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Keenan TE, Tan-Wasielewski Z, Trippa L, Kochupurakkal B, Guerriero JL, Tahara RK, Winship G, Osmani W, Andrews C, Conway JR, He MX, Pastorello R, Tracy A, Godin RE, Overmoyer BA, Winer EP, Mittendorf EA, Shapiro GI, Van Allen EM, Tolaney SM. Abstract P3-10-08: A phase II study of cisplatin and the Wee1 inhibitor adavosertib in metastatic triple-negative breast cancer (mTNBC). Cancer Res 2020. [DOI: 10.1158/1538-7445.sabcs19-p3-10-08] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: mTNBC progresses rapidly on first-line chemotherapy. For instance, in the TNT trial, median progression-free survival (PFS) was 3 months on first-line carboplatin. Selective inhibition of Wee1, a negative regulator of the G2 cell cycle checkpoint, may enhance the efficacy of DNA-damaging agents by reducing DNA damage repair. We report the results of the first phase II study assessing the efficacy of the Wee1 inhibitor adavosertib (AZD-1775) with cisplatin in mTNBC.
Methods: mTNBC patients (pts) with 0-1 prior lines of chemotherapy in the metastatic setting were eligible. Pts received cisplatin 75 mg/m2 IV followed by combination therapy 21 d later with cisplatin plus adavosertib 200 mg oral twice daily x 5 doses over 2.5 d every 21 d. Tumor biopsies were mandatory for patients with safely accessible tumors, and occurred 5-48 h after monotherapy and 5-8 h after the last adavosertib dose in the first combination therapy cycle. The study used a Simon optimal two-stage design that had 90% power to detect the difference between null (20%) and alternative (40%) response rates with a one-sided type I error of 0.1. The primary endpoint was objective response rate (ORR): an ORR > 30% would identify the regimen as worthy of further study. Key secondary endpoints were PFS and overall survival (OS). Exploratory analyses evaluated the association of response, defined as clinical benefit rate (CBR) > 6 months (CR + PR + SD > 6 mos), with transcriptional and immunostaining profiles of on-treatment tumors (n = 16), as well as with targeted panel genomic alterations in archival tissue. Tumor immune cell composition was assessed by CIBERSORT.
Results: 34 pts initiated protocol therapy; median age was 56 yrs, 2 (6%) pts had known BRCA2 mutations, and 14 (41%) had 1 prior line of chemotherapy. Median follow-up was 13 mos. ORR was 29% (3 CR + 7 PR), median PFS 4.9 months (95% CI, 2.3-5.8 mos), CBR 35%, and preliminary OS 14.0 mos (95% CI, 11.8-21.8 mos). All-cause AEs occurred in 100% of pts (G3-4, 56%; most commonly diarrhea, 21%), including one death due to sepsis possibly related to study therapy. The primary tumor of the longest responding patient had a possible biallelic loss-of-function alteration (missense mutation and loss of heterozygosity) in the homologous recombination-related gene FANCM. In Hallmark gene set enrichment analyses of 26 on-treatment biopsies across 16 pts, responding tumors (n = 4) demonstrated enriched expression of immune response gene sets (allograft rejection FDR q < 0.001, IL2-STAT5 signaling FDR q = 0.001, inflammatory response FDR q = 0.003), while non-responding tumors (n = 12) showed enrichment of cell cycle gene sets (E2F targets FDR q < 0.001, G2M checkpoint FDR q < 0.001). In the same on-treatment biopsies, responding tumors (n = 4) had higher tumor infiltrating lymphocytes (46% v. 29%, Mann-Whitney p = 0.04) and lower M0 macrophages (3% v. 17%, Mann-Whitney p = 0.04) than non-responding tumors (n =12). Updated data, including OS and tissue immunostaining results, will be presented.
Conclusions: Among mTNBC pts, the combination of adavosertib and cisplatin was associated with a 29% ORR, failing to meet the pre-determined ORR of > 30% required to support further investigation. Responses were associated with immune-related gene expression and TILs detected by RNA sequencing.
Citation Format: Tanya E. Keenan, Zhenying Tan-Wasielewski, Lorenzo Trippa, Bose Kochupurakkal, Jennifer L. Guerriero, Rie K. Tahara, Grace Winship, Wafa Osmani, Chelsea Andrews, Jake R. Conway, Meng X He, Ricardo Pastorello, Adam Tracy, Robert E. Godin, Beth A. Overmoyer, Eric P. Winer, Elizabeth A. Mittendorf, Geoffrey I Shapiro, Eliezer M Van Allen, Sara M Tolaney. A phase II study of cisplatin and the Wee1 inhibitor adavosertib in metastatic triple-negative breast cancer (mTNBC) [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P3-10-08.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Meng X He
- 1Dana-Farber Cancer Institute, Boston, MA
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Kamran SC, Lennerz JK, Margolis CA, Liu D, Reardon B, Wankowicz SA, Van Seventer EE, Tracy A, Wo JY, Carter SL, Willers H, Corcoran RB, Hong TS, Van Allen EM. Integrative Molecular Characterization of Resistance to Neoadjuvant Chemoradiation in Rectal Cancer. Clin Cancer Res 2019; 25:5561-5571. [PMID: 31253631 PMCID: PMC6744983 DOI: 10.1158/1078-0432.ccr-19-0908] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/08/2019] [Accepted: 06/21/2019] [Indexed: 12/18/2022]
Abstract
PURPOSE Molecular properties associated with complete response or acquired resistance to concurrent chemotherapy and radiotherapy (CRT) are incompletely characterized.Experimental Design: We performed integrated whole-exome/transcriptome sequencing and immune infiltrate analysis on rectal adenocarcinoma tumors prior to neoadjuvant CRT (pre-CRT) and at time of resection (post-CRT) in 17 patients [8 complete/partial responders, 9 nonresponders (NR)]. RESULTS CRT was not associated with increased tumor mutational burden or neoantigen load and did not alter the distribution of established somatic tumor mutations in rectal cancer. Concurrent KRAS/TP53 mutations (KP) associated with NR tumors and were enriched for an epithelial-mesenchymal transition transcriptional program. Furthermore, NR was associated with reduced CD4/CD8 T-cell infiltrates and a post-CRT M2 macrophage phenotype. Absence of any local tumor recurrences, KP/NR status predicted worse progression-free survival, suggesting that local immune escape during or after CRT with specific genomic features contributes to distant progression. CONCLUSIONS Overall, while CRT did not impact genomic profiles, CRT impacted the tumor immune microenvironment, particularly in resistant cases.
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Affiliation(s)
- Sophia C Kamran
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Jochen K Lennerz
- Department of Pathology, Center for Integrated Diagnostics, Massachusetts General Hospital, Boston, Massachusetts
| | - Claire A Margolis
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - David Liu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Brendan Reardon
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Stephanie A Wankowicz
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Emily E Van Seventer
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Adam Tracy
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Jennifer Y Wo
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Scott L Carter
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Joint Center for Cancer Precision Medicine, Dana-Farber Cancer Institute/Brigham and Women's Hospital, Boston, Massachusetts
| | - Henning Willers
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ryan B Corcoran
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Theodore S Hong
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts.
| | - Eliezer M Van Allen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
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Keenan T, Liu D, Elmarakeby H, Stover D, Kochupurakkal B, Tracy A, Danielczyk E, Anderson L, Andrews C, Reardon B, Overmoyer B, Winer E, Zheleva D, Chiao J, Blake D, Allen EV, Shapiro GI, Tolaney S. Abstract CT050: Expansion cohort of Phase I study of oral sapacitabine and oral seliciclib in patients with metastatic breast cancer and BRCA1/2 mutations. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-ct050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Sapacitabine, a nucleoside analog, and seliciclib, a cyclin-dependent kinase 2/9 inhibitor, constitute a novel oral regimen aimed at augmenting DNA damage and impairing cell cycle checkpoints. The initial phase I cohort investigating this combination demonstrated a 25% response rate in BRCA carriers. Hence, we developed an expansion cohort to assess the safety and efficacy of this regimen in patients with metastatic breast cancer and BRCA1/2 mutations.
Methods: We enrolled 20 patients with HER2-negative metastatic breast cancer and germline or somatic BRCA1/2 mutations, who were treated with sapacitabine 50 mg twice daily for days 1-7 followed by seliciclib 800 mg twice daily for days 8-10 of a 21-day cycle. Baseline or archival biopsies underwent RAD51 immunohistochemistry to assess for functional homologous recombination proficiency. Available tissue was sent for whole exome and transcriptome sequencing, and pre- and post-treatment blood was submitted for cell-free DNA sequencing to assess for genomic correlates of response.
Results: Participants received a median of 2 prior lines of chemotherapy for metastatic disease. Of the 9 patients who received a prior platinum agent, 6 progressed on this therapy. In addition to chemotherapy, 7 patients received and progressed on a prior PARP inhibitor. The overall response rate for sapacitabine and seliciclib in this cohort was 10%, consisting of 2 patients with partial responses lasting 4.7 and 9.0 months, respectively. The clinical benefit rate (CR + PR + SD ≥ 6 months) was 30%, and durations of stable disease ≥ 6 months ranged from 7.4 to 11.7 months. For all patients, median PFS was 3.7 months. The most frequent grade 3/4 adverse events were neutropenia (25% of patients), transaminitis (20%), and rash (10%). No patients who progressed on prior PARP inhibitor therapy and 6 of 13 patients (46%) with no history of PARP inhibitor resistance experienced clinical benefit (p = 0.052 by Fisher’s exact test). In contrast, 1 of 6 patients (17%) who progressed on prior platinum chemotherapy and 5 of 14 patients (36%) with no history of platinum resistance experienced clinical benefit (p = 0.61 by Fisher’s exact test). Notably, the tumors of some resistant patients harbored BRCA reversion mutations. Additional genomic analyses and RAD51 immunohistochemistry will be presented.
Conclusions: The combination of sapacitabine and seliciclib was safe and led to durable clinical benefit in some patients with metastatic breast cancer and BRCA1/2 mutations. Prior progression on PARP inhibitors predicted resistance to this combination, associated in some cases with BRCA reversion mutations. Based on these results, the combination of sapacitabine and the PARP inhibitor olaparib is now being investigated in patients with PARP-naïve metastatic HER2-negative breast cancer and germline BRCA1/2 mutations.
Citation Format: Tanya Keenan, David Liu, Haitham Elmarakeby, Daniel Stover, Bose Kochupurakkal, Adam Tracy, Elaine Danielczyk, Leilani Anderson, Chelsea Andrews, Brendan Reardon, Beth Overmoyer, Eric Winer, Daniella Zheleva, Judy Chiao, David Blake, Eliezer Van Allen, Geoffrey I. Shapiro, Sara Tolaney. Expansion cohort of Phase I study of oral sapacitabine and oral seliciclib in patients with metastatic breast cancer and BRCA1/2 mutations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr CT050.
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Affiliation(s)
| | - David Liu
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | - Daniel Stover
- 2Ohio State University Comprehensive Cancer Center, Columbus, OH
| | | | | | | | | | | | | | | | - Eric Winer
- 1Dana-Farber Cancer Institute, Boston, MA
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4
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Amin-Mansour A, George S, Sioletic S, Carter SL, Rosenberg M, Taylor-Weiner A, Stewart C, Chevalier A, Seepo S, Tracy A, Getz G, Hornick JL, Nucci MR, Quade B, Demetri GD, Raut CP, Garraway LA, Van Allen EM, Wagner AJ. Genomic Evolutionary Patterns of Leiomyosarcoma and Liposarcoma. Clin Cancer Res 2019; 25:5135-5142. [PMID: 31164371 DOI: 10.1158/1078-0432.ccr-19-0271] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 03/27/2019] [Accepted: 05/30/2019] [Indexed: 01/08/2023]
Abstract
PURPOSE Leiomyosarcoma and liposarcoma are common subtypes of soft tissue sarcoma (STS). Patients with metastatic leiomyosarcoma or dedifferentiated liposarcoma (DDLPS) typically have worse outcomes compared with localized leiomyosarcoma or well-differentiated liposarcoma (WDLPS). A better understanding of genetic changes between primary/metastatic leiomyosarcoma and between WDLPS/DDLPS may provide insight into their genetic evolution. EXPERIMENTAL DESIGN We interrogated whole-exome sequencing (WES) from "trios" of normal tissue, primary tumor, and metastatic tumor from individual patients with leiomyosarcoma (n = 9), and trios of normal tissue, well-differentiated tumor, and dedifferentiated tumor from individual patients with liposarcoma (n = 19). Specifically, we performed mutational, copy number, and tumor evolution analyses on these cohorts and compared patterns among leiomyosarcoma and liposarcoma trios. RESULTS Leiomyosarcoma cases harbored shared drivers through a typical parent/child relationship where the metastatic tumor was derived from the primary tumor. In contrast, while all liposarcoma cases shared the characteristic focal chromosome 12 amplicon, most paired liposarcoma cases did not share additional mutations, suggesting a divergent evolutionary pattern from a common precursor. No highly recurrent genomic alterations from WES were identified that could be implicated as driving the progression of disease in either sarcoma subtype. CONCLUSIONS From a genomic perspective, leiomyosarcoma metastases contain genetic alterations that are also found in primary tumors. WDLPS and DDLPS, however, appear to divergently evolve from a common precursor harboring 12q amplification, rather than as a transformation to a higher-grade tumor. Further efforts to identify specific drivers of these distinct evolutionary patterns may inform future translational and clinical research in STS.
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Affiliation(s)
- Ali Amin-Mansour
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Suzanne George
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Stefano Sioletic
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Scott L Carter
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Mara Rosenberg
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | | | - Chip Stewart
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Aaron Chevalier
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Sara Seepo
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Adam Tracy
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Gad Getz
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Jason L Hornick
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Marisa R Nucci
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Bradley Quade
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - George D Demetri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Ludwig Center at Harvard, Harvard Medical School, Boston, Massachusetts
| | - Chandrajit P Raut
- Department of Surgery, Brigham and Women's Hospital, Boston, Massachusetts
| | - Levi A Garraway
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Eliezer M Van Allen
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts. .,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Andrew J Wagner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
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5
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Bandopadhayay P, Piccioni F, O'Rourke R, Ho P, Gonzalez EM, Buchan G, Qian K, Gionet G, Girard E, Coxon M, Rees MG, Brenan L, Dubois F, Shapira O, Greenwald NF, Pages M, Balboni Iniguez A, Paolella BR, Meng A, Sinai C, Roti G, Dharia NV, Creech A, Tanenbaum B, Khadka P, Tracy A, Tiv HL, Hong AL, Coy S, Rashid R, Lin JR, Cowley GS, Lam FC, Goodale A, Lee Y, Schoolcraft K, Vazquez F, Hahn WC, Tsherniak A, Bradner JE, Yaffe MB, Milde T, Pfister SM, Qi J, Schenone M, Carr SA, Ligon KL, Kieran MW, Santagata S, Olson JM, Gokhale PC, Jaffe JD, Root DE, Stegmaier K, Johannessen CM, Beroukhim R. Neuronal differentiation and cell-cycle programs mediate response to BET-bromodomain inhibition in MYC-driven medulloblastoma. Nat Commun 2019; 10:2400. [PMID: 31160565 PMCID: PMC6546744 DOI: 10.1038/s41467-019-10307-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 04/25/2019] [Indexed: 12/26/2022] Open
Abstract
BET-bromodomain inhibition (BETi) has shown pre-clinical promise for MYC-amplified medulloblastoma. However, the mechanisms for its action, and ultimately for resistance, have not been fully defined. Here, using a combination of expression profiling, genome-scale CRISPR/Cas9-mediated loss of function and ORF/cDNA driven rescue screens, and cell-based models of spontaneous resistance, we identify bHLH/homeobox transcription factors and cell-cycle regulators as key genes mediating BETi's response and resistance. Cells that acquire drug tolerance exhibit a more neuronally differentiated cell-state and expression of lineage-specific bHLH/homeobox transcription factors. However, they do not terminally differentiate, maintain expression of CCND2, and continue to cycle through S-phase. Moreover, CDK4/CDK6 inhibition delays acquisition of resistance. Therefore, our data provide insights about the mechanisms underlying BETi effects and the appearance of resistance and support the therapeutic use of combined cell-cycle inhibitors with BETi in MYC-amplified medulloblastoma.
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Affiliation(s)
- Pratiti Bandopadhayay
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Pediatrics, Harvard Medical School, Boston, USA
| | | | - Ryan O'Rourke
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Patricia Ho
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Elizabeth M Gonzalez
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Graham Buchan
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Kenin Qian
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Gabrielle Gionet
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Emily Girard
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Margo Coxon
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | | | - Lisa Brenan
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Frank Dubois
- Broad Institute of MIT and Harvard, Cambridge, USA
- Division of Cancer Biology, Dana-Farber Cancer Institute, Boston, USA
| | - Ofer Shapira
- Broad Institute of MIT and Harvard, Cambridge, USA
- Division of Cancer Biology, Dana-Farber Cancer Institute, Boston, USA
| | - Noah F Greenwald
- Broad Institute of MIT and Harvard, Cambridge, USA
- Division of Cancer Biology, Dana-Farber Cancer Institute, Boston, USA
- Department of Neurosurgery, Brigham and Women's Hospital, Boston, USA
| | - Melanie Pages
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Amanda Balboni Iniguez
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Brenton R Paolella
- Broad Institute of MIT and Harvard, Cambridge, USA
- Division of Cancer Biology, Dana-Farber Cancer Institute, Boston, USA
| | - Alice Meng
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - Claire Sinai
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - Giovanni Roti
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Medicine and Surgery, Hematology and BMT, University of Parma, Parma, Italy
| | - Neekesh V Dharia
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Pediatrics, Harvard Medical School, Boston, USA
| | | | | | - Prasidda Khadka
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Pediatrics, Harvard Medical School, Boston, USA
| | - Adam Tracy
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Hong L Tiv
- Experimental Therapeutics Core and Belfer Center for Applied Cancer Science, Boston, USA
| | - Andrew L Hong
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Pediatrics, Harvard Medical School, Boston, USA
| | - Shannon Coy
- Department of Pathology, Brigham and Women's Hospital, Boston, USA
| | - Rumana Rashid
- Department of Pathology, Brigham and Women's Hospital, Boston, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, USA
| | - Jia-Ren Lin
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, USA
- Ludwig Center for Cancer Research at Harvard, Harvard Medical School, Boston, USA
| | - Glenn S Cowley
- Broad Institute of MIT and Harvard, Cambridge, USA
- Discovery Science, Janssen Research and Development (Johnson & Johnson), Spring House, PA, USA
| | - Fred C Lam
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, USA
| | - Amy Goodale
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Yenarae Lee
- Broad Institute of MIT and Harvard, Cambridge, USA
| | | | | | - William C Hahn
- Broad Institute of MIT and Harvard, Cambridge, USA
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA
- Department of Medicine, Harvard Medical School, Boston, USA
| | | | - James E Bradner
- Broad Institute of MIT and Harvard, Cambridge, USA
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA
- Department of Medicine, Harvard Medical School, Boston, USA
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Michael B Yaffe
- Broad Institute of MIT and Harvard, Cambridge, USA
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, USA
| | - Till Milde
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- CCU Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, Center for Child and Adolescent Medicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-Oncology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Jun Qi
- Division of Cancer Biology, Dana-Farber Cancer Institute, Boston, USA
| | | | | | - Keith L Ligon
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, USA
- Department of Medicine, Harvard Medical School, Boston, USA
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, USA
- Department of Pathology, Boston Children's Hospital, Boston, USA
| | - Mark W Kieran
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Department of Pediatrics, Harvard Medical School, Boston, USA
| | - Sandro Santagata
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, USA
| | - James M Olson
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Prafulla C Gokhale
- Experimental Therapeutics Core and Belfer Center for Applied Cancer Science, Boston, USA
| | | | - David E Root
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Kimberly Stegmaier
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
- Department of Pediatrics, Harvard Medical School, Boston, USA
| | | | - Rameen Beroukhim
- Broad Institute of MIT and Harvard, Cambridge, USA.
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, USA.
- Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA.
- Department of Medicine, Harvard Medical School, Boston, USA.
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6
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Pagès M, Rotem D, Gydush G, Reed S, Rhoades J, Ha G, Lo C, Tracy A, Jones R, Becker S, Haller M, Chi S, Kieran M, Goumnerova L, Love C, Ligon K, Wright K, Adalsteinsson V, Beroukhim R, Bandopadhayay P. GENE-07. LIQUID BIOPSY DETECTION OF GENOMIC ALTERATIONS IN PEDIATRIC BRAIN TUMORS FROM CELL-FREE DNA IN PERIPHERAL BLOOD, CSF, AND URINE. Neuro Oncol 2019. [DOI: 10.1093/neuonc/noz036.078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Mélanie Pagès
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
| | | | | | | | | | - Gavin Ha
- Broad Institute, Cambridge, MA, USA
| | - Chris Lo
- Broad Institute, Cambridge, MA, USA
| | | | - Robert Jones
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
| | - Sarah Becker
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
| | - Michaela Haller
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
| | - Susan Chi
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Boston Children’s Hospital, Boston, MA, USA
| | - Mark Kieran
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Boston Children’s Hospital, Boston, MA, USA
| | - Liliana Goumnerova
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Boston Children’s Hospital, Boston, MA, USA
| | | | - Keith Ligon
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
- Boston Children’s Hospital, Boston, MA, USA
| | - Karen Wright
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Boston Children’s Hospital, Boston, MA, USA
| | - Viktor Adalsteinsson
- Broad Institute, Cambridge, MA, USA
- Massachussets Institute of Technology, Cambridge, MA, USA
| | - Rameen Beroukhim
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Pratiti Bandopadhayay
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
- Boston Children’s Hospital, Boston, MA, USA
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7
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Hong AL, Tseng YY, Wala JA, Kim WJ, Kynnap BD, Doshi MB, Kugener G, Sandoval GJ, Howard TP, Li J, Yang X, Tillgren M, Ghandi M, Sayeed A, Deasy R, Ward A, McSteen B, Labella KM, Keskula P, Tracy A, Connor C, Clinton CM, Church AJ, Crompton BD, Janeway KA, Van Hare B, Sandak D, Gjoerup O, Bandopadhayay P, Clemons PA, Schreiber SL, Root DE, Gokhale PC, Chi SN, Mullen EA, Roberts CW, Kadoch C, Beroukhim R, Ligon KL, Boehm JS, Hahn WC. Renal medullary carcinomas depend upon SMARCB1 loss and are sensitive to proteasome inhibition. eLife 2019; 8:44161. [PMID: 30860482 PMCID: PMC6436895 DOI: 10.7554/elife.44161] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 03/03/2019] [Indexed: 12/11/2022] Open
Abstract
Renal medullary carcinoma (RMC) is a rare and deadly kidney cancer in patients of African descent with sickle cell trait. We have developed faithful patient-derived RMC models and using whole-genome sequencing, we identified loss-of-function intronic fusion events in one SMARCB1 allele with concurrent loss of the other allele. Biochemical and functional characterization of these models revealed that RMC requires the loss of SMARCB1 for survival. Through integration of RNAi and CRISPR-Cas9 loss-of-function genetic screens and a small-molecule screen, we found that the ubiquitin-proteasome system (UPS) was essential in RMC. Inhibition of the UPS caused a G2/M arrest due to constitutive accumulation of cyclin B1. These observations extend across cancers that harbor SMARCB1 loss, which also require expression of the E2 ubiquitin-conjugating enzyme, UBE2C. Our studies identify a synthetic lethal relationship between SMARCB1-deficient cancers and reliance on the UPS which provides the foundation for a mechanism-informed clinical trial with proteasome inhibitors. Renal medullary carcinoma (RMC for short) is a rare type of kidney cancer that affects teenagers and young adults. These patients are usually of African descent and carry one of the two genetic changes that cause sickle cell anemia. RMC is an aggressive disease without effective treatments and patients survive, on average, for only six to eight months after their diagnosis. Recent genetic studies found that most RMC cells have mutations that prevent them from producing a protein called SMARCB1. SMARCB1 normally acts as a so-called tumor suppressor, preventing cells from becoming cancerous. However, it was not clear whether RMCs always have to lose SMARCB1 if they are to survive and grow. Often, diseases are studied using laboratory-grown cells and tissues that have certain features of the disease. No such models had been created for RMC, which has slowed efforts to understand how the disease develops and find new treatments for it. Hong et al. therefore worked with patients to develop new lines of cells that can be used to study RMC in the laboratory. These RMC cells started dying when they were given copies of the SMARCB1 gene, which supports the theory that RMCs have to lose SMARCB1 in order to grow. Hong et al. then used a set of genetic reagents that can suppress or delete genes that are targeted by drugs, and followed this by testing a range of drugs on the RMC cells. Drugs and genetic reagents that reduced the activity of the proteasome – the structure inside cells that gets rid of old or unwanted proteins – caused the RMC cells to die. These proteasome inhibitor drugs also killed other kinds of cancer cells with SMARCB1 mutations. Proteasome inhibitors are already used to treat different types of cancer. Potentially, a clinical trial could be run to see if they will treat patients whose cancers lack SMARCB1. Further work is also needed to determine the exact link between SMARCB1 and the proteasome.
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Affiliation(s)
- Andrew L Hong
- Boston Children's Hospital, Boston, United States.,Dana-Farber Cancer Institute, Boston, United States.,Broad Institute of Harvard and MIT, Cambridge, United States
| | - Yuen-Yi Tseng
- Broad Institute of Harvard and MIT, Cambridge, United States
| | - Jeremiah A Wala
- Broad Institute of Harvard and MIT, Cambridge, United States
| | - Won-Jun Kim
- Dana-Farber Cancer Institute, Boston, United States
| | | | - Mihir B Doshi
- Broad Institute of Harvard and MIT, Cambridge, United States
| | | | - Gabriel J Sandoval
- Dana-Farber Cancer Institute, Boston, United States.,Broad Institute of Harvard and MIT, Cambridge, United States
| | | | - Ji Li
- Dana-Farber Cancer Institute, Boston, United States
| | - Xiaoping Yang
- Broad Institute of Harvard and MIT, Cambridge, United States
| | | | - Mahmhoud Ghandi
- Broad Institute of Harvard and MIT, Cambridge, United States
| | - Abeer Sayeed
- Broad Institute of Harvard and MIT, Cambridge, United States
| | - Rebecca Deasy
- Broad Institute of Harvard and MIT, Cambridge, United States
| | - Abigail Ward
- Boston Children's Hospital, Boston, United States.,Dana-Farber Cancer Institute, Boston, United States
| | - Brian McSteen
- Rare Cancer Research Foundation, Durham, United States
| | | | - Paula Keskula
- Broad Institute of Harvard and MIT, Cambridge, United States
| | - Adam Tracy
- Broad Institute of Harvard and MIT, Cambridge, United States
| | - Cora Connor
- RMC Support, North Charleston, United States
| | - Catherine M Clinton
- Boston Children's Hospital, Boston, United States.,Dana-Farber Cancer Institute, Boston, United States
| | | | - Brian D Crompton
- Boston Children's Hospital, Boston, United States.,Dana-Farber Cancer Institute, Boston, United States.,Broad Institute of Harvard and MIT, Cambridge, United States
| | - Katherine A Janeway
- Boston Children's Hospital, Boston, United States.,Dana-Farber Cancer Institute, Boston, United States
| | | | - David Sandak
- Rare Cancer Research Foundation, Durham, United States
| | - Ole Gjoerup
- Dana-Farber Cancer Institute, Boston, United States
| | - Pratiti Bandopadhayay
- Boston Children's Hospital, Boston, United States.,Dana-Farber Cancer Institute, Boston, United States.,Broad Institute of Harvard and MIT, Cambridge, United States
| | - Paul A Clemons
- Broad Institute of Harvard and MIT, Cambridge, United States
| | | | - David E Root
- Broad Institute of Harvard and MIT, Cambridge, United States
| | | | - Susan N Chi
- Boston Children's Hospital, Boston, United States.,Dana-Farber Cancer Institute, Boston, United States
| | - Elizabeth A Mullen
- Boston Children's Hospital, Boston, United States.,Dana-Farber Cancer Institute, Boston, United States
| | | | - Cigall Kadoch
- Dana-Farber Cancer Institute, Boston, United States.,Broad Institute of Harvard and MIT, Cambridge, United States
| | - Rameen Beroukhim
- Dana-Farber Cancer Institute, Boston, United States.,Broad Institute of Harvard and MIT, Cambridge, United States.,Brigham and Women's Hospital, Boston, United States
| | - Keith L Ligon
- Dana-Farber Cancer Institute, Boston, United States.,Broad Institute of Harvard and MIT, Cambridge, United States.,Brigham and Women's Hospital, Boston, United States
| | - Jesse S Boehm
- Broad Institute of Harvard and MIT, Cambridge, United States
| | - William C Hahn
- Dana-Farber Cancer Institute, Boston, United States.,Broad Institute of Harvard and MIT, Cambridge, United States.,Brigham and Women's Hospital, Boston, United States
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8
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Pages M, Rotem D, Gydush G, Reed S, Rhoades J, Ha G, Lo C, Tracy A, Jones R, Becker S, Haller M, Chi S, Kieran M, Goumnerova L, Love JC, Ligon K, Bandopadhayay P, Wright K, Adalsteinsson VA, Beroukhim R. INNV-22. LIQUID BIOPSY DETECTION OF GENOMIC ALTERATIONS IN PEDIATRIC BRAIN TUMORS FROM CELL FREE DNA IN PERIPHERAL BLOOD, CSF, AND URINE. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy148.595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Mélanie Pages
- Dana-Farber Cancer Institute / Boston Childrens Cancer and Blood Disorders Center, Boston, MA, USA
| | | | | | | | | | - Gavin Ha
- Broad Institute, Cambridge, MA, USA
| | - Chris Lo
- Broad Institute, Cambridge, MA, USA
| | | | - Robert Jones
- Dana-Farber Cancer Institute / Boston Childrens Cancer and Blood Disorders Center, Boston, MA, USA
| | - Sarah Becker
- Dana-Farber Cancer Institute / Boston Childrens Cancer and Blood Disorders Center, Boston, MA, USA
| | - Michaela Haller
- Dana-Farber Cancer Institute / Boston Childrens Cancer and Blood Disorders Center, Boston, MA, USA
| | - Susan Chi
- Dana-Farber Cancer Institute / Boston Childrens Cancer and Blood Disorders Center / Boston Childrens Hospital, Boston, MA, USA
| | - Mark Kieran
- Dana-Farber Cancer Institute / Boston Childrens Cancer and Blood Disorders Center / Boston Childrens Hospital, Boston, MA, USA
| | - Liliana Goumnerova
- Dana-Farber Cancer Institute / Boston Childrens Cancer and Blood Disorders Center / Boston Childrens Hospital, Boston, MA, USA
| | | | - Keith Ligon
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | - Karen Wright
- Dana-Farber Cancer Institute / Boston Childrens Hospital, Boston, MA, USA
| | | | - Rameen Beroukhim
- Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
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9
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Pages M, Rotem D, Gydush G, Reed S, Rhoades J, Ha G, Lo C, Tracy A, Jones R, Becker S, Haller M, Chi S, Kieran M, Goumnerova L, Love JC, Ligon KL, Bandopadhayay P, Wright K, Adalsteinsson VA, Beroukhim R. TBIO-18. LIQUID BIOPSY DETECTION OF GENOMIC ALTERATIONS IN PEDIATRIC BRAIN TUMORS FROM CELL FREE DNA IN PERIPHERAL BLOOD, CSF, AND URINE. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy059.706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Melanie Pages
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
| | | | | | | | | | - Gavin Ha
- Broad Institute, Cambridge, MA, USA
| | - Chris Lo
- Broad Institute, Cambridge, MA, USA
| | | | - Robert Jones
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
| | - Sarah Becker
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
| | - Michaela Haller
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
| | - Susan Chi
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Boston Children’s Hospital, Boston, MA, USA
| | - Mark Kieran
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Boston Children’s Hospital, Boston, MA, USA
| | - Liliana Goumnerova
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Boston Children’s Hospital, Boston, MA, USA
| | | | - Keith L Ligon
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Boston Children’s Hospital, Boston, MA, USA
| | - Pratiti Bandopadhayay
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Boston Children’s Hospital, Boston, MA, USA
| | - Karen Wright
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Boston Children’s Hospital, Boston, MA, USA
| | - Viktor A Adalsteinsson
- Broad Institute, Cambridge, MA, USA
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rameen Beroukhim
- Dana-Farber Cancer Institute/Boston Children’s Cancer and Blood Disorders Center, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
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10
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Miao D, Margolis CA, Gao W, Voss MH, Li W, Martini DJ, Norton C, Bossé D, Wankowicz SM, Cullen D, Horak C, Wind-Rotolo M, Tracy A, Giannakis M, Hodi FS, Drake CG, Ball MW, Allaf ME, Snyder A, Hellmann MD, Ho T, Motzer RJ, Signoretti S, Kaelin WG, Choueiri TK, Van Allen EM. Genomic correlates of response to immune checkpoint therapies in clear cell renal cell carcinoma. Science 2018; 359:801-806. [PMID: 29301960 PMCID: PMC6035749 DOI: 10.1126/science.aan5951] [Citation(s) in RCA: 788] [Impact Index Per Article: 131.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 10/30/2017] [Accepted: 12/15/2017] [Indexed: 12/20/2022]
Abstract
Immune checkpoint inhibitors targeting the programmed cell death 1 receptor (PD-1) improve survival in a subset of patients with clear cell renal cell carcinoma (ccRCC). To identify genomic alterations in ccRCC that correlate with response to anti-PD-1 monotherapy, we performed whole-exome sequencing of metastatic ccRCC from 35 patients. We found that clinical benefit was associated with loss-of-function mutations in the PBRM1 gene (P = 0.012), which encodes a subunit of the PBAF switch-sucrose nonfermentable (SWI/SNF) chromatin remodeling complex. We confirmed this finding in an independent validation cohort of 63 ccRCC patients treated with PD-1 or PD-L1 (PD-1 ligand) blockade therapy alone or in combination with anti-CTLA-4 (cytotoxic T lymphocyte-associated protein 4) therapies (P = 0.0071). Gene-expression analysis of PBAF-deficient ccRCC cell lines and PBRM1-deficient tumors revealed altered transcriptional output in JAK-STAT (Janus kinase-signal transducers and activators of transcription), hypoxia, and immune signaling pathways. PBRM1 loss in ccRCC may alter global tumor-cell expression profiles to influence responsiveness to immune checkpoint therapy.
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Affiliation(s)
- Diana Miao
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | - Claire A Margolis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | - Wenhua Gao
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Martin H Voss
- Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Weill Cornell Medical College, New York, NY 10065, USA
| | - Wei Li
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Dylan J Martini
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Craig Norton
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Dominick Bossé
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Stephanie M Wankowicz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | - Dana Cullen
- Bristol-Myers Squibb, New York, NY 10154, USA
| | | | | | - Adam Tracy
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | - Marios Giannakis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | - Frank Stephen Hodi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Mark W Ball
- James Buchanan Brady Urological Institute and Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Mohamad E Allaf
- James Buchanan Brady Urological Institute and Department of Urology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | | | - Matthew D Hellmann
- Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Weill Cornell Medical College, New York, NY 10065, USA
| | - Thai Ho
- Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Robert J Motzer
- Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Weill Cornell Medical College, New York, NY 10065, USA
| | - Sabina Signoretti
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - William G Kaelin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Howard Hughes Medical Institute, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
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11
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Rheinbay E, Parasuraman P, Grimsby J, Tiao G, Engreitz JM, Kim J, Lawrence MS, Taylor-Weiner A, Rodriguez-Cuevas S, Rosenberg M, Hess J, Stewart C, Maruvka YE, Stojanov P, Cortes ML, Seepo S, Cibulskis C, Tracy A, Pugh TJ, Lee J, Zheng Z, Ellisen LW, Iafrate AJ, Boehm JS, Gabriel SB, Meyerson M, Golub TR, Baselga J, Hidalgo-Miranda A, Shioda T, Bernards A, Lander ES, Getz G. Recurrent and functional regulatory mutations in breast cancer. Nature 2017; 547:55-60. [PMID: 28658208 DOI: 10.1038/nature22992] [Citation(s) in RCA: 211] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 05/28/2017] [Indexed: 12/24/2022]
Abstract
Genomic analysis of tumours has led to the identification of hundreds of cancer genes on the basis of the presence of mutations in protein-coding regions. By contrast, much less is known about cancer-causing mutations in non-coding regions. Here we perform deep sequencing in 360 primary breast cancers and develop computational methods to identify significantly mutated promoters. Clear signals are found in the promoters of three genes. FOXA1, a known driver of hormone-receptor positive breast cancer, harbours a mutational hotspot in its promoter leading to overexpression through increased E2F binding. RMRP and NEAT1, two non-coding RNA genes, carry mutations that affect protein binding to their promoters and alter expression levels. Our study shows that promoter regions harbour recurrent mutations in cancer with functional consequences and that the mutations occur at similar frequencies as in coding regions. Power analyses indicate that more such regions remain to be discovered through deep sequencing of adequately sized cohorts of patients.
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Affiliation(s)
- Esther Rheinbay
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02124, USA.,Massachusetts General Hospital Center for Cancer Research, Charlestown, Massachusetts 02129, USA
| | - Prasanna Parasuraman
- Massachusetts General Hospital Center for Cancer Research, Charlestown, Massachusetts 02129, USA
| | - Jonna Grimsby
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02124, USA
| | - Grace Tiao
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02124, USA
| | - Jesse M Engreitz
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02124, USA.,Division of Health Sciences and Technology, MIT, Cambridge, Massachusetts 02139, USA
| | - Jaegil Kim
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02124, USA
| | - Michael S Lawrence
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02124, USA.,Massachusetts General Hospital Center for Cancer Research, Charlestown, Massachusetts 02129, USA
| | | | | | - Mara Rosenberg
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02124, USA
| | - Julian Hess
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02124, USA
| | - Chip Stewart
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02124, USA
| | - Yosef E Maruvka
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02124, USA.,Massachusetts General Hospital Center for Cancer Research, Charlestown, Massachusetts 02129, USA
| | - Petar Stojanov
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02124, USA
| | - Maria L Cortes
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02124, USA
| | - Sara Seepo
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02124, USA
| | - Carrie Cibulskis
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02124, USA
| | - Adam Tracy
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02124, USA
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network and the Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Jesse Lee
- Massachusetts General Hospital Center for Cancer Research, Charlestown, Massachusetts 02129, USA
| | - Zongli Zheng
- Massachusetts General Hospital Center for Cancer Research, Charlestown, Massachusetts 02129, USA
| | - Leif W Ellisen
- Massachusetts General Hospital Center for Cancer Research, Charlestown, Massachusetts 02129, USA.,Harvard Medical School, Boston, Massachusetts 02115, USA
| | - A John Iafrate
- Massachusetts General Hospital Center for Cancer Research, Charlestown, Massachusetts 02129, USA
| | - Jesse S Boehm
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02124, USA
| | - Stacey B Gabriel
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02124, USA
| | - Matthew Meyerson
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02124, USA.,Harvard Medical School, Boston, Massachusetts 02115, USA.,Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Todd R Golub
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02124, USA.,Harvard Medical School, Boston, Massachusetts 02115, USA.,Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Jose Baselga
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | | | - Toshi Shioda
- Massachusetts General Hospital Center for Cancer Research, Charlestown, Massachusetts 02129, USA
| | - Andre Bernards
- Massachusetts General Hospital Center for Cancer Research, Charlestown, Massachusetts 02129, USA
| | - Eric S Lander
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02124, USA
| | - Gad Getz
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02124, USA.,Massachusetts General Hospital Center for Cancer Research, Charlestown, Massachusetts 02129, USA.,Harvard Medical School, Boston, Massachusetts 02115, USA.,Massachusetts General Hospital, Department of Pathology, Boston, Massachusetts 02114, USA
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12
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Bandopadhayay P, Paolella B, O’Rourke R, Ho P, Greenwald N, Sharpira O, Pantel S, Bagul M, Tracy A, Roti G, Balboni A, Vazquez F, Ligon K, Piccioni F, Stegmaier K, Johannessen C, Beroukhim R. TRTH-15. RESISTANCE MECHANISMS TO BET-BROMODOMAIN INHIBITION IN MYC-AMPLIFIED MEDULLOBLASTOMA. Neuro Oncol 2017. [DOI: 10.1093/neuonc/nox083.227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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13
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Affiliation(s)
- A Tracy
- Medical Department, G. and J. Weir, Ltd., Glasgow
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14
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Cheng J, Sun S, Tracy A, Hubbell E, Morris J, Valmeekam V, Kimbrough A, Cline MS, Liu G, Shigeta R, Kulp D, Siani-Rose MA. NetAffx Gene Ontology Mining Tool: a visual approach for microarray data analysis. Bioinformatics 2004; 20:1462-3. [PMID: 14962933 DOI: 10.1093/bioinformatics/bth087] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
SUMMARY The NetAffx Gene Ontology (GO) Mining Tool is a web-based, interactive tool that permits traversal of the GO graph in the context of microarray data. It accepts a list of Affymetrix probe sets and renders a GO graph as a heat map colored according to significance measurements. The rendered graph is interactive, with nodes linked to public web sites and to lists of the relevant probe sets. The GO Mining Tool provides visualization combining biological annotation with expression data, encompassing thousands of genes in one interactive view. AVAILABILITY GO Mining Tool is freely available at http://www.affymetrix.com/analysis/query/go_analysis.affx
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Affiliation(s)
- Jill Cheng
- Affymetrix Corporation, Bioinformatics, 6550 Vallejo Street, Suite 100, Emeryville, CA 94608, USA.
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15
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Rojdev R, Krikorian R, Feldman D, Tracy A, Williams C. Working memory and concept formation on the tower of London task. Arch Clin Neuropsychol 1998. [DOI: 10.1093/arclin/13.1.32a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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16
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Staner L, Tracy A, Dramaix M, Genevrois C, Vanderelst M, Vilane A, Bauwens F, Pardoen D, Mendlewicz J. Clinical and psychosocial predictors of recurrence in recovered bipolar and unipolar depressives: a one-year controlled prospective study. Psychiatry Res 1997; 69:39-51. [PMID: 9080544 DOI: 10.1016/s0165-1781(96)03021-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Unipolar and bipolar patients with a chronic illness pattern were investigated to evaluate the relevance of clinical and psychosocial risk factors to predict subsequent recurrence. Self-esteem, social adjustment, social support and attributional style were assessed in 27 recovered bipolar patients, 24 recovered unipolar patients maintained on lithium or antidepressant prophylaxis and 26 healthy controls. They were further interviewed every 2 months in a 1-year period in order to diagnose affective episodes according to Research Diagnostic Criteria. Survival analyses and Cox's regressions demonstrated that being a unipolar patient and showing poor social adjustment were the strongest predictors of the occurrence of affective episodes. Self-esteem, social support, attributional style and clinical characteristics, such as age at illness onset, number of previous episodes or of previous hospitalizations and presence of affective disorder in first-degree relatives, were not found to be risk factors for further recurrence. This study stresses the importance of social adjustment in evaluating the outcome of affectively ill patients maintained on medication prophylaxis.
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Affiliation(s)
- L Staner
- Department of Psychiatry, Centre Hospitalier, Luxembourg, Grand Duchy of Luxembourg.
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17
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Abstract
BACKGROUND Unipolar and bipolar patients with a chronic illness pattern were investigated to determine whether they experienced a higher number of life events prior to the onset of recurrent affective episodes. METHOD The study participants consisted of 27 recovered bipolar patients, 24 recovered unipolar patients and 26 healthy control subjects. Life events and psychiatric status were assessed by bimonthly interviews over the period of one year using the Inventory for Recent Life Events and the Research Diagnostic Criteria. RESULTS In both unipolar and bipolar patients, analyses revealed no significant differences in the number of life events experienced, irrespective of whether the patients had presented with a depressive episode of at least minor intensity during the study (all P > 0.1). Specifically, an increase in marital problems was observed in bipolar patients prior to the onset of recurrent hypomanic and manic episodes (P = 0.06). CONCLUSION The causal association between life events and the onset of depression, shown to be relevant in non-chronically depressed subjects, does not apply in chronic affective disorders. In addition, our results suggest that marital events have an impact on the onset of recurrent hypomanic and manic episodes.
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Affiliation(s)
- D Pardoen
- Free University of Brussels, University Clinic of Brussels, Belgium
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18
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Abstract
The hypothesis of a low self-esteem in depressive patients was tested using the Rosenberg Self-Esteem Scale in 24 recovered unipolar and 27 recovered bipolar patients, compared with a normal control group of 26 subjects matched for age and sex. The hypothesis was confirmed only for unipolars; bipolar patients presented a self-esteem score not significantly different from normal scores. Self-esteem was not related to clinical characteristics of the affective disorder, suggesting that low self-esteem may be a basic component of a depression-prone personality. The investigation of the relationship between self-esteem and social adjustment confirmed the presence of social conformism in bipolar patients and rigidly set low self-esteem in unipolar patients. These results should stimulate the evaluation of different psychotherapeutic treatments in the long-term psychosocial management of affectively ill patients.
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Affiliation(s)
- D Pardoen
- Department of Psychiatry, University Clinics of Brussels, Erasme Hospital, Belgium
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Tracy A, Bauwens F, Martin F, Pardoen D, Mendlewicz J. Attributional style and depression: a controlled comparison of remitted unipolar and bipolar patients. Br J Clin Psychol 1992; 31:83-4. [PMID: 1559120 DOI: 10.1111/j.2044-8260.1992.tb00970.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Attributional style was investigated in remitted affective disorder patients (23 unipolars and 26 bipolars) and 26 non-psychiatric controls. We found a specific cognitive vulnerability in unipolars. Unipolars attributed negative events to causes that were more stable--but not more internal nor more global--than bipolars and controls, and did not attach more importance to these events. Attributional vulnerability seemed more apparent in patients with longer histories of depression.
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Affiliation(s)
- A Tracy
- Department of Psychiatry, Cliniques Universitaires de Bruxelles, Hôpital Erasme, Belgium
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Bauwens F, Tracy A, Pardoen D, Vander Elst M, Mendlewicz J. Social adjustment of remitted bipolar and unipolar out-patients. A comparison with age- and sex-matched controls. Br J Psychiatry 1991; 159:239-44. [PMID: 1773240 DOI: 10.1192/bjp.159.2.239] [Citation(s) in RCA: 88] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Various areas of social adjustment were compared using the Social Adjustment Scale in 27 remitted bipolars, 24 remitted unipolars and 25 normal controls matched for age and sex. Scores for global adjustment and for social and leisure activities were significantly worse in patients than in controls. The maladjustment in social and leisure activities appeared only in 'contact with friends' for bipolar patients and 'diminished social interactions' for unipolar patients. Unipolar patients differed significantly from controls on the items investigating sexual adjustment. In unipolars, social maladjustment seemed to be independent of the course of the disease; in bipolars, it was partly related to the mean number of lifetime episodes and current residual symptoms.
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Affiliation(s)
- F Bauwens
- Department of Psychiatry, Erasme Hospital, Brussels, Belgium
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