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Sicinska E, Kola VSR, Kerfoot JA, Taddei ML, Al-Ibraheemi A, Hsieh YH, Church AJ, Landesman-Bollag E, Landesman Y, Hemming ML. ASPSCR1::TFE3 Drives Alveolar Soft Part Sarcoma by Inducing Targetable Transcriptional Programs. Cancer Res 2024:743240. [PMID: 38657118 DOI: 10.1158/0008-5472.can-23-2115] [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] [Received: 07/15/2023] [Revised: 02/09/2024] [Accepted: 04/19/2024] [Indexed: 04/26/2024]
Abstract
Alveolar soft part sarcoma (ASPS) is a rare mesenchymal malignancy driven by the ASPSCR1::TFE3 fusion. A better understanding of the mechanisms by which this oncogenic transcriptional regulator drives cancer growth is needed to help identify potential therapeutic targets. Here, we characterized the transcriptional and chromatin landscapes of ASPS tumors and preclinical models, identifying the essential role of ASPSCR1::TFE3 in tumor cell viability by regulating core transcriptional programs involved in cell proliferation, angiogenesis, and mitochondrial biology. ASPSCR1::TFE3 directly interacted with key epigenetic regulators at enhancers and promoters to support ASPS-associated transcription. Among the effector programs driven by ASPSCR1::TFE3, cell proliferation was driven by high levels of cyclin D1 expression. Disruption of cyclin D1/CDK4 signaling led to loss of ASPS proliferative capacity, and combined inhibition of CDK4/6 and angiogenesis halted tumor growth in xenografts. These results define the ASPS oncogenic program, reveal mechanisms by which ASPSCR1::TFE3 controls tumor biology, and identify a strategy for therapeutically targeting tumor cell-intrinsic vulnerabilities.
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Affiliation(s)
- Ewa Sicinska
- Dana-Farber Cancer Institute, Boston, MA, United States
| | | | | | | | | | - Yi-Hsuan Hsieh
- University of Massachusetts Chan Medical School, Worcester, MA, United States
| | | | | | | | - Matthew L Hemming
- University of Massachusetts Chan Medical School, Worcester, MA, United States
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2
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Schaefer IM, Hemming ML, Lundberg MZ, Serrata MP, Goldaracena I, Liu N, Yin P, Paulo JA, Gygi SP, George S, Morgan JA, Bertagnolli MM, Sicinska ET, Chu C, Zheng S, Mariño-Enríquez A, Hornick JL, Raut CP, Ou WB, Demetri GD, Saka SK, Fletcher JA. Concurrent inhibition of CDK2 adds to the anti-tumour activity of CDK4/6 inhibition in GIST. Br J Cancer 2022; 127:2072-2085. [PMID: 36175617 PMCID: PMC9681737 DOI: 10.1038/s41416-022-01990-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 04/22/2022] [Revised: 09/07/2022] [Accepted: 09/12/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Advanced gastrointestinal stromal tumour (GIST) is characterised by genomic perturbations of key cell cycle regulators. Oncogenic activation of CDK4/6 results in RB1 inactivation and cell cycle progression. Given that single-agent CDK4/6 inhibitor therapy failed to show clinical activity in advanced GIST, we evaluated strategies for maximising response to therapeutic CDK4/6 inhibition. METHODS Targeted next-generation sequencing and multiplexed protein imaging were used to detect cell cycle regulator aberrations in GIST clinical samples. The impact of inhibitors of CDK2, CDK4 and CDK2/4/6 was determined through cell proliferation and protein detection assays. CDK-inhibitor resistance mechanisms were characterised in GIST cell lines after long-term exposure. RESULTS We identify recurrent genomic aberrations in cell cycle regulators causing co-activation of the CDK2 and CDK4/6 pathways in clinical GIST samples. Therapeutic co-targeting of CDK2 and CDK4/6 is synergistic in GIST cell lines with intact RB1, through inhibition of RB1 hyperphosphorylation and cell proliferation. Moreover, RB1 inactivation and a novel oncogenic cyclin D1 resulting from an intragenic rearrangement (CCND1::chr11.g:70025223) are mechanisms of acquired CDK-inhibitor resistance in GIST. CONCLUSIONS These studies establish the biological rationale for CDK2 and CDK4/6 co-inhibition as a therapeutic strategy in patients with advanced GIST, including metastatic GIST progressing on tyrosine kinase inhibitors.
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Affiliation(s)
- Inga-Marie Schaefer
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Matthew L Hemming
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Sarcoma Center, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA, USA
| | - Meijun Z Lundberg
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Matthew P Serrata
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Isabel Goldaracena
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Ninning Liu
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Suzanne George
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Sarcoma Center, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA, USA
| | - Jeffrey A Morgan
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Sarcoma Center, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA, USA
| | - Monica M Bertagnolli
- Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ewa T Sicinska
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Chen Chu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Shanshan Zheng
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Adrian Mariño-Enríquez
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jason L Hornick
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Sarcoma Center, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA, USA
| | - Chandrajit P Raut
- Sarcoma Center, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA, USA
- Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Wen-Bin Ou
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - George D Demetri
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Sarcoma Center, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
| | - Sinem K Saka
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Jonathan A Fletcher
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Sarcoma Center, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Boston, MA, USA
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3
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Schaefer IM, Hemming ML, Lundberg MZ, Serrata MP, Goldaracena I, Liu N, Yin P, Paulo JA, Gygi SP, George S, Morgan JA, Bertagnolli MM, Sicinska ET, Mariño-Enríquez A, Hornick JL, Raut CP, Demetri GD, Ou WB, Saka SK, Fletcher JA. Abstract A013: CDK2 and CDK4/6 inhibition in GIST: Mechanisms of response and resistance. Clin Cancer Res 2022. [DOI: 10.1158/1557-3265.sarcomas22-a013] [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
Advanced GIST is characterized by genomic perturbations of key cell cycle regulators. Oncogenic activation of CDK4/6 results in RB1 inactivation and cell cycle progression. Given that single-agent CDK4/6 inhibitor (CDK4/6i) therapy failed to show clinical activity in advanced GIST, we evaluated strategies for maximizing response to therapeutic CDK4/6 inhibition. Targeted next-generation sequencing and multiplexed protein imaging were used to detect cell cycle regulator aberrations in GIST clinical samples (N=18), including 8 metastatic TKI-resistant GISTs. Multiple metastases were analyzed in 3 patients. The impact of CDK2i (CDK2 inhibitor-II), CDK4/6i (palbociclib or abemaciclib), and CDK2/4/6i (PF-06873600) was determined through cell proliferation and protein detection assays in vitro and in vivo. Mechanisms of acquired CDK2i and CDK4/6i resistance were characterized in GIST cell lines after long-term exposure. The results demonstrate recurrent genomic aberrations in cell cycle regulators causing co-activation of the CDK2 and CDK4/6 pathways. Identical aberrations of p16, RB1, and TP53 were present in all metastases from 3 patients. We show that therapeutic co-targeting of CDK2 and CDK4/6 is synergistic in GIST cell lines with intact RB1, through inhibition of RB1 hyperphosphorylation and cell proliferation (P<0.01). Intact RB1 predicted response to treatment, whereas RB1-deficient models were resistant. Moreover, we identify RB1 inactivation and a novel oncogenic cyclin D1 resulting from an intragenic rearrangement (CCND1::chr11.g:70025223) as mechanisms of acquired CDK inhibitor resistance in GIST. The CCND1 rearrangement deleted the cyclin D1 C-terminal Thr286 and Thr288 residues which mediate cyclin D1 proteasomal degradation, resulting in overexpression of an abnormal cyclin D1. CDK inhibitor resistance properties were corroborated by lentiviral transduction of the CCND1 fusion gene into fusion-negative GIST, leiomyosarcoma, and breast cancer cells. These studies establish the biologic rationale for CDK2 and CDK4/6 co-inhibition as therapeutic strategy in patients with advanced GIST, including patients with metastatic GIST progressing on TKIs. In addition, these findings expand the spectrum of potential CDK inhibitor resistance mechanisms with translational potential for improving cell cycle targeted therapies in other cancer types.
Citation Format: Inga-Marie Schaefer, Matthew L. Hemming, Meijun Z. Lundberg, Matthew P. Serrata, Isabel Goldaracena, Ninning Liu, Peng Yin, Joao A. Paulo, Steven P. Gygi, Suzanne George, Jeffrey A. Morgan, Monica M. Bertagnolli, Ewa T. Sicinska, Adrian Mariño-Enríquez, Jason L. Hornick, Chandrajit P. Raut, George D. Demetri, Wen-Bin Ou, Sinem K. Saka, Jonathan A. Fletcher. CDK2 and CDK4/6 inhibition in GIST: Mechanisms of response and resistance [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr A013.
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Affiliation(s)
| | | | | | - Matthew P. Serrata
- 3Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA,
| | - Isabel Goldaracena
- 3Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA,
| | - Ninning Liu
- 3Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA,
| | - Peng Yin
- 3Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA,
| | | | | | | | | | | | | | | | | | | | | | - Wen-Bin Ou
- 1Brigham and Women's Hospital, Boston, MA,
| | - Sinem K. Saka
- 5European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
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Hemming ML, Benson MR, Loycano MA, Anderson JA, Andersen JL, Taddei ML, Krivtsov AV, Aubrey BJ, Cutler JA, Hatton C, Sicinska E, Armstrong SA. MOZ and Menin-MLL Complexes Are Complementary Regulators of Chromatin Association and Transcriptional Output in Gastrointestinal Stromal Tumor. Cancer Discov 2022; 12:1804-1823. [PMID: 35499757 PMCID: PMC9453853 DOI: 10.1158/2159-8290.cd-21-0646] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 03/23/2022] [Accepted: 04/27/2022] [Indexed: 01/09/2023]
Abstract
Gastrointestinal stromal tumor (GIST) is commonly characterized by activating mutations in the receptor tyrosine kinase KIT. Tyrosine kinase inhibitors are the only approved therapy for GIST, and complementary treatment strategies are urgently needed. As GIST lacks oncogene amplification and relies upon an established network of transcription factors, we hypothesized that unique chromatin-modifying enzymes are essential in orchestrating the GIST epigenome. We identified through genome-scale CRISPR screening that MOZ and Menin-MLL chromatin regulatory complexes are cooperative and unique dependencies in GIST. These complexes were enriched at GIST-relevant genes and regulated their transcription. Inhibition of MOZ and Menin-MLL complexes decreased GIST cell proliferation by disrupting interactions with transcriptional/chromatin regulators, such as DOT1L. MOZ and Menin inhibition caused significant reductions in tumor burden in vivo, with superior effects observed with combined Menin and KIT inhibition. These results define unique chromatin regulatory dependencies in GIST and identify potential therapeutic strategies for clinical application. SIGNIFICANCE Although many malignancies rely on oncogene amplification, GIST instead depends upon epigenetic regulation of KIT and other essential genes. Utilizing genome-scale CRISPR dependency screens, we identified complementary chromatin-modifying complexes essential to GIST and characterize the consequences of their disruption, elucidating a novel therapeutic approach to this disease. This article is highlighted in the In This Issue feature, p. 1599.
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Affiliation(s)
- Matthew L Hemming
- Department of Medical Oncology, Sarcoma Center, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Morgan R Benson
- Department of Pediatric Oncology and Division of Hematology/Oncology, Dana-Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Michael A Loycano
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Justin A Anderson
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Jessica L Andersen
- Department of Medical Oncology, Sarcoma Center, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Madeleine L Taddei
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Andrei V Krivtsov
- Department of Pediatric Oncology and Division of Hematology/Oncology, Dana-Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Brandon J Aubrey
- Department of Pediatric Oncology and Division of Hematology/Oncology, Dana-Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Jevon A Cutler
- Department of Pediatric Oncology and Division of Hematology/Oncology, Dana-Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Charlie Hatton
- Department of Pediatric Oncology and Division of Hematology/Oncology, Dana-Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Ewa Sicinska
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Scott A Armstrong
- Department of Pediatric Oncology and Division of Hematology/Oncology, Dana-Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts
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5
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Schaefer IM, Lundberg MZ, Hemming ML, Saka SK, Serrata MP, Goldaracena I, Liu N, Yin P, Paulo JA, Gygi S, Demetri GD, Sicinska E, Mariño-Enríquez A, Hornick JL, Raut CP, Ou WB, Fletcher JA. Abstract 5648: Response and resistance to CDK2 and CDK4/6 inhibition in GIST. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-5648] [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
Gastrointestinal stromal tumor (GIST) is the most common GI sarcoma and is generally initiated by KIT or PDGFRA mutations which are compelling therapeutic targets for tyrosine kinase inhibitors (TKI). However, the emergence of secondary mutations results in clinical resistance to available TKIs. GIST progression is driven by genomic events which incrementally target the p16-CDK4/6-RB1 and p14-TP53-RB1 pathways to create CDK4/6 and CDK2 oncogenic co-dependency. Based on limited efficacy of single-agent CDK4/6-inhibitor (CDK4/6i) therapy in GIST, we evaluated strategies of co-targeting CDK2 and CDK4/6. Multiplexed protein imaging (via Immuno-SABER) was validated for the detection of cell cycle regulator aberrations in GIST clinical samples (N=18), 7 of which were TKI-resistant, and including 3 patients in whom multiple metastases were analyzed. The impact of various CDK perturbants using CDK2i (CDK2 inhibitor-II), CDK4/6i (palbociclib or abemaciclib), and CDK2/4/6i (PF-06873600) was determined through cell proliferation and protein detection assays in GIST cell lines and murine xenografts. Mechanisms of acquired CDK2i and CDK4/6i resistance were characterized in GIST cell lines after long-term exposure. Abnormal expression/biallelic inactivation of CDKN2A/p16, RB1, and TP53 were identified in 7 (39%), 2 (11%), and 2 (11%) of 18 GISTs, respectively. Identical aberrations of p16, RB1, and TP53 were present in all metastases from 3 patients. Since 5 of 7 RB1-intact advanced GISTs had co-dysregulation of the CDK2 and CDK4/6 pathways, we evaluated co-inhibition of CDK2 and CDK4/6 in vitro and in vivo which inhibited cell proliferation (P<0.01) and RB1 hyperphosphorylation. Intact RB1 predicted response to treatment, whereas RB1-deficient models were resistant. Two resistant sub-lines emerged after 11 and 14 months of palbociclib exposure: one with biallelic genomic RB1 inactivation and the other with the first known example of a cyclin D1 coding sequence fusion with oncogenic properties (CCND1::chr11.g:70025223). The CCND1 fusion deleted the cyclin D1 C-terminal Thr286 and Thr288 residues which mediate cyclin D1 proteasomal degradation, resulting in overexpression of an abnormal cyclin D1. Palbociclib-resistance properties were corroborated by lentiviral transduction of the CCND1 fusion gene into fusion-negative GIST, leiomyosarcoma, and breast cancer cells. CDK2 and CDK4/6 pathway perturbations with retained RB1 are frequent in advanced GIST and can be conserved across metastases, creating a compelling biologic rationale for therapeutic cell cycle restoration. We show that co-inhibition of CDK2 and CDK4/6 is synergistic in GIST and highlight RB1 inactivation and a novel oncogenic cyclin D1 as mechanisms of acquired CDKi resistance. Hence, combination therapies targeting CDK2 and CDK4/6 with correlative biomarkers predictive of response should be evaluated in patients with metastatic or TKI-resistant GIST.
Citation Format: Inga-Marie Schaefer, Meijun Z. Lundberg, Matthew L. Hemming, Sinem K. Saka, Matthew P. Serrata, Isabel Goldaracena, Ninning Liu, Peng Yin, Joao A. Paulo, Steven Gygi, George D. Demetri, Ewa Sicinska, Adrian Mariño-Enríquez, Jason L. Hornick, Chandrajit P. Raut, Wen-Bin Ou, Jonathan A. Fletcher. Response and resistance to CDK2 and CDK4/6 inhibition in GIST [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5648.
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Affiliation(s)
| | | | | | - Sinem K. Saka
- 3European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Matthew P. Serrata
- 4Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA
| | - Isabel Goldaracena
- 4Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA
| | - Ninning Liu
- 4Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA
| | - Peng Yin
- 4Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA
| | | | | | | | - Ewa Sicinska
- 2Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | | | - Jason L. Hornick
- 1Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | | | - Wen-Bin Ou
- 1Brigham and Women's Hospital, Harvard Medical School, Boston, MA
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Zaiken MC, Flynn R, Paz KG, Rhee SY, Jin S, Mohamed FA, Saha A, Thangavelu G, Park PMC, Hemming ML, Sage PT, Sharpe AH, DuPage M, Bluestone JA, Panoskaltsis-Mortari A, Cutler CS, Koreth J, Antin JH, Soiffer RJ, Ritz J, Luznik L, Maillard I, Hill GR, MacDonald KPA, Munn DH, Serody JS, Murphy WJ, Kean LS, Zhang Y, Bradner JE, Qi J, Blazar BR. BET-bromodomain and EZH2 inhibitor-treated chronic GVHD mice have blunted germinal centers with distinct transcriptomes. Blood 2022; 139:2983-2997. [PMID: 35226736 PMCID: PMC9101246 DOI: 10.1182/blood.2021014557] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 10/25/2021] [Accepted: 02/09/2022] [Indexed: 01/26/2023] Open
Abstract
Despite advances in the field, chronic graft-versus-host-disease (cGVHD) remains a leading cause of morbidity and mortality following allogenic hematopoietic stem cell transplant. Because treatment options remain limited, we tested efficacy of anticancer, chromatin-modifying enzyme inhibitors in a clinically relevant murine model of cGVHD with bronchiolitis obliterans (BO). We observed that the novel enhancer of zeste homolog 2 (EZH2) inhibitor JQ5 and the BET-bromodomain inhibitor JQ1 each improved pulmonary function; impaired the germinal center (GC) reaction, a prerequisite in cGVHD/BO pathogenesis; and JQ5 reduced EZH2-mediated H3K27me3 in donor T cells. Using conditional EZH2 knockout donor cells, we demonstrated that EZH2 is obligatory for the initiation of cGVHD/BO. In a sclerodermatous cGVHD model, JQ5 reduced the severity of cutaneous lesions. To determine how the 2 drugs could lead to the same physiological improvements while targeting unique epigenetic processes, we analyzed the transcriptomes of splenic GCB cells (GCBs) from transplanted mice treated with either drug. Multiple inflammatory and signaling pathways enriched in cGVHD/BO GCBs were reduced by each drug. GCBs from JQ5- but not JQ1-treated mice were enriched for proproliferative pathways also seen in GCBs from bone marrow-only transplanted mice, likely reflecting their underlying biology in the unperturbed state. In conjunction with in vivo data, these insights led us to conclude that epigenetic targeting of the GC is a viable clinical approach for the treatment of cGVHD, and that the EZH2 inhibitor JQ5 and the BET-bromodomain inhibitor JQ1 demonstrated clinical potential for EZH2i and BETi in patients with cGVHD/BO.
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Affiliation(s)
- Michael C Zaiken
- Division of Blood & Marrow Transplant & Cellular Therapy, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN
| | - Ryan Flynn
- Division of Blood & Marrow Transplant & Cellular Therapy, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN
| | - Katelyn G Paz
- Division of Blood & Marrow Transplant & Cellular Therapy, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN
| | - Stephanie Y Rhee
- Division of Blood & Marrow Transplant & Cellular Therapy, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN
| | - Sujeong Jin
- Division of Blood & Marrow Transplant & Cellular Therapy, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN
| | - Fathima A Mohamed
- Division of Blood & Marrow Transplant & Cellular Therapy, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN
| | - Asim Saha
- Division of Blood & Marrow Transplant & Cellular Therapy, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN
| | - Govindarajan Thangavelu
- Division of Blood & Marrow Transplant & Cellular Therapy, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN
| | - Paul M C Park
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
| | - Matthew L Hemming
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
| | - Peter T Sage
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA
- Evergrande Center for Immunologic Diseases, Harvard Medical School-Brigham and Women's Hospital, Boston, MA
| | - Arlene H Sharpe
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA
- Evergrande Center for Immunologic Diseases, Harvard Medical School-Brigham and Women's Hospital, Boston, MA
| | - Michel DuPage
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA
| | | | - Angela Panoskaltsis-Mortari
- Division of Blood & Marrow Transplant & Cellular Therapy, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN
| | | | | | | | - Robert J Soiffer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | | | - Leo Luznik
- Department of Oncology, Sidney Kimmel Cancer Center, Baltimore, MD
| | - Ivan Maillard
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Geoffrey R Hill
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- Division of Medical Oncology, University of Washington, Seattle, WA
| | - Kelli P A MacDonald
- Department of Immunology, Queensland Institute of Medical Research (QIMR), University of Queensland, Brisbane, QLD, Australia
| | - David H Munn
- Georgia Cancer Center, Augusta University, Augusta, GA
| | - Jonathan S Serody
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
| | - William J Murphy
- Department of Dermatology, School of Medicine, University of California, Davis, Sacramento, CA
| | - Leslie S Kean
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, MA
| | - Yi Zhang
- Fels Institute for Cancer Research and Molecular Biology, Department of Microbiology and Immunology, Temple University, Philadelphia, PA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA; and
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Bruce R Blazar
- Division of Blood & Marrow Transplant & Cellular Therapy, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN
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7
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Hemming ML, Bhola P, Loycano MA, Anderson JA, Taddei ML, Doyle LA, Lavrova E, Andersen JL, Klega KS, Benson MR, Crompton BD, Raut CP, George S, Letai A, Demetri GD, Sicinska E. Preclinical modeling of leiomyosarcoma identifies susceptibility to transcriptional CDK inhibitors through antagonism of E2F-driven oncogenic gene expression. Clin Cancer Res 2022; 28:2397-2408. [PMID: 35325095 DOI: 10.1158/1078-0432.ccr-21-3523] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 02/15/2022] [Accepted: 03/22/2022] [Indexed: 11/16/2022]
Abstract
PURPOSE Leiomyosarcoma (LMS) is a neoplasm characterized by smooth muscle differentiation, complex copy-number alterations, tumor suppressor loss and the absence of recurrent driver mutations. Clinical management for advanced disease relies on the use of empiric cytotoxic chemotherapy with limited activity, and novel targeted therapies supported by preclinical research on LMS biology are urgently needed. A lack of fidelity of established LMS cell lines to their mesenchymal neoplasm of origin has limited translational understanding of this disease, and few other preclinical models have been established. Here, we characterize LMS patient derived xenograft (PDX) models of LMS, assessing fidelity to their tumors of origin and performing preclinical evaluation of candidate therapies. EXPERIMENTAL DESIGN We implanted 49 LMS surgical samples into immunocompromised mice. Engrafting tumors were characterized by histology, targeted next-generation sequencing, RNA-seq and ultra-low passage whole-genome sequencing. Candidate therapies were selected based on prior evidence of pathway activation or high-throughput dynamic BH3 profiling. RESULTS We show that LMS PDX maintain the histologic appearance, copy-number alterations and transcriptional program of their parental tumors across multiple xenograft passages. Transcriptionally, LMS PDX co-cluster with paired LMS patient-derived samples and differ primarily in host-related immunologic and microenvironment signatures. We identify susceptibility of LMS PDX to transcriptional CDK inhibition, which disrupts an E2F-driven oncogenic transcriptional program and inhibits tumor growth. CONCLUSIONS Our results establish LMS PDX as valuable preclinical models and identify strategies to discover novel vulnerabilities in this disease. These data support the clinical assessment of transcriptional CDK inhibitors as a therapeutic strategy for LMS patients.
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Affiliation(s)
| | - Patrick Bhola
- Dana-Farber Cancer Institute, Boston, MA, United States
| | | | | | | | - Leona A Doyle
- Brigham and Women's Hospital, Boston, MA, United States
| | | | | | - Kelly S Klega
- Dana-Farber Cancer Institute, Boston, MA, United States
| | | | - Brian D Crompton
- Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, United States
| | - Chandrajit P Raut
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | | | - Anthony Letai
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, United States
| | | | - Ewa Sicinska
- Dana-Farber Cancer Institute, Boston, MA, United States
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8
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Cousin S, Blay JY, Garcia IB, de Bono JS, Le Tourneau C, Moreno V, Trigo J, Hann CL, Azad AA, Im SA, Cassier PA, French CA, Italiano A, Keedy VL, Plummer R, Sablin MP, Hemming ML, Ferron-Brady G, Wyce A, Khaled A, Datta A, Foley SW, McCabe MT, Wu Y, Horner T, Kremer BE, Dhar A, O'Dwyer PJ, Shapiro GI, Piha-Paul SA. Safety, pharmacokinetic, pharmacodynamic and clinical activity of molibresib for the treatment of nuclear protein of the testis carcinoma and other cancers: Results of a Phase I/II open-label, dose escalation study. Int J Cancer 2021; 150:993-1006. [PMID: 34724226 DOI: 10.1002/ijc.33861] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 07/01/2021] [Accepted: 07/13/2021] [Indexed: 11/07/2022]
Abstract
Molibresib is an orally bioavailable, selective, small molecule BET protein inhibitor. Results from a first time in human study in solid tumors resulted in the selection of a 75 mg once daily dose of the besylate formulation of molibresib as the recommended Phase 2 dose (RP2D). Here we present the results of Part 2 of our study, investigating safety, pharmacokinetics, pharmacodynamics and clinical activity of molibresib at the RP2D for nuclear protein in testis carcinoma (NC), small cell lung cancer, castration-resistant prostate cancer (CRPC), triple-negative breast cancer, estrogen receptor-positive breast cancer and gastrointestinal stromal tumor. The primary safety endpoints were incidence of adverse events (AEs) and serious AEs; the primary efficacy endpoint was overall response rate. Secondary endpoints included plasma concentrations and gene set enrichment analysis (GSEA). Molibresib 75 mg once daily demonstrated no unexpected toxicities. The most common treatment-related AEs (any grade) were thrombocytopenia (64%), nausea (43%) and decreased appetite (37%); 83% of patients required dose interruptions and 29% required dose reductions due to AEs. Antitumor activity was observed in NC and CRPC (one confirmed partial response each, with observed reductions in tumor size), although predefined clinically meaningful response rates were not met for any tumor type. Total active moiety median plasma concentrations after single and repeated administration were similar across tumor cohorts. GSEA revealed that gene expression changes with molibresib varied by patient, response status and tumor type. Investigations into combinatorial approaches that use BET inhibition to eliminate resistance to other targeted therapies are warranted.
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Affiliation(s)
- Sophie Cousin
- Medical Oncology Department, Institut Bergonié, Bordeaux, France
| | - Jean-Yves Blay
- Medical Oncology Department, Centre Léon Bérard, Lyon, France
| | - Irene Braña Garcia
- Medical Oncology Department, Vall d'Hebron University Hospital, Vall d'Hebron Institut of Oncology (VHIO), Barcelona, Spain
| | - Johann S de Bono
- The Institute of Cancer Research and Royal Marsden Hospital, London, UK
| | - Christophe Le Tourneau
- Department of Drug Development and Innovation (D3i), INSERM U900 Research Unit, Institut Curie, Paris-Saclay University, Paris and Saint-Cloud, France
| | - Victor Moreno
- Medical Oncology, START Madrid-FJD, Fundación Jiménez Díaz Hospital, Madrid, Spain
| | - Jose Trigo
- Medical Oncology Department, Hospital Universitario Virgen de la Victoria y Regional, IBIMA, Málaga, Spain
| | - Christine L Hann
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Arun A Azad
- Peter MacCallum Cancer Centre, Victoria, Australia
| | - Seock-Ah Im
- Seoul National University Hospital, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | | | - Christopher A French
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Antoine Italiano
- Early Phase Trials and Sarcoma Units, Institut Bergonié, Bordeaux, France
| | - Vicki L Keedy
- Department of Medicine, Hematology and Oncology, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee, USA
| | - Ruth Plummer
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Marie-Paule Sablin
- Department of Drug Development and Innovation (D3i), INSERM U900 Research Unit, Institut Curie, Paris-Saclay University, Paris and Saint-Cloud, France
| | - Matthew L Hemming
- Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | | | | | | | | | | | | | - Yuehui Wu
- GSK, Collegeville, Pennsylvania, USA
| | | | | | | | - Peter J O'Dwyer
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Geoffrey I Shapiro
- Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Sarina A Piha-Paul
- Department of Investigational Cancer Therapeutics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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9
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Kasper B, Achee A, Schuster K, Wilson R, van Oortmerssen G, Gladdy RA, Hemming ML, Huang P, Ingham M, Jones RL, Pollack SM, Reinke D, Sanfilippo R, Schuetze SM, Somaiah N, Van Tine BA, Wilky B, Okuno S, Trent J. Unmet Medical Needs and Future Perspectives for Leiomyosarcoma Patients-A Position Paper from the National LeioMyoSarcoma Foundation (NLMSF) and Sarcoma Patients EuroNet (SPAEN). Cancers (Basel) 2021; 13:886. [PMID: 33672607 PMCID: PMC7924026 DOI: 10.3390/cancers13040886] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 01/29/2021] [Revised: 02/11/2021] [Accepted: 02/15/2021] [Indexed: 02/07/2023] Open
Abstract
As leiomyosarcoma patients are challenged by the development of metastatic disease, effective systemic therapies are the cornerstone of outcome. However, the overall activity of the currently available conventional systemic treatments and the prognosis of patients with advanced or metastatic disease are still poor, making the treatment of this patient group challenging. Therefore, in a joint effort together with patient networks and organizations, namely Sarcoma Patients EuroNet (SPAEN), the international network of sarcoma patients organizations, and the National LeioMyoSarcoma Foundation (NLMSF) in the United States, we aim to summarize state-of-the-art treatments for leiomyosarcoma patients in order to identify knowledge gaps and current unmet needs, thereby guiding the community to design innovative clinical trials and basic research and close these research gaps. This position paper arose from a leiomyosarcoma research meeting in October 2020 hosted by the NLMSF and SPAEN.
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Affiliation(s)
- Bernd Kasper
- Mannheim University Medical Center, University of Heidelberg, 68167 Mannheim, Germany
| | - Annie Achee
- National LeioMyoSarcoma Foundation (NLMSF), Denver, CO 80222, USA;
| | - Kathrin Schuster
- Sarcoma Patients EuroNet, SPAEN, 61200 Wölfersheim, Germany; (K.S.); (R.W.); (G.v.O.)
| | - Roger Wilson
- Sarcoma Patients EuroNet, SPAEN, 61200 Wölfersheim, Germany; (K.S.); (R.W.); (G.v.O.)
| | | | - Rebecca A. Gladdy
- Department of Surgery, Mount Sinai Hospital, Toronto, ON M5G 1XS, Canada;
| | | | - Paul Huang
- Institute of Cancer Research, London SM2 5NG, UK; (P.H.); (R.L.J.)
| | - Matthew Ingham
- Department of Medicine, Columbia University School of Medicine, New York, NY 10032, USA;
| | - Robin L. Jones
- Institute of Cancer Research, London SM2 5NG, UK; (P.H.); (R.L.J.)
- Royal Marsden Hospital, London SW3 6JJ, UK
| | - Seth M. Pollack
- Northwestern Medicine, Feinberg School of Medicine, Chicago, IL 60611, USA;
| | - Denise Reinke
- Sarcoma Alliance for Research through Collaboration (SARC), Ann Arbor, MI 48105, USA;
| | | | - Scott M. Schuetze
- Michigan Medicine Sarcoma Clinic, Rogel Cancer Center, Ann Arbor, MI 48109, USA;
| | - Neeta Somaiah
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Care Center, Houston, TX 77030, USA;
| | - Brian A. Van Tine
- Barnes and Jewish Hospital, Washington University in St. Louis, St. Louis, MO 63110, USA;
| | - Breelyn Wilky
- Department of Sarcoma Medical Oncology, Anschutz Medical Campus, University of Colorado, Aurora, CO 80045, USA;
| | - Scott Okuno
- Division of Medical Oncology, Mayo Clinic, Rochester, MN 55905, USA;
| | - Jonathan Trent
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136, USA;
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10
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Iida K, Abdelhamid Ahmed AH, Nagatsuma AK, Shibutani T, Yasuda S, Kitamura M, Hattori C, Abe M, Hasegawa J, Iguchi T, Karibe T, Nakada T, Inaki K, Kamei R, Abe Y, Nomura T, Andersen JL, Santagata S, Hemming ML, George S, Doi T, Ochiai A, Demetri GD, Agatsuma T. Identification and Therapeutic Targeting of GPR20, Selectively Expressed in Gastrointestinal Stromal Tumors, with DS-6157a, a First-in-Class Antibody-Drug Conjugate. Cancer Discov 2021; 11:1508-1523. [PMID: 33579785 DOI: 10.1158/2159-8290.cd-20-1434] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 01/18/2021] [Accepted: 02/10/2021] [Indexed: 11/16/2022]
Abstract
Currently, the only approved treatments for gastrointestinal stromal tumor (GIST) are tyrosine kinase inhibitors (TKI), which eventually lead to the development of secondary resistance mutations in KIT or PDGFRA and disease progression. Herein, we identified G protein-coupled receptor 20 (GPR20) as a novel non-tyrosine kinase target in GIST, developed new GPR20 IHC, and assessed GPR20 expression in cell lines, patient-derived xenografts, and clinical samples from two institutes (United States and Japan). We studied GPR20 expression stratified by treatment line, KIT expression, GIST molecular subtype, and primary tumor location. We produced DS-6157a, an anti-GPR20 antibody-drug conjugate with a novel tetrapeptide-based linker and DNA topoisomerase I inhibitor exatecan derivative (DXd). DS-6157a exhibited GPR20 expression-dependent antitumor activity in GIST xenograft models including a GIST model resistant to imatinib, sunitinib, and regorafenib. Preclinical pharmacokinetics and safety profile of DS-6157a support its clinical development as a potential novel GIST therapy in patients who are refractory or have resistance or intolerance to approved TKIs. SIGNIFICANCE: GPR20 is selectively expressed in GIST across all treatment lines, regardless of KIT/PDGFRA genotypes. We generated DS-6157a, a DXd-based antibody-drug conjugate that exhibited antitumor activity in GIST models by a different mode of action than currently approved TKIs, showing favorable pharmacokinetics and safety profiles.This article is highlighted in the In This Issue feature, p. 1307.
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Affiliation(s)
- Kenji Iida
- Daiichi Sankyo, Co., Ltd., Tokyo, Japan.
| | - Amr H Abdelhamid Ahmed
- Sarcoma and Bone Oncology Division, Medical Oncology Department, Dana-Farber Cancer Institute, Boston, Massachusetts
- Ludwig Center at Harvard, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Akiko Kawano Nagatsuma
- Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Japan
| | | | | | | | | | | | | | | | | | | | | | | | - Yuki Abe
- Daiichi Sankyo, Co., Ltd., Tokyo, Japan
| | - Taisei Nomura
- National Institutes of Biomedical Innovations, Health and Nutrition, Osaka, Japan
| | - Jessica L Andersen
- Sarcoma and Bone Oncology Division, Medical Oncology Department, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Sandro Santagata
- Ludwig Center at Harvard, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Matthew L Hemming
- Sarcoma and Bone Oncology Division, Medical Oncology Department, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Suzanne George
- Sarcoma and Bone Oncology Division, Medical Oncology Department, Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Toshihiko Doi
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Atsushi Ochiai
- Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Japan
| | - George D Demetri
- Sarcoma and Bone Oncology Division, Medical Oncology Department, Dana-Farber Cancer Institute, Boston, Massachusetts
- Ludwig Center at Harvard, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
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11
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Hemming ML, Coy S, Lin JR, Andersen JL, Przybyl J, Mazzola E, Abdelhamid Ahmed AH, van de Rijn M, Sorger PK, Armstrong SA, Demetri GD, Santagata S. HAND1 and BARX1 Act as Transcriptional and Anatomic Determinants of Malignancy in Gastrointestinal Stromal Tumor. Clin Cancer Res 2021; 27:1706-1719. [PMID: 33451979 DOI: 10.1158/1078-0432.ccr-20-3538] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/21/2020] [Accepted: 01/06/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Gastrointestinal stromal tumor (GIST) arises from interstitial cells of Cajal (ICC) or their precursors, which are present throughout the gastrointestinal tract. Although gastric GIST is commonly indolent and small intestine GIST more aggressive, a molecular understanding of disease behavior would inform therapy decisions in GIST. Although a core transcription factor (TF) network is conserved across GIST, accessory TFs HAND1 and BARX1 are expressed in a disease state-specific pattern. Here, we characterize two divergent transcriptional programs maintained by HAND1 and BARX1, and evaluate their association with clinical outcomes. EXPERIMENTAL DESIGN We evaluated RNA sequencing and TF chromatin immunoprecipitation with sequencing in GIST samples and cultured cells for transcriptional programs associated with HAND1 and BARX1. Multiplexed tissue-based cyclic immunofluorescence and IHC evaluated tissue- and cell-level expression of TFs and their association with clinical factors. RESULTS We show that HAND1 is expressed in aggressive GIST, modulating KIT and core TF expression and supporting proliferative cellular programs. In contrast, BARX1 is expressed in indolent and micro-GISTs. HAND1 and BARX1 expression were superior predictors of relapse-free survival, as compared with standard risk stratification, and they predict progression-free survival on imatinib. Reflecting the developmental origins of accessory TF programs, HAND1 was expressed solely in small intestine ICCs, whereas BARX1 expression was restricted to gastric ICCs. CONCLUSIONS Our results define anatomic and transcriptional determinants of GIST and molecular origins of clinical phenotypes. Assessment of HAND1 and BARX1 expression in GIST may provide prognostic information and improve clinical decisions on the administration of adjuvant therapy.
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Affiliation(s)
- Matthew L Hemming
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts. .,Sarcoma Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Shannon Coy
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Jia-Ren Lin
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts.,Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Jessica L Andersen
- Sarcoma Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | | | - Emanuele Mazzola
- Department of Data Science, Dana-Farber Cancer Institute and Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Amr H Abdelhamid Ahmed
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts.,Sarcoma Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | | | - Peter K Sorger
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts.,Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts.,Ludwig Center at Harvard, Boston, Massachusetts
| | - Scott A Armstrong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - George D Demetri
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts.,Sarcoma Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Ludwig Center at Harvard, Boston, Massachusetts
| | - Sandro Santagata
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts. .,Department of Systems Biology, Harvard Medical School, Boston, Massachusetts.,Ludwig Center at Harvard, Boston, Massachusetts
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12
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Hemming ML, Fan C, Raut CP, Demetri GD, Armstrong SA, Sicinska E, George S. Oncogenic Gene-Expression Programs in Leiomyosarcoma and Characterization of Conventional, Inflammatory, and Uterogenic Subtypes. Mol Cancer Res 2020; 18:1302-1314. [PMID: 32518213 PMCID: PMC7484251 DOI: 10.1158/1541-7786.mcr-20-0197] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [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: 02/28/2020] [Revised: 04/17/2020] [Accepted: 06/03/2020] [Indexed: 12/25/2022]
Abstract
Leiomyosarcoma (LMS) is a mesenchymal neoplasm with complex copy-number alterations and characteristic loss of tumor suppressor genes without known recurrent activating mutations. Clinical management of advanced LMS relies on chemotherapy and complementary palliative approaches, and research efforts to date have had limited success identifying clinically actionable biomarkers or targeted therapeutic vulnerabilities. To explore the biological underpinning of LMS, we evaluated gene-expression patterns of this disease in comparison with diverse sarcomas, nonmesenchymal neoplasms, and normal myogenic tissues. We identified a recurrent gene-expression program in LMS, with evidence of oncogenic evolution of an underlying smooth-muscle lineage-derived program characterized by activation of E2F1 and downstream effectors. Recurrently amplified or highly expressed genes in LMS were identified, including IGF1R and genes involved in retinoid signaling pathways. Though the majority of expressed transcripts were conserved across LMS samples, three separate subtypes were identified that were enriched for muscle-associated transcripts (conventional LMS), immune markers (inflammatory LMS), or a uterine-like gene-expression program (uterogenic LMS). Each of these subtypes expresses a unique subset of genes that may be useful in the management of LMS: IGF1R was enriched in conventional LMS, worse disease-specific survival was observed in inflammatory LMS, and prolactin was elaborated by uterogenic LMS. These results extend our understanding of LMS biology and identify several strategies and challenges for further translational investigation. IMPLICATIONS: LMS has a recurrent oncogenic transcriptional program and consists of molecular subtypes with biological and possible clinical implications.
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Affiliation(s)
- Matthew L Hemming
- Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Changyu Fan
- Department of Informatics and Analytics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Chandrajit P Raut
- Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - George D Demetri
- Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
- Ludwig Center at Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Scott A Armstrong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Ewa Sicinska
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Suzanne George
- Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
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13
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Iida K, Abdelhamid AH, Nagatsuma AK, Shibutani T, Yasuda S, Kitamura M, Hattori C, Abe M, Hasegawa J, Iguchi T, Karibe T, Nakada T, Inaki K, Kamei R, Abe Y, Andersen JL, Santagata S, Hemming ML, George S, Doi T, Ochiai A, Demetri GD, Agatsuma T. Abstract 5181: Therapeutic targeting of GPR20, selectively expressed in gastrointestinal stromal tumor (GIST), with DS-6157a, an antibody-drug conjugate (ADC). Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-5181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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
More than 85% of GISTs are driven by activating mutations in KIT proto-oncogene receptor tyrosine kinase (KIT) or platelet-derived growth factor receptor alpha (PDGFRA). Currently, the only approved treatments for GIST are KIT directed tyrosine kinase inhibitors (TKIs). However, treatment with approved TKIs eventually results in disease progression most often due to the development of secondary resistance mutations in KIT. In addition, these agents have limited activity in PDGFRA mutant GIST and KIT/PDGFRA wild type (WT) GIST as primary therapy. Therefore, it is essential to develop novel therapeutic strategies with different modes of action in advanced GIST. G protein-coupled receptor 20 (GPR20) is an orphan GPCR selectively and abundantly expressed in GIST. GPR20 expression is regulated by FOXF1 and ETV1, transcription factors that play critical roles in KIT-driven GIST initiation, proliferation, and survival. We hypothesize that GPR20 is a potential therapeutic target for ADC development for the treatment of GIST. In this study, 1) GPR20 and KIT protein expression was assessed by IHC staining on GIST samples from DFCI (n=144) and NCCHE (n=100) as well as on normal and malignant tissue microarrays obtained commercially, and 2) an anti-GPR20 ADC (DS-6157a) was generated to evaluate antitumor activity in GIST models and to assess safety. GPR20 was expressed in more than 88% of the GIST samples analyzed, with higher expression levels in samples that: (I) received multiple treatment lines compared to naïve/early treated samples, (II) expressed higher KIT levels, (III) were small intestinal GIST, and/or (IV) had no KIT mutation, including succinate dehydrogenase (SDH) deficient GIST and neurofibromatosis type 1 (NF1)-associated GIST. The interstitial cells of Cajal were the only normal cells positive for GPR20. Normal mast cells expressed KIT but not GPR20. DS-6157a is an ADC composed of a humanized anti-GPR20 antibody, a Gly-Gly-Phe-Gly tetra-peptide-based linker, and a DNA topoisomerase I (TOP1) inhibitor Dxd. DS-6157a exhibited GPR20 expression-dependent cell growth-inhibitory activity and induced tumor regression with dosing at 3 to 10 mg/kg in multiple GIST xenograft models. In addition, DS-6157a showed antitumor activity in a GIST patient-derived xenograft model that was resistant to imatinib, sunitinib, and regorafenib. In vitro, DS-6157a induced TOP1 inhibitor-associated markers of DNA damage (phosphorylation of Chk1) and apoptosis (cleaved PARP) in GPR20 expressing cells. In preclinical toxicology studies using rats and cynomolgus monkeys, the pharmacokinetics and safety profile of DS-6157a were favorable at up to 200 mg/kg and 30 mg/kg, respectively. These data support the clinical development of DS-6157a as a potential novel GIST therapy with activity in patients that are resistant, refractory, or intolerant to approved TKIs.
Citation Format: Kenji Iida, Amr H. Abdelhamid, Akiko Kawano Nagatsuma, Tomoko Shibutani, Satoru Yasuda, Michiko Kitamura, Chiharu Hattori, Manabu Abe, Jun Hasegawa, Takuma Iguchi, Tsuyoshi Karibe, Takashi Nakada, Koichiro Inaki, Reiko Kamei, Yuki Abe, Jessica L. Andersen, Sandro Santagata, Matthew L. Hemming, Suzanne George, Toshihiko Doi, Atsushi Ochiai, George D. Demetri, Toshinori Agatsuma. Therapeutic targeting of GPR20, selectively expressed in gastrointestinal stromal tumor (GIST), with DS-6157a, an antibody-drug conjugate (ADC) [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5181.
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Affiliation(s)
- Kenji Iida
- 1Daiichi Sankyo, Co., Ltd., Tokyo, Japan
| | | | - Akiko Kawano Nagatsuma
- 3Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Kashiwa, Japan
| | | | | | | | | | - Manabu Abe
- 1Daiichi Sankyo, Co., Ltd., Tokyo, Japan
| | | | | | | | | | | | | | - Yuki Abe
- 1Daiichi Sankyo, Co., Ltd., Tokyo, Japan
| | | | | | | | | | - Toshihiko Doi
- 6National Cancer Center Hospital East (NCCHE), Kashiwa, Japan
| | - Atsushi Ochiai
- 3Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Kashiwa, Japan
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14
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Hemming ML, Nathenson MJ, Lin JR, Mei S, Du Z, Malik K, Marino-Enriquez A, Jagannathan JP, Sorger PK, Bertagnolli M, Sicinska E, Demetri GD, Santagata S. Response and mechanisms of resistance to larotrectinib and selitrectinib in metastatic undifferentiated sarcoma harboring oncogenic fusion of NTRK1. JCO Precis Oncol 2020; 4:79-90. [PMID: 32133433 PMCID: PMC7055910 DOI: 10.1200/po.19.00287] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Matthew L Hemming
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael J Nathenson
- Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Jia-Ren Lin
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.,Ludwig Center at Harvard, Boston, Massachusetts, USA
| | - Shaolin Mei
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.,Ludwig Center at Harvard, Boston, Massachusetts, USA
| | - Ziming Du
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Karan Malik
- Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Adrian Marino-Enriquez
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jyothi P Jagannathan
- Department of Imaging, Dana-Farber Cancer Institute, Harvard Medical School, and Department of Radiology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.,Ludwig Center at Harvard, Boston, Massachusetts, USA.,Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Monica Bertagnolli
- Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ewa Sicinska
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - George D Demetri
- Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA.,Ludwig Center at Harvard, Boston, Massachusetts, USA
| | - Sandro Santagata
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.,Ludwig Center at Harvard, Boston, Massachusetts, USA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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15
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Hemming ML, Heinrich MC, Bauer S, George S. Translational insights into gastrointestinal stromal tumor and current clinical advances. Ann Oncol 2019; 29:2037-2045. [PMID: 30101284 DOI: 10.1093/annonc/mdy309] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Gastrointestinal stromal tumor (GIST) is the most common soft tissue sarcoma of the gastrointestinal tract and, in the vast majority of cases, is characterized by activating mutations in KIT or, less commonly, PDGFRA. Mutations in these type III receptor tyrosine kinases (RTKs) account for over 85% of GIST cases, and the majority of KIT primary mutations respond to treatment with the tyrosine kinase inhibitor (TKI) imatinib. However, drug resistance develops over time, most commonly due to secondary kinase mutations. Sunitinib and regorafenib are approved for the treatment of imatinib-resistant GIST in the second and third lines, respectively. However, resistance to these agents also develops and new therapeutic options are needed. In addition, a small number of GISTs harbor primary activating mutations that are resistant to currently available TKIs, highlighting an additional unmet medical need. Several novel and selective TKIs that overcome known mechanisms of resistance in GIST have been developed and show promise in early clinical trials. Additional emerging targeted therapies in GIST include modulation of cellular signaling pathways downstream of KIT, antibodies targeting KIT and PDGFRA and immune checkpoint inhibitors. These advancements highlight the rapid evolution in the understanding of this malignancy and provide perspective on the encouraging horizon of current and forthcoming therapeutic strategies for GIST.
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Affiliation(s)
- M L Hemming
- Department of Medical Oncology, Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, USA
| | - M C Heinrich
- VA Health Care System and Knight Cancer Institute, Oregon Health and Science University, Oregon, USA
| | - S Bauer
- Sarcoma Center, Western German Cancer Center and German Cancer Consortium (DKTK), Essen, Germany
| | - S George
- Department of Medical Oncology, Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, USA.
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16
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Flavahan WA, Drier Y, Johnstone SE, Hemming ML, Tarjan DR, Hegazi E, Shareef SJ, Javed NM, Raut CP, Eschle BK, Gokhale PC, Hornick JL, Sicinska ET, Demetri GD, Bernstein BE. Altered chromosomal topology drives oncogenic programs in SDH-deficient GISTs. Nature 2019; 575:229-233. [PMID: 31666694 PMCID: PMC6913936 DOI: 10.1038/s41586-019-1668-3] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 09/10/2019] [Indexed: 12/22/2022]
Abstract
Epigenetic aberrations are widespread in cancer, yet the underlying
mechanisms and causality remain poorly understood1-3.
A subset of gastrointestinal stromal tumors (GISTs) lack canonical kinase
mutations but instead have succinate dehydrogenase (SDH)-deficiency and global
DNA hyper-methylation4,5. Here we associate this hyper-methylation
with changes in genome topology that activate oncogenic programs. To investigate
epigenetic alterations systematically, we mapped DNA methylation, CTCF
insulators, enhancers, and chromosome topology in KIT-mutant,
PDGFRA-mutant, and SDH-deficient GISTs. Although these
respective subtypes shared similar enhancer landscapes, we identified hundreds
of putative insulators where DNA methylation replaced CTCF binding in
SDH-deficient GISTs. We focused on a disrupted insulator that normally
partitions a core GIST super-enhancer from the FGF4 oncogene.
Recurrent loss of this insulator alters locus topology in SDH-deficient GISTs,
allowing aberrant physical interaction between enhancer and oncogene.
CRISPR-mediated excision of the corresponding CTCF motifs in an SDH-intact GIST
model disrupted the boundary and strongly up-regulated FGF4
expression. We also identified a second recurrent insulator loss event near the
KIT oncogene, which is also highly expressed across
SDH-deficient GISTs. Finally, we established a patient-derived xenograft (PDX)
from an SDH-deficient GIST that faithfully maintains the epigenetics of the
parental tumor, including hyper-methylation and insulator defects. This PDX
model is highly sensitive to FGF receptor (FGFR) inhibitor, and more so to
combined FGFR and KIT inhibition, validating the functional significance of the
underlying epigenetic lesions. Our study reveals how epigenetic alterations can
drive oncogenic programs in the absence of canonical kinase mutations, with
implications for mechanistic targeting of aberrant pathways in cancers.
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Affiliation(s)
- William A Flavahan
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yotam Drier
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,The Lautenberg Center for Immunology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University, Jerusalem, Israel.
| | - Sarah E Johnstone
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Matthew L Hemming
- Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School Boston, Boston, MA, USA
| | - Daniel R Tarjan
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Esmat Hegazi
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sarah J Shareef
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nauman M Javed
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Chandrajit P Raut
- Department of Surgery, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Benjamin K Eschle
- Experimental Therapeutics Core, Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Prafulla C Gokhale
- Experimental Therapeutics Core, Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jason L Hornick
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Ewa T Sicinska
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - George D Demetri
- Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School Boston, Boston, MA, USA. .,Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.
| | - Bradley E Bernstein
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.
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17
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Hemming ML, Klega KS, Rhoades J, Ha G, Acker KE, Andersen JL, Thai E, Nag A, Thorner AR, Raut CP, George S, Crompton BD. Detection of Circulating Tumor DNA in Patients With Leiomyosarcoma With Progressive Disease. JCO Precis Oncol 2019; 2019. [PMID: 30793095 DOI: 10.1200/po.18.00235] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Purpose Leiomyosarcoma (LMS) is a soft tissue sarcoma characterized by multiple copy number alterations (CNAs) and without common recurrent single nucleotide variants. We evaluated the feasibility of detecting circulating tumor DNA (ctDNA) with next-generation sequencing in a cohort of patients with LMS whose tumor burden ranged from no evidence of disease to metastatic progressive disease. Patients and Methods Cell-free DNA in plasma samples and paired genomic DNA from resected tumors were evaluated from patients with LMS by ultra-low passage whole genome sequencing (ULP-WGS). Sequencing reads were aligned to the human genome and CNAs identified in cell-free DNA and tumor DNA by ichorCNA software to determine the presence of ctDNA. Clinical data were reviewed to assess disease burden and clinicopathologic features. Results We identified LMS ctDNA in eleven of sixteen patients (69%) with disease progression and total tumor burden over 5 cm. Sixteen patients with stable disease or low disease burden at the time of blood draw were found to have no detectable ctDNA. Higher ctDNA fraction of total cell-free DNA was associated with increasing tumor size and disease progression. Conserved CNAs were found between primary tumors and ctDNA in each case, and recurrent CNAs were found across LMS samples. ctDNA levels declined following resection of progressive disease in one case and became detectable upon disease relapse in another individual patient. Conclusion These results suggest that ctDNA, assayed by a widely available sequencing approach, may be useful as a biomarker for a subset of uterine and extrauterine LMS. Higher levels of ctDNA correlate with tumor size and disease progression. Liquid biopsies may assist in guiding treatment decisions, monitoring response to systemic therapy, surveying for disease recurrence and differentiating benign and malignant smooth muscle tumors.
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Affiliation(s)
- Matthew L Hemming
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Kelly S Klega
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts, USA
| | - Justin Rhoades
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Gavin Ha
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Kate E Acker
- Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Jessica L Andersen
- Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Edwin Thai
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Anwesha Nag
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Aaron R Thorner
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Chandrajit P Raut
- Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Suzanne George
- Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Brian D Crompton
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts, USA.,Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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18
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Hemming ML, Lawlor MA, Andersen JL, Hagan T, Chipashvili O, Scott TG, Raut CP, Sicinska E, Armstrong SA, Demetri GD, Bradner JE. Enhancer Domains in Gastrointestinal Stromal Tumor Regulate KIT Expression and Are Targetable by BET Bromodomain Inhibition. Cancer Res 2019; 79:994-1009. [PMID: 30630822 DOI: 10.1158/0008-5472.can-18-1888] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 12/04/2018] [Accepted: 01/07/2019] [Indexed: 12/31/2022]
Abstract
Gastrointestinal stromal tumor (GIST) is a mesenchymal neoplasm characterized by activating mutations in the related receptor tyrosine kinases KIT and PDGFRA. GIST relies on expression of these unamplified receptor tyrosine kinase (RTK) genes through a large enhancer domain, resulting in high expression levels of the oncogene required for tumor growth. Although kinase inhibition is an effective therapy for many patients with GIST, disease progression from kinase-resistant mutations is common and no other effective classes of systemic therapy exist. In this study, we identify regulatory regions of the KIT enhancer essential for KIT gene expression and GIST cell viability. Given the dependence of GIST upon enhancer-driven expression of RTKs, we hypothesized that the enhancer domains could be therapeutically targeted by a BET bromodomain inhibitor (BBI). Treatment of GIST cells with BBIs led to cell-cycle arrest, apoptosis, and cell death, with unique sensitivity in GIST cells arising from attenuation of the KIT enhancer domain and reduced KIT gene expression. BBI treatment in KIT-dependent GIST cells produced genome-wide changes in the H3K27ac enhancer landscape and gene expression program, which was also seen with direct KIT inhibition using a tyrosine kinase inhibitor (TKI). Combination treatment with BBI and TKI led to superior cytotoxic effects in vitro and in vivo, with BBI preventing tumor growth in TKI-resistant xenografts. Resistance to select BBI in GIST was attributable to drug efflux pumps. These results define a therapeutic vulnerability and clinical strategy for targeting oncogenic kinase dependency in GIST. SIGNIFICANCE: Expression and activity of mutant KIT is essential for driving the majority of GIST neoplasms, which can be therapeutically targeted using BET bromodomain inhibitors.
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Affiliation(s)
- Matthew L Hemming
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts. .,Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Matthew A Lawlor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jessica L Andersen
- Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Timothy Hagan
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Otari Chipashvili
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Thomas G Scott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Chandrajit P Raut
- Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ewa Sicinska
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Scott A Armstrong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - George D Demetri
- Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Ludwig Center at Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
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19
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Hemming ML, Lawlor MA, Andersen JL, Hagan T, Chipashvili O, Scott TG, Raut CP, Sicinska E, Armstrong SA, Demetri GD, Bradner JE, Ganz PA, Tomlinson G, Olopade OI, Couch FJ, Wang X, Lindor NM, Pankratz VS, Radice P, Manoukian S, Peissel B, Zaffaroni D, Barile M, Viel A, Allavena A, Dall'Olio V, Peterlongo P, Szabo CI, Zikan M, Claes K, Poppe B, Foretova L, Mai PL, Greene MH, Rennert G, Lejbkowicz F, Glendon G, Ozcelik H, Andrulis IL, Thomassen M, Gerdes AM, Sunde L, Cruger D, Birk Jensen U, Caligo M, Friedman E, Kaufman B, Laitman Y, Milgrom R, Dubrovsky M, Cohen S, Borg A, Jernström H, Lindblom A, Rantala J, Stenmark-Askmalm M, Melin B, Nathanson K, Domchek S, Jakubowska A, Lubinski J, Huzarski T, Osorio A, Lasa A, Durán M, Tejada MI, Godino J, Benitez J, Hamann U, Kriege M, Hoogerbrugge N, van der Luijt RB, van Asperen CJ, Devilee P, Meijers-Heijboer EJ, Blok MJ, Aalfs CM, Hogervorst F, Rookus M, Cook M, Oliver C, Frost D, Conroy D, Evans DG, Lalloo F, Pichert G, Davidson R, Cole T, Cook J, Paterson J, Hodgson S, Morrison PJ, Porteous ME, Walker L, Kennedy MJ, Dorkins H, Peock S, Godwin AK, Stoppa-Lyonnet D, de Pauw A, Mazoyer S, Bonadona V, Lasset C, Dreyfus H, Leroux D, Hardouin A, Berthet P, Faivre L, Loustalot C, Noguchi T, Sobol H, Rouleau E, Nogues C, Frénay M, Vénat-Bouvet L, Hopper JL, Daly MB, Terry MB, John EM, Buys SS, Yassin Y, Miron A, Goldgar D, Singer CF, Dressler AC, Gschwantler-Kaulich D, Pfeiler G, Hansen TVO, Jønson L, Agnarsson BA, Kirchhoff T, Offit K, Devlin V, Dutra-Clarke A, Piedmonte M, Rodriguez GC, Wakeley K, Boggess JF, Basil J, Schwartz PE, Blank SV, Toland AE, Montagna M, Casella C, Imyanitov E, Tihomirova L, Blanco I, Lazaro C, Ramus SJ, Sucheston L, Karlan BY, Gross J, Schmutzler R, Wappenschmidt B, Engel C, Meindl A, Lochmann M, Arnold N, Heidemann S, Varon-Mateeva R, Niederacher D, Sutter C, Deissler H, Gadzicki D, Preisler-Adams S, Kast K, Schönbuchner I, Caldes T, de la Hoya M, Aittomäki K, Nevanlinna H, Simard J, Spurdle AB, Holland H, Chen X, Platte R, Chenevix-Trench G, Easton DF. Enhancer Domains in Gastrointestinal Stromal Tumor Regulate KIT Expression and Are Targetable by BET Bromodomain Inhibition. Cancer Res 2019. [PMID: 18483246 DOI: 10.1158/0008-5472] [Citation(s) in RCA: 655] [Impact Index Per Article: 131.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Gastrointestinal stromal tumor (GIST) is a mesenchymal neoplasm characterized by activating mutations in the related receptor tyrosine kinases KIT and PDGFRA. GIST relies on expression of these unamplified receptor tyrosine kinase (RTK) genes through a large enhancer domain, resulting in high expression levels of the oncogene required for tumor growth. Although kinase inhibition is an effective therapy for many patients with GIST, disease progression from kinase-resistant mutations is common and no other effective classes of systemic therapy exist. In this study, we identify regulatory regions of the KIT enhancer essential for KIT gene expression and GIST cell viability. Given the dependence of GIST upon enhancer-driven expression of RTKs, we hypothesized that the enhancer domains could be therapeutically targeted by a BET bromodomain inhibitor (BBI). Treatment of GIST cells with BBIs led to cell-cycle arrest, apoptosis, and cell death, with unique sensitivity in GIST cells arising from attenuation of the KIT enhancer domain and reduced KIT gene expression. BBI treatment in KIT-dependent GIST cells produced genome-wide changes in the H3K27ac enhancer landscape and gene expression program, which was also seen with direct KIT inhibition using a tyrosine kinase inhibitor (TKI). Combination treatment with BBI and TKI led to superior cytotoxic effects in vitro and in vivo, with BBI preventing tumor growth in TKI-resistant xenografts. Resistance to select BBI in GIST was attributable to drug efflux pumps. These results define a therapeutic vulnerability and clinical strategy for targeting oncogenic kinase dependency in GIST. SIGNIFICANCE: Expression and activity of mutant KIT is essential for driving the majority of GIST neoplasms, which can be therapeutically targeted using BET bromodomain inhibitors.
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Affiliation(s)
- Matthew L Hemming
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts. .,Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Matthew A Lawlor
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jessica L Andersen
- Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Timothy Hagan
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Otari Chipashvili
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Thomas G Scott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Chandrajit P Raut
- Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ewa Sicinska
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Scott A Armstrong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - George D Demetri
- Center for Sarcoma and Bone Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Ludwig Center at Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
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20
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Brien GL, Remillard D, Shi J, Hemming ML, Chabon J, Wynne K, Dillon ET, Cagney G, Van Mierlo G, Baltissen MP, Vermeulen M, Qi J, Fröhling S, Gray NS, Bradner JE, Vakoc CR, Armstrong SA. Targeted degradation of BRD9 reverses oncogenic gene expression in synovial sarcoma. eLife 2018; 7:41305. [PMID: 30431433 PMCID: PMC6277197 DOI: 10.7554/elife.41305] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [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: 08/21/2018] [Accepted: 11/11/2018] [Indexed: 12/14/2022] Open
Abstract
Synovial sarcoma tumours contain a characteristic fusion protein, SS18-SSX, which drives disease development. Targeting oncogenic fusion proteins presents an attractive therapeutic opportunity. However, SS18-SSX has proven intractable for therapeutic intervention. Using a domain-focused CRISPR screen we identified the bromodomain of BRD9 as a critical functional dependency in synovial sarcoma. BRD9 is a component of SS18-SSX containing BAF complexes in synovial sarcoma cells; and integration of BRD9 into these complexes is critical for cell growth. Moreover BRD9 and SS18-SSX co-localize extensively on the synovial sarcoma genome. Remarkably, synovial sarcoma cells are highly sensitive to a novel small molecule degrader of BRD9, while other sarcoma subtypes are unaffected. Degradation of BRD9 induces downregulation of oncogenic transcriptional programs and inhibits tumour progression in vivo. We demonstrate that BRD9 supports oncogenic mechanisms underlying the SS18-SSX fusion in synovial sarcoma and highlight targeted degradation of BRD9 as a potential therapeutic opportunity in this disease.
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Affiliation(s)
- Gerard L Brien
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, United States.,Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - David Remillard
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, United States.,Department of Cancer Biology, Dana Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, United States
| | - Junwei Shi
- Department of Cancer Biology, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Matthew L Hemming
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, United States.,Department of Medical Oncology, Dana Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, United States
| | - Jonathon Chabon
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, United States
| | - Kieran Wynne
- School of Biomolecular and Biomedical Science and Conway Institute, University College Dublin, Dublin, Ireland
| | - Eugène T Dillon
- School of Biomolecular and Biomedical Science and Conway Institute, University College Dublin, Dublin, Ireland
| | - Gerard Cagney
- School of Biomolecular and Biomedical Science and Conway Institute, University College Dublin, Dublin, Ireland
| | - Guido Van Mierlo
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Marijke P Baltissen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Jun Qi
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, United States
| | - Stefan Fröhling
- German Cancer Consortium, Heidelberg, Germany.,Section for Personalized Oncology, Heidelberg University Hospital, Heidelberg, Germany.,Division of Translational Oncology, National Center for Tumor Diseases Heidelberg and German Cancer Research Center, Heidelberg, Germany
| | - Nathanael S Gray
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, United States
| | - James E Bradner
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, United States
| | | | - Scott A Armstrong
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, United States
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21
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Flavahan WA, Drier Y, Johnstone SE, Tarjan DR, Hegazi E, Sicinska ET, Hemming ML, Raut CP, Hornick JL, Demetri GD, Bernstein BE. Abstract 2996: Insulator dysfunction and epigenetic oncogene activation in SDH-deficient gastrointestinal stromal tumor. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-2996] [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
Metabolic lesions with profound effects on epigenetic regulation are widely implicated in cancer, yet the mechanistic links between this epigenetic dysregulation and tumorigenesis remain unclear. Succinate dehydrogenase (SDH) deficiency, responsible for a subset of gastrointestinal stromal tumors (GISTs), causes accumulation of the metabolite succinate and DNA hypermethylation. We identified convergent mechanisms involving altered chromosomal conformation and pseudo-hypoxia that mediate the tumorigenic effects of SDH deficiency in GIST. To investigate epigenetic alterations in this disease, we created epigenetic maps of 14 clinical GIST specimens; including KIT and PDGFRA mutant, and SDH-deficient tumors. We characterized the landscapes of enhancers, genetic regulatory elements which can drive gene expression, through histone H3 lysine 27 acetylation chromatin immunoprecipitation sequencing (ChIP-seq). We characterized both the DNA methylation and CTCF occupancy of insulators, elements which help control chromatin conformation and restrict enhancer-gene interactions, through hybrid selection bisulfite sequencing and CTCF ChIP-seq, respectively. Analyzing these data, we uncovered thousands of putative insulators where DNA methylation replaced CTCF binding in SDH-deficient GISTs. One of the strongest disrupted insulators protected the receptor tyrosine kinase and known driver of GIST, c-KIT, from a nearby superenhancer. Chromatin conformation studies confirmed an SDH-deficient-specific interaction of this superenhancer with the KIT gene. CRISPR-mediated excision of the insulator in an SDH-intact GIST model resulted in enhancer interaction and KIT upregulation. Immunohistochemical studies confirm strong expression of c-KIT in SDH-deficient GIST clinical samples. SDH deficiency has also been reported to cause pseudohypoxia in tumors. We confirmed that the enhancer landscape of SDH-deficient tumors had a signature of pseudohypoxia. Additionally, following pseudohypoxia induction in a SDH-intact GIST model, the c-KIT ligand Stem Cell Factor (SCF/KITLG) was upregulated 12-fold. While activating KIT mutations drive the majority (~75%) of GIST tumors and are mutually exclusive with SDH deficiency, we show that a primary consequence of SDH loss is in fact induction of KIT signaling. Our findings demonstrate how metabolic lesions can provide alternate epigenetic mechanisms to activate classic tumorigenic pathways in the absence of canonical genetic mutations.
Citation Format: William A. Flavahan, Yotam Drier, Sarah E. Johnstone, Daniel R. Tarjan, Esmat Hegazi, Ewa T. Sicinska, Matthew L. Hemming, Chandrajit P. Raut, Jason L. Hornick, George D. Demetri, Bradley E. Bernstein. Insulator dysfunction and epigenetic oncogene activation in SDH-deficient gastrointestinal stromal tumor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2996.
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Hemming ML, Elias JE, Gygi SP, Selkoe DJ. Proteomic profiling of gamma-secretase substrates and mapping of substrate requirements. PLoS Biol 2009; 6:e257. [PMID: 18942891 PMCID: PMC2570425 DOI: 10.1371/journal.pbio.0060257] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Accepted: 09/12/2008] [Indexed: 11/18/2022] Open
Abstract
The presenilin/γ-secretase complex, an unusual intramembrane aspartyl protease, plays an essential role in cellular signaling and membrane protein turnover. Its ability to liberate numerous intracellular signaling proteins from the membrane and also mediate the secretion of amyloid-β protein (Aβ) has made modulation of γ-secretase activity a therapeutic goal for cancer and Alzheimer disease. Although the proteolysis of the prototypical substrates Notch and β-amyloid precursor protein (APP) has been intensely studied, the full spectrum of substrates and the determinants that make a transmembrane protein a substrate remain unclear. Using an unbiased approach to substrate identification, we surveyed the proteome of a human cell line for targets of γ-secretase and found a relatively small population of new substrates, all of which are type I transmembrane proteins but have diverse biological roles. By comparing these substrates to type I proteins not regulated by γ-secretase, we determined that besides a short ectodomain, γ-secretase requires permissive transmembrane and cytoplasmic domains to bind and cleave its substrates. In addition, we provide evidence for at least two mechanisms that can target a substrate for γ cleavage: one in which a substrate with a short ectodomain is directly cleaved independent of sheddase association, and a second where a substrate requires ectodomain shedding to instruct subsequent γ-secretase processing. These findings expand our understanding of the mechanisms of substrate selection as well as the diverse cellular processes to which γ-secretase contributes. All cells face the challenge of removing transmembrane proteins from the lipid bilayer for the purpose of signaling or degradation. One molecular solution to this problem is the multiprotein enzyme complex γ-secretase, which is able to hydrolyze several known transmembrane proteins within the hydrophobic lipid environment. Due to its central role in the pathogenesis of Alzheimer disease, modulation of γ-secretase activity has become a therapeutic goal. However, the number and diversity of proteins that can be cleaved by this protease remain unknown, and the attributes that target these proteins to γ-secretase are unclear. In this study, we used an unbiased approach to substrate identification and surveyed the proteome for targets of γ-secretase. Of the thousands of proteins detectable, only a relative few were substrates of γ-secretase, all of which were type I transmembrane proteins. In addition to validating several of these novel substrates, we compared them to other proteins that we identified as nonsubstrates and determined that there are specific domains that can activate or inhibit γ-secretase processing. These findings should advance our understanding of the many cellular processes regulated by γ-secretase and may offer insights into how γ-secretase can be exploited for therapeutic purposes. Using an unbiased quantitative proteomics approach, novel substrate targets for the protease γ-secretase are identified and analyzed to determine which domains enable their cleavage.
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Affiliation(s)
- Matthew L Hemming
- Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Joshua E Elias
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Dennis J Selkoe
- Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- * To whom correspondence should be addressed. E-mail:
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Hemming ML, Patterson M, Reske-Nielsen C, Lin L, Isacson O, Selkoe DJ. Reducing amyloid plaque burden via ex vivo gene delivery of an Abeta-degrading protease: a novel therapeutic approach to Alzheimer disease. PLoS Med 2007; 4:e262. [PMID: 17760499 PMCID: PMC1952204 DOI: 10.1371/journal.pmed.0040262] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2007] [Accepted: 07/18/2007] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Understanding the mechanisms of amyloid-beta protein (Abeta) production and clearance in the brain has been essential to elucidating the etiology of Alzheimer disease (AD). Chronically decreasing brain Abeta levels is an emerging therapeutic approach for AD, but no such disease-modifying agents have achieved clinical validation. Certain proteases are responsible for the catabolism of brain Abeta in vivo, and some experimental evidence suggests they could be used as therapeutic tools to reduce Abeta levels in AD. The objective of this study was to determine if enhancing the clearance of Abeta in the brain by ex vivo gene delivery of an Abeta-degrading protease can reduce amyloid plaque burden. METHODS AND FINDINGS We generated a secreted form of the Abeta-degrading protease neprilysin, which significantly lowers the levels of naturally secreted Abeta in cell culture. We then used an ex vivo gene delivery approach utilizing primary fibroblasts to introduce this soluble protease into the brains of beta-amyloid precursor protein (APP) transgenic mice with advanced plaque deposition. Brain examination after cell implantation revealed robust clearance of plaques at the site of engraftment (72% reduction, p = 0.0269), as well as significant reductions in plaque burden in both the medial and lateral hippocampus distal to the implantation site (34% reduction, p = 0.0020; and 55% reduction, p = 0.0081, respectively). CONCLUSIONS Ex vivo gene delivery of an Abeta-degrading protease reduces amyloid plaque burden in transgenic mice expressing human APP. These results support the use of Abeta-degrading proteases as a means to therapeutically lower Abeta levels and encourage further exploration of ex vivo gene delivery for the treatment of Alzheimer disease.
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Affiliation(s)
- Matthew L Hemming
- Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Michaela Patterson
- Neuroregeneration Laboratories, McLean Hospital and Harvard University Udall Parkinson's Disease Research Center of Excellence, Belmont, Massachusetts, United States of America
| | - Casper Reske-Nielsen
- Neuroregeneration Laboratories, McLean Hospital and Harvard University Udall Parkinson's Disease Research Center of Excellence, Belmont, Massachusetts, United States of America
| | - Ling Lin
- Neuroregeneration Laboratories, McLean Hospital and Harvard University Udall Parkinson's Disease Research Center of Excellence, Belmont, Massachusetts, United States of America
| | - Ole Isacson
- Neuroregeneration Laboratories, McLean Hospital and Harvard University Udall Parkinson's Disease Research Center of Excellence, Belmont, Massachusetts, United States of America
| | - Dennis J Selkoe
- Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- * To whom correspondence should be addressed. E-mail:
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Hemming ML, Selkoe DJ, Farris W. Effects of prolonged angiotensin-converting enzyme inhibitor treatment on amyloid beta-protein metabolism in mouse models of Alzheimer disease. Neurobiol Dis 2007; 26:273-81. [PMID: 17321748 PMCID: PMC2377010 DOI: 10.1016/j.nbd.2007.01.004] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [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: 10/24/2006] [Revised: 01/12/2007] [Accepted: 01/14/2007] [Indexed: 01/21/2023] Open
Abstract
Genetic and pathologic studies have associated angiotensin-converting enzyme (ACE) with Alzheimer disease. Previously, we and others have reported that ACE degrades in vitro the amyloid beta-protein (Abeta), a putative upstream initiator of Alzheimer disease. These studies support the hypothesis that deficiency in ACE-mediated Abeta proteolysis could increase Alzheimer disease risk and raise the question of whether ACE inhibitors, a commonly prescribed class of anti-hypertensive medications, can elevate Abeta levels in vivo. To test this hypothesis, we administered the ACE inhibitor captopril to two lines of APP transgenic mice harboring either low levels of Abeta or high levels of Abeta with associated plaque deposition. In both models, we show that captopril does not affect cerebral Abeta levels in either soluble or insoluble pools. Furthermore, we find no change in plaque deposition or in peripheral Abeta levels. Data from these Alzheimer models suggest that captopril and similar ACE inhibitors do not cause Abeta accumulation in vivo.
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Affiliation(s)
| | - Dennis J. Selkoe
- Address correspondence to: Dennis J. Selkoe, Harvard Institutes of Medicine 730, 77 Ave. Louis Pasteur, Boston, MA 02115, Tel. 617 525-5200; Fax. 617 525-5252; E-mail. ; or Wesley Farris, Department of Neurology, Pittsburgh Institute for Neurodegenerative Diseases, 3501 Fifth Ave, BST3-7019, Pittsburgh, PA 15260. Tel: 412-383-5832; Fax. 412-648-7223; E-mail.
| | - Wesley Farris
- Address correspondence to: Dennis J. Selkoe, Harvard Institutes of Medicine 730, 77 Ave. Louis Pasteur, Boston, MA 02115, Tel. 617 525-5200; Fax. 617 525-5252; E-mail. ; or Wesley Farris, Department of Neurology, Pittsburgh Institute for Neurodegenerative Diseases, 3501 Fifth Ave, BST3-7019, Pittsburgh, PA 15260. Tel: 412-383-5832; Fax. 412-648-7223; E-mail.
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Abstract
Human genetic data have associated angiotensin-converting enzyme (ACE) with Alzheimer disease (AD), and purified ACE has been reported to cleave synthetic amyloid beta-protein (Abeta) in vitro. Whether deficiency in ACE activity, arising from genetic alteration or pharmacological inhibition, can decrease Abeta degradation and allow Abeta accumulation in intact cells is unknown. We cloned ACE from human neuroblastoma cells and showed that it had posttranslational processing and enzymatic activity typical of the endogenous protease. Cellular expression of ACE promoted degradation of naturally secreted Abeta40 and Abeta42, leading to significant clearance of both species. Using site-directed mutagenesis, we determined that both active sites within ACE contribute to Abeta clearance, and an ACE construct bearing mutations in each catalytic domain had no effect on Abeta levels. Pharmacological inhibition of ACE with a widely prescribed drug, captopril, promoted the accumulation of cell-derived Abeta in the media of beta-amyloid precursor-protein expressing cells. Together, these results show that ACE can lower the levels of secreted Abeta in living cells and that this effect is blocked by inhibiting the protease's activity with an ACE inhibitor. This work, combined with the genetic studies, supports the hypothesis that ACE may modulate the susceptibility to and progression of AD via degradation of Abeta. Our data encourage further analyses of the ACE gene for disease association and raise the question of whether currently prescribed ACE inhibitors could elevate cerebral Abeta levels in humans.
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Affiliation(s)
- Matthew L Hemming
- Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
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Farris W, Leissring MA, Hemming ML, Chang AY, Selkoe DJ. Alternative splicing of human insulin-degrading enzyme yields a novel isoform with a decreased ability to degrade insulin and amyloid beta-protein. Biochemistry 2005; 44:6513-25. [PMID: 15850385 DOI: 10.1021/bi0476578] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [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] [Indexed: 11/28/2022]
Abstract
Deletion of insulin-degrading enzyme (IDE) in mice causes accumulation of cerebral amyloid beta-protein (Abeta), hyperinsulinemia, and glucose intolerance. Together with genetic linkage and allelic association of IDE to Alzheimer's disease (AD) and type 2 diabetes mellitus (DM2), these findings suggest that IDE hypofunction could mediate human disease. To date, no coding mutations have been found in the canonical isoform of IDE, suggesting that pathological mutations could exist in undiscovered exons or regulatory regions, including untranslated regions (UTRs). However, neither isoforms arising from alternative splicing nor the UTRs have been described. Here, we systematically characterize human IDE mRNAs, identify a novel splice form, and compare its subcellular distribution, kinetic properties, and ability to degrade Abeta to the known isoform. Six distinct human IDE transcripts were identified, with most of the variance attributable to alternative polyadenylation sites. In the novel spliceoform, an exon we designate "15b" replaces the canonical exon "15a", and the resultant variant is widely expressed. Subcellular fractionation, immunofluorescent confocal microscopy, and immunogold-electron microscopy reveal that the 15b-IDE protein occurs in both cytosol and mitochondria. Organelle targeting of both isoforms is determined by which of two translation start sites is used, and only those isoforms utilizing the second site regulate levels of secreted Abeta. 15b-IDE can exist as a heterodimer with the 15a isoform or as a homodimer. The apparent K(m) values of recombinant 15b-IDE for both insulin and Abeta are significantly higher and the k(cat) and catalytic efficiency markedly lower than those of 15a-IDE. In accord, cells coexpressing beta-amyloid precursor protein (APP) and 15b-IDE accumulated significantly more Abeta in their media than those expressing APP and 15a-IDE. Our results identify a novel, catalytically inefficient form of IDE expressed in brain and non-neural tissues and recommend novel regions of the IDE gene in which to search for mutations predisposing patients to AD and DM2.
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Affiliation(s)
- Wesley Farris
- Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
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Winrow CJ, Hemming ML, Allen DM, Quistad GB, Casida JE, Barlow C. Loss of neuropathy target esterase in mice links organophosphate exposure to hyperactivity. Nat Genet 2003; 33:477-85. [PMID: 12640454 DOI: 10.1038/ng1131] [Citation(s) in RCA: 145] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2002] [Accepted: 02/21/2003] [Indexed: 11/08/2022]
Abstract
Neuropathy target esterase (NTE) is involved in neural development and is the target for neurodegeneration induced by selected organophosphorus pesticides and chemical warfare agents. We generated mice with disruptions in Nte, the gene encoding NTE. Nte(-/-) mice die after embryonic day 8, and Nte(+/-) mice have lower activity of Nte in the brain and higher mortality when exposed to the Nte-inhibiting compound ethyl octylphosphonofluoridate (EOPF) than do wild-type mice. Nte(+/-) and wild-type mice treated with 1 mg per kg of body weight of EOPF have elevated motor activity, showing that even minor reduction of Nte activity leads to hyperactivity. These studies show that genetic or chemical reduction of Nte activity results in a neurological phenotype of hyperactivity in mammals and indicate that EOPF toxicity occurs directly through inhibition of Nte without the requirement for Nte gain of function or aging.
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Affiliation(s)
- Christopher J Winrow
- The Salk Institute for Biological Studies, The Laboratory of Genetics, 10010 North Torrey Pines Road, La Jolla, California 92037, USA
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