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Yang G, Lu T, Weisenberger DJ, Liang G. The Multi-Omic Landscape of Primary Breast Tumors and Their Metastases: Expanding the Efficacy of Actionable Therapeutic Targets. Genes (Basel) 2022; 13:genes13091555. [PMID: 36140723 PMCID: PMC9498783 DOI: 10.3390/genes13091555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/08/2022] [Accepted: 08/23/2022] [Indexed: 12/02/2022] Open
Abstract
Breast cancer (BC) mortality is almost exclusively due to metastasis, which is the least understood aspect of cancer biology and represents a significant clinical challenge. Although we have witnessed tremendous advancements in the treatment for metastatic breast cancer (mBC), treatment resistance inevitably occurs in most patients. Recently, efforts in characterizing mBC revealed distinctive genomic, epigenomic and transcriptomic (multi-omic) landscapes to that of the primary tumor. Understanding of the molecular underpinnings of mBC is key to understanding resistance to therapy and the development of novel treatment options. This review summarizes the differential molecular landscapes of BC and mBC, provides insights into the genomic heterogeneity of mBC and highlights the therapeutically relevant, multi-omic features that may serve as novel therapeutic targets for mBC patients.
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Affiliation(s)
- Guang Yang
- School of Sciences, China Pharmaceutical University, Nanjing 211121, China
- China Grand Enterprises, Beijing 100101, China
| | - Tao Lu
- School of Sciences, China Pharmaceutical University, Nanjing 211121, China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211121, China
| | - Daniel J. Weisenberger
- Department of Biochemistry and Molecular Medicine, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
| | - Gangning Liang
- Department of Urology, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
- Correspondence:
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Sher G, Salman NA, Khan AQ, Prabhu KS, Raza A, Kulinski M, Dermime S, Haris M, Junejo K, Uddin S. Epigenetic and breast cancer therapy: Promising diagnostic and therapeutic applications. Semin Cancer Biol 2020; 83:152-165. [PMID: 32858230 DOI: 10.1016/j.semcancer.2020.08.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 08/17/2020] [Accepted: 08/17/2020] [Indexed: 12/24/2022]
Abstract
The global burden of breast cancer (BC) is increasing significantly. This trend is caused by several factors such as late diagnosis, limited treatment options for certain BC subtypes, drug resistance which all lead to poor clinical outcomes. Recent research has reported the role of epigenetic alterations in the mechanism of BC pathogenesis and its hallmarks include drug resistance and stemness features. The understanding of these modifications and their significance in the management of BC carcinogenesis is challenging and requires further attention. Nevertheless, it promises to provide novel insight needed for utilizing these alterations as potential diagnostic, prognostic markers, predict treatment efficacy, as well as therapeutic agents. This highlights the importance of continuing research development to further advance the existing knowledge on epigenetics and BC carcinogenesis to overcome the current challenges. Hence, this review aims to shed light and discuss the current state of epigenetics research in the diagnosis and management of BC.
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Affiliation(s)
- Gulab Sher
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, P.O. Box 3050, Qatar
| | - Nadia Aziz Salman
- Kingston University London, School of Life Science, Pharmacy and Chemistry, SEC Faculty, Kingston, upon Thames, London, KT1 2EE, UK
| | - Abdul Q Khan
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, P.O. Box 3050, Qatar
| | - Kirti S Prabhu
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, P.O. Box 3050, Qatar
| | - Afsheen Raza
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, P.O. Box 3050, Qatar
| | - Michal Kulinski
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, P.O. Box 3050, Qatar
| | - Said Dermime
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, P.O. Box 3050, Qatar
| | - Mohammad Haris
- Functional and Molecular Imaging Laboratory, Sidra Medicine, P.O. Box 26999, Qatar; Laboratory Animal Research Center, Qatar University, Doha, P.O. Box 2713, Qatar
| | - Kulsoom Junejo
- General Surgery Department, Hamad General Hospital, Hamad Medical Corporation, Doha, P.O. Box 3050, Qatar
| | - Shahab Uddin
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, P.O. Box 3050, Qatar; Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, P.O. Box 3050, Qatar.
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3
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Mitchell E, Jindal S, Chan T, Narasimhan J, Sivagnanam S, Gray E, Chang YH, Weinmann S, Schedin P. Loss of myoepithelial calponin-1 characterizes high-risk ductal carcinoma in situ cases, which are further stratified by T cell composition. Mol Carcinog 2020; 59:701-712. [PMID: 32134153 PMCID: PMC7317523 DOI: 10.1002/mc.23171] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/14/2020] [Accepted: 02/15/2020] [Indexed: 12/15/2022]
Abstract
A hallmark of ductal carcinoma in situ (DCIS) progression is a loss of the surrounding ductal myoepithelium. However, whether compromise in myoepithelial differentiation, rather than overt cellular loss, can be used to predict the risk of DCIS progression is unknown. Here we address this question utilizing pure and mixed DCIS cases (N = 30) as surrogates for DCIS at low and high risk for progression, respectively. We used multiplex immunohistochemical staining to evaluate the relationship between myoepithelial cell differentiation and lymphoid immune cell types associated with poor prognostic DCIS. Our results show that myoepithelial calponin-1 discriminates between pure and mixed DCIS lesions better than histological subtype, presence of necrosis, or nuclear grade. Additionally, focal loss of myoepithelial cells associated with increased PD-1+CD8+ T cells, which suggests a link between the myoepithelium and immune surveillance. To identify associations between calponin-1 expression and immune response, we performed unsupervised hierarchical clustering of myoepithelial and immune cell biomarkers on 219 DCIS lesions from 30 cases. Notably, the majority of pure (low-risk) DCIS lesions clustered in a high calponin-1, T cell low group, whereas the majority of mixed (high-risk) DCIS lesions clustered in a low calponin-1, T cell high group, specifically with CD8+ and PD-1+CD8+ T cells. However, a subset of pure DCIS lesions had a similar calponin-1 and immune signature as the majority of mixed DCIS lesions, which have low calponin-1 and T cell enrichment-raising the possibility that these pure DCIS lesions might be at a high risk for progression.
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Affiliation(s)
- Elizabeth Mitchell
- Department of Cell, Developmental, and Cancer BiologyOregon Health and Science UniversityPortlandOregon
| | - Sonali Jindal
- Department of Cell, Developmental, and Cancer BiologyOregon Health and Science UniversityPortlandOregon
- Cancer Prevention and Control, Knight Cancer InstituteOregon Health and Science UniversityPortlandOregon
| | - Tiffany Chan
- Department of Cell, Developmental, and Cancer BiologyOregon Health and Science UniversityPortlandOregon
| | - Jayasri Narasimhan
- Department of Cell, Developmental, and Cancer BiologyOregon Health and Science UniversityPortlandOregon
| | - Shamilene Sivagnanam
- Computational Biology Program, Department of Cell, Developmental, and Cancer BiologyOregon Health and Science UniversityPortlandOregon
| | - Elliot Gray
- Department of Biomedical Engineering, Oregon Center for Spatial Systems BiomedicineOregon Health and Science UniversityPortlandOregon
| | - Young Hwan Chang
- Department of Biomedical Engineering, Oregon Center for Spatial Systems BiomedicineOregon Health and Science UniversityPortlandOregon
| | - Sheila Weinmann
- Center for Health ResearchKaiser Permanente NorthwestPortlandOregon
| | - Pepper Schedin
- Department of Cell, Developmental, and Cancer BiologyOregon Health and Science UniversityPortlandOregon
- Cancer Prevention and Control, Knight Cancer InstituteOregon Health and Science UniversityPortlandOregon
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4
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Prognostic role of immune infiltrates in breast ductal carcinoma in situ. Breast Cancer Res Treat 2019; 177:17-27. [PMID: 31134489 DOI: 10.1007/s10549-019-05272-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 05/06/2019] [Indexed: 01/13/2023]
Abstract
PURPOSE Ductal carcinoma in situ (DCIS) of the breast is often regarded as a non-obligate precursor to invasive breast carcinoma but current diagnostic tools are unable to accurately predict the invasive potential of DCIS. Infiltration of immune cells into the tumour and its microenvironment is often an early event at the site of tumourigenesis. These immune infiltrates may be potential predictive and/or prognostic biomarkers for DCIS. This review aims to discuss recent findings pertaining to the potential prognostic significance of immune infiltrates as well as their evaluation in DCIS. METHODS A literature search on PubMed was conducted up to 28th January 2019. Search terms used were "DCIS", "ductal carcinoma in situ", "immune", "immunology", "TIL", "TIL assessment", and "tumour-infiltrating lymphocyte". Search filters for "Most Recent" and "English" were applied. Information from published papers related to the research topic were synthesised and summarised for this review. RESULTS Studies have revealed that immune infiltrates play a role in the biology and microenvironment of DCIS, as well as treatment response. There is currently no consensus on the evaluation of TILs in DCIS for clinical application. CONCLUSIONS This review highlights the recent findings on the potential influence and prognostic value of immunological processes on DCIS progression, as well as the evaluation of TILs in DCIS. Further characterisation of the immune milieu of DCIS is recommended to better understand the immune response in DCIS progression and recurrence.
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Gorringe KL, Fox SB. Ductal Carcinoma In Situ Biology, Biomarkers, and Diagnosis. Front Oncol 2017; 7:248. [PMID: 29109942 PMCID: PMC5660056 DOI: 10.3389/fonc.2017.00248] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 10/02/2017] [Indexed: 12/21/2022] Open
Abstract
Ductal carcinoma in situ (DCIS) is an often-diagnosed breast disease and a known, non-obligate, precursor to invasive breast carcinoma. In this review, we explore the clinical and pathological features of DCIS, fundamental elements of DCIS biology including gene expression and genetic events, the relationship of DCIS with recurrence and invasive breast cancer, and the interaction of DCIS with the microenvironment. We also survey how these various elements are being used to solve the clinical conundrum of how to optimally treat a disease that has potential to progress, and yet is also likely over-treated in a significant proportion of cases.
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Affiliation(s)
- Kylie L. Gorringe
- Cancer Genomics Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Stephen B. Fox
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
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Deb S, Gorringe KL, Pang JMB, Byrne DJ, Takano EA, Dobrovic A, Fox SB. BRCA2 carriers with male breast cancer show elevated tumour methylation. BMC Cancer 2017; 17:641. [PMID: 28893223 PMCID: PMC5594583 DOI: 10.1186/s12885-017-3632-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 08/28/2017] [Indexed: 12/19/2022] Open
Abstract
Background Male breast cancer (MBC) represents a poorly characterised group of tumours, the management of which is largely based on practices established for female breast cancer. However, recent studies demonstrate biological and molecular differences likely to impact on tumour behaviour and therefore patient outcome. The aim of this study was to investigate methylation of a panel of commonly methylated breast cancer genes in familial MBCs. Methods 60 tumours from 3 BRCA1 and 25 BRCA2 male mutation carriers and 32 males from BRCAX families were assessed for promoter methylation by methylation-sensitive high resolution melting in a panel of 10 genes (RASSF1A, TWIST1, APC, WIF1, MAL, RARβ, CDH1, RUNX3, FOXC1 and GSTP1). An average methylation index (AMI) was calculated for each case comprising the average of the methylation of the 10 genes tested as an indicator of overall tumour promoter region methylation. Promoter hypermethylation and AMI were correlated with BRCA carrier mutation status and clinicopathological parameters including tumour stage, grade, histological subtype and disease specific survival. Results Tumours arising in BRCA2 mutation carriers showed significantly higher methylation of candidate genes, than those arising in non-BRCA2 familial MBCs (average AMI 23.6 vs 16.6, p = 0.01, 45% of genes hypermethylated vs 34%, p < 0.01). RARβ methylation and AMI-high status were significantly associated with tumour size (p = 0.01 and p = 0.02 respectively), RUNX3 methylation with invasive carcinoma of no special type (94% vs 69%, p = 0.046) and RASSF1A methylation with coexistence of high grade ductal carcinoma in situ (33% vs 6%, p = 0.02). Cluster analysis showed MBCs arising in BRCA2 mutation carriers were characterised by RASSF1A, WIF1, RARβ and GTSP1 methylation (p = 0.02) whereas methylation in BRCAX tumours showed no clear clustering to particular genes. TWIST1 methylation (p = 0.001) and AMI (p = 0.01) were prognostic for disease specific survival. Conclusions Increased methylation defines a subset of familial MBC and with AMI may be a useful prognostic marker. Methylation might be predictive of response to novel therapeutics that are currently under investigation in other cancer types. Electronic supplementary material The online version of this article (10.1186/s12885-017-3632-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Siddhartha Deb
- Molecular Pathology Research and Development Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Vic, Parkville, 3010, Australia
| | - Kylie L Gorringe
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Vic, Parkville, 3010, Australia.,Cancer Genomics Program, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia.,Department of Pathology, University of Melbourne, Parkville, VIC, 3012, Australia
| | - Jia-Min B Pang
- Molecular Pathology Research and Development Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - David J Byrne
- Molecular Pathology Research and Development Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Elena A Takano
- Molecular Pathology Research and Development Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
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- Kathleen Cuningham Foundation Consortium for research into Familial Breast Cancer, Peter MacCallum Cancer Centre, Melbourne, 3000, Australia
| | - Alexander Dobrovic
- Molecular Pathology Research and Development Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia.,Department of Pathology, University of Melbourne, Parkville, VIC, 3012, Australia.,Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, 3084, Australia.,School of Cancer Medicine, La Trobe University, Bundoora, VIC, 3084, Australia
| | - Stephen B Fox
- Molecular Pathology Research and Development Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia. .,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Vic, Parkville, 3010, Australia. .,Department of Pathology, University of Melbourne, Parkville, VIC, 3012, Australia. .,School of Cancer Medicine, La Trobe University, Bundoora, VIC, 3084, Australia.
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7
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Chen Y, Marotti JD, Jenson EG, Onega TL, Johnson KC, Christensen BC. Concordance of DNA methylation profiles between breast core biopsy and surgical excision specimens containing ductal carcinoma in situ (DCIS). Exp Mol Pathol 2017; 103:78-83. [PMID: 28711544 DOI: 10.1016/j.yexmp.2017.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 07/10/2017] [Indexed: 01/12/2023]
Abstract
The utility and reliability of assessing molecular biomarkers for translational applications on pre-operative core biopsy specimens assume consistency of molecular profiles with larger surgical specimens. Whether DNA methylation in ductal carcinoma in situ (DCIS), measured in core biopsy and surgical specimens are similar, remains unclear. Here, we compared genome-scale DNA methylation measured in matched core biopsy and surgical specimens from DCIS, including specific DNA methylation biomarkers of subsequent invasive cancer. DNA was extracted from guided 2mm cores of formalin fixed paraffin embedded (FFPE) specimens, bisulfite-modified, and measured on the Illumina HumanMethylation450 BeadChip. DNA methylation profiles of core biopsies exhibited high concordance with matched surgical specimens. Within-subject variability in DNA methylation was significantly lower than between-subject variability (all P<2.20E-16). In 641 CpGs whose methylation was related with increased hazard of invasive breast cancer, lower within-subject than between-subject variability was observed in 92.3% of the study participants (P<0.05). Between patient-matched core biopsy and surgical specimens, <0.6% of CpGs measured had changes in median DNA methylation >15%, and a pathway analysis of these CpGs indicated enrichment for genes related with wound healing. Our results indicate that DNA methylation measured in core biopsies are representative of the matched surgical specimens and suggest that DCIS biomarkers measured in core biopsies can inform clinical decision-making.
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Affiliation(s)
- Youdinghuan Chen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA; Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA.
| | - Jonathan D Marotti
- Department of Pathology and Laboratory Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA; Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Erik G Jenson
- Department of Pathology and Laboratory Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Tracy L Onega
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Kevin C Johnson
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA; Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA; Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA; Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA.
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Shakeri H, Gharesouran J, Fakhrjou A, Esfahani A, Mohaddes Ardebili SM. DNA methylation assessment as a prognostic factor in invasive breast cancer using methylation-specific multiplex ligation dependent probe amplification. EXCLI JOURNAL 2016; 15:11-20. [PMID: 27065772 PMCID: PMC4822054 DOI: 10.17179/excli2015-485] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 12/05/2015] [Indexed: 12/17/2022]
Abstract
DNA methylation of promoter regions is a common molecular mechanism for inactivation of tumor suppressor genes that participates in carcinogenesis. Determining the methylation status of genes in cancer and their association with clinical features play an essential role in early diagnosis, prognosis and determine appropriate treatment for patients. The purpose of the present study was to evaluate the methylation of tumor suppressor genes in patients with invasive ductal carcinoma (IDC). Furthermore, we evaluated the association between clinical parameters and DNA methylation as a biomarker in diagnostic IDC patients. The methylation-specific multiplex ligation dependent probe amplification (MS-MLPA) assay was used to analyze the methylation profile of 24 genes in formalin-fixed paraffin embedded (FFPE) tissue samples from 75 patients with IDC. Each of the patients showed a distinctive methylation profile. We observed higher methylation in the RASSF1 (48 %), CDH13 (44 %) and GSTP1 (36 %) genes. Some of the methylated genes were associated with clinical features. Methylation of GSTP1 (P=0.028) and RASSF1 (P=0.012) were related with lymph node metastasis. Methylation of GSTP1 (P=0.005) was associated with high histological grade. Moreover, concurrent methylation of GSTP1 and CDH13 was observed in IDC patients (p<0.001). Hierarchical cluster analysis based on the methylation profile revealed two main clusters of patients, the highly methylated cluster being significantly associated with high histological grade and lymph node metastasis. The results of this study indicate that the methylation status of RASSF1 and CDH13 and GSTP1 can be a prognostic marker to better management of IDC patients.
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Affiliation(s)
- Halaleh Shakeri
- Hematology & Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Biochemistry and Clinical Laboratories, Division of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jalal Gharesouran
- Department of Biochemistry and Clinical Laboratories, Division of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ashraf Fakhrjou
- Department of Pathology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali Esfahani
- Hematology & Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Seyyed Mojtaba Mohaddes Ardebili
- Hematology & Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Biochemistry and Clinical Laboratories, Division of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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9
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MiRNAs and Other Epigenetic Changes as Biomarkers in Triple Negative Breast Cancer. Int J Mol Sci 2015; 16:28347-76. [PMID: 26633365 PMCID: PMC4691037 DOI: 10.3390/ijms161226090] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 10/30/2015] [Accepted: 11/12/2015] [Indexed: 02/06/2023] Open
Abstract
Triple negative breast cancer (TNBC) is characterised by the lack of receptors for estrogen (ER), progesterone (PR), and human epidermal growth factor 2 (HER2). Since it cannot be treated by current endocrine therapies which target these receptors and due to its aggressive nature, it has one of the worst prognoses of all breast cancer subtypes. The only treatments remain chemo- and/or radio-therapy and surgery and because of this, novel biomarkers or treatment targets are urgently required to improve disease outcomes. MicroRNAs represent an attractive candidate for targeted therapies against TNBC, due to their natural ability to act as antisense interactors and regulators of entire gene sets involved in malignancy and their superiority over mRNA profiling to accurately classify disease. Here we review the current knowledge regarding miRNAs as biomarkers in TNBC and their potential use as therapeutic targets in this disease. Further, we review other epigenetic changes and interactions of these changes with microRNAs in this breast cancer subtype, which may lead to the discovery of new treatment targets for TNBC.
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10
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Mardekian SK, Bombonati A, Palazzo JP. Ductal carcinoma in situ of the breast: the importance of morphologic and molecular interactions. Hum Pathol 2015; 49:114-23. [PMID: 26826418 DOI: 10.1016/j.humpath.2015.11.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 11/02/2015] [Accepted: 11/05/2015] [Indexed: 12/21/2022]
Abstract
Ductal carcinoma in situ (DCIS) of the breast is a lesion characterized by significant heterogeneity, in terms of morphology, immunohistochemical staining, molecular signatures, and clinical expression. For some patients, surgical excision provides adequate treatment, but a subset of patients will experience recurrence of DCIS or progression to invasive ductal carcinoma (IDC). Recent years have seen extensive research aimed at identifying the molecular events that characterize the transition from normal epithelium to DCIS and IDC. Tumor epithelial cells, myoepithelial cells, and stromal cells undergo alterations in gene expression, which are most important in the early stages of breast carcinogenesis. Epigenetic modifications, such as DNA methylation, together with microRNA alterations, play a major role in these genetic events. In addition, tumor proliferation and invasion is facilitated by the lesional microenvironment, which includes stromal fibroblasts and macrophages that secrete growth factors and angiogenesis-promoting substances. Characterization of DCIS on a molecular level may better account for the heterogeneity of these lesions and how this manifests as differences in patient outcome and response to therapy. Molecular assays originally developed for assessing likelihood of recurrence in IDC are recently being applied to DCIS, with promising results. In the future, the classification of DCIS will likely incorporate molecular findings along with histologic and immunohistochemical features, allowing for personalized prognostic information and therapeutic options for patients with DCIS. This review summarizes current data regarding the molecular characterization of DCIS and discusses the potential clinical relevance.
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MESH Headings
- Animals
- Biomarkers, Tumor/analysis
- Biomarkers, Tumor/genetics
- Biopsy
- Breast Neoplasms/chemistry
- Breast Neoplasms/genetics
- Breast Neoplasms/pathology
- Breast Neoplasms/therapy
- Carcinoma/chemistry
- Carcinoma/genetics
- Carcinoma/pathology
- Carcinoma, Intraductal, Noninfiltrating/chemistry
- Carcinoma, Intraductal, Noninfiltrating/genetics
- Carcinoma, Intraductal, Noninfiltrating/pathology
- Carcinoma, Intraductal, Noninfiltrating/therapy
- Disease Progression
- Epigenesis, Genetic
- Female
- Gene Expression Regulation, Neoplastic
- Genetic Predisposition to Disease
- Humans
- Immunohistochemistry
- Mastectomy
- Molecular Diagnostic Techniques
- Neoplasm Recurrence, Local
- Phenotype
- Predictive Value of Tests
- Reproducibility of Results
- Treatment Outcome
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Affiliation(s)
- Stacey K Mardekian
- Department of Pathology, Thomas Jefferson University, Philadelphia, PA 19107.
| | - Alessandro Bombonati
- Department of Pathology, Albert Einstein Medical Center, Philadelphia, PA 19141.
| | - Juan P Palazzo
- Department of Pathology, Thomas Jefferson University, Philadelphia, PA 19107.
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11
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Johnson KC, Koestler DC, Fleischer T, Chen P, Jenson EG, Marotti JD, Onega T, Kristensen VN, Christensen BC. DNA methylation in ductal carcinoma in situ related with future development of invasive breast cancer. Clin Epigenetics 2015. [PMID: 26213588 PMCID: PMC4514996 DOI: 10.1186/s13148-015-0094-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background Ductal carcinoma in situ (DCIS) is a heterogeneous, pre-invasive lesion associated with an increased risk for future invasive ductal carcinoma. However, accurate risk stratification for development of invasive disease and appropriate treatment decisions remain clinical challenges. DNA methylation alterations are early events in the progression of cancer and represent emerging molecular markers that may predict invasive recurrence more accurately than traditional measures of DCIS prognosis. Results We measured DNA methylation using the Illumina HumanMethylation450K array of estrogen-receptor positive DCIS (n = 40) and adjacent-normal (n = 15) tissues from subjects in the New Hampshire Mammography Network longitudinal breast imaging registry. We identified locus-specific methylation differences between DCIS and matched adjacent-normal tissue (95,609 CpGs, Q < 0.05). Among 40 DCIS cases, 13 later developed invasive disease and we identified 641 CpG sites that exhibited differential DNA methylation (P < 0.01 and median |∆β| > 0.1) in these cases compared with age-matched subjects without invasive disease. The set of differentially methylated CpG loci associated with disease progression was enriched in homeobox-containing genes (P = 1.3E-09) and genes involved with limb morphogenesis (P = 1.0E-05). In an independent cohort, a subset of genes with progression-related differential methylation between DCIS and invasive breast cancer were confirmed. Further, the functional relevance of these genes’ regulation by methylation was demonstrated in early stage breast cancers from The Cancer Genome Atlas database. Conclusions This work contributes to the understanding of epigenetic alterations that occur in DCIS and illustrates the potential of DNA methylation as markers of DCIS progression. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0094-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kevin C Johnson
- Department of Pharmacology and Toxicology, Geisel School of Medicine at Dartmouth, HB 7650, Remsen 611, Hanover, NH 03755 USA ; Department of Epidemiology, Geisel School of Medicine at Dartmouth, HB 7650, Remsen 611, Hanover, NH 03755 USA
| | - Devin C Koestler
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, KS USA
| | - Thomas Fleischer
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway ; The K.G. Jebsen Center for Breast Cancer, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Panpan Chen
- Department of Pharmacology and Toxicology, Geisel School of Medicine at Dartmouth, HB 7650, Remsen 611, Hanover, NH 03755 USA ; Department of Epidemiology, Geisel School of Medicine at Dartmouth, HB 7650, Remsen 611, Hanover, NH 03755 USA
| | - Erik G Jenson
- Department of Pathology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755 USA
| | - Jonathan D Marotti
- Department of Pathology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755 USA
| | - Tracy Onega
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, HB 7650, Remsen 611, Hanover, NH 03755 USA ; Department of Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH 03755 USA ; The Dartmouth Institute, Geisel School of Medicine at Dartmouth, Lebanon, NH 03766 USA
| | - Vessela N Kristensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway ; The K.G. Jebsen Center for Breast Cancer, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway ; Department of Clinical Molecular Biology (EpiGen), Medical Division, Akershus Hospital, Lørenskog, Norway
| | - Brock C Christensen
- Department of Pharmacology and Toxicology, Geisel School of Medicine at Dartmouth, HB 7650, Remsen 611, Hanover, NH 03755 USA ; Department of Epidemiology, Geisel School of Medicine at Dartmouth, HB 7650, Remsen 611, Hanover, NH 03755 USA ; Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Hanover, NH 03755 USA
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12
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Pang JMB, Deb S, Takano EA, Byrne DJ, Jene N, Boulghourjian A, Holliday A, Millar E, Lee CS, O'Toole SA, Dobrovic A, Fox SB. Methylation profiling of ductal carcinoma in situ and its relationship to histopathological features. Breast Cancer Res 2014; 16:423. [PMID: 25331261 PMCID: PMC4303108 DOI: 10.1186/s13058-014-0423-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 07/30/2014] [Indexed: 12/14/2022] Open
Abstract
Introduction DNA methylation is a well-studied biomarker in invasive breast cancer, but its role in ductal carcinoma in situ (DCIS) is less well characterized. The aims of this study are to assess the methylation profile in DCIS for a panel of well-characterized genes that are frequently methylated in breast cancer, to investigate the relationship of methylation with pathological features, and to perform a proof-of-principle study to evaluate the practicality of methylation as a biomarker in diagnostic DCIS material. Methods Promoter CpG island methylation for a panel of 11 breast cancer-related genes was performed by methylation-sensitive high resolution melting (MS-HRM). Formalin-fixed, paraffin-embedded (FFPE) biopsies from 72 samples of pure DCIS (DCIS occurring in the absence of synchronous invasive carcinoma), 10 samples of mixed DCIS (DCIS adjacent to invasive carcinoma), and 18 samples of normal breast epithelium adjacent to a DCIS lesion were micro-dissected prior to DNA extraction. Results Methylation was seen for all the tested genes except BRCA1. RASSF1A was the most frequently methylated gene (90% of DCIS samples) and its methylation was associated with comedo necrosis (p = 0.018). Cluster analysis based on the methylation profile revealed four groups, the highly methylated cluster being significantly associated with high nuclear grade, HER2 amplification, negative estrogen receptor (ER) α status, and negative progesterone receptor (PgR) status, (p = 0.038, p = 0.018, p <0.001, p = 0.001, respectively). Methylation of APC (p = 0.017), CDH13 (p = 0.017), and RARβ (p <0.001) was associated with negative ERα status. Methylation of CDH13 (p <0.001), and RARβ (p = 0.001) was associated with negative PgR status. Methylation of APC (p = 0.013) and CDH13 (p = 0.026) was associated with high nuclear grade. Methylation of CDH13 (p = 0.009), and RARβ (p = 0.042) was associated with HER2-amplification. Conclusions DNA methylation can be assessed in FFPE-derived samples using suitable methodologies. Methylation of a panel of genes that are known to be methylated in invasive breast cancer was able to classify DCIS into distinct groups and was differentially associated with phenotypic features in DCIS. Electronic supplementary material The online version of this article (doi:10.1186/s13058-014-0423-9) contains supplementary material, which is available to authorized users.
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Fleischer T, Frigessi A, Johnson KC, Edvardsen H, Touleimat N, Klajic J, Riis ML, Haakensen VD, Wärnberg F, Naume B, Helland A, Børresen-Dale AL, Tost J, Christensen BC, Kristensen VN. Genome-wide DNA methylation profiles in progression to in situ and invasive carcinoma of the breast with impact on gene transcription and prognosis. Genome Biol 2014. [PMID: 25146004 PMCID: PMC4165906 DOI: 10.1186/s13059-014-0435-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Ductal carcinoma in situ (DCIS) of the breast is a precursor of invasive breast carcinoma. DNA methylation alterations are thought to be an early event in progression of cancer, and may prove valuable as a tool in clinical decision making and for understanding neoplastic development. RESULTS We generate genome-wide DNA methylation profiles of 285 breast tissue samples representing progression of cancer, and validate methylation changes between normal and DCIS in an independent dataset of 15 normal and 40 DCIS samples. We also validate a prognostic signature on 583 breast cancer samples from The Cancer Genome Atlas. Our analysis reveals that DNA methylation profiles of DCIS are radically altered compared to normal breast tissue, involving more than 5,000 genes. Changes between DCIS and invasive breast carcinoma involve around 1,000 genes. In tumors, DNA methylation is associated with gene expression of almost 3,000 genes, including both negative and positive correlations. A prognostic signature based on methylation level of 18 CpGs is associated with survival of breast cancer patients with invasive tumors, as well as with survival of patients with DCIS and mixed lesions of DCIS and invasive breast carcinoma. CONCLUSIONS This work demonstrates that changes in the epigenome occur early in the neoplastic progression, provides evidence for the possible utilization of DNA methylation-based markers of progression in the clinic, and highlights the importance of epigenetic changes in carcinogenesis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Vessela N Kristensen
- Department of Genetics, Institute for Cancer Research, OUS Radiumhospitalet, Montebello, Oslo, 0310, Norway.
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14
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Fleischer T, Frigessi A, Johnson KC, Edvardsen H, Touleimat N, Klajic J, Riis ML, Haakensen VD, Wärnberg F, Naume B, Helland A, Børresen-Dale AL, Tost J, Christensen BC, Kristensen VN. Genome-wide DNA methylation profiles in progression to in situ and invasive carcinoma of the breast with impact on gene transcription and prognosis. Genome Biol 2014; 15:435. [PMID: 25146004 DOI: 10.1186/preaccept-2333349012841587] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 08/08/2014] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Ductal carcinoma in situ (DCIS) of the breast is a precursor of invasive breast carcinoma. DNA methylation alterations are thought to be an early event in progression of cancer, and may prove valuable as a tool in clinical decision making and for understanding neoplastic development. RESULTS We generate genome-wide DNA methylation profiles of 285 breast tissue samples representing progression of cancer, and validate methylation changes between normal and DCIS in an independent dataset of 15 normal and 40 DCIS samples. We also validate a prognostic signature on 583 breast cancer samples from The Cancer Genome Atlas. Our analysis reveals that DNA methylation profiles of DCIS are radically altered compared to normal breast tissue, involving more than 5,000 genes. Changes between DCIS and invasive breast carcinoma involve around 1,000 genes. In tumors, DNA methylation is associated with gene expression of almost 3,000 genes, including both negative and positive correlations. A prognostic signature based on methylation level of 18 CpGs is associated with survival of breast cancer patients with invasive tumors, as well as with survival of patients with DCIS and mixed lesions of DCIS and invasive breast carcinoma. CONCLUSIONS This work demonstrates that changes in the epigenome occur early in the neoplastic progression, provides evidence for the possible utilization of DNA methylation-based markers of progression in the clinic, and highlights the importance of epigenetic changes in carcinogenesis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Vessela N Kristensen
- Department of Genetics, Institute for Cancer Research, OUS Radiumhospitalet, Montebello, Oslo, 0310, Norway.
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Du M, Su XM, Zhang T, Xing YJ. Aberrant promoter DNA methylation inhibits bone morphogenetic protein 2 expression and contributes to drug resistance in breast cancer. Mol Med Rep 2014; 10:1051-5. [PMID: 24866720 DOI: 10.3892/mmr.2014.2276] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 03/17/2014] [Indexed: 11/06/2022] Open
Abstract
Bone morphogenetic protein 2 (BMP2) is a growth factor that is involved in the development and progression of various types of cancer. However, the epigenetic regulation of the expression of BMP2 and the association between BMP2 expression and drug resistance in breast cancer remains to be elucidated. The present study reported that the expression of BMP2 was significantly decreased in primary breast cancer samples and the MCF‑7/ADR breast cancer mulitdrug resistance cell line, which was closely associated with its promoter DNA methylation status. The expression of BMP2 in MCF‑7/ADR cells markedly increased when treated with 5‑Aza‑2'‑deoxycytidine. Knockdown of BMP2 by specific small interfering RNA enhanced the chemoresistance of the MCF‑7 breast cancer cell line. These findings indicated that epigenetic silencing of BMP2 in breast cancer may be involved in breast cancer progression and drug resistance, and provided a novel prognostic marker and therapeutic strategy for breast cancer.
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Affiliation(s)
- Min Du
- Department of Oncology, PLA General Hospital of Chengdu Military Region, Chengdu, Sichuan 610083, P.R. China
| | - Xiao-Mei Su
- Department of Oncology, PLA General Hospital of Chengdu Military Region, Chengdu, Sichuan 610083, P.R. China
| | - Tao Zhang
- Department of Oncology, PLA General Hospital of Chengdu Military Region, Chengdu, Sichuan 610083, P.R. China
| | - Yong-Jun Xing
- Affiliated Stomatological Hospital, PLA General Hospital of Chengdu Military Region, Chengdu, Sichuan 610083, P.R. China
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Tsang JYS, Tse GMK. Narrowing down the focus: what are the main predictive markers for ductal carcinoma in situ? BREAST CANCER MANAGEMENT 2014. [DOI: 10.2217/bmt.14.9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
SUMMARY Ductal carcinoma in situ accounts for approximately a quarter of newly diagnosed breast cancer nowadays. It is not life threatening per se, but confers an increased risk for subsequent invasive cancers. Optimal management should be based on the tumor characteristics and tailored to the risk of subsequent recurrence and invasive events. Prediction for recurrence risk has been determined mainly with clinical and histopathologic factors. However, they are imperfect, probably owing to the lack of standardized methods for assessment. Ongoing efforts have been shifted to the use of molecular factors, as well as prediction of noninvasive and invasive recurrences separately. These molecular factors seem to be more powerful in predicting invasive and noninvasive recurrence. However, their emerging roles still need to be validated.
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Affiliation(s)
- Julia YS Tsang
- Department of Anatomical & Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong
| | - Gary MK Tse
- Department of Anatomical & Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong
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