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Puca L, Bareja R, Prandi D, Shaw R, Benelli M, Karthaus WR, Hess J, Sigouros M, Donoghue A, Kossai M, Gao D, Cyrta J, Sailer V, Vosoughi A, Pauli C, Churakova Y, Cheung C, Deonarine LD, McNary TJ, Rosati R, Tagawa ST, Nanus DM, Mosquera JM, Sawyers CL, Chen Y, Inghirami G, Rao RA, Grandori C, Elemento O, Sboner A, Demichelis F, Rubin MA, Beltran H. Patient derived organoids to model rare prostate cancer phenotypes. Nat Commun 2018; 9:2404. [PMID: 29921838 PMCID: PMC6008438 DOI: 10.1038/s41467-018-04495-z] [Citation(s) in RCA: 227] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 04/25/2018] [Indexed: 12/25/2022] Open
Abstract
A major hurdle in the study of rare tumors is a lack of existing preclinical models. Neuroendocrine prostate cancer is an uncommon and aggressive histologic variant of prostate cancer that may arise de novo or as a mechanism of treatment resistance in patients with pre-existing castration-resistant prostate cancer. There are few available models to study neuroendocrine prostate cancer. Here, we report the generation and characterization of tumor organoids derived from needle biopsies of metastatic lesions from four patients. We demonstrate genomic, transcriptomic, and epigenomic concordance between organoids and their corresponding patient tumors. We utilize these organoids to understand the biologic role of the epigenetic modifier EZH2 in driving molecular programs associated with neuroendocrine prostate cancer progression. High-throughput organoid drug screening nominated single agents and drug combinations suggesting repurposing opportunities. This proof of principle study represents a strategy for the study of rare cancer phenotypes.
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Means AL, Freeman TJ, Zhu J, Woodbury LG, Marincola-Smith P, Wu C, Meyer AR, Weaver CJ, Padmanabhan C, An H, Zi J, Wessinger BC, Chaturvedi R, Brown TD, Deane NG, Coffey RJ, Wilson KT, Smith JJ, Sawyers CL, Goldenring JR, Novitskiy SV, Washington MK, Shi C, Beauchamp RD. Epithelial Smad4 Deletion Up-Regulates Inflammation and Promotes Inflammation-Associated Cancer. Cell Mol Gastroenterol Hepatol 2018; 6:257-276. [PMID: 30109253 PMCID: PMC6083016 DOI: 10.1016/j.jcmgh.2018.05.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 05/18/2018] [Indexed: 02/08/2023]
Abstract
Background & Aims Chronic inflammation is a predisposing condition for colorectal cancer. Many studies to date have focused on proinflammatory signaling pathways in the colon. Understanding the mechanisms that suppress inflammation, particularly in epithelial cells, is critical for developing therapeutic interventions. Here, we explored the roles of transforming growth factor β (TGFβ) family signaling through SMAD4 in colonic epithelial cells. Methods The Smad4 gene was deleted specifically in adult murine intestinal epithelium. Colitis was induced by 3 rounds of dextran sodium sulfate in drinking water, after which mice were observed for up to 3 months. Nontransformed mouse colonocyte cell lines and colonoid cultures and human colorectal cancer cell lines were analyzed for responses to TGFβ1 and bone morphogenetic protein 2. Results Dextran sodium sulfate treatment was sufficient to drive carcinogenesis in mice lacking colonic Smad4 expression, with resulting tumors bearing striking resemblance to human colitis-associated carcinoma. Loss of SMAD4 protein was observed in 48% of human colitis-associated carcinoma samples as compared with 19% of sporadic colorectal carcinomas. Loss of Smad4 increased the expression of inflammatory mediators within nontransformed mouse colon epithelial cells in vivo. In vitro analysis of mouse and human colonic epithelial cell lines and organoids indicated that much of this regulation was cell autonomous. Furthermore, TGFβ signaling inhibited the epithelial inflammatory response to proinflammatory cytokines. Conclusions TGFβ suppresses the expression of proinflammatory genes in the colon epithelium, and loss of its downstream mediator, SMAD4, is sufficient to initiate inflammation-driven colon cancer. Transcript profiling: GSE100082.
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Key Words
- AOM, azoxymethane
- APC, adenomatous polyposis coli
- BMP, bone morphogenetic protein
- CAC, colitis-associated carcinoma
- CCL20, Chemokine (C-C motif) ligand 20
- CRC, colorectal cancer
- CRISPR/Cas9, Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9
- Colitis-Associated Carcinoma
- DMEM, Dulbecco's modified Eagle medium
- DSS, dextran sodium sulfate
- FBS, fetal bovine serum
- FDR, false discovery rate
- GFP, green fluorescent protein
- HBSS, Hank's balanced salt solution
- IBD, inflammatory bowel disease
- IL, interleukin
- IMCS4fl/fl, immortalized mouse colonoctye cell line with loxP-flanked Smad4 alleles
- IMCS4null, immortalized mouse colonocyte cell line with deletion of the Smad4 alleles
- LPS, lipopolysaccharide
- PBS, phosphate-buffered saline
- PE, phycoerythrin
- R-SMAD, Receptor-SMAD
- SFG, retroviral vector
- STAT3, signal transducer and activator of transcription 3
- TGFβ
- TGFβ, transforming growth factor β
- TNF, tumor necrosis factor
- Tumor Necrosis Factor
- UC, ulcerative colitis
- WNT, wingless-type mouse mammary tumor virus integration site
- YAMC, young adult mouse colon epithelial cells
- mRNA, messenger RNA
- sgRNA, single-guide RNA
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Abida W, Cheng ML, Armenia J, Middha S, Autio KA, Rathkopf DE, Morris MJ, Danila DC, Slovin SF, Carbone E, Hullings M, Hechtman JF, Reuter VE, Berger MF, Kantoff PW, Sawyers CL, Schultz N, Solit DB, Gopalan A, Scher HI. Microsatellite instability in prostate cancer and response to immune checkpoint blockade. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.5020] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Armenia J, Wankowicz SAM, Liu D, Gao J, Kundra R, Reznik E, Chatila WK, Chakravarty D, Han GC, Coleman I, Montgomery B, Pritchard C, Morrissey C, Barbieri CE, Beltran H, Sboner A, Zafeiriou Z, Miranda S, Bielski CM, Penson AV, Tolonen C, Huang FW, Robinson D, Wu YM, Lonigro R, Garraway LA, Demichelis F, Kantoff PW, Taplin ME, Abida W, Taylor BS, Scher HI, Nelson PS, de Bono JS, Rubin MA, Sawyers CL, Chinnaiyan AM, Schultz N, Van Allen EM. The long tail of oncogenic drivers in prostate cancer. Nat Genet 2018; 50:645-651. [PMID: 29610475 PMCID: PMC6107367 DOI: 10.1038/s41588-018-0078-z] [Citation(s) in RCA: 529] [Impact Index Per Article: 88.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 01/26/2018] [Indexed: 01/05/2023]
Abstract
Comprehensive genomic characterization of prostate cancer has identified recurrent alterations in genes involved in androgen signaling, DNA repair, and PI3K signaling, among others. However, larger and uniform genomic analysis may identify additional recurrently mutated genes at lower frequencies. Here we aggregate and uniformly analyze exome sequencing data from 1,013 prostate cancers. We identify and validate a new class of E26 transformation-specific (ETS)-fusion-negative tumors defined by mutations in epigenetic regulators, as well as alterations in pathways not previously implicated in prostate cancer, such as the spliceosome pathway. We find that the incidence of significantly mutated genes (SMGs) follows a long-tail distribution, with many genes mutated in less than 3% of cases. We identify a total of 97 SMGs, including 70 not previously implicated in prostate cancer, such as the ubiquitin ligase CUL3 and the transcription factor SPEN. Finally, comparing primary and metastatic prostate cancer identifies a set of genomic markers that may inform risk stratification.
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Settleman J, Sawyers CL, Hunter T. Challenges in validating candidate therapeutic targets in cancer. eLife 2018; 7:e32402. [PMID: 29417929 PMCID: PMC5805407 DOI: 10.7554/elife.32402] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 01/20/2018] [Indexed: 12/18/2022] Open
Abstract
More than 30 published articles have suggested that a protein kinase called MELK is an attractive therapeutic target in human cancer, but three recent reports describe compelling evidence that it is not. These reports highlight the caveats associated with some of the research tools that are commonly used to validate candidate therapeutic targets in cancer research.
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Luo J, Attard G, Balk SP, Bevan C, Burnstein K, Cato L, Cherkasov A, De Bono JS, Dong Y, Gao AC, Gleave M, Heemers H, Kanayama M, Kittler R, Lang JM, Lee RJ, Logothetis CJ, Matusik R, Plymate S, Sawyers CL, Selth LA, Soule H, Tilley W, Weigel NL, Zoubeidi A, Dehm SM, Raj GV. Role of Androgen Receptor Variants in Prostate Cancer: Report from the 2017 Mission Androgen Receptor Variants Meeting. Eur Urol 2017; 73:715-723. [PMID: 29258679 DOI: 10.1016/j.eururo.2017.11.038] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 11/28/2017] [Indexed: 12/17/2022]
Abstract
CONTEXT Although a number of studies have demonstrated the importance of constitutively active androgen receptor variants (AR-Vs) in prostate cancer, questions still remain about the precise role of AR-Vs in the progression of castration-resistant prostate cancer (CRPC). OBJECTIVE Key stakeholders and opinion leaders in prostate cancer convened on May 11, 2017 in Boston to establish the current state of the field of AR-Vs. EVIDENCE ACQUISITION The meeting "Mission Androgen Receptor Variants" was the second of its kind sponsored by the Prostate Cancer Foundation (PCF). This invitation-only event was attended by international leaders in the field and representatives from sponsoring organizations (PCF and industry sponsors). Eighteen faculty members gave short presentations, which were followed by in-depth discussions. Discussions focused on three thematic topics: (1) potential of AR-Vs as biomarkers of therapeutic resistance; (2) role of AR-Vs as functionally active CRPC progression drivers; and (3) utility of AR-Vs as therapeutic targets in CRPC. EVIDENCE SYNTHESIS The three meeting organizers synthesized this meeting report, which is intended to summarize major data discussed at the meeting and identify key questions as well as strategies for addressing these questions. There was a critical consensus that further study of the AR-Vs is an important research focus in CRPC. Contrasting views and emphasis, each supported by data, were presented at the meeting, discussed among the participants, and synthesized in this report. CONCLUSIONS This article highlights the state of knowledge and outlines the most pressing questions that need to be addressed to advance the AR-V field. PATIENT SUMMARY Although further investigation is needed to delineate the role of androgen receptor (AR) variants in metastatic castration-resistant prostate cancer, advances in measurement science have enabled development of blood-based tests for treatment selection. Detection of AR variants (eg, AR-V7) identified a patient population with poor outcomes to existing AR-targeting therapies, highlighting the need for novel therapeutic agents currently under development.
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Liu X, Grogan TR, Hieronymus H, Hashimoto T, Mottahedeh J, Cheng D, Zhang L, Huang K, Stoyanova T, Park JW, Shkhyan RO, Nowroozizadeh B, Rettig MB, Sawyers CL, Elashoff D, Horvath S, Huang J, Witte ON, Goldstein AS. Low CD38 Identifies Progenitor-like Inflammation-Associated Luminal Cells that Can Initiate Human Prostate Cancer and Predict Poor Outcome. Cell Rep 2017; 17:2596-2606. [PMID: 27926864 PMCID: PMC5367888 DOI: 10.1016/j.celrep.2016.11.010] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 09/27/2016] [Accepted: 10/28/2016] [Indexed: 12/19/2022] Open
Abstract
Inflammation is a risk factor for prostate cancer, but the mechanisms by which inflammation increases that risk are poorly understood. Here, we demonstrate that low expression of CD38 identifies a progenitor-like subset of luminal cells in the human prostate. CD38lo luminal cells are enriched in glands adjacent to inflammatory cells and exhibit epithelial nuclear factor κB (NF-κB) signaling. In response to oncogenic transformation, CD38lo luminal cells can initiate human prostate cancer in an in vivo tissue-regeneration assay. Finally, the CD38lo luminal phenotype and gene signature are associated with disease progression and poor outcome in prostate cancer. Our results suggest that prostate inflammation expands the pool of progenitor-like target cells susceptible to tumorigenesis.
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Hieronymus H, Iaquinta PJ, Wongvipat J, Gopalan A, Murali R, Mao N, Carver BS, Sawyers CL. Deletion of 3p13-14 locus spanning FOXP1 to SHQ1 cooperates with PTEN loss in prostate oncogenesis. Nat Commun 2017; 8:1081. [PMID: 29057879 PMCID: PMC5651901 DOI: 10.1038/s41467-017-01198-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 08/25/2017] [Indexed: 01/01/2023] Open
Abstract
A multigenic locus at 3p13-14, spanning FOXP1 to SHQ1, is commonly deleted in prostate cancer and lost broadly in a range of cancers but has unknown significance to oncogenesis or prognosis. Here, we report that FOXP1-SHQ1 deletion cooperates with PTEN loss to accelerate prostate oncogenesis and that loss of component genes correlates with prostate, breast, and head and neck cancer recurrence. We demonstrate that Foxp1-Shq1 deletion accelerates prostate tumorigenesis in mice in combination with Pten loss, consistent with the association of FOXP1-SHQ1 and PTEN loss observed in human cancers. Tumors with combined Foxp1-Shq1 and Pten deletion show increased proliferation and anaplastic dedifferentiation, as well as mTORC1 hyperactivation with reduced Akt phosphorylation. Foxp1-Shq1 deletion restores expression of AR target genes repressed in tumors with Pten loss, circumventing PI3K-mediated repression of the androgen axis. Moreover, FOXP1-SHQ1 deletion has prognostic relevance, with cancer recurrence associated with combined loss of PTEN and FOXP1-SHQ1 genes.
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Shah N, Wang P, Wongvipat J, Karthaus WR, Abida W, Armenia J, Rockowitz S, Drier Y, Bernstein BE, Long HW, Freedman ML, Arora VK, Zheng D, Sawyers CL. Regulation of the glucocorticoid receptor via a BET-dependent enhancer drives antiandrogen resistance in prostate cancer. eLife 2017; 6. [PMID: 28891793 PMCID: PMC5593504 DOI: 10.7554/elife.27861] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 08/24/2017] [Indexed: 12/18/2022] Open
Abstract
In prostate cancer, resistance to the antiandrogen enzalutamide (Enz) can occur through bypass of androgen receptor (AR) blockade by the glucocorticoid receptor (GR). In contrast to fixed genomic alterations, here we show that GR-mediated antiandrogen resistance is adaptive and reversible due to regulation of GR expression by a tissue-specific enhancer. GR expression is silenced in prostate cancer by a combination of AR binding and EZH2-mediated repression at the GR locus, but is restored in advanced prostate cancers upon reversion of both repressive signals. Remarkably, BET bromodomain inhibition resensitizes drug-resistant tumors to Enz by selectively impairing the GR signaling axis via this enhancer. In addition to revealing an underlying molecular mechanism of GR-driven drug resistance, these data suggest that inhibitors of broadly active chromatin-readers could have utility in nuanced clinical contexts of acquired drug resistance with a more favorable therapeutic index.
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Mandelker D, Zhang L, Kemel Y, Stadler ZK, Joseph V, Zehir A, Pradhan N, Arnold A, Walsh MF, Li Y, Balakrishnan AR, Syed A, Prasad M, Nafa K, Carlo MI, Cadoo KA, Sheehan M, Fleischut MH, Salo-Mullen E, Trottier M, Lipkin SM, Lincoln A, Mukherjee S, Ravichandran V, Cambria R, Galle J, Abida W, Arcila ME, Benayed R, Shah R, Yu K, Bajorin DF, Coleman JA, Leach SD, Lowery MA, Garcia-Aguilar J, Kantoff PW, Sawyers CL, Dickler MN, Saltz L, Motzer RJ, O'Reilly EM, Scher HI, Baselga J, Klimstra DS, Solit DB, Hyman DM, Berger MF, Ladanyi M, Robson ME, Offit K. Mutation Detection in Patients With Advanced Cancer by Universal Sequencing of Cancer-Related Genes in Tumor and Normal DNA vs Guideline-Based Germline Testing. JAMA 2017; 318:825-835. [PMID: 28873162 PMCID: PMC5611881 DOI: 10.1001/jama.2017.11137] [Citation(s) in RCA: 329] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
IMPORTANCE Guidelines for cancer genetic testing based on family history may miss clinically actionable genetic changes with established implications for cancer screening or prevention. OBJECTIVE To determine the proportion and potential clinical implications of inherited variants detected using simultaneous sequencing of the tumor and normal tissue ("tumor-normal sequencing") compared with genetic test results based on current guidelines. DESIGN, SETTING, AND PARTICIPANTS From January 2014 until May 2016 at Memorial Sloan Kettering Cancer Center, 10 336 patients consented to tumor DNA sequencing. Since May 2015, 1040 of these patients with advanced cancer were referred by their oncologists for germline analysis of 76 cancer predisposition genes. Patients with clinically actionable inherited mutations whose genetic test results would not have been predicted by published decision rules were identified. Follow-up for potential clinical implications of mutation detection was through May 2017. EXPOSURE Tumor and germline sequencing compared with the predicted yield of targeted germline sequencing based on clinical guidelines. MAIN OUTCOMES AND MEASURES Proportion of clinically actionable germline mutations detected by universal tumor-normal sequencing that would not have been detected by guideline-directed testing. RESULTS Of 1040 patients, the median age was 58 years (interquartile range, 50.5-66 years), 65.3% were male, and 81.3% had stage IV disease at the time of genomic analysis, with prostate, renal, pancreatic, breast, and colon cancer as the most common diagnoses. Of the 1040 patients, 182 (17.5%; 95% CI, 15.3%-19.9%) had clinically actionable mutations conferring cancer susceptibility, including 149 with moderate- to high-penetrance mutations; 101 patients tested (9.7%; 95% CI, 8.1%-11.7%) would not have had these mutations detected using clinical guidelines, including 65 with moderate- to high-penetrance mutations. Frequency of inherited mutations was related to case mix, stage, and founder mutations. Germline findings led to discussion or initiation of change to targeted therapy in 38 patients tested (3.7%) and predictive testing in the families of 13 individuals (1.3%), including 6 for whom genetic evaluation would not have been initiated by guideline-based testing. CONCLUSIONS AND RELEVANCE In this referral population with selected advanced cancers, universal sequencing of a broad panel of cancer-related genes in paired germline and tumor DNA samples was associated with increased detection of individuals with potentially clinically significant heritable mutations over the predicted yield of targeted germline testing based on current clinical guidelines. Knowledge of these additional mutations can help guide therapeutic and preventive interventions, but whether all of these interventions would improve outcomes for patients with cancer or their family members requires further study. TRIAL REGISTRATION clinicaltrials.gov Identifier: NCT01775072.
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Hieronymus H, Iaquinta PJ, Wongvipat J, Gopalan A, Murali R, Mao N, Carver BS, Sawyers CL. Abstract 1537: 3p13-14 FOXP1-SHQ1 deletion spanning multiple potential tumor suppressor genes cooperates with PTEN loss in cancer. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-1537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The recurrent 3p13-14 deletion spanning from FOXP1 to SHQ1 occurs frequently in prostate cancer and is broadly lost in a range of cancer types, but this deletion has unknown tumor suppressive potential. FOXP1-SHQ1 deletion significantly co-occurs with PTEN loss in prostate cancer and other cancers. We find that FOXP1-SHQ1 deletion cooperates with PTEN loss to accelerate prostate cancer development in mice, resulting in tumors with increased proliferation and highly anaplastic dedifferentiation. FOXP1-SHQ1 deletion in these PTEN null tumors results in selective mTORC1 pathway hyperactivation beyond that mediated by PTEN loss alone. FOXP1-SHQ1 deletion also partially rescues AR target gene inhibition caused by PTEN loss, circumventing the repression of the androgen axis seen upon PI3K pathway activation. Clinically, combined FOXP1 and PTEN loss is associated with increased prostate cancer recurrence, and this finding extends to other cancer types, most notably breast cancer.
Citation Format: Haley Hieronymus, Philip J. Iaquinta, John Wongvipat, Anuradha Gopalan, Rajmohan Murali, Ninghui Mao, Brett S. Carver, Charles L. Sawyers. 3p13-14 FOXP1-SHQ1 deletion spanning multiple potential tumor suppressor genes cooperates with PTEN loss in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1537. doi:10.1158/1538-7445.AM2017-1537
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Mu P, Zhang Z, Benelli M, Karthaus W, Hoover E, Chen CC, Wongvipat J, Ku SY, Gao D, Cao Z, Shah N, Adams E, Abida W, Watson P, Prandi D, Huang CH, Stanchina ED, Lowe S, Ellis L, Beltran H, Rubin M, Goodrich D, Demichelis F, Sawyers CL. Abstract 4165: SOX2 promotes lineage plasticity and antiandrogen resistance in TP53 and RB1 deficient prostate cancer. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-4165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Some cancers evade targeted therapies through a mechanism known as lineage plasticity, whereby tumor cells acquire phenotypic characteristics of a cell lineage whose survival no longer depends on the drug target. Here we show, using in vitro and in vivo prostate cancer models, that these tumors can develop resistance to the antiandrogen drug enzalutamide by a phenotypic shift from androgen receptor (AR) dependent luminal epithelial cells to AR independent basal-like cells. This lineage plasticity is enabled by loss of TP53 and RB1 function, is mediated by increased expression of the reprogramming transcription factor SOX2 and can be reversed by restoring TP53 and RB1 function or by inhibiting SOX2 expression. Thus, mutations in tumor suppressor genes can create a state of increased cellular plasticity that, when challenged with antiandrogen therapy, promotes resistance through lineage switching.
Citation Format: Ping Mu, Zeda Zhang, Matteo Benelli, Wouter Karthaus, Elizebeth Hoover, Chi-Chao Chen, John Wongvipat, Sheng-Yu Ku, Dong Gao, Zhen Cao, Neel Shah, Elizabeth Adams, Wassim Abida, Philip Watson, Davide Prandi, Chun-Hao Huang, Elisa de Stanchina, Scott Lowe, Leigh Ellis, Himisha Beltran, Mark Rubin, David Goodrich, Francesca Demichelis, Charles L. Sawyers. SOX2 promotes lineage plasticity and antiandrogen resistance in TP53 and RB1 deficient prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4165. doi:10.1158/1538-7445.AM2017-4165
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Schram A, Won HH, Andre F, Arnedos M, Meric - Bernstam F, Bedard PL, Shaw KR, Horlings H, Micheel C, Park BH, Mann G, Lalani AS, Smyth L, Solit DB, Schrag D, Levy MA, Rollins BJ, Routbort M, Sawyers CL, Lepisto E, Berger MF, Hyman DM. Abstract LB-103: Landscape of somatic ERBB2 Mutations: Findings from AACR GENIE and comparison to ongoing ERBB2 mutant basket study. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-lb-103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: AACR GENIE is an international data-sharing project that aggregates clinical-grade cancer genomic data. As a demonstration of utility, we evaluated the landscape of ERBB2 mutations in the first 18,486 patients included in this registry and compared it to the first 100 patients enrolled in an ongoing international Phase 2 SUMMIT ‘basket’ study of the pan-HER inhibitor neratinib in ERBB2 mutant solid tumors (NCT01953926). Results: ERBB2 mutations were identified in 2.8% (519/18,486) of patients in the GENIE cohort and observed at all participating centers. In total, there were 482 missense, 66 indels, 19 truncating mutations, and 14 structural variants. A total of 263 unique missense mutations were observed including 12 at previously identified hotspots which accounted for 69.2% of all missense mutations. 35 unique cancer types were represented. The tumor types with the highest proportion of ERBB2 mutations were bladder (12.8%, 82/641), breast (3.9%, 87/2230), colorectal (3.3%, 70/2102), and NSCLC (3%, 90/3006). Among patients with copy number data available (91%) 11% had concurrent ERBB2 amplification, most often in breast cancer. The most frequently observed alterations in ERBB2, adjusted for differing exon coverage between panels, was S310F/Y in 0.46% of the GENIE cohort (12.6% of samples with ERBB2 alterations), Y772_A775dup in 0.21% (6.9%), R678Q in 0.17% (4.5%), L755S in 0.16% (5.2%), V777L in 0.12% (3.8%), and V842I in 0.09% (3.1%). The distribution of specific ERBB2 variants differed significantly by tumor type with exon 20 insertions being most common in NSCLC (44.4%, 40/90), L755S (18.9%, 11/92) in breast, S310F/Y (26.9%, 28/104) in bladder, and V842I (13.9%, 10/72) in colorectal cancer. Structural variants included intragenic deletions (n=4) and fusions involving various partners including GRB7 (n=2), and one each of C1orf87, PPIL6, HEXIM2, THRA, ASIC2, BCA3, WIPF2. The frequencies of ERBB2 mutant cancer types observed in the GENIE cohort were generally comparable to those enrolled to the neratinib basket study including NSCLC (17 vs 22%, respectively), breast (16.4 vs 24%), bladder (15.5 vs 14%), colorectal (13.2 vs 17%), and endometrial (4.2 vs 6%). At the variant level, S310F/Y was less prevalent in GENIE compared to the neratinib study (12.6 vs 24%) while all other mutations were generally similar including L755S (5.2 vs 9%), R678Q (4.5 vs 2%), Y772_A775dup (6.9 vs 13%), V777L (3.8 vs 9%), and V842I (3.1 vs 6%). Conclusion: GENIE confirms that a diversity of ERBB2 mutations are prevalent across a variety of tumor types in patients with advanced cancer. The genomic landscape of ERBB2 mutations was largely similar in the population based GENIE cohort and the neratinib SUMMIT study, providing the first direct evidence that basket study enrollment accurately reflects the true landscape of the target alteration.
Citation Format: Alison Schram, Helen H. Won, Fabrice Andre, Monica Arnedos, Funda Meric - Bernstam, Philippe L. Bedard, Kenna R. Shaw, Hugo Horlings, Christine Micheel, Ben Ho Park, Grace Mann, Alshad S. Lalani, Lillian Smyth, David B. Solit, Deborah Schrag, Mia A. Levy, Barrett J. Rollins, Mark Routbort, Charles L. Sawyers, Eva Lepisto, Michael F. Berger, David M. Hyman, on behalf of the AACR Project GENIE Consortium. Landscape of somatic ERBB2 Mutations: Findings from AACR GENIE and comparison to ongoing ERBB2 mutant basket study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-103. doi:10.1158/1538-7445.AM2017-LB-103
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Abida W, Armenia J, Gopalan A, Brennan R, Walsh M, Barron D, Danila D, Rathkopf D, Morris M, Slovin S, McLaughlin B, Curtis K, Hyman DM, Durack JC, Solomon SB, Arcila ME, Zehir A, Syed A, Gao J, Chakravarty D, Vargas HA, Robson ME, Vijai J, Offit K, Donoghue MT, Abeshouse AA, Kundra R, Heins ZJ, Penson AV, Harris C, Taylor BS, Ladanyi M, Mandelker D, Zhang L, Reuter VE, Kantoff PW, Solit DB, Berger MF, Sawyers CL, Schultz N, Scher HI. Prospective Genomic Profiling of Prostate Cancer Across Disease States Reveals Germline and Somatic Alterations That May Affect Clinical Decision Making. JCO Precis Oncol 2017; 2017:PO.17.00029. [PMID: 28825054 PMCID: PMC5558263 DOI: 10.1200/po.17.00029] [Citation(s) in RCA: 208] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
PURPOSE A long natural history and a predominant osseous pattern of metastatic spread are impediments to the adoption of precision medicine in patients with prostate cancer. To establish the feasibility of clinical genomic profiling in the disease, we performed targeted deep sequencing of tumor and normal DNA from patients with locoregional, metastatic non-castrate, and metastatic castration-resistant prostate cancer (CRPC). METHODS Patients consented to genomic analysis of their tumor and germline DNA. A hybridization capture-based clinical assay was employed to identify single nucleotide variations, small insertions and deletions, copy number alterations and structural rearrangements in over 300 cancer-related genes in tumors and matched normal blood. RESULTS We successfully sequenced 504 tumors from 451 patients with prostate cancer. Potentially actionable alterations were identified in DNA damage repair (DDR), PI3K, and MAP kinase pathways. 27% of patients harbored a germline or a somatic alteration in a DDR gene that may predict for response to PARP inhibition. Profiling of matched tumors from individual patients revealed that somatic TP53 and BRCA2 alterations arose early in tumors from patients who eventually developed metastatic disease. In contrast, comparative analysis across disease states revealed that APC alterations were enriched in metastatic tumors, while ATM alterations were specifically enriched in CRPC. CONCLUSION Through genomic profiling of prostate tumors representing the disease clinical spectrum, we identified a high frequency of potentially actionable alterations and possible drivers of disease initiation, metastasis and castration-resistance. Our findings support the routine use of tumor and germline DNA profiling for patients with advanced prostate cancer, for the purpose of guiding enrollment in targeted clinical trials and counseling families at increased risk of malignancy.
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Cerami E, Baras AS, Guinney J, Lepisto E, Pugh TJ, Schultz N, Stricker T, Sweeney SM, Veer LJV, Meijer GA, Andre F, Velculescu VE, Shaw KR, Levy MA, Bedard PL, Rollins BJ, Sawyers CL. Abstract LB-102: Landscape analysis of the initial data release from AACR Project GENIE. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-lb-102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
AACR Project Genomics Evidence Neoplasia Information Exchange (GENIE) is a multi-phase, multi-year, international data-sharing consortium whose goal is to generate an evidence base for precision cancer medicine by integrating and linking clinical-grade cancer genomic data with clinical outcome data for tens of thousands of cancer patients treated at multiple institutions worldwide. The project fulfills an unmet need in oncology by providing the statistical power necessary to identify novel therapeutic targets, to understand genomic determinants of response to therapy, to design new biomarker-driven clinical trials and ultimately, to improve clinical decision-making and the care delivered to patients. Here we describe the goals, structure and data standards of the GENIE consortium and conclusions from a high-level analysis of the first public release of genomic and limited clinical data from approximately 19,000 patients treated at eight cancer centers obtained during this initial phase of the project. We also explore the clinical utility of these genomic data by examining rates of clinical actionability across multiple cancer types and by estimating patient enrollment rates to the NCI MATCH Trial. Based on yearly rates of sequencing at each of the eight founding institutions, together with the planned addition of new members, we estimate the GENIE database could grow to >100,000 samples within five years. Consistent with the goals of the proposed Cancer Moonshot National Cancer Data Ecosystem, GENIE is committed to the principles of generating interoperable, open access data that can be widely shared across the entire scientific community.
Citation Format: Ethan Cerami, Alexander S. Baras, Justin Guinney, Eva Lepisto, Trevor J. Pugh, Nikolaus Schultz, Thomas Stricker, Shawn M. Sweeney, Laura J. van't Veer, Gerrit A. Meijer, Fabrice Andre, Victor E. Velculescu, Kenna R. Shaw, Mia A. Levy, Philippe L. Bedard, Barrett J. Rollins, Charles L. Sawyers, on behalf of the AACR Project GENIE Consortium. Landscape analysis of the initial data release from AACR Project GENIE [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-102. doi:10.1158/1538-7445.AM2017-LB-102
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Ku SY, Rosario S, Wang Y, Mu P, Seshadri M, Goodrich Z, Goodrich M, Labbé DP, Gomez EC, Wang J, Long HW, Xu B, Brown M, Loda M, Sawyers CL, Ellis L, Goodrich DG. Abstract 2170: Rb1 suppresses prostate cancer metastasis and lineage plasticity underlying castration resistance. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-2170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Androgen deprivation therapy (ADT) is an effective treatment for metastatic prostate cancer (mPCa), but patients eventually relapse with ADT resistant disease. Well-characterized mechanisms of ADT resistance include AR amplification, intra-tumoral androgen synthesis, AR splice variants, and growth receptor bypass. All of these mechanisms function to maintain sufficient AR signaling for tumor growth and survival. Improved ADT like abiraterone acetate (AA) and enzalutamide (Enza) were developed to combat such resistance mechanisms associated with alterations in androgen receptor or androgen metabolism. While AA and Enza extend survival, clinical benefits are short-lived. A new form of resistance is increasingly appreciated in patients relapsing from AA or Enza, histologic transformation of prostate adenocarcinoma (PADC) to neuroendocrine prostate cancer (NEPC) variants. NEPC is lethal and the survival time is less than a year as effective targeted therapy is unavailable. NEPC typically exhibits reduced AR expression, increased expression of neuroendocrine markers, and visceral metastasis in the absence of rising PSA. Of note, NEPC possesses the similar genome rearrangements with adjacent PADC cells, indicating they share clonal origin. Thus, NEPC may arise by histologic transformation of PADC. Underlying mechanisms of histologic transformation are not understood and experimental models are limited, hindering development of effective remedies. RB1 loss is common in NEPC, but rare in PADC; genetic profiling shows human NEPC exhibit elevated levels of several epigenetic modifiers. We hypothesize that transdifferentiation from PADC to NEPC in the context of RB1 loss is due to epigenetic alterations and can be reversed or blocked by epigenetic targeted therapies. We established several genetically engineered mouse models (GEMMs) to test the role of Rb1, and we find Rb1 loss causes metastatic progression of PADC initiated by Pten deficiency. This Rb1/Pten deficient (DKO) PADC exhibits expression markers for both PADC and NEPC as seen in human patients. Yet, these tumors are sensitive to ADT but relapse with low AR expression and acquired Trp53 mutations. RNA profiling demonstrates the phenotype of DKO tumors is similar to human NEPC. Both human and mouse NEPC is accompanied by increased expression of epigenetic reprogramming factors like Sox2 and Ezh2. Clinically relevant Ezh2 inhibitors GSK126 and EPZ6438 can restore Enza sensitivity by reversing neuroendocrine transformation. This finding has been genetically validated using short-hairpin RNA(shRNA) in vitro. These results uncover genetic mutations driving prostate cancer lineage plasticity and suggest an epigenetic approach for extending the clinical benefits of ADT.
Citation Format: Sheng-Yu Ku, Spencer Rosario, Yanqing Wang, Ping Mu, Mukund Seshadri, Zachary Goodrich, Maxwell Goodrich, David P. Labbé, Eduardo Cortez Gomez, Jianmin Wang, Henry W. Long, Bo Xu, Myles Brown, Massimo Loda, Charles L. Sawyers, Leigh Ellis, David G. Goodrich. Rb1 suppresses prostate cancer metastasis and lineage plasticity underlying castration resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2170. doi:10.1158/1538-7445.AM2017-2170
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Lawler M, Haussler D, Siu LL, Haendel MA, McMurry JA, Knoppers BM, Chanock SJ, Calvo F, The BT, Walia G, Banks I, Yu PP, Staudt LM, Sawyers CL. Sharing Clinical and Genomic Data on Cancer - The Need for Global Solutions. N Engl J Med 2017; 376:2006-2009. [PMID: 28538124 DOI: 10.1056/nejmp1612254] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Wise D, Armenia J, Chen Y, Nelson P, Schultz N, Sawyers CL, Scher HI. The immunomodulatory protein Dickkopf-1 (DKK1) defines a non-neuroendocrine subtype of metastatic castration-resistant prostate cancer (mCRPC) with low AR and low PSA expression. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.5054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
5054 Background: Advanced stagemCRPC can manifest AR-signaling independent growth typified by loss of AR and/or PSA expression in the absence of neuroendocrine (NE) features on biopsy. We sought to identify therapeutically relevant biomarkers of this highly resistant prostate cancer subtype. Methods: An unbiased differential gene expression analysis of non-neuroendocrine mCRPC biopsies was carried out comparing patients with ARlow to patients with ARhigh disease in a discovery cohort (SU2C/PCF, 18 pts: 8 ARlow, 10 ARhigh) and validation cohort (Fred Hutchinson, 76 pts: 12 ARlow, 64 ARhigh). The AR and NE status of the biopsies were defined by AR and PSA mRNA expression and gene signatures representative of AR activity and NE lineage. An RNA sequencing-based signature of immune cell subsets was calculated using the Cibersort algorithm. Results: Differential gene expression analysis identified the secreted Wnt antagonist, DKK1, as significantly upregulated in ARlow cases compared to ARhigh cases (11.2 RPKM vs. 0.28 RPKM, p < 0.03) in our discovery cohort and confirmed in our validation cohort (9.2 FPKM vs. 0.99 FPKM, p < 0.001). DKK1 protein was also found to be increased in non-neuroendocrine ARlow relative to ARhigh prostate cancer in vitro cell and organoid models (858 pg/mg total protein vs. 2 pg/mg total protein, p < 0.05) and patient-derived xenografts (28.6 FPKM vs. 0.78 FPKM, p < 0.0001). Consistent with the role of DKK1 as a negative modulator of anti-tumor immunity, patient biopsies with the highest quartile of DKK1 expression showed an RNA signature consistent with lower levels of active NK cells (0.2% vs. 1.8%, p < 0.005), and lower levels of CD8+ T cells (3.7% vs. 9.7%, p< 0.005) compared to those with the lowest quartile of DKK1 expression. Conclusions: DKK1 represents a secreted biomarker that is disproportionately enriched in non-neuroendocrine mCRPCs that lack AR expression. Because DKK1 has been implicated as a suppressor of anti-tumor immunity and is a target of an existing neutralizing antibody, our results support the clinical evaluation of the role of DKK1 blockade in DKK1-positive AR-negative prostate cancer.
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Armenia J, Mullane SA, Gao J, Chakravarty D, Kundra R, Huang FW, Han GC, Robinson D, Garraway LA, Nelson P, Rubin MA, Taplin ME, Abida W, Sawyers CL, Chinnaiyan AM, Kantoff PW, De Bono JS, Schultz N, Van Allen EM. The long tail of significantly mutated genes in prostate cancer. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.6_suppl.131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
131 Background: The mutational landscapes of primary and metastatic PCa have been robustly analyzed in multiple whole exome sequencing (WES) studies. We hypothesized that an aggregate, uniform analysis of all data generated to date would enable discovery of new significantly mutated genes and pathways not previously associated with PCa, and shed more light onto the genetic differences between primary and metastatic PCa. Methods: We assembled and uniformly analyzed a cohort of 1,021 tumor and matched germline primary and metastatic PCa whole exomes (686 primary, 335 metastatic), and performed mutational significance analysis using statistical and biological approaches to determine which genes and pathways are recurrently altered. Results: We identified 117 significantly mutated genes (Mutsig q<0.1) in PCa, which included many novel genes and pathways. These include epigenetic modifiers [KMT2C (6%), KMT2D (6%), and KDM6A (2.7%)], regulators of the SWI/SNF complex [SMARCA1 (1.1%), ARID1A (1.5%), ARID1B (1.3%), ARID2 (1.3%), and PBRM1 (0.7%)], and the splicing pathway [SF3B1 (1.1%) and U2AF1 (0.5%)]. In addition, we identified mutations in FUBP1 (0.4%), a splicing regulator involved in the regulation of MDM2 splicing. We also found truncating mutations in SPEN, a hormone inducible transcriptional repressor, in 2.8% of samples, similar to the frequency observed in breast tumors. Finally, a comparison of primary and metastatic samples enabled discovery of a genetic profile associated with metastatic disease, including AR amplifications and mutations, and loss of TP53, PTEN, and RB1. At lower frequency, metastatic tumors showed enrichment in mutations in MLLs (KMT2C/D), APC, CDK12, BRCA2, CTNNB1, and amplifications of MYC and CCND1. Conclusions: Through aggregation and uniform genomic analysis, we refined the map of somatic mutations in PCa and identified cancer genes and pathways not previously associated with this disease. Our findings may inform patient stratification and translational investigation.
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Wasserman I, Lee LH, Shia J, Wu C, Chen X, Guillem JG, Paty P, Weiser MR, Nash GM, Temple LKF, Saltz L, Yaeger RD, Barlas A, Manova-Todorova KO, Vakiani E, Elghouayel AE, Kemeny NE, Garcia-Aguilar J, Sawyers CL, Smith JJ. SMAD4 loss in colorectal cancer: Correlation with recurrence, chemoresistance, and immune infiltrate. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.4_suppl.587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
587 Background: Few markers reliably identify colorectal cancer (CRC) patients at risk of recurrence and death. SMAD4 loss occurs in 10-20% of cases and has shown promise in identifying high-risk stage II/III patients. We examined SMAD4 status and association with clinical/pathologic features in 446 stage I-IV CRC patients at Memorial Sloan Kettering (MSK). Methods: Patients undergoing curative resection were included (1981-2010). Familial polyposis syndrome patients and those with inadequate tissue were excluded. Tissue microarrays were constructed (n=364). Immunohistochemistry for SMAD4 and mismatch repair (MMR) proteins was completed. SMAD4 nuclear stain intensity was scored (scale=0-3; 0=loss). On whole sections, MMR proteins (present or absent), tumor-infiltrating lymphocytes (TILs) and peritumoral lymphocyte aggregates (PLAs) were scored (scale=0-3). Associations between clinical/pathologic features and SMAD4 loss vs. retention were analyzed. Kaplan-Meier estimates and log-rank test were used for recurrence-free and overall survival analyses (RFS and OS). Results: SMAD4 loss was noted in 13%. Median age at diagnosis was 53 years, and 51% were male. The cohort consisted of 61% hindgut tumors and 62% stage II/III patients. With up to 33 years of follow-up, the mean was 6 years. SMAD4 loss correlated with higher tumor and nodal stage, adjuvant therapy use, and lower TIL and PLA scores (p<0.04 for all). Unlike prior studies, no significant differences in OS based on SMAD4 status across the entire cohort were noted; however, older patients (>median) were noted to have worse OS with SMAD4 loss (p<0.01). SMAD4 loss did correlate with worse RFS (p=0.02), persisting even when excluding MMR-deficient patients. Additionally, SMAD4 loss was associated with worse RFS in both the adjuvant chemotherapy group (median RFS=3.8 vs. 13 years; p=0.06) and the resection-only group (median RFS=4.2 years vs. not yet reached; p< 0.01). Conclusions: SMAD4 loss correlates with worse RFS and resistance to adjuvant therapy. SMAD4 loss also correlates with lower TIL and PLA scores. Future work will address chemoresistance mechanisms, relevance to adjuvant therapy use, and loss of immune infiltrate in SMAD4-null tumors.
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Ku SY, Rosario S, Wang Y, Mu P, Seshadri M, Goodrich ZW, Goodrich MM, Labbé DP, Gomez EC, Wang J, Long HW, Xu B, Brown M, Loda M, Sawyers CL, Ellis L, Goodrich DW. Rb1 and Trp53 cooperate to suppress prostate cancer lineage plasticity, metastasis, and antiandrogen resistance. Science 2017; 355:78-83. [PMID: 28059767 PMCID: PMC5367887 DOI: 10.1126/science.aah4199] [Citation(s) in RCA: 706] [Impact Index Per Article: 100.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 12/05/2016] [Indexed: 12/20/2022]
Abstract
Prostate cancer relapsing from antiandrogen therapies can exhibit variant histology with altered lineage marker expression, suggesting that lineage plasticity facilitates therapeutic resistance. The mechanisms underlying prostate cancer lineage plasticity are incompletely understood. Studying mouse models, we demonstrate that Rb1 loss facilitates lineage plasticity and metastasis of prostate adenocarcinoma initiated by Pten mutation. Additional loss of Trp53 causes resistance to antiandrogen therapy. Gene expression profiling indicates that mouse tumors resemble human prostate cancer neuroendocrine variants; both mouse and human tumors exhibit increased expression of epigenetic reprogramming factors such as Ezh2 and Sox2. Clinically relevant Ezh2 inhibitors restore androgen receptor expression and sensitivity to antiandrogen therapy. These findings uncover genetic mutations that enable prostate cancer progression; identify mouse models for studying prostate cancer lineage plasticity; and suggest an epigenetic approach for extending clinical responses to antiandrogen therapy.
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Mu P, Zhang Z, Benelli M, Karthaus WR, Hoover E, Chen CC, Wongvipat J, Ku SY, Gao D, Cao Z, Shah N, Adams EJ, Abida W, Watson PA, Prandi D, Huang CH, de Stanchina E, Lowe SW, Ellis L, Beltran H, Rubin MA, Goodrich DW, Demichelis F, Sawyers CL. SOX2 promotes lineage plasticity and antiandrogen resistance in TP53- and RB1-deficient prostate cancer. Science 2017; 355:84-88. [PMID: 28059768 PMCID: PMC5247742 DOI: 10.1126/science.aah4307] [Citation(s) in RCA: 675] [Impact Index Per Article: 96.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 11/27/2016] [Indexed: 12/17/2022]
Abstract
Some cancers evade targeted therapies through a mechanism known as lineage plasticity, whereby tumor cells acquire phenotypic characteristics of a cell lineage whose survival no longer depends on the drug target. We use in vitro and in vivo human prostate cancer models to show that these tumors can develop resistance to the antiandrogen drug enzalutamide by a phenotypic shift from androgen receptor (AR)-dependent luminal epithelial cells to AR-independent basal-like cells. This lineage plasticity is enabled by the loss of TP53 and RB1 function, is mediated by increased expression of the reprogramming transcription factor SOX2, and can be reversed by restoring TP53 and RB1 function or by inhibiting SOX2 expression. Thus, mutations in tumor suppressor genes can create a state of increased cellular plasticity that, when challenged with antiandrogen therapy, promotes resistance through lineage switching.
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Gao D, Zhan Y, Di W, Moore AR, Sher JJ, Guan Y, Wang S, Zhang Z, Murphy DA, Sawyers CL, Chi P, Chen Y. A Tmprss2-CreERT2 Knock-In Mouse Model for Cancer Genetic Studies on Prostate and Colon. PLoS One 2016; 11:e0161084. [PMID: 27536883 PMCID: PMC4990297 DOI: 10.1371/journal.pone.0161084] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 07/31/2016] [Indexed: 01/29/2023] Open
Abstract
Fusion between TMPRSS2 and ERG, placing ERG under the control of the TMPRSS2 promoter, is the most frequent genetic alteration in prostate cancer, present in 40–50% of cases. The fusion event is an early, if not initiating, event in prostate cancer, implicating the TMPRSS2-positive prostate epithelial cell as the cancer cell of origin in fusion-positive prostate cancer. To introduce genetic alterations into Tmprss2-positive cells in mice in a temporal-specific manner, we generated a Tmprss2-CreERT2 knock-in mouse. We found robust tamoxifen-dependent Cre activation in the prostate luminal cells but not basal epithelial cells, as well as epithelial cells of the bladder and gastrointestinal (GI) tract. The knock-in allele on the Tmprss2 locus does not noticeably impact prostate, bladder, or gastrointestinal function. Deletion of Pten in Tmprss2-positive cells of adult mice generated neoplasia only in the prostate, while deletion of Apc in these cells generated neoplasia only in the GI tract. These results suggest that this new Tmprss2-CreERT2 mouse model will be a useful resource for genetic studies on prostate and colon.
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Abida W, Walsh MF, Armenia J, Vijai J, Gopalan A, Brennan R, Curtis K, Arcila M, Danila D, Arnold A, Rathkopf D, Morris MJ, Robson M, Slovin S, Hyman D, Durack J, Solomon SB, Vargas HA, Taylor B, Reuter V, Solit D, Berger MF, Offit K, Sawyers CL, Schultz N, Scher HI. Abstract LB-070: Next generation sequencing of prostate cancer reveals germline and somatic alterations detected at diagnosis and at metastasis that may impact clinical decision making. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-lb-070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: The TCGA and SU2C/PCF projects have allowed for the identification of molecular alterations in primary and metastatic castration-resistant prostate cancer (mCRPC), respectively, through whole exome sequencing of highly curated tissue samples. To explore the frequency of these alteration at clinical scale, we have used a next-generation sequencing assay called MSK-IMPACT that is targeted to 410 cancer-associated genes to profile the tumors and germline of patients (pts) with prostate cancer across the disease spectrum.
Methods: Prostate cancer pts enrolled on an IRB-approved protocol for tumor genomic profiling, with optional consent for germline DNA analysis. Fresh or archived fixed tumors and matched germline samples underwent targeted DNA sequencing and analysis of somatic mutations and copy number alterations (CNAs) using MSK-IMPACT. Germline analysis was performed according to ACMG guidelines for patients who consented.
Results: We successfully sequenced 300 tumors from 259 pts, including 171 primary and 129 metastatic samples, evaluated at MSKCC between 2/2014 and 8/2015. We identified actionable somatic alterations in >60% of pts, including in the PI3K/AKT pathway (25% of pts), the MAP kinase pathway (5% of pts) and the Wnt pathway (15% of pts). We found that 26% of pts harbor a tumor somatic alteration in a gene involved in DNA damage repair (DDR). Of the 140 pts who consented to germline DNA analysis, germline pathogenic mutations were identified in BRCA2 (9% of pts), CHEK2 (5% of pts), ATM (2.1% of pts), and in BRCA1, PALB2 or PMS2 (<1% of pts). Additional germline alterations were identified in BRIP1, NBN, JAK2, and FH totaling a 21% rate of germline pathogenic mutations. Overall, for patients who underwent germline and tumor somatic analysis, a 26% alteration frequency was identified in BRCA1/2, ATM or CHEK2 either in the germline or somatically. Furthermore, TP53 and BRCA somatic alterations found in men with metastatic disease were also detected in previously sampled matched primary tumors, suggesting that these alterations occur as early events in tumorigenesis.
Conclusions: In addition to confirming that actionable genomic alterations are common in men with advanced prostate cancer, two additional findings emerge that could influence clinical decision making in patients at the time of diagnosis with primary disease. First, we report a high frequency of germline pathogenic mutations, including in the DDR genes BRCA2/1, CHEK2 and ATM, that could impact treatment decisions (e.g., with PARP inhibitors) and screening of family members. Second, the fact that somatic TP53 and BRCA alterations are present in matched primary samples of patients who subsequently develop metastatic diseases suggests that early detection of these alterations may be prognostic.
Citation Format: Wassim Abida, Michael F. Walsh, Joshua Armenia, Joseph Vijai, Anuradha Gopalan, Ryan Brennan, Kristen Curtis, Maria Arcila, Daniel Danila, Angela Arnold, Dana Rathkopf, Michael J. Morris, Mark Robson, Susin Slovin, David Hyman, Jeremy Durack, Stephen B. Solomon, Herbert A. Vargas, Barry Taylor, Victor Reuter, David Solit, Michael F. Berger, Kenneth Offit, Charles L. Sawyers, Nikolaus Schultz, Howard I. Scher. Next generation sequencing of prostate cancer reveals germline and somatic alterations detected at diagnosis and at metastasis that may impact clinical decision making. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-070.
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