Saranya Akumalla1, Russell Madison1, Douglas I Lin1, Alexa B Schrock1, Evgeny Yakirevich2, Mark Rosenzweig1, Arjun V Balar3, Garrett M Frampton1, Claire Edgerly1, Rachel L Erlich1, Vincent A Miller1, Shridar Ganesan4, Jeffrey S Ross1,5, Siraj M Ali6. 1. Foundation Medicine, Cambridge, Massachusetts, USA. 2. Department of Pathology, Rhode Island Hospital, Alpert Medical School of Brown University, Providence, Rhode Island, USA. 3. Perlmutter Cancer Center, NYU Langone Health, New York, New York, USA. 4. Rutgers Cancer Institute of New Jersey and Rutgers Robert Wood Johnson Medical School, Rutgers University, New Brunswick, New Jersey, USA. 5. Department of Urology Pathology and Laboratory Medicine, Upstate Medical Center, Syracuse, New York, USA. 6. Foundation Medicine, Cambridge, Massachusetts, USA, SMALIMDPHD@gmail.com.
Abstract
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.
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.
Authors: Lingxin Zhang; Daniel Lubin; John H Sinard; Brendan C Dickson; Cristina R Antonescu; Hao Wu; Roheena Z Panni; Snjezana Dogan; Brian R Untch; Ronald A Ghossein; Bin Xu Journal: Head Neck Pathol Date: 2022-02-26
Authors: Ergin Erginoz; Halit Eren Taskin; Gokce Hande Cavus; Abdullah Kagan Zengin Journal: Medicine (Baltimore) Date: 2021-12-17 Impact factor: 1.817
Authors: Daniela C Salles; Kaushal Asrani; Juhyung Woo; Thiago Vidotto; Hans B Liu; Igor Vidal; Andres Matoso; George J Netto; Pedram Argani; Tamara L Lotan Journal: J Pathol Date: 2022-03-29 Impact factor: 9.883