgroundSelf-citationvan Belzen, I. A. E. M., Schönhuth, A., Kemmeren, P., & Hehir‐Kwa, J. Y. (2021) · npj Precision Oncology · doi:10.1038/s41698-021-00155-6 · Cited by 95 · see citing works
Structural Variation in Cancer: Role, Prevalence, and Mechanisms
Cosenza, M. R., Rodríguez–Martín, B., & Korbel, J. O. (2022) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-120121-101149 · Cited by 92 · see citing works
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“%) had evidence of focal TD.”
BackgroundMethodInfluentialSelf-citationDarolutamide is a potent androgen receptor antagonist with strong efficacy in prostate cancer models
Sugawara, T., Baumgart, S. J., Nevedomskaya, E., Reichert, K., Steuber, H., Lejeune, P., Mumberg, D., & Haendler, B. (2019) · International Journal of Cancer · doi:10.1002/ijc.32242 · Cited by 92 · see citing works
“For the AR N/C interaction assay, HCT-116 cells were seeded into 6-well plates and transfected 1 day later with 2 μg of pFR-Luc reporter vector, and 250 ng of pCMV-AD-AR (2-554) and pCMV-BD-AR(665-918) plasmids.”
MethodA noncanonical AR addiction drives enzalutamide resistance in prostate cancer
He, Y., Wei, T., Ye, Z., Orme, J. J., Lin, D., Sheng, H., Fazli, L., Karnes, R. J., Jiménez, R. E., Wang, L., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-21860-7 · Cited by 92 · see citing works
Illuminating the noncoding genome in cancer
Zhang, X., & Meyerson, M. M. (2020) · Nature Cancer · doi:10.1038/s43018-020-00114-3 · Cited by 85 · see citing works
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Self-citationCDK12 phosphorylates 4E-BP1 to enable mTORC1-dependent translation and mitotic genome stabilityPreprint
Choi, S. H., Martinez, T. F., Kim, S., Donaldson, C. J., Shokhirev, M. N., Saghatelian, A., & Jones, K. A. (2019) · Genes & Development · doi:10.1101/gad.322339.118 · Cited by 83 · see citing works
Targeting DNA Damage Response in Prostate and Breast Cancer
Wengner, A. M., Scholz, A., & Haendler, B. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21218273 · Cited by 78 · see citing works
“been described for an enhancer of the AR potentially responsible for disease progression on androgen pathway inhibitors [44,45].”
BackgroundAggarwal, R. R., Quigley, D. A., Huang, J., Zhang, L., Beer, T. M., Rettig, M. B., Reiter, R. E., Gleave, M. E., THOMAS, G. V., Foye, A., et al. (2019) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-18-1101 · Cited by 80 · see citing works
Malihi, P. D., Graf, R. P., Rodríguez, Á., Ramesh, N., Lee, J. S. H., Sutton, R., Jiles, R., Velasco, C. R., Sei, E., Kolatkar, A. R., et al. (2020) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-19-4100 · Cited by 78 · see citing works
“A probable explanation for some of the AR-expressing mCRPC cases with no or low-level AR amplification may have been the presence of amplification in the enhancer region upstream of AR (5, 6).”
BackgroundCDK12: A Potent Target and Biomarker for Human Cancer Therapy
Liang, S., Hu, L., Wu, Z., Chen, Z., Liu, S., Xu, X., & Qian, A. (2020) · Cells · doi:10.3390/cells9061483 · Cited by 75 · see citing works
“Recent studies also show that inactivation of CDK12 (biallelic inactivation) is associated with a global tandem duplication phenotype [72,73].”
BackgroundSokol, E. S., Pavlick, D. C., Frampton, G. M., Ross, J. S., Miller, V. A., Ali, S. M., Lotan, T. L., Pardoll, D. M., Chung, J., & Antonarakis, E. S. (2019) · The Oncologist · doi:10.1634/theoncologist.2019-0214 · Cited by 76 · see citing works
“In ovarian and prostate cancers, CDK12 loss-of-function (CDK12-LOF) alterations are not associated with a homologous recombination deficiency (HRD) phenotype but are instead associated with the tandem-duplicator phenotype (TDP), a genomic signature characterized by focal tandem duplications (FTDs) with a bimodal size…”
BackgroundMethodResultInfluentialAndrogen receptor and MYC equilibration centralizes on developmental super-enhancer
Guo, H., Wu, Y., Nouri, M., Spisák, S., Russo, J. W., Sowalsky, A. G., Pomerantz, M. M., Wei, Z., Korthauer, K. D., Seo, J.-H., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-27077-y · Cited by 73 · see citing works
Accelerating precision medicine in metastatic prostate cancer
Mateo, J., McKay, R. R., Abida, W. M., Aggarwal, R. R., Alumkal, J. J., Alva, A. S., Feng, F. Y.-C., Gao, X. Y., Graff, J. N., Hussain, M., et al. (2020) · Nature Cancer · doi:10.1038/s43018-020-00141-0 · Cited by 74 · see citing works
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Hwang, J. H., Seo, J.-H., Beshiri, M. L., Wankowicz, S. A. M., Liu, D., Cheung, A. T. M., Li, J., Qiu, X., Hong, A. L., Botta, G., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.10.068 · Cited by 71 · see citing works
“, 2015) or its enhancer (Takeda et al., 2018; Viswanathan et al., 2018) are frequently observed in metastatic castration-resistant prostate cancer (mCRPC).”
BackgroundSelf-citationThe role of the histone H3 variant CENPA in prostate cancer
Saha, A. K., Contreras-Galindo, R., Niknafs, Y. S., Iyer, M. K., Qin, T., Padmanabhan, K., Siddiqui, J., Palande, M., Wang, C., Qian, B., et al. (2020) · Journal of Biological Chemistry · doi:10.1074/jbc.ra119.010080 · Cited by 69 · see citing works
“CENPA is infrequently mutated and amplified in metastatic prostate cancer (40, 41).”
Noncoding mutations target cis-regulatory elements of the FOXA1 plexus in prostate cancer
Zhou, S., Hawley, J. R., Soares, F., Grillo, G., Teng, M., Tonekaboni, S. A. M., Hua, J. T., Kron, K. J., Mazrooei, P., Ahmed, M., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-14318-9 · Cited by 68 · see citing works
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Oncogenic CDK13 mutations impede nuclear RNA surveillance
Insco, M. L., Abraham, B. J., Dubbury, S. J., Kaltheuner, I. H., Dust, S., Wu, C., Chen, K. Y., Liu, D., Bellaousov, S., Cox, A. M., et al. (2023) · Science · doi:10.1126/science.abn7625 · Cited by 65 · see citing works
“9%), cancer cell lines (8%) Prostate, ovarian (64, 65) .”
BackgroundGonthier, K., Poluri, R. T. K., & Audet‐Walsh, É. (2019) · The Journal of Steroid Biochemistry and Molecular Biology · doi:10.1016/j.jsbmb.2019.04.016 · Cited by 67 · see citing works
Ghildiyal, R., Sawant, M., Renganathan, A., Mahajan, K. N., Kim, E. H., Luo, J., Dang, H. X., Maher, C. A., Feng, F. Y.-C., & Mahajan, N. P. (2021) · Cancer Research · doi:10.1158/0008-5472.can-20-3845 · Cited by 66 · see citing works
PTEN‐PI3K pathway alterations in advanced prostate cancer and clinical implications
Choudhury, A. D. (2022) · The Prostate · doi:10.1002/pros.24372 · Cited by 66 · see citing works
“deletions for PTEN because of normal cell contamination, and may not detect certain structural alterations detectable through linked‐ read genome sequencing.(31)”
BackgroundSelf-citationZhao, R., Lv, Y., Feng, T., Zhang, R., Ge, L., Pan, J., Han, B., Song, G., & Wang, L. (2022) · The Prostate · doi:10.1002/pros.24308 · Cited by 64 · see citing works
“However, all patients will ultimately relapse with incurable castration‐ resistant prostate cancer (CRPC).(1) Previous studies demonstrated that lipid metabolism was altered during the development of CRPC, and an increase in intratumoral essential polyunsaturated fatty acids (PUFAs) was observed.”
BackgroundInsight into Recent Advances in Degrading Androgen Receptor for Castration-Resistant Prostate Cancer
Chen, Q., Munoz, E., & Ashong, D. (2024) · Cancers · doi:10.3390/cancers16030663 · Cited by 64 · see citing works
A Practical Guide for Structural Variation Detection in the Human Genome
Yang, L. (2020) · Current Protocols in Human Genetics · doi:10.1002/cphg.103 · Cited by 63 · see citing works
“For example, linked-read sequencing was used to resolve haplotypes and somatic SVs in metastatic castration-resistant prostate cancers (Viswanathan et al., 2018).”
MethodSperger, J. M., Emamekhoo, H., McKay, R. R., Stahlfeld, C. N., Singh, A., Chen, X. E., Kwak, L., Gilsdorf, C. S., Wolfe, S. K., Wei, X. X., et al. (2021) · Journal of Clinical Oncology · doi:10.1200/jco.21.00169 · Cited by 61 · see citing works
Self-citationZhang, Y., Ming, A., Wang, J., Chen, W., & Fang, Z. (2024) · Pharmacological Research · doi:10.1016/j.phrs.2024.107234 · Cited by 63 · see citing works
Androgen receptor-binding sites are highly mutated in prostate cancer
Morova, T., McNeill, D. R., Lallous, N., Gönen, M., Dalal, K., Wilson, D. M. I., Gürsoy, A., Keskin, Ö., & Lack, N. (2020) · Nature Communications · doi:10.1038/s41467-020-14644-y · Cited by 52 · see citing works
Aneuploidy and complex genomic rearrangements in cancer evolution
Baker, T. M., Waise, S., Tarabichi, M., & Loo, P. V. (2024) · Nature Cancer · doi:10.1038/s43018-023-00711-y · Cited by 59 · see citing works
“Chromoplexy chains often co-occur with other rearrangement patterns, such as chromothripsis (discussed below) and may have a causal role in some of these events 114,117,134,135 .”
The landscape of RNA polymerase II–associated chromatin interactions in prostate cancer
Ramanand, S. G., Chen, Y., Yuan, J., Daescu, K., Lambros, M. B. K., Houlahan, K. E., Carreira, S., Yuan, W., Baek, G., Sharp, A., et al. (2020) · Journal of Clinical Investigation · doi:10.1172/jci134260 · Cited by 57 · see citing works
Genomic Profiling of Prostate Cancer: An Updated Review
Hatano, K., & Nonomura, N. (2021) · The World Journal of Men s Health · doi:10.5534/wjmh.210072 · Cited by 51 · see citing works
Dong, Q., Qiu, H., Piao, C., Li, Z., & Cui, X. (2023) · Journal of Experimental & Clinical Cancer Research · doi:10.1186/s13046-023-02774-2 · Cited by 52 · see citing works
Clinical Applications of Liquid Biopsy in Prostate Cancer: From Screening to Predictive Biomarker
Ionescu, F., Zhang, J., & Wang, L. (2022) · Cancers · doi:10.3390/cancers14071728 · Cited by 50 · see citing works
Burris, T. P., de Vera, I. M. S., Côté, I., Flaveny, C. A., Wanninayake, U. S., Chatterjee, A., Walker, J. K., Steinauer, N., Zhang, J., Coons, L. A., et al. (2023) · Pharmacological Reviews · doi:10.1124/pharmrev.121.000436 · Cited by 53 · see citing works
Targeting the androgen receptor and overcoming resistance in prostate cancer
Einstein, D. J., Arai, S., & Balk, S. P. (2019) · Current Opinion in Oncology · doi:10.1097/cco.0000000000000520 · Cited by 50 · see citing works
Androgen Receptor-Mediated Transcription in Prostate Cancer
Özturan, D., Morova, T., & Lack, N. A. (2022) · Cells · doi:10.3390/cells11050898 · Cited by 50 · see citing works
New Prognostic Biomarkers in Metastatic Castration-Resistant Prostate Cancer
Conteduca, V., Mosca, A., Brighi, N., Giorgi, U. D., & Rescigno, P. (2021) · Cells · doi:10.3390/cells10010193 · Cited by 48 · see citing works
“Its alterations are found in nearly 10% of mCRPC patients [6,60], but its loss does not determine the same mutational signature as BRCA1 or BRCA2 biallelic loss [74,75].”
BackgroundFuture directions for precision oncology in prostate cancer
Mizuno, K., & Beltran, H. (2022) · The Prostate · doi:10.1002/pros.24354 · Cited by 46 · see citing works
“In CRPC, amplification of an upstream enhancer of the androgen receptor (AR) gene leads to resistance to AR pathway inhibitor (ARPI) therapy.(4,15,16) A comprehensive analysis of nearly 200 patients with metastatic CRPC defined distinct genomic subgroups by WGS, including a cluster with a”
BackgroundHa, S., Luo, G., & Xiang, H. (2022) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.2c01487 · Cited by 48 · see citing works
Structural variants shape driver combinations and outcomes in pediatric high-grade glioma
Dubois, F. P. B., Shapira, O., Greenwald, N. F., Zack, T. I., Wala, J. A., Tsai, J. W., Crane, A., Baguette, A., Hadjadj, D., Harutyunyan, A. S., et al. (2022) · Nature Cancer · doi:10.1038/s43018-022-00403-z · Cited by 39 · see citing works
Self-citationTakayama, K., Kosaka, T., Suzuki, T., Hongo, H., Oya, M., Fujimura, T., Suzuki, Y., & Inoue, S. (2021) · Nature Communications · doi:10.1038/s41467-021-23974-4 · Cited by 45 · see citing works
Liu, Y., Wu, Z., Zhou, J. R., Ramadurai, D. K. A., Mortenson, K. L., Aguilera-Jimenez, E., Yan, Y., Yang, X., Taylor, A. M., Varley, K. E., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-27055-4 · Cited by 43 · see citing works
Zhao, S. G., Bootsma, M., Zhou, S., Shrestha, R., Moreno-Rodriguez, T., Lundberg, A., Pan, C., Arlidge, C., Hawley, J. R., Foye, A., et al. (2024) · Nature Genetics · doi:10.1038/s41588-024-01826-3 · Cited by 42 · see citing works
“A plateau of amplification and 5hmC/hypomethylation of both the AR gene itself and its regulatory plexus of coampli-fied enhancers, is thought to be a critical driver of overexpression and resistance to therapies targeting AR 4,5,7,11,12 .”
Self-citationGermain, L., Lafront, C., Paquette, V., Neveu, B., Paquette, J., Pouliot, F., & Audet‐Walsh, É. (2023) · Nature Reviews Urology · doi:10.1038/s41585-023-00726-1 · Cited by 43 · see citing works
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Application of long-read sequencing to the detection of structural variants in human cancer genomes
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“In 2018, Viswanathan et al. performed a linked-read whole-genome sequencing of 23 metastatic castration-resistant prostate cancers using biopsy specimens [50].”
BackgroundTang, S., Sethunath, V., Metaferia, N. Y., Nogueira, M. F., Gallant, D. S., Garner, E. R., Lairson, L. A., Penney, C. M., Li, J., Gelbard, M. K., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.110417 · Cited by 42 · see citing works
Self-citationCDK12: cellular functions and therapeutic potential of versatile player in cancer
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“The CDK12-specific focal tandem duplications with a high number of duplications and fusions can lead to the differential expression of oncogenic drivers such as CCND1 or AR (androgen receptor) or c-MYC enhancers as a secondary genetic event of CDK12 inactivation (88,89,111).”
BackgroundRecent Discoveries in the Androgen Receptor Pathway in Castration-Resistant Prostate Cancer
Obinata, D., Lawrence, M. G., Takayama, K., Choo, N., Risbridger, G. P., Takahashi, S., & Inoue, S. (2020) · Frontiers in Oncology · doi:10.3389/fonc.2020.581515 · Cited by 42 · see citing works
“Amplifications of the AR and its enhancer are associated with higher levels of AR expression, and over-expressing the AR in prostate cancer cell lines causes enzalutamide-resistance (20, 21).”
BackgroundDNA repair defects in prostate cancer: impact for screening, prognostication and treatment
Warner, E. W., Yip, S., Chi, K. N., & Wyatt, A. W. (2018) · British Journal of Urology · doi:10.1111/bju.14576 · Cited by 42 · see citing works
Darolutamide antagonizes androgen signaling by blocking enhancer and super‐enhancer activation
Baumgart, S. J., Nevedomskaya, E., Lesche, R., Newman, R., Mumberg, D., & Haendler, B. (2020) · Molecular Oncology · doi:10.1002/1878-0261.12693 · Cited by 40 · see citing works
“Indeed, a majority of metastatic PCa lesions have amplification of the AR gene and/or of an upstream regulatory enhancer element (Quigley et al., 2018; Robinson et al., 2011; Takeda et al., 2018; Viswanathan et al., 2018).”
BackgroundThe genetic evolution of acral melanoma
Wang, M., Fukushima, S., Sheen, Y., Ramelyte, E., Cruz‐Pacheco, N., Shi, C., Liu, S., Banik, I., Aquino, J. D., Acosta, M. S., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-50233-z · Cited by 39 · see citing works
“Tumor purity and ploidy were resolved by using the following formula 49 : Here ρ and φ represent tumorpurity and ploidy, respectively.”
Larsson, P., Khaja, A. S. S., Semenas, J., Wang, T., Sarwar, M., Dizeyi, N., Simoulis, A., Hedblom, A., Wai, S. N., Ødum, N., et al. (2019) · International Journal of Cancer · doi:10.1002/ijc.32607 · Cited by 38 · see citing works
“recently reported to be associated with inactivated tumor suppressor PTEN, a negative regulator of PI3K/AKT pathways.(3,4)”
Background
- Authors
- Viswanathan, S. R., Ha, G., Hoff, A. M., Wala, J. A., Carrot-Zhang, J., Whelan, C. W., Haradhvala, N. J., Freeman, S. S., Reed, S. C., Rhoades, J., Polak, P., Cipicchio, M., Wankowicz, S. A., Wong, A., Kamath, T., Zhang, Z., Gydush, G. J., Rotem, D., Love, J. C., Getz, G., Gabriel, S., Zhang, C.-Z., Dehm, S. M., Nelson, P. S., Van Allen, E. M., Choudhury, A. D., Adalsteinsson, V. A., Beroukhim, R., Taplin, M.-E., & Meyerson, M.
- Affiliations
- Broad Institute (US)
- Icahn School of Medicine at Mount Sinai (US)
- Dana-Farber Cancer Institute (US)
- University of Minnesota (US)
- Fred Hutch Cancer Center (US)
- Harvard University (US)
- Corresponding author
- Meyerson, Matthew
- ORCID
- Viswanathan, Srinivas R.
- Ha, Gavin
- Hoff, Andreas M.
- Wala, Jeremiah A.
- Whelan, Christopher W.
- Haradhvala, Nicholas J.
- Freeman, Samuel S.
- Reed, Sarah C.
- Rhoades, Justin
- Polak, Paz
- Cipicchio, Michelle
- Wankowicz, Stephanie A.
- Wong, Alicia
- Kamath, Tushar
- Zhang, Zhenwei
- Rotem, Denisse
- Love, J. Christopher
- Getz, Gad
- Gabriel, Stacey
- Zhang, Cheng-Zhong
- Dehm, Scott M.
- Nelson, Peter S.
- Choudhury, Atish D.
- Adalsteinsson, Viktor A.
- Beroukhim, Rameen
- Taplin, Mary-Ellen
- Meyerson, Matthew
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2018-07
- Volume
- 174
- Issue
- 2
- Pages
- 433-447.e19
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC6046279
- OpenAlex
- W2807985734
- Cited by
- 365
- References
- 65
- Citations by year
- 2026: 17 · 2025: 28 · 2024: 47 · 2023: 48 · 2022: 59 · 2021: 51 · 2020: 53 · 2019: 45 · 2018: 16
- FWCI
- 31.27
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- www.elsevier.com/open-access/userlicense/1.0/ (vor, 376 d)
- doi.org/10.15223/policy-017 (stm-asf)
- doi.org/10.15223/policy-037 (stm-asf)
- doi.org/10.15223/policy-012 (stm-asf)
- doi.org/10.15223/policy-029 (stm-asf)
- doi.org/10.15223/policy-004 (stm-asf)
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc-nd)
- Funders
- Department of Defense (W81XWH-17-1-0358)
- Prostate Cancer Foundation Young Investigator Award
- Canadian Institutes of Health Research (MFE-140389)
- Norwegian Cancer Society (PR-2007-0166)
- NIH (K08 CA188615, R01CA174777, P01CA163227, NIH R01 CA215489)
- NCI (R35 CA197568)
- PCF-V Foundation
- Movember
- PCF
- Gerstner Family Foundation
- Prostate SPORE (P50CA097186)
- Fund for Innovation in Cancer Informatics
- American Cancer Society Research Professorship
- American Association for Cancer Research (SU2C-AACR-DT0712)
- Topics
- Health Sciences › Medicine › Pulmonary and Respiratory Medicine › Prostate Cancer Treatment and Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Keywords
- castration-resistant prostate cancer, metastatic prostate cancer, tandem duplication, genome rearrangement, cell-free DNA, linked-read sequencing
- MeSH terms
- Whole Genome Sequencing, Aged, Anilides, Enhancer Elements, Genetic, Haplotypes, Humans, Male, Middle Aged, Neoplasm Metastasis, Phenotype, Pyridines, Receptors, Androgen, Gene Rearrangement, Genes, myc, Prostate-Specific Antigen, Cyclin-Dependent Kinases, Gene Duplication, Protein Kinase Inhibitors, PTEN Phosphohydrolase, Genetic Loci, Prostatic Neoplasms, Castration-Resistant
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