1
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Thomas NJ, Luck C, Shlimon N, Ponce RK, Kosibaty Z, Okimoto RA. Mapping chromatin state and transcriptional response in CIC-DUX4 undifferentiated round cell sarcoma. bioRxiv 2023:2023.10.11.561932. [PMID: 37873100 PMCID: PMC10592754 DOI: 10.1101/2023.10.11.561932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
CIC-DUX4 is a rare and understudied transcription factor fusion oncoprotein. CIC-DUX4 co-opts native gene targets to drive a lethal form of human sarcoma. The molecular underpinnings that lead to oncogenic reprograming and CIC-DUX4 sarcomagenesis remain largely undefined. Through an integrative ChIP and RNA-Seq analysis using patient-derived CIC-DUX4 cells, we define CIC-DUX4 mediated chromatin states and function. We show that CIC-DUX4 primarily localizes to proximal and distal cis-regulatory elements where it associates with active histone marks. Our findings nominate key signaling pathways and molecular targets that enable CIC-DUX4 to mediate tumor cell survival. Collectively, our data demonstrate how the CIC-DUX4 fusion oncoprotein impacts chromatin state and transcriptional responses to drive an oncogenic program in undifferentiated sarcoma. Significance CIC-DUX4 sarcoma is a rare and lethal sarcoma that affects children, adolescent young adults, and adults. CIC-DUX4 sarcoma is associated with rapid metastatic dissemination and relative insensitivity to chemotherapy. There are no current standard-of-care therapies for CIC-DUX4 sarcoma leading to universally poor outcomes for patients. Through a deep mechanistic understanding of how the CIC-DUX4 fusion oncoprotein reprograms chromatin state and function, we aim to improve outcomes for CIC-DUX4 patients.
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2
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Gupta N, Song H, Wu W, Ponce RK, Lin YK, Kim JW, Small EJ, Feng FY, Huang FW, Okimoto RA. The CIC-ERF co-deletion underlies fusion-independent activation of ETS family member, ETV1, to drive prostate cancer progression. eLife 2022; 11:77072. [PMID: 36383412 PMCID: PMC9668335 DOI: 10.7554/elife.77072] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 01/14/2022] [Accepted: 10/16/2022] [Indexed: 11/13/2022] Open
Abstract
Human prostate cancer can result from chromosomal rearrangements that lead to aberrant ETS gene expression. The mechanisms that lead to fusion-independent ETS factor upregulation and prostate oncogenesis remain relatively unknown. Here, we show that two neighboring transcription factors, Capicua (CIC) and ETS2 repressor factor (ERF), which are co-deleted in human prostate tumors can drive prostate oncogenesis. Concurrent CIC and ERF loss commonly occur through focal genomic deletions at chromosome 19q13.2. Mechanistically, CIC and ERF co-bind the proximal regulatory element and mutually repress the ETS transcription factor, ETV1. Targeting ETV1 in CIC and ERF-deficient prostate cancer limits tumor growth. Thus, we have uncovered a fusion-independent mode of ETS transcriptional activation defined by concurrent loss of CIC and ERF.
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Affiliation(s)
- Nehal Gupta
- Department of Medicine, University of California, San Francisco, United States
| | - Hanbing Song
- Department of Medicine, University of California, San Francisco, United States
| | - Wei Wu
- Department of Medicine, University of California, San Francisco, United States
| | - Rovingaile K Ponce
- Department of Medicine, University of California, San Francisco, United States
| | - Yone K Lin
- Department of Medicine, University of California, San Francisco, United States
| | - Ji Won Kim
- Department of Medicine, University of California, San Francisco, United States
| | - Eric J Small
- Department of Medicine, University of California, San Francisco, United States.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, United States
| | - Felix Y Feng
- Department of Medicine, University of California, San Francisco, United States.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, United States.,Department of Radiation Oncology, University of California, San Francisco, United States
| | - Franklin W Huang
- Department of Medicine, University of California, San Francisco, United States.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, United States
| | - Ross A Okimoto
- Department of Medicine, University of California, San Francisco, United States.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, United States
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3
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Bennett NK, Nakaoka HJ, Laurent D, Okimoto RA, Sei Y, Horvai AE, Bivona TG, ten Hoeve J, Graeber TG, Nakamura K, Nakamura JL. Primary and metastatic tumors exhibit systems-level differences in dependence on mitochondrial respiratory function. PLoS Biol 2022; 20:e3001753. [PMID: 36137002 PMCID: PMC9498964 DOI: 10.1371/journal.pbio.3001753] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 09/30/2021] [Accepted: 07/12/2022] [Indexed: 11/18/2022] Open
Abstract
The Warburg effect, aerobic glycolysis, is a hallmark feature of cancer cells grown in culture. However, the relative roles of glycolysis and respiratory metabolism in supporting in vivo tumor growth and processes such as tumor dissemination and metastatic growth remain poorly understood, particularly on a systems level. Using a CRISPRi mini-library enriched for mitochondrial ribosomal protein and respiratory chain genes in multiple human lung cancer cell lines, we analyzed in vivo metabolic requirements in xenograft tumors grown in distinct anatomic contexts. While knockdown of mitochondrial ribosomal protein and respiratory chain genes (mito-respiratory genes) has little impact on growth in vitro, tumor cells depend heavily on these genes when grown in vivo as either flank or primary orthotopic lung tumor xenografts. In contrast, respiratory function is comparatively dispensable for metastatic tumor growth. RNA-Seq and metabolomics analysis of tumor cells expressing individual sgRNAs against mito-respiratory genes indicate overexpression of glycolytic genes and increased sensitivity of glycolytic inhibition compared to control when grown in vitro, but when grown in vivo as primary tumors these cells down-regulate glycolytic mechanisms. These studies demonstrate that discrete perturbations of mitochondrial respiratory chain function impact in vivo tumor growth in a context-specific manner with differential impacts on primary and metastatic tumors.
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Affiliation(s)
- Neal K. Bennett
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, California, United States of America
| | - Hiroki J. Nakaoka
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California, United States of America
| | - Danny Laurent
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California, United States of America
| | - Ross A. Okimoto
- Department of Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Yoshitaka Sei
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, California, United States of America
| | - Andrew E. Horvai
- Department of Pathology, University of California, San Francisco, San Francisco, California, United States of America
| | - Trever G. Bivona
- Department of Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Johanna ten Hoeve
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, UCLA Metabolomics Center, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Thomas G. Graeber
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, UCLA Metabolomics Center, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Ken Nakamura
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, California, United States of America
- Graduate Programs in Neuroscience and Biomedical Sciences, University of California, San Francisco, San Francisco, California, United States of America
- Department of Neurology, University of California, San Francisco, San Francisco, California, United States of America
| | - Jean L. Nakamura
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California, United States of America
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4
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Gounder MM, Agaram NP, Trabucco SE, Robinson V, Ferraro RA, Millis SZ, Krishnan A, Lee J, Attia S, Abida W, Drilon A, Chi P, Angelo SPD, Dickson MA, Keohan ML, Kelly CM, Agulnik M, Chawla SP, Choy E, Chugh R, Meyer CF, Myer PA, Moore JL, Okimoto RA, Pollock RE, Ravi V, Singh AS, Somaiah N, Wagner AJ, Healey JH, Frampton GM, Venstrom JM, Ross JS, Ladanyi M, Singer S, Brennan MF, Schwartz GK, Lazar AJ, Thomas DM, Maki RG, Tap WD, Ali SM, Jin DX. Clinical genomic profiling in the management of patients with soft tissue and bone sarcoma. Nat Commun 2022; 13:3406. [PMID: 35705558 PMCID: PMC9200814 DOI: 10.1038/s41467-022-30496-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 05/04/2022] [Indexed: 02/07/2023] Open
Abstract
There are more than 70 distinct sarcomas, and this diversity complicates the development of precision-based therapeutics for these cancers. Prospective comprehensive genomic profiling could overcome this challenge by providing insight into sarcomas' molecular drivers. Through targeted panel sequencing of 7494 sarcomas representing 44 histologies, we identify highly recurrent and type-specific alterations that aid in diagnosis and treatment decisions. Sequencing could lead to refinement or reassignment of 10.5% of diagnoses. Nearly one-third of patients (31.7%) harbor potentially actionable alterations, including a significant proportion (2.6%) with kinase gene rearrangements; 3.9% have a tumor mutational burden ≥10 mut/Mb. We describe low frequencies of microsatellite instability (<0.3%) and a high degree of genome-wide loss of heterozygosity (15%) across sarcomas, which are not readily explained by homologous recombination deficiency (observed in 2.5% of cases). In a clinically annotated subset of 118 patients, we validate actionable genetic events as therapeutic targets. Collectively, our findings reveal the genetic landscape of human sarcomas, which may inform future development of therapeutics and improve clinical outcomes for patients with these rare cancers.
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Affiliation(s)
- Mrinal M Gounder
- Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Weill Cornell Medical College, New York, NY, USA.
| | | | | | | | - Richard A Ferraro
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | | | - Anita Krishnan
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jessica Lee
- Foundation Medicine, Inc., Cambridge, MA, USA
| | | | - Wassim Abida
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Alexander Drilon
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Ping Chi
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Sandra P D' Angelo
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Mark A Dickson
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Mary Lou Keohan
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Ciara M Kelly
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | | | - Sant P Chawla
- Sarcoma Center of Santa Monica, Santa Monica, CA, USA
| | - Edwin Choy
- Massachusetts General Hospital, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | - Christian F Meyer
- Johns Hopkins Sidney Kimmel Comprehensive Center, Baltimore, MD, USA
| | - Parvathi A Myer
- Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | - Ross A Okimoto
- University of California at San Francisco, San Francisco, CA, USA
| | | | - Vinod Ravi
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Arun S Singh
- University of California at Los Angeles, Los Angeles, CA, USA
| | - Neeta Somaiah
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andrew J Wagner
- Harvard Medical School, Boston, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - John H Healey
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | | | | | - Jeffrey S Ross
- Foundation Medicine, Inc., Cambridge, MA, USA
- Albany Medical College, Albany, NY, USA
| | - Marc Ladanyi
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samuel Singer
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Murray F Brennan
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Gary K Schwartz
- Herbert Irving Cancer Center, Columbia University, New York, NY, USA
| | | | - David M Thomas
- Garvan Institute of Medical Research, Darlinghurst,, NSW, Australia
| | - Robert G Maki
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - William D Tap
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Siraj M Ali
- Foundation Medicine, Inc., Cambridge, MA, USA
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5
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Nanjo S, Wu W, Karachaliou N, Blakely CM, Suzuki J, Chou YT, Ali SM, Kerr DL, Olivas VR, Shue J, Rotow J, Mayekar MK, Haderk F, Chatterjee N, Urisman A, Yeo JC, Skanderup AJ, Tan AC, Tam WL, Arrieta O, Hosomichi K, Nishiyama A, Yano S, Kirichok Y, Tan DS, Rosell R, Okimoto RA, Bivona TG. Deficiency of the splicing factor RBM10 limits EGFR inhibitor response in EGFR mutant lung cancer. J Clin Invest 2022; 132:145099. [PMID: 35579943 PMCID: PMC9246391 DOI: 10.1172/jci145099] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 10/19/2020] [Accepted: 05/13/2022] [Indexed: 11/18/2022] Open
Abstract
Molecularly targeted cancer therapy has improved outcomes for patients with cancer with targetable oncoproteins, such as mutant EGFR in lung cancer. Yet, the long-term survival of these patients remains limited, because treatment responses are typically incomplete. One potential explanation for the lack of complete and durable responses is that oncogene-driven cancers with activating mutations of EGFR often harbor additional co-occurring genetic alterations. This hypothesis remains untested for most genetic alterations that co-occur with mutant EGFR. Here, we report the functional impact of inactivating genetic alterations of the mRNA splicing factor RNA-binding motif 10 (RBM10) that co-occur with mutant EGFR. RBM10 deficiency decreased EGFR inhibitor efficacy in patient-derived EGFR-mutant tumor models. RBM10 modulated mRNA alternative splicing of the mitochondrial apoptotic regulator Bcl-x to regulate tumor cell apoptosis during treatment. Genetic inactivation of RBM10 diminished EGFR inhibitor–mediated apoptosis by decreasing the ratio of (proapoptotic) Bcl-xS to (antiapoptotic) Bcl-xL isoforms of Bcl-x. RBM10 deficiency was a biomarker of poor response to EGFR inhibitor treatment in clinical samples. Coinhibition of Bcl-xL and mutant EGFR overcame the resistance induced by RBM10 deficiency. This study sheds light on the role of co-occurring genetic alterations and on the effect of splicing factor deficiency on the modulation of sensitivity to targeted kinase inhibitor cancer therapy.
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Affiliation(s)
- Shigeki Nanjo
- Department of Medicine, University of California, San Francisco, San Francisco, United States of America
| | - Wei Wu
- Department of Medicine, University of California, San Francisco, San Francisco, United States of America
| | - Niki Karachaliou
- Cancer Biology and Precision Medicine Program, Germans Trias i Pujol Research Institute and Hospital, Badalona, Spain
| | - Collin M Blakely
- Department of Medicine, University of California, San Francisco, San Francisco, United States of America
| | - Junji Suzuki
- Department of Physiology, University of California, San Francisco, San Francisco, United States of America
| | - Yu-Ting Chou
- Department of Medicine, University of California, San Francisco, San Francisco, United States of America
| | - Siraj M Ali
- Foundation Medicine, Inc., Foundation Medicine, Inc., Cambridge, United States of America
| | - D Lucas Kerr
- Department of Medicine, University of California, San Francisco, San Francisco, United States of America
| | - Victor R Olivas
- Department of Medicine, University of California, San Francisco, San Francisco, United States of America
| | - Jonathan Shue
- Department of Medicine, University of California, San Francisco, San Francisco, United States of America
| | - Julia Rotow
- Department of Medicine, University of California, San Francisco, San Francisco, United States of America
| | - Manasi K Mayekar
- Department of Medicine, University of California, San Francisco, San Francisco, United States of America
| | - Franziska Haderk
- Department of Medicine, University of California, San Francisco, San Francisco, United States of America
| | - Nilanjana Chatterjee
- Department of Medicine, University of California, San Francisco, San Francisco, United States of America
| | - Anatoly Urisman
- Department of Pathology, University of California, San Francisco, San Francisco, United States of America
| | - Jia Chi Yeo
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Anders J Skanderup
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Aaron C Tan
- Division of Medical Oncology, National Cancer Center Singapore, Singapore, Singapore
| | - Wai Leong Tam
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Oscar Arrieta
- Thoracic Oncology Unit, National Cancer Center Institute (INCan), México City, Mexico
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomic, Kanazawa Universuty, Kanazawa, Japan
| | - Akihiro Nishiyama
- Division of Medical Oncology, Kanazawa University Cancer Research Institute, Kanazawa, Japan
| | - Seiji Yano
- Kanazawa University Cancer Research Institute, Kanazawa, Japan
| | - Yuriy Kirichok
- Department of Physiology, University of California, San Francisco, San Francisco, United States of America
| | - Daniel Sw Tan
- Division of Medical Oncology, National Cancer Center Singapore, Singapore, Singapore
| | - Rafael Rosell
- Cancer Biology and Precision Medicine Program, Germans Trias i Pujol Research Institute and Hospital, Badalona, Spain
| | - Ross A Okimoto
- Department of Medicine, University of California, San Francisco, San Francisco, United States of America
| | - Trever G Bivona
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, United States of America
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6
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Ponce RKM, Thomas NJ, Bui NQ, Kondo T, Okimoto RA. WEE1 kinase is a therapeutic vulnerability in CIC-DUX4 undifferentiated sarcoma. JCI Insight 2022; 7:152293. [PMID: 35315355 PMCID: PMC8986087 DOI: 10.1172/jci.insight.152293] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 06/15/2021] [Accepted: 02/09/2022] [Indexed: 01/08/2023] Open
Abstract
CIC-DUX4 rearrangements define an aggressive and chemotherapy-insensitive subset of undifferentiated sarcomas. The CIC-DUX4 fusion drives oncogenesis through direct transcriptional upregulation of cell cycle and DNA replication genes. Notably, CIC-DUX4–mediated CCNE1 upregulation compromises the G1/S transition to confer a dependence on the G2/M cell cycle checkpoint. Through an integrative transcriptional and kinase activity screen using patient-derived specimens, we now show that CIC-DUX4 sarcomas depend on the G2/M checkpoint regulator WEE1 as part of an adaptive survival mechanism. Specifically, CIC-DUX4 sarcomas depended on WEE1 activity to limit DNA damage and unscheduled mitotic entry. Consequently, genetic or pharmacologic WEE1 inhibition in vitro and in vivo led to rapid DNA damage–associated apoptotic induction of patient-derived CIC-DUX4 sarcomas. Thus, we identified WEE1 as a vulnerability targetable by therapeutic intervention in CIC-DUX4 sarcomas.
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Affiliation(s)
| | | | - Nam Q Bui
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Tadashi Kondo
- Division of Rare Cancer Research, National Cancer Center Research Institute, Tokyo, Japan
| | - Ross A Okimoto
- Department of Medicine, UCSF, San Francisco, California, USA.,Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
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7
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Wustrack RL, Shao E, Sheridan J, Zimel M, Cho SJ, Horvai AE, Luong D, Kwek SS, Fong L, Okimoto RA. Tumor morphology and location associate with immune cell composition in pleomorphic sarcoma. Cancer Immunol Immunother 2021; 70:3031-3040. [PMID: 33864502 PMCID: PMC8423706 DOI: 10.1007/s00262-021-02935-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 11/10/2020] [Accepted: 03/31/2021] [Indexed: 01/04/2023]
Abstract
Background Soft-tissue sarcomas (STS) are a rare group of mesenchymal malignancies that account for approximately 1% of adult human cancer. Undifferentiated pleomorphic sarcoma (UPS) is one of the most common subtypes of adult STS. Clinical stratification of UPS patients has not evolved for decades and continues to rely on tumor-centric metrics including tumor size and depth. Our understanding of how the tumor microenvironment correlates to these clinicopathologic parameters remains limited. Methods Here, we performed single-cell flow cytometric immune-based profiling of 15 freshly resected UPS tumors and integrated this analysis with clinical, histopathologic, and outcomes data using both a prospective and retrospective cohort of UPS patients. Results We uncovered a correlation between physiologic and anatomic properties of UPS tumors and the composition of immune cells in the tumor microenvironment. Specifically, we identified an inverse correlation between tumor-infiltrating CD8 + T cells and UPS tumor size; and a positive correlation between tumor-infiltrating CD8 + T cells and overall survival. Moreover, we demonstrate an association between anatomical location (deep or superficial) and frequency of CD4 + PD1hi infiltrating T cells in UPS tumors. Conclusions Our study provides an immune-based analysis of the tumor microenvironment in UPS patients and describes the different composition of tumor infiltrating lymphocytes based on size and tumor depth. Supplementary Information The online version contains supplementary material available at 10.1007/s00262-021-02935-2.
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Affiliation(s)
- Rosanna L Wustrack
- Department of Orthopedic Surgery, University of California, San Francisco, USA
| | - Evans Shao
- Division of Hematology and Oncology, Department of Medicine, University of California, 513 Parnassus Avenue, HSW1201, San Francisco, CA, 94143, USA
| | - Joey Sheridan
- Department of Orthopedic Surgery, University of California, San Francisco, USA
| | - Melissa Zimel
- Department of Orthopedic Surgery, University of California, San Francisco, USA
| | - Soo-Jin Cho
- Department of Pathology, University of California, San Francisco, USA
| | - Andrew E Horvai
- Department of Pathology, University of California, San Francisco, USA
| | - Diamond Luong
- Division of Hematology and Oncology, Department of Medicine, University of California, 513 Parnassus Avenue, HSW1201, San Francisco, CA, 94143, USA.,Helen Diller Comprehensive Cancer Center, University of California, San Francisco, USA.,Parker Institute of Cancer Immunotherapy, University of California, San Francisco, USA
| | - Serena S Kwek
- Division of Hematology and Oncology, Department of Medicine, University of California, 513 Parnassus Avenue, HSW1201, San Francisco, CA, 94143, USA.,Helen Diller Comprehensive Cancer Center, University of California, San Francisco, USA.,Parker Institute of Cancer Immunotherapy, University of California, San Francisco, USA
| | - Lawrence Fong
- Division of Hematology and Oncology, Department of Medicine, University of California, 513 Parnassus Avenue, HSW1201, San Francisco, CA, 94143, USA. .,Helen Diller Comprehensive Cancer Center, University of California, San Francisco, USA. .,Parker Institute of Cancer Immunotherapy, University of California, San Francisco, USA.
| | - Ross A Okimoto
- Division of Hematology and Oncology, Department of Medicine, University of California, 513 Parnassus Avenue, HSW1201, San Francisco, CA, 94143, USA. .,Helen Diller Comprehensive Cancer Center, University of California, San Francisco, USA.
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8
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Quinn JJ, Jones MG, Okimoto RA, Nanjo S, Chan MM, Yosef N, Bivona TG, Weissman JS. Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts. Science 2021; 371:eabc1944. [PMID: 33479121 PMCID: PMC7983364 DOI: 10.1126/science.abc1944] [Citation(s) in RCA: 127] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 09/23/2020] [Accepted: 12/17/2020] [Indexed: 12/11/2022]
Abstract
Detailed phylogenies of tumor populations can recount the history and chronology of critical events during cancer progression, such as metastatic dissemination. We applied a Cas9-based, single-cell lineage tracer to study the rates, routes, and drivers of metastasis in a lung cancer xenograft mouse model. We report deeply resolved phylogenies for tens of thousands of cancer cells traced over months of growth and dissemination. This revealed stark heterogeneity in metastatic capacity, arising from preexisting and heritable differences in gene expression. We demonstrate that these identified genes can drive invasiveness and uncovered an unanticipated suppressive role for KRT17 We also show that metastases disseminated via multidirectional tissue routes and complex seeding topologies. Overall, we demonstrate the power of tracing cancer progression at subclonal resolution and vast scale.
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Affiliation(s)
- Jeffrey J Quinn
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- Inscripta, Inc., Boulder, CO, USA
| | - Matthew G Jones
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- Biological and Medical Informatics Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Integrative Program in Quantitative Biology, University of California, San Francisco, San Francisco, CA, USA
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Ross A Okimoto
- UCSF Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Shigeki Nanjo
- UCSF Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Michelle M Chan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Nir Yosef
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.
- Department of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, CA, USA
- Chan Zuckerberg Biohub Investigator, San Francisco, CA, USA
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Cambridge, MA, USA
| | - Trever G Bivona
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
- UCSF Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA
- Whitehead Institute, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
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9
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Nothdurft S, Thumser-Henner C, Breitenbücher F, Okimoto RA, Dorsch M, Opitz CA, Sadik A, Esser C, Hölzel M, Asthana S, Forster J, Beisser D, Kalmbach S, Grüner BM, Bivona TG, Schramm A, Schuler M. Functional screening identifies aryl hydrocarbon receptor as suppressor of lung cancer metastasis. Oncogenesis 2020; 9:102. [PMID: 33214553 PMCID: PMC7677369 DOI: 10.1038/s41389-020-00286-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 02/03/2020] [Revised: 10/22/2020] [Accepted: 10/30/2020] [Indexed: 02/08/2023] Open
Abstract
Lung cancer mortality largely results from metastasis. Despite curative surgery many patients with early-stage non-small cell lung cancer ultimately succumb to metastatic relapse. Current risk reduction strategies based on cytotoxic chemotherapy and radiation have only modest activity. Against this background, we functionally screened for novel metastasis modulators using a barcoded shRNA library and an orthotopic lung cancer model. We identified aryl hydrocarbon receptor (AHR), a sensor of xenobiotic chemicals and transcription factor, as suppressor of lung cancer metastasis. Knockdown of endogenous AHR induces epithelial–mesenchymal transition signatures, increases invasiveness of lung cancer cells in vitro and metastasis formation in vivo. Low intratumoral AHR expression associates with inferior outcome of patients with resected lung adenocarcinomas. Mechanistically, AHR triggers ATF4 signaling and represses matrix metalloproteinase activity, both counteracting metastatic programs. These findings link the xenobiotic defense system with control of lung cancer progression. AHR-regulated pathways are promising targets for innovative anti-metastatic strategies.
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Affiliation(s)
- Silke Nothdurft
- Laboratory of Molecular Oncology, Department of Medical Oncology, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Clotilde Thumser-Henner
- Laboratory of Molecular Oncology, Department of Medical Oncology, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Frank Breitenbücher
- Laboratory of Molecular Oncology, Department of Medical Oncology, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Ross A Okimoto
- Department of Medicine, University of California, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Madeleine Dorsch
- Laboratory of Molecular Tumor Pathology, Department of Medical Oncology, West German Cancer Center, University Hospital Essen, Essen, Germany
| | - Christiane A Opitz
- DKTK Brain Cancer Metabolism Group, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Neurology Clinic and National Center for Tumor Diseases, University Hospital of Heidelberg, Heidelberg, Germany
| | - Ahmed Sadik
- DKTK Brain Cancer Metabolism Group, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Faculty of Bioscience, Heidelberg University, Heidelberg, Germany
| | - Charlotte Esser
- IUF-Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
| | - Michael Hölzel
- Institute of Experimental Oncology, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Saurabh Asthana
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Jan Forster
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, Essen, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniela Beisser
- Department of Biodiversity, University Duisburg-Essen, Essen, Germany
| | - Sophie Kalmbach
- Laboratory of Molecular Oncology, Department of Medical Oncology, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Barbara M Grüner
- Laboratory of Molecular Tumor Pathology, Department of Medical Oncology, West German Cancer Center, University Hospital Essen, Essen, Germany.,German Cancer Consortium (DKTK), Partner Site University Hospital Essen, Essen, Germany
| | - Trever G Bivona
- Department of Medicine, University of California, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Alexander Schramm
- Laboratory of Molecular Oncology, Department of Medical Oncology, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, Essen, Germany.
| | - Martin Schuler
- Laboratory of Molecular Oncology, Department of Medical Oncology, West German Cancer Center, University Hospital Essen, University Duisburg-Essen, Essen, Germany.,German Cancer Consortium (DKTK), Partner Site University Hospital Essen, Essen, Germany
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10
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Wu W, Okimoto RA, Blakely CM, Fraser J, Bivona TG. Targeted DNA sequencing analysis to reveal genetic diversity and androgen-receptor alteration in advanced EGFR mutant lung adenocarcinoma. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.9526] [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: 11/20/2022] Open
Abstract
9526 Background: Lung cancer remains the leading cause of death from cancer around the world. Several oncogenic drivers have been identified from large cancer genome projects focused mainly on profiling early-stage lung cancers. Targeted therapies have been developed for specific activated driver gene mutations and are used in advanced-stage patients. For instance, advanced EGFR mutant lung cancer is primarily treated with EGFR tyrosine receptor inhibitors (TKIs). However, resistance remains an obstacle to durable anti-tumor control. We hypothesize that concurrent genetic alterations co-exiting with EGFR driver mutations contribute to the failure of EGFR TKI therapy. Methods: To understand the complexity and diversity of genetic alterations present in EGFR mutant advanced lung cancers, we utilized 660 EGFR mutant advanced lung adenocarcinomas samples with targeted DNA sequencing from Foundation Medicine, 394 cases from MSK-IMPACT dataset, along with TCGA lung cancer data. We performed systematic co-mutation analysis, molecular simulation, functional annotation and pathway enrichment analysis. Results: We updated mutational profiling on EGFR gene with hotspots at exon 18, 19, 20 and 21. Among them, EGFR L858R, exon19 deletion, T790M and G719A are top ranking alleles among EGFR mutations. Interestingly, a subset (n = 26 cases) of EGFR T790M mutations parallel with other EGFR mutations, which could affect the TKI binding pocket as inferred by molecular simulations. Furthermore, in advanced lung cancer EGFR mutations co-occurred with known oncogenic mutations in KRAS, MET, NF-1, MAP2K1, ERBB2, and ALK/ROS-1/RET fusions. Functional annotation suggests that concurrent mutated genes and copy number alterations in advanced EGFR mutant lung cancer were enriched in signatures of epigenetic modifiers, genome instability, WNT signaling, and RNA splicing. Compared to early stage TCGA-lung adenocarcinomas, Cell cycle, DNA repair, WNT signaling and androgen receptor-mediated signaling pathways are predominantly altered in advanced EGFR mutant lung cancers. Conclusions: We characterized the genetic landscape of advanced EGFR-mutant lung adenocarcinomas and further dissected concurrent mutated genes with EGFR driver mutations. Our findings provide a rational for polytherapy roadmap for testing in advanced EGFR-mutant lung cancer.
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Affiliation(s)
- Wei Wu
- University of California, San Francisco, San Francisco, CA
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11
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Okimoto RA, Wu W, Nanjo S, Olivas V, Lin YK, Ponce RK, Oyama R, Kondo T, Bivona TG. CIC-DUX4 oncoprotein drives sarcoma metastasis and tumorigenesis via distinct regulatory programs. J Clin Invest 2019; 129:3401-3406. [PMID: 31329165 DOI: 10.1172/jci126366] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [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: 11/21/2018] [Accepted: 05/24/2019] [Indexed: 12/31/2022] Open
Abstract
Transcription factor fusion genes create oncoproteins that drive oncogenesis and represent challenging therapeutic targets. Understanding the molecular targets by which such fusion oncoproteins promote malignancy offers an approach to develop rational treatment strategies to improve clinical outcomes. Capicua-double homeobox 4 (CIC-DUX4) is a transcription factor fusion oncoprotein that defines certain undifferentiated round cell sarcomas with high metastatic propensity and poor clinical outcomes. The molecular targets regulated by the CIC-DUX4 oncoprotein that promote this aggressive malignancy remain largely unknown. We demonstrated that increased expression of ETS variant 4 (ETV4) and cyclin E1 (CCNE1) occurs via neomorphic, direct effects of CIC-DUX4 and drives tumor metastasis and survival, respectively. We uncovered a molecular dependence on the CCNE-CDK2 cell cycle complex that renders CIC-DUX4-expressing tumors sensitive to inhibition of the CCNE-CDK2 complex, suggesting a therapeutic strategy for CIC-DUX4-expressing tumors. Our findings highlight a paradigm of functional diversification of transcriptional repertoires controlled by a genetically aberrant transcriptional regulator, with therapeutic implications.
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Affiliation(s)
- Ross A Okimoto
- Department of Medicine.,Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA
| | | | | | | | | | | | - Rieko Oyama
- Division of Rare Cancer Research, National Cancer Center Research Institute, Tokyo, Japan
| | - Tadashi Kondo
- Division of Rare Cancer Research, National Cancer Center Research Institute, Tokyo, Japan
| | - Trever G Bivona
- Department of Medicine.,Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, USA.,Cellular and Molecular Pharmacology, UCSF, San Francisco, California, USA
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12
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Okimoto RA, Wu W, Bivona TG. Abstract B24: Molecular and functional dissection of the CIC-DUX4 fusion in undifferentiated round cell sarcoma. Clin Cancer Res 2018. [DOI: 10.1158/1557-3265.sarcomas17-b24] [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
CIC-DUX4 soft-tissue tumors are an aggressive subset of undifferentiated round cell sarcomas that arise in children and young adults. The cytogenetic hallmark, (t(4;19) or t(10;19)), of this tumor is a chromosomal translocation that fuses the transcription factor, Capicua (CIC), with the double homeobox 4 protein, DUX4. Despite morphologic similarities to Ewing sarcoma, CIC-DUX4 sarcomas are clinically distinct with rapid development of lethal metastatic disease and chemoinsensitivity. The unique cytogenetic and clinical features that distinguish CIC-DUX4 sarcomas from other small round cell tumors provide a unique opportunity to identify and rationally target this population to improve clinical outcomes.
To meet this need, we are taking a systematic functional approach to identify critical CIC-DUX4 targets that promote tumor progression and metastasis. Leveraging a comparative transcriptional analysis between cytogenetically distinct small round cell sarcomas, we reveal that the CIC-DUX4 fusion activates highly conserved molecular networks to control tumor growth and metastatic capacity. Using an orthotopic soft-tissue sarcoma model, we show that CIC-DUX4 induces ETV4 expression to drive invasion and metastasis. Genetic silencing of ETV4 in CIC-DUX4 expressing tumors limits tumor dissemination without a profound impact on tumor cell growth. These findings suggest that CIC-DUX4 enhances metastasis and tumor growth through distinct transcriptional repertoires. Consistent with this, we identify multiple components of the cell cycle machinery that are transcriptionally regulated by CIC-DUX4 expression. Specifically, the CIC-DUX4 fusion co-opts native CIC-binding specificity to transcriptionally activate these cell cycle target genes. Altogether, our molecular and functional dissection of the CIC-DUX4 fusion reveals highly conserved CIC-regulated transcriptional targets that promote tumor growth and metastasis. We aim to pharmacologically exploit these key CIC-DUX4-dependent transcriptional nodes to improve outcomes for this population with few therapeutic options.
Citation Format: Ross A. Okimoto, Wei Wu, Trever G. Bivona. Molecular and functional dissection of the CIC-DUX4 fusion in undifferentiated round cell sarcoma [abstract]. In: Proceedings of the AACR Conference on Advances in Sarcomas: From Basic Science to Clinical Translation; May 16-19, 2017; Philadelphia, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(2_Suppl):Abstract nr B24.
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Affiliation(s)
| | - Wei Wu
- University of California, San Francisco, San Francisco, CA
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13
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Affiliation(s)
- Ross A Okimoto
- a Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco , San Francisco , CA , USA.,b Department of Medicine , University of California at San Francisco , San Francisco , CA , USA
| | - Trever G Bivona
- a Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco , San Francisco , CA , USA.,b Department of Medicine , University of California at San Francisco , San Francisco , CA , USA
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14
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Okimoto RA, Breitenbuecher F, Olivas VR, Wu W, Gini B, Hofree M, Asthana S, Hrustanovic G, Flanagan J, Tulpule A, Blakely CM, Haringsma HJ, Simmons AD, Gowen K, Suh J, Miller VA, Ali S, Schuler M, Bivona TG. Inactivation of Capicua drives cancer metastasis. Nat Genet 2017; 49:87-96. [PMID: 27869830 PMCID: PMC5195898 DOI: 10.1038/ng.3728] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [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: 07/28/2016] [Accepted: 10/25/2016] [Indexed: 12/23/2022]
Abstract
Metastasis is the leading cause of death in people with lung cancer, yet the molecular effectors underlying tumor dissemination remain poorly defined. Through the development of an in vivo spontaneous lung cancer metastasis model, we show that the developmentally regulated transcriptional repressor Capicua (CIC) suppresses invasion and metastasis. Inactivation of CIC relieves repression of its effector ETV4, driving ETV4-mediated upregulation of MMP24, which is necessary and sufficient for metastasis. Loss of CIC, or an increase in levels of its effectors ETV4 and MMP24, is a biomarker of tumor progression and worse outcomes in people with lung and/or gastric cancer. Our findings reveal CIC as a conserved metastasis suppressor, highlighting new anti-metastatic strategies that could potentially improve patient outcomes.
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Affiliation(s)
- Ross A. Okimoto
- Department of Medicine, University of California, San Francisco, San Francisco, CA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
| | - Frank Breitenbuecher
- Department of Medical Oncology, West German Cancer Center, University Hospital Essen, Essen, Germany
| | - Victor R. Olivas
- Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Wei Wu
- Department of Medicine, University of California, San Francisco, San Francisco, CA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
| | - Beatrice Gini
- Department of Medicine, University of California, San Francisco, San Francisco, CA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
| | - Matan Hofree
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Saurabh Asthana
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
| | - Gorjan Hrustanovic
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
| | - Jennifer Flanagan
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
| | - Asmin Tulpule
- Department of Medicine, University of California, San Francisco, San Francisco, CA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
| | - Collin M. Blakely
- Department of Medicine, University of California, San Francisco, San Francisco, CA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
| | | | | | - Kyle Gowen
- Foundation Medicine, Cambridge, Massachusetts
| | - James Suh
- Foundation Medicine, Cambridge, Massachusetts
| | | | - Siraj Ali
- Foundation Medicine, Cambridge, Massachusetts
| | - Martin Schuler
- Department of Medical Oncology, West German Cancer Center, University Hospital Essen, Essen, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Trever G. Bivona
- Department of Medicine, University of California, San Francisco, San Francisco, CA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA
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15
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Abstract
Two recent studies validate the LMNA-NTRK1 fusion as an oncogenic driver and therapeutic target of TRK inhibitors. The LMNA-NTRK1 fusion occurs at low frequency across multiple tumor types. The studies highlight the increasing need to develop molecular biomarker-based clinical trials across cancer subtypes.
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Affiliation(s)
- Ross A Okimoto
- Department of Medicine, Division of Hematology and Oncology, University of California, San Francisco, San Francisco, California. Helen Diller Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Trever G Bivona
- Department of Medicine, Division of Hematology and Oncology, University of California, San Francisco, San Francisco, California. Helen Diller Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California.
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16
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Premasekharan G, Gilbert E, Okimoto RA, Hamirani A, Lindquist KJ, Ngo VT, Roy R, Hough J, Edwards M, Paz R, Foye A, Sood R, Copren KA, Gubens M, Small EJ, Bivona TG, Collisson EA, Friedlander TW, Paris PL. An improved CTC isolation scheme for pairing with downstream genomics: Demonstrating clinical utility in metastatic prostate, lung and pancreatic cancer. Cancer Lett 2016; 380:144-52. [PMID: 27343980 DOI: 10.1016/j.canlet.2016.06.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [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: 04/06/2016] [Revised: 06/16/2016] [Accepted: 06/17/2016] [Indexed: 12/29/2022]
Abstract
Improvements in technologies to yield purer circulating tumor cells (CTCs) will enable a broader range of clinical applications. We have previously demonstrated the use of a commercially available cell-adhesion matrix (CAM) assay to capture invasive CTCs (iCTCs). To improve the purity of the isolated iCTCs, here we used fluorescence-activated cell sorting (FACS) in combination with the CAM assay (CAM + FACS). Our results showed an increase of median purity from the CAM assay to CAM + FACS for the spiked-in cell lines and patient samples analyzed from three different metastatic cancer types: castration resistant prostate cancer (mCRPC), non-small cell lung cancer (mNSCLC) and pancreatic ductal adenocarcinoma cancer (mPDAC). Copy number profiles for spiked-in mCRPC cell line and mCRPC patient iCTCs were similar to expected mCRPC profiles and a matched biopsy. A somatic epidermal growth factor receptor (EGFR) mutation specific to mNSCLC was observed in the iCTCs recovered from EGFR(+) mNSCLC cell lines and patient samples. Next-generation sequencing (NGS) of spiked-in pancreatic cancer cell line and mPDAC patient iCTCs showed mPDAC common mutations. CAM + FACS iCTC enrichment enables multiple downstream genomic characterizations across different tumor types.
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Affiliation(s)
- Gayatri Premasekharan
- Department of Urology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Elizabeth Gilbert
- Department of Urology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Ross A Okimoto
- Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Ashiya Hamirani
- Department of Urology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Karla J Lindquist
- Department of Urology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Vy T Ngo
- Department of Urology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Ritu Roy
- Computational Biology Core, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Jeffrey Hough
- Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Matthew Edwards
- Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Rosa Paz
- Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Adam Foye
- Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Riddhi Sood
- Genome Analysis Core, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Kirsten A Copren
- Genome Analysis Core, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Matthew Gubens
- Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Eric J Small
- Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Trever G Bivona
- Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Eric A Collisson
- Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Terence W Friedlander
- Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Pamela L Paris
- Department of Urology, University of California, San Francisco (UCSF), San Francisco, CA, USA; Division of Hematology & Oncology, University of California, San Francisco (UCSF), San Francisco, CA, USA.
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17
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Affiliation(s)
- Ross A Okimoto
- Division of Hematology/Oncology, University of California, San Francisco, CA
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18
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Abstract
The AXL receptor tyrosine kinase and its ligand, Gas6, regulate key processes in lung cancer growth, metastasis, and epithelial–mesenchymal transition-associated drug resistance. Gas6 and AXL expression have been correlated with poor prognosis and advanced clinical stage in patients with lung cancer, and targeting the Gas6/AXL pathway demonstrates antitumor activity, decreases cellular invasion, and restores sensitivity in de novo and acquired drug resistance models. These findings implicate AXL as a promising therapeutic target in lung cancer. In this review, we explore the role of AXL in lung cancer progression, from tumor development to disseminated disease, and highlight the current clinical landscape of anti-AXL therapeutics.
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Affiliation(s)
- Ross A Okimoto
- Division of Hematology and Medical Oncology, University of California San Francisco, San Francisco, CA, USA
| | - Trever G Bivona
- Division of Hematology and Medical Oncology, University of California San Francisco, San Francisco, CA, USA; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
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19
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Abstract
The identification of molecular subtypes of non-small-cell lung cancer has transformed the clinical management of this disease. This is best exemplified by the clinical success of targeting the EGFR or ALK with tyrosine kinase inhibitors in the front-line setting. Our ability to further improve patient outcomes with biomarker-based targeted therapies will depend on a more comprehensive genetic platform that can rationally interrogate the cancer genome of an individual patient. Novel technologies, including multiplex genotyping and next-generation sequencing are rapidly evolving and will soon challenge the oncologist with a wealth of genetic information for each patient. Although there are many barriers to overcome, the integration of these genetic platforms into clinical care has the potential to transform the management of lung cancer through improved molecular categorization, patient stratification, and drug development, thereby, improving clinical outcomes through personalized lung cancer medicine.
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Affiliation(s)
- Ross A Okimoto
- Division of Hematology & Medical Oncology, University of California San Francisco, San Francisco, CA, USA
| | - Trever G Bivona
- Division of Hematology & Medical Oncology, University of California San Francisco, San Francisco, CA, USA ; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
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20
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Abstract
PURPOSE OF REVIEW Tyrosine kinase inhibitors (TKIs) have revolutionized the treatment of chronic myeloid leukemia (CML) and are now widely accepted as the initial therapy of choice in this disease, supplanting interferon and allogeneic stem cell transplantation. There are currently three drugs approved by the US Food and Drug Administration (FDA) for front-line treatment of CML: imatinib, nilotinib, and dasatinib. A fourth drug, bosutinib, may also win FDA approval in 2011. The goal of this review is to summarize the most recent information on initial treatment of CML and to aid clinicians in managing newly diagnosed CML patients. RECENT FINDINGS Phase III studies comparing imatinib with nilotinib or dasatinib in newly diagnosed CML were published in June 2010, leading to accelerated FDA approval for both of these 'second-generation' TKIs for initial therapy of CML. There are significant differences between the agents in terms of frequency and rate of responses, progression-free survival, and side-effects. However, the follow-up period on these trials is short, and there are as yet no significant differences in overall survival. Guidelines for monitoring CML patients on TKI therapy have been recently revised. SUMMARY Management of newly diagnosed CML patients in the coming decade will begin to resemble antibiotic treatment of infection, with therapy individualized based on patient risk factors, co-morbidities, and tolerability. In addition, the cost of therapy will emerge as an important consideration as generic imatinib becomes available in 2015. In this context, clinical trials to guide decision-making in newly diagnosed CML patients are needed.
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Affiliation(s)
- Ross A. Okimoto
- Department of Medicine, Tufts Medical Center, Boston, MA USA
| | - Richard A. Van Etten
- Department of Medicine, Tufts Medical Center, Boston, MA USA
- Division of Hematology/Oncology, Tufts Medical Center, Boston, MA USA
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21
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Hur J, Bell DW, Dean KL, Coser KR, Hilario PC, Okimoto RA, Tobey EM, Smith SL, Isselbacher KJ, Shioda T. Regulation of expression of BIK proapoptotic protein in human breast cancer cells: p53-dependent induction of BIK mRNA by fulvestrant and proteasomal degradation of BIK protein. Cancer Res 2006; 66:10153-61. [PMID: 17047080 DOI: 10.1158/0008-5472.can-05-3696] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Induction of mRNA for BIK proapoptotic protein by doxorubicin or gamma-irradiation requires the DNA-binding transcription factor activity of p53. In MCF7 cells, pure antiestrogen fulvestrant also induces BIK mRNA and apoptosis. Here, we provide evidence that, in contrast to doxorubicin or gamma-irradiation, fulvestrant induction of BIK mRNA is not a direct effect of the transcriptional activity of p53, although p53 is necessary for this induction. It is known that p53 up-regulated modulator of apoptosis (PUMA) mRNA is induced directly by the transcriptional activity of p53. Whereas gamma-irradiation induced both BIK and PUMA mRNA, only BIK mRNA was induced by fulvestrant. Whereas both fulvestrant and doxorubicin induced BIK mRNA, only doxorubicin enhanced the DNA-binding activity of p53 and induced PUMA mRNA. Small interfering RNA (siRNA) suppression of p53 expression as well as overexpression of dominant-negative p53 effectively inhibited the fulvestrant induction of BIK mRNA, protein, and apoptosis. Transcriptional activity of a 2-kb BIK promoter, which contained an incomplete p53-binding sequence, was not affected by fulvestrant when tested by reporter assay. Fulvestrant neither affected the stability of the BIK mRNA transcripts. Interestingly, other human breast cancer cells, such as ZR75-1, constitutively expressed BIK mRNA even without fulvestrant. In these cells, however, BIK protein seemed to be rapidly degraded by proteasome, and siRNA suppression of BIK in ZR75-1 cells inhibited apoptosis induced by MG132 proteasome inhibitor. These results suggest that expression of BIK in human breast cancer cells is regulated at the mRNA level by a mechanism involving a nontranscriptional activity of p53 and by proteasomal degradation of BIK protein.
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MESH Headings
- Antineoplastic Agents/pharmacology
- Antineoplastic Agents, Hormonal/pharmacology
- Apoptosis Regulatory Proteins/biosynthesis
- Apoptosis Regulatory Proteins/genetics
- Breast Neoplasms/drug therapy
- Breast Neoplasms/genetics
- Breast Neoplasms/metabolism
- Cell Line, Tumor
- Doxorubicin/pharmacology
- Estradiol/analogs & derivatives
- Estradiol/pharmacology
- Fulvestrant
- Gamma Rays
- Gene Expression Regulation, Neoplastic/drug effects
- Gene Expression Regulation, Neoplastic/radiation effects
- Humans
- Leupeptins/pharmacology
- Membrane Proteins/biosynthesis
- Membrane Proteins/genetics
- Mitochondrial Proteins
- Promoter Regions, Genetic
- Proteasome Endopeptidase Complex/metabolism
- Proteasome Inhibitors
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- Receptors, Estrogen/biosynthesis
- Transcription, Genetic/drug effects
- Transcription, Genetic/radiation effects
- Tumor Suppressor Protein p53/genetics
- Tumor Suppressor Protein p53/metabolism
- Tumor Suppressor Protein p53/physiology
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Affiliation(s)
- Jingyung Hur
- Department of Tumor Biology, Massachusetts General Hospital Center for Cancer Research, Charlestown, Massachusetts 02129, USA
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Kwak EL, Jankowski J, Thayer SP, Lauwers GY, Brannigan BW, Harris PL, Okimoto RA, Haserlat SM, Dris coll DR, Ferry D, Muir B, Settleman J, Fuchs CS, Kulke MH, Ryan DP, Clark JW, Sgroi DC, Haber DA, Bell DW. Epidermal growth factor receptor kinase domain mutations in esophageal and pancreatic adenocarcinomas. Clin Cancer Res 2006; 12:4283-7. [PMID: 16857803 PMCID: PMC3807136 DOI: 10.1158/1078-0432.ccr-06-0189] [Citation(s) in RCA: 132] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PURPOSE Specific activating mutations within the epidermal growth factor receptor (EGFR) identify a subset of non-small cell lung cancers with dramatic sensitivity to the specific tyrosine kinase inhibitors (TKI), gefitinib and erlotinib. Despite the abundant expression of EGFR protein in a broad range of epithelial cancers, EGFR mutations have not been reported in a substantial fraction of other cancers. Given recent reports of TKI-responsive cases of esophageal and pancreatic cancer, this study was designed to determine the prevalence of EGFR mutations in these gastrointestinal cancers. EXPERIMENTAL DESIGN We sequenced exons 18 to 21 of EGFR from 21 cases of Barrett's esophagus, 5 cases of high-grade esophageal dysplasia, 17 cases of esophageal adenocarcinoma, and 55 cases of pancreatic adenocarcinoma. Subsets of esophageal (n = 7) and pancreatic cancer cases (n = 5) were obtained from patients who were subsequently treated with gefitinib or erlotinib-capecitabine, respectively. RESULTS Mutations of EGFR were identified in two esophageal cancers (11.7%), three cases of Barrett's esophagus (14.2%), and two pancreatic cancers (3.6%). The mutations consisted of the recurrent missense L858R and in-frame deletion delE746-A750, previously characterized as activating EGFR mutations in non-small cell lung cancer. We also identified the TKI drug resistance-associated EGFR T790M mutation in an untreated case of Barrett's esophagus and the corresponding adenocarcinoma. CONCLUSION The presence of activating mutations within EGFR in both esophageal and pancreatic adenocarcinomas defines a previously unrecognized subset of gastrointestinal tumors in which EGFR signaling may play an important biological role. EGFR mutations in premalignant lesions of Barrett's esophagus also point to these as an early event in transformation of the esophageal epithelium. The role of genotype-directed TKI therapy should be tested in prospective clinical trials.
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Affiliation(s)
- Eunice L. Kwak
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts
| | - Janusz Jankowski
- Department of Clinical Pharmacology, Oxford University, Oxford, United Kingdom
| | - Sarah P. Thayer
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School
| | - Gregory Y. Lauwers
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School
| | - Brian W. Brannigan
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts
| | - Patricia L. Harris
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts
| | - Ross A. Okimoto
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts
| | - Sara M. Haserlat
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts
| | - David R. Dris coll
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts
| | - David Ferry
- Oncology Centre, Royal Wolverhampton Hospital, Wolverhampton, United Kingdom
| | - Beth Muir
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School
| | - Jeff Settleman
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts
| | - Charles S. Fuchs
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Matthew H. Kulke
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - David P. Ryan
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts
| | - Jeff W. Clark
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts
| | - Dennis C. Sgroi
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School
| | - Daniel A. Haber
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts
| | - Daphne W. Bell
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts
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23
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Smolen GA, Muir B, Mohapatra G, Barmettler A, Kim WJ, Rivera MN, Haserlat SM, Okimoto RA, Kwak E, Dahiya S, Garber JE, Bell DW, Sgroi DC, Chin L, Deng CX, Haber DA. Frequent met oncogene amplification in a Brca1/Trp53 mouse model of mammary tumorigenesis. Cancer Res 2006; 66:3452-5. [PMID: 16585167 DOI: 10.1158/0008-5472.can-05-4181] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [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] [Indexed: 11/16/2022]
Abstract
In a screen for gene copy number alterations in mouse mammary tumors initiated by loss of the Brca1 and Trp53 genes, we observed that the majority (11 of 15; 73%) had high-level amplification of wild-type Met, encoding a growth factor receptor implicated in tumor progression. Met amplification was localized to unstable double minute chromosomes and was uniquely found in mouse breast tumors driven by loss of Brca1 and Trp53. Whereas analogous MET amplification was not found in human breast cancers, the identification of a dominant somatic genetic lesion in the Brca1/Trp53 mouse model suggests that recurrent secondary hits may also exist in BRCA1-initiated human breast cancer.
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Affiliation(s)
- Gromoslaw A Smolen
- Massachusetts General Hospital Cancer Center, Harvard Medical School, 13th Street, Charlestown, MA 02129, USA
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24
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Cohen EEW, Lingen MW, Martin LE, Harris PL, Brannigan BW, Haserlat SM, Okimoto RA, Sgroi DC, Dahiya S, Muir B, Clark JR, Rocco JW, Vokes EE, Haber DA, Bell DW. Response of some head and neck cancers to epidermal growth factor receptor tyrosine kinase inhibitors may be linked to mutation of ERBB2 rather than EGFR. Clin Cancer Res 2006; 11:8105-8. [PMID: 16299242 DOI: 10.1158/1078-0432.ccr-05-0926] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.4] [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: 11/16/2022]
Abstract
PURPOSE Small-molecule tyrosine kinase inhibitors (TKI) of the epidermal growth factor receptor (EGFR) have shown modest yet reproducible response rates in patients with squamous cell carcinoma of the head and neck (SCCHN). Somatic mutations in EGFR have recently been shown to be predictive of a clinical response in patients with non-small cell lung cancer (NSCLC) treated with these inhibitors. The objective of this study was to determine if such mutations, or recently reported mutations in ERBB2, also underlie EGFR-TKI responsiveness in SCCHN patients. EXPERIMENTAL DESIGN We sequenced the kinase domain of EGFR and exon 20 of ERBB2 in tumor specimens from eight responsive patients. In addition, mutational analysis was done on tumor specimens from nine gefitinib nonresponders and 65 unselected cases of SCCHN. RESULTS None of eight TKI-responsive specimens had mutations within the kinase domain of EGFR. EGFR amplification was also not associated with drug responsiveness. However, a single responsive case had a somatic missense mutation within exon 20 of ERBB2. CONCLUSION Our data indicate that unlike NSCLC, EGFR kinase mutations are rare in unselected cases of SCCHN within the United States and are not linked to gefitinib or erlotinib responses in SCCHN. Alternative mechanisms, including ERBB2 mutations, may underlie responsiveness in this tumor type.
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Affiliation(s)
- Ezra E W Cohen
- Department of Medicine, University of Chicago, Illinois, USA
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25
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Smolen GA, Sordella R, Muir B, Mohapatra G, Barmettler A, Archibald H, Kim WJ, Okimoto RA, Bell DW, Sgroi DC, Christensen JG, Settleman J, Haber DA. Amplification of MET may identify a subset of cancers with extreme sensitivity to the selective tyrosine kinase inhibitor PHA-665752. Proc Natl Acad Sci U S A 2006; 103:2316-21. [PMID: 16461907 PMCID: PMC1413705 DOI: 10.1073/pnas.0508776103] [Citation(s) in RCA: 425] [Impact Index Per Article: 23.6] [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: 01/07/2023] Open
Abstract
The success of molecular targeted therapy in cancer may depend on the selection of appropriate tumor types whose survival depends on the drug target, so-called "oncogene addiction." Preclinical approaches to defining drug-responsive subsets are needed if initial clinical trials are to be directed at the most susceptible patient population. Here, we show that gastric cancer cells with high-level stable chromosomal amplification of the growth factor receptor MET are extraordinarily susceptible to the selective inhibitor PHA-665752. Although MET activation has primarily been linked with tumor cell migration and invasiveness, the amplified wild-type MET in these cells is constitutively activated, and its continued signaling is required for cell survival. Treatment with PHA-665752 triggers massive apoptosis in 5 of 5 gastric cancer cell lines with MET amplification but in 0 of 12 without increased gene copy numbers (P = 0.00016). MET amplification may thus identify a subset of epithelial cancers that are uniquely sensitive to disruption of this pathway and define a patient group that is appropriate for clinical trials of targeted therapy using MET inhibitors.
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Affiliation(s)
| | | | - Beth Muir
- Department of Pathology, Molecular Pathology Research Unit, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129; and
| | - Gayatry Mohapatra
- Department of Pathology, Molecular Pathology Research Unit, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129; and
| | - Anne Barmettler
- Department of Pathology, Molecular Pathology Research Unit, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129; and
| | | | | | | | | | - Dennis C. Sgroi
- Department of Pathology, Molecular Pathology Research Unit, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129; and
| | | | | | - Daniel A. Haber
- *Cancer Center and
- To whom correspondence should be addressed at:
Massachusetts General Hospital Cancer Center, Building 149, 13th Street, Charlestown, MA 02129. E-mail:
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26
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Bell DW, Gore I, Okimoto RA, Godin-Heymann N, Sordella R, Mulloy R, Sharma SV, Brannigan BW, Mohapatra G, Settleman J, Haber DA. Inherited susceptibility to lung cancer may be associated with the T790M drug resistance mutation in EGFR. Nat Genet 2005; 37:1315-6. [PMID: 16258541 DOI: 10.1038/ng1671] [Citation(s) in RCA: 370] [Impact Index Per Article: 19.5] [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: 06/24/2005] [Accepted: 09/12/2005] [Indexed: 11/09/2022]
Abstract
Somatic activating mutations in EGFR identify a subset of non-small cell lung cancer that respond to tyrosine kinase inhibitors. Acquisition of drug resistance is linked to a specific secondary somatic mutation, EGFR T790M. Here we describe a family with multiple cases of non-small cell lung cancer associated with germline transmission of this mutation. Four of six tumors analyzed showed a secondary somatic activating EGFR mutation, arising in cis with the germline EGFR mutation T790M. These observations implicate altered EGFR signaling in genetic susceptibility to lung cancer.
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Affiliation(s)
- Daphne W Bell
- Massachusetts General Hospital Cancer Center, Harvard Medical School, 13th Street, Charlestown, Massachusetts 02129, USA
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27
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Bell DW, Lynch TJ, Haserlat SM, Harris PL, Okimoto RA, Brannigan BW, Sgroi DC, Muir B, Riemenschneider MJ, Iacona RB, Krebs AD, Johnson DH, Giaccone G, Herbst RS, Manegold C, Fukuoka M, Kris MG, Baselga J, Ochs JS, Haber DA. Epidermal growth factor receptor mutations and gene amplification in non-small-cell lung cancer: molecular analysis of the IDEAL/INTACT gefitinib trials. J Clin Oncol 2005; 23:8081-92. [PMID: 16204011 DOI: 10.1200/jco.2005.02.7078] [Citation(s) in RCA: 527] [Impact Index Per Article: 27.7] [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: 11/20/2022] Open
Abstract
PURPOSE Most cases of non-small-cell lung cancer (NSCLC) with dramatic responses to gefitinib have specific activating mutations in the epidermal growth factor receptor (EGFR), but the predictive value of these mutations has not been defined in large clinical trials. The goal of this study was to determine the contribution of molecular alterations in EGFR to response and survival within the phase II (IDEAL) and phase III (INTACT) trials of gefitinib. PATIENTS AND METHODS We analyzed the frequency of EGFR mutations in lung cancer specimens from both the IDEAL and INTACT trials and compared it with EGFR gene amplification, another genetic abnormality in NSCLC. RESULTS EGFR mutations correlated with previously identified clinical features of gefitinib response, including adenocarcinoma histology, absence of smoking history, female sex, and Asian ethnicity. No such association was seen in patients whose tumors had EGFR amplification, suggesting that these molecular markers identify different biologic subsets of NSCLC. In the IDEAL trials, responses to gefitinib were seen in six of 13 tumors (46%) with an EGFR mutation, two of seven tumors (29%) with amplification, and five of 56 tumors (9%) with neither mutation nor amplification (P = .001 for either EGFR mutation or amplification v neither abnormality). Analysis of the INTACT trials did not show a statistically significant difference in response to gefitinib plus chemotherapy according to EGFR genotype. CONCLUSION EGFR mutations and, to a lesser extent, amplification appear to identify distinct subsets of NSCLC with an increased response to gefitinib. The combination of gefitinib with chemotherapy does not improve survival in patients with these molecular markers.
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Affiliation(s)
- Daphne W Bell
- Massachusetts General Hospital Cancer Center and Department of Pathology, Harvard Medical School, Charlestown, MA 02129, USA
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28
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Kwak EL, Sordella R, Bell DW, Godin-Heymann N, Okimoto RA, Brannigan BW, Harris PL, Driscoll DR, Fidias P, Lynch TJ, Rabindran SK, McGinnis JP, Wissner A, Sharma SV, Isselbacher KJ, Settleman J, Haber DA. Irreversible inhibitors of the EGF receptor may circumvent acquired resistance to gefitinib. Proc Natl Acad Sci U S A 2005; 102:7665-70. [PMID: 15897464 PMCID: PMC1129023 DOI: 10.1073/pnas.0502860102] [Citation(s) in RCA: 757] [Impact Index Per Article: 39.8] [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] [Indexed: 01/14/2023] Open
Abstract
Non-small cell lung cancers (NSCLCs) with activating mutations in the kinase domain of the epidermal growth factor receptor (EGFR) demonstrate dramatic, but transient, responses to the reversible tyrosine kinase inhibitors gefitinib (Iressa) and erlotinib (Tarceva). Some recurrent tumors have a common secondary mutation in the EGFR kinase domain, T790M, conferring drug resistance, but in other cases the mechanism underlying acquired resistance is unknown. In studying multiple sites of recurrent NSCLCs, we detected T790M in only a small percentage of tumor cells. To identify additional mechanisms of acquired resistance to gefitinib, we used NSCLC cells harboring an activating EGFR mutation to generate multiple resistant clones in vitro. These drug-resistant cells demonstrate continued dependence on EGFR and ERBB2 signaling for their viability and have not acquired secondary EGFR mutations. However, they display increased internalization of ligand-activated EGFR, consistent with altered receptor trafficking. Although gefitinib-resistant clones are cross-resistant to related anilinoquinazolines, they demonstrate sensitivity to a class of irreversible inhibitors of EGFR. These inhibitors also show effective inhibition of signaling by T790M-mutant EGFR and killing of NSCLC cells with the T790M mutation. Both mechanisms of gefitinib resistance are therefore circumvented by irreversible tyrosine kinase inhibitors. Our findings suggest that one of these, HKI-272, may prove highly effective in the treatment of EGFR-mutant NSCLCs, including tumors that have become resistant to gefitinib or erlotinib.
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Affiliation(s)
- Eunice L Kwak
- Center for Molecular Therapeutics, Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
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29
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Lynch TJ, Bell DW, Sordella R, Gurubhagavatula S, Okimoto RA, Brannigan BW, Harris PL, Haserlat SM, Supko JG, Haluska FG, Louis DN, Christiani DC, Settleman J, Haber DA. Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib. N Engl J Med 2004; 350:2129-39. [PMID: 15118073 DOI: 10.1056/nejmoa040938] [Citation(s) in RCA: 8589] [Impact Index Per Article: 429.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND Most patients with non-small-cell lung cancer have no response to the tyrosine kinase inhibitor gefitinib, which targets the epidermal growth factor receptor (EGFR). However, about 10 percent of patients have a rapid and often dramatic clinical response. The molecular mechanisms underlying sensitivity to gefitinib are unknown. METHODS We searched for mutations in the EGFR gene in primary tumors from patients with non-small-cell lung cancer who had a response to gefitinib, those who did not have a response, and those who had not been exposed to gefitinib. The functional consequences of identified mutations were evaluated after the mutant proteins were expressed in cultured cells. RESULTS Somatic mutations were identified in the tyrosine kinase domain of the EGFR gene in eight of nine patients with gefitinib-responsive lung cancer, as compared with none of the seven patients with no response (P<0.001). Mutations were either small, in-frame deletions or amino acid substitutions clustered around the ATP-binding pocket of the tyrosine kinase domain. Similar mutations were detected in tumors from 2 of 25 patients with primary non-small-cell lung cancer who had not been exposed to gefitinib (8 percent). All mutations were heterozygous, and identical mutations were observed in multiple patients, suggesting an additive specific gain of function. In vitro, EGFR mutants demonstrated enhanced tyrosine kinase activity in response to epidermal growth factor and increased sensitivity to inhibition by gefitinib. CONCLUSIONS A subgroup of patients with non-small-cell lung cancer have specific mutations in the EGFR gene, which correlate with clinical responsiveness to the tyrosine kinase inhibitor gefitinib. These mutations lead to increased growth factor signaling and confer susceptibility to the inhibitor. Screening for such mutations in lung cancers may identify patients who will have a response to gefitinib.
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Affiliation(s)
- Thomas J Lynch
- Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston 02129, USA
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