1
|
Rasmussen SV, Wozniak A, Lathara M, Goldenberg JM, Samudio BM, Bickford LR, Nagamori K, Wright H, Woods AD, Chauhan S, Lee CJ, Rudzinski ER, Swift MK, Kondo T, Fisher DE, Imyanitov E, Machado I, Llombart-Bosch A, Andrulis IL, Gokgoz N, Wunder J, Mirotaki H, Nakamura T, Srinivasa G, Thway K, Jones RL, Huang PH, Berlow NE, Schöffski P, Keller C. Functional genomics of human clear cell sarcoma: genomic, transcriptomic and chemical biology landscape for clear cell sarcoma. Br J Cancer 2023; 128:1941-1954. [PMID: 36959380 PMCID: PMC10147623 DOI: 10.1038/s41416-023-02222-0] [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: 06/03/2022] [Revised: 02/14/2023] [Accepted: 02/24/2023] [Indexed: 03/25/2023] Open
Abstract
BACKGROUND Systemic therapy for metastatic clear cell sarcoma (CCS) bearing EWSR1-CREB1/ATF1 fusions remains an unmet clinical need in children, adolescents, and young adults. METHODS To identify key signaling pathway vulnerabilities in CCS, a multi-pronged approach was taken: (i) genomic and transcriptomic landscape analysis, (ii) integrated chemical biology interrogations, (iii) development of CREB1/ATF1 inhibitors, and (iv) antibody-drug conjugate testing (ADC). The first approach encompassed DNA exome and RNA deep sequencing of the largest human CCS cohort yet reported consisting of 47 patient tumor samples and 8 cell lines. RESULTS Sequencing revealed recurrent mutations in cell cycle checkpoint, DNA double-strand break repair or DNA mismatch repair genes, with a correspondingly low to intermediate tumor mutational burden. DNA multi-copy gains with corresponding high RNA expression were observed in CCS tumor subsets. CCS cell lines responded to the HER3 ADC patritumab deruxtecan in a dose-dependent manner in vitro, with impaired long term cell viability. CONCLUSION These studies of the genomic, transcriptomic and chemical biology landscape represent a resource 'atlas' for the field of CCS investigation and drug development. CHK inhibitors are identified as having potential relevance, CREB1 inhibitors non-dependence of CCS on CREB1 activity was established, and the potential utility of HER3 ADC being used in CCS is found.
Collapse
Affiliation(s)
| | - Agnieszka Wozniak
- University Hospitals Leuven, Department of General Medical Oncology, and Laboratory of Experimental Oncology, KU Leuven, Leuven Cancer Institute, Leuven, Belgium
| | | | | | | | | | - Kiyo Nagamori
- Children's Cancer Therapy Development Institute, Beaverton, OR, USA
| | | | - Andrew D Woods
- Children's Cancer Therapy Development Institute, Beaverton, OR, USA
| | - Shefali Chauhan
- Children's Cancer Therapy Development Institute, Beaverton, OR, USA
| | - Che-Jui Lee
- University Hospitals Leuven, Department of General Medical Oncology, and Laboratory of Experimental Oncology, KU Leuven, Leuven Cancer Institute, Leuven, Belgium
| | - Erin R Rudzinski
- Department of Pathology, Seattle Children's Hospital, Seattle, WA, USA
| | - Michael K Swift
- Children's Cancer Therapy Development Institute, Beaverton, OR, USA
| | - Tadashi Kondo
- Division of Rare Cancer Research, National Cancer Center Research Institute, Tokyo, Japan
| | - David E Fisher
- Department of Hematology/Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Evgeny Imyanitov
- N.N. Petrov National Medicine Research Center of Oncology, St. Petersburg, Russia
| | - Isidro Machado
- Pathology Department, Instituto Valenciano de Oncología and Patologika Laboratorio, Hospital QuironSalud, Valencia, Spain
| | | | - Irene L Andrulis
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Nalan Gokgoz
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Jay Wunder
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
- University Musculoskeletal Oncology Unit, Mount Sinai Hospital, Toronto, ON, Canada
- Division of Orthopaedic Surgery, Department of Surgery, University of Toronto, Toronto, Canada
| | | | - Takuro Nakamura
- The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | | | - Khin Thway
- Sarcoma Unit, Royal Marsden Hospital, Division of Molecular Pathology, Institute of Cancer Research, London, UK
| | - Robin L Jones
- Sarcoma Unit, Royal Marsden Hospital, Division of Clinical Studies, Institute of Cancer Research, London, UK
| | - Paul H Huang
- Sarcoma Unit, Royal Marsden Hospital, Division of Molecular Pathology, Institute of Cancer Research, London, UK.
| | - Noah E Berlow
- Children's Cancer Therapy Development Institute, Beaverton, OR, USA.
| | - Patrick Schöffski
- University Hospitals Leuven, Department of General Medical Oncology, and Laboratory of Experimental Oncology, KU Leuven, Leuven Cancer Institute, Leuven, Belgium
| | - Charles Keller
- Children's Cancer Therapy Development Institute, Beaverton, OR, USA.
| |
Collapse
|