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Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer
Open accessAbstract
SUMMARY While mutations affecting protein-coding regions have been examined across many cancers, structural variants at the genome-wide level are still poorly defined. Through integrative deep whole genome and transcriptome analysis of 101 castration-resistant prostate cancer metastases (109X tumor / 38X normal coverage), we identified structural variants altering critical regulators of tumorigenesis and progression not detectable by exome approaches. Notably, we observed amplification of an intergenic enhancer region 624 kilobases upstream of the androgen receptor (AR) in 81% of patients, correlating with increased AR expression. Tandem duplication hotspots also occur near MYC, in lncRNAs associated with post-translational MYC regulation. Classes of structural variations were linked to distinct DNA repair deficiencies, suggesting their etiology, including associations of CDK12 mutation with tandem duplications, TP53 inactivation with inverted rearrangements and chromothripsis, and BRCA2 inactivation with deletions. Together, these observations provide a comprehensive view of how structural variations affect critical regulators in metastatic prostate cancer.
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“Most PCas express AR throughout the course of the disease2–5”
From Genome-scale CRISPR screens identify PTGES3 as a direct modulator of androgen receptor function in advanced prostate cancer (2025) · cites this paper as [2]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“The androgen receptor (AR) is a critical driver of prostate cancer (PCa).”
From Genome-scale CRISPR screens identify PTGES3 as a direct modulator of androgen receptor function in advanced prostate cancer (2025) · cites this paper as [2]
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“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 [2]
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“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 [2]
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“However, deep deletions (primarily of BRCA2; Supplementary Fig. 23) occurred much more frequently in prostate cancer (33%) compared to other cancer types, consistent with previous observations28.”
From Pan-cancer landscape of homologous recombination deficiency. (2020) · cites this paper as [28]
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CHD1 Is a 5q21 Tumor Suppressor Required for ERG Rearrangement in Prostate Cancer
Burkhardt, L., Fuchs, S., Krohn, A., Masser, S., Mäder, M., Kluth, M., Bachmann, F., Huland, H., Steuber, T. P., Graefen, M., et al. (2013) · Cancer Research · doi:10.1158/0008-5472.can-12-1342 · Cited by 218 · cited 5×
“ETS gene family activations weremutually exclusive with activating alterations in the RAS/MAPK pathway members (p = 0.01, Fisher’s exact test) and with inactivation of SPOP and CHD1 (Barbieri et al., 2012; Burkhardt et al., 2013; Huang et al., 2012).”
InfluentialCanvas: versatile and scalable detection of copy number variants
Roller, E., Ivakhno, S., Lee, S., Royce, T., & Tanner, S. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw163 · Cited by 206
Blattner, M., Liu, D., Robinson, B. D., Huang, D., Poliakov, A., Gao, D., Nataraj, S., Deonarine, L. D., Augello, M. A., Sailer, V., et al. (2017) · Cancer Cell · doi:10.1016/j.ccell.2017.02.004 · Cited by 204
Self-citationKron, K. J., Murison, A. J., Zhou, S., Huang, V., Yamaguchi, T. N., Shiah, Y.-J., Fraser, M. E., van der Kwast, T., Boutros, P. C., Bristow, R. G., et al. (2017) · Nature Genetics · doi:10.1038/ng.3930 · Cited by 189 · cited 1×
“Previously published data from 19 primary prostate tumors revealed that the minimally targeted region at the upstream peak was enriched for H3K27ac histone modifications (Kron et al., 2017) (Figure 2A, middle and bottom).”
Chromothripsis and Human Disease: Piecing Together the Shattering Process
Maher, C. A., & Wilson, R. K. (2012) · Cell · doi:10.1016/j.cell.2012.01.006 · Cited by 159 · cited 1×
“all undergone chromothripsis, the shattering and subsequent reconstruction of a single chromosome (Figure 3C, right; Figure 3D, orange points) (Fraser et al., 2017; Maher and Wilson, 2012; Stephens et al., 2011; Zack et al., 2013) (Figure 3B, right).”
Self-citationPopova, T., Manié, E., Boeva, V., Battistella, A., Goundiam, O., Smith, N. K., Mueller, C. R., Raynal, V., Mariani, O., Sastre-Garau, X., et al. (2016) · Cancer Research · doi:10.1158/0008-5472.can-15-2128 · Cited by 130 · cited 1×
“These results were consistent with results previously reported in ovarian cancer (Popova et al., 2016).”
Recurrent deletion of CHD1 in prostate cancer with relevance to cell invasiveness
Huang, S., Gulzar, Z. G., Salari, K., Lapointe, J., Brooks, J. D., & Pollack, J. R. (2011) · Oncogene · doi:10.1038/onc.2011.590 · Cited by 109 · cited 5×
“ETS gene family activations weremutually exclusive with activating alterations in the RAS/MAPK pathway members (p = 0.01, Fisher’s exact test) and with inactivation of SPOP and CHD1 (Barbieri et al., 2012; Burkhardt et al., 2013; Huang et al., 2012).”
InfluentialThe lncRNAs PCGEM1 and PRNCR1 are not implicated in castration resistant prostate cancer
Prensner, J. R., Sahu, A., Iyer, M. K., Malik, R., Chandler, B. C., Asangani, I. A., Poliakov, A., Vergara, I. A., Alshalalfa, M., Jenkins, R. B., et al. (2014) · Oncotarget · doi:10.18632/oncotarget.1846 · Cited by 100 · cited 1×
“Although PRNCR1 is unlikely to be implicated in mCRPC pathogenesis (Prensner et al., 2014), PCAT-1 has been shown to upregulate cMyc protein levels post-translationally (Prensner et al.”
Self-citationHeterogeneity in the inter-tumor transcriptome of high risk prostate cancer
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Self-citation
Flagged first, then by citations
1 of the 73 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
Genomic correlates of clinical outcome in advanced prostate cancer
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Self-citationA decade of clinical development of PARP inhibitors in perspective
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Protein degraders enter the clinic — a new approach to cancer therapy
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Structural variation in the sequencing era
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Metadata
- Authors
- 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., Playdle, D., Barnard, T. J., Zhang, L., Zhang, J., Youngren, J. F., Cieslik, M. P., Parolia, A., Beer, T. M., Thomas, G., Chi, K. N., Gleave, M., Lack, N. A., Zoubeidi, A., Reiter, R. E., Rettig, M. B., Witte, O., Ryan, C. J., Fong, L., Kim, W., Friedlander, T., Chou, J., Li, H., Das, R., Li, H., Moussavi-Baygi, R., Goodarzi, H., Gilbert, L. A., Lara, P. N., Evans, C. P., Goldstein, T. C., Stuart, J. M., Tomlins, S. A., Spratt, D. E., Cheetham, R. K., Cheng, D. T., Farh, K., Gehring, J. S., Hakenberg, J., Liao, A., Febbo, P. G., Shon, J., Sickler, B., Batzoglou, S., Knudsen, K. E., He, H. H., Huang, J., Wyatt, A. W., Dehm, S. M., Ashworth, A., Chinnaiyan, A. M., Maher, C. A., Small, E. J., & Feng, F. Y.
- Affiliations
- University of California, San Francisco (US)
- Washington University in St. Louis (US)
- University of Michigan (US)
- Oregon Health & Science University (US)
- BC Cancer Agency (CA)
- University of British Columbia (CA)
- University of California, Los Angeles (US)
- University of Minnesota (US)
- University of California Davis Medical Center (US)
- University of California, Santa Cruz (US)
- Illumina (United States) (US)
- Thomas Jefferson University (US)
- University Health Network (CA)
- Duke University (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Chinnaiyan, Arul M.
- Maher, Christopher A.
- Small, Eric J.
- Feng, Felix Y.
- ORCID
- Quigley, David A.
- Dang, Ha X.
- Zhao, Shuang G.
- Lloyd, Paul
- Aggarwal, Rahul
- Alumkal, Joshi J.
- Foye, Adam
- Kothari, Vishal
- Perry, Marc D.
- Zhang, Li
- Zhang, Jin
- Youngren, Jack F.
- Cieslik, Marcin P.
- Parolia, Abhijit
- Beer, Tomasz M.
- Thomas, George
- Chi, Kim N.
- Gleave, Martin
- Lack, Nathan A.
- Zoubeidi, Amina
- Reiter, Robert E.
- Rettig, Matthew B.
- Witte, Owen
- Ryan, Charles J.
- Fong, Lawrence
- Kim, Won
- Friedlander, Terence
- Chou, Jonathan
- Li, Haolong
- Das, Rajdeep
- Li, Hui
- Goodarzi, Hani
- Gilbert, Luke A.
- Lara, Primo N.
- Evans, Christopher P.
- Goldstein, Theodore C.
- Stuart, Joshua M.
- Tomlins, Scott A.
- Spratt, Daniel E.
- Farh, Kyle
- Gehring, Julian S.
- Hakenberg, Jörg
- Shon, John
- Sickler, Brad
- Batzoglou, Serafim
- Knudsen, Karen E.
- He, Housheng H.
- Huang, Jiaoti
- Wyatt, Alexander W.
- Dehm, Scott M.
- Ashworth, Alan
- Chinnaiyan, Arul M.
- Maher, Christopher A.
- Small, Eric J.
- Feng, Felix Y.
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2018-07
- Volume
- 174
- Issue
- 3
- Pages
- 758-769.e9
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC6425931
- OpenAlex
- W2884001931
- Semantic Scholar
- c72ffe522bd85597687b47e4d3db90ec72b4fc80
- Cited by
- 733
- References
- 73
- Citations by year
- 2026: 48 · 2025: 73 · 2024: 102 · 2023: 107 · 2022: 94 · 2021: 110 · 2020: 102 · 2019: 81 · 2018: 15
- FWCI
- 58.02
- Type
- journal article
- Language
- en
- Update notices
- erratum (2018-10-18)
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- Stand Up To Cancer-Prostate Cancer Foundation Prostate Cancer Dream Team Award (SU2C-AACR-DT0812, SU2C-AACR-DT0712)
- Movember Foundation
- Goldberg-Benioff Research Fund for Prostate Cancer Translational Biology
- Prostate Cancer Foundation Challenge
- V Foundation
- BRCA Foundation Young Investigator Award
- Department of Defense (W81XWH-16-1-0747, W81XWH-15-1-0562, PC160429, W81XWH-17-1-0192)
- Early Detection Research Network (U01 CA214170)
- Prostate SPORE (P50 CA186786, P50 CA097186)
- NIH (R01CA174777)
- NCI T32 (CA108462)
- Prostate Cancer Foundation Young Investigator Awards
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Prostate Cancer Treatment and Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- castration-resistant prostate cancer, metastatic prostate cancer, structural variants, androgen receptor, c-Myc, tandem duplication, long non-coding RNA, DNA repair deficiency, CDK12, TP53, chromothripsis, BRCA2
- MeSH terms
- Whole Genome Sequencing, Aged, Aged, 80 and over, Humans, Male, Middle Aged, Mutation, Neoplasm Metastasis, Prostatic Neoplasms, Receptors, Androgen, Tumor Suppressor Protein p53, Proto-Oncogene Proteins c-myc, Cyclin-Dependent Kinases, Tandem Repeat Sequences, Gene Expression Profiling, Genomics, BRCA2 Protein, Genomic Structural Variation, DNA Copy Number Variations, Exome
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