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Nishimura T, Kakiuchi N, Yoshida K, Sakurai T, Kataoka TR, Kondoh E, Chigusa Y, Kawai M, Sawada M, Inoue T, Takeuchi Y, Maeda H, Baba S, Shiozawa Y, Saiki R, Nakagawa MM, Nannya Y, Ochi Y, Hirano T, Nakagawa T, Inagaki-Kawata Y, Aoki K, Hirata M, Nanki K, Matano M, Saito M, Suzuki E, Takada M, Kawashima M, Kawaguchi K, Chiba K, Shiraishi Y, Takita J, Miyano S, Mandai M, Sato T, Takeuchi K, Haga H, Toi M, Ogawa S. Evolutionary histories of breast cancer and related clones. Nature 2023; 620:607-614. [PMID: 37495687 PMCID: PMC10432280 DOI: 10.1038/s41586-023-06333-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 06/15/2023] [Indexed: 07/28/2023]
Abstract
Recent studies have documented frequent evolution of clones carrying common cancer mutations in apparently normal tissues, which are implicated in cancer development1-3. However, our knowledge is still missing with regard to what additional driver events take place in what order, before one or more of these clones in normal tissues ultimately evolve to cancer. Here, using phylogenetic analyses of multiple microdissected samples from both cancer and non-cancer lesions, we show unique evolutionary histories of breast cancers harbouring der(1;16), a common driver alteration found in roughly 20% of breast cancers. The approximate timing of early evolutionary events was estimated from the mutation rate measured in normal epithelial cells. In der(1;16)(+) cancers, the derivative chromosome was acquired from early puberty to late adolescence, followed by the emergence of a common ancestor by the patient's early 30s, from which both cancer and non-cancer clones evolved. Replacing the pre-existing mammary epithelium in the following years, these clones occupied a large area within the premenopausal breast tissues by the time of cancer diagnosis. Evolution of multiple independent cancer founders from the non-cancer ancestors was common, contributing to intratumour heterogeneity. The number of driver events did not correlate with histology, suggesting the role of local microenvironments and/or epigenetic driver events. A similar evolutionary pattern was also observed in another case evolving from an AKT1-mutated founder. Taken together, our findings provide new insight into how breast cancer evolves.
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Affiliation(s)
- Tomomi Nishimura
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Next-generation Clinical Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Breast Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Nobuyuki Kakiuchi
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- The Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kenichi Yoshida
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Division of Cancer Evolution, National Cancer Center Research Institute, Tokyo, Japan
| | - Takaki Sakurai
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
- Department of Diagnostic Pathology, Osaka Red Cross Hospital, Osaka, Japan
| | - Tatsuki R Kataoka
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
- Department of Pathology, Iwate Medical University, Iwate, Japan
| | - Eiji Kondoh
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Obstetrics and Gynecology Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Yoshitsugu Chigusa
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masahiko Kawai
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | | | | | - Yasuhide Takeuchi
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
| | - Hirona Maeda
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
| | - Satoko Baba
- Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
- Division of Pathology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
- Department of Pathology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yusuke Shiozawa
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ryunosuke Saiki
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masahiro M Nakagawa
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Next-generation Clinical Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yasuhito Nannya
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Division of Hematopoietic Disease Control, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yotaro Ochi
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tomonori Hirano
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Tomoe Nakagawa
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Yukiko Inagaki-Kawata
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Breast Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kosuke Aoki
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masahiro Hirata
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
| | - Kosaku Nanki
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Mami Matano
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Megumu Saito
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
- Osaka Research Center for Drug Discovery, Otsuka Pharmaceutical Company, Limited, Osaka, Japan
| | - Eiji Suzuki
- Department of Breast Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Breast Surgery Department, Kobe City Medical Center General Hospital, Hyogo, Japan
| | - Masahiro Takada
- Department of Breast Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masahiro Kawashima
- Department of Breast Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kosuke Kawaguchi
- Department of Breast Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kenichi Chiba
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Yuichi Shiraishi
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Satoru Miyano
- Department of Integrated Analytics, M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Masaki Mandai
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Toshiro Sato
- Department of Organoid Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Kengo Takeuchi
- Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
- Division of Pathology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
- Department of Pathology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Hironori Haga
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
| | - Masakazu Toi
- Department of Breast Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumour Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.
- Department of Medicine, Centre for Haematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden.
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Lee JJK, Jung YL, Cheong TC, Espejo Valle-Inclan J, Chu C, Gulhan DC, Ljungström V, Jin H, Viswanadham VV, Watson EV, Cortés-Ciriano I, Elledge SJ, Chiarle R, Pellman D, Park PJ. ERα-associated translocations underlie oncogene amplifications in breast cancer. Nature 2023; 618:1024-1032. [PMID: 37198482 PMCID: PMC10307628 DOI: 10.1038/s41586-023-06057-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 04/05/2023] [Indexed: 05/19/2023]
Abstract
Focal copy-number amplification is an oncogenic event. Although recent studies have revealed the complex structure1-3 and the evolutionary trajectories4 of oncogene amplicons, their origin remains poorly understood. Here we show that focal amplifications in breast cancer frequently derive from a mechanism-which we term translocation-bridge amplification-involving inter-chromosomal translocations that lead to dicentric chromosome bridge formation and breakage. In 780 breast cancer genomes, we observe that focal amplifications are frequently connected to each other by inter-chromosomal translocations at their boundaries. Subsequent analysis indicates the following model: the oncogene neighbourhood is translocated in G1 creating a dicentric chromosome, the dicentric chromosome is replicated, and as dicentric sister chromosomes segregate during mitosis, a chromosome bridge is formed and then broken, with fragments often being circularized in extrachromosomal DNAs. This model explains the amplifications of key oncogenes, including ERBB2 and CCND1. Recurrent amplification boundaries and rearrangement hotspots correlate with oestrogen receptor binding in breast cancer cells. Experimentally, oestrogen treatment induces DNA double-strand breaks in the oestrogen receptor target regions that are repaired by translocations, suggesting a role of oestrogen in generating the initial translocations. A pan-cancer analysis reveals tissue-specific biases in mechanisms initiating focal amplifications, with the breakage-fusion-bridge cycle prevalent in some and the translocation-bridge amplification in others, probably owing to the different timing of DNA break repair. Our results identify a common mode of oncogene amplification and propose oestrogen as its mechanistic origin in breast cancer.
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Affiliation(s)
- Jake June-Koo Lee
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Youngsook Lucy Jung
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Taek-Chin Cheong
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Chong Chu
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Doga C Gulhan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
| | - Viktor Ljungström
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Hu Jin
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | | | - Emma V Watson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Isidro Cortés-Ciriano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Stephen J Elledge
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Roberto Chiarle
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - David Pellman
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.
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3
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de Boer M, Verschuur-Maes AHJ, Moelans C, van Diest PJ. Papillomatous breast lesions with atypical columnar cell features. J Clin Pathol 2023; 76:228-233. [PMID: 36693714 DOI: 10.1136/jcp-2022-208389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 12/29/2022] [Indexed: 01/26/2023]
Abstract
AIMS Columnar cell lesions (CCLs) are recognised breast cancer precursor lesions. Intraductal papillomas are usually lined by benign (polyclonal) cells. Although papillomas with monoclonal lesions (atypical ductal hyperplasia (ADH)/ductal carcinoma in situ (DCIS)) have been described, CCLs have not been described in papillomas. METHODS We present two papillary breast lesions lined by a single layer of luminal cells resembling atypical CCL/flat epithelial atypia (FEA). We compared these two lesions with 13 benign intraductal papillomas, and 2 papillomas with ADH/DCIS grade 1 features as controls were immunohistochemically stained for the oestrogen receptor alpha (oestrogen receptor) and progesterone receptors (PR), cytokeratin 5 (CK5) and cyclin D1. RESULTS Oestrogen receptor/PR expression was variable, with areas with ≥85% hormone receptor positivity in both morphologically normal papillomas and papillomas with ADH. In ADH areas, CK5 expression was seen in ≤5% of cells while cyclin D1 expression was high (>60%). The two papillary lesions with FEA were 100% oestrogen receptor and 90% cyclin D1 positive, and low on PR/CK5. There was only one morphologically normal papilloma with similar areas of low CK5 (5%) and high cyclin D1 expression; in all other morphologically benign papillomas CK5 expression varied between 10% and 50% and cyclin D1 expression was ≤50%. The papillary lesion with FEA that could be tested showed 16q losses, the hallmark genetic change in low nuclear grade breast neoplasias, in contrast to nine morphologically benign papillomas that could be tested. CONCLUSION We present two papillomatous breast lesions with atypical CCL morphology and 16q loss, for which we propose the term papillary FEA.
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Affiliation(s)
- Mirthe de Boer
- Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Cathy Moelans
- Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Paul J van Diest
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
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4
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Machine learning-based image analysis for accelerating the diagnosis of complicated preneoplastic and neoplastic ductal lesions in breast biopsy tissues. Breast Cancer Res Treat 2021; 188:649-659. [PMID: 33934277 DOI: 10.1007/s10549-021-06243-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/21/2021] [Indexed: 10/21/2022]
Abstract
PURPOSE Diagnosis of breast preneoplastic and neoplastic lesions is difficult due to their similar morphology in breast biopsy specimens. To diagnose these lesions, pathologists perform immunohistochemical analysis and consult with expert breast pathologists. These additional examinations are time-consuming and expensive. Artificial intelligence (AI)-based image analysis has recently improved, and may help in ordinal pathological diagnosis. Here, we showed the significance of machine learning-based image analysis of breast preneoplastic and neoplastic lesions for facilitating high-throughput diagnosis. METHODS Images were obtained from normal mammary glands, hyperplastic lesions, preneoplastic lesions and neoplastic lesions, such as usual ductal hyperplasia (UDH), columnar cell lesion (CCL), ductal carcinoma in situ (DCIS), and DCIS with comedo necrosis (comedo DCIS) in breast biopsy specimens. The original enhanced convoluted neural network (CNN) system was used for analyzing the pathological images. RESULTS The AI-based image analysis provided the following area under the curve values (AUC): normal lesion versus DCIS, 0.9902; DCIS versus comedo DCIS, 0.9942; normal lesion versus CCL, 0.9786; and UDH versus DCIS, 1.000. Multiple comparison analysis showed precision and recall scores similar to those of single comparison analysis. Based on the gradient-weighted class activation mapping (Grad-CAM) used to visualize the important regions reflecting the result of CNN analysis, the ratio of stromal tissue in the whole weighted area was significantly higher in UDH and CCL than that in DCIS. CONCLUSIONS These analyses may provide a more accurate and rapid pathological diagnosis of patients. Moreover, Grad-CAM identifies uncharted important histological characteristics for newer pathological findings and targets of research for understanding diseases.
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Kutasovic JR, McCart Reed AE, Sokolova A, Lakhani SR, Simpson PT. Morphologic and Genomic Heterogeneity in the Evolution and Progression of Breast Cancer. Cancers (Basel) 2020; 12:E848. [PMID: 32244556 PMCID: PMC7226487 DOI: 10.3390/cancers12040848] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 03/25/2020] [Accepted: 03/26/2020] [Indexed: 12/13/2022] Open
Abstract
: Breast cancer is a remarkably complex and diverse disease. Subtyping based on morphology, genomics, biomarkers and/or clinical parameters seeks to stratify optimal approaches for management, but it is clear that every breast cancer is fundamentally unique. Intra-tumour heterogeneity adds further complexity and impacts a patient's response to neoadjuvant or adjuvant therapy. Here, we review some established and more recent evidence related to the complex nature of breast cancer evolution. We describe morphologic and genomic diversity as it arises spontaneously during the early stages of tumour evolution, and also in the context of treatment where the changing subclonal architecture of a tumour is driven by the inherent adaptability of tumour cells to evolve and resist the selective pressures of therapy.
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Affiliation(s)
- Jamie R. Kutasovic
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, Brisbane 4029, Australia; (J.R.K.); (A.E.M.R.); (A.S.); (S.R.L.)
- QIMR Berghofer Medical Research Institute, Herston 4006, Australia
| | - Amy E. McCart Reed
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, Brisbane 4029, Australia; (J.R.K.); (A.E.M.R.); (A.S.); (S.R.L.)
- QIMR Berghofer Medical Research Institute, Herston 4006, Australia
| | - Anna Sokolova
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, Brisbane 4029, Australia; (J.R.K.); (A.E.M.R.); (A.S.); (S.R.L.)
- Pathology Queensland, The Royal Brisbane & Women’s Hospital, Herston, Brisbane 4029, Australia
| | - Sunil R. Lakhani
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, Brisbane 4029, Australia; (J.R.K.); (A.E.M.R.); (A.S.); (S.R.L.)
- Pathology Queensland, The Royal Brisbane & Women’s Hospital, Herston, Brisbane 4029, Australia
| | - Peter T. Simpson
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, Brisbane 4029, Australia; (J.R.K.); (A.E.M.R.); (A.S.); (S.R.L.)
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Guillet C, Rechsteiner M, Bellini E, Choschzick M, Moskovszky L, Dedes K, Papassotiropoulos B, Varga Z. Juvenile papillomatosis of the breast (Swiss cheese disease) has frequent associations with PIK3CA and/or AKT1 mutations. Hum Pathol 2020; 98:64-73. [PMID: 32088208 DOI: 10.1016/j.humpath.2020.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 02/02/2020] [Accepted: 02/16/2020] [Indexed: 12/22/2022]
Abstract
Juvenile papillomatosis (JP), the so-called Swiss cheese disease, is a rare benign breast disease of young adults. An association (up to 28%) with breast cancer within the family of affected patients has been reported. A multinodular cystic breast mass lesion and calcifications characterizes JP in imaging studies. The histological picture is diverse and comprises multiple intraductal papillomas, usual ductal hyperplasia, ductectasias, perifocal sclerosing adenosis, and calcification. Patients with complete excision of JP lesions have an excellent follow-up; breast cancer develops only on a very low subset of patients. Molecular background of JP has not been investigated until now. In this study, we addressed mutational analysis of JP cases and correlated these results with follow-up and family history in context with a comprehensive review of the JP literature. We identified 13 cases fulfilling the criteria of JP. All patients were women with a median age of 38 years (26-50 years). Follow-up information was available for 11 of 13 patients. Sufficient paraffin-embedded tissue and good DNA quality for next-generation sequencing (NGS) was available for 10 patients. Paraffin blocks were microdissected in the area of intraductal proliferative disease; the tissue cores underwent NGS analysis using the Oncomine Comprehensive Panel. In 5 of 10 patients, we found PIK3CA mutations; in 2 of 10 patients, we found AKT1 mutations in known hot spot regions. Further mutations in MET, FGFR3, PTEN, ATM, NF1, and GNAS genes were detected in individual patients. Some of these mutations were present at high allele frequencies suggesting germ line mutations. Two of 3 patients with positive family history had PIK3CA mutation; one patient with positive family history had an AKT1 mutation. One patient who subsequently developed invasive ductal carcinoma in the contralateral breast possibly had a germ line ATM mutation. Our results confirm hot spot mutations in PIK3CA and AKT1 genes in JP associated with positive family history for breast cancer, although these mutations are not specific for JP. The genetic link between JP, positive family history, and subsequent risk of breast cancer needs to be analyzed in further studies.
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Affiliation(s)
- Carole Guillet
- Institute of Pathology and Molecular Pathology, University Hospital Zurich, 8091, Switzerland; Clinic of Dermatology, University Hospital Zurich, 8091, Switzerland
| | - Markus Rechsteiner
- Institute of Pathology and Molecular Pathology, University Hospital Zurich, 8091, Switzerland
| | - Elisa Bellini
- Institute of Pathology and Molecular Pathology, University Hospital Zurich, 8091, Switzerland
| | - Matthias Choschzick
- Institute of Pathology and Molecular Pathology, University Hospital Zurich, 8091, Switzerland
| | - Linda Moskovszky
- Institute of Pathology and Molecular Pathology, University Hospital Zurich, 8091, Switzerland
| | - Konstantin Dedes
- Clinic of Gynecology, University Hospital Zurich, 8091, Switzerland
| | | | - Zsuzsanna Varga
- Institute of Pathology and Molecular Pathology, University Hospital Zurich, 8091, Switzerland.
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7
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Lin CY, Vennam S, Purington N, Lin E, Varma S, Han S, Desa M, Seto T, Wang NJ, Stehr H, Troxell ML, Kurian AW, West RB. Genomic landscape of ductal carcinoma in situ and association with progression. Breast Cancer Res Treat 2019; 178:307-316. [PMID: 31420779 PMCID: PMC6800639 DOI: 10.1007/s10549-019-05401-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 08/07/2019] [Indexed: 01/07/2023]
Abstract
PURPOSE The detection rate of breast ductal carcinoma in situ (DCIS) has increased significantly, raising the concern that DCIS is overdiagnosed and overtreated. Therefore, there is an unmet clinical need to better predict the risk of progression among DCIS patients. Our hypothesis is that by combining molecular signatures with clinicopathologic features, we can elucidate the biology of breast cancer progression, and risk-stratify patients with DCIS. METHODS Targeted exon sequencing with a custom panel of 223 genes/regions was performed for 125 DCIS cases. Among them, 60 were from cases having concurrent or subsequent invasive breast cancer (IBC) (DCIS + IBC group), and 65 from cases with no IBC development over a median follow-up of 13 years (DCIS-only group). Copy number alterations in chromosome 1q32, 8q24, and 11q13 were analyzed using fluorescence in situ hybridization (FISH). Multivariable logistic regression models were fit to the outcome of DCIS progression to IBC as functions of demographic and clinical features. RESULTS We observed recurrent variants of known IBC-related mutations, and the most commonly mutated genes in DCIS were PIK3CA (34.4%) and TP53 (18.4%). There was an inverse association between PIK3CA kinase domain mutations and progression (Odds Ratio [OR] 10.2, p < 0.05). Copy number variations in 1q32 and 8q24 were associated with progression (OR 9.3 and 46, respectively; both p < 0.05). CONCLUSIONS PIK3CA kinase domain mutations and the absence of copy number gains in DCIS are protective against progression to IBC. These results may guide efforts to distinguish low-risk from high-risk DCIS.
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MESH Headings
- Aged
- Aged, 80 and over
- Carcinoma, Ductal, Breast/genetics
- Carcinoma, Ductal, Breast/pathology
- Carcinoma, Ductal, Breast/therapy
- Carcinoma, Intraductal, Noninfiltrating/genetics
- Carcinoma, Intraductal, Noninfiltrating/pathology
- DNA Copy Number Variations
- Female
- Genetic Predisposition to Disease
- Genome-Wide Association Study/methods
- Genomics/methods
- Humans
- In Situ Hybridization, Fluorescence
- Middle Aged
- Neoplasm Metastasis
- Neoplasm Staging
- Tumor Burden
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Affiliation(s)
- Chieh-Yu Lin
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology and Immunology, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Sujay Vennam
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Natasha Purington
- Department of Medicine, Quantitative Sciences Unit, Stanford University, Stanford, CA, USA
| | - Eric Lin
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Sushama Varma
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Summer Han
- Department of Medicine, Quantitative Sciences Unit, Stanford University, Stanford, CA, USA
| | - Manisha Desa
- Department of Medicine and of Biomedical Data Science, Quantitative Sciences Unit, Stanford University, Stanford, CA, USA
| | - Tina Seto
- Research Information Technology, Stanford University School of Medicine, Stanford, CA, USA
| | - Nicholas J Wang
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
| | - Henning Stehr
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Megan L Troxell
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Allison W Kurian
- Departments of Medicine and of Health Research and Policy, Stanford University School of Medicine, Stanford, CA, USA
| | - Robert B West
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
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Bhargava R, Florea AV, Pelmus M, Jones MW, Bonaventura M, Wald A, Nikiforova M. Breast Tumor Resembling Tall Cell Variant of Papillary Thyroid Carcinoma: A Solid Papillary Neoplasm With Characteristic Immunohistochemical Profile and Few Recurrent Mutations. Am J Clin Pathol 2017; 147:399-410. [PMID: 28375433 DOI: 10.1093/ajcp/aqx016] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES Breast tumor resembling tall cell variant of papillary thyroid carcinoma (BTRPTC) is a rare breast lesion that is unrelated to thyroid carcinoma. Morphologically, it shows a solid papillary lesion with bland cytology, eosinophilic/amphophilic secretions, nuclear grooves, reversal of nuclear polarity (recently described), and nuclear inclusions. Clinical course is often uneventful with few exceptions reported in the literature. Herein, we report three additional cases. METHODS Immunohistochemical staining and next-generation sequencing was performed on all three cases. RESULTS The lesional cells on all cases were positive for cytokeratin 5 and S100, with weak expression/lack of estrogen receptor. No staining was observed for myoepithelial markers (p63 and myosin heavy chain) around the lesion. IDH2 mutations were identified in two cases at nucleotide 172 (cases 1 and 3). ATM gene mutation was identified in cases 2 and 3 and PIK3CA mutation in case 3. All patients are currently without disease. CONCLUSIONS BTRPTC is a slow-growing neoplastic lesion that needs to be distinguished from other papillary lesions for optimizing therapy.
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Affiliation(s)
- Rohit Bhargava
- From the Magee-Womens Hospital of University of Pittsburgh Medical Center, Pittsburgh, PA
| | | | | | - Miroslawa W Jones
- From the Magee-Womens Hospital of University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Marguerite Bonaventura
- From the Magee-Womens Hospital of University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Abigail Wald
- University of Pittsburgh Medical Center-Presbyterian, Pittsburgh, PA
| | - Marina Nikiforova
- University of Pittsburgh Medical Center-Presbyterian, Pittsburgh, PA
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9
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Pang JMB, Gorringe KL, Fox SB. Ductal carcinoma in situ - update on risk assessment and management. Histopathology 2016; 68:96-109. [PMID: 26768032 DOI: 10.1111/his.12796] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 07/31/2015] [Indexed: 12/20/2022]
Abstract
Ductal carcinoma in situ (DCIS) accounts for ~20-25% of breast cancers. While DCIS is not life-threatening, it may progress to invasive carcinoma over time, and treatment intended to prevent invasive progression may itself cause significant morbidity. Accurate risk assessment is therefore necessary to avoid over- or undertreatment of an individual patient. In this review we will outline the evidence for current management of DCIS, discuss approaches to DCIS risk assessment and challenges facing identification of novel DCIS biomarkers.
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Affiliation(s)
- Jia-Min B Pang
- Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne, Vic., Australia.,Department of Pathology, University of Melbourne, Melbourne, Vic., Australia
| | - Kylie L Gorringe
- Department of Pathology, University of Melbourne, Melbourne, Vic., Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Vic., Australia.,Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Vic., Australia
| | - Stephen B Fox
- Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne, Vic., Australia.,Department of Pathology, University of Melbourne, Melbourne, Vic., Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Vic., Australia
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10
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Liau JY, Lee YH, Tsai JH, Yuan CT, Chu CY, Hong JB, Sheen YS. FrequentPIK3CAactivating mutations in nipple adenomas. Histopathology 2016; 70:195-202. [DOI: 10.1111/his.13043] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 07/19/2016] [Indexed: 12/13/2022]
Affiliation(s)
- Jau-Yu Liau
- Department of Pathology; National Taiwan University Hospital and National Taiwan University College of Medicine; Taipei Taiwan
- Graduate Institute of Pathology; National Taiwan University College of Medicine; Taipei Taiwan
| | - Yi-Hsuan Lee
- Department of Pathology; National Taiwan University Hospital and National Taiwan University College of Medicine; Taipei Taiwan
| | - Jia-Huei Tsai
- Department of Pathology; National Taiwan University Hospital and National Taiwan University College of Medicine; Taipei Taiwan
- Graduate Institute of Pathology; National Taiwan University College of Medicine; Taipei Taiwan
| | - Chang-Tsu Yuan
- Department of Pathology; National Taiwan University Hospital and National Taiwan University College of Medicine; Taipei Taiwan
| | - Chia-Yu Chu
- Department of Dermatology; National Taiwan University Hospital and National Taiwan University College of Medicine; Taipei Taiwan
| | - Jin-Bon Hong
- Department of Dermatology; National Taiwan University Hospital and National Taiwan University College of Medicine; Taipei Taiwan
| | - Yi-Shuan Sheen
- Department of Dermatology; National Taiwan University Hospital and National Taiwan University College of Medicine; Taipei Taiwan
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11
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Rudolph M, Anzeneder T, Schulz A, Beckmann G, Byrne AT, Jeffers M, Pena C, Politz O, Köchert K, Vonk R, Reischl J. AKT1 (E17K) mutation profiling in breast cancer: prevalence, concurrent oncogenic alterations, and blood-based detection. BMC Cancer 2016; 16:622. [PMID: 27515171 PMCID: PMC4982009 DOI: 10.1186/s12885-016-2626-1] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 07/26/2016] [Indexed: 12/30/2022] Open
Abstract
Background The single hotspot mutation AKT1 [G49A:E17K] has been described in several cancers, with the highest incidence observed in breast cancer. However, its precise role in disease etiology remains unknown. Methods We analyzed more than 600 breast cancer tumor samples and circulating tumor DNA for AKT1E17K and alterations in other cancer-associated genes using Beads, Emulsions, Amplification, and Magnetics digital polymerase chain reaction technology and targeted exome sequencing. Results Overall AKT1E17K mutation prevalence was 6.3 % and not correlated with age or menopausal stage. AKT1E17K mutation frequency tended to be lower in patients with grade 3 disease (1.9 %) compared with those with grade 1 (11.1 %) or grade 2 (6 %) disease. In two cohorts of patients with advanced metastatic disease, 98.0 % (n = 50) and 97.1 % (n = 35) concordance was obtained between tissue and blood samples for the AKT1E17K mutation, and mutation capture rates of 66.7 % (2/3) and 85.7 % (6/7) in blood versus tissue samples were observed. Although AKT1-mutant tumor specimens were often found to harbor concurrent alterations in other driver genes, a subset of specimens harboring AKT1E17K as the only known driver alteration was also identified. Initial follow-up survival data suggest that AKT1E17K could be associated with increased mortality. These findings warrant additional long-term follow-up. Conclusions The data suggest that AKT1E17K is the most likely disease driver in certain breast cancer patients. Blood-based mutation detection is achievable in advanced-stage disease. These findings underpin the need for a further enhanced-precision medicine paradigm in the treatment of breast cancer. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2626-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marion Rudolph
- Bayer Pharma AG, Muellerstrasse 178, 13353, Berlin, Germany.
| | | | - Anke Schulz
- Bayer Pharma AG, Muellerstrasse 178, 13353, Berlin, Germany
| | - Georg Beckmann
- Bayer Pharma AG, Muellerstrasse 178, 13353, Berlin, Germany
| | - Annette T Byrne
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland.,At the time of manuscript preparation, the author was on a Science Foundation Ireland-funded industry secondment, Bayer HealthCare Pharmaceuticals, Whippany, NJ, USA
| | | | - Carol Pena
- Bayer HealthCare Pharmaceuticals, Whippany, NJ, USA
| | - Oliver Politz
- Bayer Pharma AG, Muellerstrasse 178, 13353, Berlin, Germany
| | - Karl Köchert
- Bayer Pharma AG, Muellerstrasse 178, 13353, Berlin, Germany
| | - Richardus Vonk
- Bayer Pharma AG, Muellerstrasse 178, 13353, Berlin, Germany
| | - Joachim Reischl
- Bayer Pharma AG, Muellerstrasse 178, 13353, Berlin, Germany.,AstraZeneca R&D, Personalized Healthcare and Biomarkers, Gothenburg, Sweden
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12
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Targeted next generation sequencing of parotid gland cancer uncovers genetic heterogeneity. Oncotarget 2016; 6:18224-37. [PMID: 26053092 PMCID: PMC4627247 DOI: 10.18632/oncotarget.4015] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 05/14/2015] [Indexed: 12/12/2022] Open
Abstract
Salivary gland cancer represents a heterogeneous group of malignant tumors. Due to their low incidence and the existence of multiple morphologically defined subtypes, these tumors are still poorly understood with regard to their molecular pathogenesis and therapeutically relevant genetic alterations. Performing a systematic and comprehensive study covering 13 subtypes of salivary gland cancer, next generation sequencing was done on 84 tissue samples of parotid gland cancer using multiplex PCR for enrichment of cancer related gene loci covering hotspots of 46 cancer genes. Mutations were identified in 22 different genes. The most frequent alterations affected TP53, followed by RAS genes, PIK3CA, SMAD4 and members of the ERB family. HRAS mutations accounted for more than 90% of RAS mutations, occurring especially in epithelial-myoepithelial carcinomas and salivary duct carcinomas. Additional mutations in PIK3CA also affected particularly epithelial-myoepithelial carcinomas and salivary duct carcinomas, occurring simultaneously with HRAS mutations in almost all cases, pointing to an unknown and therapeutically relevant molecular constellation. Interestingly, 14% of tumors revealed mutations in surface growth factor receptor genes including ALK, HER2, ERBB4, FGFR, cMET and RET, which might prove to be targetable by new therapeutic agents. 6% of tumors revealed mutations in SMAD4. In summary, our data provide novel insight into the fundamental molecular heterogeneity of salivary gland cancer, relevant in terms of tumor classification and the establishment of targeted therapeutic concepts.
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13
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Defining the Prognostic and Predictive Role of PIK3CA Mutations: Sifting Through the Conflicting Data. CURRENT BREAST CANCER REPORTS 2016. [DOI: 10.1007/s12609-016-0215-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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14
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Liau JY, Lan J, Hong JB, Tsai JH, Kuo KT, Chu CY, Sheen YS, Huang WC. Frequent PIK3CA-activating mutations in hidradenoma papilliferums. Hum Pathol 2016; 55:57-62. [PMID: 27184479 DOI: 10.1016/j.humpath.2016.04.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 04/05/2016] [Accepted: 04/21/2016] [Indexed: 12/12/2022]
Abstract
Hidradenoma papilliferum (HP) is a benign epithelial tumor most commonly seen in the vulva. It is proposed to be derived from the anogenital mammary-like glands and is histologically very similar to the mammary intraductal papilloma (IP). Approximately 60% of mammary IPs have activating mutations in either PIK3CA or AKT1, with each gene accounting for 30% of cases. In this study, we screened the mutation statuses of PIK3CA, AKT1, RAS, and BRAF in 30 HPs. The results showed that activating mutations in either PIK3CA or AKT1 were identified in 20 tumors (67%); 19 tumors had PIK3CA mutations (63%; 13 in exon 20 and 6 in exon 9), and 1 had an AKT1 E17K mutation (3%). BRAF V600E mutation was found in an HP that also had a PIK3CA H1047R mutation. No RAS mutation was found. The mutation status was not correlated with the degree of epithelial cell hyperplasia. We conclude that although there might be site-related variations in the mutation frequencies of PIK3CA and AKT1 genes, HP is histologically and also genetically very similar to the mammary IP, suggesting that HP can be viewed as the extramammary counterpart of mammary IP.
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Affiliation(s)
- Jau-Yu Liau
- Department of Pathology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei 10002, Taiwan; Graduate Institute of Pathology, National Taiwan University College of Medicine, Taipei 10051, Taiwan
| | - Jui Lan
- Department of Pathology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83301, Taiwan
| | - Jin-Bon Hong
- Department of Dermatology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei 10002, Taiwan
| | - Jia-Huei Tsai
- Department of Pathology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei 10002, Taiwan; Graduate Institute of Pathology, National Taiwan University College of Medicine, Taipei 10051, Taiwan
| | - Kuan-Tin Kuo
- Department of Pathology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei 10002, Taiwan
| | - Chia-Yu Chu
- Department of Dermatology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei 10002, Taiwan
| | - Yi-Shuan Sheen
- Department of Dermatology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei 10002, Taiwan
| | - Wen-Chang Huang
- Department of Pathology, Wan Fang Hospital, Taipei Medical University, Taipei 11696, Taiwan.
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15
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Jahn SW, Kashofer K, Thüringer A, Abete L, Winter E, Eidenhammer S, Viertler C, Tavassoli F, Moinfar F. Mutation Profiling of Usual Ductal Hyperplasia of the Breast Reveals Activating Mutations Predominantly at Different Levels of the PI3K/AKT/mTOR Pathway. THE AMERICAN JOURNAL OF PATHOLOGY 2016; 186:15-23. [PMID: 26718977 DOI: 10.1016/j.ajpath.2015.09.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Revised: 08/29/2015] [Accepted: 09/28/2015] [Indexed: 01/05/2023]
Abstract
Usual ductal hyperplasia (UDH) of the breast is generally regarded as a nonneoplastic proliferation, albeit loss of heterozygosity has long been reported in a part of these lesions. To gain deeper insights into the molecular drivers of these lesions, an extended mutation profiling was performed. The coding regions of 409 cancer-related genes were investigated by next-generation sequencing in 16 cases of UDH, nine unassociated with neoplasia (classic) and seven arising within papillomas. Phosphatidylinositol 3-kinase/AKT/mammalian target of rapamycin (mTOR) activation was investigated by phosphorylated AKT, mTOR, and S6 immunohistochemistry. Of 16 lesions, 10 (63%) were mutated; 56% of classic lesions were unassociated with neoplasia, and 71% of lesions arose in papillomas. Fourteen missense mutations were detected: PIK3CA [6 (43%) of 14], AKT1 [2 (14%) of 14], as well as GNAS, MTOR, PIK3R1, LPHN3, LRP1B, and IGF2R [each 1 (7%) of 14]. Phosphorylated mTOR was seen in 83% and phosphorylated S6 in 86% of evaluable lesions (phospho-AKT staining was technically uninterpretable). In conclusion, UDH displays mutations of the phosphatidylinositol 3-kinase/AKT/mTOR axis at different levels, with PIK3R1, MTOR, and GNAS mutations not previously described. Specifically, oncogenic G-protein activation represents a yet unrecognized route to proliferation in UDH. On the basis of evidence of activating mutations, loss of heterozygosity, and a mass forming proliferation, we propose that UDH is most appropriately viewed as an early neoplastic intraductal proliferation.
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Affiliation(s)
- Stephan W Jahn
- Institute of Pathology, Medical University of Graz, Graz, Austria.
| | - Karl Kashofer
- Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Andrea Thüringer
- Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Luca Abete
- Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Elke Winter
- Institute of Pathology, Medical University of Graz, Graz, Austria
| | | | | | - Fattaneh Tavassoli
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut
| | - Farid Moinfar
- Institute of Pathology, Medical University of Graz, Graz, Austria; Department of Pathology, Hospital of the Sisters of Charity, Linz, Austria
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16
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Eberle CA, Piscuoglio S, Rakha EA, Ng CKY, Geyer FC, Edelweiss M, Sakr RA, Weigelt B, Reis-Filho JS, Ellis IO. Infiltrating epitheliosis of the breast: characterization of histological features, immunophenotype and genomic profile. Histopathology 2016; 68:1030-9. [PMID: 26497122 DOI: 10.1111/his.12897] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 10/21/2015] [Indexed: 01/01/2023]
Abstract
AIMS Infiltrating epitheliosis is a rare complex sclerosing lesion (CSL) of the breast, characterized by infiltrating ducts immersed in a scleroelastotic stroma and filled with cells having architectural and cytological patterns reminiscent of those of usual ductal hyperplasia. In this study we sought to define the molecular characteristics of infiltrating epitheliosis. METHODS AND RESULTS Eight infiltrating epitheliosis, adjacent breast lesions (one usual ductal hyperplasia, one papilloma, one micropapillary ductal carcinoma in situ and one low-grade adenosquamous carcinoma), and corresponding normal breast tissue from each case were microdissected and subjected to massively parallel sequencing analysis targeting all coding regions of 254 genes mutated recurrently in breast cancer and/or related to DNA repair. Mutations in components of the PI3K pathway were found in all infiltrating epitheliosis samples, seven of which harboured PIK3CA hotspot mutations, while the remaining case displayed a PIK3R1 somatic mutation. CONCLUSIONS Somatic mutations affecting PI3K pathway genes were found to be highly prevalent in infiltrating epitheliosis, suggesting that these lesions may be neoplastic rather than hyperplastic. The landscape of somatic genetic alterations found in infiltrating epitheliosis is similar to that of radial scars/CSLs, suggesting that infiltrating epitheliosis may represent one end of this spectrum of lesions.
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Affiliation(s)
- Carey A Eberle
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Salvatore Piscuoglio
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Emad A Rakha
- Department of Histopathology, Nottingham University Hospitals, Nottingham, UK
| | - Charlotte K Y Ng
- 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.,Department of Pathology, Hospital Israelita Albert Einstein, Instituto Israelita de Ensino e Pesquisa, São Paulo, Brazil
| | - Marcia Edelweiss
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rita A Sakr
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - 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
| | - Ian O Ellis
- Department of Histopathology, Nottingham University Hospitals, Nottingham, UK
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17
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Novel mutations in neuroendocrine carcinoma of the breast: possible therapeutic targets. Appl Immunohistochem Mol Morphol 2015; 23:97-103. [PMID: 25679062 DOI: 10.1097/pdm.0b013e3182a40fd1] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Primary neuroendocrine carcinoma of the breast is a rare variant, accounting for only 2% to 5% of diagnosed breast cancers, and may have relatively aggressive behavior. Mutational profiling of invasive ductal breast cancers has yielded potential targets for directed cancer therapy, yet most studies have not included neuroendocrine carcinomas. In a tissue microarray screen, we found a 2.4% prevalence (9/372) of neuroendocrine breast carcinoma, including several with lobular morphology. We then screened primary or metastatic neuroendocrine breast carcinomas (excluding papillary and mucinous) for mutations in common cancer genes using polymerase chain reaction-mass spectroscopy (643 hotspot mutations across 53 genes), or semiconductor-based next-generation sequencing analysis (37 genes). Mutations were identified in 5 of 15 tumors, including 3 with PIK3CA exon 9 E542K mutations, 2 of which also harbored point mutations in FGFR family members (FGFR1 P126S, FGFR4 V550M). Single mutations were found in each of KDR (A1065T) and HRAS (G12A). PIK3CA mutations are common in other types of breast carcinoma. However, FGFR and RAS family mutations are exceedingly rare in the breast cancer literature. Likewise, activating mutations in the receptor tyrosine kinase KDR (VEGFR2) have been reported in angiosarcomas and non-small cell lung cancers; the KDR A1065T mutation is reported to be sensitive to VEGFR kinase inhibitors, and fibroblast growth factor receptor inhibitors are in trials. Our findings demonstrate the utility of broad-based genotyping in the study of rare tumors such as neuroendocrine breast cancer.
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18
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Afghahi A, Forgó E, Mitani AA, Desai M, Varma S, Seto T, Rigdon J, Jensen KC, Troxell ML, Gomez SL, Das AK, Beck AH, Kurian AW, West RB. Chromosomal copy number alterations for associations of ductal carcinoma in situ with invasive breast cancer. Breast Cancer Res 2015; 17:108. [PMID: 26265211 PMCID: PMC4534146 DOI: 10.1186/s13058-015-0623-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 07/24/2015] [Indexed: 01/07/2023] Open
Abstract
INTRODUCTION Screening mammography has contributed to a significant increase in the diagnosis of ductal carcinoma in situ (DCIS), raising concerns about overdiagnosis and overtreatment. Building on prior observations from lineage evolution analysis, we examined whether measuring genomic features of DCIS would predict association with invasive breast carcinoma (IBC). The long-term goal is to enhance standard clinicopathologic measures of low- versus high-risk DCIS and to enable risk-appropriate treatment. METHODS We studied three common chromosomal copy number alterations (CNA) in IBC and designed fluorescence in situ hybridization-based assay to measure copy number at these loci in DCIS samples. Clinicopathologic data were extracted from the electronic medical records of Stanford Cancer Institute and linked to demographic data from the population-based California Cancer Registry; results were integrated with data from tissue microarrays of specimens containing DCIS that did not develop IBC versus DCIS with concurrent IBC. Multivariable logistic regression analysis was performed to describe associations of CNAs with these two groups of DCIS. RESULTS We examined 271 patients with DCIS (120 that did not develop IBC and 151 with concurrent IBC) for the presence of 1q, 8q24 and 11q13 copy number gains. Compared to DCIS-only patients, patients with concurrent IBC had higher frequencies of CNAs in their DCIS samples. On multivariable analysis with conventional clinicopathologic features, the copy number gains were significantly associated with concurrent IBC. The state of two of the three copy number gains in DCIS was associated with a risk of IBC that was 9.07 times that of no copy number gains, and the presence of gains at all three genomic loci in DCIS was associated with a more than 17-fold risk (P = 0.0013). CONCLUSIONS CNAs have the potential to improve the identification of high-risk DCIS, defined by presence of concurrent IBC. Expanding and validating this approach in both additional cross-sectional and longitudinal cohorts may enable improved risk stratification and risk-appropriate treatment in DCIS.
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Affiliation(s)
- Anosheh Afghahi
- Department of Medicine, Stanford University School of Medicine, 291 Campus Drive, Stanford, CA, 94305, USA.
| | - Erna Forgó
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA.
| | - Aya A Mitani
- Department of Medicine, Stanford University School of Medicine, 291 Campus Drive, Stanford, CA, 94305, USA.
| | - Manisha Desai
- Department of Medicine, Stanford University School of Medicine, 291 Campus Drive, Stanford, CA, 94305, USA.
| | - Sushama Varma
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA.
| | - Tina Seto
- Department of Medicine, Stanford University School of Medicine, 291 Campus Drive, Stanford, CA, 94305, USA.
| | - Joseph Rigdon
- Department of Medicine, Stanford University School of Medicine, 291 Campus Drive, Stanford, CA, 94305, USA.
| | - Kristin C Jensen
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA.
- Pathology and Laboratory Medicine, Palo Alto Veterans Affairs Health Care System, 795 Willow Road, Palo Alto, CA, 94025, USA.
| | - Megan L Troxell
- Department of Pathology, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR, 97239, USA.
| | - Scarlett Lin Gomez
- Department of Health Research and Policy, Stanford University School of Medicine, 900 Blake Wilbur Drive, Stanford, CA, 94305, USA.
- Cancer Prevention Institute of California (CPIC), 2201 Walnut Avenue, Fremont, CA, 94538, USA.
| | - Amar K Das
- Department of Medicine, Stanford University School of Medicine, 291 Campus Drive, Stanford, CA, 94305, USA.
- Department of Psychiatry and The Dartmouth Institute for Health Policy and Clinical Practice, Geisel School of Medicine, 1 Rope Ferry Road, Lebanon, NH, 03755, USA.
| | - Andrew H Beck
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, 330 Brookline Avenue, Boston, MA, 02215, USA.
| | - Allison W Kurian
- Department of Medicine, Stanford University School of Medicine, 291 Campus Drive, Stanford, CA, 94305, USA.
- Department of Health Research and Policy, Stanford University School of Medicine, 900 Blake Wilbur Drive, Stanford, CA, 94305, USA.
| | - Robert B West
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA.
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19
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Pang JMB, Gorringe KL, Wong SQ, Dobrovic A, Campbell IG, Fox SB. Appraisal of the technologies and review of the genomic landscape of ductal carcinoma in situ of the breast. Breast Cancer Res 2015; 17:80. [PMID: 26078038 PMCID: PMC4469314 DOI: 10.1186/s13058-015-0586-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Ductal carcinoma in situ is a biologically diverse entity. Whereas some lesions are cured by local surgical excision, others recur as in situ disease or progress to invasive carcinoma with subsequent potential for metastatic spread. Reliable prognostic biomarkers are therefore desirable for appropriate clinical management but remain elusive. In common with invasive breast cancer, ductal carcinoma in situ exhibits many genomic changes, predominantly copy number alterations. Although studies have revealed the genomic heterogeneity within individual ductal carcinoma in situ lesions and the association of certain copy number alterations with nuclear grade, none of the genomic changes defined so far is consistently associated with invasive transformation or recurrence risk in pure ductal carcinoma in situ. This article will review the current landscape of genomic alterations in ductal carcinoma in situ and their potential as prognostic biomarkers together with the technologies used to define these.
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Affiliation(s)
- Jia-Min B Pang
- Department of Pathology, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, VIC, 3002, Australia. .,Department of Pathology, University of Melbourne, Grattan Street, Parkville, Melbourne, VIC, 3010, Australia.
| | - Kylie L Gorringe
- Department of Pathology, University of Melbourne, Grattan Street, Parkville, Melbourne, VIC, 3010, Australia. .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Grattan Street, Parkville, Melbourne, VIC, 3010, Australia. .,Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, VIC, 3002, Australia.
| | - Stephen Q Wong
- Department of Pathology, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, VIC, 3002, Australia. .,Translational Research Laboratory, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, VIC, 3002, Australia.
| | - Alexander Dobrovic
- Department of Pathology, University of Melbourne, Grattan Street, Parkville, Melbourne, VIC, 3010, Australia. .,Translational Genomics & Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Studley Road, Heidelberg, VIC, 3084, Australia.
| | - Ian G Campbell
- Department of Pathology, University of Melbourne, Grattan Street, Parkville, Melbourne, VIC, 3010, Australia. .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Grattan Street, Parkville, Melbourne, VIC, 3010, Australia. .,Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, VIC, 3002, Australia.
| | - Stephen B Fox
- Department of Pathology, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, VIC, 3002, Australia. .,Department of Pathology, University of Melbourne, Grattan Street, Parkville, Melbourne, VIC, 3010, Australia. .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Grattan Street, Parkville, Melbourne, VIC, 3010, Australia.
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20
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Abstract
Phosphatidylinositol 3-kinases (PI3Ks) include members of a unique and conserved family of intracellular lipid kinases that phosphorylate the 3-hydroxyl group of phosphatidylinositols and phosphoinositides. The resultant activation of many intracellular signalling pathways regulates various biological functions such as cell metabolism, survival, growth, proliferation, polarity, and apoptosis. PI3Ks are classified into three types: class I, II, and III. Of them, class I PI3K is most widely studied and plays an important role in the development and progression of tumours. In this review, we describe PI3K family members and their functions, especially the subunits of class I PI3K, their alterations in cancers, as well as PI3K inhibitors and their clinical trial status in cancer-targeted therapy.
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Affiliation(s)
- Wenli Cui
- 1Department of Pathology, Fudan University Shanghai Cancer Center 2Department of Oncology, Shanghai Medical College, Fudan University 3Institute of Pathology, Fudan University, Shanghai 4Department of Pathology, First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang Uygur Autonomous Region, PR China
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Weng Z, Spies N, Zhu SX, Newburger DE, Kashef-Haghighi D, Batzoglou S, Sidow A, West RB. Cell-lineage heterogeneity and driver mutation recurrence in pre-invasive breast neoplasia. Genome Med 2015; 7:28. [PMID: 25918554 PMCID: PMC4410742 DOI: 10.1186/s13073-015-0146-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 02/26/2015] [Indexed: 12/12/2022] Open
Abstract
Background All cells in an individual are related to one another by a bifurcating lineage tree, in which each node is an ancestral cell that divided into two, each branch connects two nodes, and the root is the zygote. When a somatic mutation occurs in an ancestral cell, all its descendants carry the mutation, which can then serve as a lineage marker for the phylogenetic reconstruction of tumor progression. Using this concept, we investigate cell lineage relationships and genetic heterogeneity of pre-invasive neoplasias compared to invasive carcinomas. Methods We deeply sequenced over a thousand phylogenetically informative somatic variants in 66 morphologically independent samples from six patients that represent a spectrum of normal, early neoplasia, carcinoma in situ, and invasive carcinoma. For each patient, we obtained a highly resolved lineage tree that establishes the phylogenetic relationships among the pre-invasive lesions and with the invasive carcinoma. Results The trees reveal lineage heterogeneity of pre-invasive lesions, both within the same lesion, and between histologically similar ones. On the basis of the lineage trees, we identified a large number of independent recurrences of PIK3CA H1047 mutations in separate lesions in four of the six patients, often separate from the diagnostic carcinoma. Conclusions Our analyses demonstrate that multi-sample phylogenetic inference provides insights on the origin of driver mutations, lineage heterogeneity of neoplastic proliferations, and the relationship of genomically aberrant neoplasias with the primary tumors. PIK3CA driver mutations may be comparatively benign inducers of cellular proliferation. Electronic supplementary material The online version of this article (doi:10.1186/s13073-015-0146-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ziming Weng
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305 USA ; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Noah Spies
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305 USA ; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Shirley X Zhu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Daniel E Newburger
- Biomedical Informatics Training Program, Stanford University, Stanford, CA 94305 USA
| | | | - Serafim Batzoglou
- Department of Computer Science, Stanford University, Stanford, CA 94305 USA
| | - Arend Sidow
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305 USA ; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Robert B West
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305 USA
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Brunner AL, Li J, Guo X, Sweeney RT, Varma S, Zhu SX, Li R, Tibshirani R, West RB. A shared transcriptional program in early breast neoplasias despite genetic and clinical distinctions. Genome Biol 2014; 15:R71. [PMID: 24887547 PMCID: PMC4072957 DOI: 10.1186/gb-2014-15-5-r71] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 05/23/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The earliest recognizable stages of breast neoplasia are lesions that represent a heterogeneous collection of epithelial proliferations currently classified based on morphology. Their role in the development of breast cancer is not well understood but insight into the critical events at this early stage will improve efforts in breast cancer detection and prevention. These microscopic lesions are technically difficult to study so very little is known about their molecular alterations. RESULTS To characterize the transcriptional changes of early breast neoplasia, we sequenced 3'- end enriched RNAseq libraries from formalin-fixed paraffin-embedded tissue of early neoplasia samples and matched normal breast and carcinoma samples from 25 patients. We find that gene expression patterns within early neoplasias are distinct from both normal and breast cancer patterns and identify a pattern of pro-oncogenic changes, including elevated transcription of ERBB2, FOXA1, and GATA3 at this early stage. We validate these findings on a second independent gene expression profile data set generated by whole transcriptome sequencing. Measurements of protein expression by immunohistochemistry on an independent set of early neoplasias confirms that ER pathway regulators FOXA1 and GATA3, as well as ER itself, are consistently upregulated at this early stage. The early neoplasia samples also demonstrate coordinated changes in long non-coding RNA expression and microenvironment stromal gene expression patterns. CONCLUSIONS This study is the first examination of global gene expression in early breast neoplasia, and the genes identified here represent candidate participants in the earliest molecular events in the development of breast cancer.
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Sakr RA, Weigelt B, Chandarlapaty S, Andrade VP, Guerini-Rocco E, Giri D, Ng CKY, Cowell CF, Rosen N, Reis-Filho JS, King TA. PI3K pathway activation in high-grade ductal carcinoma in situ--implications for progression to invasive breast carcinoma. Clin Cancer Res 2014; 20:2326-37. [PMID: 24634376 PMCID: PMC4015460 DOI: 10.1158/1078-0432.ccr-13-2267] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
PURPOSE To assess the prevalence of phosphoinositide 3-kinase (PI3K) pathway alterations in pure high-grade ductal carcinoma in situ (DCIS) and DCIS associated with invasive breast cancer (IBC), and to determine whether DCIS and adjacent IBCs harbor distinct PI3K pathway aberrations. EXPERIMENTAL DESIGN Eighty-nine cases of pure high-grade DCIS and 119 cases of high-grade DCIS associated with IBC were characterized according to estrogen receptor (ER) and HER2 status, subjected to immunohistochemical analysis of PTEN, INPP4B, phosphorylated (p)AKT and pS6 expression, and to microdissection followed by Sequenom genotyping of PIK3CA and AKT1 hotspot mutations. RESULTS Alterations affecting the PI3K pathway were found in a subset of pure DCIS and DCIS adjacent to IBC. A subtype-matched comparison of pure DCIS and DCIS adjacent to IBC revealed that PIK3CA hotspot mutations and pAKT expression were significantly more prevalent in ER-positive/HER2-negative DCIS adjacent to IBC (P values, 0.005 and 0.043, respectively), and that in ER-negative/HER2-positive cases INPP4B loss of expression was more frequently observed in pure DCIS (a P value of 0.013). No differences in the parameters analyzed were observed in a pairwise comparison of the in situ and invasive components of cases of DCIS and adjacent IBC. Analysis of the PIK3CA-mutant allelic frequencies in DCIS and synchronous IBC revealed cases in which PIK3CA mutations were either restricted to the DCIS or to the invasive components. CONCLUSION Molecular aberrations affecting the PI3K pathway may play a role in the progression from high-grade DCIS to IBC in a subset of cases (e.g., a subgroup of ER-positive/HER2-negative lesions).
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Affiliation(s)
- Rita A. Sakr
- Breast Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Sarat Chandarlapaty
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Victor P. Andrade
- Breast Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Elena Guerini-Rocco
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Dilip Giri
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Charlotte K. Y. Ng
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Catherine F. Cowell
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Neal Rosen
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, 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
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Tari A. King
- Breast Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
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24
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Frequent phosphatidylinositol-3-kinase mutations in proliferative breast lesions. Mod Pathol 2014; 27:740-50. [PMID: 24186142 DOI: 10.1038/modpathol.2013.197] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 09/09/2013] [Accepted: 09/10/2013] [Indexed: 01/08/2023]
Abstract
The phosphatidylinositol-3-kinase pathway is one of the most commonly altered molecular pathways in invasive breast carcinoma, with phosphatidylinositol-3-kinase catalytic subunit (PIK3CA) mutations in 25% of invasive carcinomas. Ductal carcinoma in situ (DCIS), benign papillomas, and small numbers of columnar cell lesions harbor an analogous spectrum of PIK3CA and AKT1 mutations, yet there is little data on usual ductal hyperplasia and atypical ductal and lobular neoplasias. We screened 192 formalin-fixed paraffin-embedded breast lesions from 75 patients for point mutations using a multiplexed panel encompassing 643 point mutations across 53 genes, including 58 PIK3CA substitutions. PIK3CA point mutations were identified in 31/62 (50%) proliferative lesions (usual ductal hyperplasia and columnar cell change), 10/14 (71%) atypical hyperplasias (atypical ductal hyperplasia and flat epithelial atypia), 7/16 (44%) lobular neoplasias (atypical lobular hyperplasia and lobular carcinoma in situ), 10/21 (48%) DCIS, and 13/37 (35%) invasive carcinomas. In genotyping multiple lesions of different stage from the same patient/specimen, we found considerable heterogeneity; most notably, in 12 specimens the proliferative lesion was PIK3CA mutant but the concurrent carcinoma was wild type. In 11 additional specimens, proliferative epithelium and cancer contained different point mutations. The frequently discordant genotypes of usual ductal hyperplasia/columnar cell change and concurrent carcinoma support a role for PIK3CA-activating point mutations in breast epithelial proliferation, perhaps more so than transformation. Further, these data suggest that proliferative breast lesions are heterogeneous and may represent non-obligate precursors of invasive carcinoma.
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MAST2 and NOTCH1 translocations in breast carcinoma and associated pre-invasive lesions. Hum Pathol 2013; 44:2837-44. [PMID: 24140425 DOI: 10.1016/j.humpath.2013.08.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 07/30/2013] [Accepted: 08/02/2013] [Indexed: 11/21/2022]
Abstract
There are several mutations and structural variations common to breast cancer. Many of these genomic changes are thought to represent driver mutations in oncogenesis. Less well understood is how and when these changes take place in breast cancer development. Previous studies have identified gene rearrangements in the microtubule-associated serine-threonine kinase (MAST) and NOTCH gene families in 5% to 7% of invasive breast cancers. Some of these translocations can be detected by fluorescence in situ hybridization (FISH) allowing for examination of the correlation between these genomic changes and concurrent morphologic changes in early breast neoplasia. NOTCH and MAST gene rearrangements were identified by FISH in a large series of breast cancer cases organized on tissue microarrays (TMA). When translocations were identified by TMA, we performed full cross-section FISH to evaluate concurrent pre-invasive lesions. FISH break-apart assays were designed for NOTCH1 and MAST2 gene rearrangements. Translocations were identified in 16 cases of invasive carcinoma; 10 with MAST2 translocations (2.0%) and 6 cases with NOTCH1 translocations (1.2%). Whole section FISH analysis of these cases demonstrated that the translocations are present in the majority of concurrent ductal carcinoma in situ (DCIS) (6/8). When DCIS wasn't associated with an invasive component, it was never translocated (0/170, P=.0048). We have confirmed the presence of MAST and NOTCH family gene rearrangements in invasive breast carcinoma, and show that FISH studies can effectively be used with TMAs to screen normal, pre-invasive, and coexisting invasive disease. Our findings suggest that these translocations occur during the transition to DCIS and/or invasive carcinoma.
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Abstract
Morphologic "special types" of breast carcinomas have been recognized for many years, and their molecular and genetic properties have not been specifically studied until recently. Lobular carcinoma lacks functional E-cadherin expression but shares molecular similarities with low-grade invasive ductal carcinomas. Papillary carcinoma is relatively rare, and molecular features are just being elucidated. We report a case of concurrent invasive lobular and papillary carcinoma, the latter with extensive nodal involvement. Multiplex screening for activating point mutations identified different point mutations in the distinct morphologic components: lobular PIK3CA H1047R, papillary; PIK3CA Q546P, and IDH1 R132H. These molecular data favor coincidental "collision tumors" over clonal evolution. The IDH1 R132H point mutation is common in gliomas and acute myelogenous leukemia, but this has not been previously reported in breast carcinoma. The characterization of activating point mutations in morphologic special types of breast carcinoma may suggest avenues amenable to targeted therapy.
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27
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Newburger DE, Kashef-Haghighi D, Weng Z, Salari R, Sweeney RT, Brunner AL, Zhu SX, Guo X, Varma S, Troxell ML, West RB, Batzoglou S, Sidow A. Genome evolution during progression to breast cancer. Genome Res 2013; 23:1097-108. [PMID: 23568837 PMCID: PMC3698503 DOI: 10.1101/gr.151670.112] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cancer evolution involves cycles of genomic damage, epigenetic deregulation, and increased cellular proliferation that eventually culminate in the carcinoma phenotype. Early neoplasias, which are often found concurrently with carcinomas and are histologically distinguishable from normal breast tissue, are less advanced in phenotype than carcinomas and are thought to represent precursor stages. To elucidate their role in cancer evolution we performed comparative whole-genome sequencing of early neoplasias, matched normal tissue, and carcinomas from six patients, for a total of 31 samples. By using somatic mutations as lineage markers we built trees that relate the tissue samples within each patient. On the basis of these lineage trees we inferred the order, timing, and rates of genomic events. In four out of six cases, an early neoplasia and the carcinoma share a mutated common ancestor with recurring aneuploidies, and in all six cases evolution accelerated in the carcinoma lineage. Transition spectra of somatic mutations are stable and consistent across cases, suggesting that accumulation of somatic mutations is a result of increased ancestral cell division rather than specific mutational mechanisms. In contrast to highly advanced tumors that are the focus of much of the current cancer genome sequencing, neither the early neoplasia genomes nor the carcinomas are enriched with potentially functional somatic point mutations. Aneuploidies that occur in common ancestors of neoplastic and tumor cells are the earliest events that affect a large number of genes and may predispose breast tissue to eventual development of invasive carcinoma.
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Affiliation(s)
- Daniel E Newburger
- Biomedical Informatics Training Program, Stanford, California 94305, USA
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28
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Novel method for PIK3CA mutation analysis: locked nucleic acid--PCR sequencing. J Mol Diagn 2013; 15:312-8. [PMID: 23541593 DOI: 10.1016/j.jmoldx.2012.12.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 12/14/2012] [Accepted: 12/20/2012] [Indexed: 01/08/2023] Open
Abstract
Somatic mutations in PIK3CA are commonly seen in invasive breast cancer and several other carcinomas, occurring in three hotspots: codons 542 and 545 of exon 9 and in codon 1047 of exon 20. We designed a locked nucleic acid (LNA)-PCR sequencing assay to detect low levels of mutant PIK3CA DNA with attention to avoiding amplification of a pseudogene on chromosome 22 that has >95% homology to exon 9 of PIK3CA. We tested 60 FFPE breast DNA samples with known PIK3CA mutation status (48 cases had one or more PIK3CA mutations, and 12 were wild type) as identified by PCR-mass spectrometry. PIK3CA exons 9 and 20 were amplified in the presence or absence of LNA-oligonucleotides designed to bind to the wild-type sequences for codons 542, 545, and 1047, and partially suppress their amplification. LNA-PCR sequencing confirmed all 51 PIK3CA mutations; however, the mutation detection rate by standard Sanger sequencing was only 69% (35 of 51). Of the 12 PIK3CA wild-type cases, LNA-PCR sequencing detected three additional H1047R mutations in "normal" breast tissue and one E545K in usual ductal hyperplasia. Histopathological review of these three normal breast specimens showed columnar cell change in two (both with known H1047R mutations) and apocrine metaplasia in one. The novel LNA-PCR shows higher sensitivity than standard Sanger sequencing and did not amplify the known pseudogene.
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29
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Flatley E, Ang D, Warrick A, Beadling C, Corless CL, Troxell ML. PIK3CA-AKT pathway mutations in micropapillary breast carcinoma. Hum Pathol 2013; 44:1320-7. [PMID: 23352210 DOI: 10.1016/j.humpath.2012.10.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2012] [Revised: 10/24/2012] [Accepted: 10/26/2012] [Indexed: 12/20/2022]
Abstract
Micropapillary carcinoma of the breast is associated with increased rates of lymph node metastasis and lymphovascular invasion. While activating point mutations in PIK3CA (encoding phosphatidylinositol-3-kinase catalytic subunit) or AKT1 are found in 25% to 30% of invasive ductal carcinomas, the mutational profile of invasive micropapillary carcinomas has not been characterized in detail. Micropapillary carcinomas, concurrent metastatic and precursor breast lesions from 19 patients were identified. Lesional tissue was punched from paraffin-tissue blocks, and genomic DNA was extracted and screened for a large panel of known hotspot mutations using multiplex polymerase chain reaction and mass-spectroscopy analysis (643 mutations in 53 genes). Hotspot point mutations were identified in 35% (7/20) of micropapillary breast carcinomas, including PIK3CA exons 7, 9 and 20 hotspots, as well as the AKT1 plekstrin homology domain mutation (E17K); mutations in TP53 and KRAS were each found in a single patient. In 6 patients, micropapillary and non-micropapillary components of the same tumor were separately tested, yielding concordant results in five; one had a wild type micropapillary component, but a PIK3CA mutation in the invasive ductal component. Concurrent lymph node metastases were mostly wild type (2/8 mutant). Accompanying ductal carcinoma in situ had point mutations in 45% (5/11), mostly concordant with invasive carcinoma; however, mutational status of other breast proliferative lesions was generally discordant with accompanying carcinoma. The rate of PIK3CA mutations in this series of micropapillary carcinomas is similar to invasive ductal carcinomas; however, there may be an enrichment of AKT1 mutations (10%). The non-micropapillary components and precursor lesions occasionally had different mutations.
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Affiliation(s)
- Ellen Flatley
- Department of Pathology, Oregon Health & Science University, Portland, OR 97239, USA
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30
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Kehr EL, Jorns JM, Ang D, Warrick A, Neff T, Degnin M, Lewis R, Beadling C, Corless CL, Troxell ML. Mucinous breast carcinomas lack PIK3CA and AKT1 mutations. Hum Pathol 2012; 43:2207-12. [DOI: 10.1016/j.humpath.2012.03.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 03/06/2012] [Accepted: 03/07/2012] [Indexed: 10/28/2022]
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31
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Huang WS, Wang TB, He Y, Chen YJ, Zhong SL, Tan M. Phosphoinositide-3-kinase, catalytic, alpha polypeptide RNA interference inhibits growth of colon cancer cell SW948. World J Gastroenterol 2012; 18:3458-64. [PMID: 22807617 PMCID: PMC3396200 DOI: 10.3748/wjg.v18.i26.3458] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 05/09/2012] [Accepted: 05/13/2012] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the gene knock-down effect by the phosphoinositide-3-kinase, catalytic, alpha polypeptide (PIK3CA)-targeted double-stranded RNA (dsRNA) and its effect on cell proliferation and cycle distribution in SW948.
METHODS: Two PIK3CA-targeted dsRNAs were constructed and transfected into SW948 cells. Transfections were performed using lipofectamineTM 2000. The transfection effectiveness was calculated basing on the rate of fluorescence cell of SW948 at 6 h after transfection. Total messenger RNA was extracted from these cells using the RNeasy kit, and semiquantitative reverse transcription polymerase chain reaction was performed to detect the down-regulation of PIK3CA, AKT1, MYC, and CCND1 gene expression. Cells were harvested, proteins were resolved, and western blot was employed to detect the expression levels of PIK3CA, AKT1, MYC, and CCND1 gene. Cell proliferation was assessed by 3-(4,5)-dimethylthiahiazo (-z-y1)-3,5-di-phenytetrazoliumromide assay and the inhibition rate was calculated. Soft agar colony formation assay was performed basing on colonies greater than 60 μm in diameter at ×100 magnification. The effect on cell cycle distribution and apoptosis was assessed by flow cytometry. All experiments were performed in triplicate.
RESULTS: Green fluorescence was observed in SW948 cell transfected with plasmid Pgenesil-1, and the transfection effectiveness was about 65%. Forty-eight hours post-transfection, mRNA expression of PIK3CA in SW948 cells was 0.51 ± 0.04 vs 0.49 ± 0.03 vs 0.92 ± 0.01 vs 0.93 ± 0.03 (P = 0.001 ) in Pgenesil-CA1, Pgenesil-CA2, negative and blank group respectively. mRNA expression of AKT1 was 0.50 ± 0.03 vs 0.48 ± 0.01 vs 0.93 ± 0.04 vs 0.92 ± 0.02 (P = 0.000) in Pgenesil-CA1, Pgenesil-CA2, negative and blank group respectively. mRNA expression of MYC was 0.49 ± 0.01 vs 0.50 ± 0.04 vs 0.90 ± 0.02 vs 0.91 ± 0.03 (P = 0.001) in the four groups respectively. mRNA expression of CCND1 was 0.45 ± 0.02 vs 0.51 ± 0.01 vs 0.96 ± 0.03 vs 0.98 ± 0.01 (P = 0.001) in the four groups respectively. The protein level of PIK3CA was 0.53 ± 0.01 vs 0.54 ± 0.02 vs 0.92 ± 0.03 vs 0.91 ± 0.02 (P = 0.001) in Pgenesil-CA1, Pgenesil-CA2, negative and blank group respectively. The protein level of AKT1 in the four groups was 0.49 ± 0.02 vs 0.55 ± 0.03 vs 0.94 ± 0.03 vs 0.95 ± 0.04, P = 0.000). The protein level of MYC in the four groups was 0.51 ± 0.03 vs 0.52 ± 0.04 vs 0.92 ± 0.02 vs 0.95 ± 0.01 (P = 0.000). The protein level of CCND1 in the four groups was 0.54 ± 0.04 vs 0.56 ± 0.03 vs 0.93 ± 0.01 vs 0.93 ± 0.03 (P = 0.000). Both Pgenesil-CA1 and Pgenesil-CA2 plasmids significantly suppressed the growth of SW948 cells when compared with the negative or blank group at 48 h after transfection (29% vs 25% vs 17% vs 14%, P = 0.001), 60 h after transfection (38% vs 34% vs 19% vs 16%, P = 0.001), and 72 h after transfection (53% vs 48% vs 20% vs 17%, P = 0.000). Numbers of colonies in negative, blank, CA1, and CA2 groups were 42 ± 4, 45 ± 5, 8 ± 2, and 10 ± 3, respectively (P = 0.000). There were more than 4.5 times colonies in the blank and negative control groups as there were in the CA1 and CA2 groups. In addition, the colonies in blank and negative control groups were also larger than those in the CA1 and CA2 groups. The percentage of cells in the CA1 and CA2 groups was significantly higher in G0/G1 phase, but lower in S and G2/M phase when compared with the negative and control groups. Moreover, cell apoptosis rates in the CA1 and CA2 groups were 5.11 ± 0.32 and 4.73 ± 0.32, which were significantly higher than those in negative (0.95 ± 0.11, P = 0.000) and blank groups (0.86 ± 0.13, P = 0.001). No significant difference was found between CA1 and CA2 groups in cell cycle distribution and apoptosis.
CONCLUSION: PIK3CA-targeted short hairpin RNAs can block the phosphoinositide 3-kinase-Akt signaling pathway and inhibit cell growth, increase apoptosis, and induce cell cycle arrest in the PIK3CA-mutant colon cancer SW948 cells.
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