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Published on: July 25, 2020
Characterization of Clinical Cases of Malignant PEComa via Comprehensive Genomic Profiling of DNA and RNA
Saranya Akumalla1, Russell Madison1, Douglas I Lin1
1Foundation Medicine, Cambridge, Massachusetts, USA.
Purpose:
Perivascular epithelioid cell tumor (PEComa) is a rare mesenchymal soft tissue neoplasm often linked to mTOR pathway activation via TSC2 mutation. We analyzed a series of 31 consecutive metastatic PEComa (mPEComa) cases using a combined DNA/RNA hybrid capture-based comprehensive genomic profiling (CGP) assay to assess the genomic landscape of mPEComa.
Patients And Methods:
Formalin-fixed, paraffin-embedded (FFPE) blocks or slides were obtained from tumors from 31 unique patients with mPEC-oma. DNA and RNA were extracted and CGP was performed on 405 genes using a targeted next-generation sequencing (NGS) assay in a CLIA-certified lab.
Results:
All cases had locally advanced or metastatic disease, and 58% of patients were female with a median age of 50 years (range 8-76), and 17 and 14 specimens were from primary and metastatic sites, respectively. One hundred genomic alterations were identified in the cohort, with an average of 3.2 genomic alterations/case including alterations in TSC2 32.3% of cases (10), TSC1 9.6% (3), TFE3 16.1% (5, all fusions), and folliculin (FLCN) 6.4% (2), with all occurring in mutually exclusive fashion. Of TSC2 mutant cases, 70% had biallelic inactivation of this locus, as were 100% of TSC1 mutant cases. Two TSC1/2 wildtype cases harbored truncating mutations in FLCN, both of which were under LOH. Five TFE3 fusion cases were identified including the novel 5' fusion partner ZC3H4.
Conclusions:
We describe for the first time mPEComa cases with FLCN mutations under LOH, further characterizing dysregulation of the mTOR pathway as a unifying theme in mPEC-oma. Cumulatively, we demonstrate the feasibility and potential utility of segregating mPEComa by TSC, TFE3, and FLCN status via CGP in clinical care.
Insights
Genomic profiling of metastatic perivascular epithelioid cell tumors (mPEComa) reveals mTOR pathway dysregulation. Mutations in TSC1, TSC2, TFE3, and FLCN are key drivers, guiding potential therapeutic strategies for this rare cancer.
Area of Science:
- Oncology
- Genetics
- Pathology
Background:
- Perivascular epithelioid cell tumor (PEComa) is a rare mesenchymal neoplasm.
- mTOR pathway activation, often via TSC2 mutation, is frequently implicated in PEComa pathogenesis.
Purpose of the Study:
- To comprehensively analyze the genomic landscape of metastatic PEComa (mPEComa).
- To identify key genomic alterations driving mPEComa using comprehensive genomic profiling (CGP).
Main Methods:
- 31 consecutive mPEComa cases were analyzed using a combined DNA/RNA hybrid capture-based CGP assay.
- Targeted next-generation sequencing (NGS) of 405 genes was performed on DNA and RNA extracted from formalin-fixed, paraffin-embedded (FFPE) tumor samples.
Main Results:
- 100 genomic alterations were identified across 31 mPEComa cases.
- Alterations in TSC2 (32.3%), TSC1 (9.6%), TFE3 (16.1% as fusions), and FLCN (6.4%) were observed, often mutually exclusive.
- Biallelic inactivation was common in TSC1/2 mutant cases, and novel FLCN mutations under loss of heterozygosity (LOH) were identified in TSC1/2 wildtype cases.
Conclusions:
- Dysregulation of the mTOR pathway is a unifying theme in mPEComa.
- FLCN mutations under LOH represent a newly characterized mechanism in mPEComa.
- CGP can effectively segregate mPEComa cases by TSC, TFE3, and FLCN status, aiding clinical management.
