Establishment of multiplex RT-PCR to detect fusion genes for the diagnosis of Ewing sarcoma

[Practical Guidance on the Detection of NTRK Fusions in Sarcomas: Current Status and Diagnostic Challenges]

Sarcomas are a rare and heterogeneous group of mesenchymal malignant tumors and account for approximately 1% of all adult cancers and around 20% of all pediatric solid tumors in Europe. Technology advances have enabled a more accurate and efficient characterization of the molecular mechanisms underlying the pathogenesis of sarcoma subtypes and revealed novel and unexpected therapeutic targets with prognostic/predictive biomarkers, namely the neurotrophic tyrosine receptor kinase (NTRK) gene fusion. The NTRK fusion assessment has recently become a standard part of management for patients with unresectable locally advanced or metastatic cancers and has been identified in various tumor types. In the more prevalent adult and pediatric sarcomas, NTRK fusions are present in 1% and 20%, respectively, and in more than 90% of very rare subsets of tumors. The inhibition of TRK activity with first-generation TRK inhibitors has been found to be effective and well tolerated in adult and pediatric patients, independently of the tumor type. Overall, the therapeutic benefit to those patients compensates for the difficulties of identifying NTRK gene fusions. However, the rarity and diagnostic complexity of NTRK gene fusions raise several questions and challenges for clinicians. To address these issues, an expert panel of medical and pediatric oncologists, radiologists, surgeons, orthopedists, and pathologists reviewed the recent literature and discussed the current status and challenges, proposing a diagnostic algorithm for identifying NTRK fusion sarcomas. The aim of this article is to review the updated information on this issue and to provide the experts' recommendations and practical guidance on the optimal management of patients with soft tissue sarcomas, infantile fibrosarcoma, gastrointestinal stromal tumors, and osteosarcoma.

Development, optimization and application of a universal fluorescence multiplex PCR-based assay to detect BCOR genetic alterations in pediatric tumors

BACKGROUND

A number of genetic aberrations are associated with the BCL6-correpresor gene (BCOR), including internal tandem duplications (ITDs) and gene fusions (BCOR::CCNB3 and BCOR::MAML3), as well as YWHAE::NUTM2, which are found in clear cell sarcoma of the kidney (CCSK), sarcoma with BCOR genetic alterations, primitive myxoid mesenchymal tumor of infancy, and high-grade neuroepithelial tumors in children. Detecting these gene aberrations is crucial for tumor diagnosis. ITDs can be identified by Sanger sequencing or agarose gel electrophoresis. However, gene fusions are usually detected through reverse transcription-polymerase chain reaction (RT-PCR) or fluorescence in situ hybridization. Methods that analyze these variants simultaneously in a sensitive and convenient manner are lacking in clinical practice.

METHODS

This study validated a Universal Fluorescence Multiplex PCR-based assay that assessed BCOR ITDs, BCOR::CCNB3, BCOR::MAML3 and YWHAE::NUTM2 fusions simultaneously.

RESULTS

The assay achieved a detection threshold of 10 copies for fusion genes and 0.32 ng genomic DNA for BCOR ITDs. The performance of this assay was also tested in a cohort of 43 pediatric tumors (17 undifferentiated small round cell sarcomas, and 26 tumors with a histological diagnosis of CCSK). In total, 20 BCOR ITDs, 4 BCOR::CCNB3 and one YWHAE::NUTM2 were detected. When compared with the final diagnosis, the assay achieved 93% sensitivity and 100% specificity.

CONCLUSIONS

Accordingly, this assay provided an effective and convenient method for detecting BCOR- and YWHAE-related abnormalities in tumors.

Molecular testing of soft tissue tumors

BACKGROUND

The diagnosis of soft tissue tumors is challenging, especially when the evaluable material procured is limited. As a result, diagnostic ancillary testing is frequently needed. Moreover, there is a trend in soft tissue pathology toward increasing use of molecular results for tumor classification and prognostication. Hence, diagnosing newer tumor entities such as CIC-rearranged sarcoma explicitly requires molecular testing. Molecular testing can be accomplished by in situ hybridization, polymerase chain reaction, as well as next generation sequencing, and more recently such testing can even be accomplished leveraging an immunohistochemical proxy.

CONCLUSION

This review evaluates the role of different molecular tests in characterizing soft tissue tumors belonging to various cytomorphologic categories that have been sampled by small biopsy and cytologic techniques.