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Spano M, Davis-Hayes C, Hameed M, Benayed R, Hwang S. NTRK-rearranged spindle cell neoplasm: Initial observation of imaging appearance and clinicopathologic correlation. Clin Imaging 2024; 110:110134. [PMID: 38631176 DOI: 10.1016/j.clinimag.2024.110134] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 03/07/2024] [Accepted: 03/10/2024] [Indexed: 04/19/2024]
Abstract
OBJECTIVE To explore pre-treatment imaging findings of neurotrophic tyrosine receptor kinase (NTRK)-rearranged spindle cell neoplasm, an emerging group of molecularly defined soft tissue tumors and summarize the clinical course, including TRK inhibitor therapy response. MATERIALS AND METHODS This retrospective study included 8 women and 4 men with NTRK-rearranged spindle cell neoplasm (median age, 35.5 years, range, 0-66). Available pre-treatment MRI, CT, PET, and US imaging were reviewed. Tumor histology and the patients' clinical course were reviewed. RESULTS Primary tumors were located within the soft tissue, lungs, kidney, and breast with soft tissue being the most prevalent site (n = 6). Pre-treatment MRI (n = 4) revealed linear hypointense signal foci and contrast enhancement in all patients with hemorrhage in half of the tumors. A tail sign (n = 1) and fluid levels (n = 1) were less frequent. Ultrasound showed well-marginated hypoechoic masses with internal flow. Primary tumors were all non-calcified on CT (4/4). Metastases were FDG-avid (4/4). Among the 8 patients who developed metastasis, 7 developed pulmonary metastases. All four patients who received NTRK inhibitor therapy showed an initial decrease in tumor size or FDG uptake. CONCLUSION NTRK-rearranged neoplasms may occur as enhancing masses with linear hypointense signal foci on MRI and FDG avid metastases on PET. Pulmonary metastases were frequent in our study. Initial treatment response is observed in most patients.
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Affiliation(s)
- Matthew Spano
- Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, United States of America.
| | - Cecilia Davis-Hayes
- Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, United States of America.
| | - Meera Hameed
- Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, United States of America.
| | - Ryma Benayed
- AstraZeneca, 430 East 29 Street, New York, NY 10016, United States of America.
| | - Sinchun Hwang
- Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, United States of America.
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2
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Krystel-Whittemore M, Petrova-Drus K, Ptashkin RN, Ewalt MD, Yao J, Liu Y, Zhu M, Benhamida J, Durham B, Kumar J, Nafa K, Kiecka I, Bowman AS, Gedvilaite E, Casanova J, Lin YT, Mohanty AS, Rana S, Rema AB, Rijo I, Chaves N, Salazar P, Yun A, Lachhander S, Wang W, Haque MS, Xiao W, Roshal M, Giralt S, Salles G, Rampal R, Stein EM, Perales MA, Horwitz S, Jakubowski A, Ponce D, Markova A, Birsoy O, Mandelker D, Mantha S, Dogan A, Benayed R, Ladanyi M, Berger MF, Brannon AR, Zehir A, Vanderbilt C, Arcila ME. Cell-free DNA from nail clippings as source of normal control for genomic studies in hematologic malignancies. Haematologica 2024. [PMID: 38450530 DOI: 10.3324/haematol.2024.285054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Indexed: 03/08/2024] Open
Abstract
Comprehensive genomic sequencing is becoming a critical component in the assessment of hematologic malignancies, with broad implications for patient management. In this context, unequivocally discriminating somatic from germline events is challenging but greatly facilitated by matched analysis of tumor:normal pairs. In contrast to solid tumors, conventional sources of normal control (peripheral blood, buccal swabs, saliva) could be highly involved by the neoplastic process, rendering them unsuitable. In this work we describe our real-world experience using cell free DNA (cfDNA) isolated from nail clippings as an alternate source of normal control, through the dedicated review of 2,610 tumor:nail pairs comprehensively sequenced by MSK-IMPACT-heme. Overall, we find nail cfDNA is a robust source of germline control for paired genomic studies. In a subset of patients, nail DNA may have tumor DNA contamination, reflecting unique attributes of the hematologic disease and transplant history. Contamination is generally low level, but significantly more common among patients with myeloid neoplasms (20.5%; 304/1482) compared to lymphoid diseases (5.4%; 61/1128) and particularly enriched in myeloproliferative neoplasms with marked myelofibrosis. When identified in patients with lymphoid and plasma-cell neoplasms, mutations commonly reflected a myeloid profile and correlated with a concurrent/evolving clonal myeloid neoplasm. For nails collected after allogeneic stem-cell transplantation, donor DNA was identified in 22% (11/50). In this cohort, an association with recent history of graft-vs-host disease was identified. These findings should be considered as a potential limitation for the use of nail as normal control but could also provide important diagnostic information regarding the disease process.
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Affiliation(s)
| | - Kseniya Petrova-Drus
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ryan N Ptashkin
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mark D Ewalt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - JinJuan Yao
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ying Liu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Menglei Zhu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jamal Benhamida
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Benjamin Durham
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jyoti Kumar
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Khedoudja Nafa
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Iwona Kiecka
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Anita S Bowman
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Erika Gedvilaite
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jacklyn Casanova
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yun-Te Lin
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Abhinita S Mohanty
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Satshil Rana
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Anoop Balakrishnan Rema
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ivelise Rijo
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nelio Chaves
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Paulo Salazar
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Anita Yun
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sean Lachhander
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Wei Wang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mohammad S Haque
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Wenbin Xiao
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mikhail Roshal
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sergio Giralt
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Gilles Salles
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Raajit Rampal
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Eytan M Stein
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Steven Horwitz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ann Jakubowski
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Doris Ponce
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Alina Markova
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ozge Birsoy
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Diana Mandelker
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Simon Mantha
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Dogan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ryma Benayed
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Marc Ladanyi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael F Berger
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - A Rose Brannon
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Chad Vanderbilt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Maria E Arcila
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.
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3
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Yang SR, Gedvilaite E, Ptashkin R, Chang J, Ziegler J, Mata DA, Villafania LB, Nafa K, Hechtman JF, Benayed R, Zehir A, Benhamida J, Arcila ME, Mandelker D, Rudin CM, Paik PK, Drilon A, Schoenfeld AJ, Ladanyi M. Microsatellite Instability and Mismatch Repair Deficiency Define a Distinct Subset of Lung Cancers Characterized by Smoking Exposure, High Tumor Mutational Burden, and Recurrent Somatic MLH1 Inactivation. J Thorac Oncol 2024; 19:409-424. [PMID: 37838086 PMCID: PMC10939956 DOI: 10.1016/j.jtho.2023.10.004] [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: 08/05/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 10/16/2023]
Abstract
INTRODUCTION Microsatellite instability (MSI) and mismatch repair (MMR) deficiency represent a distinct oncogenic process and predict response to immune checkpoint inhibitors (ICIs). The clinicopathologic features of MSI-high (MSI-H) and MMR deficiency (MMR-D) in lung cancers remain poorly characterized. METHODS MSI status from 5171 patients with NSCLC and 315 patients with SCLC was analyzed from targeted next-generation sequencing data using two validated bioinformatic pipelines. RESULTS MSI-H and MMR-D were identified in 21 patients with NSCLC (0.41%) and six patients with SCLC (1.9%). Notably, all patients with NSCLC had a positive smoking history, including 11 adenocarcinomas. Compared with microsatellite stable cases, MSI-H was associated with exceptionally high tumor mutational burden (37.4 versus 8.5 muts/Mb, p < 0.0001), MMR mutational signatures (43% versus 0%, p < 0.0001), and somatic biallelic alterations in MLH1 (52% versus 0%, p < 0.0001). Loss of MLH1 and PMS2 expression by immunohistochemistry was found in MLH1 altered and wild-type cases. Similarly, the majority of patients with MSI-H SCLC had evidence of MLH1 inactivation, including two with MLH1 promoter hypermethylation. A single patient with NSCLC with a somatic MSH2 mutation had Lynch syndrome as confirmed by the presence of a germline MSH2 mutation. Among patients with advanced MSI-H lung cancers treated with ICIs, durable clinical benefit was observed in three of eight patients with NSCLC and two of two patients with SCLC. In NSCLC, STK11, KEAP1, and JAK1 were mutated in nonresponders but wild type in responders. CONCLUSIONS We present a comprehensive clinicogenomic landscape of MSI-H lung cancers and reveal that MSI-H defines a rare subset of lung cancers associated with smoking, high tumor mutational burden, and MLH1 inactivation. Although durable clinical benefit to ICI was observed in some patients, the broad range of responses suggests that clinical activity may be modulated by co-mutational landscapes.
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Affiliation(s)
- Soo-Ryum Yang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Erika Gedvilaite
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ryan Ptashkin
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jason Chang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - John Ziegler
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Douglas A Mata
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Liliana B Villafania
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Khedoudja Nafa
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jaclyn F Hechtman
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ryma Benayed
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ahmet Zehir
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jamal Benhamida
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria E Arcila
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Diana Mandelker
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Charles M Rudin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Paul K Paik
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alexander Drilon
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Adam J Schoenfeld
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
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4
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Ptashkin RN, Ewalt MD, Jayakumaran G, Kiecka I, Bowman AS, Yao J, Casanova J, Lin YTD, Petrova-Drus K, Mohanty AS, Bacares R, Benhamida J, Rana S, Razumova A, Vanderbilt C, Balakrishnan Rema A, Rijo I, Son-Garcia J, de Bruijn I, Zhu M, Lachhander S, Wang W, Haque MS, Seshan VE, Wang J, Liu Y, Nafa K, Borsu L, Zhang Y, Aypar U, Suehnholz SP, Chakravarty D, Park JH, Abdel-Wahab O, Mato AR, Xiao W, Roshal M, Yabe M, Batlevi CL, Giralt S, Salles G, Rampal R, Tallman M, Stein EM, Younes A, Levine RL, Perales MA, van den Brink MRM, Dogan A, Ladanyi M, Berger MF, Brannon AR, Benayed R, Zehir A, Arcila ME. Enhanced clinical assessment of hematologic malignancies through routine paired tumor and normal sequencing. Nat Commun 2023; 14:6895. [PMID: 37898613 PMCID: PMC10613284 DOI: 10.1038/s41467-023-42585-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 10/16/2023] [Indexed: 10/30/2023] Open
Abstract
Genomic profiling of hematologic malignancies has augmented our understanding of variants that contribute to disease pathogenesis and supported development of prognostic models that inform disease management in the clinic. Tumor only sequencing assays are limited in their ability to identify definitive somatic variants, which can lead to ambiguity in clinical reporting and patient management. Here, we describe the MSK-IMPACT Heme cohort, a comprehensive data set of somatic alterations from paired tumor and normal DNA using a hybridization capture-based next generation sequencing platform. We highlight patterns of mutations, copy number alterations, and mutation signatures in a broad set of myeloid and lymphoid neoplasms. We also demonstrate the power of appropriate matching to make definitive somatic calls, including in patients who have undergone allogeneic stem cell transplant. We expect that this resource will further spur research into the pathobiology and clinical utility of clinical sequencing for patients with hematologic neoplasms.
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Affiliation(s)
- Ryan N Ptashkin
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- C2i Genomics, New York, NY, USA
| | - Mark D Ewalt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Gowtham Jayakumaran
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Guardant Health, Palo Alto, CA, USA
| | - Iwona Kiecka
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anita S Bowman
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - JinJuan Yao
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jacklyn Casanova
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yun-Te David Lin
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kseniya Petrova-Drus
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Abhinita S Mohanty
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ruben Bacares
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jamal Benhamida
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Satshil Rana
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anna Razumova
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chad Vanderbilt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anoop Balakrishnan Rema
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ivelise Rijo
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Julie Son-Garcia
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ino de Bruijn
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Menglei Zhu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sean Lachhander
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wei Wang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mohammad S Haque
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Venkatraman E Seshan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jiajing Wang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ying Liu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Khedoudja Nafa
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Laetitia Borsu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yanming Zhang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Umut Aypar
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sarah P Suehnholz
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Debyani Chakravarty
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jae H Park
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Omar Abdel-Wahab
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anthony R Mato
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wenbin Xiao
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mikhail Roshal
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mariko Yabe
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Connie Lee Batlevi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sergio Giralt
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gilles Salles
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Raajit Rampal
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Martin Tallman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
| | - Eytan M Stein
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anas Younes
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Oncology R&D, AstraZeneca, New York, NY, USA
| | - Ross L Levine
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Miguel-Angel Perales
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Marcel R M van den Brink
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ahmet Dogan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc Ladanyi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael F Berger
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - A Rose Brannon
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ryma Benayed
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Oncology R&D, AstraZeneca, New York, NY, USA
| | - Ahmet Zehir
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Oncology R&D, AstraZeneca, New York, NY, USA.
| | - Maria E Arcila
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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5
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Franch-Expósito S, Mehine M, Ptashkin RN, Bolton KL, Bandlamudi C, Srinivasan P, Zhang L, Goodell MA, Gedvilaite E, Menghrajani K, Sánchez-Vela P, Mandelker D, Comen E, Norton L, Benayed R, Gao T, Papaemmanuil E, Taylor B, Levine R, Offit K, Stadler Z, Berger MF, Zehir A. Associations Between Cancer Predisposition Mutations and Clonal Hematopoiesis in Patients With Solid Tumors. JCO Precis Oncol 2023; 7:e2300070. [PMID: 37561983 PMCID: PMC10581611 DOI: 10.1200/po.23.00070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/31/2023] [Accepted: 07/05/2023] [Indexed: 08/12/2023] Open
Abstract
PURPOSE Clonal hematopoiesis (CH), the expansion of clones in the hematopoietic system, has been linked to different internal and external features such as aging, genetic ancestry, smoking, and oncologic treatment. However, the interplay between mutations in known cancer predisposition genes and CH has not been thoroughly examined in patients with solid tumors. METHODS We used prospective tumor-blood paired sequencing data from 46,906 patients who underwent Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT) testing to interrogate the associations between CH and rare pathogenic or likely pathogenic (P/LP) germline variants. RESULTS We observed an enrichment of CH-positive patients among those carrying P/LP germline mutations and identified a significant association between P/LP germline variants in ATM and CH. Germline and CH comutation patterns in ATM, TP53, and CHEK2 suggested biallelic inactivation as a potential mediator of clonal expansion. Moreover, we observed that CH-PPM1D mutations, similar to somatic tumor-associated PPM1D mutations, were depleted in patients with P/LP germline mutations in the DNA damage response (DDR) genes ATM, CHEK2, and TP53. Patients with solid tumors and harboring P/LP germline mutations, CH mutations, and mosaicism chromosomal alterations might be at an increased risk of developing secondary leukemia while germline variants in TP53 were identified as an independent risk factor (hazard ratio, 36; P < .001) for secondary leukemias. CONCLUSION Our results suggest a close relationship between inherited variants and CH mutations within the DDR genes in patients with solid tumors. Associations identified in this study might translate into enhanced clinical surveillance for CH and associated comorbidities in patients with cancer harboring these germline mutations.
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Affiliation(s)
- Sebastià Franch-Expósito
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Miika Mehine
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ryan N. Ptashkin
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- C2i Genomics, New York, NY
| | - Kelly L. Bolton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Chaitanya Bandlamudi
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Preethi Srinivasan
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Natera Inc, San Carlos, CA
| | - Linda Zhang
- Department of Molecular and Cellular Biology, Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX
| | - Margaret A. Goodell
- Department of Molecular and Cellular Biology, Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX
| | - Erika Gedvilaite
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kamal Menghrajani
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Pablo Sánchez-Vela
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Diana Mandelker
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Elizabeth Comen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Larry Norton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ryma Benayed
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Precision Medicine and Biosamples, AstraZeneca, New York, NY
| | - Teng Gao
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Elli Papaemmanuil
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Barry Taylor
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ross Levine
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Zsofia Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael F. Berger
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Precision Medicine and Biosamples, AstraZeneca, New York, NY
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6
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Nykaza IR, Febres-Aldana CA, Lin ST, Benayed R, Mullaney K, Cocco E, Iasonos A, Ladanyi M, Drilon AE, Murciano-Goroff YR. Abstract 3931: BRD4, BRD3, NSD3, and ZNF532 fusions in histologies beyond NUT carcinomas: Investigation of a large pan-cancer cohort. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-3931] [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: 04/07/2023]
Abstract
Abstract
Background: NUT rearrangements drive NUT carcinomas (NCs), which are rare, poorly differentiated tumors with a survival from diagnosis of ~6-7 months. Common NUT fusion partners (NCFPs) include BRD4, BRD3, NSD3, and ZNF532, which are associated with epigenetic changes leading to tumor growth. Recent clinical trials have aimed to address NCs, but little is known about fusions involving NCFPs in other histologies. We characterized NCFPs in a large, pan-cancer cohort.
Methods: The MSK-IMPACT (DNA sequencing; n=71,423) and MSK-Fusion (RNA sequencing; n=10,897) clinical cohorts were mined to identify patients (pts) with all forms of structural variants (SVs) involving NCFPs, detected between April, 2015 and June, 2022. The targeted NGS panels included BRD4 and NSD3 only; detection of BRD3 and ZNF532 SVs was possible for fusions with a partner present on either panel. SVs were manually reviewed to identify in-frame fusions with oncogenic potential if critical domains present in NC fusions were conserved. Pts were followed through July 2022 and manual chart review enabled assessment of treatment history and clinical outcomes.
Results: SVs involving NCFP genes were detected in 182 (BRD4=110, NSD3=61, BRD3=8 and ZNF532=3) pts (0.002%). Putative NCFP fusions not involving any of the NUT gene family members comprised a total of 20 fusions with likely oncogenic potential including 11 with BRD4 (55%), 5 with NSD3 (25%), 3 with ZNF532 (15%), and 1 with BRD3 (5%). BRD4::NOTCH3 and ZNF532::MALT1 were the most enriched fusions, present in 3 samples each. The most common histologies were breast (3 ductal; 1 lobular), lung (2 squamous cell carcinoma, 1 adenocarcinoma and 1 mixed histology), and colon and esophageal adenocarcinoma (2 samples each). Median age at diagnosis was 62. 11 (55%) pts were female and 9 (45%) were male. 13 (65%) pts ultimately were diagnosed with stage IV disease and had a median overall survival from stage IV diagnosis of 2.5 years (95% CI: 1.41, NR). DNA sequencing in 19/20 tumors revealed a mean tumor mutational burden (TMB) of 5.0 mut/Mb including 15 with low TMB (<10) and 3 with high TMB (>10). No tumor showed microsatellite instability (MSI-high). TP53 mutations were the most common co-alteration, found in 11 (58%) cases. 18/20 pts received systemic therapy; 18 (90%) received cytotoxic chemotherapy and/or mAb therapy, including 13 (65%) who received a platinum. 8 pts (40%) received immunotherapy (IO), and 4 (20%) received small molecule inhibitors. No pts received BET inhibitors. Among pts who received IO, median time to treatment discontinuation was 64 days (95% CI: 20, NR).
Conclusion: Tumor sequencing from a large cohort reveals potential oncogenic fusions involving BRD4, BRD3, NSD3, and ZNF532 across multiple histologies. Further biological characterization of their oncogenicity and potential targetability is warranted.
Citation Format: Ian R. Nykaza, Christopher A. Febres-Aldana, Sabrina T. Lin, Ryma Benayed, Kerry Mullaney, Emiliano Cocco, Alexia Iasonos, Marc Ladanyi, Alexander E. Drilon, Yonina R. Murciano-Goroff. BRD4, BRD3, NSD3, and ZNF532 fusions in histologies beyond NUT carcinomas: Investigation of a large pan-cancer cohort. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3931.
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Affiliation(s)
| | | | | | - Ryma Benayed
- 2Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Emiliano Cocco
- 3University of Miami Miller School of Medicine, Miami, FL
| | | | - Marc Ladanyi
- 2Memorial Sloan Kettering Cancer Center, New York, NY
| | - Alexander E. Drilon
- 4Weill Cornell Medical College and Memorial Sloan Kettering Cancer Center, New York, NY
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Abramson DH, Mandelker DL, Brannon AR, Dunkel IJ, Benayed R, Berger MF, Arcila ME, Ladanyi M, Friedman DN, Jayakumaran G, Diosdado MS, Robbins MA, Haggag-Lindgren D, Shukla N, Walsh MF, Kothari P, Tsui DWY, Francis JH. Mutant-RB1 circulating tumor DNA in the blood of unilateral retinoblastoma patients: What happens during enucleation surgery: A pilot study. PLoS One 2023; 18:e0271505. [PMID: 36735656 PMCID: PMC9897525 DOI: 10.1371/journal.pone.0271505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/04/2022] [Indexed: 02/04/2023] Open
Abstract
Cell free DNA (cfDNA) and circulating tumor cell free DNA (ctDNA) from blood (plasma) are increasingly being used in oncology for diagnosis, monitoring response, identifying cancer causing mutations and detecting recurrences. Circulating tumor RB1 DNA (ctDNA) is found in the blood (plasma) of retinoblastoma patients at diagnosis before instituting treatment (naïve). We investigated ctDNA in naïve unilateral patients before enucleation and during enucleation (6 patients/ 8 mutations with specimens collected 5-40 minutes from severing the optic nerve) In our cohort, following transection the optic nerve, ctDNA RB1 VAF was measurably lower than pre-enucleation levels within five minutes, 50% less within 15 minutes and 90% less by 40 minutes.
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Affiliation(s)
- David H. Abramson
- Department of Surgery, Ophthalmic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Department of Ophthalmology, Weill Cornell Medical Center, New York, New York, United States of America
- * E-mail:
| | - Diana L. Mandelker
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - A. Rose Brannon
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Ira J. Dunkel
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Department of Pediatrics, Weill Cornell Medical Center, New York, New York, United States of America
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Michael F. Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Maria E. Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Danielle Novetsky Friedman
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Gowtham Jayakumaran
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Monica S. Diosdado
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Melissa A. Robbins
- Department of Surgery, Ophthalmic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Dianna Haggag-Lindgren
- Department of Surgery, Ophthalmic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Neerav Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Michael F. Walsh
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Prachi Kothari
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Dana W. Y. Tsui
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, United States of America
| | - Jasmine H. Francis
- Department of Surgery, Ophthalmic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Department of Ophthalmology, Weill Cornell Medical Center, New York, New York, United States of America
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8
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Giraldo NA, Drill E, Satravada BA, Dika IE, Brannon AR, Dermawan J, Mohanty A, Ozcan K, Chakravarty D, Benayed R, Vakiani E, Abou-Alfa GK, Kundra R, Schultz N, Li BT, Berger MF, Harding JJ, Ladanyi M, O’Reilly EM, Jarnagin W, Vanderbilt C, Basturk O, Arcila ME. Comprehensive Molecular Characterization of Gallbladder Carcinoma and Potential Targets for Intervention. Clin Cancer Res 2022; 28:5359-5367. [PMID: 36228155 PMCID: PMC9772093 DOI: 10.1158/1078-0432.ccr-22-1954] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/04/2022] [Accepted: 10/11/2022] [Indexed: 01/24/2023]
Abstract
PURPOSE Gallbladder carcinoma (GBC) is an uncommon and aggressive disease, which remains poorly defined at a molecular level. Here, we aimed to characterize the molecular landscape of GBC and identify markers with potential prognostic and therapeutic implications. EXPERIMENTAL DESIGN GBC samples were analyzed using the MSK-IMPACT (Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets) platform (targeted NGS assay that analyzes 505 cancer-associated genes). Variants with therapeutic implications were identified using OncoKB database. The associations between recurrent genetic alterations and clinicopathologic characteristics (Fisher exact tests) or overall survival (univariate Cox regression) were evaluated. P values were adjusted for multiple testing. RESULTS Overall, 244 samples (57% primary tumors and 43% metastases) from 233 patients were studied (85% adenocarcinomas, 10% carcinomas with squamous differentiation, and 5% neuroendocrine carcinomas). The most common oncogenic molecular alterations appeared in the cell cycle (TP53 63% and CDKN2A 21%) and RTK_RAS pathways (ERBB2 15% and KRAS 11%). No recurrent structural variants were identified. There were no differences in the molecular landscape of primary and metastasis samples. Variants in SMAD4 and STK11 independently associated with reduced survival in patients with metastatic disease. Alterations considered clinically actionable in GBC or other solid tumor types (e.g., NTRK1 fusions or oncogenic variants in ERBB2, PIK3CA, or BRCA1/2) were identified in 35% of patients; 18% of patients with metastatic disease were treated off-label or enrolled in a clinical trial based on molecular findings. CONCLUSIONS GBC is a genetically diverse malignancy. This large-scale genomic analysis revealed alterations with potential prognostic and therapeutic implications and provides guidance for the development of targeted therapies.
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Affiliation(s)
- Nicolas A. Giraldo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Esther Drill
- Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Baby A Satravada
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Imane El Dika
- Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Weill Medical College at Cornell University, 1275 York Avenue, New York, NY, 10065, USA
| | - A. Rose Brannon
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Josephine Dermawan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Abhinita Mohanty
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Kerem Ozcan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Debyani Chakravarty
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Efsevia Vakiani
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Ghassan K. Abou-Alfa
- Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Weill Medical College at Cornell University, 1275 York Avenue, New York, NY, 10065, USA
| | - Ritika Kundra
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Nikolaus Schultz
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Bob T. Li
- Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Weill Medical College at Cornell University, 1275 York Avenue, New York, NY, 10065, USA
| | - Michael F. Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - James J. Harding
- Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Weill Medical College at Cornell University, 1275 York Avenue, New York, NY, 10065, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Eileen M. O’Reilly
- Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Weill Medical College at Cornell University, 1275 York Avenue, New York, NY, 10065, USA
| | - William Jarnagin
- Surgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Weill Medical College at Cornell University, 1275 York Avenue, New York, NY, 10065, USA
| | - Chad Vanderbilt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Olca Basturk
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Weill Medical College at Cornell University, 1275 York Avenue, New York, NY, 10065, USA
| | - Maria E. Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Weill Medical College at Cornell University, 1275 York Avenue, New York, NY, 10065, USA
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9
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Van Egeren D, Kohli K, Warner JL, Bedard PL, Riely G, Lepisto E, Schrag D, LeNoue-Newton M, Catalano P, Kehl KL, Michor F, Fiandalo M, Foti M, Khotskaya Y, Lee J, Peters N, Sweeney S, Abraham J, Brenton JD, Caldas C, Doherty G, Nimmervoll B, Pinilla K, Martin JE, Rueda OM, Sammut SJ, Silva D, Cao K, Heath AP, Li M, Lilly J, MacFarland S, Maris JM, Mason JL, Morgan AM, Resnick A, Welsh M, Zhu Y, Johnson B, Li Y, Sholl L, Beaudoin R, Biswas R, Cerami E, Cushing O, Dand D, Ducar M, Gusev A, Hahn WC, Haigis K, Hassett M, Janeway KA, Jänne P, Jawale A, Johnson J, Kehl KL, Kumari P, Laucks V, Lepisto E, Lindeman N, Lindsay J, Lueders A, Macconaill L, Manam M, Mazor T, Miller D, Newcomb A, Orechia J, Ovalle A, Postle A, Quinn D, Reardon B, Rollins B, Shivdasani P, Tramontano A, Van Allen E, Van Nostrand SC, Bell J, Datto MB, Green M, Hubbard C, McCall SJ, Mettu NB, Strickler JH, Andre F, Besse B, Deloger M, Dogan S, Italiano A, Loriot Y, Ludovic L, Michels S, Scoazec J, Tran-Dien A, Vassal G, Freeman CE, Hsiao SJ, Ingham M, Pang J, Rabadan R, Roman LC, Carvajal R, DuBois R, Arcila ME, Benayed R, Berger MF, Bhuiya M, Brannon AR, Brown S, Chakravarty D, Chu C, de Bruijn I, Galle J, Gao J, Gardos S, Gross B, Kundra R, Kung AL, Ladanyi M, Lavery JA, Li X, Lisman A, Mastrogiacomo B, McCarthy C, Nichols C, Ochoa A, Panageas KS, Philip J, Pillai S, Riely GJ, Rizvi H, Rudolph J, Sawyers CL, Schrag D, Schultz N, Schwartz J, Sheridan R, Solit D, Wang A, Wilson M, Zehir A, Zhang H, Zhao G, Ahmed L, Bedard PL, Bruce JP, Chow H, Cooke S, Del Rossi S, Felicen S, Hakgor S, Jagannathan P, Kamel-Reid S, Krishna G, Leighl N, Lu Z, Nguyen A, Oldfield L, Plagianakos D, Pugh TJ, Rizvi A, Sabatini P, Shah E, Singaravelan N, Siu L, Srivastava G, Stickle N, Stockley T, Tang M, Virtaenen C, Watt S, Yu C, Bernard B, Bifulco C, Cramer JL, Lee S, Piening B, Reynolds S, Slagel J, Tittel P, Urba W, VanCampen J, Weerasinghe R, Acebedo A, Guinney J, Guo X, Hunter-Zinck H, Yu T, Dang K, Anagnostou V, Baras A, Brahmer J, Gocke C, Scharpf RB, Tao J, Velculescu VE, Alexander S, Bailey N, Gold P, Bierkens M, de Graaf J, Hudeček J, Meijer GA, Monkhorst K, Samsom KG, Sanders J, Sonke G, ten Hoeve J, van de Velde T, van den Berg J, Voest E, Steinhardt G, Kadri S, Pankhuri W, Wang P, Segal J, Moung C, Espinosa-Mendez C, Martell HJ, Onodera C, Quintanar Alfaro A, Sweet-Cordero EA, Talevich E, Turski M, Van’t Veer L, Wren A, Aguilar S, Dienstmann R, Mancuso F, Nuciforo P, Tabernero J, Viaplana C, Vivancos A, Anderson I, Chaugai S, Coco J, Fabbri D, Johnson D, Jones L, Li X, Lovly C, Mishra S, Mittendorf K, Wen L, Yang YJ, Ye C, Holt M, LeNoue-Newton ML, Micheel CM, Park BH, Rubinstein SM, Stricker T, Wang L, Warner J, Guan M, Jin G, Liu L, Topaloglu U, Urtis C, Zhang W, D’Eletto M, Hutchison S, Longtine J, Walther Z. Genomic analysis of early-stage lung cancer reveals a role for TP53 mutations in distant metastasis. Sci Rep 2022; 12:19055. [PMID: 36351964 PMCID: PMC9646734 DOI: 10.1038/s41598-022-21448-1] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 09/27/2022] [Indexed: 11/10/2022] Open
Abstract
Patients with non-small cell lung cancer (NSCLC) who have distant metastases have a poor prognosis. To determine which genomic factors of the primary tumor are associated with metastasis, we analyzed data from 759 patients originally diagnosed with stage I-III NSCLC as part of the AACR Project GENIE Biopharma Collaborative consortium. We found that TP53 mutations were significantly associated with the development of new distant metastases. TP53 mutations were also more prevalent in patients with a history of smoking, suggesting that these patients may be at increased risk for distant metastasis. Our results suggest that additional investigation of the optimal management of patients with early-stage NSCLC harboring TP53 mutations at diagnosis is warranted in light of their higher likelihood of developing new distant metastases.
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Affiliation(s)
- Debra Van Egeren
- grid.65499.370000 0001 2106 9910Department of Data Science, Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Systems Biology, Harvard Medical School, Boston, MA USA ,grid.2515.30000 0004 0378 8438Stem Cell Program, Boston Children’s Hospital, Boston, MA USA ,grid.5386.8000000041936877XDepartment of Medicine, Weill Cornell Medicine, New York, NY USA
| | - Khushi Kohli
- grid.65499.370000 0001 2106 9910Department of Data Science, Dana-Farber Cancer Institute, Boston, MA USA
| | - Jeremy L. Warner
- grid.152326.10000 0001 2264 7217Department of Medicine, Vanderbilt University, Nashville, TN USA ,grid.152326.10000 0001 2264 7217Department of Biomedical Informatics, Vanderbilt University, Nashville, TN USA
| | - Philippe L. Bedard
- grid.17063.330000 0001 2157 2938Department of Medicine, University of Toronto, Toronto, ON Canada
| | - Gregory Riely
- grid.51462.340000 0001 2171 9952Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Eva Lepisto
- grid.65499.370000 0001 2106 9910Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.429426.f0000 0000 9350 5788Present Address: Multiple Myeloma Research Foundation, Norwalk, CT USA
| | - Deborah Schrag
- grid.51462.340000 0001 2171 9952Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Michele LeNoue-Newton
- grid.412807.80000 0004 1936 9916Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN USA
| | - Paul Catalano
- grid.65499.370000 0001 2106 9910Department of Data Science, Dana-Farber Cancer Institute, Boston, MA USA
| | - Kenneth L. Kehl
- grid.65499.370000 0001 2106 9910Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA USA
| | - Franziska Michor
- grid.65499.370000 0001 2106 9910Department of Data Science, Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA USA ,grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.38142.3c000000041936754XDepartment of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA USA ,grid.65499.370000 0001 2106 9910The Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XThe Ludwig Center at Harvard, Boston, MA USA
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Jee J, Lebow ES, Yeh R, Das JP, Namakydoust A, Paik PK, Chaft JE, Jayakumaran G, Rose Brannon A, Benayed R, Zehir A, Donoghue M, Schultz N, Chakravarty D, Kundra R, Madupuri R, Murciano-Goroff YR, Tu HY, Xu CR, Martinez A, Wilhelm C, Galle J, Daly B, Yu HA, Offin M, Hellmann MD, Lito P, Arbour KC, Zauderer MG, Kris MG, Ng KK, Eng J, Preeshagul I, Victoria Lai W, Fiore JJ, Iqbal A, Molena D, Rocco G, Park BJ, Lim LP, Li M, Tong-Li C, De Silva M, Chan DL, Diakos CI, Itchins M, Clarke S, Pavlakis N, Lee A, Rekhtman N, Chang J, Travis WD, Riely GJ, Solit DB, Gonen M, Rusch VW, Rimner A, Gomez D, Drilon A, Scher HI, Shah SP, Berger MF, Arcila ME, Ladanyi M, Levine RL, Shen R, Razavi P, Reis-Filho JS, Jones DR, Rudin CM, Isbell JM, Li BT. Overall survival with circulating tumor DNA-guided therapy in advanced non-small-cell lung cancer. Nat Med 2022; 28:2353-2363. [PMID: 36357680 PMCID: PMC10338177 DOI: 10.1038/s41591-022-02047-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 09/16/2022] [Indexed: 11/12/2022]
Abstract
Circulating tumor DNA (ctDNA) sequencing guides therapy decisions but has been studied mostly in small cohorts without sufficient follow-up to determine its influence on overall survival. We prospectively followed an international cohort of 1,127 patients with non-small-cell lung cancer and ctDNA-guided therapy. ctDNA detection was associated with shorter survival (hazard ratio (HR), 2.05; 95% confidence interval (CI), 1.74-2.42; P < 0.001) independently of clinicopathologic features and metabolic tumor volume. Among the 722 (64%) patients with detectable ctDNA, 255 (23%) matched to targeted therapy by ctDNA sequencing had longer survival than those not treated with targeted therapy (HR, 0.63; 95% CI, 0.52-0.76; P < 0.001). Genomic alterations in ctDNA not detected by time-matched tissue sequencing were found in 25% of the patients. These ctDNA-only alterations disproportionately featured subclonal drivers of resistance, including RICTOR and PIK3CA alterations, and were associated with short survival. Minimally invasive ctDNA profiling can identify heterogeneous drivers not captured in tissue sequencing and expand community access to life-prolonging therapy.
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Affiliation(s)
- Justin Jee
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Emily S Lebow
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Randy Yeh
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jeeban P Das
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Paul K Paik
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Jamie E Chaft
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | | | - A Rose Brannon
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ryma Benayed
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ahmet Zehir
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mark Donoghue
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - Ritika Kundra
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - Hai-Yan Tu
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Chong-Rui Xu
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | | | - Clare Wilhelm
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jesse Galle
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bobby Daly
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Helena A Yu
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Michael Offin
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Matthew D Hellmann
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Piro Lito
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Kathryn C Arbour
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Marjorie G Zauderer
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Mark G Kris
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Kenneth K Ng
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Juliana Eng
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Isabel Preeshagul
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - W Victoria Lai
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - John J Fiore
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Afsheen Iqbal
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Daniela Molena
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Gaetano Rocco
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Bernard J Park
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Lee P Lim
- Resolution Bioscience, Agilent Technologies, Kirkland, WA, USA
| | - Mark Li
- Resolution Bioscience, Agilent Technologies, Kirkland, WA, USA
| | - Candace Tong-Li
- GenesisCare, University of Sydney, Sydney, Australia
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - David L Chan
- GenesisCare, University of Sydney, Sydney, Australia
| | | | | | | | - Nick Pavlakis
- GenesisCare, University of Sydney, Sydney, Australia
| | - Adrian Lee
- GenesisCare, University of Sydney, Sydney, Australia
| | - Natasha Rekhtman
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Jason Chang
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - William D Travis
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Gregory J Riely
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - David B Solit
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Mithat Gonen
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Valerie W Rusch
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Andreas Rimner
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Daniel Gomez
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Alexander Drilon
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Howard I Scher
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Sohrab P Shah
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Maria E Arcila
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Marc Ladanyi
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Ross L Levine
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Ronglai Shen
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pedram Razavi
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Jorge S Reis-Filho
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - David R Jones
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Charles M Rudin
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - James M Isbell
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Bob T Li
- Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Weill Cornell Medicine, Cornell University, New York, NY, USA.
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11
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Dermawan JK, Torrence D, Lee CH, Villafania L, Mullaney KA, DiNapoli S, Sukhadia P, Benayed R, Borsu L, Agaram NP, Nash GM, Dickson BC, Benhamida J, Antonescu CR. EWSR1::YY1 fusion positive peritoneal epithelioid mesothelioma harbors mesothelioma epigenetic signature: Report of 3 cases in support of an emerging entity. Genes Chromosomes Cancer 2022; 61:592-602. [PMID: 35665561 PMCID: PMC9811235 DOI: 10.1002/gcc.23074] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/26/2022] [Accepted: 05/29/2022] [Indexed: 01/07/2023] Open
Abstract
Mesothelioma is a rare, aggressive malignant neoplasm of mesothelial origin. A small subset of peritoneal mesothelioma is driven by recurrent gene fusions, mostly EWSR1/FUS::ATF1 fusions, with predilection for young adults. To date, only two cases of mesothelioma harboring EWSR1::YY1 fusions have been described. We present three additional cases of EWSR1::YY1-fused peritoneal mesotheliomas, two localized and one diffuse, all occurring in the peritoneum of middle-aged adults (2 females and 1 male), and discovered incidentally by imaging or during surgery performed for unrelated reasons. None presented with symptoms or had a known history of asbestos exposure. All three cases were cellular epithelioid neoplasms with heterogeneous architectural patterns comprising mostly solid nests and sheets with variably papillary and trabecular areas against collagenous stroma. Cytologically, the cells were monomorphic, polygonal, epithelioid cells with dense eosinophilic cytoplasm and centrally located nuclei. Overt mitotic activity or tumor necrosis was absent. All cases showed strong diffuse immunoreactivity for pancytokeratin, CK7, and nuclear WT1, patchy to negative calretinin, retained BAP1 expression, and were negative for Ber-EP4 and MOC31. RNA-sequencing confirmed in-frame gene fusion transcripts involving EWSR1 exon 7/8 and YY1 exon 2/3. By unsupervised clustering analysis, the methylation profiles of EWSR1::YY1-fused mesotheliomas clustered similarly with EWSR1/FUS::ATF1-fused mesotheliomas and conventional mesotheliomas, suggesting a mesothelioma epigenetic signature. All three patients underwent surgical resection or cytoreductive surgery of the masses. On follow-up imaging, no recurrence or progression of disease was identified. Our findings suggest that EWSR1::YY1-fusion defines a small subset of peritoneal epithelioid mesothelioma in middle-aged adults without history of asbestos exposure.
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Affiliation(s)
- Josephine K. Dermawan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dianne Torrence
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Cheng-Han Lee
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Liliana Villafania
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kerry A. Mullaney
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sara DiNapoli
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Purvil Sukhadia
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ryma Benayed
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Laetitia Borsu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Narasimhan P. Agaram
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Garrett M. Nash
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Brendan C. Dickson
- Department of Pathology and Laboratory Medicine, Sinai Health System, Toronto, Ontario, Canada
| | - Jamal Benhamida
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Cristina R. Antonescu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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12
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Elkrief A, Ogura K, Bowman AS, Koche RP, Benayed R, Mauguen A, Mattar MS, Khodos I, de Stanchina E, Meyers PA, Healey JH, Tap WD, Shukla N, Hameed M, Zehir A, Sawyers C, Bose R, Slotkin E, Ladanyi M. Abstract B023: Prospective clinical genomic profiling of ewing sarcoma: ERF and FGFR1 mutations as recurrent secondary alterations of potential biological and therapeutic relevance. Clin Cancer Res 2022. [DOI: 10.1158/1557-3265.sarcomas22-b023] [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
Background: Ewing Sarcoma (ES) is a primitive sarcoma defined by EWSR1–ETS fusions as the primary driver alteration. To expand our understanding of the genetic and molecular characterization of ES, we conducted a comprehensive analysis of clinical genomic profiling data on tumors from 113 patients using the MSK-IMPACT platform (Integrated Mutation Profiling of Actionable Cancer Targets). Methods: The dataset consisted of ES patients prospectively tested with the FDA-cleared MSK-IMPACT large panel, hybrid capture-based NGS assay. To assess the functional significance of ERF loss, we generated ES cell lines with increased expression of ERF as well as lines with knockdown of ERF. We assessed cell viability, clonogenic growth, and motility and performed transcriptomic and epigenetic analyses. Finally, we validated our findings in vivo using cell line xenografts. Results: Unlike previous ES genomic cohorts, ours included more adult patients (>18 years of age) and more patients with advanced stage at presentation. TP53, STAG2, and CDKN2A were the most common alterations and were associated with worse overall survival at 5-years. Notably, 3% had activating FGFR1 alterations (1 amplification and 2 hotspot activating kinase domain mutations). Mining data generated using a targeted RNAseq assay that includes FGFR1 based on the Archer Anchored Multiplex PCR technology, FGFR1 was highly expressed in the ES cohort (N=42). The 2 patients with activating FGFR1 mutations had relatively high expression of FGFR1. The second novel subset of patients in our cohort were defined by recurrent secondary alterations in ERF, which encodes an ETS domain transcriptional repressor, in 7% of patients (5 truncating mutations, 1 deep deletion, 2 missense mutations). ERF alterations were non-overlapping with STAG2 alterations, suggesting a potentially important biologic role in ES. As the functional significance of FGFR1 mutation in ES has been previously studied, we focused our functional studies on the role of ERF status in ES. In vitro, increased expression of ERF decreased tumor cell growth, colony formation, and motility in two ES cell lines, while ERF loss induced cellular proliferation and clonogenic growth. Transcriptomic analysis of cell lines with ERF loss revealed increased expression of genes and pathways associated with aggressive tumor biology, and epigenetic, chromatin-based studies revealed that ERF competes with EWSR1-FLI1 at ETS binding sites. Conclusion: Our study reveals a previously unexplored role of ERF loss-of-function in ES. Older age in our cohort, and a higher proportion of patients with advanced disease at presentation, could potentially explain the finding of ERF alterations which were associated with aggressive tumor biology in our preclinical studies. Our functional analyses of how ERF modulates EWSR1-FLI1 oncogenicity may open a new window into the pathobiology of ES. Moreover, our data suggest that 3% of ES patients harbor activating FGFR1 mutations, the first targetable kinase alteration in this sarcoma.
Citation Format: Arielle Elkrief, Koichi Ogura, Anita S. Bowman, Richard P. Koche, Ryma Benayed, Audrey Mauguen, Marissa S. Mattar, Inna Khodos, Elisa de Stanchina, Paul A. Meyers, John H. Healey, William D. Tap, Neerav Shukla, Meera Hameed, Ahmet Zehir, Charles Sawyers, Rohit Bose, Emily Slotkin, Marc Ladanyi. Prospective clinical genomic profiling of ewing sarcoma: ERF and FGFR1 mutations as recurrent secondary alterations of potential biological and therapeutic relevance [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr B023.
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Affiliation(s)
| | - Koichi Ogura
- 1Memorial Sloan Kettering Cancer Center, New York, NY,
| | | | | | - Ryma Benayed
- 1Memorial Sloan Kettering Cancer Center, New York, NY,
| | | | | | - Inna Khodos
- 1Memorial Sloan Kettering Cancer Center, New York, NY,
| | | | | | | | | | - Neerav Shukla
- 1Memorial Sloan Kettering Cancer Center, New York, NY,
| | - Meera Hameed
- 1Memorial Sloan Kettering Cancer Center, New York, NY,
| | - Ahmet Zehir
- 1Memorial Sloan Kettering Cancer Center, New York, NY,
| | | | - Rohit Bose
- 2University of California, San Francisco (UCSF), San Francisco, CA
| | - Emily Slotkin
- 1Memorial Sloan Kettering Cancer Center, New York, NY,
| | - Marc Ladanyi
- 1Memorial Sloan Kettering Cancer Center, New York, NY,
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13
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Dermawan JK, Vanoli F, Herviou L, Sung YS, Zhang L, Singer S, Tap WD, Benayed R, Bale TA, Benhamida JK, Dickson BC, Antonescu CR. Comprehensive genomic profiling of EWSR1/FUS::CREB translocation-associated tumors uncovers prognostically significant recurrent genetic alterations and methylation-transcriptional correlates. Mod Pathol 2022; 35:1055-1065. [PMID: 35347249 PMCID: PMC9329182 DOI: 10.1038/s41379-022-01023-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [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: 09/14/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 12/22/2022]
Abstract
To elucidate the mechanisms underlying the divergent clinicopathologic spectrum of EWSR1/FUS::CREB translocation-associated tumors, we performed a comprehensive genomic analysis of fusion transcript variants, recurrent genetic alterations (mutations, copy number alterations), gene expression, and methylation profiles across a large cohort of tumor types. The distribution of the EWSR1/FUS fusion partners-ATF1, CREB1, and CREM-and exon involvement was significantly different across different tumor types. Our targeted sequencing showed that secondary genetic events are associated with tumor type rather than fusion type. Of the 39 cases that underwent targeted NGS testing, 18 (46%) had secondary OncoKB mutations or copy number alterations (29 secondary genetic events in total), of which 15 (52%) were recurrent. Secondary recurrent, but mutually exclusive, TERT promoter and CDKN2A mutations were identified only in clear cell sarcoma (CCS) and associated with worse overall survival. CDKN2A/B homozygous deletions were recurrent in angiomatoid fibrous histiocytoma (AFH) and restricted to metastatic cases. mRNA upregulation of MITF, CDH19, PARVB, and PFKP was found in CCS, compared to AFH, and correlated with a hypomethylated profile. In contrast, S100A4 and XAF1 were differentially upregulated and hypomethylated in AFH but not CCS. Unsupervised clustering of methylation profiles revealed that CREB family translocation-associated tumors form neighboring but tight, distinct clusters. A sarcoma methylation classifier was able to accurately match 100% of CCS cases to the correct methylation class; however, it was suboptimal when applied to other histologies. In conclusion, our comprehensive genomic profiling of EWSR1/FUS::CREB translocation-associated tumors uncovered mostly histotype, rather than fusion-type associated correlations in transcript variants, prognostically significant secondary genetic alterations, and gene expression and methylation patterns.
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Affiliation(s)
| | - Fabio Vanoli
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Laurie Herviou
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yun-Shao Sung
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lei Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samuel Singer
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - William D. Tap
- Department of Medicine, Sarcoma Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tejus A. Bale
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jamal K. Benhamida
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Brendan C. Dickson
- Department of Pathology and Laboratory Medicine, Sinai Health System, Toronto, Ontario, Canada
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14
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Ogura K, Elkrief A, Bowman AS, Koche RP, de Stanchina E, Benayed R, Mauguen A, Mattar MS, Khodos I, Meyers PA, Healey JH, Tap WD, Hameed M, Zehir A, Shukla N, Sawyers C, Bose R, Slotkin E, Ladanyi M. Prospective Clinical Genomic Profiling of Ewing Sarcoma: ERF and FGFR1 Mutations as Recurrent Secondary Alterations of Potential Biologic and Therapeutic Relevance. JCO Precis Oncol 2022; 6:e2200048. [PMID: 35952322 PMCID: PMC9384944 DOI: 10.1200/po.22.00048] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ewing sarcoma (ES) is a primitive sarcoma defined by EWSR1-ETS fusions as the primary driver alteration. To better define the landscape of cooperating secondary genetic alterations in ES, we analyzed clinical genomic profiling data of 113 patients with ES, a cohort including more adult patients (> 18 years) and more patients with advanced stage at presentation than previous genomic cohorts.
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Affiliation(s)
- Koichi Ogura
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Arielle Elkrief
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Anita S Bowman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Elisa de Stanchina
- Anti-tumor Assessment Core Facility, Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY.,AstraZeneca Pharmaceuticals, Wilmington, DE
| | - Audrey Mauguen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Marissa S Mattar
- Anti-tumor Assessment Core Facility, Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Inna Khodos
- Anti-tumor Assessment Core Facility, Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Paul A Meyers
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - John H Healey
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Surgery, Orthopaedic Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - William D Tap
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Meera Hameed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY.,AstraZeneca Pharmaceuticals, Wilmington, DE
| | - Neerav Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Charles Sawyers
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY.,HHMI, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Rohit Bose
- Department of Anatomy, University of California, San Francisco, San Francisco, CA.,Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA.,Department of Urology, University of California, San Francisco, San Francisco, CA.,Benioff Initiative for Prostate Cancer Research, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Emily Slotkin
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
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15
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Dessources K, Miller KM, Kertowidjojo E, Da Cruz Paula A, Zou Y, Selenica P, da Silva EM, Benayed R, Ashley CW, Abu-Rustum NR, Dogan S, Soslow RA, Hensley ML, Weigelt B, Chiang S. ESR1 hotspot mutations in endometrial stromal sarcoma with high-grade transformation and endocrine treatment. Mod Pathol 2022; 35:972-978. [PMID: 34961764 PMCID: PMC9234101 DOI: 10.1038/s41379-021-01003-5] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/30/2021] [Accepted: 12/15/2021] [Indexed: 01/13/2023]
Abstract
High-grade endometrial stromal sarcomas (HGESSs) are more aggressive and have higher rates of resistance to endocrine therapy than low-grade endometrial stromal sarcomas (LGESSs). The pathogenesis of hormonal resistance in these lesions has yet to be defined. Here we sought to histologically and genetically characterize 3 LGESSs and their recurrences that underwent histologic high-grade transformation following endocrine therapy. For this, DNA from primary tumors and select subsequent recurrences were subject to massively parallel sequencing targeting 468 cancer-related genes. Somatic mutation analyses were performed using validated bioinformatics methods. In addition, RNA from each case was evaluated for the presence of gene fusions using targeted RNA-sequencing. All patients initially presented with LGESS, developed HGESS recurrences, and received at least 2 lines of hormonal suppressive therapy. Gene fusions classically described as associated with LGESS were identified in all 3 cases, including JAZF1-PHF1, EPC1-PHF1 and JAZF1-SUZ12 fusions for Cases 1, 2 and 3, respectively. Targeted sequencing analysis revealed that none of the primary LGESS, however the HGESS recurrences of Cases 1 and 3, and the LGESS and HGESS recurrences of Case 2 post endocrine treatment harbored ESR1 p.Y537S hotspot mutations. These ESR1 ligand-binding domain mutations have been found as a mechanism of acquired endocrine resistance in breast cancer. Also, a reduction in estrogen receptor (ER) expression was observed in recurrences. Our findings suggest that the ESR1 p.Y537S hotspot mutation in LGESS with histologic high-grade transformation may be associated with endocrine resistance in these lesions. Furthermore, our data suggest that genetic analyses may be performed in recurrent LGESS following hormonal therapy, development of high-grade morphology, and/or altered/diminished ER expression.
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Affiliation(s)
- Kimberly Dessources
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kathryn M Miller
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Arnaud Da Cruz Paula
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Youran Zou
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Edaise M da Silva
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Charles W Ashley
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nadeem R Abu-Rustum
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Snjezana Dogan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert A Soslow
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Martee L Hensley
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Sarah Chiang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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Kotecha RR, Gedvilaite E, Ptashkin R, Knezevic A, Murray S, Johnson I, Shapnik N, Feldman DR, Carlo MI, Shah NJ, Dunigan M, Huberman K, Benayed R, Zehir A, Berger MF, Ladanyi M, Tsui DWY, Motzer RJ, Lee CH, Voss MH. Matched Molecular Profiling of Cell-Free DNA and Tumor Tissue in Patients With Advanced Clear Cell Renal Cell Carcinoma. JCO Precis Oncol 2022; 6:e2200012. [PMID: 35797508 PMCID: PMC9489165 DOI: 10.1200/po.22.00012] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE The clinical utility of cell-free DNA (cfDNA) as a biomarker for advanced clear cell renal cell carcinoma (ccRCC) remains unclear. We evaluated the validity of cfDNA-based genomic profiling in a large cohort of patients with ccRCC with matched next-generation sequencing (NGS) from primary tumor tissues. MATERIALS AND METHODS We performed paired NGS of tumor DNA and plasma cfDNA using the MSK-IMPACT platform in 110 patients with metastatic ccRCC. Tissues were profiled for variants and copy number alterations with germline comparison. Manual cross-genotyping between cfDNA and tumor tissue was performed. Deep sequencing with a higher sensitivity platform, MSK-ACCESS, was performed on a subset of cfDNA samples. Clinical data and radiographic tumor volumes were assessed to correlate cfDNA yield with treatment response and disease burden. RESULTS Tumor tissue MSK-IMPACT testing identified 582 genomic alterations (GAs) across the cohort. Using standard thresholds for de novo variant calling in cfDNA, only 24 GAs were found by MSK-IMPACT in cfDNA in 7 of 110 patients (6%). With manual cross-genotyping, 210 GAs were detectable below thresholds in 74 patients (67%). Intrapatient concordance with tumor tissue was limited, including VHL (31.6%), PBRM1 (24.1%), and TP53 (52.9%). cfDNA profiling did not identify 3p loss because of low tumor fractions. Tumor volume was associated with cfDNA allele frequency, and VHL concordance was superior for patients with greater disease burden. CONCLUSION cfDNA-based NGS profiling yielded low detection rates in this metastatic ccRCC cohort. Concordance with tumor profiling was low, even for truncal mutations such as VHL, and some findings in peripheral blood may represent clonal hematopoiesis. Routine cfDNA panel testing is not supported, and its application in biomarker efforts must account for these limitations.
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Affiliation(s)
- Ritesh R Kotecha
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Erika Gedvilaite
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ryan Ptashkin
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Andrea Knezevic
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Samuel Murray
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ian Johnson
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Natalie Shapnik
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Darren R Feldman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Maria I Carlo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Neil J Shah
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Marisa Dunigan
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kety Huberman
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael F Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Dana W Y Tsui
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Robert J Motzer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Chung-Han Lee
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Martin H Voss
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
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17
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DiNapoli SE, Spence C, Gedvilaite E, Bowman A, Diosdado M, Razumova A, Tsui D, Salles GA, Batlevi C, von Keudell G, Ptashkin R, Zehir A, Berger M, Brannon AR, Benayed R, Arcila M. Abstract 56: MSK-ACCESS Heme: A cell-free DNA next-generation sequencing assay to identify somatic alterations in patients with lymphoma. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-56] [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
Next-generation sequencing of cell-free DNA (cfDNA) can be used to noninvasively assess and monitor patients with lymphoma. Here, we describe the preliminary validation of MSK-ACCESS Heme (Memorial Sloan Kettering-Analysis of Circulating cfDNA to Examine Somatic Status), a cfDNA assay that employs unique molecular indexing and ultra-deep sequencing to detect somatic alterations in 117 genes related to hematologic malignancies. To our knowledge, this is the first report of a clinical-grade cfDNA assay developed specifically for hematologic malignancies.
Overall assay performance was assessed using 53 validation samples (26 normal samples and 27 cfDNA samples with somatic variants). Initial accuracy studies showed excellent correlation with the reference next-generation sequencing method (MSK-ACCESS Solid), detecting 32/32 (100%) of expected variants with a variant allele frequency over 1%. The limit of detection was assessed using standard samples, with detection of variants down to 0.5% variant allele frequency. Results were highly concordant in both inter- and intra-assay reproducibility studies.
Overall, these data indicate that MSK-ACCESS Heme is a robust cfDNA-based assay that can be used to detect variants at low frequency with high reproducibility. Future work sequencing additional samples will be performed to further assess the performance of the panel.
Citation Format: Sara E. DiNapoli, Coleman Spence, Erika Gedvilaite, Anita Bowman, Monica Diosdado, Anna Razumova, Dana Tsui, Gilles A. Salles, Connie Batlevi, Gottfried von Keudell, Ryan Ptashkin, Ahmet Zehir, Michael Berger, A Rose Brannon, Ryma Benayed, Maria Arcila. MSK-ACCESS Heme: A cell-free DNA next-generation sequencing assay to identify somatic alterations in patients with lymphoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 56.
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Affiliation(s)
| | | | | | - Anita Bowman
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Anna Razumova
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Dana Tsui
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | - Ryan Ptashkin
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Ryma Benayed
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Maria Arcila
- 1Memorial Sloan Kettering Cancer Center, New York, NY
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Bandlamudi C, Chatila WK, Smith SA, Nandakumar S, Bielski C, Nguyen B, Walch HS, Kreitzer CK, Arora KS, Ngoc TT, Mehine M, Ostrovnaya I, de Bruijn I, Woo HJ, Kundra R, Fong CJ, Rana S, Zhao G, Zhang M, Zucker MR, Zhang H, Ptashkin R, Brannon R, Reznik E, Gao J, Arcila ME, Benayed R, Chakravarty D, Solit D, Donoghue MT, Ladanyi M, Schultz ND, Berger MF, Zehir A. Abstract 3628: Comprehensive identification of lineage associated cancer genes in 122 histologies. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3628] [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
Although the majority of cancer genes show a high degree of specificity for certain lineages, genomic profiling of cancer patients routinely identify alterations in genes that are atypical to the presented cancer type but are canonical drivers in a different lineage. It is often unclear if these atypical drivers arose early in tumorigenesis or were acquired during progression. A complete understanding of lineage associated genes (LAGs) will enable better interpretation of the molecular etiology of each diagnosed tumor.
Here, we used a cohort of 38,912 patients across 122 cancer histologies (each with 50 or more patients) profiled for somatic alterations (mutations, copy number alterations and gene fusions) using the MSK-IMPACT assay. Tumors with TMB > 15 were already excluded. All alterations were classified as drivers using OncoKB. Allele-specific copy number calls were assessed using FACETS.
Overall, 95% of patients harbored at least one oncogenic alteration, with a median of 4 drivers per tumor. We observed widespread prevalence of drivers across lineages with each gene mutated in a median of 36 different lineages. Conversely, a median of 103 genes were mutated at least once in each lineage. Hypothesizing that cancer genes are influenced by cell of origin, we sought to identify lineages harboring significantly higher rates of drivers in a given gene compared to its pancancer driver rate. We identified 1781 significant (adjusted P < 0.05) gene and lineage associations, and an additional 109 involving genes mutated at >10% in the respective lineages but which did not reach significance were also included. Lineage-agnostic genes such as TP53 and CDKN2A were associated with a broad spectrum of lineages (90 and 55, respectively). However, overall, each gene we profiled was found to be associated with a median of 3 distinct lineages. For example, while BRAF drivers are found in nearly all histologies (n=91), it is enriched for drivers in only 8 lineages: melanoma (acral and cutaneous), thyroid (poorly differentiated, anaplastic and papillary) and bowel (mucinous adenocarc. of colon/rectum, colon adenocarc. and neuroendocrine carc. of colon/rectum). In all, nearly a third of all drivers were observed in non-associated lineages.
We next compared the somatic properties of drivers among genes in associated lineages vs. the same genes in non-associated lineages. We observed that mutations in LAGs were more often clonal (83% vs. 73%, associated vs. non-associated, P = 0) and showed enrichment for mutant allele imbalance in oncogenes (40% vs. 23%, P = 2e-111) and biallelic inactivation in tumor suppressor LAGs (71% vs. 58%, P = 4e-130). Furthermore, 93% of all OncoKB Level 1/2/3A actionable alterations, which are classified based on their histology, were in LAGs. In conclusion, our findings enable classification of drivers that are relevant for lineage-specific malignant transformation and advance our understanding of tumor biology.
Citation Format: Chaitanya Bandlamudi, Walid K. Chatila, Shaleigh A. Smith, Subhiksha Nandakumar, Craig Bielski, Bastien Nguyen, Henry S. Walch, Christoph K. Kreitzer, Kanika S. Arora, Tran Thinh Ngoc, Miika Mehine, Irina Ostrovnaya, Ino de Bruijn, Hyung Jun Woo, Ritika Kundra, Christopher J. Fong, Satshil Rana, Gaofei Zhao, Mingxuan Zhang, Mark R. Zucker, Hongxin Zhang, Ryan Ptashkin, Rose Brannon, Eduard Reznik, JianJiong Gao, Maria E. Arcila, Ryma Benayed, Debyani Chakravarty, David Solit, Mark T. Donoghue, Marc Ladanyi, Nikolaus D. Schultz, Michael F. Berger, Ahmet Zehir. Comprehensive identification of lineage associated cancer genes in 122 histologies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3628.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Miika Mehine
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Ino de Bruijn
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Hyung Jun Woo
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ritika Kundra
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Satshil Rana
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Gaofei Zhao
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Hongxin Zhang
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ryan Ptashkin
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Rose Brannon
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Eduard Reznik
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - JianJiong Gao
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Ryma Benayed
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - David Solit
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Marc Ladanyi
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Ahmet Zehir
- 1Memorial Sloan Kettering Cancer Center, New York, NY
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19
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Giraldo NA, Mohanty A, Vanderbilt C, Brannon R, Benayed R, Vakiani E, Abou-Alfa G, Harding J, Dika IE, Schultz N, Li B, Berger MF, Ladanyi M, O'Reilly E, Jarnagin W, Basturk O, Arcila M. Abstract 82: Molecular characterization of gallbladder cancer. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-82] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Gallbladder carcinomas (GBC) are rare and aggressive neoplasms. Previous studies in small GBC cohorts have suggested potential molecular alterations associated with poor prognosis, however, a comprehensive understanding of the recurrent genetic events in this cancer type is very limited. In this study, we aim to characterize in detail the recurrent molecular alterations in GBC and their association with pathologic and clinical characteristics.
Material and Methods: We studied the prevalence of somatic mutations and copy number alterations (CNA) in n=244 GBC samples (54% primary, 56% metastatic), collected from 2014 to 2021, and sequenced with the targeted NGS panel MSK-IMPACT. We assessed the correlation of the recurrent genomic variants with several pathologic (e.g., T stage, N stage, grade, histologic subtypes) and clinical characteristics (e.g., clinical stage) using Fisher's exact test. We also used Cox Proportional-Hazards modeling to assess the correlation between genetic variants and patient overall survival (OS).
Results: The most common histologic subtypes in this GCB cohort included adenocarcinomas NOS (83%), carcinomas with squamous differentiation (9%), high-grade carcinomas (4%), and carcinomas with neuroendocrine differentiation (3%). Most patients were diagnosed with stage IV (65%) and stage III (11%) disease at the time of biopsy/resection, and the mean OS survival was 29.4 months. The most commonly mutated genes were TP53 (59%), SMAD4 (21%), ARID1A (19%), PIK3CA (10%), KRAS (7%), and ERBB2 (7%). Potentially recurrent oncogenic CNAs included deep deletions in CDKN2A (14%) and CDKN2B (14%), and amplifications in MDM2 (12%), ERBB2 (10%), CCNE1 (9%), MYC (7%), and KRAS (7%). RB1, PBRM1, and CTNNB1 variants were more common in cases with neuroendocrine differentiation, whereas alterations in IKZF1 and AGO2 were enriched in cases with squamous differentiation. The most significant event associated with shorted OS was chromosome 12q13-15 amplification i.e., CDK4 p=0.03 HR=2 [95% CI 1-3.6] and MDM2 p=0.05 HR=1.6 [1-2.5], which associated with a median OS of 20 months (vs. 34 months in the wild-type). Genomic variants associated with longer OS included ERBB2 (p=0.006 HR=0.2 [0.06-0.6]), KMT2C (p=0.03 HR=0.2 [0.1-0.9]) and KMT2D (p=0.01 HR=0.2 [0.04-0.7]) mutations, and CDK12 amplification (p=0.04 HR=0.4 [0.2-0.96]). Although ERBB2 amplification was not associated with prognosis, co-amplification of CDK12 and ERBB2 (chromosome 17q12) was frequently observed (Pearson correlation r=0.8).
Conclusions: This large-scale genomic analysis reveals recurrent genomic events potentially associated with prognosis in GBC, including single nucleotide variants in ERBB2, KMT2C, and KMT2D, in addition to CNAs in chromosome 12q13-15 and 17q12 regions. This effort will continue to include a detailed analysis of recurrent structural variants, loss of heterozygosity loci, and analysis of the microbiota in this GBC cohort.
Citation Format: Nicolas A. Giraldo, Abhinita Mohanty, Chad Vanderbilt, Rose Brannon, Ryma Benayed, Efsevia Vakiani, Ghassan Abou-Alfa, James Harding, Imane El Dika, Nikolaus Schultz, Bob Li, Michael F. Berger, Marc Ladanyi, Eileen O'Reilly, William Jarnagin, Olca Basturk, Maria Arcila. Molecular characterization of gallbladder cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 82.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Bob Li
- 1Memorial Sloan Kettering, New York, NY
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20
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Murciano-Goroff YR, Kannan S, Chang JC, Benayed R, Blokhin I, Rekhtman N, Sisk AE, Gibson J, Judka L, Kaplanis L, Merrill M, Sgroe E, Verma CS, Drilon A, Cocco E. Abstract 5239: Switching inhibitor class overcomes crizotinib resistance in a MET fusion-positive NSCLC with a novel acquired MET G1090A mutation. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-5239] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Purpose: MET fusions are oncogenic drivers of multiple cancers including non-small cell lung cancer (NSCLC). While MET fusion-positive tumors can be sensitive to MET tyrosine kinase inhibitors (TKI), to date no mechanisms of TKI resistance have been identified or characterized for MET fusion-positive disease.
Experimental Design: Serial targeted genomic sequencing (MSK-IMPACT) was performed in clinical samples from a MET fusion-positive NSCLC treated with the type Ia MET TKI crizotinib. Structural modeling and in vitro kinase assays were used to characterize crizotinib resistance and to test the activity of MET inhibitors with alternative binding modes.
Results: A novel MET G1090A resistance mutation was identified in a patient with a CD47-MET-rearranged NSCLC after crizotinib progression. In silico structural modeling and simulations indicated that the 2,6-dichloro-3-fluorophenyl moiety present on crizotinib directly binds to the side chain of the Y1230 residue in the activation loop of the MET wild type (WT) kinase. In the MET G1090A mutant kinase, the position of the Y1230 residue is predicted to be flipped roughly 180°. As a result, the interaction between crizotinib and Y1230 is compromised; this in turn is predicted to reduce crizotinib’s binding affinity for the mutant kinase. Similar results were obtained when MET WT and G1090A mutant kinases were modeled in complex with selective type Ib MET TKI (i.e., capmatinib, savolitinib and tepotinib). Conversely, we found that type II agents (i.e., cabozantinib and foretinib) were not predicted to interact with Y1230. Therefore, their binding affinity to the mutant MET kinase was predicted to be retained. In vitro kinase assays performed using titrations of crizotinib and capmatinib (representative type I agents) and of cabozantinib (representative type II agent) showed that all three TKI were active against the MET WT kinase (calculated IC50 of 2.5nM, 3.89nM and 1.59nM, respectively). However, the calculated IC50 for crizotinib and capmatinib were 6.04- and 48.4-fold higher than the calculated IC50 for cabozantinib against the MET G1090A mutant kinase. Consistent with the prediction of type II inhibitor activity, the patient was transitioned to cabozantinib. A marked clinical, radiographic, and metabolic response was observed.
Conclusions: In MET fusion-positive cancers, the novel MET G1090A resistance mutation drives resistance to type I MET kinase inhibition. Drug binding mode switching to type II MET inhibition overcomes preclinical and clinical resistance, highlighting the need for further rational type II inhibitor development.
Citation Format: Yonina R. Murciano-Goroff, Srinivasaraghavan Kannan, Jason C. Chang, Ryma Benayed, Ilya Blokhin, Natasha Rekhtman, Ann Elizabeth Sisk, Jaime Gibson, Lia Judka, Lauren Kaplanis, Madeline Merrill, Erica Sgroe, Chandra S. Verma, Alexander Drilon, Emiliano Cocco. Switching inhibitor class overcomes crizotinib resistance in a MET fusion-positive NSCLC with a novel acquired MET G1090A mutation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5239.
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Affiliation(s)
| | - Srinivasaraghavan Kannan
- 2Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | | | - Ryma Benayed
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | - Jaime Gibson
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Lia Judka
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Erica Sgroe
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Chandra S. Verma
- 4Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | | | - Emiliano Cocco
- 5University of Miami, Sylvester Cancer Center, Miami, FL
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Hill K, Miller AM, Li BK, Bouvier N, Li S, Alano T, Doe-Tetteh S, Huereca C, DiNapoli S, Lee A, Szalontay L, Riviere-Cazaux C, Burns TC, Haque S, Bale T, Benhamida J, Dogan S, Vanderbilt C, Ross D, Chang J, Donzelli M, Dunkel IJ, Sait SF, Khakoo Y, Gilheeney S, Souweidane M, Greenfield J, Berger M, Benayed R, Arcila ME, Ladanyi M, Mellinghoff I, Karajannis M. PATH-16. Noninvasive diagnosis of gliomas through CSF cfDNA sequencing in pediatric and adolescent and young adult (AYA) patients. Neuro Oncol 2022. [DOI: 10.1093/neuonc/noac079.600] [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: 11/15/2022] Open
Abstract
Abstract
PURPOSE: A subset of pediatric, adolescent and young adult (AYA) gliomas are located in the brainstem, eloquent locations, or present with diffuse/leptomeningeal disease, and are associated with high risk and low yield of biopsy. At the same time, accurate molecular diagnosis is necessary to direct optimal therapy. In such cases, analysis of cell free DNA (cfDNA) form cerebral spinal fluid (CSF) may represent a diagnostic alternative to biopsy. METHODS: We investigated the utility of CSF cfDNA sequencing through a stepwise approach, using clinically validated, targeted molecular assays. Testing was performed using a broad hybrid capture next generation sequencing assay (MSK-IMPACT) and subsequent targeted digital droplet PCR in a subset of cases. RESULTS: We analyzed 17 CSF samples from 17 pediatric (n=6) and AYA (n=11) glioma patients with primary or recurrent disease. Thirteen had tumors located within the brainstem, and four had leptomeningeal involvement. Somatic alterations were detected in 12/17 samples (71%). In 3/4 patients with leptomeningeal involvement, cfDNA testing revealed a BRAF fusion consistent with the diagnosis of diffuse leptomeningeal glioneuronal tumor (DLGNT). Among the 13 patients with brainstem involvement, four had somatic H3 K27M mutations, three had IDH mutations, and one had TP53 and ATRX mutations; five patients had no detectable mutations. CONCLUSION: In our analysis, we found that established glioma hotspot mutations were able to be detected within the CSF. We propose that in patients for whom tissue biopsy is high risk, not feasible, or tissue was nondiagnostic, CSF cfDNA sequencing has a substantial diagnostic yield and should be considered as a valuable novel diagnostic tool. Ongoing research is aiming to further increase the sensitivity of cfDNA testing, especially in patients with very low levels of CSF cfDNA.
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Affiliation(s)
- Katherine Hill
- Memorial Sloan Kettering Cancer Center, New York , NY , USA
| | | | | | - Nancy Bouvier
- Memorial Sloan Kettering Cancer Center, New York , NY , USA
| | - Shanita Li
- Memorial Sloan Kettering Cancer Center, New York , NY , USA
| | - Tina Alano
- Memorial Sloan Kettering Cancer Center, New York , NY , USA
| | | | | | - Sara DiNapoli
- Memorial Sloan Kettering Cancer Center, New York , NY , USA
| | - Alex Lee
- Memorial Sloan Kettering Cancer Center, New York , NY , USA
| | | | | | | | - Sofia Haque
- Memorial Sloan Kettering Cancer Center, New York , NY , USA
| | - Tejus Bale
- Memorial Sloan Kettering Cancer Center, New York , NY , USA
| | | | - Snjezana Dogan
- Memorial Sloan Kettering Cancer Center, New York , NY , USA
| | | | - Dara Ross
- Memorial Sloan Kettering Cancer Center, New York , NY , USA
| | - Jason Chang
- Memorial Sloan Kettering Cancer Center, New York , NY , USA
| | - Maria Donzelli
- Memorial Sloan Kettering Cancer Center, New York , NY , USA
| | - Ira J Dunkel
- Memorial Sloan Kettering Cancer Center, New York , NY , USA
| | | | - Yasmin Khakoo
- Memorial Sloan Kettering Cancer Center, New York , NY , USA
| | | | - Mark Souweidane
- Memorial Sloan Kettering Cancer Center, New York , NY , USA
- Weill Cornell Medical College, New York , NY , USA
| | - Jeffrey Greenfield
- Memorial Sloan Kettering Cancer Center, New York , NY , USA
- Weill Cornell Medical College, New York , NY , USA
| | - Michael Berger
- Memorial Sloan Kettering Cancer Center, New York , NY , USA
| | - Ryma Benayed
- Memorial Sloan Kettering Cancer Center, New York , NY , USA
| | - Maria E Arcila
- Memorial Sloan Kettering Cancer Center, New York , NY , USA
| | - Marc Ladanyi
- Memorial Sloan Kettering Cancer Center, New York , NY , USA
| | - Ingo Mellinghoff
- Memorial Sloan Kettering Cancer Center, New York , NY , USA
- Weill Cornell Medical College, New York , NY , USA
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22
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Chu YH, Barbee J, Yang SR, Chang JC, Liang P, Mullaney K, Chan R, Salazar P, Benayed R, Offin M, Drilon A, Ladanyi M, Nafa K, Arcila ME. Clinical Utility and Performance of an Ultrarapid Multiplex RNA-Based Assay for Detection of ALK, ROS1, RET, and NTRK1/2/3 Rearrangements and MET Exon 14 Skipping Alterations. J Mol Diagn 2022; 24:642-654. [PMID: 35430374 DOI: 10.1016/j.jmoldx.2022.03.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 01/14/2022] [Accepted: 03/03/2022] [Indexed: 11/19/2022] Open
Abstract
Several kinase fusions are established targetable drivers in lung cancers. However, rapid and comprehensive detection remains challenging because of diverse partner genes and breakpoints. We assess the clinical utility and performance of a rapid microfluidic multiplex real-time PCR-based assay for simultaneous query of fusions involving ALK, ROS1, RET, and NTRK1/2/3, as well as MET exon 14 skipping, using a 3-hour automated process. Dual analytic strategies were utilized: fusion-specific amplification and 3' to 5' expression imbalance. One-hundred and forty-three independent, formalin-fixed, paraffin-embedded tumor samples (112 surgical specimens, 31 cytologic cell blocks) were analyzed: 133 with known kinase gene alterations and 10 negative samples based on clinically validated next-generation sequencing. Testing was successful in 142 (99%) cases. The assay demonstrated a sensitivity of 97% (28/29), 100% (31/31), 92% (22/24), 81% (22/27), and 100% (20/20) for ALK, RET, ROS1, and NTRK1/2/3 rearrangements and MET exon 14 skipping alterations, respectively, with 100% specificity for all. Concordant results were achieved in specimens aged up to 5 years, with >10% tumor, and inputs of at least 9 mm2 (surgical specimens) and 9000 cells (cytologic cell blocks). The assay enables rapid screening for clinically actionable kinase alterations with quicker turnaround and lower tissue requirements compared with immunohistochemistry and molecular methods, while also circumventing the infrastructure dependencies associated with next-generation sequencing and fluorescence in situ hybridization.
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Affiliation(s)
- Ying-Hsia Chu
- Department of Pathology and Laboratory Medicine, Molecular Diagnostic Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jada Barbee
- Department of Pathology and Laboratory Medicine, Molecular Diagnostic Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Soo-Ryum Yang
- Department of Pathology and Laboratory Medicine, Molecular Diagnostic Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jason C Chang
- Department of Pathology and Laboratory Medicine, Molecular Diagnostic Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Priscilla Liang
- Department of Pathology and Laboratory Medicine, Molecular Diagnostic Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kerry Mullaney
- Department of Pathology and Laboratory Medicine, Molecular Diagnostic Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Roger Chan
- Department of Pathology and Laboratory Medicine, Molecular Diagnostic Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Paulo Salazar
- Department of Pathology and Laboratory Medicine, Molecular Diagnostic Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ryma Benayed
- Department of Pathology and Laboratory Medicine, Molecular Diagnostic Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael Offin
- Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alexander Drilon
- Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Marc Ladanyi
- Department of Pathology and Laboratory Medicine, Molecular Diagnostic Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Khedoudja Nafa
- Department of Pathology and Laboratory Medicine, Molecular Diagnostic Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria E Arcila
- Department of Pathology and Laboratory Medicine, Molecular Diagnostic Service, Memorial Sloan Kettering Cancer Center, New York, New York.
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23
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Momeni-Boroujeni A, Yousefi E, Gupta S, Benayed R, Berger MF, Ladanyi M, Monroe R, Kim J, Jungbluth A, Weigelt B, Park KJ. Evaluation of TERT mRNA expression using RNAscope®: A potential histopathologic diagnostic and prognostic tool. Pathol Res Pract 2022; 233:153892. [DOI: 10.1016/j.prp.2022.153892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/07/2022] [Indexed: 11/29/2022]
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24
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Rosenzweig J, Pillai PM, Prockop S, Benayed R, Eidenschink Brodersen L, Najfeld V, Loken MR, Zhang Y, Shukla N. Acute myeloid leukemia with an MN1-ETV6 fusion in a young child with Down syndrome. Cold Spring Harb Mol Case Stud 2022; 8:a006167. [PMID: 35483876 PMCID: PMC9059786 DOI: 10.1101/mcs.a006167] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/16/2022] [Indexed: 11/24/2022] Open
Abstract
Myeloid leukemia of Down syndrome (ML-DS) in young children is associated with distinct clinical and biological features and is typically initiated with oncogenic mutations in the X-linked megakaryocytic transcription factor GATA1. Here we present a 3-yr-old child with DS diagnosed with acute myeloid leukemia (AML), which lacks typical immunophenotypic and molecular characteristics of ML-DS, including GATA1 mutations. The leukemic blasts were found to have an MN1-ETV6 gene fusion, a high-risk oncofusion not previously described in DS patients. This report highlights the importance of immunophenotypic, cytogenetic, and molecular characterization of ML-DS for identification of rare cases with unique features that may benefit from treatment protocols that are more intensive than those developed for patients with typical GATA1 mutant ML-DS.
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Affiliation(s)
- Jaclyn Rosenzweig
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Pallavi M Pillai
- Department of Pediatrics, Division of Pediatric Hematology-Oncology, Mount Sinai Kravis Children's Hospital, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Susan Prockop
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | | | - Vesna Najfeld
- Department of Medicine and Pathology, Tumor Cytogenomics, Icahn School of Medicine at Mount Sinai Hospital, New York, New York 10029, USA
| | | | - Yanming Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Neerav Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
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25
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Ferguson DC, Mata DA, Tay TKY, Traina TA, Gucalp A, Chandarlapaty S, D’Alfonso TM, Brogi E, Mullaney K, Ladanyi M, Arcila ME, Benayed R, Ross DS. Androgen receptor splice variant-7 in breast cancer: clinical and pathologic correlations. Mod Pathol 2022; 35:396-402. [PMID: 34593966 PMCID: PMC8863633 DOI: 10.1038/s41379-021-00924-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 09/05/2021] [Accepted: 09/06/2021] [Indexed: 11/09/2022]
Abstract
Androgen receptor (AR) inhibitor therapy is a developing treatment for AR-positive breast cancer (BC) with ongoing clinical trials. AR splice variant-7 (AR-V7) is a truncated variant of AR that leads to AR inhibitor therapy resistance in prostate cancer; recent studies have identified AR-V7 in BC and theorized that AR-V7 can have a similar impact. This study assessed the prevalence and clinicopathologic features associated with AR-V7 in a large BC cohort. BC samples were evaluated by MSK-Fusion targeted RNAseq for AR-V7 detection and MSK-IMPACT targeted DNAseq, including triple-negative tumors with no driver alteration and estrogen receptor-positive/ESR1 wildtype tumors progressing on therapy. Among 196 primary and metastatic/recurrent cases (196 RNAseq, 194DNAseq), 9.7% (19/196) were AR-V7 positive and 90.3% (177/196) AR-V7 negative. All AR-V7 positive BC were AR-positive by immunohistochemistry (19/19). The prevalence of AR-V7 by receptor subtype (N = 189) was: 18% (12/67) in ER-/PgR-/HER2-negative BC, 3.7% (4/109) in ER-positive/HER2-negative BC, and 15.4% (2/13) in HER2-positive BC; AR-V7 was detected in one ER-positive/HER2-unknown BC. Apocrine morphology was observed in 42.1% (8/19) of AR-V7 positive BC and 3.4% (6/177) AR-V7 negative BC (P < 0.00001). Notably, AR-V7 was detected in 2 primary BC and 7 metastatic/recurrent BC patients with no prior endocrine therapy. We conclude that positive AR IHC and apocrine morphology are pathologic features that may indicate testing for AR-V7 is warranted in both primary and metastatic BC in the appropriate clinical context. The study findings further encourage the assessment of AR-V7 as a predictive biomarker for AR antagonist benefit in ongoing clinical BC trials.
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Affiliation(s)
- Donna C. Ferguson
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Douglas A. Mata
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Timothy KY. Tay
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tiffany A. Traina
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ayca Gucalp
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sarat Chandarlapaty
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Timothy M. D’Alfonso
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Edi Brogi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kerry Mullaney
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria E. Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dara S. Ross
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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26
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Miller AM, Szalontay L, Bouvier N, Hill K, Ahmad H, Rafailov J, Lee AJ, Rodriguez-Sanchez MI, Yildirim O, Patel A, Bale TA, Benhamida JK, Benayed R, Arcila ME, Donzelli M, Dunkel IJ, Gilheeney SW, Khakoo Y, Kramer K, Sait SF, Greenfield JP, Souweidane MM, Haque S, Mauguen A, Berger MF, Mellinghoff IK, Karajannis MA. Next-generation sequencing of cerebrospinal fluid for clinical molecular diagnostics in pediatric, adolescent and young adult brain tumor patients. Neuro Oncol 2022; 24:1763-1772. [PMID: 35148412 PMCID: PMC9527510 DOI: 10.1093/neuonc/noac035] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Safe sampling of central nervous system tumor tissue for diagnostic purposes may be difficult if not impossible, especially in pediatric patients, and an unmet need exists to develop less invasive diagnostic tests. METHODS We report our clinical experience with minimally invasive molecular diagnostics using a clinically validated assay for sequencing of cerebrospinal fluid (CSF) cell-free DNA (cfDNA). All CSF samples were collected as part of clinical care, and results reported to both clinicians and patients/families. RESULTS We analyzed 64 CSF samples from 45 pediatric, adolescent and young adult (AYA) patients (pediatric = 25; AYA = 20) with primary and recurrent brain tumors across 12 histopathological subtypes including high-grade glioma (n = 10), medulloblastoma (n = 10), pineoblastoma (n = 5), low-grade glioma (n = 4), diffuse leptomeningeal glioneuronal tumor (DLGNT) (n = 4), retinoblastoma (n = 4), ependymoma (n = 3), and other (n = 5). Somatic alterations were detected in 30/64 samples (46.9%) and in at least one sample per unique patient in 21/45 patients (46.6%). CSF cfDNA positivity was strongly associated with the presence of disseminated disease at the time of collection (81.5% of samples from patients with disseminated disease were positive). No association was seen between CSF cfDNA positivity and the timing of CSF collection during the patient's disease course. CONCLUSIONS We identified three general categories where CSF cfDNA testing provided additional relevant diagnostic, prognostic, and/or therapeutic information, impacting clinical assessment and decision making: (1) diagnosis and/or identification of actionable alterations; (2) monitor response to therapy; and (3) tracking tumor evolution. Our findings support broader implementation of clinical CSF cfDNA testing in this population to improve care.
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Affiliation(s)
| | | | - Nancy Bouvier
- Pediatric Translational Medicine Program, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Katherine Hill
- Pediatric Translational Medicine Program, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Hamza Ahmad
- Pediatric Translational Medicine Program, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Johnathan Rafailov
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Alex J Lee
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - M Irene Rodriguez-Sanchez
- Pediatric Translational Medicine Program, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Onur Yildirim
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Arti Patel
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Tejus A Bale
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jamal K Benhamida
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Maria E Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Maria Donzelli
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ira J Dunkel
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Stephen W Gilheeney
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Yasmin Khakoo
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Kim Kramer
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Sameer F Sait
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jeffrey P Greenfield
- Department of Pediatrics, Weill Cornell Medical College, New York, New York, USA,Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA,Department of Neurological Surgery, Weill Cornell Medical College, New York, New York, USA,Department of Neurological Surgery, Columbia University Irving Medical Center, New York, New York, USA
| | - Mark M Souweidane
- Department of Pediatrics, Weill Cornell Medical College, New York, New York, USA,Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA,Department of Neurological Surgery, Weill Cornell Medical College, New York, New York, USA,Department of Neurological Surgery, Columbia University Irving Medical Center, New York, New York, USA
| | - Sofia Haque
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Audrey Mauguen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Michael F Berger
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ingo K Mellinghoff
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA,Department of Pharmacology, Weill Cornell Medical College, New York, New York, USA
| | - Matthias A Karajannis
- Corresponding Author: Matthias A. Karajannis, MD, MS, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY 10065, USA ()
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27
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Petrova-Drus K, Quesada AE, Bowman AS, Ptashkin R, Yao J, Arcila ME, Ho C, Moung C, Regalado J, Benayed R, Benhamida JK, Galera PK, Dogan A, Vanderbilt C. Quantitative Off-Target Detection of Epstein-Barr Virus-Derived DNA in Routine Molecular Profiling of Hematopoietic Neoplasms by Panel-Based Hybrid-Capture Next-Generation Sequencing. J Mol Diagn 2022; 24:69-78. [PMID: 34801704 PMCID: PMC8802759 DOI: 10.1016/j.jmoldx.2021.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/31/2021] [Accepted: 10/04/2021] [Indexed: 01/03/2023] Open
Abstract
Epstein-Barr virus (EBV) is associated with hematologic and solid tumors. We utilized a hybridization capture-based next-generation sequencing (NGS) platform targeting 400 genes associated with hematological malignancies to detect and quantify nontargeted viral-derived EBV reads that aligned to the EBV reference contig (NC_007605). We evaluated 5234 samples from 3636 unique patients with hematological neoplasms and found that 100 samples (1.9%) in 93 unique patients had ≥6 EBV reads (range, 6 to 32,325; mean, 827.5; median, 54). Most (n = 73, 73%) represented known EBV-associated conditions, and the most common was post-transplant lymphoproliferative disorders (n = 21, 29%). Documented EBV viremia was found in 4 of 27 samples with a moderate quantity of EBV reads and conditions not known to be EBV associated, whereas suspected viremia or low-level activation was likely in the remaining 23 samples. A good correlation (Spearman r = 0.8; 95% CI, 0.74-0.85) was found between EBV reads by NGS and systematic semiquantitative EBV-encoded RNA in situ hybridization in 162 available samples, particularly at greater EBV involvement. An optimal threshold for significant morphologic EBV involvement was found to be ≥10 reads by the receiver operating characteristic analysis (area under the curve, 0.990; 95% CI, 0.9974%-1.000%). Thus, in addition to mutational analysis, hybrid-capture-based NGS panels can detect and quantitate off-target EBV-derived viral DNA, which correlates well with morphology.
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Affiliation(s)
- Kseniya Petrova-Drus
- Address correspondence to Kseniya Petrova-Drus, M.D., Ph.D., Memorial Sloan Kettering Cancer Center, Department of Pathology, 1275 York Ave., C-563-C, New York, NY 10065.
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28
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Pareja F, Ptashkin RN, Brown DN, Derakhshan F, Selenica P, da Silva EM, Gazzo AM, Da Cruz Paula A, Breen K, Shen R, Marra A, Zehir A, Benayed R, Berger MF, Ceyhan-Birsoy O, Jairam S, Sheehan M, Patel U, Kemel Y, Casanova-Murphy J, Schwartz CJ, Vahdatinia M, Comen E, Borsu L, Pei X, Riaz N, Abramson DH, Weigelt B, Walsh MF, Hadjantonakis AK, Ladanyi M, Offit K, Stadler ZK, Robson ME, Reis-Filho JS, Mandelker D. Cancer Causative Mutations Occurring in Early Embryogenesis. Cancer Discov 2021; 12:949-957. [DOI: 10.1158/2159-8290.cd-21-1110] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/21/2021] [Accepted: 12/20/2021] [Indexed: 11/16/2022]
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29
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Mondaca S, Lebow ES, Namakydoust A, Razavi P, Reis-Filho JS, Shen R, Offin M, Tu HY, Murciano-Goroff Y, Xu C, Makhnin A, Martinez A, Pavlakis N, Clarke S, Itchins M, Lee A, Rimner A, Gomez D, Rocco G, Chaft JE, Riely GJ, Rudin CM, Jones DR, Li M, Shaffer T, Hosseini SA, Bertucci C, Lim LP, Drilon A, Berger MF, Benayed R, Arcila ME, Isbell JM, Li BT. Corrigendum to "Clinical utility of next-generation sequencing-based ctDNA testing for common and novel ALK fusions" [Lung Cancer 159 (2021) 66-73]. Lung Cancer 2021; 162:210. [PMID: 34625293 PMCID: PMC10551809 DOI: 10.1016/j.lungcan.2021.09.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Sebastian Mondaca
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA; Department of Hematology and Oncology, Pontificia Universidad Católica de Chile, Diagonal Paraguay 362 6th Fl, Rm 609, Santiago, Chile.
| | - Emily S Lebow
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Azadeh Namakydoust
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Pedram Razavi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Ronglai Shen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering, 1275 York Avenue, New York, NY, USA
| | - Michael Offin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Hai-Yan Tu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA; Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, 106 Zhongshan Er Road, Guangzhou, China
| | - Yonina Murciano-Goroff
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Chongrui Xu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA; Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, 106 Zhongshan Er Road, Guangzhou, China
| | - Alex Makhnin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Andres Martinez
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Nick Pavlakis
- GenesisCare (formerly Northern Cancer Institute), University of Sydney, NSW 2109, Australia
| | - Stephen Clarke
- GenesisCare (formerly Northern Cancer Institute), University of Sydney, NSW 2109, Australia
| | - Malinda Itchins
- GenesisCare (formerly Northern Cancer Institute), University of Sydney, NSW 2109, Australia
| | - Adrian Lee
- GenesisCare (formerly Northern Cancer Institute), University of Sydney, NSW 2109, Australia
| | - Andreas Rimner
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Daniel Gomez
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Gaetano Rocco
- Department of Surgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Jamie E Chaft
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Gregory J Riely
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Charles M Rudin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - David R Jones
- Department of Surgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Mark Li
- Resolution Bioscience, 550 Kirkland Way #200, Kirkland, WA, USA
| | - Tristan Shaffer
- Resolution Bioscience, 550 Kirkland Way #200, Kirkland, WA, USA
| | | | | | - Lee P Lim
- Resolution Bioscience, 550 Kirkland Way #200, Kirkland, WA, USA
| | - Alexander Drilon
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Michael F Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA; Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York NY, USA
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Maria E Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - James M Isbell
- Department of Surgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Bob T Li
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA.
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Al-Obaidy KI, Bridge JA, Cheng L, Sumegi J, Reuter VE, Benayed R, Hameed M, Williamson SR, Hes O, Alruwaii FI, Segal JP, Wanjari P, Idrees MT, Nassiri M, Eble JN, Grignon DJ. EWSR1-PATZ1 fusion renal cell carcinoma: a recurrent gene fusion characterizing thyroid-like follicular renal cell carcinoma. Mod Pathol 2021; 34:1921-1934. [PMID: 34099871 DOI: 10.1038/s41379-021-00833-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 05/12/2021] [Accepted: 05/12/2021] [Indexed: 02/07/2023]
Abstract
Thyroid-like follicular renal cell carcinoma is an uncommon kidney tumor with no distinct molecular alteration described to date. This cohort of eight women with mean and median ages of 45 and 46 years, respectively (range 19-65 years), had unencapsulated, well-circumscribed tumors composed of tightly packed anastomosing follicle-like cysts filled with eosinophilic colloid-like material and lined by cuboidal cells with high nuclear to cytoplasmic ratios, oval to elongated nuclei with perpendicular arrangement toward the lumens, and prominent nuclear overlapping. The stroma between these was minimal with the exception of two tumors. Calcifications and necrosis were absent. Immunohistochemically, the tumors were positive for KRT19 (7/7), PAX8 (5/5), cyclin D1 (6/6), KRT7 (5/7), and AMACR (1/5; focal, weak), and were negative for WT1, TTF1 (transcription termination factor-1), and thyroglobulin. In three of three tumors tested molecularly, EWSR1-PATZ1 fusion was identified by RNA sequencing and confirmed by RT-PCR and Sanger sequencing. Over a follow-up period of 1-7 years, no evidence of recurrence or metastasis has been detected. The EWSR1-PATZ1 fusion has been recognized as a recurrent alteration in a subset of round to spindle cell sarcomas with EWSR1-non-ETS fusions (EWSR1-PATZ1 sarcoma) and in several central nervous system tumors. The finding of an EWSR1-PATZ1 fusion in all three of the thyroid-like follicular renal cell carcinomas for which sufficient tissue was available for genomic profiling provides the first distinct molecular abnormality in thyroid-like follicular renal cell carcinomas, supporting its designation as a distinct diagnostic entity.
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Affiliation(s)
- Khaleel I Al-Obaidy
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Julia A Bridge
- Division of Molecular Pathology, ProPath, Dallas, TX, USA.,Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Liang Cheng
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Janos Sumegi
- The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Victor E Reuter
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Meera Hameed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Ondrej Hes
- Department of Pathology, Charles University Hospital Pilsen, Pilsen, Czech Republic
| | - Fatimah I Alruwaii
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jeremy P Segal
- Department of Pathology, University of Chicago Medical Center, Chicago, IL, USA
| | - Pankhuri Wanjari
- Department of Pathology, University of Chicago Medical Center, Chicago, IL, USA
| | - Muhammad T Idrees
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Mehdi Nassiri
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - John N Eble
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - David J Grignon
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
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31
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Kyi C, Friedman CF, Mueller JJ, Benayed R, Ladanyi M, Arcila M, Yang SR, Hensley ML, Chiang S. Uterine mesenchymal tumors harboring ALK fusions and response to ALK-targeted therapy. Gynecol Oncol Rep 2021; 37:100852. [PMID: 34522753 PMCID: PMC8427213 DOI: 10.1016/j.gore.2021.100852] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 08/21/2021] [Indexed: 12/21/2022] Open
Abstract
Inflammatory myofibroblastic tumor (IMT) of the uterus is a rare but aggressive malignancy that is often misdiagnosed. Approximately 50% of uterine IMTs (UMT) harbor rearrangements involving the ALK gene on chromosome 2p23 with subsequent overexpression of the ALK protein. Molecular characterization and wider availability of immunohistochemistry (IHC) and next generation sequencing (NGS) have improved clinical recognition and accurate diagnosis of UMT. The discovery of ALK fusions as a genomic driver led to the FDA approval of ALK inhibitors in ALK-altered lung cancers, but there are limited data to date on the spectrum of ALK fusions or patterns of response and resistance to ALK inhibitors in ALK-altered UMT. In this report we describe the genomic and histopathological characteristics and the response to ALK-targeted therapy in four patients with UMT. In all four patients, clinical activity of ALK inhibition was observed, with durable responses lasting 12 months or more. Moreover, three patients derived benefit from a second-generation ALK inhibitor after progression of disease or intolerance to the first-generation inhibitor crizotinib. Our report advocates for consideration of expanding the current National Comprehensive Cancer Network (NCCN) guidelines to include later-generation ALK inhibitors for the treatment of ALK-rearranged UMTs.
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Affiliation(s)
- Chrisann Kyi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States.,Weill Cornell Medical College, New York, NY, United States
| | - Claire F Friedman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States.,Weill Cornell Medical College, New York, NY, United States
| | - Jennifer J Mueller
- Weill Cornell Medical College, New York, NY, United States.,Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Maria Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Soo Ryum Yang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Martee L Hensley
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States.,Weill Cornell Medical College, New York, NY, United States
| | - Sarah Chiang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, United States
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32
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Varghese AM, Singh I, Singh R, Kunte S, Chou JF, Capanu M, Wong W, Lowery MA, Stadler ZK, Salo-Mullen E, Saadat LV, Wei AC, Reyngold M, Basturk O, Benayed R, Mandelker D, Iacobuzio-Donahue CA, Kelsen DP, Park W, Yu KH, O’Reilly EM. Early-Onset Pancreas Cancer: Clinical Descriptors, Genomics, and Outcomes. J Natl Cancer Inst 2021; 113:1194-1202. [PMID: 33755158 PMCID: PMC8418394 DOI: 10.1093/jnci/djab038] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [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] [Received: 10/01/2020] [Revised: 12/05/2020] [Accepted: 02/12/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Recent evidence suggests a rising incidence of cancer in younger individuals. Herein, we report the epidemiologic, pathologic, and molecular characteristics of a patient cohort with early-onset pancreas cancer (EOPC). METHODS Institutional databases were queried for demographics, treatment history, genomic results, and outcomes. Overall survival from date of diagnosis was estimated using Kaplan-Meier method. RESULTS Between 2008 and 2018, 450 patients with EOPC were identified at Memorial Sloan Kettering. Median overall survival was 16.3 (95% confidence interval [CI] = 14.6 to 17.7) months in the entire cohort and 11.3 (95% CI = 10.2 to 12.2) months for patients with stage IV disease at diagnosis. Of the patients, 132 (29.3% of the cohort) underwent somatic testing; 21 of 132 (15.9%) had RAS wild-type cancers with identification of several actionable alterations, including ETV6-NTRK3, TPR-NTRK1, SCLA5-NRG1, and ATP1B1-NRG1 fusions, IDH1 R132C mutation, and mismatch repair deficiency. A total of 138 patients (30.7% of the cohort) underwent germline testing; 44 of 138 (31.9%) had a pathogenic germline variant (PGV), and 27.5% harbored alterations in cancer susceptibility genes. Of patients seen between 2015 and 2018, 30 of 193 (15.5%) had a PGV. Among 138 who underwent germline testing, those with a PGV had a reduced all-cause mortality compared with patients without a PGV controlling for stage and year of diagnosis (hazard ratio = 0.42, 95% CI = 0.26 to 0.69). CONCLUSIONS PGVs are present in a substantial minority of patients with EOPC. Actionable somatic alterations were identified frequently in EOPC, enriched in the RAS wild-type subgroup. These observations underpin the recent guidelines for universal germline testing and somatic profiling in pancreatic ductal adenocarcinoma.
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Affiliation(s)
- Anna M Varghese
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- David M. Rubenstein Center for Pancreas Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Isha Singh
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rituraj Singh
- Department of Medicine, Indiana University School of Medicine, Fort Wayne, IN, USA
| | - Siddharth Kunte
- Department of Medicine, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Joanne F Chou
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marinela Capanu
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Winston Wong
- Department of Medicine, Columbia University Herbert Irving Comprehensive Cancer Center, New York, NY, USA
| | - Maeve A Lowery
- School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Zsofia K Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Erin Salo-Mullen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lily V Saadat
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alice C Wei
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marsha Reyngold
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Olca Basturk
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Diana Mandelker
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christine A Iacobuzio-Donahue
- David M. Rubenstein Center for Pancreas Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David P Kelsen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- David M. Rubenstein Center for Pancreas Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Wungki Park
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- David M. Rubenstein Center for Pancreas Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Kenneth H Yu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- David M. Rubenstein Center for Pancreas Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Eileen M O’Reilly
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- David M. Rubenstein Center for Pancreas Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
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Mondaca S, Lebow ES, Namakydoust A, Razavi P, Reis-Filho JS, Shen R, Offin M, Tu HY, Murciano-Goroff Y, Xu C, Makhnin A, Martinez A, Pavlakis N, Clarke S, Itchins M, Lee A, Rimner A, Gomez D, Rocco G, Chaft JE, Riely GJ, Rudin CM, Jones DR, Li M, Shaffer T, Hosseini SA, Bertucci C, Lim LP, Drilon A, Berger MF, Benayed R, Arcila ME, Isbell JM, Li BT. Clinical utility of next-generation sequencing-based ctDNA testing for common and novel ALK fusions. Lung Cancer 2021; 159:66-73. [PMID: 34311346 DOI: 10.1016/j.lungcan.2021.06.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 03/10/2021] [Revised: 06/16/2021] [Accepted: 06/24/2021] [Indexed: 10/20/2022]
Abstract
OBJECTIVES Liquid biopsy for plasma circulating tumor DNA (ctDNA) next-generation sequencing (NGS) can detect ALK fusions, though data on clinical utility of this technology in the real world is limited. MATERIALS AND METHODS Patients with lung cancer without known oncogenic drivers or who had acquired resistance to therapy (n = 736) underwent prospective plasma ctDNA NGS. A subset of this cohort (n = 497) also had tissue NGS. We evaluated ALK fusion detection, turnaround time (TAT), plasma and tissue concordance, matching to therapy, and treatment response. RESULTS ctDNA identified an ALK fusion in 21 patients (3%) with a variety of breakpoints and fusion partners, including EML4, CLTC, and PON1, a novel ALK fusion partner. TAT for ctDNA NGS was shorter than tissue NGS (10 vs. 20 days; p < 0.001). Among ALK fusions identified by ctDNA, 93% (13/14, 95% CI 66%-99%) were concordant with tissue evaluation. Among ALK fusions detected by tissue NGS, 54% (13/24, 95% CI 33%-74%) were concordant with plasma ctDNA. ctDNA matched patients to ALK-directed therapy with subsequent clinical response, including four patients matched on the basis of ctDNA results alone due to inadequate or delayed tissue testing. Serial ctDNA analysis detected MET amplification (n = 2) and ALK G1202R mutation (n = 2) as mechanisms of acquired resistance to ALK-directed therapy. CONCLUSION Our findings support a complementary role for ctDNA in detection of ALK fusions and other alterations at diagnosis and therapeutic resistance settings.
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Affiliation(s)
- Sebastian Mondaca
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA; Department of Hematology and Oncology, Pontificia Universidad Católica de Chile, Diagonal Paraguay 362 6th Fl, Rm 609, Santiago, Chile.
| | - Emily S Lebow
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Azadeh Namakydoust
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Pedram Razavi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Ronglai Shen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering, 1275 York Avenue, New York, NY, USA
| | - Michael Offin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Hai-Yan Tu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA; Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, 106 Zhongshan Er Road, Guangzhou, China
| | - Yonina Murciano-Goroff
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Chongrui Xu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA; Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, 106 Zhongshan Er Road, Guangzhou, China
| | - Alex Makhnin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Andres Martinez
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Nick Pavlakis
- GenesisCare (formerly Northern Cancer Institute), University of Sydney, Macquarie University NSW 2109, Australia
| | - Stephen Clarke
- GenesisCare (formerly Northern Cancer Institute), University of Sydney, Macquarie University NSW 2109, Australia
| | - Malinda Itchins
- GenesisCare (formerly Northern Cancer Institute), University of Sydney, Macquarie University NSW 2109, Australia
| | - Adrian Lee
- GenesisCare (formerly Northern Cancer Institute), University of Sydney, Macquarie University NSW 2109, Australia
| | - Andreas Rimner
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Daniel Gomez
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Gaetano Rocco
- Department of Surgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Jamie E Chaft
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Gregory J Riely
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Charles M Rudin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - David R Jones
- Department of Surgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Mark Li
- Resolution Bioscience, 550 Kirkland Way #200, Kirkland, WA, USA
| | - Tristan Shaffer
- Resolution Bioscience, 550 Kirkland Way #200, Kirkland, WA, USA
| | | | | | - Lee P Lim
- Resolution Bioscience, 550 Kirkland Way #200, Kirkland, WA, USA
| | - Alexander Drilon
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Michael F Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA; Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York NY, USA
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Maria E Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - James M Isbell
- Department of Surgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA
| | - Bob T Li
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA.
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Chang JC, Offin M, Falcon C, Brown D, Houck-Loomis BR, Meng F, Rudneva VA, Won HH, Amir S, Montecalvo J, Desmeules P, Kadota K, Adusumilli PS, Rusch VW, Teed S, Sabari JK, Benayed R, Nafa K, Borsu L, Li BT, Schram AM, Arcila ME, Travis WD, Ladanyi M, Drilon A, Rekhtman N. Comprehensive Molecular and Clinicopathologic Analysis of 200 Pulmonary Invasive Mucinous Adenocarcinomas Identifies Distinct Characteristics of Molecular Subtypes. Clin Cancer Res 2021; 27:4066-4076. [PMID: 33947695 PMCID: PMC8282731 DOI: 10.1158/1078-0432.ccr-21-0423] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/27/2021] [Accepted: 04/30/2021] [Indexed: 02/06/2023]
Abstract
PURPOSE Invasive mucinous adenocarcinoma (IMA) is a unique subtype of lung adenocarcinoma, characterized genomically by frequent KRAS mutations or specific gene fusions, most commonly involving NRG1. Comprehensive analysis of a large series of IMAs using broad DNA- and RNA-sequencing methods is still lacking, and it remains unclear whether molecular subtypes of IMA differ clinicopathologically. EXPERIMENTAL DESIGN A total of 200 IMAs were analyzed by 410-gene DNA next-generation sequencing (MSK-IMPACT; n = 136) or hotspot 8-oncogene genotyping (n = 64). Driver-negative cases were further analyzed by 62-gene RNA sequencing (MSK-Fusion) and those lacking fusions were further tested by whole-exome sequencing and whole-transcriptome sequencing (WTS). RESULTS Combined MSK-IMPACT and MSK-Fusion testing identified mutually exclusive driver alterations in 96% of IMAs, including KRAS mutations (76%), NRG1 fusions (7%), ERBB2 alterations (6%), and other less common events. In addition, WTS identified a novel NRG2 fusion (F11R-NRG2). Overall, targetable gene fusions were identified in 51% of KRAS wild-type IMAs, leading to durable responses to targeted therapy in some patients. Compared with KRAS-mutant IMAs, NRG1-rearranged tumors exhibited several more aggressive characteristics, including worse recurrence-free survival (P < 0.0001). CONCLUSIONS This is the largest molecular study of IMAs to date, where we demonstrate the presence of a major oncogenic driver in nearly all cases. This study is the first to document more aggressive characteristics of NRG1-rearranged IMAs, ERBB2 as the third most common alteration, and a novel NRG2 fusion in these tumors. Comprehensive molecular testing of KRAS wild-type IMAs that includes fusion testing is essential, given the high prevalence of alterations with established and investigational targeted therapies in this subset.
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Affiliation(s)
- Jason C Chang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael Offin
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Christina Falcon
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David Brown
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Brian R Houck-Loomis
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Fanli Meng
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Vasilisa A Rudneva
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Helen H Won
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sharon Amir
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Joseph Montecalvo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Patrice Desmeules
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kyuichi Kadota
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Surgery, Thoracic Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Prasad S Adusumilli
- Department of Surgery, Thoracic Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Valerie W Rusch
- Department of Surgery, Thoracic Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sarah Teed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Cell Biology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Joshua K Sabari
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Khedoudja Nafa
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Laetitia Borsu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Bob T Li
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alison M Schram
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria E Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - William D Travis
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alexander Drilon
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Early Drug Development Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Natasha Rekhtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
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Yang SR, Chang JC, Leduc C, Tan KS, Dogan S, Benayed R, Borsu L, Offin M, Drilon A, Travis WD, Arcila ME, Ladanyi M, Rekhtman N. Invasive Mucinous Adenocarcinomas With Spatially Separate Lung Lesions: Analysis of Clonal Relationship by Comparative Molecular Profiling. J Thorac Oncol 2021; 16:1188-1199. [PMID: 33839364 PMCID: PMC8240964 DOI: 10.1016/j.jtho.2021.03.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [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: 01/25/2021] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Pulmonary invasive mucinous adenocarcinomas (IMAs) often present with spatially separate lung lesions. Clonal relationship between such lesions, particularly those involving contralateral lobes, is not well established. Here, we used comparative genomic profiling to address this question. METHODS Patients with genomic analysis performed on two IMAs located in different lung regions were identified. Molecular assays included DNA-based next-generation sequencing (NGS) for 410 to 468 genes (Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets), RNA-based NGS for 62 genes (Memorial Sloan Kettering-Fusion), or non-NGS assays. RESULTS Comparative genomic profiling was performed on two separate IMAs in 24 patients, of whom 19 had contralateral lesions. Tumors from all but one patient shared matching driver alterations, including KRAS (n = 19), NRG1 (n = 2), ERBB2 (n = 1) or BRAF (n = 1). In addition, in patients with paired tumors profiled by NGS (n = 12), shared driver alterations were accompanied by up to 4 (average 2.6) other identical mutations, further supporting the clonal relationship between the tumors. Only in a single patient separate IMAs harbored entirely nonoverlapping mutation profiles, supporting clonally unrelated, distinct primary tumors. Notably, in a subset of patients (n = 3), molecular testing confirmed a clonal relationship between the original resected IMAs and subsequent contralateral IMA presenting after an extremely long latency (8.1-11.7 y). CONCLUSIONS Comparative molecular profiling supports that nearly all separate pulmonary IMA lesions represent intrapulmonary spread arising from a single tumor and documents a subset with a remarkably protracted course of intrapulmonary progression. This study reinforces the unique biology and clinical behavior of IMAs while further highlighting the value of genomic testing for clarifying the clonal relationship between multiple lung carcinomas.
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Affiliation(s)
- Soo-Ryum Yang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jason C Chang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Charles Leduc
- Department of Pathology and Cellular Biology, University of Montreal, Montreal, Quebec, Canada
| | - Kay See Tan
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Snjezana Dogan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Laetitia Borsu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael Offin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alexander Drilon
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - William D Travis
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria E Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Natasha Rekhtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
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Rose Brannon A, Jayakumaran G, Diosdado M, Patel J, Razumova A, Hu Y, Meng F, Haque M, Sadowska J, Murphy BJ, Baldi T, Johnson I, Ptashkin R, Hasan M, Srinivasan P, Rema AB, Rijo I, Agarunov A, Won H, Perera D, Brown DN, Samoila A, Jing X, Gedvilaite E, Yang JL, Stephens DP, Dix JM, DeGroat N, Nafa K, Syed A, Li A, Lebow ES, Bowman AS, Ferguson DC, Liu Y, Mata DA, Sharma R, Yang SR, Bale T, Benhamida JK, Chang JC, Dogan S, Hameed MR, Hechtman JF, Moung C, Ross DS, Vakiani E, Vanderbilt CM, Yao J, Razavi P, Smyth LM, Chandarlapaty S, Iyer G, Abida W, Harding JJ, Krantz B, O'Reilly E, Yu HA, Li BT, Rudin CM, Diaz L, Solit DB, Arcila ME, Ladanyi M, Loomis B, Tsui D, Berger MF, Zehir A, Benayed R. Enhanced specificity of clinical high-sensitivity tumor mutation profiling in cell-free DNA via paired normal sequencing using MSK-ACCESS. Nat Commun 2021; 12:3770. [PMID: 34145282 PMCID: PMC8213710 DOI: 10.1038/s41467-021-24109-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [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: 12/02/2020] [Accepted: 05/26/2021] [Indexed: 12/13/2022] Open
Abstract
Circulating cell-free DNA from blood plasma of cancer patients can be used to non-invasively interrogate somatic tumor alterations. Here we develop MSK-ACCESS (Memorial Sloan Kettering - Analysis of Circulating cfDNA to Examine Somatic Status), an NGS assay for detection of very low frequency somatic alterations in 129 genes. Analytical validation demonstrated 92% sensitivity in de-novo mutation calling down to 0.5% allele frequency and 99% for a priori mutation profiling. To evaluate the performance of MSK-ACCESS, we report results from 681 prospective blood samples that underwent clinical analysis to guide patient management. Somatic alterations are detected in 73% of the samples, 56% of which have clinically actionable alterations. The utilization of matched normal sequencing allows retention of somatic alterations while removing over 10,000 germline and clonal hematopoiesis variants. Our experience illustrates the importance of analyzing matched normal samples when interpreting cfDNA results and highlights the importance of cfDNA as a genomic profiling source for cancer patients. Liquid biopsies allow the non-invasive detection of somatic mutations from tumours. Here, the authors develop and test MSK-ACCESS, an NGS-based clinical assay for identifying low frequency mutations in 129 genes and describe how it benefits patients in the clinic.
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Affiliation(s)
- A Rose Brannon
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gowtham Jayakumaran
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Monica Diosdado
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Juber Patel
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anna Razumova
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yu Hu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fanli Meng
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mohammad Haque
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Justyna Sadowska
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Brian J Murphy
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tessara Baldi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ian Johnson
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ryan Ptashkin
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maysun Hasan
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Preethi Srinivasan
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Ivelise Rijo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Aaron Agarunov
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Helen Won
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dilmi Perera
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David N Brown
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Aliaksandra Samoila
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Xiaohong Jing
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Erika Gedvilaite
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Julie L Yang
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dennis P Stephens
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jenna-Marie Dix
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicole DeGroat
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Khedoudja Nafa
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Aijazuddin Syed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alan Li
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Emily S Lebow
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anita S Bowman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Donna C Ferguson
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ying Liu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Douglas A Mata
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rohit Sharma
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Soo-Ryum Yang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tejus Bale
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jamal K Benhamida
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jason C Chang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Snjezana Dogan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Meera R Hameed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christine Moung
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dara S Ross
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Efsevia Vakiani
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chad M Vanderbilt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - JinJuan Yao
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pedram Razavi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lillian M Smyth
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sarat Chandarlapaty
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gopa Iyer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wassim Abida
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - James J Harding
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Benjamin Krantz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eileen O'Reilly
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Helena A Yu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bob T Li
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Charles M Rudin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Luis Diaz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David B Solit
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria E Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Brian Loomis
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dana Tsui
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael F Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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Miller A, Szalontay L, Bouvier N, Ahmed H, Hill K, Rafailov J, Lee A, Rodriguez-Sanchez I, Yildirim O, Patel A, Bale T, Benayed R, Arcila M, Donzelli M, Dunkel I, Gilheeney S, Khakoo Y, Kramer K, Sait SF, Greenfield J, Souweidane M, Haque S, Mauguen A, Berger M, Mellinghoff I, Karajannis M. EPCT-21. NEXT-GENERATION SEQUENCING OF CEREBROSPINAL FLUID FOR CLINICAL MOLECULAR DIAGNOSTICS IN ADOLESCENT AND YOUNG ADULT (AYA) BRAIN TUMOR PATIENTS. Neuro Oncol 2021. [PMCID: PMC8168217 DOI: 10.1093/neuonc/noab090.207] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Purpose Pediatric central nervous system tumors remain a leading cause of cancer-related death in children and adolescents. Safe sampling of tumor tissue for diagnostic purposes may be challenging. Subclinical detection of disease prior to clinical or imaging progression may provide opportunity for earlier intervention and ultimately improve overall survival. Additionally, our understanding of molecular evolution in response to therapy remains limited, given the rarity of serial sampling of tumor tissue. Methods We report our experience with minimally invasive molecular diagnostics using a validated next generation sequencing assay for sequencing of cerebrospinal fluid (CSF) cell-free DNA (cfDNA) obtained at the time of surgery, by intraventricular catheter or lumbar puncture. All CSF samples were collected as part of clinical care, and results reported to both clinicians and patients/families. Results We analyzed 64 CSF samples from 45 pediatric and adolescent and young adult (AYA) patients (pediatric=25; AYA=20) with primary and recurrent brain tumors across 12 histopathological subtypes including high-grade glioma (n=10), medulloblastoma (n=10), pineoblastoma (n=5), low grade glioma (n=4), diffuse leptomeningeal glioneuronal tumor (DLGNT) (n=4), metastatic retinoblastoma (n=4), ependymoma (n=3), and other (n=5). Somatic alterations were detected in 28/64 samples (44.4%) and in at least one sample per unique patient in 22/45 patients (48.8%). CSF cfDNA positivity was strongly associated with the presence of disseminated disease at the time of collection (86.3%). No association was seen between CSF cfDNA positivity and the timing of CSF collection during the patient’s disease course. Conclusion We identified four general categories where CSF cfDNA testing provided additional relevant diagnostic, prognostic, and/or therapeutic information, impacting clinical assessment and decision making: 1) diagnosis; 2) identification of actionable alterations; 3) track response to therapy; and 4) monitoring tumor evolution. Our findings support broader implementation of clinical CSF cfDNA testing in this population that may improve care.
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Affiliation(s)
| | - Luca Szalontay
- Columbia University Irving Medical Center, New York, NY, USA
| | - Nancy Bouvier
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hamza Ahmed
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Katherine Hill
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Alex Lee
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Onur Yildirim
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arti Patel
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tejus Bale
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ryma Benayed
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria Arcila
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria Donzelli
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ira Dunkel
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New, York, USA
| | - Stephen Gilheeney
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New, York, USA
| | - Yasmin Khakoo
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New, York, USA
| | - Kim Kramer
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New, York, USA
| | - Sameer F Sait
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New, York, USA
| | - Jeffrey Greenfield
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New, York, USA
| | - Mark Souweidane
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New, York, USA
| | - Sofia Haque
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Audrey Mauguen
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael Berger
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ingo Mellinghoff
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New, York, USA
| | - Matthias Karajannis
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New, York, USA
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38
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Tsui DWY, Cheng ML, Shady M, Yang JL, Stephens D, Won H, Srinivasan P, Huberman K, Meng F, Jing X, Patel J, Hasan M, Johnson I, Gedvilaite E, Houck-Loomis B, Socci ND, Selcuklu SD, Seshan VE, Zhang H, Chakravarty D, Zehir A, Benayed R, Arcila M, Ladanyi M, Funt SA, Feldman DR, Li BT, Razavi P, Rosenberg J, Bajorin D, Iyer G, Abida W, Scher HI, Rathkopf D, Viale A, Berger MF, Solit DB. Tumor fraction-guided cell-free DNA profiling in metastatic solid tumor patients. Genome Med 2021; 13:96. [PMID: 34059130 PMCID: PMC8165771 DOI: 10.1186/s13073-021-00898-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [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: 03/02/2020] [Accepted: 04/27/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Cell-free DNA (cfDNA) profiling is increasingly used to guide cancer care, yet mutations are not always identified. The ability to detect somatic mutations in plasma depends on both assay sensitivity and the fraction of circulating DNA in plasma that is tumor-derived (i.e., cfDNA tumor fraction). We hypothesized that cfDNA tumor fraction could inform the interpretation of negative cfDNA results and guide the choice of subsequent assays of greater genomic breadth or depth. METHODS Plasma samples collected from 118 metastatic cancer patients were analyzed with cf-IMPACT, a modified version of the FDA-authorized MSK-IMPACT tumor test that can detect genomic alterations in 410 cancer-associated genes. Shallow whole genome sequencing (sWGS) was also performed in the same samples to estimate cfDNA tumor fraction based on genome-wide copy number alterations using z-score statistics. Plasma samples with no somatic alterations detected by cf-IMPACT were triaged based on sWGS-estimated tumor fraction for analysis with either a less comprehensive but more sensitive assay (MSK-ACCESS) or broader whole exome sequencing (WES). RESULTS cfDNA profiling using cf-IMPACT identified somatic mutations in 55/76 (72%) patients for whom MSK-IMPACT tumor profiling data were available. A significantly higher concordance of mutational profiles and tumor mutational burden (TMB) was observed between plasma and tumor profiling for plasma samples with a high tumor fraction (z-score≥5). In the 42 patients from whom tumor data was not available, cf-IMPACT identified mutations in 16/42 (38%). In total, cf-IMPACT analysis of plasma revealed mutations in 71/118 (60%) patients, with clinically actionable alterations identified in 30 (25%), including therapeutic targets of FDA-approved drugs. Of the 47 samples without alterations detected and low tumor fraction (z-score<5), 29 had sufficient material to be re-analyzed using a less comprehensive but more sensitive assay, MSK-ACCESS, which revealed somatic mutations in 14/29 (48%). Conversely, 5 patients without alterations detected by cf-IMPACT and with high tumor fraction (z-score≥5) were analyzed by WES, which identified mutational signatures and alterations in potential oncogenic drivers not covered by the cf-IMPACT panel. Overall, we identified mutations in 90/118 (76%) patients in the entire cohort using the three complementary plasma profiling approaches. CONCLUSIONS cfDNA tumor fraction can inform the interpretation of negative cfDNA results and guide the selection of subsequent sequencing platforms that are most likely to identify clinically-relevant genomic alterations.
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Affiliation(s)
- Dana W Y Tsui
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
- Weill Cornell Medical College, Weill Cornell University, New York, USA.
- Present Address: PetDx, Inc., La Jolla, USA.
| | - Michael L Cheng
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
- Present Address: Dana-Farber Cancer Institute, Harvard Medical School, Boston, USA
| | - Maha Shady
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Present Address: Graduate School of Arts and Sciences, Harvard University, Cambridge, USA
| | - Julie L Yang
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Dennis Stephens
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Helen Won
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Preethi Srinivasan
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Kety Huberman
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Fanli Meng
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Xiaohong Jing
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Present Address: NYU Langone Health, New York, USA
| | - Juber Patel
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Maysun Hasan
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Ian Johnson
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Erika Gedvilaite
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Brian Houck-Loomis
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Nicholas D Socci
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - S Duygu Selcuklu
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Venkatraman E Seshan
- Department of Epidemiology-Biostatistics, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Hongxin Zhang
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Debyani Chakravarty
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Maria Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Samuel A Funt
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Darren R Feldman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Bob T Li
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Pedram Razavi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Jonathan Rosenberg
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Dean Bajorin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Gopa Iyer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Wassim Abida
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Howard I Scher
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Dana Rathkopf
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Agnes Viale
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Michael F Berger
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Weill Cornell Medical College, Weill Cornell University, New York, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA
| | - David B Solit
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA.
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA.
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39
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Jee J, Lebow ES, Murciano-Goroff YR, Jayakumaran G, Shen R, Brannon AR, Benayed R, Namakydoust A, Offin M, Paik PK, Yu HA, Donoghue M, Zehir A, Drilon AE, Solit DB, Jones DR, Rudin CM, Berger MF, Isbell JM, Li BT. Overall survival with circulating tumor DNA-guided therapy in advanced non-small cell lung cancer. J Clin Oncol 2021. [DOI: 10.1200/jco.2021.39.15_suppl.9009] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
9009 Background: The effectiveness of circulating tumor DNA (ctDNA) at matching patients to life prolonging therapy has been studied mostly in small cohorts with limited follow up. The prognostic value of ctDNA alterations, particularly those absent on tissue, is also unclear. To address these questions, we studied survival outcomes in a prospective cohort of patients (N = 1002) with non-small cell lung cancer (NSCLC). Methods: Adults with metastatic or recurrent NSCLC were eligible if they had no known driver mutation or a known driver with progression following targeted therapy. Patients were enrolled at Memorial Sloan Kettering Cancer Center (New York, NY) starting October 21, 2016; analysis here is from a snapshot November 1, 2020. All patients had ctDNA sequenced via the Resolution ctDx Lung platform. To reduce inclusion of incidental germline mutations, we excluded non-functionally significant mutations with an allele frequency 35-65% that were present in gnomAD. Patients could also receive, at their provider’s discretion, tissue sequencing with MSK-IMPACT, which filters germline and clonal hematopoietic (CH) mutations with matched white blood cell sequencing. We performed survival analyses using Cox proportional hazards models from time of diagnosis of advanced disease to death, left truncating at time of study entry. Results: Of 1002 patients, 348 (35%) were treated with targeted therapy; in 181 of these (52%) the targetable alteration was detected in ctDNA. Patients treated with targeted therapy had prolonged survival whether matched by tissue-based methods (HR 0.39, 95%CI 0.30-0.51) or ctDNA (HR 0.47, 95%CI 0.37-0.61). These benefits persisted across multiple subgroups. ctDNA alterations themselves were associated with worse survival (HR 2.2, 95%CI 1.8-2.8), in a manner that scaled with allele fraction and burden. Of 401 patients with time-matched tissue sampling, 62 (15%) had ctDNA alterations that were absent on IMPACT (“unique” ctDNA alterations). Three such patients had unique ctDNA EGFR T790M mutations leading to changes in therapy. However, unique ctDNA alterations were generally associated with worse survival than no ctDNA alterations (HR 2.5, 95%CI 1.7-3.7) and even tissue-matched ctDNA alterations (HR 1.7, 95%CI 1.1-2.4). Of 98 unique ctDNA mutations, 48 (49%) were detectable in tissue at subthreshold levels, 12 (12%) were filtered by IMPACT as CH or germline, and 38 mutations (39%) were absent even at subthreshold levels. ctDNA alteration burden correlated with radiographic disease extent. In multivariate models with radiographic disease extent and other clinical variables, ctDNA alterations were the strongest independent predictor of worse survival. Conclusions: Our results show that ctDNA may match patients to life-prolonging targeted therapy and have prognostic importance. ctDNA may provide data about a patient’s cancer missed by spatially restricted tissue sequencing. Clinical trial information: NCT01775072.
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Affiliation(s)
- Justin Jee
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | - Ronglai Shen
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Ryma Benayed
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Michael Offin
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Paul K. Paik
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | | | - Mark Donoghue
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Alexander E. Drilon
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY
| | | | | | | | | | | | - Bob T. Li
- Memorial Sloan Kettering Cancer Center, New York, NY
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40
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Abramson DH, Mandelker D, Francis JH, Dunkel IJ, Brannon AR, Benayed R, Berger MF, Arcila ME, Ladanyi M, Friedman DN, Jayakumaran G, Diosdado MS, Robbins MA, Haggag-Lindgren D, Shukla N, Walsh M, Kothari P, Tsui DW. Retrospective Evaluation of Somatic Alterations in Cell-Free DNA from Blood in Retinoblastoma. Ophthalmology Science 2021; 1:100015. [PMID: 36246006 PMCID: PMC9560572 DOI: 10.1016/j.xops.2021.100015] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 03/11/2021] [Accepted: 03/11/2021] [Indexed: 12/18/2022]
Abstract
Purpose Analysis of circulating tumor DNA (ctDNA) in the plasma of patients with retinoblastoma and simulating lesions. Design Retrospective cross-sectional study of the association of plasma ctDNA from retinoblastoma and simulating lesions with disease course. Participants Fifty-eight Memorial Sloan Kettering Cancer Center patients with retinoblastoma comprising 68 plasma ctDNA samples and 5 with retinoblastoma-simulating lesions. Methods The ctDNA analyzed with hybridization capture and next-generation sequencing in blood (plasma) of patients who had retinoblastoma or simulating lesions were evaluated for association with clinical course of the disease. Main Outcome Measures Presence or absence of molecular aberrations in the RB1 gene and correlations with clinical features. Results RB1 cell-free DNA (cfDNA) was detected in 16 of 19 patients with newly diagnosed, untreated intraocular retinoblastoma and in 3 of 3 patients with newly diagnosed, untreated metastatic disease. It was also present in 3 patients with recurrent intraocular disease before therapy, but was not present in patients with recurrent disease who received intra-arterial chemotherapy, nor in 21 patients who had undergone enucleation for unilateral disease. In 1 patient who had delayed treatment (insurance reasons) and showed rapid growth of the intraocular tumor, the variant allele frequency increased in 1 month from 0.34% to 2.48%. No RB1 mutations were detected in the cfDNA from plasma of patients with simulating lesions (3 with Coats disease and 1 with persistent fetal vasculature [PFV]). In 2 patients, we identified 2 independent RB1 mutations in plasma. Conclusions Mutations in RB1 were found in the cfDNA from blood of patients with newly diagnosed, untreated retinoblastoma and in patients who showed disease recurrence in the eye after prior treatment, but not in unilateral retinoblastoma after enucleation Levels of ctDNA increase in patients with progressive disease who did not receive any treatment. High plasma cfDNA levels were detected in patients with newly diagnosed metastatic disease, and these levels decreased after systemic chemotherapy was administered. Further validation is needed for measuring the somatic alterations in cfDNA from blood in retinoblastoma that could provide a promising method of monitoring patients in the future.
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Affiliation(s)
- David H. Abramson
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Ophthalmology, Weill Cornell Medical Center, New York, New York
- Correspondence: David H. Abramson, MD, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065.
| | - Diana Mandelker
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jasmine H. Francis
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Ophthalmology, Weill Cornell Medical Center, New York, New York
| | - Ira J. Dunkel
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pediatrics, Weill Cornell Medical College, New York, New York
| | - A. Rose Brannon
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F. Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria E. Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Gowtham Jayakumaran
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Monica S. Diosdado
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Melissa A. Robbins
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Neerav Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael Walsh
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Prachi Kothari
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Dana W.Y. Tsui
- Department of Pathology, Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
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41
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Yang SR, Aypar U, Rosen EY, Mata DA, Benayed R, Mullaney K, Jayakumaran G, Zhang Y, Frosina D, Drilon A, Ladanyi M, Jungbluth AA, Rekhtman N, Hechtman JF. A Performance Comparison of Commonly Used Assays to Detect RET Fusions. Clin Cancer Res 2021; 27:1316-1328. [PMID: 33272981 PMCID: PMC8285056 DOI: 10.1158/1078-0432.ccr-20-3208] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [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: 08/17/2020] [Revised: 10/23/2020] [Accepted: 11/30/2020] [Indexed: 01/02/2023]
Abstract
PURPOSE Selpercatinib and pralsetinib induce deep and durable responses in patients with advanced RET fusion-positive lung and thyroid cancer. RET fusion testing strategies with rapid and reliable results are critical given recent FDA approval. Here, we assess various clinical assays in a large pan-cancer cohort. EXPERIMENTAL DESIGN Tumors underwent DNA-based next-generation sequencing (NGS) with reflex to RNA-based NGS if no mitogenic driver or if a RET structural variant of unknown significance (SVUS) were present. Canonical DNA-level RET fusions and RNA-confirmed RET fusions were considered true fusions. Break-apart FISH and IHC performance were assessed in subgroups. RESULTS A total of 171 of 41,869 patients with DNA NGS harbored RET structural variants, including 139 canonical fusions and 32 SVUS. Twelve of 32 (37.5%) SVUS were transcribed into RNA-level fusions, resulting in 151 oncogenic RET fusions. The most common RET fusion-positive tumor types were lung (65.6%) and thyroid (23.2%). The most common partners were KIF5B (45%), CCDC6 (29.1%), and NCOA4 (13.3%). DNA NGS showed 100% (46/46) sensitivity and 99.6% (4,459/4,479) specificity. FISH showed 91.7% (44/48) sensitivity, with lower sensitivity for NCOA4-RET (66.7%, 8/12). A total of 87.5% (7/8) of RET SVUS negative for RNA-level fusions demonstrated rearrangement by FISH. The sensitivity of IHC varied by fusion partner: KIF5B sensitivity was highest (100%, 31/31), followed by CCDC6 (88.9%, 16/18) and NCOA4 (50%, 6/12). Specificity of RET IHC was 82% (73/89). CONCLUSIONS Although DNA sequencing has high sensitivity and specificity, RNA sequencing of RET SVUS is necessary. Both FISH and IHC demonstrated lower sensitivity for NCOA4-RET fusions.
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Affiliation(s)
- Soo-Ryum Yang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Umut Aypar
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ezra Y Rosen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Douglas A Mata
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kerry Mullaney
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Gowtham Jayakumaran
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yanming Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Denise Frosina
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alexander Drilon
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Achim A Jungbluth
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Natasha Rekhtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
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42
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Quesada AE, Zhang Y, Ptashkin R, Ho C, Horwitz S, Benayed R, Dogan A, Arcila ME. Next generation sequencing of breast implant-associated anaplastic large cell lymphomas reveals a novel STAT3-JAK2 fusion among other activating genetic alterations within the JAK-STAT pathway. Breast J 2021; 27:314-321. [PMID: 33660353 DOI: 10.1111/tbj.14205] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [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: 08/07/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 12/29/2022]
Abstract
Breast implant associated anaplastic large cell lymphoma (BIA-ALCL) is a distinct type of ALCL, and a new provisional entity by the 2016 revision of the World Health Organization (WHO) classification of tumors of hematopoietic and lymphoid tissues. In contrast to systemic and primary cutaneous ALCLs, BIA-ALCLs have been genetically characterized by the absence of fusions and frequent activation of the JAK-STAT3 pathway through mutations in JAK1 and STAT3. In this study, we report the results of the genetic profiling of 9 BIA-ALCL cases supporting the role of the JAK-STAT pathway activation in this entity, including the identification of an activating STAT3-JAK2 fusion similar to those recently reported in T-cell lymphoproliferative disorders of the gastrointestinal tract. To our knowledge, this is the first fusion reported in BIA-ALCL, providing further insight into the overall genetic landscape of this rare entity as well as uncovering potential options for targeted therapy in cases with advanced disease.
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Affiliation(s)
- Andrés E Quesada
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yanming Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ryan Ptashkin
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Caleb Ho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Steven Horwitz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ahmet Dogan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria E Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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43
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Yao J, Xu L, Aypar U, Meyerson HJ, Londono D, Gao Q, Baik J, Dietz J, Benayed R, Sigler A, Yabe M, Dogan A, Arcila ME, Roshal M, Zhang Y, Mauro MJ, Xiao W. Myeloid/lymphoid neoplasms with eosinophilia/ basophilia and ETV6-ABL1 fusion: cell-of-origin and response to tyrosine kinase inhibition. Haematologica 2021; 106:614-618. [PMID: 32299902 PMCID: PMC7849580 DOI: 10.3324/haematol.2020.249649] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 04/09/2020] [Indexed: 01/22/2023] Open
Affiliation(s)
- JinJuan Yao
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Lianrong Xu
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Umut Aypar
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Howard J Meyerson
- Department of Pathology, University Hospitals of Cleveland, Cleveland, OH, USA
| | - Dory Londono
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Qi Gao
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Jeeyeon Baik
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - James Dietz
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Allison Sigler
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Mariko Yabe
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Ahmet Dogan
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Maria E Arcila
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Mikhail Roshal
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Yanming Zhang
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Michael J Mauro
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Wenbin Xiao
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
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44
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Gao T, Ptashkin R, Bolton KL, Sirenko M, Fong C, Spitzer B, Menghrajani K, Ossa JEA, Zhou Y, Bernard E, Levine M, Martinez JSM, Zhang Y, Franch-Expósito S, Patel M, Braunstein LZ, Kelly D, Yabe M, Benayed R, Caltabellotta NM, Philip J, Paraiso E, Mantha S, Solit DB, Diaz LA, Berger MF, Klimek V, Levine RL, Zehir A, Devlin SM, Papaemmanuil E. Interplay between chromosomal alterations and gene mutations shapes the evolutionary trajectory of clonal hematopoiesis. Nat Commun 2021; 12:338. [PMID: 33436578 PMCID: PMC7804935 DOI: 10.1038/s41467-020-20565-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [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: 07/24/2020] [Accepted: 12/01/2020] [Indexed: 01/03/2023] Open
Abstract
Stably acquired mutations in hematopoietic cells represent substrates of selection that may lead to clonal hematopoiesis (CH), a common state in cancer patients that is associated with a heightened risk of leukemia development. Owing to technical and sample size limitations, most CH studies have characterized gene mutations or mosaic chromosomal alterations (mCAs) individually. Here we leverage peripheral blood sequencing data from 32,442 cancer patients to jointly characterize gene mutations (n = 14,789) and mCAs (n = 383) in CH. Recurrent composite genotypes resembling known genetic interactions in leukemia genomes underlie 23% of all detected autosomal alterations, indicating that these selection mechanisms are operative early in clonal evolution. CH with composite genotypes defines a patient group at high risk of leukemia progression (3-year cumulative incidence 14.6%, CI: 7-22%). Multivariable analysis identifies mCA as an independent risk factor for leukemia development (HR = 14, 95% CI: 6-33, P < 0.001). Our results suggest that mCA should be considered in conjunction with gene mutations in the surveillance of patients at risk of hematologic neoplasms.
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Affiliation(s)
- Teng Gao
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Center for Computational Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Ryan Ptashkin
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Kelly L Bolton
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Maria Sirenko
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Center for Computational Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Christopher Fong
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Center for Computational Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Barbara Spitzer
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Kamal Menghrajani
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Juan E Arango Ossa
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Center for Computational Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Yangyu Zhou
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Center for Computational Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Elsa Bernard
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Center for Computational Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Max Levine
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Center for Computational Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Juan S Medina Martinez
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Center for Computational Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Yanming Zhang
- Department of Pathology, Cytogenetics Laboratory, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Sebastià Franch-Expósito
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Minal Patel
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Lior Z Braunstein
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Daniel Kelly
- Department of Information Systems, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Mariko Yabe
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Nicole M Caltabellotta
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - John Philip
- Department of Health Informatics, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Ederlinda Paraiso
- Center for Strategy & Innovation, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Simon Mantha
- Department of Medicine, Hematology Service, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - David B Solit
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
- Department of Medicine, Solid Tumor Division, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Luis A Diaz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
- Program in Precision Interception and Prevention, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Michael F Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Virginia Klimek
- Department of Medicine, Hematology Service, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
- Weill Cornell Medical College, 407 E 61st St, New York, NY, 10065, USA
| | - Ross L Levine
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
- Program in Precision Interception and Prevention, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Sean M Devlin
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Elli Papaemmanuil
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Center for Computational Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA.
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA.
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA.
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA.
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45
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Selenica P, Conlon N, Gonzalez C, Frosina D, Jungbluth AA, Beets-Tan RGH, Rao MK, Zhang Y, Benayed R, Ladanyi M, Solit DB, Chiang S, Hyman DM, Hensley ML, Soslow RA, Weigelt B, Murali R. Genomic Profiling Aids Classification of Diagnostically Challenging Uterine Mesenchymal Tumors With Myomelanocytic Differentiation. Am J Surg Pathol 2021; 45:77-92. [PMID: 32889887 PMCID: PMC8276853 DOI: 10.1097/pas.0000000000001572] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [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] [Indexed: 12/13/2022]
Abstract
Although diagnosis of high-grade uterine mesenchymal tumors (UMTs) exhibiting classic morphologic features is straightforward, diagnosis is more challenging in tumors in which prototypical features are poorly developed, focal, and/or coexist with features seen in other neoplasms. Here, we sought to define the repertoire of somatic genetic alterations in diagnostically challenging UMTs with myomelanocytic differentiation, including some reported as perivascular epithelioid cell tumors (PEComas). In 17 samples from 15 women, the tumors were histologically heterogenous. Immunohistochemical expression of at least 1 melanocytic marker (HMB45, Melan-A, or MiTF) was identified in all tumors, and of myogenic markers (desmin or smooth muscle actin) in most tumors. Targeted massively parallel sequencing revealed several genetic alterations, most commonly in TP53 (41% mutation, 12% deletion), TSC2 (29% mutation, 6% deletion), RB1 (18% deletion), ATRX (24% mutation), MED12 (12% mutation), BRCA2 (12% deletion), CDKN2A (6% deletion) as well as FGFR3, NTRK1, and ERBB3 amplification (each 6%). Gene rearrangements (JAZF1-SUZ12; DNAJB6-PLAG1; and SFPQ-TFE3) were identified in 3 tumors. Integrating histopathologic, immunohistochemical, and genetic findings, tumors from 4 patients were consistent with malignant PEComa (1 TFE3-rearranged); 6 were classified as leiomyosarcomas; 3 showed overlapping features of PEComa and other sarcoma types (leiomyosarcoma or low-grade endometrial stromal sarcoma); and 2 were classified as sarcoma, not otherwise specified. Our findings suggest that diagnostically challenging UMTs with myomelanocytic differentiation represent a heterogenous group of neoplasms which harbor a diverse repertoire of somatic genetic alterations; these genetic alterations can aid classification.
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Affiliation(s)
- Pier Selenica
- Departments of Pathology
- GROW School for Oncology and Developmental Biology
| | - Niamh Conlon
- Departments of Pathology
- Department of Pathology, Cork University Hospital, Cork, Ireland
| | | | | | | | - Regina G. H. Beets-Tan
- GROW School for Oncology and Developmental Biology
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | - David B. Solit
- Department of Radiology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Medicine
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46
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Gupta S, Vanderbilt CM, Lin YT, Benhamida JK, Jungbluth AA, Rana S, Momeni-Boroujeni A, Chang JC, Mcfarlane T, Salazar P, Mullaney K, Middha S, Zehir A, Gopalan A, Bale TA, Ganly I, Arcila ME, Benayed R, Berger MF, Ladanyi M, Dogan S. A Pan-Cancer Study of Somatic TERT Promoter Mutations and Amplification in 30,773 Tumors Profiled by Clinical Genomic Sequencing. J Mol Diagn 2020; 23:253-263. [PMID: 33285287 DOI: 10.1016/j.jmoldx.2020.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 10/15/2020] [Accepted: 11/10/2020] [Indexed: 01/20/2023] Open
Abstract
TERT gene promoter mutations are known in multiple cancer types. Other TERT alterations remain poorly characterized. Sequencing data from 30,773 tumors analyzed by a hybridization capture next-generation sequencing assay (Memorial Sloan Kettering Cancer Center Integrated Mutation Profiling of Actionable Cancer Targets) were analyzed for the presence of TERT alterations. Promoter rearrangements (500 bases upstream of the transcriptional start site), hypermethylation (n = 57), and gene expression (n = 155) were evaluated for a subset of cases. Mutually exclusive and recurrent promoter mutations were identified at three hot spots upstream of the transcriptional start site in 11.3% of cases (-124: 74%; -146: 24%; and -138: <2%). Mutually exclusive amplification events were identified in another 2.3% of cases, whereas mutually exclusive rearrangements proximal to the TERT gene were seen in 24 cases. The highest incidence of TERT promoter mutations was seen in cutaneous melanoma (82%), whereas amplification events significantly outnumbered promoter mutations in well-differentiated/dedifferentiated liposarcoma (14.1% versus 2.4%) and adrenocortical carcinoma (13.6% versus 4.5%). Gene expression analysis suggests that the highest levels of gene expression are seen in cases with amplifications and rearrangements. Hypermethylation events upstream of the TERT coding sequence were not mutually exclusive with known pathogenic alterations. Studies aimed at defining the prevalence and prognostic impact of TERT alterations should incorporate other pathogenic TERT alterations as these may impact telomerase function.
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Affiliation(s)
- Sounak Gupta
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Chad M Vanderbilt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yun-Te Lin
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jamal K Benhamida
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Achim A Jungbluth
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Satshil Rana
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Jason C Chang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Tiffany Mcfarlane
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Paulo Salazar
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kerry Mullaney
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sumit Middha
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Anuradha Gopalan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Tejus A Bale
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ian Ganly
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria E Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Snjezana Dogan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
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47
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Ogura K, Somwar R, Hmeljak J, Magnan H, Benayed R, Momeni Boroujeni A, Bowman AS, Mattar MS, Khodos I, de Stanchina E, Jungbluth A, Asher M, Odintsov I, Hartono AB, LaQuaglia MP, Slotkin E, Pratilas CA, Lee SB, Spraggon L, Ladanyi M. Therapeutic Potential of NTRK3 Inhibition in Desmoplastic Small Round Cell Tumor. Clin Cancer Res 2020; 27:1184-1194. [PMID: 33229458 DOI: 10.1158/1078-0432.ccr-20-2585] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/27/2020] [Accepted: 11/18/2020] [Indexed: 12/12/2022]
Abstract
PURPOSE Desmoplastic small round cell tumor (DSRCT) is a highly lethal intra-abdominal sarcoma of adolescents and young adults. DSRCT harbors a t(11;22)(p13:q12) that generates the EWSR1-WT1 chimeric transcription factor, the key oncogenic driver of DSRCT. EWSR1-WT1 rewires global gene expression networks and activates aberrant expression of targets that together mediate oncogenesis. EWSR1-WT1 also activates a neural gene expression program. EXPERIMENTAL DESIGN Among these neural markers, we found prominent expression of neurotrophic tyrosine kinase receptor 3 (NTRK3), a druggable receptor tyrosine kinase. We investigated the regulation of NTRK3 by EWSR1-WT1 and its potential as a therapeutic target in vitro and in vivo, the latter using novel patient-derived models of DSRCT. RESULTS We found that EWSR1-WT1 binds upstream of NTRK3 and activates its transcription. NTRK3 mRNA is highly expressed in DSRCT compared with other major chimeric transcription factor-driven sarcomas and most DSRCTs are strongly immunoreactive for NTRK3 protein. Remarkably, expression of NTRK3 kinase domain mRNA in DSRCT is also higher than in cancers with NTRK3 fusions. Abrogation of NTRK3 expression by RNAi silencing reduces growth of DSRCT cells and pharmacologic targeting of NTRK3 with entrectinib is effective in both in vitro and in vivo models of DSRCT. CONCLUSIONS Our results indicate that EWSR1-WT1 directly activates NTRK3 expression in DSRCT cells, which are dependent on its expression and activity for growth. Pharmacologic inhibition of NTRK3 by entrectinib significantly reduces growth of DSRCT cells both in vitro and in vivo, providing a rationale for clinical evaluation of NTRK3 as a therapeutic target in DSRCT.
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Affiliation(s)
- Koichi Ogura
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Romel Somwar
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Julija Hmeljak
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Heather Magnan
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Anita S Bowman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marissa S Mattar
- Anti-tumor Assessment Core Facility, Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Inna Khodos
- Anti-tumor Assessment Core Facility, Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elisa de Stanchina
- Anti-tumor Assessment Core Facility, Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Achim Jungbluth
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marina Asher
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Igor Odintsov
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alifiani B Hartono
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Michael P LaQuaglia
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Emily Slotkin
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Christine A Pratilas
- Division of Pediatric Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland
| | - Sean Bong Lee
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Lee Spraggon
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York. .,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
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48
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Guo R, Offin M, Brannon AR, Chang J, Chow A, Delasos L, Girshman J, Wilkins O, McCarthy CG, Makhnin A, Falcon C, Scott K, Tian Y, Cecchi F, Hembrough T, Alex D, Shen R, Benayed R, Li BT, Rudin CM, Kris MG, Arcila ME, Rekhtman N, Paik P, Zehir A, Drilon A. MET Exon 14-altered Lung Cancers and MET Inhibitor Resistance. Clin Cancer Res 2020; 27:799-806. [PMID: 33172896 DOI: 10.1158/1078-0432.ccr-20-2861] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/17/2020] [Accepted: 11/04/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE MET tyrosine kinase inhibitors (TKIs) can achieve modest clinical outcomes in MET exon 14-altered lung cancers, likely secondary to primary resistance. Mechanisms of primary resistance remain poorly characterized and comprehensive proteomic analyses have not previously been performed. EXPERIMENTAL DESIGN We performed hybrid capture-based DNA sequencing, targeted RNA sequencing, cell-free DNA sequencing, selected reaction monitoring mass spectrometry (SRM-MS), and immunohistochemistry on patient samples of MET exon 14-altered lung cancers treated with a MET TKI. Associations between overall response rate (ORR), progression-free survival (PFS), and putative genomic alterations and MET protein expression were evaluated. RESULTS Seventy-five of 168 MET exon 14-altered lung cancers received a MET TKI. Previously undescribed (zygosity, clonality, whole-genome duplication) and known (copy-number focality, tumor mutational burden, mutation region/type) genomic factors were not associated with ORR/PFS (P > 0.05). In contrast, MET expression was associated with MET TKI benefit. Only cases with detectable MET expression by SRM-MS (N = 15) or immunochemistry (N = 22) responded to MET TKI therapy, and cancers with H-score ≥ 200 had a higher PFS than cancers below this cutoff (10.4 vs. 5.5 months, respectively; HR, 3.87; P = 0.02). CONCLUSIONS In MET exon 14-altered cancers treated with a MET TKI, a comprehensive analysis of previously unknown and known genomic factors did not identify a genomic mechanism of primary resistance. Instead, MET expression correlated with benefit, suggesting the potential role of interrogating the proteome in addition to the genome in confirmatory prospective trials.
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Affiliation(s)
- Robin Guo
- Thoracic Oncology, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Early Drug Development Services, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael Offin
- Thoracic Oncology, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York
| | - A Rose Brannon
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jason Chang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Andrew Chow
- Thoracic Oncology, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lukas Delasos
- Department of Medicine, UConn Health, Farmington, Connecticut
| | - Jeffrey Girshman
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Olivia Wilkins
- Thoracic Oncology, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Caroline G McCarthy
- Thoracic Oncology, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alex Makhnin
- Thoracic Oncology, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Christina Falcon
- Thoracic Oncology, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | | | | | | | - Deepu Alex
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ronglai Shen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering, New York, New York
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Bob T Li
- Thoracic Oncology, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Early Drug Development Services, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York
| | - Charles M Rudin
- Thoracic Oncology, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mark G Kris
- Thoracic Oncology, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York
| | - Maria E Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Natasha Rekhtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Paul Paik
- Thoracic Oncology, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alexander Drilon
- Thoracic Oncology, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York. .,Early Drug Development Services, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York
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49
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Mata DA, Benhamida JK, Lin AL, Vanderbilt CM, Yang SR, Villafania LB, Ferguson DC, Jonsson P, Miller AM, Tabar V, Brennan CW, Moss NS, Sill M, Benayed R, Mellinghoff IK, Rosenblum MK, Arcila ME, Ladanyi M, Bale TA. Genetic and epigenetic landscape of IDH-wildtype glioblastomas with FGFR3-TACC3 fusions. Acta Neuropathol Commun 2020; 8:186. [PMID: 33168106 PMCID: PMC7653727 DOI: 10.1186/s40478-020-01058-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 10/13/2020] [Indexed: 01/29/2023] Open
Abstract
A subset of glioblastomas (GBMs) harbors potentially druggable oncogenic FGFR3-TACC3 (F3T3) fusions. However, their associated molecular and clinical features are poorly understood. Here we analyze the frequency of F3T3-fusion positivity, its associated genetic and methylation profiles, and its impact on survival in 906 IDH-wildtype GBM patients. We establish an F3T3 prevalence of 4.1% and delineate its associations with cancer signaling pathway alterations. F3T3-positive GBMs had lower tumor mutational and copy-number alteration burdens than F3T3-wildtype GBMs. Although F3T3 fusions were predominantly mutually exclusive with other oncogenic RTK pathway alterations, they did rarely co-occur with EGFR amplification. They were less likely to harbor TP53 alterations. By methylation profiling, they were more likely to be assigned the mesenchymal or RTK II subclass. Despite being older at diagnosis and having similar frequencies of MGMT promoter hypermethylation, patients with F3T3-positive GBMs lived about 8 months longer than those with F3T3-wildtype tumors. While consistent with IDH-wildtype GBM, F3T3-positive GBMs exhibit distinct biological features, underscoring the importance of pursuing molecular studies prior to clinical trial enrollment and targeted treatment.
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50
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Miller A, Szalontay L, Ahmad H, Bouvier N, Rodriguez-Sanchez I, Bale T, Benayed R, Arcila M, Donzelli M, Dunkel I, Gilheeney S, Khakoo Y, Kramer K, Sait SF, Souweidane M, Mellinghoff I, Karajannis M. BIOM-56. THE INTEGRATION OF A LIQUID BIOPSY PROGRAM INTO THE CARE OF PEDIATRIC BRAIN TUMOR PATIENTS. Neuro Oncol 2020. [DOI: 10.1093/neuonc/noaa215.053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Pediatric CNS tumors remain the leading cause of cancer-related death in children and adolescents. Safe sampling of tumor tissue for diagnostic purposes may be difficult if not impossible. Detection of minimal residual or recurrent disease prior to definitive clinical or radiographic progression may allow earlier initiation of novel therapies and ultimately improve overall survival. Given the rarity of serial sampling of tumor tissue, our understanding of molecular evolution in response to therapy remains limited. Recent technological advances have led to the development of “liquid biopsy” assays, which detect cell-free DNA (cfDNA) in blood, cerebrospinal fluid (CSF) or other bodily fluids. Here, we report our initial clinical experience with the recently established MSK Kids pediatric neuro-oncology liquid-biopsy program at Memorial Sloan Kettering Cancer Center (MSKCC) using MSK-IMPACT, which is clinically validated by the New York State Department of Health for CSF cell-free DNA (cfDNA)vprofiling. All CSF samples were collected as part of clinical care, and results reported to both clinicians and patients/families. Samples from 29 unique patients were sequenced. Histopathology included high-grade glioma (5); low-grade glioma (2); medulloblastoma (8); pineoblastoma (3); retinoblastoma (4); other (7). CSF cfDNA could be detected in 18/42 samples (43%) and 12/29 patients (34%). CSF cfDNA was more commonly detected in higher-grade, disseminated tumors such as high-grade glioma (60%), medulloblastoma (38%), and pineoblastoma (100%). Low-grade lesions without leptomeningeal involvement did not result in detectable CSF cfDNA shedding (86% were negative). In a subset of patients, MSK-IMPACT identified previously unrecognized molecular actionable targets (e.g. BRAF-KIAA1549 fusion); or the detection of “minimal residual disease” prior to the detection of tumor recurrence by conventional diagnostics, impacting clinical care decisions. Future directions include integration of CSF cfDNA into prospective clinical trials as a correlative biomarker.
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Affiliation(s)
| | - Luca Szalontay
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hamza Ahmad
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nancy Bouvier
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Tejus Bale
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ryma Benayed
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria Arcila
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria Donzelli
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ira Dunkel
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Yasmin Khakoo
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kim Kramer
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Mark Souweidane
- NY Presbyterian Hospital/Weill Cornell Medical Center, New York, NY, USA
| | | | - Matthias Karajannis
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY, USA
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