title: Massively parallel sequencing of phyllodes tumours of the breast reveals actionable mutations, and TERT promoter hotspot mutations and TERT gene amplification as likely drivers of progression.
abstract: Phyllodes tumours (PTs) are breast fibroepithelial lesions that are graded based on histological criteria as benign, borderline or malignant. PTs may recur locally. Borderline PTs and malignant PTs may metastasize to distant sites. Breast fibroepithelial lesions, including PTs and fibroadenomas, are characterized by recurrent MED12 exon 2 somatic mutations. We sought to define the repertoire of somatic genetic alterations in PTs and whether these may assist in the differential diagnosis of these lesions. We collected 100 fibroadenomas, 40 benign PTs, 14 borderline PTs and 22 malignant PTs; six, six and 13 benign, borderline and malignant PTs, respectively, and their matched normal tissue, were subjected to targeted massively parallel sequencing (MPS) using the MSK-IMPACT sequencing assay. Recurrent MED12 mutations were found in 56% of PTs; in addition, mutations affecting cancer genes (eg TP53, RB1, SETD2 and EGFR) were exclusively detected in borderline and malignant PTs. We found a novel recurrent clonal hotspot mutation in the TERT promoter (-124 C>T) in 52% and TERT gene amplification in 4% of PTs. Laser capture microdissection revealed that these mutations were restricted to the mesenchymal component of PTs. Sequencing analysis of the entire cohort revealed that the frequency of TERT alterations increased from benign (18%) to borderline (57%) and to malignant PTs (68%; p < 0.01), and TERT alterations were associated with increased levels of TERT mRNA (p < 0.001). No TERT alterations were observed in fibroadenomas. An analysis of TERT promoter sequencing and gene amplification distinguished PTs from fibroadenomas with a sensitivity and a positive predictive value of 100% (CI 95.38-100%) and 100% (CI 85.86-100%), respectively, and a sensitivity and a negative predictive value of 39% (CI 28.65-51.36%) and 68% (CI 60.21-75.78%), respectively. Our results suggest that TERT alterations may drive the progression of PTs, and may assist in the differential diagnosis between PTs and fibroadenomas. Copyright © 2015 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
authors.affiliation: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA.
authors.forename: Salvatore
authors.initials: S
authors.lastname: Piscuoglio
authors.affiliation: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA.
authors.forename: Charlotte Ky
authors.initials: CK
authors.lastname: Ng
authors.affiliation: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA.
authors.forename: Melissa
authors.initials: M
authors.lastname: Murray
authors.affiliation: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA.
authors.forename: Kathleen A
authors.initials: KA
authors.lastname: Burke
authors.affiliation: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA.
authors.forename: Marcia
authors.initials: M
authors.lastname: Edelweiss
authors.affiliation: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA.|Department of Pathology, Hospital Israelita Albert Einstein, Instituto Israelita de Ensino e Pesquisa, São Paulo, Brazil.
authors.forename: Felipe C
authors.initials: FC
authors.lastname: Geyer
authors.affiliation: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA.
authors.forename: Gabriel S
authors.initials: GS
authors.lastname: Macedo
authors.affiliation: Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, USA.
authors.forename: Akiko
authors.initials: A
authors.lastname: Inagaki
authors.affiliation: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA.|Department of Pathology, Patras General Hospital, Greece.
authors.forename: Anastasios D
authors.initials: AD
authors.lastname: Papanastasiou
authors.affiliation: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA.
authors.forename: Luciano G
authors.identifier: http://orcid.org/0000-0002-9625-1183
authors.initials: LG
authors.lastname: Martelotto
authors.affiliation: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA.|Department of Medical Sciences, University of Turin, Italy.
authors.forename: Caterina
authors.initials: C
authors.lastname: Marchio
authors.affiliation: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA.
authors.forename: Raymond S
authors.initials: RS
authors.lastname: Lim
authors.affiliation: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA.
authors.forename: Rafael A
authors.initials: RA
authors.lastname: Ioris
authors.affiliation: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA.
authors.forename: Pooja K
authors.initials: PK
authors.lastname: Nahar
authors.affiliation: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA.
authors.forename: Ino De
authors.initials: ID
authors.lastname: Bruijn
authors.affiliation: Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA.
authors.forename: Lillian
authors.initials: L
authors.lastname: Smyth
authors.affiliation: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA.
authors.forename: Muzaffar
authors.initials: M
authors.lastname: Akram
authors.affiliation: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA.
authors.forename: Dara
authors.initials: D
authors.lastname: Ross
authors.affiliation: Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, USA.
authors.forename: John H
authors.initials: JH
authors.lastname: Petrini
authors.affiliation: Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA.
authors.forename: Larry
authors.initials: L
authors.lastname: Norton
authors.affiliation: Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA.|Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, USA.|Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA.
authors.forename: David B
authors.initials: DB
authors.lastname: Solit
authors.affiliation: Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA.|Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA.
authors.forename: Jose
authors.initials: J
authors.lastname: Baselga
authors.affiliation: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA.
authors.forename: Edi
authors.initials: E
authors.lastname: Brogi
authors.affiliation: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA.|Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA.
authors.forename: Marc
authors.initials: M
authors.lastname: Ladanyi
authors.affiliation: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA.
authors.forename: Britta
authors.initials: B
authors.lastname: Weigelt
authors.affiliation: Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA.
authors.forename: Jorge S
authors.initials: JS
authors.lastname: Reis-Filho
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics* / Q000473:pathology*; D003937:Diagnosis, Differential; D005260:Female; D018226:Fibroadenoma / Q000175:diagnosis / Q000473:pathology*; D005784:Gene Amplification / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D009154:Mutation / Q000235:genetics*; D009364:Neoplasm Recurrence, Local / Q000175:diagnosis / Q000235:genetics / Q000473:pathology*; D003557:Phyllodes Tumor / Q000175:diagnosis / Q000473:pathology*; D011401:Promoter Regions, Genetic; D019098:Telomerase / Q000235:genetics*
chemical_list: C509186:TERT protein, human; D019098:Telomerase
keywords: gene amplification; massively parallel sequencing; mutation; phyllodes tumour; promoter; telomerase
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