Massively parallel sequencing of phyllodes tumours of the breast reveals actionable mutations, and <i><scp>TERT</scp></i> promoter hotspot mutations and <i>TERT</i> gene amplification as likely drivers of progression

Piscuoglio, Salvatore; Ng, Charlotte K.Y.; Murray, Melissa P.; Burke, Kathleen A.; Edelweiss, Marcia; Geyer, Felipe C.; Macedo, Gabriel S.; Inagaki, Akiko; Papanastasiou, Anastasios D.; Martelotto, Luciano G.; Marchiò, Caterina; Lim, Raymond S.; Ioris, Rafael A; Nahar, Pooja K.; Bruijn, Ino de; Smyth, Lillian M.; Akram, Muzaffar; Ross, Dara S.; Petrini, John H.J.; Norton, Larry; Solit, David B.; Baselga, José; Brogi, Edi; Ladanyi, Marc; Weigelt, Britta; Reis‐Filho, Jorge S.

doi:10.1002/path.4672

Cited by 111 publications

(197 citation statements)

References 59 publications

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“…DNA was extracted from microdissected tumor and normal samples using the DNeasy Blood and Tissue Kit (Qiagen) following the manufacturer’s guidelines. Tumor and matched germline DNA from SPCRP10 and SPCRP13 were subjected to WES on a Illumina HiSeq2000 at the Integrated Genomics Operation (IGO) at MSKCC (14), and tumor DNA from SPCRP5 and SPCRP11 to Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT) sequencing assay (15) targeting all exons and selected regulatory regions and introns of 410 key cancer genes on a Illumina HiSeq2500 (16). Massively parallel sequencing analysis was performed as previously described (Supplementary Methods; refs.…”

Section: Methodsmentioning

confidence: 99%

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IDH2 Mutations Define a Unique Subtype of Breast Cancer with Altered Nuclear Polarity

et al. 2016

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Solid papillary carcinoma with reverse polarity (SPCRP) is a rare breast cancer subtype with an obscure etiology. In this study, we sought to describe its unique histopathologic features and to identify the genetic alterations that underpin SPCRP using massively parallel whole-exome and targeted sequencing. The morphologic and immunohistochemical features of SPCRP support the invasive nature of this subtype. Ten of 13 (77%) SPCRPs harbored hotspot mutations at R172 of the isocitrate dehydrogenase IDH2, of which 8 of 10 displayed concurrent pathogenic mutations affecting PIK3CA or PIK3R1. One of the IDH2 wild-type SPCRPs harbored a TET2 Q548* truncating mutation coupled with a PIK3CA H1047R mutation. Functional studies demonstrated that IDH2 and PIK3CA hotspot mutations are likely drivers of SPCRP, resulting in its reversed nuclear polarization phenotype. Our results offer a molecular definition of SPCRP as a distinct breast cancer subtype. Concurrent IDH2 and PIK3CA mutations may help diagnose SPCRP and possibly direct effective treatment.

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Section: Methodsmentioning

confidence: 99%

“…Massively parallel sequencing analysis was performed as previously described (Supplementary Methods; refs. 16, 17). WES and MSK-IMPACT data have been submitted to SRA under the accessions SRP066429 and SRP066430, respectively.…”

Section: Methodsmentioning

confidence: 99%

IDH2 Mutations Define a Unique Subtype of Breast Cancer with Altered Nuclear Polarity

et al. 2016

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“…Tumor and normal DNA samples were subjected to targeted capture massively parallel sequencing at the MSKCC Integrated Genomics Operation, using the MSK Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT) sequencing assay targeting all exons and selected introns of 341 key cancer genes, 32,33 as well as a sequencing assay targeting all exons of 254 genes recurrently mutated in breast cancer and related to DNA repair 34 (Supplementary Table 3). Of the 595 genes captured, 107 genes were common to both targeted capture sequencing assays (i.e.…”

Section: Methodsmentioning

confidence: 99%

Genetic events in the progression of adenoid cystic carcinoma of the breast to high-grade triple-negative breast cancer

et al. 2016

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Adenoid cystic carcinoma of the breast is a rare histologic type of triple-negative breast cancer with an indolent clinical behavior, often driven by the MYB-NFIB fusion gene. Here we sought to define the repertoire of somatic genetic alterations in two adenoid cystic carcinomas associated with high-grade triple-negative breast cancer. The different components of each case were subjected to copy number profiling and massively parallel sequencing targeting all exons and selected regulatory and intronic regions of 488 genes. Reverse transcription PCR and fluorescence in situ hybridization were employed to investigate the presence of the MYB-NFIB translocation. The MYB-NFIB fusion gene was detected in both adenoid cystic carcinomas and their associated high-grade triple-negative breast cancer components. Whilst the distinct components of both cases displayed similar patterns of gene copy number alterations, massively parallel sequencing analysis revealed intra-tumor genetic heterogeneity. In case 1, progression from the trabecular adenoid cystic carcinoma to the high-grade triple-negative breast cancer was found to involve clonal shifts with enrichment of mutations affecting EP300, NOTCH1, ERBB2 and FGFR1 in the high-grade triple-negative breast cancer. In case 2, a clonal KMT2C mutation was present in the cribriform adenoid cystic carcinoma, solid adenoid cystic carcinoma and high-grade triple-negative breast cancer components, whereas a mutation affecting MYB was present only in the solid and high-grade triple-negative breast cancer areas and additional three mutations targeting STAG2, KDM6A and CDK12 were restricted to the high-grade triple-negative breast cancer. In conclusion, adenoid cystic carcinomas of the breast with high-grade transformation are underpinned by MYB-NFIB fusion gene, and, akin to other forms of cancer, may be constituted by a mosaic of cancer cell clones at diagnosis. The progression from adenoid cystic carcinoma to high-grade triple-negative breast cancer of no special type may involve the selection of neoplastic clones and/ or the acquisition of additional genetic alterations.

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“…6,21 Details of the sequencing analysis and primer sequences are available in the Supplementary Methods and Supplementary Table 5.…”

Section: Methodsmentioning

confidence: 99%

“…13,14 Interestingly, the frequency of MED12 mutations appears to diminish with increasing PT grade, 4–6 whereas the frequency of the TERT −124C>T promoter hotspot mutation and/or TERT gene amplification has been shown to increase according to the histologic grade of PTs, with significantly lower rates in benign (18%) than in borderline (57%) and malignant PTs (68%). 6 On the basis of these observations, we have posited that genetic alterations affecting TERT rather than MED12 mutations may have a role in the progression of PTs. 6 …”

Section: Introductionmentioning

confidence: 99%

Massively parallel sequencing analysis of synchronous fibroepithelial lesions supports the concept of progression from fibroadenoma to phyllodes tumor

et al. 2016

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Phyllodes tumors (PTs) and fibroadenomas (FAs) are fibroepithelial lesions (FELs) of the breast. Although mutations affecting exon 2 of MED12 are highly recurrent in FAs and PTs, TERT promoter hotspot mutations are frequently found in PTs but are vanishingly rare in FAs. Malignant transformation of benign PTs is well-documented, but the progression from FA to PT remains a matter of contention. Here we report on the somatic genetic alterations in multiple ipsilateral synchronous FELs (three FAs, one benign PT, and one malignant PT) occurring in the same patient. DNA samples extracted from each tumor and matched normal tissue were subjected to targeted massively parallel sequencing using the Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT) assay. This analysis revealed MED12 mutations in all lesions. One FA and the benign PT harbored a MED12Gly44Val mutation, whereas another FA and the malignant PT displayed a MED12Gly44Asp mutation. The remaining FA had an independent distinct MED12Gly44Cys mutation. A formal clonality analysis suggested a clonal relationship between the FELs with identical MED12 mutations (P<0.05). A clonal TERT promoter hotspot mutation was identified exclusively in the malignant PT. The identification of distinct MED12 mutations in multifocal ipsilateral and synchronous FELs supports the notion that co-existing mammary fibroepithelial tumors can arise independently. Conversely, the co-existence of identical MED12 mutations indicates clonal relatedness among FAs and PTs, corroborating the hypothesis that FAs may constitute the substrate from which PTs develop. Our findings also support the notion that acquisition of TERT promoter mutations may drive the progression of FELs.

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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

Cited by 111 publications

References 59 publications

IDH2 Mutations Define a Unique Subtype of Breast Cancer with Altered Nuclear Polarity

IDH2 Mutations Define a Unique Subtype of Breast Cancer with Altered Nuclear Polarity

Genetic events in the progression of adenoid cystic carcinoma of the breast to high-grade triple-negative breast cancer

Massively parallel sequencing analysis of synchronous fibroepithelial lesions supports the concept of progression from fibroadenoma to phyllodes tumor

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