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Muller KE, Marotti JD. Genotype-phenotype associations in breast pathology: Achievements of the past quarter century. Breast J 2020; 26:1123-1131. [PMID: 32367572 DOI: 10.1111/tbj.13861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 09/18/2019] [Indexed: 12/27/2022]
Abstract
The first genotype-phenotype relationship in breast pathology developed in 1994 with the discovery of the CDH1 gene. This finding eventually provided biological insight into the characteristic morphology of invasive lobular carcinoma. Subsequent investigative efforts have uncovered additional molecular alterations largely responsible for the histology of several breast neoplasms including secretory carcinoma, adenoid cystic carcinoma, tall cell carcinoma with reversed polarity, fibroepithelial lesions, and most recently, adenomyoepithelioma. Evaluation of the genomic landscape of other special types of breast cancer with distinctive growth patterns, such as invasive mucinous carcinoma, have yet to uncover recurring cytogenetic and/or molecular alterations. Despite the lack of a hallmark alteration in mucinous carcinoma, it is important to note the relative decrease in PIK3CA mutations compared with invasive carcinoma of no special type. In this review, we describe the clinical and pathologic features of breast tumors with recognized genotype-phenotype correlations and summarize the molecular alterations of mucinous carcinoma.
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Affiliation(s)
- Kristen E Muller
- Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.,Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Jonathan D Marotti
- Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.,Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
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52
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Rakha EA, Pareja FG. New Advances in Molecular Breast Cancer Pathology. Semin Cancer Biol 2020; 72:102-113. [PMID: 32259641 DOI: 10.1016/j.semcancer.2020.03.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 12/12/2022]
Abstract
Breast cancer (BC) comprises a diverse spectrum of diseases featuring distinct presentation, morphological, biological, and clinical phenotypes. BC behaviour and response to therapy also vary widely. Current evidence indicates that traditional prognostic and predictive classification systems are insufficient to reflect the biological and clinical heterogeneity of BC. Advancements in high-throughput molecular techniques and bioinformatics have contributed to the improved understanding of BC biology, refinement of molecular taxonomies and the development of novel prognostic and predictive molecular assays. Molecular testing has also become increasingly important in the diagnosis and treatment of BC in the era of precision medicine. Despite the enormous amount of research work to develop and refine BC molecular prognostic and predictive assays, it is still in evolution and proper incorporation of these molecular tests into clinical practice to guide patient's management remains a challenge. With the increasing use of more sophisticated high throughput molecular techniques, large amounts of data will continue to emerge, which could potentially lead to identification of novel therapeutic targets and allow more precise classification systems that can accurately predict outcome and response to therapy. In this review, we provide an update on the molecular classification of BC and molecular prognostic assays. Companion diagnostics, contribution of massive parallel sequencing and the use of liquid biopsy are also highlighted.
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Affiliation(s)
- Emad A Rakha
- Department of Histopathology, Division of Cancer and Stem Cells, School of Medicine, The University of Nottingham and Nottingham University Hospitals NHS Trust, Nottingham City Hospital, Nottingham, NG5 1PB, UK.
| | - Fresia G Pareja
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
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PTEN Expression as a Complementary Biomarker for Mismatch Repair Testing in Breast Cancer. Int J Mol Sci 2020; 21:ijms21041461. [PMID: 32098071 PMCID: PMC7073136 DOI: 10.3390/ijms21041461] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 02/18/2020] [Accepted: 02/19/2020] [Indexed: 02/07/2023] Open
Abstract
Mismatch repair (MMR) analysis in breast cancer may help to inform immunotherapy decisions but it lacks breast-specific guidelines. Unlike in other neoplasms, MMR protein loss shows intra-tumor heterogeneity and it is not mirrored by microsatellite instability in the breast. Additional biomarkers can improve MMR clinical testing. Phosphatase and tensin homolog (PTEN) inactivation is an early oncogenic event that is associated with MMR deficiency (dMMR) in several tumors. Here, we sought to characterize the diagnostic utility of PTEN expression analysis for MMR status assessment in breast cancer. A total of 608 breast cancers were profiled for their MMR and PTEN status. Proteins expression and distribution were analyzed by immunohistochemistry (IHC) on tissue microarrays and confirmed on full sections; PTEN copy number alterations were detected using a real-time PCR assay. Overall, 78 (12.8%) cases were MMR-heterogeneous (hMMR), while all patterns of PTEN expression showed no intra-tumor heterogeneity. Wild-type PTEN expression was observed in 15 (18.5%) dMMR tumors (p < 0.0001). Survival analyses revealed significant correlations between MMR-proficient (pMMR), PTEN expression, and a better outcome. The positive predictive value of PTEN-retained status for pMMR ranged from 94.6% in estrogen receptor (ER)+/HER2- tumors to 100% in HER2-amplified and ER-/HER2- cases. We propose a novel diagnostic algorithm where PTEN expression analysis can be employed to identify pMMR breast cancers.
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54
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Slodkowska E, Xu B, Kos Z, Bane A, Barnard M, Zubovits J, Iyengar P, Faragalla H, Turbin D, Williams P, Barnes PJ, Mulligan AM. Predictors of Outcome in Mammary Adenoid Cystic Carcinoma: A Multi-Institutional Study. Am J Surg Pathol 2020; 44:214-223. [PMID: 31567278 DOI: 10.1097/pas.0000000000001378] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Mammary adenoid cystic carcinoma (ACC) is a rare subtype of breast cancer with a favorable prognosis. Here we report on predictors of outcome based on a detailed morphologic review and analysis of 108 mammary ACC. Sixty-four tumors (59.2%) were pure conventional ACC, 23 (21.3%) were pure basaloid ACC. Follow-up was available for 87 patients (median: 51 mo). Eighteen patients (20.7%) developed recurrence: 7 (8%) had local recurrence and 14 (16%) had distant metastasis. Two patients died of disease, 1 died of an unrelated cause, 14 were alive with disease (including 8 in palliative care), and 70 (80.5%) were alive with no evidence of disease. Of 90 patients with known lymph node (LN) status 9 (10%) had nodal involvement (all with basaloid ACC). Distant metastases in patients with predominantly basaloid ACC compared with pure conventional ACC were more common (40% vs. 7.7%) and occurred earlier (22 vs. 84 mo). The following factors were found to be predictive of recurrence-free survival: positive margin, Nottingham grade, neovascularization, basaloid component, perineural invasion, lymphovascular invasion, >30% solid growth, necrosis and LN involvement; the first 3 remained statistically significant on multivariate analysis. Factors predictive of distant disease-free survival were neovascularization, Nottingham grade, lymphovascular invasion, solid component >50%, LN involvement, basaloid component >50%, tumor necrosis, perineural invasion, and final margin. Only neovascularization remained statistically significant on multivariate analysis. Basaloid ACC is an aggressive variant of mammary ACC with more frequent nodal involvement and higher incidence of distant spread. LN staging should be performed for all mammary basaloid ACC.
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Affiliation(s)
- Elzbieta Slodkowska
- Department of Anatomic Pathology, Sunnybrook Health Sciences Centre, University of Toronto
| | - Bin Xu
- Department of Anatomic Pathology, Sunnybrook Health Sciences Centre, University of Toronto
| | - Zuzana Kos
- Department of Anatomic Pathology, The Ottawa Hospital and University of Ottawa, Ottawa
| | - Anita Bane
- Department of Anatomic Pathology, Cambridge Memorial Hospital, Cambridge
| | - Maja Barnard
- Department of Anatomic Pathology, Sunnybrook Health Sciences Centre, University of Toronto
- Department of Anatomic Pathology, North York General Hospital
| | - Judit Zubovits
- Department of Anatomic Pathology, Sunnybrook Health Sciences Centre, University of Toronto
- Department of Anatomic Pathology, Scarborough Health Network, Scarborough
| | - Pratibha Iyengar
- Department of Anatomic Pathology, Sunnybrook Health Sciences Centre, University of Toronto
- Department of Anatomic Pathology, Trillium Health Partners, Mississauga
| | - Hala Faragalla
- Department of Anatomic Pathology, Sunnybrook Health Sciences Centre, University of Toronto
- Department of Anatomic Pathology, St. Michael's Hospital
| | - Dmitry Turbin
- Department of Anatomic Pathology, St. Paul's Hospital, Vancouver, BC
| | - Phillip Williams
- Department of Anatomic Pathology, Juravinski Hospital and McMaster University, Hamilton, ON
| | - Penny J Barnes
- Department of Anatomic Pathology, Nova Scotia Health Authority and Dalhousie University, Halifax, NS, Canada
| | - Anna Marie Mulligan
- Department of Anatomic Pathology, Sunnybrook Health Sciences Centre, University of Toronto
- Department of Anatomic Pathology, University Health Network, Toronto
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Identification of recurrent FHL2-GLI2 oncogenic fusion in sclerosing stromal tumors of the ovary. Nat Commun 2020; 11:44. [PMID: 31896750 PMCID: PMC6940380 DOI: 10.1038/s41467-019-13806-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 11/26/2019] [Indexed: 12/29/2022] Open
Abstract
Sclerosing stromal tumor (SST) of the ovary is a rare type of sex cord-stromal tumor (SCST), whose genetic underpinning is currently unknown. Here, using whole-exome, targeted capture and RNA-sequencing, we report recurrent FHL2-GLI2 fusion genes in 65% (17/26) of SSTs and other GLI2 rearrangements in additional 15% (4/26) SSTs, none of which are detected in other types of SCSTs (n = 48) or common cancer types (n = 9,950). The FHL2-GLI2 fusions result in transcriptomic activation of the Sonic Hedgehog (SHH) pathway in SSTs. Expression of the FHL2-GLI2 fusion in vitro leads to the acquisition of phenotypic characteristics of SSTs, increased proliferation, migration and colony formation, and SHH pathway activation. Targeted inhibition of the SHH pathway results in reversal of these oncogenic properties, indicating its role in the pathogenesis of SSTs. Our results demonstrate that the FHL2-GLI2 fusion is likely the oncogenic driver of SSTs, defining a genotypic–phenotypic correlation in ovarian neoplasms. Little is known about the genetics of sclerosing stromal tumor of the ovary, a rare type of sex cord-stromal tumor. Here, the authors use sequencing strategies to show that in a cohort of 26 tumor samples 65% carry a FHL2-GLI2 fusion gene and demonstrate in vitro that the fusion gene has oncogenic properties.
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Zhang S, Huang S, Zhang H, Li D, Li X, Cheng Y, Liu Q, Xu L, Wang Y, Liu Y, Li T. Histo- and clinico-pathological analysis of a large series of triple-negative breast cancer in a single center in China: Evidences on necessity of histological subtyping and grading. Chin J Cancer Res 2020; 32:580-595. [PMID: 33223753 PMCID: PMC7666778 DOI: 10.21147/j.issn.1000-9604.2020.05.03] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Objective To investigate histo-pathological distribution and clinico-pathological significance in a large Chinese triple-negative breast cancer (TNBC) patients serials based on the latest understanding of its clinico-pathological diversity, and to provide more information to clinicians to improve precision of individualized treatment of TNBC. Methods A retrospective analysis was performed on patients with TNBC at Breast Disease Center, Peking University First Hospital between January 2010 and December 2019. Histo- and clinico-pathological characteristics were analyzed by Chi-square test and Student’s t-test, and prognoses were calculated using Kaplan-Meier method and a Cox proportionate hazards model. Bonferroni correction was used to correct for multiple comparison.
Results Conventional type of TNBC (cTNBC) were identified in 73.7% of 582 TNBC, while special type of TNBC (sTNBC) were 26.3%, including 71 apocrine carcinoma, 20 medullary carcinoma, 31 metaplastic carcinoma, 18 invasive lobular carcinoma, 7 invasive micropapillary carcinoma, 5 adenoid cystic carcinoma and 1 acinic cell carcinoma. Compared to sTNBC, cTNBC was associated with high histologic grade (P<0.001) and lower androgen receptor (AR) expression (P<0.001). TNM stage of low-grade cTNBC was significantly lower than that of high-grade cTNBC (P=0.002). Although no significant difference, there was a trend that the rate of 5-year disease-free survival (DFS) and 5-year overall survival (OS) were longer in high-grade cTNBC than in high-grade sTNBC (P=0.091 and 0.518), and were longer in low-grade sTNBC than in high-grade sTNBC (P=0.051 and 0.350). Metaplastic carcinomas showed larger tumor size (P=0.008) and higher proliferative Ki67 index (P=0.004) than cTNBCs. Conclusions Results from our cohort imply that sub-categorization or subtyping and histological grading could be meaningful in pathological evaluation of TNBC, and need to be clarified in more large collections of TNBC.
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Affiliation(s)
- Shuang Zhang
- Department of Pathology, Peking University First Hospital, Beijing 100034, China
| | - Sixia Huang
- Department of Pathology, Peking University First Hospital, Beijing 100034, China
| | - Hong Zhang
- Department of Pathology, Peking University First Hospital, Beijing 100034, China
| | - Dong Li
- Department of Pathology, Peking University First Hospital, Beijing 100034, China
| | - Xin Li
- Department of Pathology, Peking University First Hospital, Beijing 100034, China
| | - Yuanjia Cheng
- Breast Disease Center, Peking University First Hospital, Beijing 100034, China
| | - Qian Liu
- Breast Disease Center, Peking University First Hospital, Beijing 100034, China
| | - Ling Xu
- Breast Disease Center, Peking University First Hospital, Beijing 100034, China
| | - Yue Wang
- Breast Disease Center, Peking University First Hospital, Beijing 100034, China
| | - Yinhua Liu
- Breast Disease Center, Peking University First Hospital, Beijing 100034, China
| | - Ting Li
- Department of Pathology, Peking University First Hospital, Beijing 100034, China
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Abstract
Next-generation sequencing (NGS) has become the primary technology for discovering gene fusions. Decreasing NGS costs have resulted in a growing quantity of patients with whole transcriptome sequencing (RNA-seq) and whole genome sequencing (WGS) data. We developed a gene fusion discovery tool, INTEGRATE, that leverages both RNA-seq and WGS data to reconstruct gene fusion junctions and genomic breakpoints by split-read alignment. INTEGRATE has become widely adopted by the larger cancer research community to discover biologically and clinically relevant gene fusions. Here we explain the rationale driving the development of the INTEGRATE tool and describe the detailed practical procedures for applying INTEGRATE to discover gene fusions using NGS data. INTEGRATE can be applied to both combined data and RNA-seq only data.
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Affiliation(s)
- Jin Zhang
- Department of Radiation Oncology, Siteman Cancer Center, Institute for Informatics, Washington University School of Medicine, St. Louis, MO, USA
| | - Christopher A Maher
- Division of Oncology, Department of Internal Medicine, Siteman Cancer Center, McDonell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA. .,Department of Biomedical Engineering, University School of Medicine, St. Louis, MO, USA.
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MYB-NFIB gene fusion in prostatic basal cell carcinoma: clinicopathologic correlates and comparison with basal cell adenoma and florid basal cell hyperplasia. Mod Pathol 2019; 32:1666-1674. [PMID: 31189999 DOI: 10.1038/s41379-019-0297-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/29/2019] [Accepted: 05/06/2019] [Indexed: 11/08/2022]
Abstract
Prostatic basal cell carcinoma is a malignant neoplasm composed of basaloid cells forming infiltrative nests and tubules, which may potentially be misdiagnosed as benign basal cell proliferations (i.e., florid basal cell hyperplasia or basal cell adenoma) and also closely resembles adenoid cystic carcinoma of the salivary gland. MYB-NFIB gene rearrangement occurs in 30-86% of salivary gland adenoid cystic carcinomas. We sought to further characterize MYB gene rearrangement in prostatic basal cell carcinoma and correlate MYB-NFIB fusion status with other clinicopathologic characteristics. To this end, FISH analysis for MYB-NFIB gene fusion using fusion probes was performed on formalin-fixed, paraffin-embedded tissue sections from prostatic basal cell carcinoma (n = 30), florid basal cell hyperplasia (n = 18), and basal cell adenoma (n = 4). Fourteen of 30 (47%) cases of basal cell carcinoma were positive for MYB-NFIB gene fusion FISH, and no cases of benign basal cell proliferations were positive (p < 0.05). FISH-positive patients (mean age = 63 years, range: 35-81) tended to be younger than FISH-negative patients (mean age = 70 years, range: 55-93). Most FISH-positive cases demonstrated adenoid cystic carcinoma-like morphology (57%), and most FISH-negative cases demonstrated nonadenoid cystic carcinoma-like morphology (93%); one case (FISH-positive) demonstrated areas with both adenoid cystic carcinoma-like and nonadenoid cystic carcinoma-like morphology. FISH-positive cases more frequently demonstrated perineural invasion (50% vs. 14%, p < 0.05) compared to FISH-negative cases. Conversely, tall basal cells (i.e., neoplastic cells at least two times taller than wide) were more frequent in FISH-negative cases than FISH-positive cases (93% vs. 36%, p < 0.05). Approximately, 50% of prostatic basal cell carcinoma harbor MYB-NFIB gene fusion. The majority of these cases were characterized by adenoid cystic carcinoma-like morphology, perineural invasion, and lack tall basal cells. Florid basal cell hyperplasia and basal cell adenoma are negative for MYB-NFIB gene fusion.
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Pang W, Wang Z, Jin X, Zhang Q. Adenoid cystic carcinoma of the breast in a male: A case report. Medicine (Baltimore) 2019; 98:e16760. [PMID: 31393393 PMCID: PMC6708915 DOI: 10.1097/md.0000000000016760] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 06/06/2019] [Accepted: 07/16/2019] [Indexed: 01/27/2023] Open
Abstract
RATIONALE Adenoid cystic carcinoma (ACC) of the breast is an infrequent neoplasm, and the occurrence in males is rare. Therefore, diagnostic and therapeutic challenges are inevitable. PATIENT CONCERNS Herein, we present a case of a 44-year-old man with a tumor on his right breast that he had known about for 6 years. DIAGNOSES The patient underwent a lumpectomy, and the histological examination confirmed a diagnosis of ACC. INTERVENTIONS Modified radical mastectomy was subsequently conducted in the patient. No positive lymph nodes were observed in the postoperative pathological examination. Following the surgery, the patient received adjuvant chemotherapy. OUTCOMES The patient remained recurrence-free at 26 months. LESSONS Compared to female breast ACC, male breast ACC may behave differently biologically and have a different prognosis. Our case will provide more diagnostic and treatment experience to deal with this disease.
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Yi X, Yang Y, Wu P, Xu X, Li W. Alternative splicing events during adipogenesis from hMSCs. J Cell Physiol 2019; 235:304-316. [PMID: 31206189 DOI: 10.1002/jcp.28970] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/28/2019] [Accepted: 05/29/2019] [Indexed: 12/22/2022]
Abstract
Adipogenesis, the developmental process of progenitor-cell differentiating into adipocytes, leads to fat metabolic disorders. Alternative splicing (AS), a ubiquitous regulatory mechanism of gene expression, allows the generation of more than one unique messenger RNA (mRNA) species from a single gene. Till now, alternative splicing events during adipogenesis from human mesenchymal stem cells (hMSCs) are not yet fully elucidated. We performed RNA-Seq coupled with bioinformatics analysis to identify the differentially expressed AS genes and events during adipogenesis from hMSCs. A global survey separately identified 1262, 1181, 1167, and 1227 ASE involved in the most common types of AS including cassette exon, alt3, and alt5, especially with cassette exon the most prevalent, at 7, 14, 21, and 28 days during adipogenesis. Interestingly, 122 differentially expressed ASE referred to 118 genes, and the three genes including ACTN1 (alt3 and cassette), LRP1 (alt3 and alt5), and LTBP4 (cassette, cassette_multi, and unknown), appeared in multiple AS types of ASE during adipogenesis. Except for all the identified ASE of LRP1 occurred in the extracellular topological domain, alt3 (84) in transmembrane domain significantly differentially expressed was the potential key event during adipogenesis. Overall, we have, for the first time, conducted the global transcriptional profiling during adipogenesis of hMSCs to identify differentially expressed ASE and ASE-related genes. This finding would provide extensive ASE as the regulator of adipogenesis and the potential targets for future molecular research into adipogenesis-related metabolic disorders.
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Affiliation(s)
- Xia Yi
- Jiangxi Provincial Key Laboratory of Systems Biomedicine, Jiujiang University, Jiujiang, China
| | - Yunzhong Yang
- Beijing Yuanchuangzhilian Techonlogy Development Co., Ltd, Beijing, China
| | - Ping Wu
- Jiangxi Provincial Key Laboratory of Systems Biomedicine, Jiujiang University, Jiujiang, China
| | - Xiaoyuan Xu
- Jiangxi Provincial Key Laboratory of Systems Biomedicine, Jiujiang University, Jiujiang, China
| | - Weidong Li
- Jiangxi Provincial Key Laboratory of Systems Biomedicine, Jiujiang University, Jiujiang, China
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Pareja F, Selenica P, Brown DN, Sebastiao APM, da Silva EM, Da Cruz Paula A, Del A, Fu L, Weigelt B, Brogi E, Reis-Filho JS, Wen HY. Micropapillary variant of mucinous carcinoma of the breast shows genetic alterations intermediate between those of mucinous carcinoma and micropapillary carcinoma. Histopathology 2019; 75:139-145. [PMID: 30843622 DOI: 10.1111/his.13853] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 02/21/2019] [Accepted: 03/04/2019] [Indexed: 12/19/2022]
Abstract
AIMS Micropapillary variant of mucinous carcinoma of the breast (MPMC) is a rare histological form of oestrogen receptor (ER)-positive invasive carcinoma that is characterised by micropapillary clusters of tumour cells in lakes of extracellular mucin. The aims of this study were to determine the genetic alterations underpinning MPMCs, and to determine whether they overlap with those of mucinous carcinomas and/or invasive micropapillary carcinomas. METHODS AND RESULTS DNA from five MPMCs was subjected to whole-exome sequencing. Somatic mutations, copy number alterations and mutational signatures were determined with state-of-the-art bioinformatics methods. No mutations in genes significantly mutated in breast cancer, including TP53, PIK3CA, GATA3, and MAP3K1, were detected. We identified copy number alterations that have been reported in invasive micropapillary carcinomas, such as recurrent gains in 1q, 6p, 8q, and 10q, and recurrent losses in 16q, 11q, and 13q, as well as a recurrent 8p12-8p11.2 amplification encompassing FGFR1. Like mucinous carcinomas, three of the five MPMCs analysed lacked PIK3CA mutations, 1q gains, and 16q losses, which are the hallmark genetic alterations of ER-positive breast cancers, whereas two MPMCs harboured 16q losses and/or a complex pattern of copy number alterations similar to those found in breast-invasive micropapillary carcinomas. CONCLUSIONS MPMCs are heterogeneous at the genetic level; some tumours show a pattern of somatic genetic alterations similar to those of mucinous carcinomas, whereas others resemble invasive micropapillary carcinomas at the genetic level. These findings suggest that MPMCs may not constitute one histological subtype, but rather a convergent phenotype that can stem from mucinous carcinomas or invasive micropapillary carcinomas.
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Affiliation(s)
- Fresia Pareja
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David N Brown
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ana P M Sebastiao
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Edaise M da Silva
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arnaud Da Cruz Paula
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Angela Del
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Li Fu
- Department of Breast Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Edi Brogi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hannah Y Wen
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Lopez G, Costanza J, Colleoni M, Fontana L, Ferrero S, Miozzo M, Fusco N. Molecular Insights into the Classification of Luminal Breast Cancers: The Genomic Heterogeneity of Progesterone-Negative Tumors. Int J Mol Sci 2019; 20:E510. [PMID: 30691046 PMCID: PMC6386970 DOI: 10.3390/ijms20030510] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/22/2019] [Accepted: 01/23/2019] [Indexed: 12/17/2022] Open
Abstract
Estrogen receptor (ER)-positive progesterone receptor (PR)-negative breast cancers are infrequent but clinically challenging. Despite the volume of genomic data available on these tumors, their biology remains poorly understood. Here, we aimed to identify clinically relevant subclasses of ER+/PR- breast cancers based on their mutational landscape. The Cancer Genomics Data Server was interrogated for mutational and clinical data of all ER+ breast cancers with information on PR status from The Cancer Genome Atlas (TCGA), Memorial Sloan Kettering (MSK), and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) projects. Clustering analysis was performed using gplots, ggplot2, and ComplexHeatmap packages. Comparisons between groups were performed using the Student's t-test and the test of Equal or Given Proportions. Survival curves were built according to the Kaplan⁻Meier method; differences in survival were assessed with the log-rank test. A total of 3570 ER+ breast cancers (PR- n = 959, 27%; PR+ n = 2611, 73%) were analyzed. Mutations in well-known cancer genes such as TP53, GATA3, CDH1, HER2, CDH1, and BRAF were private to or enriched for in PR- tumors. Mutual exclusivity analysis revealed the presence of four molecular clusters with significantly different prognosis on the basis of PIK3CA and TP53 status. ER+/PR- breast cancers are genetically heterogeneous and encompass a variety of distinct entities in terms of prognostic and predictive information.
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Affiliation(s)
- Gianluca Lopez
- Division of Pathology, Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, 20122 Milan, Italy.
- School of Pathology, University of Milan, 20122, Milan, Italy.
| | - Jole Costanza
- Research Laboratory Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122, Milan, Italy.
| | - Matteo Colleoni
- Division of Pathology, Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, 20122 Milan, Italy.
| | - Laura Fontana
- Medical Genetics, Department of Pathophysiology and Transplantation, University of Milan, 20122, Milan, Italy.
| | - Stefano Ferrero
- Division of Pathology, Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, 20122 Milan, Italy.
- Pathology, Department of Biomedical, Surgical, and Dental Sciences, University of Milan, 20122, Milan, Italy.
| | - Monica Miozzo
- Research Laboratory Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122, Milan, Italy.
- Medical Genetics, Department of Pathophysiology and Transplantation, University of Milan, 20122, Milan, Italy.
| | - Nicola Fusco
- Division of Pathology, Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, 20122 Milan, Italy.
- Pathology, Department of Biomedical, Surgical, and Dental Sciences, University of Milan, 20122, Milan, Italy.
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Pareja F, Geyer FC, Brown DN, Sebastião APM, Gularte-Mérida R, Li A, Edelweiss M, Da Cruz Paula A, Selenica P, Wen HY, Jungbluth AA, Varga Z, Palazzo J, Rubin BP, Ellis IO, Brogi E, Rakha EA, Weigelt B, Reis-Filho JS. Assessment of HMGA2 and PLAG1 rearrangements in breast adenomyoepitheliomas. NPJ Breast Cancer 2019; 5:6. [PMID: 30675516 PMCID: PMC6338730 DOI: 10.1038/s41523-018-0101-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 11/27/2018] [Indexed: 02/08/2023] Open
Abstract
Breast adenomyoepitheliomas (AMEs) are rare epithelial-myoepithelial neoplasms that may occasionally produce myxochondroid matrix, akin to pleomorphic adenomas (PAs). Regardless of their anatomic location, PAs often harbor rearrangements involving HMGA2 or PLAG1. We have recently shown that the repertoire of somatic genetic alterations of AMEs varies according to their estrogen receptor (ER) status; whilst the majority of ER-positive AMEs display mutually exclusive PIK3CA or AKT1 hotspot mutations, up to 60% of ER-negative AMEs harbor concurrent HRAS Q61 hotspot mutations and mutations affecting either PIK3CA or PIK3R1. Here, we hypothesized that a subset of AMEs lacking these somatic genetic alterations could be underpinned by oncogenic fusion genes, in particular those involving HMGA2 or PLAG1. Therefore, we subjected 13 AMEs to RNA-sequencing for fusion discovery (n = 5) and/or fluorescence in situ hybridization (FISH) analysis for HMGA2 and PLAG1 rearrangements (n = 13). RNA-sequencing revealed an HMGA2-WIF1 fusion gene in an ER-positive AME lacking HRAS, PIK3CA and AKT1 somatic mutations. This fusion gene, which has been previously described in salivary gland PAs, results in a chimeric transcript composed of exons 1-5 of HMGA2 and exons 3-10 of WIF1. No additional in-frame fusion genes or HMGA2 or PLAG1 rearrangements were identified in the remaining AMEs analyzed. Our results demonstrate that a subset of AMEs lacking mutations affecting HRAS and PI3K pathway-related genes may harbor HMGA2-WIF1 fusion genes, suggesting that a subset of breast AMEs may be genetically related to PAs or that a subset of AMEs may originate in the context of a PA.
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Affiliation(s)
- Fresia Pareja
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Felipe C. Geyer
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - David N. Brown
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | | | | | - Anqi Li
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Marcia Edelweiss
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Arnaud Da Cruz Paula
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Hannah Y. Wen
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Achim A. Jungbluth
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Zsuzsanna Varga
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Juan Palazzo
- Department of Pathology, Thomas Jefferson University Hospital, Philadelphia, PA USA
| | - Brian P. Rubin
- Department of Pathology, Cleveland Clinic, Cleveland, OH USA
| | - Ian O. Ellis
- Department of Pathology, University of Nottingham, Nottingham, UK
| | - Edi Brogi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Emad A. Rakha
- Department of Pathology, University of Nottingham, Nottingham, UK
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Jorge S. Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
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McCart Reed AE, Kalita-De Croft P, Kutasovic JR, Saunus JM, Lakhani SR. Recent advances in breast cancer research impacting clinical diagnostic practice. J Pathol 2019; 247:552-562. [PMID: 30426489 DOI: 10.1002/path.5199] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 10/29/2018] [Accepted: 11/09/2018] [Indexed: 12/17/2022]
Abstract
During the last decade, the genomics revolution has driven critical advances in molecular oncology and pathology, and a deeper appreciation of heterogeneity that is beginning to reshape our thinking around diagnostic classification. Recent developments have seen existing classification systems modified and improved where possible, gene-based diagnostics implemented and tumour-immune interactions modulated. We present a detailed discussion of this progress, including advances in the understanding of breast tumour classification, e.g. mixed ductal-lobular tumours and the spectrum of triple-negative breast cancer. The latest information on clinical trials and the implementation of gene-based diagnostics, including MammaPrint and Oncotype Dx and others, is synthesised, and emerging targeted therapies, as well as the burgeoning immuno-oncology field, and their relevance in breast cancer, are discussed. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Amy E McCart Reed
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Priyakshi Kalita-De Croft
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Jamie R Kutasovic
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Jodi M Saunus
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Sunil R Lakhani
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, Australia.,Pathology Queensland, The Royal Brisbane & Women's Hospital, Brisbane, Australia
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65
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Endo Y, Kuwamoto S, Ohira T, Matsushita M, Matsushige T, Fukuhara T, Nakamoto S, Hayashi K, Kugoh H, Hirooka Y. Possible Relationship Between MYBL1 Alterations and Specific Primary Sites in Adenoid Cystic Carcinoma: A Clinicopathological and Molecular Study of 36 Cases. Yonago Acta Med 2019. [DOI: 10.33160/yam.2019.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Yukari Endo
- *Department of Pathology, Tottori University Hospital, Yonago 683-8504, Japan
- †Department of Pathobiological Science and Technology, School of Health Sciences, Tottori University Faculty of Medicine, Yonago 683-8503, Japan
| | - Satoshi Kuwamoto
- *Department of Pathology, Tottori University Hospital, Yonago 683-8504, Japan
| | - Takahito Ohira
- ‡Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Sciences, Tottori University, Yonago 683-8503, Japan
| | - Michiko Matsushita
- †Department of Pathobiological Science and Technology, School of Health Sciences, Tottori University Faculty of Medicine, Yonago 683-8503, Japan
| | - Takahiro Matsushige
- *Department of Pathology, Tottori University Hospital, Yonago 683-8504, Japan
| | - Takahiro Fukuhara
- §Division of Otolaryngology, Head and Neck Surgery, Department of Sensory and Motor Organs, School of Medicine, Tottori University Faculty of Medicine, Yonago 683-8504, Japan
| | - Shu Nakamoto
- Department of Pathology, Tottori Prefectural Central Hospital, Tottori 680-0901, Japan
| | - Kazuhiko Hayashi
- ¶Division of Molecular Pathology, Department of Pathology, School of Medicine, Tottori University Faculty of Medicine, Yonago 683-8503, Japan
| | - Hiroyuki Kugoh
- ‡Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Sciences, Tottori University, Yonago 683-8503, Japan
| | - Yasuaki Hirooka
- *Department of Pathology, Tottori University Hospital, Yonago 683-8504, Japan
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66
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Baraban E, Zhang PJ, Jaffer S, Lubin D, Feldman M, Bleiweiss IJ, Nayak A. MYB
rearrangement and immunohistochemical expression in adenomyoepithelioma of the breast: a comparison with adenoid cystic carcinoma. Histopathology 2018; 73:897-903. [DOI: 10.1111/his.13708] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 07/11/2018] [Indexed: 01/24/2023]
Affiliation(s)
- Ezra Baraban
- Department of Pathology and Laboratory Medicine; Perelman School of Medicine and Hospital of the University of Pennsylvania; Pennsylvania PA USA
| | - Paul J Zhang
- Department of Pathology and Laboratory Medicine; Perelman School of Medicine and Hospital of the University of Pennsylvania; Pennsylvania PA USA
| | - Shabnam Jaffer
- Department of Pathology; Mount Sinai Hospital and Icahn School of Medicine; New York NY USA
| | - Daniel Lubin
- Department of Pathology and Laboratory Medicine; Perelman School of Medicine and Hospital of the University of Pennsylvania; Pennsylvania PA USA
| | - Michael Feldman
- Department of Pathology and Laboratory Medicine; Perelman School of Medicine and Hospital of the University of Pennsylvania; Pennsylvania PA USA
| | - Ira J Bleiweiss
- Department of Pathology and Laboratory Medicine; Perelman School of Medicine and Hospital of the University of Pennsylvania; Pennsylvania PA USA
| | - Anupma Nayak
- Department of Pathology and Laboratory Medicine; Perelman School of Medicine and Hospital of the University of Pennsylvania; Pennsylvania PA USA
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Loss-of-function mutations in ATP6AP1 and ATP6AP2 in granular cell tumors. Nat Commun 2018; 9:3533. [PMID: 30166553 PMCID: PMC6117336 DOI: 10.1038/s41467-018-05886-y] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 08/02/2018] [Indexed: 12/21/2022] Open
Abstract
Granular cell tumors (GCTs) are rare tumors that can arise in multiple anatomical locations, and are characterized by abundant intracytoplasmic granules. The genetic drivers of GCTs are currently unknown. Here, we apply whole-exome sequencing and targeted sequencing analysis to reveal mutually exclusive, clonal, inactivating somatic mutations in the endosomal pH regulators ATP6AP1 or ATP6AP2 in 72% of GCTs. Silencing of these genes in vitro results in impaired vesicle acidification, redistribution of endosomal compartments, and accumulation of intracytoplasmic granules, recapitulating the cardinal phenotypic characteristics of GCTs and providing a novel genotypic–phenotypic correlation. In addition, depletion of ATP6AP1 or ATP6AP2 results in the acquisition of oncogenic properties. Our results demonstrate that inactivating mutations of ATP6AP1 and ATP6AP2 are likely oncogenic drivers of GCTs and underpin the genesis of the intracytoplasmic granules that characterize them, providing a genetic link between endosomal pH regulation and tumorigenesis. Granular cell tumors (GCTs) are rare tumors that arise in multiple anatomical locations. Here, the authors investigate the genomics of GCTs, finding inactivating somatic mutations in ATP6AP1 or ATP6AP2 in 72% of the 82 GCTs analyzed. In vitro manipulation of these genes recapitulated GCT phenotypes in cellular models.
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68
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Andreasen S. Molecular features of adenoid cystic carcinoma with an emphasis on microRNA expression. APMIS 2018; 126 Suppl 140:7-57. [DOI: 10.1111/apm.12828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Simon Andreasen
- Department of Otorhinolaryngology and Maxillofacial Surgery; Zealand University Hospital; Køge Denmark
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