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Prevalence of NTRK Fusions in Canadian Solid Tumour Cancer Patients. Mol Diagn Ther 2023; 27:87-103. [PMID: 36194351 PMCID: PMC9531629 DOI: 10.1007/s40291-022-00617-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/04/2022] [Indexed: 02/04/2023]
Abstract
INTRODUCTION Neurotrophic tyrosine receptor kinase (NTRK) gene fusions occur in ~ 0.3% of all solid tumours but are enriched in some rare tumour types. Tropomyosin receptor kinase (TRK) inhibitors larotrectinib and entrectinib are approved as tumour-agnostic therapies for solid tumours harbouring NTRK fusions. METHODS This study investigated the prevalence of NTRK fusions in Canadian patients and also aimed to help guide NTRK testing paradigms through analysis of data reported from a national clinical diagnostic testing program between September 2019 and July 2021. RESULTS Of 1,687 patients included in the final analysis, NTRK fusions were detected in 0.71% (n = 12) of patients representing salivary gland carcinoma (n = 3), soft tissue sarcoma (n = 3), CNS (n = 3), and one in each of melanoma, lung, and colorectal cancer. All three salivary gland carcinomas contained ETV6-NTRK3 fusions. Thirteen (0.77%) clinically actionable incidental findings were also detected. Two of the 13 samples containing incidental findings were NTRK fusion-positive (GFOD1-NTRK2, FGFR3-TACC3 in a glioblastoma and AFAP1-NTRK2, BRAF c.1799T>A in a glioma). The testing algorithm screened most patient samples via pan-TRK immunohistochemistry (IHC), whereas samples from the central nervous system (CNS), pathognomonic cancers, and confirmed/ putative NTRK fusion-positive samples identified under research protocols were reflexed straight to next-generation sequencing (NGS). CONCLUSION These findings highlight the benefit and practicality of a diagnostic testing program to identify patients suitable for tumour-agnostic TRK inhibitor therapies, as well as other targeted therapies, due to clinically actionable incidental findings identified. Collectively, these findings may inform future guidance on selecting the appropriate testing approach per tumour type and on optimal NTRK testing algorithms.
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Torre M, Vasudevaraja V, Serrano J, DeLorenzo M, Malinowski S, Blandin AF, Pages M, Ligon AH, Dong F, Meredith DM, Nasrallah MP, Horbinski C, Dahiya S, Ligon KL, Santi M, Ramkissoon SH, Filbin MG, Snuderl M, Alexandrescu S. Molecular and clinicopathologic features of gliomas harboring NTRK fusions. Acta Neuropathol Commun 2020; 8:107. [PMID: 32665022 PMCID: PMC7362646 DOI: 10.1186/s40478-020-00980-z] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 06/24/2020] [Indexed: 01/07/2023] Open
Abstract
Fusions involving neurotrophic tyrosine receptor kinase (NTRK) genes are detected in ≤2% of gliomas and can promote gliomagenesis. The remarkable therapeutic efficacy of TRK inhibitors, which are among the first Food and Drug Administration-approved targeted therapies for NTRK-fused gliomas, has generated significant clinical interest in characterizing these tumors. In this multi-institutional retrospective study of 42 gliomas with NTRK fusions, next generation DNA sequencing (n = 41), next generation RNA sequencing (n = 1), RNA-sequencing fusion panel (n = 16), methylation profile analysis (n = 18), and histologic evaluation (n = 42) were performed. All infantile NTRK-fused gliomas (n = 7) had high-grade histology and, with one exception, no other significant genetic alterations. Pediatric NTRK-fused gliomas (n = 13) typically involved NTRK2, ranged from low- to high-histologic grade, and demonstrated histologic overlap with desmoplastic infantile ganglioglioma, pilocytic astrocytoma, ganglioglioma, and glioblastoma, among other entities, but they rarely matched with high confidence to known methylation class families or with each other; alterations involving ATRX, PTEN, and CDKN2A/2B were present in a subset of cases. Adult NTRK-fused gliomas (n = 22) typically involved NTRK1 and had predominantly high-grade histology; genetic alterations involving IDH1, ATRX, TP53, PTEN, TERT promoter, RB1, CDKN2A/2B, NF1, and polysomy 7 were common. Unsupervised principal component analysis of methylation profiles demonstrated no obvious grouping by histologic grade, NTRK gene involved, or age group. KEGG pathway analysis detected methylation differences in genes involved in PI3K/AKT, MAPK, and other pathways. In summary, the study highlights the clinical, histologic, and molecular heterogeneity of NTRK-fused gliomas, particularly when stratified by age group.
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Affiliation(s)
- Matthew Torre
- grid.62560.370000 0004 0378 8294Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, 75 Francis Street, Boston, MA 02115 USA ,grid.2515.30000 0004 0378 8438Department of Pathology, Boston Children’s Hospital and Harvard Medical School, 300 Longwood Ave, Bader Building, Boston, MA 02115 USA
| | - Varshini Vasudevaraja
- grid.137628.90000 0004 1936 8753Department of Pathology, NYU Langone Health, 550 First Avenue, New York, NY 10016 USA
| | - Jonathan Serrano
- grid.137628.90000 0004 1936 8753Department of Pathology, NYU Langone Health, 550 First Avenue, New York, NY 10016 USA
| | - Michael DeLorenzo
- grid.137628.90000 0004 1936 8753Department of Pathology, NYU Langone Health, 550 First Avenue, New York, NY 10016 USA
| | - Seth Malinowski
- grid.65499.370000 0001 2106 9910Department of Oncologic Pathology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02115 USA
| | - Anne-Florence Blandin
- grid.65499.370000 0001 2106 9910Department of Oncologic Pathology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02115 USA
| | - Melanie Pages
- grid.414435.30000 0001 2200 9055Department of Neuropathology, GHU Paris Sainte-Anne Hospital, 1 Rue Cabanis, 75014 Paris, France
| | - Azra H. Ligon
- grid.62560.370000 0004 0378 8294Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, 75 Francis Street, Boston, MA 02115 USA ,grid.62560.370000 0004 0378 8294Center for Advanced Molecular Diagnostics, Brigham and Women’s Hospital and Harvard Medical School, 75 Francis Street, Boston, MA 02115 USA
| | - Fei Dong
- grid.62560.370000 0004 0378 8294Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, 75 Francis Street, Boston, MA 02115 USA
| | - David M. Meredith
- grid.62560.370000 0004 0378 8294Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, 75 Francis Street, Boston, MA 02115 USA
| | - MacLean P. Nasrallah
- grid.25879.310000 0004 1936 8972Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, 3400 Spruce Street 34th St, Philadelphia, PA 19104 USA
| | - Craig Horbinski
- grid.16753.360000 0001 2299 3507Department of Neurological Surgery, Northwestern University, Chicago, IL USA ,grid.16753.360000 0001 2299 3507Department of Pathology, Northwestern University, 303 East Chicago Avenue, Chicago, IL 60611 USA
| | - Sonika Dahiya
- grid.4367.60000 0001 2355 7002Division of Neuropathology, Department of Pathology and Immunology, Washington University School of Medicine, 660 South Euclid Avenue, Campus Box 8118, St. Louis, MO 63110 USA
| | - Keith L. Ligon
- grid.62560.370000 0004 0378 8294Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, 75 Francis Street, Boston, MA 02115 USA ,grid.2515.30000 0004 0378 8438Department of Pathology, Boston Children’s Hospital and Harvard Medical School, 300 Longwood Ave, Bader Building, Boston, MA 02115 USA ,grid.65499.370000 0001 2106 9910Department of Oncologic Pathology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02115 USA
| | - Mariarita Santi
- grid.25879.310000 0004 1936 8972Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, 3400 Spruce Street 34th St, Philadelphia, PA 19104 USA ,grid.239552.a0000 0001 0680 8770Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Shakti H. Ramkissoon
- Foundation Medicine, 7010 Kit Creek Road, Morrisville, NC 27560 USA ,grid.241167.70000 0001 2185 3318Wake Forest Comprehensive Cancer Center and Department of Pathology, Wake Forest School of Medicine, Winston-Salem, 27157 NC USA
| | - Mariella G. Filbin
- grid.38142.3c000000041936754XDepartment of Pediatric Oncology, Dana Farber Cancer Institute, Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215 USA
| | - Matija Snuderl
- grid.137628.90000 0004 1936 8753Department of Pathology, NYU Langone Health, 550 First Avenue, New York, NY 10016 USA
| | - Sanda Alexandrescu
- grid.62560.370000 0004 0378 8294Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, 75 Francis Street, Boston, MA 02115 USA ,grid.2515.30000 0004 0378 8438Department of Pathology, Boston Children’s Hospital and Harvard Medical School, 300 Longwood Ave, Bader Building, Boston, MA 02115 USA
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