1
|
Zago Baltazar R, Claerhout S, Vander Borght S, Spans L, Sciot R, Schöffski P, Hompes D, Sinnaeve F, Wafa H, Renard M, van den Hout MFCM, Vernemmen A, Libbrecht L, De Roo A, Mazzeo F, van Marcke C, Deraedt K, Bourgain C, Vanden Bempt I. Recurrent and novel fusions detected by targeted RNA sequencing as part of the diagnostic workflow of soft tissue and bone tumours. J Pathol Clin Res 2024; 10:e12376. [PMID: 38738521 PMCID: PMC11089496 DOI: 10.1002/2056-4538.12376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 03/16/2024] [Accepted: 04/15/2024] [Indexed: 05/14/2024]
Abstract
The identification of gene fusions has become an integral part of soft tissue and bone tumour diagnosis. We investigated the added value of targeted RNA-based sequencing (targeted RNA-seq, Archer FusionPlex) to our current molecular diagnostic workflow of these tumours, which is based on fluorescence in situ hybridisation (FISH) for the detection of gene fusions using 25 probes. In a series of 131 diagnostic samples targeted RNA-seq identified a gene fusion, BCOR internal tandem duplication or ALK deletion in 47 cases (35.9%). For 74 cases, encompassing 137 FISH analyses, concordance between FISH and targeted RNA-seq was evaluated. A positive or negative FISH result was confirmed by targeted RNA-seq in 27 out of 49 (55.1%) and 81 out of 88 (92.0%) analyses, respectively. While negative concordance was high, targeted RNA-seq identified a canonical gene fusion in seven cases despite a negative FISH result. The 22 discordant FISH-positive analyses showed a lower percentage of rearrangement-positive nuclei (range 15-41%) compared to the concordant FISH-positive analyses (>41% of nuclei in 88.9% of cases). Six FISH analyses (in four cases) were finally considered false positive based on histological and targeted RNA-seq findings. For the EWSR1 FISH probe, we observed a gene-dependent disparity (p = 0.0020), with 8 out of 35 cases showing a discordance between FISH and targeted RNA-seq (22.9%). This study demonstrates an added value of targeted RNA-seq to our current diagnostic workflow of soft tissue and bone tumours in 19 out of 131 cases (14.5%), which we categorised as altered diagnosis (3 cases), added precision (6 cases), or augmented spectrum (10 cases). In the latter subgroup, four novel fusion transcripts were found for which the clinical relevance remains unclear: NAB2::NCOA2, YAP1::NUTM2B, HSPA8::BRAF, and PDE2A::PLAG1. Overall, targeted RNA-seq has proven extremely valuable in the diagnostic workflow of soft tissue and bone tumours.
Collapse
Affiliation(s)
| | - Sofie Claerhout
- Department of Human GeneticsUniversity Hospitals KU LeuvenLeuvenBelgium
| | - Sara Vander Borght
- Department of Human GeneticsUniversity Hospitals KU LeuvenLeuvenBelgium
- Department of PathologyUniversity Hospitals KU LeuvenLeuvenBelgium
| | - Lien Spans
- Department of Human GeneticsUniversity Hospitals KU LeuvenLeuvenBelgium
| | - Raphael Sciot
- Department of PathologyUniversity Hospitals KU LeuvenLeuvenBelgium
| | - Patrick Schöffski
- Department of General Medical OncologyUniversity Hospitals KU LeuvenLeuvenBelgium
| | - Daphne Hompes
- Department of Surgical OncologyUniversity Hospitals KU LeuvenLeuvenBelgium
| | - Friedl Sinnaeve
- Department of Orthopaedic SurgeryUniversity Hospitals KU LeuvenLeuvenBelgium
| | - Hazem Wafa
- Department of Orthopaedic SurgeryUniversity Hospitals KU LeuvenLeuvenBelgium
| | - Marleen Renard
- Department of Paediatric Hemato‐OncologyUniversity Hospitals KU LeuvenLeuvenBelgium
| | - Mari FCM van den Hout
- Department of PathologyMaastricht University Medical Center+MaastrichtThe Netherlands
| | - Astrid Vernemmen
- Department of PathologyMaastricht University Medical Center+MaastrichtThe Netherlands
| | - Louis Libbrecht
- Department of PathologyCliniques Universitaires Saint‐LucBrusselsBelgium
- Department of PathologyAZ GroeningeKortrijkBelgium
| | - An‐Katrien De Roo
- Department of PathologyCliniques Universitaires Saint‐LucBrusselsBelgium
- Institute of Experimental and Clinical ResearchUCLouvainBrusselsBelgium
| | - Filomena Mazzeo
- Institute of Experimental and Clinical ResearchUCLouvainBrusselsBelgium
- Breast ClinicKing Albert II Cancer Institute, Cliniques Universitaires Saint‐LucBrusselsBelgium
- Department of Medical OncologyKing Albert II Cancer Institute, Cliniques Universitaires Saint‐LucBrusselsBelgium
| | - Cédric van Marcke
- Institute of Experimental and Clinical ResearchUCLouvainBrusselsBelgium
- Breast ClinicKing Albert II Cancer Institute, Cliniques Universitaires Saint‐LucBrusselsBelgium
- Department of Medical OncologyKing Albert II Cancer Institute, Cliniques Universitaires Saint‐LucBrusselsBelgium
| | - Karen Deraedt
- Department of PathologyZiekenhuis Oost‐LimburgGenkBelgium
| | | | | |
Collapse
|
2
|
Schlieben LD, Carta MG, Moskalev EA, Stöhr R, Metzler M, Besendörfer M, Meidenbauer N, Semrau S, Janka R, Grützmann R, Wiemann S, Hartmann A, Agaimy A, Haller F, Ferrazzi F. Machine Learning-Supported Diagnosis of Small Blue Round Cell Sarcomas Using Targeted RNA Sequencing. J Mol Diagn 2024; 26:387-398. [PMID: 38395409 DOI: 10.1016/j.jmoldx.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 01/25/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Small blue round cell sarcomas (SBRCSs) are a heterogeneous group of tumors with overlapping morphologic features but markedly varying prognosis. They are characterized by distinct chromosomal alterations, particularly rearrangements leading to gene fusions, whose detection currently represents the most reliable diagnostic marker. Ewing sarcomas are the most common SBRCSs, defined by gene fusions involving EWSR1 and transcription factors of the ETS family, and the most frequent non-EWSR1-rearranged SBRCSs harbor a CIC rearrangement. Unfortunately, currently the identification of CIC::DUX4 translocation events, the most common CIC rearrangement, is challenging. Here, we present a machine-learning approach to support SBRCS diagnosis that relies on gene expression profiles measured via targeted sequencing. The analyses on a curated cohort of 69 soft-tissue tumors showed markedly distinct expression patterns for SBRCS subgroups. A random forest classifier trained on Ewing sarcoma and CIC-rearranged cases predicted probabilities of being CIC-rearranged >0.9 for CIC-rearranged-like sarcomas and <0.6 for other SBRCSs. Testing on a retrospective cohort of 1335 routine diagnostic cases identified 15 candidate CIC-rearranged tumors with a probability >0.75, all of which were supported by expert histopathologic reassessment. Furthermore, the multigene random forest classifier appeared advantageous over using high ETV4 expression alone, previously proposed as a surrogate to identify CIC rearrangement. Taken together, the expression-based classifier can offer valuable support for SBRCS pathologic diagnosis.
Collapse
Affiliation(s)
- Lea D Schlieben
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany; Bavarian Cancer Research Center, Erlangen, Germany
| | - Maria Giulia Carta
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany; Bavarian Cancer Research Center, Erlangen, Germany
| | - Evgeny A Moskalev
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany; Bavarian Cancer Research Center, Erlangen, Germany
| | - Robert Stöhr
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany; Bavarian Cancer Research Center, Erlangen, Germany
| | - Markus Metzler
- Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany; Bavarian Cancer Research Center, Erlangen, Germany; Department of Pediatrics, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Manuel Besendörfer
- Department of Pediatric Surgery, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Norbert Meidenbauer
- Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany; Bavarian Cancer Research Center, Erlangen, Germany; Department of Internal Medicine 5-Hematology and Oncology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Sabine Semrau
- Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany; Bavarian Cancer Research Center, Erlangen, Germany; Department of Radiation Oncology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Rolf Janka
- Department of Radiology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Robert Grützmann
- Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany; Bavarian Cancer Research Center, Erlangen, Germany; Department of Pediatric Surgery, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Department of Surgery, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Stefan Wiemann
- Division of Molecular Genome Analysis, German Cancer Research Center, Heidelberg, Germany
| | - Arndt Hartmann
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany; Bavarian Cancer Research Center, Erlangen, Germany
| | - Abbas Agaimy
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany; Bavarian Cancer Research Center, Erlangen, Germany
| | - Florian Haller
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany; Bavarian Cancer Research Center, Erlangen, Germany
| | - Fulvia Ferrazzi
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany; Bavarian Cancer Research Center, Erlangen, Germany; Department of Nephropathology, Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.
| |
Collapse
|
3
|
Pecciarini L, Brunetto E, Grassini G, De Pascali V, Ogliari FR, Talarico A, Marra G, Magliacane G, Redegalli M, Arrigoni G, Lazzari C, Gregorc V, Bulotta A, Doglioni C, Cangi MG. Gene Fusion Detection in NSCLC Routine Clinical Practice: Targeted-NGS or FISH? Cells 2023; 12:cells12081135. [PMID: 37190044 DOI: 10.3390/cells12081135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/05/2023] [Accepted: 04/10/2023] [Indexed: 05/17/2023] Open
Abstract
The ability to identify the broadest range of targetable gene fusions is crucial to facilitate personalized therapy selection for advanced lung adenocarcinoma (LuADs) patients harboring targetable receptor tyrosine kinase (RTK) genomic alterations. In order to evaluate the most effective testing approach for LuAD targetable gene fusion detection, we analyzed 210 NSCLC selected clinical samples, comparing in situ (Fluorescence In Situ Hybridization, FISH, and ImmunoHistoChemistry, IHC) and molecular (targeted RNA Next-Generation Sequencing, NGS, and RealTime-PCR, RT-PCR) approaches. The overall concordance among these methods was high (>90%), and targeted RNA NGS was confirmed to be the most efficient technique for gene fusion identification in clinical practice, allowing the simultaneous analysis of a large set of genomic rearrangements at the RNA level. However, we observed that FISH was useful to detect targetable fusions in those samples with inadequate tissue material for molecular testing as well as in those few cases whose fusions were not identified by the RNA NGS panel. We conclude that the targeted RNA NGS analysis of LuADs allows accurate RTK fusion detection; nevertheless, standard methods such as FISH should not be dismissed, as they can crucially contribute to the completion of the molecular characterization of LuADs and, most importantly, the identification of patients as candidates for targeted therapies.
Collapse
Affiliation(s)
- Lorenza Pecciarini
- Pathology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Emanuela Brunetto
- Pathology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Greta Grassini
- Pathology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Valeria De Pascali
- Pathology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | | | - Anna Talarico
- Pathology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Giovanna Marra
- Pathology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Gilda Magliacane
- Pathology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Miriam Redegalli
- Pathology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Gianluigi Arrigoni
- Pathology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Chiara Lazzari
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Turin, Italy
| | - Vanesa Gregorc
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Turin, Italy
| | - Alessandra Bulotta
- Department of Oncology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Claudio Doglioni
- Pathology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Maria Giulia Cangi
- Pathology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| |
Collapse
|
4
|
Stockley TL, Lo B, Box A, Gomez Corredor A, DeCoteau J, Desmeules P, Feilotter H, Grafodatskaya D, Hawkins C, Huang WY, Izevbaye I, Lepine G, Papadakis AI, Park PC, Sheffield BS, Tran-Thanh D, Yip S, Sound Tsao M. Consensus Recommendations to Optimize the Detection and Reporting of NTRK Gene Fusions by RNA-Based Next-Generation Sequencing. Curr Oncol 2023; 30:3989-3997. [PMID: 37185415 PMCID: PMC10136625 DOI: 10.3390/curroncol30040302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 03/21/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
The detection of gene fusions by RNA-based next-generation sequencing (NGS) is an emerging method in clinical genetic laboratories for oncology biomarker testing to direct targeted therapy selections. A recent Canadian study (CANTRK study) comparing the detection of NTRK gene fusions on different NGS assays to determine subjects’ eligibility for tyrosine kinase TRK inhibitor therapy identified the need for recommendations for best practices for laboratory testing to optimize RNA-based NGS gene fusion detection. To develop consensus recommendations, representatives from 17 Canadian genetic laboratories participated in working group discussions and the completion of survey questions about RNA-based NGS. Consensus recommendations are presented for pre-analytic, analytic and reporting aspects of gene fusion detection by RNA-based NGS.
Collapse
|