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NTRK gene aberrations in triple-negative breast cancer: detection challenges using IHC, FISH, RT-PCR, and NGS
Federica Zito Marino1, Simona Buono1, Marco Montella1
1Pathology Unit, Department of Mental and Physical Health and Preventive Medicine, University of Campania "L. Vanvitelli", Naples, Italy.
Abstract:
Triple-negative breast cancer (TNBC) is usually an aggressive disease with a poor prognosis and limited treatment options. The neurotrophic tyrosine receptor kinase (NTRK) gene fusions are cancer type-agnostic emerging biomarkers approved by the Food and Drug Administration (FDA), USA, for the selection of patients for targeted therapy. The main aim of our study was to investigate the frequency of NTRK aberrations, i.e. fusions, gene copy number gain, and amplification, in a series of TNBC using different methods. A total of 83 TNBCs were analyzed using pan-TRK immunohistochemistry (IHC), fluorescence in situ hybridization (FISH), real-time polymerase chain reaction (RT-PCR), and RNA-based next-generation sequencing (NGS). Of 83 cases, 16 showed pan-TRK positivity although no cases had NTRK-fusions. Indeed, FISH showed four cases carrying an atypical NTRK1 pattern consisting of one fusion signal and one/more single green signals, but all cases were negative for fusion by NGS and RT-PCR testing. In addition, FISH analysis showed six cases with NTRK1 amplification, one case with NTRK2 copy number gain, and five cases with NTRK3 copy number gain, all negative for pan-TRK IHC. Our data demonstrate that IHC has a high false-positive rate for the detection of fusions and molecular testing is mandatory; there is no need to perform additional molecular tests in cases negativity for NTRK by IHC. In conclusion, the NTRK genes are not involved in fusions in TNBC, but both copy number gain and amplification are frequent events, suggesting a possible predictive role for other NTRK aberrations.
Insights
Neurotrophic tyrosine receptor kinase (NTRK) gene fusions are not found in triple-negative breast cancer (TNBC). However, NTRK gene copy number gain and amplification are frequent, suggesting potential roles for targeted therapies.
Area of Science:
- Oncology
- Genetics
- Molecular Biology
Background:
- Triple-negative breast cancer (TNBC) presents aggressive characteristics and limited therapeutic strategies.
- Neurotrophic tyrosine receptor kinase (NTRK) gene fusions are validated biomarkers for targeted cancer therapy.
- Investigating NTRK aberrations in TNBC is crucial for identifying potential treatment avenues.
Purpose of the Study:
- To determine the prevalence of NTRK aberrations, including fusions, copy number gain, and amplification, in triple-negative breast cancer.
- To evaluate the diagnostic accuracy of different methods for detecting NTRK aberrations in TNBC.
- To assess the clinical relevance of NTRK gene alterations in TNBC.
Main Methods:
- Analysis of 83 TNBC cases using pan-TRK immunohistochemistry (IHC), fluorescence in situ hybridization (FISH), real-time polymerase chain reaction (RT-PCR), and RNA-based next-generation sequencing (NGS).
- Detection of NTRK gene fusions, copy number gain, and amplification.
- Comparative analysis of results obtained from IHC, FISH, RT-PCR, and NGS.
Main Results:
- No NTRK gene fusions were detected in any of the 83 TNBC cases by NGS or RT-PCR.
- Pan-TRK IHC showed 16 positive cases, but these were confirmed as false positives for fusions.
- FISH identified NTRK1 amplification in six cases, NTRK2 copy number gain in one case, and NTRK3 copy number gain in five cases, all negative for pan-TRK IHC.
Conclusions:
- Immunohistochemistry (IHC) demonstrates a high false-positive rate for detecting NTRK fusions in TNBC.
- Molecular testing (NGS, RT-PCR) is essential for accurate NTRK fusion detection; additional tests are unnecessary if IHC is negative.
- While NTRK fusions are absent, NTRK gene copy number gain and amplification are common in TNBC, indicating potential for other NTRK-targeted therapies.
