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Lanic MD, Guérin R, Wassef M, Durdilly P, Rainville V, Sater V, Jardin F, Ruminy P, Costes-Martineau V, Laé M. Detection of salivary gland and sinonasal fusions by a next-generation sequencing based, ligation-dependent, multiplex RT-PCR assay. Histopathology 2023; 83:685-699. [PMID: 37350081 DOI: 10.1111/his.14971] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/17/2023] [Accepted: 05/23/2023] [Indexed: 06/24/2023]
Abstract
AIMS The discovery of tumour type-specific gene fusion oncogenes in benign and malignant salivary gland and sinonasal (SGSN) tumours has significantly increased our knowledge about their molecular pathology and classification. METHODS AND RESULTS We developed a new targeted multiplexed next-generation sequencing (NGS)-based method that utilizes ligation dependent reverse-transcriptase polymerase chain reaction (LD-RT-PCR) to detect oncogenic fusion transcripts involving 116 genes, leading to 96 gene fusions known to be recurrently rearranged in these tumours. In all, 180 SGSN tumours (formalin-fixed, paraffin-embedded samples, 141 specimens and 39 core needle biopsies) from the REFCORpath (French network for rare head and neck cancers) with previously identified fusion genes by fluorescent in situ hybridisation (FISH), RT-PCR, or molecular immunohistochemistry were selected to test its specificity and sensitivity and validate its diagnostic use. Tested tumours encompassed 14 major tumours types, including secretory carcinoma, mucoepidermoid carcinoma, adenoid cystic carcinoma, salivary gland intraductal carcinoma, clear cell carcinoma, pleomorphic adenoma, adamantinoma-like Ewing Sarcoma, EWSR1::COLCA2 sinonasal sarcoma, DEK::AFF2 sinonasal carcinoma, and biphenotypic sinonasal sarcoma. In-frame fusion transcripts were detected in 97.8% of cases (176/180). Gene fusion assay results correlated with conventional techniques (immunohistochemistry [IHC], FISH, and RT-PCR) in 176/180 tumours (97.8%). CONCLUSION This targeted multiplexed NGS-based LD-RT-PCR method is a robust, highly sensitive method for the detection of recurrent gene fusions from routine clinical SGSN tumours. It can be easily customized to cover new fusions. These results are promising for implementing an integrated NGS system to rapidly detect genetic aberrations, facilitating accurate, genomics-based diagnoses, and accelerate time to precision therapies in SGSN tumours.
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Affiliation(s)
- Marie-Delphine Lanic
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIROUEN, Rouen, France
| | - René Guérin
- Department of Pathology, Centre Henri Becquerel, Rouen, France
| | - Michel Wassef
- Department of Pathology, Hôpital Lariboisière, Paris, France
| | | | - Vinciane Rainville
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIROUEN, Rouen, France
| | - Vincent Sater
- Department of Pathology, Centre Henri Becquerel, Rouen, France
| | - Fabrice Jardin
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIROUEN, Rouen, France
| | - Philippe Ruminy
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIROUEN, Rouen, France
| | | | - Marick Laé
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIROUEN, Rouen, France
- Department of Pathology, Centre Henri Becquerel, Rouen, France
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Kato H, Kano S, Yasui Y, Nojiri Y, Yoshimitsu M, Nakamura M, Morita A. Effectiveness Treatment of a BRAF-ZKSCAN5 Fusion Gene Melanoma Case with Dabrafenib/Trametinib. Case Rep Oncol 2023; 16:1007-1012. [PMID: 37900828 PMCID: PMC10601785 DOI: 10.1159/000533822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 08/24/2023] [Indexed: 10/31/2023] Open
Abstract
The most important driver gene in malignant melanoma is the BRAF mutation, and molecularly targeted therapies targeting mutations, mainly V600E and V600k, are used in clinical practice. In this report, we treated a patient with malignant melanoma expressing a rare BRAF-ZKSCAN5 fusion gene with dabrafenib/trametinib. The patient was a 71-year-old female. She was diagnosed with malignant melanoma (pT4aN3M0, STAGE IIIC) of the abdomen with axillary lymph node metastasis. She underwent extended resection and axillary lymph node dissection and was treated with adjuvant therapy, but lung and mediastinal lymph node metastases developed. The patient was treated with immune checkpoint inhibitors for metastatic lesions and achieved complete remission, but relapsed and metastatic lesions appeared in the cervical lymph nodes. Next-generation sequencing revealed the BRAF-ZKSCAN5 fusion gene, and treatment with dabrafenib/trametinib was initiated. After 1 month of treatment, tumor growth stopped and the length of the tumor shrank by 22.2%, but she developed grade 3 adverse events of nausea, fatigue, and diarrhea and had difficulty exercising, forcing her to discontinue treatment after 6 weeks. The tumor continued to shrink during drug administration. This case report may provide insight into treatment options for cases in which the BRAF fusion gene was observed, which is expected to be detected in large numbers by next-generation sequencing in the future.
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Affiliation(s)
- Hiroshi Kato
- Department of Geriatric and Environmental Dermatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Shinji Kano
- Department of Geriatric and Environmental Dermatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Yukiko Yasui
- Department of Geriatric and Environmental Dermatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Yuka Nojiri
- Department of Geriatric and Environmental Dermatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Maki Yoshimitsu
- Department of Geriatric and Environmental Dermatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Motoki Nakamura
- Department of Geriatric and Environmental Dermatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Akimichi Morita
- Department of Geriatric and Environmental Dermatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
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Loo SK, Yates ME, Yang S, Oesterreich S, Lee AV, Wang X. Fusion-associated carcinomas of the breast: Diagnostic, prognostic, and therapeutic significance. Genes Chromosomes Cancer 2022; 61:261-273. [PMID: 35106856 PMCID: PMC8930468 DOI: 10.1002/gcc.23029] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 11/11/2022] Open
Abstract
Recurrent gene fusions comprise a class of viable genetic targets in solid tumors that have culminated several recent breakthrough cancer therapies. Their role in breast cancer, however, remains largely underappreciated due to the complexity of genomic rearrangements in breast malignancy. Just recently, we and others have identified several recurrent gene fusions in breast cancer with important clinical and biological implications. Examples of the most significant recurrent gene fusions to date include (1) ESR1::CCDC170 gene fusions in luminal B and endocrine-resistant breast cancer that exert oncogenic function via modulating the HER2/HER3/SRC Proto-Oncogene (SRC) complex, (2) ESR1 exon 6 fusions in metastatic disease that drive estrogen-independent estrogen-receptor transcriptional activity, (3) BCL2L14::ETV6 fusions in a more aggressive form of the triple-negative subtype that prime epithelial-mesenchymal transition and endow paclitaxel resistance, (4) the ETV6::NTRK3 fusion in secretory breast carcinoma that constitutively activates NTRK3 kinase, (5) the oncogenic MYB-NFIB fusion as a genetic driver underpinning adenoid cystic carcinomas of the breast that activates MYB Proto-Oncogene (MYB) pathway, and (6) the NOTCH/microtubule-associated serine-threonine (MAST) kinase gene fusions that activate NOTCH and MAST signaling. Importantly, these fusions are enriched in more aggressive and lethal breast cancer presentations and appear to confer therapeutic resistance. Thus, these gene fusions could be utilized as genetic biomarkers to identify patients who require more intensive treatment and surveillance. In addition, kinase fusions are currently being evaluated in breast cancer clinical trials and ongoing mechanistic investigation is exposing therapeutic vulnerabilities in patients with fusion-positive disease.
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Affiliation(s)
- Suet Kee Loo
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15232, USA
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, 15232, USA
| | - Megan E. Yates
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15232, USA
- Integrative Systems Biology Program, University of Pittsburgh, Pittsburgh, PA, 15232, USA
- Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15232, USA
| | - Sichun Yang
- Center for Proteomics and Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Steffi Oesterreich
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15232, USA
- Department of Pharmacology & Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15232, USA
| | - Adrian V. Lee
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15232, USA
- Department of Pharmacology & Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15232, USA
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, 15232, USA
| | - Xiaosong Wang
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, 15232, USA
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, 15232, USA
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, 15232, USA
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