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Cortellesi E, Savini I, Veneziano M, Gambacurta A, Catani MV, Gasperi V. Decoding the Epigenome of Breast Cancer. Int J Mol Sci 2025; 26:2605. [PMID: 40141248 PMCID: PMC11942310 DOI: 10.3390/ijms26062605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2025] [Revised: 03/06/2025] [Accepted: 03/12/2025] [Indexed: 03/28/2025] Open
Abstract
Breast cancer (BC) is the most prevalent malignancy among women, characterized by extensive heterogeneity stemming from molecular and genetic alterations. This review explores the intricate epigenetic landscape of BC, highlighting the significant role of epigenetic modifications-particularly DNA methylation, histone modifications, and the influence of non-coding RNAs-in the initiation, progression, and prognosis of the disease. Epigenetic alterations drive crucial processes, including gene expression regulation, cell differentiation, and tumor microenvironment interactions, contributing to tumorigenesis and metastatic potential. Notably, aberrations in DNA methylation patterns, including global hypomethylation and hypermethylation of CpG islands, have been associated with distinct BC subtypes, with implications for early detection and risk assessment. Furthermore, histone modifications, such as acetylation and methylation, affect cancer cell plasticity and aggressiveness by profoundly influencing chromatin dynamics and gene transcription. Finally, non-coding RNAs contribute by modulating epigenetic machinery and gene expression. Despite advances in our knowledge, clinical application of epigenetic therapies in BC is still challenging, often yielding limited efficacy when used alone. However, combining epi-drugs with established treatments shows promise for enhancing therapeutic outcomes. This review underscores the importance of integrating epigenetic insights into personalized BC treatment strategies, emphasizing the potential of epigenetic biomarkers for improving diagnosis, prognosis, and therapeutic response in affected patients.
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Affiliation(s)
- Elisa Cortellesi
- Department of Experimental Medicine, Tor Vergata University of Rome, 00133 Rome, Italy; (E.C.); (I.S.); (M.V.); (A.G.); (M.V.C.)
| | - Isabella Savini
- Department of Experimental Medicine, Tor Vergata University of Rome, 00133 Rome, Italy; (E.C.); (I.S.); (M.V.); (A.G.); (M.V.C.)
| | - Matteo Veneziano
- Department of Experimental Medicine, Tor Vergata University of Rome, 00133 Rome, Italy; (E.C.); (I.S.); (M.V.); (A.G.); (M.V.C.)
| | - Alessandra Gambacurta
- Department of Experimental Medicine, Tor Vergata University of Rome, 00133 Rome, Italy; (E.C.); (I.S.); (M.V.); (A.G.); (M.V.C.)
- NAST Centre (Nanoscience & Nanotechnology & Innovative Instrumentation), Tor Vergata University of Rome, 00133 Rome, Italy
| | - Maria Valeria Catani
- Department of Experimental Medicine, Tor Vergata University of Rome, 00133 Rome, Italy; (E.C.); (I.S.); (M.V.); (A.G.); (M.V.C.)
| | - Valeria Gasperi
- Department of Experimental Medicine, Tor Vergata University of Rome, 00133 Rome, Italy; (E.C.); (I.S.); (M.V.); (A.G.); (M.V.C.)
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2
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Wakim JG, Spakowitz AJ. Physical modeling of nucleosome clustering in euchromatin resulting from interactions between epigenetic reader proteins. Proc Natl Acad Sci U S A 2024; 121:e2317911121. [PMID: 38900792 PMCID: PMC11214050 DOI: 10.1073/pnas.2317911121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 04/15/2024] [Indexed: 06/22/2024] Open
Abstract
Euchromatin is an accessible phase of genetic material containing genes that encode proteins with increased expression levels. The structure of euchromatin in vitro has been described as a 30-nm fiber formed from ordered nucleosome arrays. However, recent advances in microscopy have revealed an in vivo euchromatin architecture that is much more disordered, characterized by variable-length linker DNA and sporadic nucleosome clusters. In this work, we develop a theoretical model to elucidate factors contributing to the disordered in vivo architecture of euchromatin. We begin by developing a 1D model of nucleosome positioning that captures the interactions between bound epigenetic reader proteins to predict the distribution of DNA linker lengths between adjacent nucleosomes. We then use the predicted linker lengths to construct 3D chromatin configurations consistent with the physical properties of DNA within the nucleosome array, and we evaluate the distribution of nucleosome cluster sizes in those configurations. Our model reproduces experimental cluster-size distributions, which are dramatically influenced by the local pattern of epigenetic marks and the concentration of reader proteins. Based on our model, we attribute the disordered arrangement of euchromatin to the heterogeneous binding of reader proteins and subsequent short-range interactions between bound reader proteins on adjacent nucleosomes. By replicating experimental results with our physics-based model, we propose a mechanism for euchromatin organization in the nucleus that impacts gene regulation and the maintenance of epigenetic marks.
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Affiliation(s)
- Joseph G. Wakim
- Department of Chemical Engineering, Stanford University, Stanford, CA94305
| | - Andrew J. Spakowitz
- Department of Chemical Engineering, Stanford University, Stanford, CA94305
- Department of Materials Science and Engineering, Stanford University, Stanford, CA94305
- Biophysics Program, Stanford University, Stanford, CA94305
- Department of Applied Physics, Stanford University, Stanford, CA94305
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3
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Thakur C, Qiu Y, Pawar A, Chen F. Epigenetic regulation of breast cancer metastasis. Cancer Metastasis Rev 2024; 43:597-619. [PMID: 37857941 DOI: 10.1007/s10555-023-10146-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 10/02/2023] [Indexed: 10/21/2023]
Abstract
Breast cancer is the most frequently diagnosed malignancy and the second leading cause of cancer-related mortality among women worldwide. Recurrent metastasis is associated with poor patient outcomes and poses a significant challenge in breast cancer therapies. Cancer cells adapting to a new tissue microenvironment is the key event in distant metastasis development, where the disseminating tumor cells are likely to acquire genetic and epigenetic alterations during the process of metastatic colonization. Despite several decades of research in this field, the exact mechanisms governing metastasis are not fully understood. However, emerging body of evidence indicates that in addition to genetic changes, epigenetic reprogramming of cancer cells and the metastatic niche are paramount toward successful metastasis. Here, we review and discuss the latest knowledge about the salient attributes of metastasis and epigenetic regulation in breast cancer and crucial research domains that need further investigation.
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Affiliation(s)
- Chitra Thakur
- Stony Brook Cancer Center, Renaissance School of Medicine, Stony Brook University, Lauterbur Drive, Stony Brook, NY, 11794, USA.
| | - Yiran Qiu
- Stony Brook Cancer Center, Renaissance School of Medicine, Stony Brook University, Lauterbur Drive, Stony Brook, NY, 11794, USA
| | - Aashna Pawar
- Stony Brook Cancer Center, Renaissance School of Medicine, Stony Brook University, Lauterbur Drive, Stony Brook, NY, 11794, USA
| | - Fei Chen
- Stony Brook Cancer Center, Renaissance School of Medicine, Stony Brook University, Lauterbur Drive, Stony Brook, NY, 11794, USA.
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4
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Zhou L, Yu CW. Epigenetic modulations in triple-negative breast cancer: Therapeutic implications for tumor microenvironment. Pharmacol Res 2024; 204:107205. [PMID: 38719195 DOI: 10.1016/j.phrs.2024.107205] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 04/23/2024] [Accepted: 04/30/2024] [Indexed: 06/01/2024]
Abstract
Triple-negative breast cancer (TNBC) is an aggressive subtype lacking estrogen receptors, progesterone receptors and lacks HER2 overexpression. This absence of critical molecular targets poses significant challenges for conventional therapies. Immunotherapy, remarkably immune checkpoint blockade, offers promise for TNBC treatment, but its efficacy remains limited. Epigenetic dysregulation, including altered DNA methylation, histone modifications, and imbalances in regulators such as BET proteins, plays a crucial role in TNBC development and resistance to treatment. Hypermethylation of tumor suppressor gene promoters and the imbalance of histone methyltransferases such as EZH2 and histone deacetylases (HDACs) profoundly influence tumor cell proliferation, survival, and metastasis. In addition, epigenetic alterations critically shape the tumor microenvironment (TME), including immune cell composition, cytokine signaling, and immune checkpoint expression, ultimately contributing to immune evasion. Targeting these epigenetic mechanisms with specific inhibitors such as EZH2 and HDAC inhibitors in combination with immunotherapy represents a compelling strategy to remodel the TME, potentially overcoming immune evasion and enhancing therapeutic outcomes in TNBC. This review aims to comprehensively elucidate the current understanding of epigenetic modulation in TNBC, its influence on the TME, and the potential of combining epigenetic therapies with immunotherapy to overcome the challenges posed by this aggressive breast cancer subtype.
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Affiliation(s)
- Linlin Zhou
- Institute of Immunotherapy, Fujian Medical University, Fuzhou, China; School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Chen-Wei Yu
- Department of Statistics and Information Science, Fu Jen Catholic University, New Taipei City, Taiwan.
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5
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Puvvula PK, Moon AM. Discovery and characterization of anti-cancer peptides from a random peptide library. PLoS One 2024; 19:e0293072. [PMID: 38349913 PMCID: PMC10863893 DOI: 10.1371/journal.pone.0293072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 10/03/2023] [Indexed: 02/15/2024] Open
Abstract
We performed a forward genetic screen to discover peptides that specifically target breast cancer cells using a Penetratin tagged, random 15mer peptide library. We identified a group of novel peptides that specifically inhibited the proliferation and survival of breast cancer cells without affecting normal primary mammary epithelial cells or fibroblasts. The intrinsic apoptotic pathway is activated by these peptides in the face of abnormal expression of numerous cell cycle regulatory genes. Associated alterations in histone marks, nuclear structure, and levels of critical RNA binding proteins vary in a peptide specific manner. This study demonstrates a novel method for the discovery of new potential therapeutic peptides.
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Affiliation(s)
- Pavan Kumar Puvvula
- Department of Molecular and Functional Genomics, Weis Center for Research, Geisinger Clinic, Danville, Pennsylvania, United States of America
| | - Anne M. Moon
- Department of Molecular and Functional Genomics, Weis Center for Research, Geisinger Clinic, Danville, Pennsylvania, United States of America
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
- The Mindich Child Health and Development Institute, Hess Center for Science and Medicine at Mount Sinai, New York, New York, United States of America
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Gabbianelli R, Shahar E, de Simone G, Rucci C, Bordoni L, Feliziani G, Zhao F, Ferrati M, Maggi F, Spinozzi E, Mahajna J. Plant-Derived Epi-Nutraceuticals as Potential Broad-Spectrum Anti-Viral Agents. Nutrients 2023; 15:4719. [PMID: 38004113 PMCID: PMC10675658 DOI: 10.3390/nu15224719] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 10/29/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
Although the COVID-19 pandemic appears to be diminishing, the emergence of SARS-CoV-2 variants represents a threat to humans due to their inherent transmissibility, immunological evasion, virulence, and invulnerability to existing therapies. The COVID-19 pandemic affected more than 500 million people and caused over 6 million deaths. Vaccines are essential, but in circumstances in which vaccination is not accessible or in individuals with compromised immune systems, drugs can provide additional protection. Targeting host signaling pathways is recommended due to their genomic stability and resistance barriers. Moreover, targeting host factors allows us to develop compounds that are effective against different viral variants as well as against newly emerging virus strains. In recent years, the globe has experienced climate change, which may contribute to the emergence and spread of infectious diseases through a variety of factors. Warmer temperatures and changing precipitation patterns can increase the geographic range of disease-carrying vectors, increasing the risk of diseases spreading to new areas. Climate change may also affect vector behavior, leading to a longer breeding season and more breeding sites for disease vectors. Climate change may also disrupt ecosystems, bringing humans closer to wildlife that transmits zoonotic diseases. All the above factors may accelerate the emergence of new viral epidemics. Plant-derived products, which have been used in traditional medicine for treating pathological conditions, offer structurally novel therapeutic compounds, including those with anti-viral activity. In addition, plant-derived bioactive substances might serve as the ideal basis for developing sustainable/efficient/cost-effective anti-viral alternatives. Interest in herbal antiviral products has increased. More than 50% of approved drugs originate from herbal sources. Plant-derived compounds offer diverse structures and bioactive molecules that are candidates for new drug development. Combining these therapies with conventional drugs could improve patient outcomes. Epigenetics modifications in the genome can affect gene expression without altering DNA sequences. Host cells can use epigenetic gene regulation as a mechanism to silence incoming viral DNA molecules, while viruses recruit cellular epitranscriptomic (covalent modifications of RNAs) modifiers to increase the translational efficiency and transcript stability of viral transcripts to enhance viral gene expression and replication. Moreover, viruses manipulate host cells' epigenetic machinery to ensure productive viral infections. Environmental factors, such as natural products, may influence epigenetic modifications. In this review, we explore the potential of plant-derived substances as epigenetic modifiers for broad-spectrum anti-viral activity, reviewing their modulation processes and anti-viral effects on DNA and RNA viruses, as well as addressing future research objectives in this rapidly emerging field.
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Affiliation(s)
- Rosita Gabbianelli
- Unit of Molecular Biology and Nutrigenomics, University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy; (R.G.); (G.d.S.); (L.B.); (G.F.); (F.Z.)
| | - Ehud Shahar
- Department of Nutrition and Natural Products, Migal—Galilee Research Institute, Kiryat Shmona 11016, Israel;
- Department of Biotechnology, Tel-Hai College, Kiryat Shmona 1220800, Israel
| | - Gaia de Simone
- Unit of Molecular Biology and Nutrigenomics, University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy; (R.G.); (G.d.S.); (L.B.); (G.F.); (F.Z.)
| | - Chiara Rucci
- Unit of Molecular Biology and Nutrigenomics, University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy; (R.G.); (G.d.S.); (L.B.); (G.F.); (F.Z.)
| | - Laura Bordoni
- Unit of Molecular Biology and Nutrigenomics, University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy; (R.G.); (G.d.S.); (L.B.); (G.F.); (F.Z.)
| | - Giulia Feliziani
- Unit of Molecular Biology and Nutrigenomics, University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy; (R.G.); (G.d.S.); (L.B.); (G.F.); (F.Z.)
| | - Fanrui Zhao
- Unit of Molecular Biology and Nutrigenomics, University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy; (R.G.); (G.d.S.); (L.B.); (G.F.); (F.Z.)
| | - Marta Ferrati
- Chemistry Interdisciplinary Project (ChIP) Research Centre, School of Pharmacy, University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy; (M.F.); (F.M.); (E.S.)
| | - Filippo Maggi
- Chemistry Interdisciplinary Project (ChIP) Research Centre, School of Pharmacy, University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy; (M.F.); (F.M.); (E.S.)
| | - Eleonora Spinozzi
- Chemistry Interdisciplinary Project (ChIP) Research Centre, School of Pharmacy, University of Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy; (M.F.); (F.M.); (E.S.)
| | - Jamal Mahajna
- Department of Nutrition and Natural Products, Migal—Galilee Research Institute, Kiryat Shmona 11016, Israel;
- Department of Biotechnology, Tel-Hai College, Kiryat Shmona 1220800, Israel
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7
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Zhou L, Wu J, Ruan M, Xiao Y, Lan H, Wu Q, Yu CW, Zhang Q. The loss of B7-H4 expression in breast cancer cells escaping from T cell cytotoxicity contributes to epithelial-to-mesenchymal transition. Breast Cancer Res 2023; 25:115. [PMID: 37794509 PMCID: PMC10548745 DOI: 10.1186/s13058-023-01721-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 09/26/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND B7 homology 4 (B7-H4), a potential target for cancer therapy, has been demonstrated to inhibit T cell cytotoxicity in the early stages of breast cancer. However, B7-H4 manipulating breast tumor immune microenvironment (TIME) in the tumor progression remains unknown. METHODS We engineered T cells with B7-H4-specific chimeric antigen receptors (CARs) and performed a T cell co-culture assay to characterize B7-H4 expression level in breast cancer cells escaping from T cell cytotoxicity. We generated B7-H4 knockout (KO) and overexpression (OE) breast cancer cells to determine the epithelial-to-mesenchymal transition (EMT) and stemness characteristics in vitro and in vivo, including tumor proliferation, migration, metastasis and chemoresistance. The Cancer Genome Atlas breast cancer database was accessed to investigate the correlation between B7-H4 expression levels and EMT characteristics in patients with breast cancer. RESULTS Our result found that B7-H4 expression level was significantly reduced in a subset of breast cancer cells that escaped from the cytotoxicity of B7-H4 CAR-T cells. Compared with wild type cells, B7-H4 KO cells prompt EMT and stemness characteristics, including migration, invasion and metastasis, and OE cells vice versa. The increase in H3K27me3 in KO cells confirmed the epigenetic reprogramming of cancer stem cells. The IC50 of doxorubicin or oxaliplatin significantly increased in KO cells, which was in agreement with a decrease in OE cells. Moreover, a trend of downregulated B7-H4 from stage I to stage II breast cancer patients indicates that the low-expressing B7-H4 breast cancer cells escaping from TIME have spread to nearby breast lymph nodes in the cancer progression. CONCLUSIONS Our study illuminates the novel role of renouncing B7-H4 in breast cancer cells through immune escape, which contributes to EMT processes and provides new insights for breast cancer treatments.
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Affiliation(s)
- Linlin Zhou
- Institute of Immunotherapy, Fujian Medical University, Fuzhou, China
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Jichun Wu
- Institute of Immunotherapy, Fujian Medical University, Fuzhou, China
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Mei Ruan
- Institute of Immunotherapy, Fujian Medical University, Fuzhou, China
| | - Yonglei Xiao
- Institute of Immunotherapy, Fujian Medical University, Fuzhou, China
| | - Hailin Lan
- Institute of Immunotherapy, Fujian Medical University, Fuzhou, China
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Qiongwen Wu
- Institute of Immunotherapy, Fujian Medical University, Fuzhou, China
| | - Chen-Wei Yu
- Institute of Immunotherapy, Fujian Medical University, Fuzhou, China.
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.
- Department of Statistics and Information Science, Fu Jen Catholic University, New Taipei City, Taiwan.
| | - Qiuyu Zhang
- Institute of Immunotherapy, Fujian Medical University, Fuzhou, China.
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.
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8
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Wang B, Zhou M, Shi YY, Chen XL, Ren YX, Yang YZ, Tang LY, Ren ZF. Survival is associated with repressive histone trimethylation markers in both HR-positive HER2-negative and triple-negative breast cancer patients. Virchows Arch 2023:10.1007/s00428-023-03534-5. [PMID: 37059917 DOI: 10.1007/s00428-023-03534-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/28/2023] [Accepted: 03/23/2023] [Indexed: 04/16/2023]
Abstract
About 30% of patients with hormone receptor (HR)-positive breast cancers and up to 50% of human epidermal growth factor receptor 2 (HER2)-positive patients develop progression due to treatment resistance, highlighting the need for more differentiated tumor classifications within the breast cancer molecular subtype to optimize the therapies. We aim to examine the roles of histone modification markers. The levels of common repressive histone markers, histone H3 lysine 9 trimethylation (H3K9me3), histone H3 lysine 27 trimethylation (H3K27me3), and histone H4 lysine 20 trimethylation (H4K20me3), in tumors were evaluated by immunohistochemistry for 914 breast cancer patients. The subjects were followed up until December 2021. Hazard ratios (HRs) for overall survival (OS) and progression-free survival (PFS) were estimated using Cox regression models. For H3K27me3, patients with the high level had a longer PFS rate (81.3%) than that with the low level (73.9%) within HR-positive/HER2-negative subtype during a follow-up of 85 months only in univariate analysis (P < 0.05). For H3K9me3, the significant association between the high level of it and the longer OS [HR = 0.57, P < 0.05] was found within HR-positive/HER2-negative subtype in multivariate analysis. For H4K20me3, patients with the high level had a longer both OS [HR = 0.38] and PFS [HR = 0.46] within HR-positive/HER2-negative subtype, while had a shorter OS [HR = 3.28] in triple-negative breast cancer (TNBC) in multivariate analysis (all P < 0.05). H3K9me3 and H3K27me3 were the potential prognostic markers for breast cancer patients with HR-positive/HER2-negative subtype. Importantly, H4K20me3 was a robust prognostic marker for both HR-positive/HER2-negative and TNBC patients.
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Affiliation(s)
- Bo Wang
- School of Public Health, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Meng Zhou
- School of Public Health, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Yue-Yu Shi
- School of Public Health, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Xing-Lei Chen
- School of Public Health, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Yue-Xiang Ren
- The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510630, China
| | - Yuan-Zhong Yang
- The Sun Yat-Sen University Cancer Center, Guangzhou, 510080, China
| | - Lu-Ying Tang
- The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510630, China.
| | - Ze-Fang Ren
- School of Public Health, Sun Yat-Sen University, Guangzhou, 510080, China.
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9
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Feng J, Meng X. Histone modification and histone modification-targeted anti-cancer drugs in breast cancer: Fundamentals and beyond. Front Pharmacol 2022; 13:946811. [PMID: 36188615 PMCID: PMC9522521 DOI: 10.3389/fphar.2022.946811] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/15/2022] [Indexed: 12/21/2022] Open
Abstract
Dysregulated epigenetic enzymes and resultant abnormal epigenetic modifications (EMs) have been suggested to be closely related to tumor occurrence and progression. Histone modifications (HMs) can assist in maintaining genome stability, DNA repair, transcription, and chromatin modulation within breast cancer (BC) cells. In addition, HMs are reversible, dynamic processes involving the associations of different enzymes with molecular compounds. Abnormal HMs (e.g. histone methylation and histone acetylation) have been identified to be tightly related to BC occurrence and development, even though their underlying mechanisms remain largely unclear. EMs are reversible, and as a result, epigenetic enzymes have aroused wide attention as anti-tumor therapeutic targets. At present, treatments to restore aberrant EMs within BC cells have entered preclinical or clinical trials. In addition, no existing studies have comprehensively analyzed aberrant HMs within BC cells; in addition, HM-targeting BC treatments remain to be further investigated. Histone and non-histone protein methylation is becoming an attractive anti-tumor epigenetic therapeutic target; such methylation-related enzyme inhibitors are under development at present. Consequently, the present work focuses on summarizing relevant studies on HMs related to BC and the possible mechanisms associated with abnormal HMs. Additionally, we also aim to analyze existing therapeutic agents together with those drugs approved and tested through pre-clinical and clinical trials, to assess their roles in HMs. Moreover, epi-drugs that target HMT inhibitors and HDAC inhibitors should be tested in preclinical and clinical studies for the treatment of BC. Epi-drugs that target histone methylation (HMT inhibitors) and histone acetylation (HDAC inhibitors) have now entered clinical trials or are approved by the US Food and Drug Administration (FDA). Therefore, the review covers the difficulties in applying HM-targeting treatments in clinics and proposes feasible approaches for overcoming such difficulties and promoting their use in treating BC cases.
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10
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Aspros KGM, Carter JM, Hoskin TL, Suman VJ, Subramaniam M, Emch MJ, Ye Z, Sun Z, Sinnwell JP, Thompson KJ, Tang X, Rodman EPB, Wang X, Nelson AW, Chernukhin I, Hamdan FH, Bruinsma ES, Carroll JS, Fernandez-Zapico ME, Johnsen SA, Kalari KR, Huang H, Leon-Ferre RA, Couch FJ, Ingle JN, Goetz MP, Hawse JR. Estrogen receptor beta repurposes EZH2 to suppress oncogenic NFκB/p65 signaling in triple negative breast cancer. NPJ Breast Cancer 2022; 8:20. [PMID: 35177654 PMCID: PMC8854734 DOI: 10.1038/s41523-022-00387-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 01/21/2022] [Indexed: 12/14/2022] Open
Abstract
Triple Negative Breast Cancer (TNBC) accounts for 15-20% of all breast cancer cases, yet is responsible for a disproportionately high percentage of breast cancer mortalities. Thus, there is an urgent need to identify novel biomarkers and therapeutic targets based on the molecular events driving TNBC pathobiology. Estrogen receptor beta (ERβ) is known to elicit anti-cancer effects in TNBC, however its mechanisms of action remain elusive. Here, we report the expression profiles of ERβ and its association with clinicopathological features and patient outcomes in the largest cohort of TNBC to date. In this cohort, ERβ was expressed in approximately 18% of TNBCs, and expression of ERβ was associated with favorable clinicopathological features, but correlated with different overall survival outcomes according to menopausal status. Mechanistically, ERβ formed a co-repressor complex involving enhancer of zeste homologue 2/polycomb repressive complex 2 (EZH2/PRC2) that functioned to suppress oncogenic NFκB/RELA (p65) activity. Importantly, p65 was shown to be required for formation of this complex and for ERβ-mediated suppression of TNBC. Our findings indicate that ERβ+ tumors exhibit different characteristics compared to ERβ- tumors and demonstrate that ERβ functions as a molecular switch for EZH2, repurposing it for tumor suppressive activities and repression of oncogenic p65 signaling.
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Affiliation(s)
- Kirsten G M Aspros
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jodi M Carter
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Tanya L Hoskin
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55905, USA
| | - Vera J Suman
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55905, USA
| | - Malayannan Subramaniam
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Michael J Emch
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Zhenqing Ye
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55905, USA
| | - Zhifu Sun
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jason P Sinnwell
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55905, USA
| | - Kevin J Thompson
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55905, USA
| | - Xiaojia Tang
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55905, USA
| | - Esther P B Rodman
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Xiyin Wang
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Adam W Nelson
- Cancer Research UK Cambridge Research Institute, University of Cambridge, Cambridge, UK
| | - Igor Chernukhin
- Cancer Research UK Cambridge Research Institute, University of Cambridge, Cambridge, UK
| | - Feda H Hamdan
- Gene Regulatory Mechanisms and Molecular Epigenetics Lab, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Elizabeth S Bruinsma
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jason S Carroll
- Cancer Research UK Cambridge Research Institute, University of Cambridge, Cambridge, UK
| | - Martin E Fernandez-Zapico
- Shulze Center for Novel Therapeutics, Division of Oncology Research, Mayo Clinic, Rochester, MN, 55905, USA
| | - Steven A Johnsen
- Gene Regulatory Mechanisms and Molecular Epigenetics Lab, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Krishna R Kalari
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55905, USA
| | - Haojie Huang
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA
- Department of Urology, Mayo Clinic, Rochester, MN, 55905, USA
| | | | - Fergus J Couch
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55905, USA
| | - James N Ingle
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Matthew P Goetz
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - John R Hawse
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA.
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11
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Borkiewicz L. Histone 3 Lysine 27 Trimethylation Signature in Breast Cancer. Int J Mol Sci 2021; 22:12853. [PMID: 34884658 PMCID: PMC8657745 DOI: 10.3390/ijms222312853] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 11/22/2021] [Accepted: 11/26/2021] [Indexed: 12/12/2022] Open
Abstract
Cancer development and progression rely on complicated genetic and also epigenetic changes which regulate gene expression without altering the DNA sequence. Epigenetic mechanisms such as DNA methylation, histone modifications, and regulation by lncRNAs alter protein expression by either promoting gene transcription or repressing it. The presence of so-called chromatin modification marks at various gene promoters and gene bodies is associated with normal cell development but also with tumorigenesis and progression of different types of cancer, including the most frequently diagnosed breast cancer. This review is focused on the significance of one of the abundant post-translational modifications of histone 3- trimethylation of lysine 27 (H3K27me3), which was shown to participate in tumour suppressor genes' silencing. Unlike other reviews in the field, here the overview of existing evidence linking H3K27me3 status with breast cancer biology and the tumour outcome is presented especially in the context of diverse breast cancer subtypes. Moreover, the potential of agents that target H3K27me3 for the treatment of this complex disease as well as H3K27 methylation in cross-talk with other chromatin modifications and lncRNAs are discussed.
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Affiliation(s)
- Lidia Borkiewicz
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, 20-059 Lublin, Poland
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12
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Markouli M, Strepkos D, Basdra EK, Papavassiliou AG, Piperi C. Prominent Role of Histone Modifications in the Regulation of Tumor Metastasis. Int J Mol Sci 2021; 22:2778. [PMID: 33803458 PMCID: PMC7967218 DOI: 10.3390/ijms22052778] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 03/08/2021] [Indexed: 12/22/2022] Open
Abstract
Tumor aggressiveness and progression is highly dependent on the process of metastasis, regulated by the coordinated interplay of genetic and epigenetic mechanisms. Metastasis involves several steps of epithelial to mesenchymal transition (EMT), anoikis resistance, intra- and extravasation, and new tissue colonization. EMT is considered as the most critical process allowing cancer cells to switch their epithelial characteristics and acquire mesenchymal properties. Emerging evidence demonstrates that epigenetics mechanisms, DNA methylation, histone modifications, and non-coding RNAs participate in the widespread changes of gene expression that characterize the metastatic phenotype. At the chromatin level, active and repressive histone post-translational modifications (PTM) in association with pleiotropic transcription factors regulate pivotal genes involved in the initiation of the EMT process as well as in intravasation and anoikis resistance, playing a central role in the progression of tumors. Herein, we discuss the main epigenetic mechanisms associated with the different steps of metastatic process, focusing in particular on the prominent role of histone modifications and the modifying enzymes that mediate transcriptional regulation of genes associated with tumor progression. We further discuss the development of novel treatment strategies targeting the reversibility of histone modifications and highlight their importance in the future of cancer therapy.
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Affiliation(s)
| | | | | | | | - Christina Piperi
- Correspondence: (A.G.P.); (C.P.); Tel.: +30-210-7462610 (C.P.); Fax: +30-210-7462703 (C.P.)
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13
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Peng Q, Weng K, Li S, Xu R, Wang Y, Wu Y. A Perspective of Epigenetic Regulation in Radiotherapy. Front Cell Dev Biol 2021; 9:624312. [PMID: 33681204 PMCID: PMC7930394 DOI: 10.3389/fcell.2021.624312] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 01/28/2021] [Indexed: 12/17/2022] Open
Abstract
Radiation therapy (RT) has been employed as a tumoricidal modality for more than 100 years and on 470,000 patients each year in the United States. The ionizing radiation causes genetic changes and results in cell death. However, since the biological mechanism of radiation remains unclear, there is a pressing need to understand this mechanism to improve the killing effect on tumors and reduce the side effects on normal cells. DNA break and epigenetic remodeling can be induced by radiotherapy. Hence the modulation of histone modification enzymes may tune the radiosensitivity of cancer cells. For instance, histone deacetylase (HDAC) inhibitors sensitize irradiated cancer cells by amplifying the DNA damage signaling and inhibiting double-strand DNA break repair to influence the irradiated cells’ survival. However, the combination of epigenetic drugs and radiotherapy has only been evaluated in several ongoing clinical trials for limited cancer types, partly due to a lack of knowledge on the potential mechanisms on how radiation induces epigenetic regulation and chromatin remodeling. Here, we review recent advances of radiotherapy and radiotherapy-induced epigenetic remodeling and introduce related technologies for epigenetic monitoring. Particularly, we exploit the application of fluorescence resonance energy transfer (FRET) biosensors to visualize dynamic epigenetic regulations in single living cells and tissue upon radiotherapy and drug treatment. We aim to bridge FRET biosensor, epigenetics, and radiotherapy, providing a perspective of using FRET to assess epigenetics and provide guidance for radiotherapy to improve cancer treatment. In the end, we discuss the feasibility of a combination of epigenetic drugs and radiotherapy as new approaches for cancer therapeutics.
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Affiliation(s)
- Qin Peng
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China.,Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States.,Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Kegui Weng
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States.,Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, United States.,Chongqing Cancer Hospital, Chongqing Cancer Institute, Chongqing University Cancer Hospital, Chongqing, China
| | - Shitian Li
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States.,Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Richard Xu
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States.,Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Yingxiao Wang
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States.,Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Yongzhong Wu
- Chongqing Cancer Hospital, Chongqing Cancer Institute, Chongqing University Cancer Hospital, Chongqing, China
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14
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Sasidharan Nair V, Saleh R, Toor SM, Taha RZ, Ahmed AA, Kurer MA, Murshed K, Abu Nada M, Elkord E. Epigenetic regulation of immune checkpoints and T cell exhaustion markers in tumor-infiltrating T cells of colorectal cancer patients. Epigenomics 2020; 12:1871-1882. [PMID: 33169618 DOI: 10.2217/epi-2020-0267] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Aim: To elucidate the epigenetic alterations behind the upregulation of immune checkpoints and T cell exhaustion markers in colorectal cancer (CRC) patients. Materials & methods: mRNA expressions of different immune checkpoint/exhaustion markers were analyzed by quantitative real-time reverse transcriptase PCR and epigenetic investigations were performed using bisulfite sequencing and chromatin immunoprecipitation quantitative PCR. Results: mRNA expressions of PD-1, TIM-3, CTLA-4, PD-L1 and TOX2 were significantly upregulated in CD4+ and CD8+ tumor-infiltrating lymphocytes and bulk CRC tumor tissues. Histone 3 lysine 9 trimethylation was downregulated and histone 3 lysine 4 trimethylation was upregulated in PD-L1 and TOX2 promoters in tumor tissues, suggesting that PD-L1 and TOX2 upregulation in CRC tumors could be mediated by activating histone 3 lysine 4 trimethylation. Conclusion: Epigenetic modifications in promoters of immune checkpoint and T cell exhaustion genes could induce their upregulation, and potentially implicate the use of epigenetic modifiers to enhance antitumor immunity in CRC patients.
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Affiliation(s)
- Varun Sasidharan Nair
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), P.O.Box: 34110, Doha, Qatar
| | - Reem Saleh
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), P.O.Box: 34110, Doha, Qatar
| | - Salman M Toor
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), P.O.Box: 34110, Doha, Qatar
| | - Rowaida Z Taha
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), P.O.Box: 34110, Doha, Qatar
| | - Ayman A Ahmed
- Department of Surgery, Hamad Medical Corporation, Doha, Qatar
| | - Mohamed A Kurer
- Department of Surgery, Hamad Medical Corporation, Doha, Qatar
| | - Khaled Murshed
- Department of Pathology, Hamad Medical Corporation, Doha, Qatar
| | | | - Eyad Elkord
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), P.O.Box: 34110, Doha, Qatar.,Biomedical Research Center, School of Science, Engineering and Environment, University of Salford, Manchester, United Kingdom
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15
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Zhuang J, Huo Q, Yang F, Xie N. Perspectives on the Role of Histone Modification in Breast Cancer Progression and the Advanced Technological Tools to Study Epigenetic Determinants of Metastasis. Front Genet 2020; 11:603552. [PMID: 33193750 PMCID: PMC7658393 DOI: 10.3389/fgene.2020.603552] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 10/09/2020] [Indexed: 12/11/2022] Open
Abstract
Metastasis is a complex process that involved in various genetic and epigenetic alterations during the progression of breast cancer. Recent evidences have indicated that the mutation in the genome sequence may not be the key factor for increasing metastatic potential. Epigenetic changes were revealed to be important for metastatic phenotypes transition with the development in understanding the epigenetic basis of breast cancer. Herein, we aim to present the potential epigenetic drivers that induce dysregulation of genes related to breast tumor growth and metastasis, with a particular focus on histone modification including histone acetylation and methylation. The pervasive role of major histone modification enzymes in cancer metastasis such as histone acetyltransferases (HAT), histone deacetylases (HDACs), DNA methyltransferases (DNMTs), and so on are demonstrated and further discussed. In addition, we summarize the recent advances of next-generation sequencing technologies and microfluidic-based devices for enhancing the study of epigenomic landscapes of breast cancer. This feature also introduces several important biotechnologists for identifying robust epigenetic biomarkers and enabling the translation of epigenetic analyses to the clinic. In summary, a comprehensive understanding of epigenetic determinants in metastasis will offer new insights of breast cancer progression and can be achieved in the near future with the development of innovative epigenomic mapping tools.
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Affiliation(s)
- Jialang Zhuang
- Biobank, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, China.,Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Qin Huo
- Biobank, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Fan Yang
- Biobank, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Ni Xie
- Biobank, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, China
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16
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Vougiouklakis T, Bernard BJ, Nigam N, Burkitt K, Nakamura Y, Saloura V. Clinicopathologic significance of protein lysine methyltransferases in cancer. Clin Epigenetics 2020; 12:146. [PMID: 33050946 PMCID: PMC7557092 DOI: 10.1186/s13148-020-00897-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 07/01/2020] [Indexed: 12/26/2022] Open
Abstract
Protein lysine methyltransferases (PKMTs) constitute a large family of approximately 50 chromatin modifiers that mono-, di- and/or tri-methylate lysine residues on histone and non-histone substrates. With the advent of The Cancer Genome Atlas, it became apparent that this family of chromatin modifiers harbors frequent genetic and expression alterations in multiple types of cancer. In this regard, past and ongoing preclinical studies have provided insight into the mechanisms of action of some of these enzymes, laying the ground for the ongoing development of PKMT inhibitors as novel anticancer therapeutics. The purpose of this review is to summarize existing data obtained by different research groups through immunohistochemical analysis of the protein expression levels of PKMTs, and their respective clinicopathologic associations. We focused on studies that used immunohistochemistry to associate protein expression levels of specific PKMTs, as well as several established histone methylation marks, with clinicopathologic features and survival outcomes in various cancer types. We also review ongoing clinical trials of PKMT inhibitors in cancer treatment. This review underscores the clinical relevance and potential of targeting the family of PKMT enzymes as the next generation of cancer therapy.
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Affiliation(s)
| | - Benjamin J Bernard
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, 41 Medlars Drive, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Nupur Nigam
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, 41 Medlars Drive, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Kyunghee Burkitt
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, 41 Medlars Drive, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Yusuke Nakamura
- Cancer Precision Medicine Research Center, Japanese Foundation for Cancer Research, Koto, Japan
| | - Vassiliki Saloura
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, 41 Medlars Drive, National Cancer Institute, Bethesda, MD, 20892, USA.
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17
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Expression of H3K4me3 and H3K9ac in breast cancer. J Cancer Res Clin Oncol 2020; 146:2017-2027. [PMID: 32468423 PMCID: PMC7324433 DOI: 10.1007/s00432-020-03265-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 05/14/2020] [Indexed: 12/19/2022]
Abstract
PURPOSE Breast cancer is the leading cause of cancer death in females. Histone modifications have been shown to have an influence on the gene expression. This study focusses on the histone modifications H3K9ac and H3K4me3 in breast cancer and their impact on survival METHODS: H3K4me3 and H3K9ac expression was immunohistochemically examined in 235 tissue samples. RESULTS Positive estrogen receptor status was correlated with a higher IRS of the nuclear (p = 0.033), and of the cytoplasmic H3K4me3 staining (p = 0.009). H3K9ac intensity was associated to the Her2 status (p = 0.045) and to poor prognosis in cells with positive Ki67 status (p = 0.013). A high intensity of nuclear H3K4me3 staining was found to be correlated with a lower 10-year-survival (p = 0.026) and with lower breast cancer-specific survival (p = 0.004). High percentage score (> 190) of H3K9ac expression was correlated to worse breast cancer-specific survival (p = 0.005). Shorter progression-free survival was found in patients with nuclear (p = 0.013) and cytoplasmic H3K4me3expression (p = 0.024) and H3K9ac expression (p = 0.023). CONCLUSION This analysis provides new evidence of histone modifications in breast cancer. High H3K4me3 and H3K9ac expression was correlated with survival rates. Further investigation of histone modifications in breast cancer could lead to a more profound understanding of the molecular mechanisms of cancer development and could result in new therapeutic strategies.
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18
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Nandy D, Rajam SM, Dutta D. A three layered histone epigenetics in breast cancer metastasis. Cell Biosci 2020; 10:52. [PMID: 32257110 PMCID: PMC7106732 DOI: 10.1186/s13578-020-00415-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 03/26/2020] [Indexed: 12/13/2022] Open
Abstract
Thanks to the advancement in science and technology and a significant number of cancer research programs being carried out throughout the world, the prevention, prognosis and treatment of breast cancer are improving with a positive and steady pace. However, a stern thoughtful attention is required for the metastatic breast cancer cases—the deadliest of all types of breast cancer, with a character of relapse even when treated. In an effort to explore the less travelled avenues, we summarize here studies underlying the aspects of histone epigenetics in breast cancer metastasis. Authoritative reviews on breast cancer epigenetics are already available; however, there is an urgent need to focus on the epigenetics involved in metastatic character of this cancer. Here we put forward a comprehensive review on how different layers of histone epigenetics comprising of histone chaperones, histone variants and histone modifications interplay to create breast cancer metastasis landscape. Finally, we propose a hypothesis of integrating histone-epigenetic factors as biomarkers that encompass different breast cancer subtypes and hence could be exploited as a target of larger population.
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Affiliation(s)
- Debparna Nandy
- Regenerative Biology Program, Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Poojappura, Thiruvananthapuram, Kerala 695014 India
| | - Sruthy Manuraj Rajam
- Regenerative Biology Program, Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Poojappura, Thiruvananthapuram, Kerala 695014 India
| | - Debasree Dutta
- Regenerative Biology Program, Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Poojappura, Thiruvananthapuram, Kerala 695014 India
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19
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Fontes-Sousa M, Lobo J, Lobo S, Salta S, Amorim M, Lopes P, Antunes L, de Sousa SP, Henrique R, Jerónimo C. Digital imaging-assisted quantification of H3K27me3 immunoexpression in luminal A/B-like, HER2-negative, invasive breast cancer predicts patient survival and risk of recurrence. Mol Med 2020; 26:22. [PMID: 32050892 PMCID: PMC7017542 DOI: 10.1186/s10020-020-0147-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 02/05/2020] [Indexed: 01/03/2023] Open
Abstract
Background Breast cancer (BC) is a major health concern and better understanding of its biology might improve treatment decisions and patient outcomes. Histone3 Lysine27 tri-methylation (H3K27me3) is a post-translational histone modification frequently associated with altered gene expression. In BC patients, lower H3K27me3 expression has been associated with worse prognosis. We assessed H3K27me3 immunoexpression with digital imaging software assistance, in a cohort of luminal-like BC patients with long-term follow-up time and evaluated its association with clinically relevant endpoints and its clinical usefulness. Methods H3K27me3 immunoexpression was assessed, by means of digital-imaging system, in archival tissue samples of 160 luminal A/B-like HER2-negative invasive BC, stages I-III. Survival analysis was performed using Kaplan-Meier and Cox regression. Cases were categorized as ‘low’ or ‘high’ expression based on cut-off defined by receiver operating characteristic (ROC) curve analysis. Results The patient cohort showed a median age of 61-years, with a median follow-up time of 11.7 years. Low H3K27me3 expression (below 85% cut-off) was significantly associated with recurrence, both in univariable (HR = 1.99, 95%CI 1.066–3.724) and multivariable analysis when adjusting for grade and age (HR = 1.89, 95%CI 1.004–3.559). A trend for higher risk of death in low H3K27me3 expression BC was observed (p = 0.069), reaching statistical significance in younger patients (p = 0.021). Conclusions H3K27me3 immunoexpression assessed by digital imaging scoring software is an independent prognosis biomarker in luminal-like BC patients and may assist in more individualized adjuvant treatment decisions, thus potentially reducing recurrences after curative-intent treatment, while sparing unnecessary toxicity.
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Affiliation(s)
- Mário Fontes-Sousa
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Institute of Oncology of Porto (IPO Porto), Research Center-LAB 3, F Bdg., 1st floor, Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal.,Department of Medical Oncology, Portuguese Institute of Oncology of Porto, Porto, Portugal
| | - João Lobo
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Institute of Oncology of Porto (IPO Porto), Research Center-LAB 3, F Bdg., 1st floor, Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal.,Department of Pathology, Portuguese Institute of Oncology of Porto, Porto, Portugal.,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar - University of Porto (ICBAS-UP), Porto, Portugal
| | - Silvana Lobo
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Institute of Oncology of Porto (IPO Porto), Research Center-LAB 3, F Bdg., 1st floor, Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Sofia Salta
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Institute of Oncology of Porto (IPO Porto), Research Center-LAB 3, F Bdg., 1st floor, Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Maria Amorim
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Institute of Oncology of Porto (IPO Porto), Research Center-LAB 3, F Bdg., 1st floor, Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - Paula Lopes
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Institute of Oncology of Porto (IPO Porto), Research Center-LAB 3, F Bdg., 1st floor, Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal.,Department of Pathology, Portuguese Institute of Oncology of Porto, Porto, Portugal
| | - Luís Antunes
- Department of Epidemiology, Portuguese Institute of Oncology of Porto, Porto, Portugal
| | - Susana Palma de Sousa
- Department of Medical Oncology, Portuguese Institute of Oncology of Porto, Porto, Portugal
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Institute of Oncology of Porto (IPO Porto), Research Center-LAB 3, F Bdg., 1st floor, Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal.,Department of Pathology, Portuguese Institute of Oncology of Porto, Porto, Portugal.,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar - University of Porto (ICBAS-UP), Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Institute of Oncology of Porto (IPO Porto), Research Center-LAB 3, F Bdg., 1st floor, Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal. .,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar - University of Porto (ICBAS-UP), Porto, Portugal.
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20
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Rahman MM, Brane AC, Tollefsbol TO. MicroRNAs and Epigenetics Strategies to Reverse Breast Cancer. Cells 2019; 8:cells8101214. [PMID: 31597272 PMCID: PMC6829616 DOI: 10.3390/cells8101214] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/04/2019] [Accepted: 10/06/2019] [Indexed: 02/07/2023] Open
Abstract
Breast cancer is a sporadic disease with genetic and epigenetic components. Genomic instability in breast cancer leads to mutations, copy number variations, and genetic rearrangements, while epigenetic remodeling involves alteration by DNA methylation, histone modification and microRNAs (miRNAs) of gene expression profiles. The accrued scientific findings strongly suggest epigenetic dysregulation in breast cancer pathogenesis though genomic instability is central to breast cancer hallmarks. Being reversible and plastic, epigenetic processes appear more amenable toward therapeutic intervention than the more unidirectional genetic alterations. In this review, we discuss the epigenetic reprogramming associated with breast cancer such as shuffling of DNA methylation, histone acetylation, histone methylation, and miRNAs expression profiles. As part of this, we illustrate how epigenetic instability orchestrates the attainment of cancer hallmarks which stimulate the neoplastic transformation-tumorigenesis-malignancy cascades. As reversibility of epigenetic controls is a promising feature to optimize for devising novel therapeutic approaches, we also focus on the strategies for restoring the epistate that favor improved disease outcome and therapeutic intervention.
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Affiliation(s)
- Mohammad Mijanur Rahman
- Department of Biology, University of Alabama at Birmingham, 1300 University Boulevard, Birmingham, AL 35294, USA.
| | - Andrew C Brane
- Department of Biology, University of Alabama at Birmingham, 1300 University Boulevard, Birmingham, AL 35294, USA.
| | - Trygve O Tollefsbol
- Department of Biology, University of Alabama at Birmingham, 1300 University Boulevard, Birmingham, AL 35294, USA.
- Comprehensive Center for Healthy Aging, University of Alabama Birmingham, 1530 3rd Avenue South, Birmingham, AL 35294, USA.
- Comprehensive Cancer Center, University of Alabama Birmingham, 1802 6th Avenue South, Birmingham, AL 35294, USA.
- Nutrition Obesity Research Center, University of Alabama Birmingham, 1675 University Boulevard, Birmingham, AL 35294, USA.
- Comprehensive Diabetes Center, University of Alabama Birmingham, 1825 University Boulevard, Birmingham, AL 35294, USA.
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21
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Li Y, Guo D, Sun R, Chen P, Qian Q, Fan H. Methylation Patterns of Lys9 and Lys27 on Histone H3 Correlate with Patient Outcome in Gastric Cancer. Dig Dis Sci 2019; 64:439-446. [PMID: 30350241 DOI: 10.1007/s10620-018-5341-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 10/16/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND Histone methylation has been considered as one of the epigenetic mechanisms of carcinogenesis and progression. Researches on the correlation between histone lysine methylation and gastric cancer (GC) will help in finding novel epigenetic biomarkers for monitoring cancers. AIMS The study detected the expression patterns of histone 3 lysine 9 dimethylation (H3K9me2), histone 3 lysine 9 trimethylation (H3K9me3), and histone 3 lysine 27 trimethylation (H3K27me3) in GC tissues and evaluated their clinical merit for GC patients. METHODS One hundred thirty-three paraffin-embedded GC samples were examined by immunohistochemistry for the histone markers: H3K9me2, H3K9me3, and H3K27me3. The relationship and clinicopathological significance of the three lysine methylations on histone H3 with GC were assessed by Paired t test, Chi-square test, Kaplan-Meier analysis with log-rank test, and Cox proportional hazard analyses. RESULTS Strong positive immunostaining of H3K9me2, H3K9me3, and H3K27me3 was observed in cancerous tissues than in their counterpart non-cancer tissues. Higher expression patterns of H3K9me2, H3K9me3, and H3K27me3 significantly related to differentiation degree, lymph nodes metastases, and pathological TNM staging in GC. The GC patients with low scoring of the three markers implied long survival period and best prognosis. In contrast, the patients' survival time was significantly shorter if their cancerous tissues presented high expression of the three markers. CONCLUSIONS H3K9me2, H3K9me3, and H3K27me3 expression patterns closely relate to clinicopathological features and may be the independent risk factors for the survival of GC patients. The combined pattern of the three markers rather than an individual marker is considered to more accurately evaluate the outcome of GC patients.
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Affiliation(s)
- Yiping Li
- Department of Medical Genetics and Developmental Biology, Medical School, The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, 210009, China.,Department of Pathology, Medical School, Southeast University, Nanjing, 210009, China
| | - Didi Guo
- Institute of Life Science, The Key Laboratory of Developmental Genes and Human Diseases, Southeast University, Nanjing, 210018, China
| | - Rui Sun
- Department of Medical Genetics and Developmental Biology, Medical School, The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, 210009, China
| | - Ping Chen
- Department of Oncology, Yancheng First People's Hospital, Yancheng, 224005, China
| | - Qi Qian
- Department of Oncology, Yancheng First People's Hospital, Yancheng, 224005, China
| | - Hong Fan
- Department of Medical Genetics and Developmental Biology, Medical School, The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, 210009, China.
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22
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Temian DC, Pop LA, Irimie AI, Berindan-Neagoe I. The Epigenetics of Triple-Negative and Basal-Like Breast Cancer: Current Knowledge. J Breast Cancer 2018; 21:233-243. [PMID: 30275851 PMCID: PMC6158152 DOI: 10.4048/jbc.2018.21.e41] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/06/2018] [Indexed: 12/15/2022] Open
Abstract
Breast cancer has the highest incidence among all malignancies diagnosed in women. Therapies have significantly improved over the years due to extensive molecular and clinical research; in a large number of cases, targeted therapies have provided better prognosis. However, one specific subtype remains elusive to targeted therapies–the triple-negative breast cancer. This immunohistochemically defined subtype is resistant to both endocrine and targeted therapies, leading to its poor prognosis. A field that is of great promise in current cancer research is epigenetics. By studying the epigenetic mechanisms underlying tumorigenesis–DNA methylation, histone modifications, and noncoding RNAs–advances in cancer treatment, diagnosis, and prevention are possible. This review aims to synthesize the epigenetic discoveries that have been made related to the triple-negative breast cancer.
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Affiliation(s)
- Daiana Cosmina Temian
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Faculty of Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Laura Ancuta Pop
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Alexandra Iulia Irimie
- Division of Dental Propaedeutics, Aesthetic, Department of Prosthetic Dentistry and Dental Materials, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania.,MedFUTURE Research Center for Advanced Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Department of Functional Genomics and Experimental Pathology, The Oncology Institute "Prof. Dr. I Chiricuta", Cluj-Napoca, Romania
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23
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Anwar T, Arellano-Garcia C, Ropa J, Chen YC, Kim HS, Yoon E, Grigsby S, Basrur V, Nesvizhskii AI, Muntean A, Gonzalez ME, Kidwell KM, Nikolovska-Coleska Z, Kleer CG. p38-mediated phosphorylation at T367 induces EZH2 cytoplasmic localization to promote breast cancer metastasis. Nat Commun 2018; 9:2801. [PMID: 30022044 PMCID: PMC6051995 DOI: 10.1038/s41467-018-05078-8] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Accepted: 05/31/2018] [Indexed: 12/19/2022] Open
Abstract
Overexpression of EZH2 in estrogen receptor negative (ER-) breast cancer promotes metastasis. EZH2 has been mainly studied as the catalytic component of the Polycomb Repressive Complex 2 (PRC2) that mediates gene repression by trimethylating histone H3 at lysine 27 (H3K27me3). However, how EZH2 drives metastasis despite the low H3K27me3 levels observed in ER- breast cancer is unknown. Here we show that in human invasive carcinomas and distant metastases, cytoplasmic EZH2 phosphorylated at T367 is significantly associated with ER- disease and low H3K27me3 levels. p38-mediated EZH2 phosphorylation at T367 promotes EZH2 cytoplasmic localization and potentiates EZH2 binding to vinculin and other cytoskeletal regulators of cell migration and invasion. Ectopic expression of a phospho-deficient T367A-EZH2 mutant is sufficient to inhibit EZH2 cytoplasmic expression, disrupt binding to cytoskeletal regulators, and reduce EZH2-mediated adhesion, migration, invasion, and development of spontaneous metastasis. These results point to a PRC2-independent non-canonical mechanism of EZH2 pro-metastatic function.
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MESH Headings
- Animals
- Breast Neoplasms/genetics
- Breast Neoplasms/mortality
- Breast Neoplasms/pathology
- Breast Neoplasms/therapy
- Carcinoma, Ductal, Breast/genetics
- Carcinoma, Ductal, Breast/mortality
- Carcinoma, Ductal, Breast/secondary
- Carcinoma, Ductal, Breast/therapy
- Cell Line, Tumor
- Cell Movement
- Enhancer of Zeste Homolog 2 Protein/antagonists & inhibitors
- Enhancer of Zeste Homolog 2 Protein/genetics
- Enhancer of Zeste Homolog 2 Protein/metabolism
- Estrogen Receptor alpha/genetics
- Estrogen Receptor alpha/metabolism
- Female
- Gene Expression Regulation, Neoplastic
- Heterografts
- Histones/genetics
- Histones/metabolism
- Humans
- Lung Neoplasms/genetics
- Lung Neoplasms/mortality
- Lung Neoplasms/secondary
- Lung Neoplasms/therapy
- Mice
- Mice, SCID
- Phosphorylation
- Polycomb Repressive Complex 2/genetics
- Polycomb Repressive Complex 2/metabolism
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- Survival Analysis
- Threonine
- p38 Mitogen-Activated Protein Kinases/antagonists & inhibitors
- p38 Mitogen-Activated Protein Kinases/genetics
- p38 Mitogen-Activated Protein Kinases/metabolism
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Affiliation(s)
- Talha Anwar
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Molecular Cellular and Pathology Training Program, University of Michigan, Ann Arbor, MI, 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, 48109, USA
- Medical Scientist Training Program, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Caroline Arellano-Garcia
- Michigan Post-baccalaureate Research Education Program, University of Michigan, Ann Arbor, MI, 48109, USA
| | - James Ropa
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Molecular Cellular and Pathology Training Program, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Yu-Chih Chen
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Hong Sun Kim
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Euisik Yoon
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Sierrah Grigsby
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Molecular Cellular and Pathology Training Program, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Venkatesha Basrur
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Andrew Muntean
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Maria E Gonzalez
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Kelley M Kidwell
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
| | | | - Celina G Kleer
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, 48109, USA.
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24
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Carlini MJ, Recouvreux MS, Simian M, Nagai MA. Gene expression profile and cancer-associated pathways linked to progesterone receptor isoform a (PRA) predominance in transgenic mouse mammary glands. BMC Cancer 2018; 18:682. [PMID: 29940887 PMCID: PMC6019805 DOI: 10.1186/s12885-018-4550-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 05/24/2018] [Indexed: 12/18/2022] Open
Abstract
Background Progesterone receptor (PR) is expressed from a single gene as two isoforms, PRA and PRB. In normal breast human tissue, PRA and PRB are expressed in equimolar ratios, but isoform ratio is altered during malignant progression, usually leading to high PRA:PRB ratios. We took advantage of a transgenic mouse model where PRA isoform is predominant (PRA transgenics) and identified the key transcriptional events and associated pathways underlying the preneoplastic phenotype in mammary glands of PRA transgenics as compared with normal wild-type littermates. Methods The transcriptomic profiles of PRA transgenics and wild-type mammary glands were generated using microarray technology. We identified differentially expressed genes and analyzed clustering, gene ontology (GO), gene set enrichment analysis (GSEA), and pathway profiles. We also performed comparisons with publicly available gene expression data sets of human breast cancer. Results We identified a large number of differentially expressed genes which were mainly associated with metabolic pathways for the PRA transgenics phenotype while inflammation- related pathways were negatively correlated. Further, we determined a significant overlap of the pathways characterizing PRA transgenics and those in breast cancer subtypes Luminal A and Luminal B and identified novel putative biomarkers, such as PDHB and LAMB3. Conclusion The transcriptional targets identified in this study should facilitate the formulation or refinement of useful molecular descriptors for diagnosis, prognosis, and therapy of breast cancer. Electronic supplementary material The online version of this article (10.1186/s12885-018-4550-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- María José Carlini
- Discipline of Oncology, Department of Radiology and Oncology, Faculty of Medicine, University of São Paulo, São Paulo, SP, 01246-903, Brazil.,Laboratory of Molecular Genetics, Center for Translational Research in Oncology, Cancer Institute of São Paulo, São Paulo, SP, 01246-000, Brazil.,Present address: Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, New York, NY, 10029, USA
| | - María Sol Recouvreux
- Instituto de Oncología "Ángel H. Roffo", Av. San Martín 5481, C1417DTB, Ciudad Autónoma de Buenos Aires, Argentina
| | - Marina Simian
- Instituto de Oncología "Ángel H. Roffo", Av. San Martín 5481, C1417DTB, Ciudad Autónoma de Buenos Aires, Argentina.,Present address: Instituto de Nanosistemas, Universidad Nacional de San Martín, Av. 25 de Mayo 1021, 1650, San Martín, Provincia de Buenos Aires, Argentina
| | - Maria Aparecida Nagai
- Discipline of Oncology, Department of Radiology and Oncology, Faculty of Medicine, University of São Paulo, São Paulo, SP, 01246-903, Brazil. .,Laboratory of Molecular Genetics, Center for Translational Research in Oncology, Cancer Institute of São Paulo, São Paulo, SP, 01246-000, Brazil.
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25
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Sasidharan Nair V, El Salhat H, Taha RZ, John A, Ali BR, Elkord E. DNA methylation and repressive H3K9 and H3K27 trimethylation in the promoter regions of PD-1, CTLA-4, TIM-3, LAG-3, TIGIT, and PD-L1 genes in human primary breast cancer. Clin Epigenetics 2018; 10:78. [PMID: 29983831 PMCID: PMC6003083 DOI: 10.1186/s13148-018-0512-1] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 06/04/2018] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND High expression of immune checkpoints in tumor microenvironment plays significant roles in inhibiting anti-tumor immunity, which is associated with poor prognosis and cancer progression. Major epigenetic modifications in both DNA and histone could be involved in upregulation of immune checkpoints in cancer. METHODS Expressions of different immune checkpoint genes and PD-L1 were assessed using qRT-PCR, and the underlying epigenetic modifications including CpG methylation and repressive histone abundance were determined using bisulfite sequencing, and histone 3 lysine 9 trimethylation (H3K9me3) and histone 3 lysine 27 trimethylation (H3K27me3) chromatin immunoprecipitation assays (ChIP), respectively. RESULTS We first assessed the expression level of six immune checkpoints/ligands and found that PD-1, CTLA-4, TIM-3, and LAG-3 were significantly upregulated in breast tumor tissues (TT), compared with breast normal tissues (NT). We investigated the epigenetic modifications beyond this upregulation in immune checkpoint genes. Interestingly, we found that CpG islands in the promoter regions of PD-1, CTLA-4, and TIM-3 were significantly hypomethylated in tumor compared with normal tissues. Additionally, CpG islands of PD-L1 promoter were completely demethylated (100%), LAG-3 were highly hypomethylated (80-90%), and TIGIT were poorly hypomethylated (20-30%), in both NT and TT. These demethylation findings are in accordance with the relative expression data that, out of all these genes, PD-L1 was highly expressed and completely demethylated and TIGIT was poorly expressed and hypermethylated in both NT and TT. Moreover, bindings of H3K9me3 and H3K27me3 were found to be reduced in the promoter loci of PD-1, CTLA-4, TIM-3, and LAG-3 in tumor tissues. CONCLUSION Our data demonstrate that both DNA and histone modifications are involved in upregulation of PD-1, CTLA-4, TIM-3, and LAG-3 in breast tumor tissue and these epigenetic modifications could be useful as diagnostic/prognostic biomarkers and/or therapeutic targets in breast cancer.
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Affiliation(s)
- Varun Sasidharan Nair
- Cancer Research Center, Qatar Biomedical Research Institute, College of Science and Engineering, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Haytham El Salhat
- Oncology Department, Al Noor Hospital, Abu Dhabi, United Arab Emirates
- Oncology Department, Tawam Hospital, Al Ain, United Arab Emirates
| | - Rowaida Z. Taha
- Cancer Research Center, Qatar Biomedical Research Institute, College of Science and Engineering, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Anne John
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Bassam R. Ali
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
- Zayed Center for Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Eyad Elkord
- Cancer Research Center, Qatar Biomedical Research Institute, College of Science and Engineering, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
- Institute of Cancer Sciences, University of Manchester, Manchester, UK
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26
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Abstract
Defects in chromatin modifiers and remodelers have been described both for hematological and solid malignancies, corroborating and strengthening the role of epigenetic aberrations in the etiology of cancer. Furthermore, epigenetic marks-DNA methylation, histone modifications, chromatin remodeling, and microRNA-can be considered potential markers of cancer development and progression. Here, we review whether altered epigenetic landscapes are merely a consequence of chromatin modifier/remodeler aberrations or a hallmark of cancer etiology. We critically evaluate current knowledge on causal epigenetic aberrations and examine to what extent the prioritization of (epi)genetic deregulations can be assessed in cancer as some type of genetic lesion characterizing solid cancer progression. We also discuss the multiple challenges in developing compounds targeting epigenetic enzymes (named epidrugs) for epigenetic-based therapies. The implementation of acquired knowledge of epigenetic biomarkers for patient stratification, together with the development of next-generation epidrugs and predictive models, will take our understanding and use of cancer epigenetics in diagnosis, prognosis, and treatment of cancer patients to a new level.
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Affiliation(s)
- Angela Nebbioso
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania "L. Vanvitelli," Napoli, Italy
| | - Francesco Paolo Tambaro
- Struttura Semplice Dipartimentale Trapianto di Midollo Osseo-Azienda Ospedialiera di Rilievo Nazionale, Santobono-Pausilipon, Napoli, Italy
| | - Carmela Dell'Aversana
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania "L. Vanvitelli," Napoli, Italy
| | - Lucia Altucci
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania "L. Vanvitelli," Napoli, Italy
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27
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Yan N, Xu L, Wu X, Zhang L, Fei X, Cao Y, Zhang F. GSKJ4, an H3K27me3 demethylase inhibitor, effectively suppresses the breast cancer stem cells. Exp Cell Res 2017; 359:405-414. [PMID: 28823831 DOI: 10.1016/j.yexcr.2017.08.024] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 08/14/2017] [Accepted: 08/16/2017] [Indexed: 12/13/2022]
Abstract
Recently, studies have been suggested that H3K27me3 is implicated with maintenance of cancer stem cells (CSCs), however, the roles of H3K27me3 in Breast cancer stem cells (BCSCs) remain poorly investigated. Here we explore the functionallities of H3K27me3 on BCSCs, we identify H3K27me3 as a negative modulator of BCSCs and suggest GSKJ4 is a promising drug targeting BCSCs. We show that the H3K27me3 level is decreased in mammosphere-derived BCSCs. In breast cancer cells, we demonstrate that GSKJ4 could markedly inhibit the proliferation. Strikingly, we show that GSKJ4 could effectively suppress BCSCs including expansion, self-renewal capacity, and the expression of stemness-related markers. Additionally, our xenograft model confirms that GSKJ4 is able to effectively inhibit the tumorigenicity of MDA-MB-231. Mechanistically, the inhibition effects of GSKJ4 on BCSCs are via inhibiting demethylases JMJD3 and UTX with methyltransferase EZH2 unchanged, which enhances H3K27me3 level. H3K27me3 activating leads to reduction of BCSCs expansion, self-renewal and global level of stemness factors. Collectively, our results provide strong supports that H3K27me3 exerts a suppressive influence on BCSCs and reveal that GSKJ4 is capable to be a prospective agent targeting BCSCs.
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Affiliation(s)
- Ningning Yan
- Department of Oncology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China; Department of Oncology, Suzhou Kowloon Hospital, Shanghai Jiaotong University School of Medicine, Suzhou 215021, China
| | - Liang Xu
- Department of Oncology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China; Prevention and Cure Center of Breast Disease, Third Hospital of Nanchang, Nanchang 33009, China
| | - Xiaobo Wu
- Prevention and Cure Center of Breast Disease, Third Hospital of Nanchang, Nanchang 33009, China
| | - Le Zhang
- Department of Oncology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China; Department of Oncology, Suzhou Kowloon Hospital, Shanghai Jiaotong University School of Medicine, Suzhou 215021, China
| | - Xiaochun Fei
- Department of Pathology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Yali Cao
- Prevention and Cure Center of Breast Disease, Third Hospital of Nanchang, Nanchang 33009, China.
| | - Fengchun Zhang
- Department of Oncology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China; Department of Oncology, Suzhou Kowloon Hospital, Shanghai Jiaotong University School of Medicine, Suzhou 215021, China.
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28
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Healey MA, Hirko KA, Beck AH, Collins LC, Schnitt SJ, Eliassen AH, Holmes MD, Tamimi RM, Hazra A. Assessment of Ki67 expression for breast cancer subtype classification and prognosis in the Nurses' Health Study. Breast Cancer Res Treat 2017; 166:613-622. [PMID: 28791482 DOI: 10.1007/s10549-017-4421-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 07/24/2017] [Indexed: 12/14/2022]
Abstract
PURPOSE Ki67 is a proliferation marker commonly assessed by immunohistochemistry in breast cancer, and it has been proposed as a clinical marker for subtype classification, prognosis, and prediction of therapeutic response. However, the clinical utility of Ki67 is limited by the lack of consensus on the optimal cut point for each application. METHODS We assessed Ki67 by immunohistochemistry using Definiens digital image analysis (DIA) in 2653 cases of incident invasive breast cancer diagnosed in the Nurses' Health Study from 1976 to 2006. Ki67 was scored as continuous percentage of positive tumor cells, and dichotomized at various cut points. Multivariable hazard ratios (HR) and 95% confidence intervals (CI) were calculated using Cox regression models for distant recurrence, breast cancer-specific mortality and overall mortality in relation to luminal subtypes defined with various Ki67 cut points, adjusting for breast cancer prognostic factors, clinico-pathologic features and treatment. RESULTS DIA was highly correlated with manual scoring of Ki67 (Spearman correlation ρ = 0.86). Mean Ki67 score was higher in grade-defined luminal B (12.6%), HER2-enriched (17.9%) and basal-like (20.6%) subtypes compared to luminal A (8.9%). In multivariable-adjusted models, luminal B tumors had higher breast cancer-specific mortality compared to luminal A cancer classified using various cut points for Ki67 positivity including the 14% cut point routinely reported in the literature (HR 1.38, 95% CI 1.11-1.72, p = 0.004). There was no significant difference in clinical outcomes for ER- tumors according to Ki67 positivity defined at various cut points. CONCLUSIONS Assessment of Ki67 in breast tumors by DIA was a robust and quantitative method. Results from this large prospective cohort study provide support for the clinical relevance of using Ki67 at the 14% cut point for luminal subtype classification and breast cancer prognosis.
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Affiliation(s)
- Megan A Healey
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
| | - Kelly A Hirko
- Department of Epidemiology and Biostatistics, College of Human Medicine, Traverse City Campus, Michigan State University, East Lansing, MI, USA
| | | | - Laura C Collins
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Stuart J Schnitt
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - A Heather Eliassen
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Michelle D Holmes
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Rulla M Tamimi
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Aditi Hazra
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA.
- Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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29
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Karsli-Ceppioglu S, Dagdemir A, Judes G, Lebert A, Penault-Llorca F, Bignon YJ, Bernard-Gallon D. The Epigenetic Landscape of Promoter Genome-wide Analysis in Breast Cancer. Sci Rep 2017; 7:6597. [PMID: 28747748 PMCID: PMC5529370 DOI: 10.1038/s41598-017-06790-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 06/19/2017] [Indexed: 12/31/2022] Open
Abstract
Breast cancer is a heterogeneous disease due to its clinico-pathological features and response to therapy. The classification of breast tumors based on their hormone receptor status and pathologic features. Post-translational histone modifications come into prominence for regulation of gene expression in cancer pathogenesis. Here, we analyzed dysregulation of H3K9ac and H3K27me3-enriched subtype-specific genes using ChIP-on-chip assay in breast cancer tumors and matched normal tissue samples. Breast cancer tumors were classified according to St Gallen Consensus 2013. Our results indicated that the promoter regions of genes modified by H3K9ac epi-mark are commonly associated with tumors with HER2-positive and TNBC subtype. H3K27me3-enriched genes were comprised of Luminal A and B1 subtypes. We constructed a network structure to elicit epigenetically regulated genes related with breast cancer progression. The central genes of the network (RUNX1, PAX3, GATA4 and DLX5) were subjected for epigenetically dysregulation in association with different breast cancer subtypes. Our study submits epigenetic mechanisms are crucial to elicit subtype-specific regulation in breast cancer and ChIP-on-chip assay provides a better understanding for breast tumorigenesis and new approaches for prevention and treatment.
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Affiliation(s)
- Seher Karsli-Ceppioglu
- Department of Oncogenetics, Centre Jean Perrin, CBRV, 28 place Henri-Dunant, 63001, Clermont-Ferrand, France.,INSERM U 1240, IMOST, 58 rue Montalembert-BP184, 63005, Clermont-Ferrand, France.,Department of Toxicology, Faculty of Pharmacy, Marmara University, Istanbul, Turkey
| | - Aslihan Dagdemir
- Department of Oncogenetics, Centre Jean Perrin, CBRV, 28 place Henri-Dunant, 63001, Clermont-Ferrand, France.,INSERM U 1240, IMOST, 58 rue Montalembert-BP184, 63005, Clermont-Ferrand, France
| | - Gaëlle Judes
- Department of Oncogenetics, Centre Jean Perrin, CBRV, 28 place Henri-Dunant, 63001, Clermont-Ferrand, France.,INSERM U 1240, IMOST, 58 rue Montalembert-BP184, 63005, Clermont-Ferrand, France
| | - André Lebert
- University Blaise Pascal, Institute Pascal UMR 6602 CNRS/UBP, 63178, Aubiere, France
| | - Frédérique Penault-Llorca
- INSERM U 1240, IMOST, 58 rue Montalembert-BP184, 63005, Clermont-Ferrand, France.,Department of Biopathology, Centre Jean Perrin, 58 rue Montalembert, 63011, Clermont-Ferrand, France
| | - Yves-Jean Bignon
- Department of Oncogenetics, Centre Jean Perrin, CBRV, 28 place Henri-Dunant, 63001, Clermont-Ferrand, France.,INSERM U 1240, IMOST, 58 rue Montalembert-BP184, 63005, Clermont-Ferrand, France
| | - Dominique Bernard-Gallon
- Department of Oncogenetics, Centre Jean Perrin, CBRV, 28 place Henri-Dunant, 63001, Clermont-Ferrand, France. .,INSERM U 1240, IMOST, 58 rue Montalembert-BP184, 63005, Clermont-Ferrand, France.
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30
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Noberini R, Longuespée R, Richichi C, Pruneri G, Kriegsmann M, Pelicci G, Bonaldi T. PAT-H-MS coupled with laser microdissection to study histone post-translational modifications in selected cell populations from pathology samples. Clin Epigenetics 2017; 9:69. [PMID: 28702092 PMCID: PMC5504751 DOI: 10.1186/s13148-017-0369-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 06/28/2017] [Indexed: 12/22/2022] Open
Abstract
Background Aberrations in histone post-translational modifications (hPTMs) have been linked with various pathologies, including cancer, and could not only represent useful biomarkers but also suggest possible targetable epigenetic mechanisms. We have recently developed an approach, termed pathology tissue analysis of histones by mass spectrometry (PAT-H-MS), that allows performing a comprehensive and quantitative analysis of histone PTMs from formalin-fixed paraffin-embedded pathology samples. Despite its great potential, the application of this technique is limited by tissue heterogeneity. Methods In this study, we further implemented the PAT-H-MS approach by coupling it with techniques aimed at reducing sample heterogeneity and selecting specific portions or cell populations within the samples, such as manual macrodissection and laser microdissection (LMD). Results When applied to the analysis of a small set of breast cancer samples, LMD-PAT-H-MS allowed detecting more marked changes between luminal A-like and triple negative patients as compared with the classical approach. These changes included not only the already known H3 K27me3 and K9me3 marks, but also H3 K36me1, which was found increased in triple negative samples and validated on a larger cohort of patients, and could represent a potential novel marker distinguishing breast cancer subtypes. Conclusions These results show the feasibility of applying techniques to reduce sample heterogeneity, including laser microdissection, to the PAT-H-MS protocol, providing new tools in clinical epigenetics and opening new avenues for the comprehensive analysis of histone post-translational modifications in selected cell populations. Electronic supplementary material The online version of this article (doi:10.1186/s13148-017-0369-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Roberta Noberini
- Center for Genomic Science of IIT@ SEMM, Istituto Italiano di Tecnologia, Via Adamello 16, 20139 Milan, Italy
| | - Rémi Longuespée
- Institute of Pathology, University of Heidelberg, Im Neuenheimer Feld 224, 69620 Heidelberg, Germany
| | - Cristina Richichi
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Giancarlo Pruneri
- Biobank for Translational Medicine Unit, Department of Pathology, European Institute of Oncology, Via Ripamonti 435, 20141 Milan, Italy.,School of Medicine, University of Milan, 20122 Milan, Italy
| | - Mark Kriegsmann
- Institute of Pathology, University of Heidelberg, Im Neuenheimer Feld 224, 69620 Heidelberg, Germany
| | - Giuliana Pelicci
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy.,Department of Translational Medicine, Piemonte Orientale University "Amedeo Avogadro", 28100 Novara, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
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Wassef M, Margueron R. The Multiple Facets of PRC2 Alterations in Cancers. J Mol Biol 2016; 429:1978-1993. [PMID: 27742591 DOI: 10.1016/j.jmb.2016.10.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 10/04/2016] [Accepted: 10/05/2016] [Indexed: 12/12/2022]
Abstract
Genome sequencing of large cohorts of tumors has revealed that mutations in genes encoding chromatin regulators are frequent in cancer. However, the precise contribution of these mutations to tumor development often remains elusive. Here, we review the current knowledge concerning the alterations of the Polycomb machinery in cancer, with a particular focus on the Polycomb repressive complex 2 (PRC2), a key chromatin modifier involved in the maintenance of transcriptional silencing. A broad variety of alterations can impair PRC2 activity; yet, overall, only one type of alteration is found in a given class of tumor. We discuss the potential impact of the various types of PRC2 alterations on gene expression. We propose that the distinct set of genes regulated by PRC2, depending on tumor etiology, constrain the type of alteration of PRC2 that can fuel tumor development. Beyond this specificity, we propose that PRC2 and, more generally, chromatin regulators act as gatekeepers of transcriptional integrity, a role that often confers a tumor-suppressive function.
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Affiliation(s)
- M Wassef
- Institut Curie, PSL Research University, - 26, rue d'Ulm, 75005 Paris, France; INSERM U934, CNRS UMR3215, Paris, France, 75005
| | - R Margueron
- Institut Curie, PSL Research University, - 26, rue d'Ulm, 75005 Paris, France; INSERM U934, CNRS UMR3215, Paris, France, 75005.
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Girotra S, Yeghiazaryan K, Golubnitschaja O. Potential biomarker panels in overall breast cancer management: advancements by multilevel diagnostics. Per Med 2016; 13:469-484. [PMID: 29767597 DOI: 10.2217/pme-2016-0020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Breast cancer (BC) prevalence has reached an epidemic scale with half a million deaths annually. Current deficits in BC management include predictive and preventive approaches, optimized screening programs, individualized patient profiling, highly sensitive detection technologies for more precise diagnostics and therapy monitoring, individualized prediction and effective treatment of BC metastatic disease. To advance BC management, paradigm shift from delayed to predictive, preventive and personalized medical services is essential. Corresponding step forwards requires innovative multilevel diagnostics procuring specific panels of validated biomarkers. Here, we discuss current instrumental advancements including genomics, proteomics, epigenetics, miRNA, metabolomics, circulating tumor cells and cancer stem cells with a focus on biomarker discovery and multilevel diagnostic panels. A list of the recommended biomarker candidates is provided.
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Townsend MK, Aschard H, De Vivo I, Michels KB, Kraft P. Genomics, Telomere Length, Epigenetics, and Metabolomics in the Nurses' Health Studies. Am J Public Health 2016; 106:1663-8. [PMID: 27459442 DOI: 10.2105/ajph.2016.303344] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
OBJECTIVES To review the contribution of the Nurses' Health Study (NHS) and NHS II to genomics, epigenetics, and metabolomics research. METHODS We performed a narrative review of the publications of the NHS and NHS II between 1990 and 2016 based on biospecimens, including blood and tumor tissue, collected from participants. RESULTS The NHS has contributed to the discovery of genetic loci influencing more than 45 complex human phenotypes, including cancers, diabetes, cardiovascular disease, reproductive characteristics, and anthropometric traits. The combination of genomewide genotype data with extensive exposure and lifestyle data has enabled the evaluation of gene-environment interactions. Furthermore, data suggest that longer telomere length increases risk of cancers not related to smoking, and that modifiable factors (e.g., diet) may have an impact on telomere length. "Omics" research in the NHS continues to expand, with epigenetics and metabolomics becoming greater areas of focus. CONCLUSIONS The combination of prospective biomarker data and broad exposure information has enabled the NHS to participate in a variety of "omics" research, contributing to understanding of the epidemiology and biology of multiple complex diseases.
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Affiliation(s)
- Mary K Townsend
- Mary K. Townsend is with the Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA. Hugues Aschard and Peter Kraft are with the Department of Epidemiology at the Harvard T. H. Chan School of Public Health, Boston. Immaculata De Vivo is with the Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School and the Department of Epidemiology at the Harvard T. H. Chan School of Public Health. Karin B. Michels is with the Channing Division of Network Medicine in the Department of Medicine and the Obstetrics and Gynecology Epidemiology Center in the Department of Obstetrics, Gynecology, and Reproductive Biology at Brigham and Women's Hospital and Harvard Medical School, and the Department of Epidemiology at the Harvard T. H. Chan School of Public Health
| | - Hugues Aschard
- Mary K. Townsend is with the Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA. Hugues Aschard and Peter Kraft are with the Department of Epidemiology at the Harvard T. H. Chan School of Public Health, Boston. Immaculata De Vivo is with the Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School and the Department of Epidemiology at the Harvard T. H. Chan School of Public Health. Karin B. Michels is with the Channing Division of Network Medicine in the Department of Medicine and the Obstetrics and Gynecology Epidemiology Center in the Department of Obstetrics, Gynecology, and Reproductive Biology at Brigham and Women's Hospital and Harvard Medical School, and the Department of Epidemiology at the Harvard T. H. Chan School of Public Health
| | - Immaculata De Vivo
- Mary K. Townsend is with the Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA. Hugues Aschard and Peter Kraft are with the Department of Epidemiology at the Harvard T. H. Chan School of Public Health, Boston. Immaculata De Vivo is with the Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School and the Department of Epidemiology at the Harvard T. H. Chan School of Public Health. Karin B. Michels is with the Channing Division of Network Medicine in the Department of Medicine and the Obstetrics and Gynecology Epidemiology Center in the Department of Obstetrics, Gynecology, and Reproductive Biology at Brigham and Women's Hospital and Harvard Medical School, and the Department of Epidemiology at the Harvard T. H. Chan School of Public Health
| | - Karin B Michels
- Mary K. Townsend is with the Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA. Hugues Aschard and Peter Kraft are with the Department of Epidemiology at the Harvard T. H. Chan School of Public Health, Boston. Immaculata De Vivo is with the Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School and the Department of Epidemiology at the Harvard T. H. Chan School of Public Health. Karin B. Michels is with the Channing Division of Network Medicine in the Department of Medicine and the Obstetrics and Gynecology Epidemiology Center in the Department of Obstetrics, Gynecology, and Reproductive Biology at Brigham and Women's Hospital and Harvard Medical School, and the Department of Epidemiology at the Harvard T. H. Chan School of Public Health
| | - Peter Kraft
- Mary K. Townsend is with the Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA. Hugues Aschard and Peter Kraft are with the Department of Epidemiology at the Harvard T. H. Chan School of Public Health, Boston. Immaculata De Vivo is with the Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School and the Department of Epidemiology at the Harvard T. H. Chan School of Public Health. Karin B. Michels is with the Channing Division of Network Medicine in the Department of Medicine and the Obstetrics and Gynecology Epidemiology Center in the Department of Obstetrics, Gynecology, and Reproductive Biology at Brigham and Women's Hospital and Harvard Medical School, and the Department of Epidemiology at the Harvard T. H. Chan School of Public Health
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miR-125b-1 is repressed by histone modifications in breast cancer cell lines. SPRINGERPLUS 2016; 5:959. [PMID: 27386402 PMCID: PMC4930440 DOI: 10.1186/s40064-016-2475-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 05/30/2016] [Indexed: 12/17/2022]
Abstract
Purpose Downregulation of miR-125b-1 is associated with poor prognosis in breast cancer patients. In this work we investigated the effect of histone modifications on the regulation of this gene promoter. Methods and results We evaluated the enrichment of two histone modifications involved in gene repression, H3K9me3 and H3K27me3, on the miR-125b-1 promoter in two breast cancer cell lines, MCF7 (luminal A subtype) and MDA-MB-231 (triple-negative subtype), compared to the non-transformed breast cell line MCF10A. H3K27me3 and H3K9me3 were enriched in MCF7 and MDA-MB-231 cells, respectively. Next, we used an EZH2 inhibitor to examine the reactivation of miR-125b-1 in MCF7 cells and evaluated the transcriptional levels of pri-miR-125b-1 and mature miR-125b by qRT-PCR. pri-miRNA and mature miRNA transcripts were both increased after treatment of MCF7 cells with the EZH2 inhibitor, whereas no effect on miR-125b-1 expression levels was observed in MDA-MB-231 and MCF10A cells. We subsequently evaluated the effect of miR-125b-1 reactivation on the expression and protein levels of BAK1, a target of miR-125b. We observed 60 and 70 % decreases in the expression and protein levels of BAK1, respectively, compared to cells that were not treated with the EZH2 inhibitor. We over-expressed KDM4B/JMJD2B to reactivate this miRNA, resulting in a three-fold increase in miR-125b expression compared with the same cell line without KDM4B/JMJD2B over-expression. Conclusion The miR-125b-1 is repressed by different epigenetic mechanisms depending on the breast cancer subtype and that miR-125b-1 reactivation specifically eliminates the effect of repressive histone modifications on the expression of an pro-apoptotic target. Electronic supplementary material The online version of this article (doi:10.1186/s40064-016-2475-z) contains supplementary material, which is available to authorized users.
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Judes G, Dagdemir A, Karsli-Ceppioglu S, Lebert A, Echegut M, Ngollo M, Bignon YJ, Penault-Llorca F, Bernard-Gallon D. H3K4 acetylation, H3K9 acetylation and H3K27 methylation in breast tumor molecular subtypes. Epigenomics 2016; 8:909-24. [DOI: 10.2217/epi-2016-0015] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Aim: Here, we investigated how the St Gallen breast molecular subtypes displayed distinct histone H3 profiles. Patients & methods: 192 breast tumors divided into five St Gallen molecular subtypes (luminal A, luminal B HER2-, luminal B HER2+, HER2+ and basal-like) were evaluated for their histone H3 modifications on gene promoters. Results: ANOVA analysis allowed to identify specific H3 signatures according to three groups of genes: hormonal receptor genes (ERS1, ERS2, PGR), genes modifying histones (EZH2, P300, SRC3) and tumor suppressor gene (BRCA1). A similar profile inside high-risk cancers (luminal B [HER2+], HER2+ and basal-like) compared with low-risk cancers including luminal A and luminal B (HER2-) were demonstrated. Conclusion: The H3 modifications might contribute to clarify the differences between breast cancer subtypes.
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Affiliation(s)
- Gaëlle Judes
- Department of Oncogenetics, Centre Jean Perrin, CBRV, 28 Place Henri Dunant, 63001 Clermont-Ferrand, France
- EA 4677 ‘ERTICA’, University of Auvergne, 63011 Clermont-Ferrand, France
| | - Aslihan Dagdemir
- Department of Oncogenetics, Centre Jean Perrin, CBRV, 28 Place Henri Dunant, 63001 Clermont-Ferrand, France
- EA 4677 ‘ERTICA’, University of Auvergne, 63011 Clermont-Ferrand, France
| | - Seher Karsli-Ceppioglu
- Department of Oncogenetics, Centre Jean Perrin, CBRV, 28 Place Henri Dunant, 63001 Clermont-Ferrand, France
- EA 4677 ‘ERTICA’, University of Auvergne, 63011 Clermont-Ferrand, France
- Department of Toxicology, Faculty of Pharmacy, Marmara University, 34668 Istanbul, Turkey
| | - André Lebert
- University Blaise Pascal, Pascal Institute UMR 6602 CNRS/UBP, 63177 Aubière, France
| | - Maureen Echegut
- Department of Toxicology, Faculty of Pharmacy, Marmara University, 34668 Istanbul, Turkey
| | - Marjolaine Ngollo
- EA 4677 ‘ERTICA’, University of Auvergne, 63011 Clermont-Ferrand, France
- Department of Toxicology, Faculty of Pharmacy, Marmara University, 34668 Istanbul, Turkey
| | - Yves-Jean Bignon
- EA 4677 ‘ERTICA’, University of Auvergne, 63011 Clermont-Ferrand, France
- Department of Toxicology, Faculty of Pharmacy, Marmara University, 34668 Istanbul, Turkey
| | - Frédérique Penault-Llorca
- EA 4677 ‘ERTICA’, University of Auvergne, 63011 Clermont-Ferrand, France
- Department of Biopathology, Centre Jean Perrin, 63011 Clermont-Ferrand, France
| | - Dominique Bernard-Gallon
- Department of Oncogenetics, Centre Jean Perrin, CBRV, 28 Place Henri Dunant, 63001 Clermont-Ferrand, France
- EA 4677 ‘ERTICA’, University of Auvergne, 63011 Clermont-Ferrand, France
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HIFI-α activation underlies a functional switch in the paradoxical role of Ezh2/PRC2 in breast cancer. Proc Natl Acad Sci U S A 2016; 113:E3735-44. [PMID: 27303043 DOI: 10.1073/pnas.1602079113] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Despite the established oncogenic function of Polycomb repressive complex 2 (PRC2) in human cancers, its role as a tumor suppressor is also evident; however, the mechanism underlying the regulation of the paradoxical functions of PRC2 in tumorigenesis is poorly understood. Here we show that hypoxia-inducible factor 1, α-subunit (HIFI-α) is a crucial modulator of PRC2 and enhancer of zeste 2 (EZH2) function in breast cancer. Interrogating the genomic expression of breast cancer indicates high HIF1A activity correlated with high EZH2 expression but low PRC2 activity in triple-negative breast cancer compared with other cancer subtypes. In the absence of HIFIA activation, PRC2 represses the expression of matrix metalloproteinase genes (MMPs) and invasion, whereas a discrete Ezh2 complexed with Forkhead box M1 (FoxM1) acts to promote the expression of MMPs. HIF1-α induction upon hypoxia results in PRC2 inactivation by selective suppression of the expression of suppressor of zeste 12 protein homolog (SUZ12) and embryonic ectoderm development (EED), leading to a functional switch toward Ezh2/FoxM1-dependent induction of the expression of MMPs and invasion. Our study suggests a tumor-suppressive function of PRC2, which is restricted by HIF1-α, and an oncogenic function of Ezh2, which cooperates with FoxM1 to promote invasion in triple-negative breast cancer.
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Bonaldi T, Noberini R. Recent advances in mass spectrometry analysis of histone post-translational modifications: potential clinical impact of the PAT-H-MS approach. Expert Rev Proteomics 2016; 13:245-50. [DOI: 10.1586/14789450.2016.1147960] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Wassef M, Rodilla V, Teissandier A, Zeitouni B, Gruel N, Sadacca B, Irondelle M, Charruel M, Ducos B, Michaud A, Caron M, Marangoni E, Chavrier P, Le Tourneau C, Kamal M, Pasmant E, Vidaud M, Servant N, Reyal F, Meseure D, Vincent-Salomon A, Fre S, Margueron R. Impaired PRC2 activity promotes transcriptional instability and favors breast tumorigenesis. Genes Dev 2015; 29:2547-62. [PMID: 26637281 PMCID: PMC4699384 DOI: 10.1101/gad.269522.115] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 11/13/2015] [Indexed: 02/06/2023]
Abstract
In this study, Wassef et al. used mouse and human models to show that the high expression of Polycomb protein EZH2 in solid tumors is a consequence, not a cause, of tumorigenesis and that low abundance or deletion of EZH2 relative to proliferation is linked to poor prognosis and transcriptional instability. Alterations of chromatin modifiers are frequent in cancer, but their functional consequences often remain unclear. Focusing on the Polycomb protein EZH2 that deposits the H3K27me3 (trimethylation of Lys27 of histone H3) mark, we showed that its high expression in solid tumors is a consequence, not a cause, of tumorigenesis. In mouse and human models, EZH2 is dispensable for prostate cancer development and restrains breast tumorigenesis. High EZH2 expression in tumors results from a tight coupling to proliferation to ensure H3K27me3 homeostasis. However, this process malfunctions in breast cancer. Low EZH2 expression relative to proliferation and mutations in Polycomb genes actually indicate poor prognosis and occur in metastases. We show that while altered EZH2 activity consistently modulates a subset of its target genes, it promotes a wider transcriptional instability. Importantly, transcriptional changes that are consequences of EZH2 loss are predominantly irreversible. Our study provides an unexpected understanding of EZH2's contribution to solid tumors with important therapeutic implications.
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Affiliation(s)
- Michel Wassef
- Institut Curie, Paris Sciences et Lettres Research University, 75005 Paris, France; U934, Institut National de la Santé et de la Recherche Médicale, 75005 Paris, France; UMR3215, Centre National de la Recherche Scientifique, 75005 Paris, France
| | - Veronica Rodilla
- Institut Curie, Paris Sciences et Lettres Research University, 75005 Paris, France; U934, Institut National de la Santé et de la Recherche Médicale, 75005 Paris, France; UMR3215, Centre National de la Recherche Scientifique, 75005 Paris, France
| | - Aurélie Teissandier
- Institut Curie, Paris Sciences et Lettres Research University, 75005 Paris, France; U900, Institut National de la Santé et de la Recherche Médicale, 75005 Paris, France; Mines ParisTech, 77300 Fontainebleau, France
| | - Bruno Zeitouni
- Institut Curie, Paris Sciences et Lettres Research University, 75005 Paris, France; U900, Institut National de la Santé et de la Recherche Médicale, 75005 Paris, France; Mines ParisTech, 77300 Fontainebleau, France
| | - Nadege Gruel
- Institut Curie, Paris Sciences et Lettres Research University, 75005 Paris, France
| | - Benjamin Sadacca
- Institut Curie, Paris Sciences et Lettres Research University, 75005 Paris, France
| | - Marie Irondelle
- Institut Curie, Paris Sciences et Lettres Research University, 75005 Paris, France
| | - Margaux Charruel
- Institut Curie, Paris Sciences et Lettres Research University, 75005 Paris, France; U934, Institut National de la Santé et de la Recherche Médicale, 75005 Paris, France; UMR3215, Centre National de la Recherche Scientifique, 75005 Paris, France
| | - Bertrand Ducos
- Laboratoire de Physique Statistique-Ecole Normale Supérieure de Paris, Centre National de la Recherche Scientifique, 75005 Paris, France; UMR 8550, Centre National de la Recherche Scientifique, 75005 Paris, France; Plateforme de PCR Quantitative à Haut Débit Genomic Paris Centre, Institut de Biologie de l'École Normale Supérieure, 75005 Paris, France
| | - Audrey Michaud
- Institut Curie, Paris Sciences et Lettres Research University, 75005 Paris, France; U934, Institut National de la Santé et de la Recherche Médicale, 75005 Paris, France; UMR3215, Centre National de la Recherche Scientifique, 75005 Paris, France
| | - Matthieu Caron
- Institut Curie, Paris Sciences et Lettres Research University, 75005 Paris, France; U934, Institut National de la Santé et de la Recherche Médicale, 75005 Paris, France; UMR3215, Centre National de la Recherche Scientifique, 75005 Paris, France
| | - Elisabetta Marangoni
- Institut Curie, Paris Sciences et Lettres Research University, 75005 Paris, France
| | - Philippe Chavrier
- Institut Curie, Paris Sciences et Lettres Research University, 75005 Paris, France
| | - Christophe Le Tourneau
- Department of Medical Oncology, Institut Curie, 75005 Paris, France; EA7285, Université de Versailles, Saint-Quentin-en-Yvelines, 78000 Versailles, France
| | - Maud Kamal
- Department of Medical Oncology, Institut Curie, 75005 Paris, France
| | - Eric Pasmant
- UMR_S745, EA7331, Institut National de la Santé et de la Recherche Médicale, 75006 Paris, France; Facultée des Sciences Pharmaceutiques et Biologiques, Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France; Service de Biochimie et Génétique Moléculaire, Assistance Publique-Hôpitaux de Paris, Hôpital Cochin, 75014 Paris, France
| | - Michel Vidaud
- UMR_S745, EA7331, Institut National de la Santé et de la Recherche Médicale, 75006 Paris, France; Facultée des Sciences Pharmaceutiques et Biologiques, Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France; Service de Biochimie et Génétique Moléculaire, Assistance Publique-Hôpitaux de Paris, Hôpital Cochin, 75014 Paris, France
| | - Nicolas Servant
- Institut Curie, Paris Sciences et Lettres Research University, 75005 Paris, France; U900, Institut National de la Santé et de la Recherche Médicale, 75005 Paris, France; Mines ParisTech, 77300 Fontainebleau, France
| | - Fabien Reyal
- Institut Curie, Paris Sciences et Lettres Research University, 75005 Paris, France
| | - Dider Meseure
- Institut Curie, Paris Sciences et Lettres Research University, 75005 Paris, France; Platform of Investigative Pathology, 75005 Paris, France
| | - Anne Vincent-Salomon
- Institut Curie, Paris Sciences et Lettres Research University, 75005 Paris, France
| | - Silvia Fre
- Institut Curie, Paris Sciences et Lettres Research University, 75005 Paris, France; U934, Institut National de la Santé et de la Recherche Médicale, 75005 Paris, France; UMR3215, Centre National de la Recherche Scientifique, 75005 Paris, France
| | - Raphaël Margueron
- Institut Curie, Paris Sciences et Lettres Research University, 75005 Paris, France; U934, Institut National de la Santé et de la Recherche Médicale, 75005 Paris, France; UMR3215, Centre National de la Recherche Scientifique, 75005 Paris, France
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Noberini R, Uggetti A, Pruneri G, Minucci S, Bonaldi T. Pathology Tissue-quantitative Mass Spectrometry Analysis to Profile Histone Post-translational Modification Patterns in Patient Samples. Mol Cell Proteomics 2015; 15:866-77. [PMID: 26463340 PMCID: PMC4813706 DOI: 10.1074/mcp.m115.054510] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Indexed: 12/18/2022] Open
Abstract
Histone post-translational modifications (hPTMs) generate a complex combinatorial code that has been implicated with various pathologies, including cancer. Dissecting such a code in physiological and diseased states may be exploited for epigenetic biomarker discovery, but hPTM analysis in clinical samples has been hindered by technical limitations. Here, we developed a method (PAThology tissue analysis of Histones by Mass Spectrometry - PAT-H-MS) that allows to perform a comprehensive, unbiased and quantitative MS-analysis of hPTM patterns on formalin-fixed paraffin-embedded (FFPE) samples. In pairwise comparisons, histone extracted from formalin-fixed paraffin-embedded tissues showed patterns similar to fresh frozen samples for 24 differentially modified peptides from histone H3. In addition, when coupled with a histone-focused version of the super-SILAC approach, this method allows the accurate quantification of modification changes among breast cancer patient samples. As an initial application of the PAThology tissue analysis of Histones by Mass Spectrometry method, we analyzed breast cancer samples, revealing significant changes in histone H3 methylation patterns among Luminal A-like and Triple Negative disease subtypes. These results pave the way for retrospective epigenetic studies that combine the power of MS-based hPTM analysis with the extensive clinical information associated with formalin-fixed paraffin-embedded archives.
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Affiliation(s)
- Roberta Noberini
- From the ‡Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, Via Adamello 16, 20139 Milan, Italy
| | - Andrea Uggetti
- §Biobank for Translational Medicine Unit, Department of Pathology, European Institute of Oncology, Via Ripamonti 435, 20141 Milano
| | - Giancarlo Pruneri
- §Biobank for Translational Medicine Unit, Department of Pathology, European Institute of Oncology, Via Ripamonti 435, 20141 Milano; ¶School of Medicine, University of Milan, 20122 Milan, Italy
| | - Saverio Minucci
- ‖Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy; **Drug Development Program, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy; ‡‡Department of Bioscience, University of Milan, 20133 Milan, Italy
| | - Tiziana Bonaldi
- ‖Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy;
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Santos JC, Ribeiro ML. Epigenetic regulation of DNA repair machinery in Helicobacter pylori-induced gastric carcinogenesis. World J Gastroenterol 2015; 21:9021-9037. [PMID: 26290630 PMCID: PMC4533035 DOI: 10.3748/wjg.v21.i30.9021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 06/02/2015] [Accepted: 07/08/2015] [Indexed: 02/06/2023] Open
Abstract
Although thousands of DNA damaging events occur in each cell every day, efficient DNA repair pathways have evolved to counteract them. The DNA repair machinery plays a key role in maintaining genomic stability by avoiding the maintenance of mutations. The DNA repair enzymes continuously monitor the chromosomes to correct any damage that is caused by exogenous and endogenous mutagens. If DNA damage in proliferating cells is not repaired because of an inadequate expression of DNA repair genes, it might increase the risk of cancer. In addition to mutations, which can be either inherited or somatically acquired, epigenetic silencing of DNA repair genes has been associated with carcinogenesis. Gastric cancer represents the second highest cause of cancer mortality worldwide. The disease develops from the accumulation of several genetic and epigenetic changes during the lifetime. Among the risk factors, Helicobacter pylori (H. pylori) infection is considered the main driving factor to gastric cancer development. Thus, in this review, we summarize the current knowledge of the role of H. pylori infection on the epigenetic regulation of DNA repair machinery in gastric carcinogenesis.
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Hudler P, Videtič Paska A, Komel R. Contemporary proteomic strategies for clinical epigenetic research and potential impact for the clinic. Expert Rev Proteomics 2015; 12:197-212. [PMID: 25719543 DOI: 10.1586/14789450.2015.1019479] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Novel proteomic methods are revealing the intricacy of the epigenetic landscape affecting gene regulation and improving our knowledge of the pathogenesis of complex diseases. Despite the enormous amount of data regarding epigenetic modifications present in DNA and histones, deciphering their biological relevance in the context of the disease and health is currently still an ongoing process. Here, we consider the relationship between epigenetic research in tumorigenesis and the prospect of knowledge transfer to clinical use, focusing primarily on the epigenetic histone post-translational modifications, which could be used as biomarkers. We additionally focus on the use of proteomic techniques in research and evaluate their usefulness in clinical setting.
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Affiliation(s)
- Petra Hudler
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, SI-1000 Ljubljana, Slovenia
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