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Bagheri M, Lee MK, Muller KE, Miller TW, Pattabiraman DR, Christensen BC. Alteration of DNA methyltransferases by eribulin elicits broad DNA methylation changes with potential therapeutic implications for triple-negative breast cancer. Epigenomics 2024; 16:293-308. [PMID: 38356412 PMCID: PMC10910603 DOI: 10.2217/epi-2023-0339] [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: 09/26/2023] [Accepted: 01/23/2024] [Indexed: 02/16/2024] Open
Abstract
Background: Triple-negative breast cancer (TNBC) is an aggressive disease with limited treatment options. Eribulin, a chemotherapeutic drug, induces epigenetic changes in cancer cells, suggesting a unique mechanism of action. Materials & methods: MDA-MB 231 cells were treated with eribulin and paclitaxel, and the samples from 53 patients treated with neoadjuvant eribulin were compared with those from 14 patients who received the standard-of-care treatment using immunohistochemistry. Results: Eribulin treatment caused significant DNA methylation changes in drug-tolerant persister TNBC cells, and it also elicited changes in the expression levels of epigenetic modifiers (DNMT1, TET1, DNMT3A/B) in vitro and in primary TNBC tumors. Conclusion: These findings provide new insights into eribulin's mechanism of action and potential biomarkers for predicting TNBC treatment response.
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Affiliation(s)
- Meisam Bagheri
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
- Dartmouth Cancer Center, Lebanon, NH 03756, USA
| | - Min Kyung Lee
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Kristen E Muller
- Dartmouth Cancer Center, Lebanon, NH 03756, USA
- Department of Pathology, Geisel School of Medicine at Dartmouth, Lebanon NH 03756, USA
| | - Todd W Miller
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
- Dartmouth Cancer Center, Lebanon, NH 03756, USA
- Department of Pharmacology & Toxicology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Diwakar R Pattabiraman
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
- Dartmouth Cancer Center, Lebanon, NH 03756, USA
| | - Brock C Christensen
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
- Department of Community & Family Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
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2
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Lin LH, Tran I, Yang Y, Shen G, Miah P, Cotzia P, Roses D, Schnabel F, Darvishian F, Snuderl M. DNA Methylation Identifies Epigenetic Subtypes of Triple-Negative Breast Cancers With Distinct Clinicopathologic and Molecular Features. Mod Pathol 2023; 36:100306. [PMID: 37595637 DOI: 10.1016/j.modpat.2023.100306] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/25/2023] [Accepted: 08/02/2023] [Indexed: 08/20/2023]
Abstract
Triple-negative breast cancers (TNBC) include diverse carcinomas with heterogeneous clinical behavior. DNA methylation is a useful tool in classifying a variety of cancers. In this study, we analyzed TNBC using DNA methylation profiling and compared the results to those of mutational analysis. DNA methylation profiling (Infinium MethylationEPIC array, Illumina) and 50-gene panel-targeted DNA sequencing were performed in 44 treatment-naïve TNBC. We identified 3 distinct DNA methylation clusters with specific clinicopathologic and molecular features. Cluster 1 (phosphoinositide 3-kinase/protein kinase B-enriched cluster; n = 9) patients were significantly older (mean age, 71 years; P = .008) with tumors that were more likely to exhibit apocrine differentiation (78%; P < .001), a lower grade (44% were grade 2), a lower proliferation index (median Ki-67, 15%; P = .002), and lower tumor-infiltrating lymphocyte fractions (median, 15%; P = .0142). Tumors carried recurrent PIK3CA and AKT1 mutations and a higher percentage of low HER-2 expression (89%; P = .033). Cluster 3 (chromosomal instability cluster; n = 28) patients were significantly younger (median age, 57 years). Tumors were of higher grade (grade 3, 93%), had a higher proliferation index (median Ki-67, 75%), and were with a high fraction of tumor-infiltrating lymphocytes (median, 30%). Ninety-one percent of the germline BRCA1/2 mutation carriers were in cluster 3, and these tumors showed the highest level of copy number alterations. Cluster 2 represented cases with intermediate clinicopathologic characteristics and no specific molecular profile (no specific molecular profile cluster; n = 7). There were no differences in relation to stage, recurrence, and survival. In conclusion, DNA methylation profiling is a promising tool to classify patients with TNBC into biologically relevant groups, which may result in better disease characterization and reveal potential targets for emerging therapies.
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Affiliation(s)
- Lawrence Hsu Lin
- Department of Pathology, New York University Langone Health and Grossman School of Medicine, New York, New York
| | - Ivy Tran
- Department of Pathology, New York University Langone Health and Grossman School of Medicine, New York, New York
| | - Yiying Yang
- Department of Pathology, New York University Langone Health and Grossman School of Medicine, New York, New York
| | - Guomiao Shen
- Department of Pathology, New York University Langone Health and Grossman School of Medicine, New York, New York
| | - Pabel Miah
- Department of Surgery, New York University Langone Health and Grossman School of Medicine, New York, New York
| | - Paolo Cotzia
- Department of Pathology, New York University Langone Health and Grossman School of Medicine, New York, New York
| | - Daniel Roses
- Department of Surgery, New York University Langone Health and Grossman School of Medicine, New York, New York
| | - Freya Schnabel
- Department of Surgery, New York University Langone Health and Grossman School of Medicine, New York, New York
| | - Farbod Darvishian
- Department of Pathology, New York University Langone Health and Grossman School of Medicine, New York, New York
| | - Matija Snuderl
- Department of Pathology, New York University Langone Health and Grossman School of Medicine, New York, New York.
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3
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Bagheri M, Lee MK, Muller KE, Miller TW, Pattabiraman DR, Christensen BC. Alteration of DNMT1/DNMT3A by eribulin elicits global DNA methylation changes with potential therapeutic implications for triple-negative breast cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.09.544426. [PMID: 37333096 PMCID: PMC10274899 DOI: 10.1101/2023.06.09.544426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Triple-negative breast cancer (TNBC) is an aggressive disease subtype with limited treatment options. Eribulin is a chemotherapeutic approved for the treatment of advanced breast cancer that has been shown to elicit epigenetic changes. We investigated the effect of eribulin treatment on genome-scale DNA methylation patterns in TNBC cells. Following repeated treatment, The results showed that eribulin-induced changes in DNA methylation patterns evident in persister cells. Eribulin also affected the binding of transcription factors to genomic ZEB1 binding sites and regulated several cellular pathways, including ERBB and VEGF signaling and cell adhesion. Eribulin also altered the expression of epigenetic modifiers including DNMT1, TET1, and DNMT3A/B in persister cells. Data from primary human TNBC tumors supported these findings: DNMT1 and DNMT3A levels were altered by eribulin treatment in human primary TNBC tumors. Our results suggest that eribulin modulates DNA methylation patterns in TNBC cells by altering the expression of epigenetic modifiers. These findings have clinical implications for using eribulin as a therapeutic agent.
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Affiliation(s)
- Meisam Bagheri
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03766
- Dartmouth Cancer Center, Lebanon, NH, 03756
| | - Min Kyung Lee
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, 03756
| | - Kristen E. Muller
- Dartmouth Cancer Center, Lebanon, NH, 03756
- Department of Pathology, Dartmouth-Hitchcock Medical Center, Lebanon NH 03756, USA
| | - Todd W. Miller
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03766
- Dartmouth Cancer Center, Lebanon, NH, 03756
| | - Diwakar R. Pattabiraman
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03766
- Dartmouth Cancer Center, Lebanon, NH, 03756
| | - Brock C. Christensen
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03766
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, 03756
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH, 03756
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4
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Zappe K, Kopic A, Scheichel A, Schier AK, Schmidt LE, Borutzki Y, Miedl H, Schreiber M, Mendrina T, Pirker C, Pfeiler G, Hacker S, Haslik W, Pils D, Bileck A, Gerner C, Meier-Menches S, Heffeter P, Cichna-Markl M. Aberrant DNA Methylation, Expression, and Occurrence of Transcript Variants of the ABC Transporter ABCA7 in Breast Cancer. Cells 2023; 12:1462. [PMID: 37296582 PMCID: PMC10252461 DOI: 10.3390/cells12111462] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/09/2023] [Accepted: 05/16/2023] [Indexed: 06/12/2023] Open
Abstract
The ABC transporter ABCA7 has been found to be aberrantly expressed in a variety of cancer types, including breast cancer. We searched for specific epigenetic and genetic alterations and alternative splicing variants of ABCA7 in breast cancer and investigated whether these alterations are associated with ABCA7 expression. By analyzing tumor tissues from breast cancer patients, we found CpGs at the exon 5-intron 5 boundary aberrantly methylated in a molecular subtype-specific manner. The detection of altered DNA methylation in tumor-adjacent tissues suggests epigenetic field cancerization. In breast cancer cell lines, DNA methylation levels of CpGs in promoter-exon 1, intron 1, and at the exon 5-intron 5 boundary were not correlated with ABCA7 mRNA levels. By qPCR involving intron-specific and intron-flanking primers, we identified intron-containing ABCA7 mRNA transcripts. The occurrence of intron-containing transcripts was neither molecular subtype-specific nor directly correlated with DNA methylation at the respective exon-intron boundaries. Treatment of breast cancer cell lines MCF-7, BT-474, SK-BR3, and MDA-MB-231 with doxorubicin or paclitaxel for 72 h resulted in altered ABCA7 intron levels. Shotgun proteomics revealed that an increase in intron-containing transcripts was associated with significant dysregulation of splicing factors linked to alternative splicing.
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Affiliation(s)
- Katja Zappe
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Antonio Kopic
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Alexandra Scheichel
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Ann-Katrin Schier
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Lukas Emanuel Schmidt
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Yasmin Borutzki
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
- Department of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Heidi Miedl
- Department of Obstetrics and Gynecology and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Martin Schreiber
- Department of Obstetrics and Gynecology and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Theresa Mendrina
- Department of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
- Center for Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Christine Pirker
- Center for Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Georg Pfeiler
- Division of Gynecology and Gynecological Oncology, Department of Obstetrics and Gynecology, Medical University of Vienna, 1090 Vienna, Austria
| | - Stefan Hacker
- Department of Plastic and Reconstructive Surgery, Medical University of Vienna, 1090 Vienna, Austria
| | - Werner Haslik
- Department of Plastic and Reconstructive Surgery, Medical University of Vienna, 1090 Vienna, Austria
| | - Dietmar Pils
- Division of Visceral Surgery, Department of General Surgery and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Andrea Bileck
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
- Joint Metabolome Facility, University of Vienna and Medical University of Vienna, 1090 Vienna, Austria
| | - Christopher Gerner
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
- Joint Metabolome Facility, University of Vienna and Medical University of Vienna, 1090 Vienna, Austria
| | - Samuel Meier-Menches
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
- Department of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
- Joint Metabolome Facility, University of Vienna and Medical University of Vienna, 1090 Vienna, Austria
| | - Petra Heffeter
- Center for Cancer Research and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Margit Cichna-Markl
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
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5
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Sofía M, Sebastián R, Emanuel C, Branham MT, Marzese DM, Matthew S, De Blas G, Rodolfo A, Michael L, María R. When left does not seem right: epigenetic and bioelectric differences between left- and right-sided breast cancer. Mol Med 2022; 28:15. [PMID: 35123413 PMCID: PMC8817536 DOI: 10.1186/s10020-022-00440-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/18/2022] [Indexed: 01/22/2023] Open
Abstract
Background During embryogenesis lateral symmetry is broken, giving rise to Left/Right (L/R) breast tissues with distinct identity. L/R-sided breast tumors exhibit consistently-biased incidence, gene expression, and DNA methylation. We postulate that a differential L/R tumor-microenvironment crosstalk generates different tumorigenesis mechanisms. Methods We performed in-silico analyses on breast tumors of public datasets, developed xenografted tumors, and conditioned MDA-MB-231 cells with L/R mammary extracts. Results We found L/R differential DNA methylation involved in embryogenic and neuron-like functions. Focusing on ion-channels, we discovered significant L/R epigenetic and bioelectric differences. Specifically, L-sided cells presented increased methylation of hyperpolarizing ion channel genes and increased Ca2+ concentration and depolarized membrane potential, compared to R-ones. Functional consequences were associated with increased proliferation in left tumors, assessed by KI67 expression and mitotic count. Conclusions Our findings reveal considerable L/R asymmetry in cancer processes, and suggest specific L/R epigenetic and bioelectric differences as future targets for cancer therapeutic approaches in the breast and many other paired organs. Supplementary Information The online version contains supplementary material available at 10.1186/s10020-022-00440-5.
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6
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Nasif D, Real S, Roqué M, Branham MT. CDC42 as an epigenetic regulator of ID4 in triple-negative breast tumors. Breast Cancer 2022; 29:562-573. [DOI: 10.1007/s12282-022-01334-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 01/09/2022] [Indexed: 12/01/2022]
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7
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Krsteski J, Gorenjak M, But I, Pakiž M, Potočnik U. Dysregulation of Synaptic Signaling Genes Is Involved in Biology of Uterine Leiomyoma. Genes (Basel) 2021; 12:1179. [PMID: 34440356 PMCID: PMC8394462 DOI: 10.3390/genes12081179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 02/07/2023] Open
Abstract
Uterine leiomyomas are tumors, which are hormone driven and originate from the smooth muscle layer of the uterine wall. In addition to known genes in leiomyoma pathogenesis, recent approaches also highlight epigenetic malfunctions as an important mechanism of gene dysregulation. RNA sequencing raw data from pair-matched normal myometrium and fibroid tumors from two independent studies were used as discovery and validation sets and reanalyzed. RNA extracted from normal myometrium and fibroid tumors from 58 Slovenian patients was used as independent confirmation of most significant differentially expressed genes. Subsequently, GWA data from leiomyoma patients were used in order to identify genetic variants at epigenetic marks. Gene Ontology analysis of the overlap of two independent RNA-seq analyses showed that NPTX1, NPTX2, CHRM2, DRD2 and CACNA1A were listed as significant for several enriched GO terms. All five genes were subsequently confirmed in the independent Slovenian cohort. Additional integration and functional analysis showed that genetic variants in these five gene regions are listed at a chromatin structure and state, predicting promoters, enhancers, DNase hypersensitivity and altered transcription factor binding sites. We identified a unique subgroup of dysregulated synaptic signaling genes involved in the biology and pathogenesis of leiomyomas, adding to the complexity of tumor biology.
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Affiliation(s)
- Jovan Krsteski
- Centre for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Taborska ulica 8, 2000 Maribor, Slovenia; (J.K.); (M.G.)
| | - Mario Gorenjak
- Centre for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Taborska ulica 8, 2000 Maribor, Slovenia; (J.K.); (M.G.)
| | - Igor But
- Department of General Gynecology and Gynecological Urology, University Clinical Centre Maribor, Ljubljanska ulica 5, 2000 Maribor, Slovenia; (I.B.); (M.P.)
| | - Maja Pakiž
- Department of General Gynecology and Gynecological Urology, University Clinical Centre Maribor, Ljubljanska ulica 5, 2000 Maribor, Slovenia; (I.B.); (M.P.)
| | - Uroš Potočnik
- Centre for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Taborska ulica 8, 2000 Maribor, Slovenia; (J.K.); (M.G.)
- Laboratory of Biochemistry, Molecular Biology and Genomics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova 17, 2000 Maribor, Slovenia
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8
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Ha CT, Cheng CY, Zheng MY, Hsu TH, Miao CC, Lee CJ, Wang HD, Pan ST, Chou YT. ID4 predicts poor prognosis and promotes BDNF-mediated oncogenesis of colorectal cancer. Carcinogenesis 2021; 42:951-960. [PMID: 33993270 DOI: 10.1093/carcin/bgab037] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 04/19/2021] [Accepted: 05/06/2021] [Indexed: 11/14/2022] Open
Abstract
Inhibitors of DNA binding and cell differentiation (ID) proteins regulate cellular differentiation and tumor progression. Whether ID family proteins serve as a linkage between pathological differentiation and cancer stemness in colorectal cancer is largely unknown. Here, the expression of ID4, but not other ID family proteins, was enriched in LGR5-high colon cancer stem cells. Its high expression was associated with poor pathological differentiation of colorectal tumors and shorter survival in patients. Knockdown of ID4 inhibited the growth and dissemination of colon cancer cells, while enhancing chemosensitivity. Through gene expression profiling analysis, brain-derived neurotrophic factor (BDNF) was identified as a downstream target of ID4 expression in colorectal cancer. BDNF knockdown decreased the growth and migration of colon cancer cells, and its expression enhanced dissemination, anoikis resistance and chemoresistance. ID4 silencing attenuated the epithelial-to-mesenchymal transition pattern in colon cancer cells. Gene cluster analysis revealed that ID4 and BDNF expression was clustered with mesenchymal markers and distant from epithelial genes. BDNF silencing decreased the expression of mesenchymal markers Vimentin, CDH2 and SNAI1. These findings demonstrated that ID4-BDNF signaling regulates colorectal cancer survival, with the potential to serve as a prognostic marker in colorectal cancer.
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Affiliation(s)
- Cam-Thu Ha
- Institute of Biotechnology, National Tsing Hua University, Hsinchu,Taiwan
| | | | - Ming-Yi Zheng
- Institute of Biotechnology, National Tsing Hua University, Hsinchu,Taiwan
| | - Tang-Hui Hsu
- Institute of Biotechnology, National Tsing Hua University, Hsinchu,Taiwan
| | - Chia-Cheng Miao
- Institute of Biotechnology, National Tsing Hua University, Hsinchu,Taiwan
| | - Chang-Jung Lee
- Institute of Biotechnology, National Tsing Hua University, Hsinchu,Taiwan
| | - Horng-Dar Wang
- Institute of Biotechnology, National Tsing Hua University, Hsinchu,Taiwan
| | - Shien-Tung Pan
- Department of Pathology, China Medical University Hsinchu Hospital, Hsinchu County, Taiwan
| | - Yu-Ting Chou
- Institute of Biotechnology, National Tsing Hua University, Hsinchu,Taiwan
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9
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Zolota V, Tzelepi V, Piperigkou Z, Kourea H, Papakonstantinou E, Argentou MI, Karamanos NK. Epigenetic Alterations in Triple-Negative Breast Cancer-The Critical Role of Extracellular Matrix. Cancers (Basel) 2021; 13:cancers13040713. [PMID: 33572395 PMCID: PMC7916242 DOI: 10.3390/cancers13040713] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 12/11/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is an aggressive subgroup of breast cancer characterized by genomic complexity and therapeutic options limited to only standard chemotherapy. Although it has been suggested that stratifying TNBC patients by pathway-specific molecular alterations may predict benefit from specific therapeutic agents, application in routine clinical practice has not yet been established. There is a growing body of the literature supporting that epigenetic modifications comprised by DNA methylation, chromatin remodeling and non-coding RNAs play a fundamental role in TNBC pathogenesis. Extracellular matrix (ECM) is a highly dynamic 3D network of macromolecules with structural and cellular regulatory roles. Alterations in the expression of ECM components result in uncontrolled matrix remodeling, thus affecting its ability to regulate vital functions of cancer cells, including proliferation, migration, adhesion, invasion and epithelial-to-mesenchymal transition (EMT). Recent molecular data highlight the major role of tumor microenvironment and ECM alterations in TNBC and approaches for targeting tumor microenvironment have recently been recognized as potential therapeutic strategies. Notably, many of the ECM/EMT modifications in cancer are largely driven by epigenetic events, highlighting the pleiotropic effects of the epigenetic network in TNBC. This article presents and critically discusses the current knowledge on the epigenetic alterations correlated with TNBC pathogenesis, with emphasis on those associated with ECM/EMT modifications, their prognostic and predictive value and their use as therapeutic targets.
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Affiliation(s)
- Vasiliki Zolota
- Department of Pathology, School of Medicine, University of Patras, 26504 Rion, Greece; (V.T.); (H.K.)
- Correspondence: ; Tel.: +30-0693613366
| | - Vasiliki Tzelepi
- Department of Pathology, School of Medicine, University of Patras, 26504 Rion, Greece; (V.T.); (H.K.)
| | - Zoi Piperigkou
- Biochemistry, Biochemical Analysis & Matrix Pathobiology Research Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, 26110 Patras, Greece; (Z.P.); (N.K.K.)
- Foundation for Research and Technology-Hellas (FORTH)/Institute of Chemical Engineering Sciences (ICE-HT), 26110 Patras, Greece
| | - Helen Kourea
- Department of Pathology, School of Medicine, University of Patras, 26504 Rion, Greece; (V.T.); (H.K.)
| | - Efthymia Papakonstantinou
- Department of Gynecology and Obstetrics School of Medicine, University of Patras, 26504 Rion, Greece;
| | - Maria-Ioanna Argentou
- Department of Surgery, School of Medicine, University of Patras, 26504 Rion, Greece;
| | - Nikos K. Karamanos
- Biochemistry, Biochemical Analysis & Matrix Pathobiology Research Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, 26110 Patras, Greece; (Z.P.); (N.K.K.)
- Foundation for Research and Technology-Hellas (FORTH)/Institute of Chemical Engineering Sciences (ICE-HT), 26110 Patras, Greece
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10
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Amirkhani Namagerdi A, d'Angelo D, Ciani F, Iannuzzi CA, Napolitano F, Avallone L, De Laurentiis M, Giordano A. Triple-Negative Breast Cancer Comparison With Canine Mammary Tumors From Light Microscopy to Molecular Pathology. Front Oncol 2020; 10:563779. [PMID: 33282730 PMCID: PMC7689249 DOI: 10.3389/fonc.2020.563779] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 10/19/2020] [Indexed: 12/12/2022] Open
Abstract
Many similar characteristics in human and dog cancers including, spontaneous development, clinical presentation, tumor heterogeneity, disease progression, and response to standard therapies have promoted the approval of this comparative model as an alternative to mice. Breast cancer represents the second most frequent neoplasm in humans after lung cancer. Triple-negative breast cancers (TNBC) constitute around 15% of all cases of breast cancer and do not express estrogen receptor (ER), progesterone receptor (PR), and do not overexpress human epidermal growth factor receptor 2 (HER2). As a result, they do not benefit from hormonal or trastuzumab-based therapy. Patients with TNBC have worse overall survival than patients with non-TNBC. Lehmann and collaborators described six different molecular subtypes of TNBC which further demonstrated its transcriptional heterogeneity. This six TNBC subtype classification has therapeutic implications. Breast cancer is the second most frequent neoplasm in sexually intact female dogs after skin cancer. Canine mammary tumors are a naturally occurring heterogeneous group of cancers that have several features in common with human breast cancer (HBC). These similarities include etiology, signaling pathway activation, and histological classification. Molecularly CMTs are more like TNBCs, and therefore dogs are powerful spontaneous models of cancer to test new therapeutic approaches, particularly for human TNBCs. More malignant tumors of the breast are more often ER and PR negative in both humans and dogs. Promising breast cancer biomarkers in both humans and canines are cancer-associated stroma (CAS), circulating tumor cells and tumor DNA (ctDNA), exosomes and miRNAs, and metabolites.
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Affiliation(s)
| | - Danila d'Angelo
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples, Italy
| | - Francesca Ciani
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples, Italy
| | | | - Francesco Napolitano
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples, Italy.,CCEINGE, Biotecnologie Avanzate, Naples, Italy
| | - Luigi Avallone
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples, Italy
| | - Michelino De Laurentiis
- Breast Oncology Division, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Naples, Italy
| | - Antonio Giordano
- Center for Biotechnology, College of Science and Technology, Sbarro Institute for Cancer Research and Molecular Medicine, Temple University, Philadelphia, PA, United States.,Department of Medical Biotechnologies, University of Siena, Siena, Italy
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11
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Wu N, Huang J, Zhang XF, Ou-Yang L, He S, Zhu Z, Xie W. Weighted Fused Pathway Graphical Lasso for Joint Estimation of Multiple Gene Networks. Front Genet 2019; 10:623. [PMID: 31396259 PMCID: PMC6662592 DOI: 10.3389/fgene.2019.00623] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 06/13/2019] [Indexed: 01/17/2023] Open
Abstract
Gene regulatory networks (GRNs) are often inferred based on Gaussian graphical models that could identify the conditional dependence among genes by estimating the corresponding precision matrix. Classical Gaussian graphical models are usually designed for single network estimation and ignore existing knowledge such as pathway information. Therefore, they can neither make use of the common information shared by multiple networks, nor can they utilize useful prior information to guide the estimation. In this paper, we propose a new weighted fused pathway graphical lasso (WFPGL) to jointly estimate multiple networks by incorporating prior knowledge derived from known pathways and gene interactions. Based on the assumption that two genes are less likely to be connected if they do not participate together in any pathways, a pathway-based constraint is considered in our model. Moreover, we introduce a weighted fused lasso penalty in our model to take into account prior gene interaction data and common information shared by multiple networks. Our model is optimized based on the alternating direction method of multipliers (ADMM). Experiments on synthetic data demonstrate that our method outperforms other five state-of-the-art graphical models. We then apply our model to two real datasets. Hub genes in our identified state-specific networks show some shared and specific patterns, which indicates the efficiency of our model in revealing the underlying mechanisms of complex diseases.
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Affiliation(s)
- Nuosi Wu
- College of Electronics and Information Engineering, Shenzhen University, Shenzhen, China
| | - Jiang Huang
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China
| | - Xiao-Fei Zhang
- School of Mathematics and Statistics, Central China Normal University, Wuhan, China
| | - Le Ou-Yang
- Guangdong Key Laboratory of Intelligent Information Processing and Shenzhen Key Laboratory of Media Security, College of Electronics and Information Engineering, Shenzhen University, Shenzhen, China
- Shenzhen Institute of Artificial Intelligence and Robotics for Society, Shenzhen, China
| | - Shan He
- School of Computer Science, University of Birmingham, Birmingham, United Kingdom
| | - Zexuan Zhu
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China
| | - Weixin Xie
- College of Electronics and Information Engineering, Shenzhen University, Shenzhen, China
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12
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Khaled N, Bidet Y. New Insights into the Implication of Epigenetic Alterations in the EMT of Triple Negative Breast Cancer. Cancers (Basel) 2019; 11:cancers11040559. [PMID: 31003528 PMCID: PMC6521131 DOI: 10.3390/cancers11040559] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/22/2019] [Accepted: 04/11/2019] [Indexed: 12/11/2022] Open
Abstract
Breast cancer is the most common cancer and leading cause of cancer death among women worldwide, encompassing a wide heterogeneity of subtypes with different clinical features. During the last two decades, the use of targeted therapies has emerged in clinical research in order to increase treatment efficiency, improve prognosis and reduce recurrence. However, the triple negative breast cancer (TNBC) subtype remains a clinical challenge, with poor prognosis since no therapeutic targets have been identified. This aggressive breast cancer entity lacks expression of oestrogen receptor (ER) and progesterone receptor (PR), and it does not overexpress human epidermal growth factor receptor 2 (HER2). The major reason for TNBC poor prognosis is early therapeutic escape from conventional treatments, leading to aggressive metastatic relapse. Metastases occur after an epithelial-mesenchymal transition EMT of epithelial cells, allowing them to break free from the primary tumour site and to colonize distant organs. Cancer-associated EMT consists not only of acquired migration and invasion ability, but involves complex and comprehensive reprogramming, including changes in metabolism, expression levels and epigenetic. Recently, many studies have considered epigenetic alterations as the primary initiator of cancer development and metastasis. This review builds a picture of the epigenetic modifications implicated in the EMT of breast cancer. It focuses on TNBC and allows comparisons with other subtypes. It emphasizes the role of the main epigenetic modifications lncRNAs, miRNAs, histone and DNA- modifications in tumour invasion and appearance of metastases. These epigenetic alterations can be considered biomarkers representing potential diagnostic and prognostic factors in order to define a global metastatic signature for TNBC.
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Affiliation(s)
| | - Yannick Bidet
- Laboratoire d'Oncologie Moléculaire, Centre Jean PERRIN et IMoST, UMR 1240, Inserm/Université Clermont Auvergne 58 rue Montalembert, 63000 Clermont-Ferrand, France.
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13
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Campoy EM, Branham MT, Mayorga LS, Roqué M. Intratumor heterogeneity index of breast carcinomas based on DNA methylation profiles. BMC Cancer 2019; 19:328. [PMID: 30953488 PMCID: PMC6451266 DOI: 10.1186/s12885-019-5550-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 03/28/2019] [Indexed: 01/02/2023] Open
Abstract
Background Cancer cells evolve and constitute heterogeneous populations that fluctuate in space and time and are subjected to selection generating intratumor heterogeneity. This phenomenon is determined by the acquisition of genetic/epigenetic alterations and their selection over time which has clinical implications on drug resistance. Methods DNA extracted from different tumor cell populations (breast carcinomas, cancer cell lines and cellular clones) were analyzed by MS-MLPA. Methylation profiles were used to generate a heterogeneity index to quantify the magnitude of epigenetic heterogeneity in these populations. Cellular clones were obtained from single cells derived of MDA-MB 231 cancer cell lines applying serial limiting dilution method and morphology was analyzed by optical microscopy and flow cytometry. Clones characteristics were examined through cellular proliferation, migration capacity and apoptosis. Heterogeneity index was also calculated from beta values derived from methylation profiles of TCGA tumors. Results The study of methylation profiles of 23 fresh breast carcinomas revealed heterogeneous allele populations in these tumor pieces. With the purpose to measure the magnitude of epigenetic heterogeneity, we developed an heterogeneity index based on methylation information and observed that all tumors present their own heterogeneity level. Applying the index calculation in pure cancer cell populations such as cancer cell lines (MDA-MB 231, MCF-7, T47D, HeLa and K-562), we also observed epigenetic heterogeneity. In addition, we detected that clones obtained from the MDA-MB 231 cancer cell line generated their own new heterogeneity over time. Using TCGA tumors, we determined that the heterogeneity index correlated with prognostic and predictive factors like tumor size (p = 0.0088), number of affected axillary nodes (p = 0.007), estrogen receptor expression (p < 0.0001) and HER2 positivity (p = 0.0007). When we analyzed molecular subtypes we found that they presented different heterogeneity levels. Interestingly, we also observed that all mentioned tumor cell populations shared a similar Heterogeneity index (HI) mean. Conclusions Our results show that each tumor presents a unique epigenetic heterogeneity level, which is associated with prognostic and predictive factors. We also observe that breast tumor subtypes differ in terms of epigenetic heterogeneity, which could serve as a new contribution to understand the different prognosis of these groups.
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Affiliation(s)
- Emanuel M Campoy
- IHEM-CONICET, Av del libertador, 80, Mendoza, Argentina. .,Facultad de Ciencias Médicas, Av del Libertador 80, Universidad Nacional de Cuyo, Mendoza, Argentina.
| | | | - Luis S Mayorga
- IHEM-CONICET, Av del libertador, 80, Mendoza, Argentina.,Facultad de Ciencias Médicas, Av del Libertador 80, Universidad Nacional de Cuyo, Mendoza, Argentina
| | - María Roqué
- IHEM-CONICET, Av del libertador, 80, Mendoza, Argentina.,Facultad de Ciencias Exactas y Naturales, Padre Jorge Contreras 1300, Universidad Nacional de Cuyo, Mendoza, Argentina
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14
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Alexandrou S, George SM, Ormandy CJ, Lim E, Oakes SR, Caldon CE. The Proliferative and Apoptotic Landscape of Basal-like Breast Cancer. Int J Mol Sci 2019; 20:ijms20030667. [PMID: 30720718 PMCID: PMC6387372 DOI: 10.3390/ijms20030667] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 01/21/2019] [Accepted: 01/28/2019] [Indexed: 02/07/2023] Open
Abstract
Basal-like breast cancer (BLBC) is an aggressive molecular subtype that represents up to 15% of breast cancers. It occurs in younger patients, and typically shows rapid development of locoregional and distant metastasis, resulting in a relatively high mortality rate. Its defining features are that it is positive for basal cytokeratins and, epidermal growth factor receptor and/or c-Kit. Problematically, it is typically negative for the estrogen receptor and human epidermal growth factor receptor 2 (HER2), which means that it is unsuitable for either hormone therapy or targeted HER2 therapy. As a result, there are few therapeutic options for BLBC, and a major priority is to define molecular subgroups of BLBC that could be targeted therapeutically. In this review, we focus on the highly proliferative and anti-apoptotic phenotype of BLBC with the goal of defining potential therapeutic avenues, which could take advantage of these aspects of tumor development.
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Affiliation(s)
- Sarah Alexandrou
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, 2010 Sydney, Australia.
| | - Sandra Marie George
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, 2010 Sydney, Australia.
| | - Christopher John Ormandy
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, 2010 Sydney, Australia.
- St. Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, 2052 Sydney, Australia.
| | - Elgene Lim
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, 2010 Sydney, Australia.
- St. Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, 2052 Sydney, Australia.
| | - Samantha Richelle Oakes
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, 2010 Sydney, Australia.
- St. Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, 2052 Sydney, Australia.
| | - C Elizabeth Caldon
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, 2010 Sydney, Australia.
- St. Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, 2052 Sydney, Australia.
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15
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Gao M, Lin Y, Liu X, Li Y, Zhang C, Wang Z, Wang Z, Wang Y, Guo Z. ISG20 promotes local tumor immunity and contributes to poor survival in human glioma. Oncoimmunology 2018; 8:e1534038. [PMID: 30713788 PMCID: PMC6343791 DOI: 10.1080/2162402x.2018.1534038] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 10/01/2018] [Accepted: 10/02/2018] [Indexed: 12/20/2022] Open
Abstract
Recent evidence has confirmed that a mutation of the isocitrate dehydrogenase (IDH) gene occurs early in gliomagenesis and contributes to suppressed immunity. The present study aimed to determine the candidate genes associated with IDH mutation status that could serve as biomarkers of immune suppression for improved prognosis prediction. Clinical information and RNA-seq gene expression data were collected for 932 glioma samples from the CGGA and TCGA databases, and differentially expressed genes in both lower-grade glioma (LGG) and glioblastoma (GBM) samples were identified according to IDH mutation status. Only one gene, interferon-stimulated exonuclease gene 20 (ISG20), with reduced expression in IDH mutant tumors, demonstrated significant prognostic value. ISG20 expression level significantly increased with increasing tumor grade, and its high expression was associated with a poor clinical outcome. Moreover, increased ISG20 expression was associated with increased infiltration of monocyte-derived macrophages and neutrophils, and suppressed adaptive immune response. ISG20 expression was also positively correlated with PD-1, PD-L1, and CTLA4 expression, along with the levels of several chemokines. We conclude that ISG20 is a useful biomarker to identify IDH-mediated immune processes in glioma and may serve as a potential therapeutic target.
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Affiliation(s)
- Mengqi Gao
- Department of Neurosurgery, the First Hospital of China Medical University, Shenyang, China
| | - Yi Lin
- Department of Neurosurgery, the First Hospital of China Medical University, Shenyang, China
| | - Xing Liu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas network, Beijing, China
| | - Yiming Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas network, Beijing, China
| | - Chuanbao Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas network, Beijing, China
| | - Zheng Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas network, Beijing, China
| | - Zhiliang Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Chinese Glioma Genome Atlas network, Beijing, China
| | - Yulin Wang
- Department of Neurosurgery, the First Hospital of China Medical University, Shenyang, China
| | - Zongze Guo
- Department of Neurosurgery, the First Hospital of China Medical University, Shenyang, China
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16
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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: 41] [Impact Index Per Article: 6.8] [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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17
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Kalinkova L, Zmetakova I, Smolkova B, Minarik G, Sedlackova T, Horvathova Kajabova V, Cierna Z, Mego M, Fridrichova I. Decreased methylation in the SNAI2 and ADAM23 genes associated with de-differentiation and haematogenous dissemination in breast cancers. BMC Cancer 2018; 18:875. [PMID: 30189837 PMCID: PMC6127923 DOI: 10.1186/s12885-018-4783-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 08/29/2018] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND In breast cancer (BC), deregulation of DNA methylation leads to aberrant expressions and functions of key regulatory genes. In our study, we investigated the relationship between the methylation profiles of genes associated with cancer invasivity and clinico-pathological parameters. In detail, we studied differences in the methylation levels between BC patients with haematogenous and lymphogenous cancer dissemination. METHODS We analysed samples of primary tumours (PTs), lymph node metastases (LNMs) and peripheral blood cells (PBCs) from 59 patients with sporadic disseminated BC. Evaluation of the DNA methylation levels of six genes related to invasivity, ADAM23, uPA, CXCL12, TWIST1, SNAI1 and SNAI2, was performed by pyrosequencing. RESULTS Among the cancer-specific methylated genes, we found lower methylation levels of the SNAI2 gene in histologic grade 3 tumours (OR = 0.61; 95% CI, 0.39-0.97; P = 0.038) than in fully or moderately differentiated cancers. We also evaluated the methylation profiles in patients with different cancer cell dissemination statuses (positivity for circulating tumour cells (CTCs) and/or LNMs). We detected the significant association between reduced DNA methylation of ADAM23 in PTs and presence of CTCs in the peripheral blood of patients (OR = 0.45; 95% CI, 0.23-0.90; P = 0.023). CONCLUSION The relationships between the decreased methylation levels of the SNAI2 and ADAM23 genes and cancer de-differentiation and haematogenous dissemination, respectively, indicate novel functions of those genes in the invasive processes. After experimental validation of the association between the lower values of SNAI2 and ADAM23 methylation and clinical features of aggressive BCs, these methylation profiles could improve the management of metastatic disease.
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Affiliation(s)
- Lenka Kalinkova
- Department of Genetics, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, v.v.i., Dubravska cesta 9, 845 05, Bratislava, Slovak Republic
| | - Iveta Zmetakova
- Department of Genetics, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, v.v.i., Dubravska cesta 9, 845 05, Bratislava, Slovak Republic
| | - Bozena Smolkova
- Department of Genetics, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, v.v.i., Dubravska cesta 9, 845 05, Bratislava, Slovak Republic
| | - Gabriel Minarik
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Sasinkova 4, 811 08, Bratislava, Slovak Republic
| | - Tatiana Sedlackova
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Sasinkova 4, 811 08, Bratislava, Slovak Republic
| | - Viera Horvathova Kajabova
- Department of Genetics, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, v.v.i., Dubravska cesta 9, 845 05, Bratislava, Slovak Republic
| | - Zuzana Cierna
- Institute of Pathological Anatomy, Faculty of Medicine, Comenius University, University Hospital, Sasinkova 4, 811 08, Bratislava, Slovak Republic
| | - Michal Mego
- 2nd Department of Oncology, Faculty of Medicine, Comenius University, National Cancer Institute, Klenova 1, 83310, Bratislava, Slovak Republic
| | - Ivana Fridrichova
- Department of Genetics, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, v.v.i., Dubravska cesta 9, 845 05, Bratislava, Slovak Republic.
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18
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Gatti V, Fierro C, Compagnone M, Giangrazi F, Markert EK, Bongiorno-Borbone L, Melino G, Peschiaroli A. ΔNp63 regulates the expression of hyaluronic acid-related genes in breast cancer cells. Oncogenesis 2018; 7:65. [PMID: 30139970 PMCID: PMC6107578 DOI: 10.1038/s41389-018-0073-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 06/20/2018] [Accepted: 07/10/2018] [Indexed: 12/16/2022] Open
Abstract
Triple negative breast cancers (TNBC) represent the most aggressive and clinically relevant breast carcinomas. On the basis of specific molecular signature, the majority of TNBC can be classified as basal-like breast carcinoma. Here, we report data showing that in basal-like breast carcinoma cells ΔNp63 is capable of sustaining the production of the hyaluronic acid (HA), one of the major component of the extracellular matrix (ECM). At molecular level, we found that ΔNp63 regulates the expression of HA-related genes, such as the HA synthase HAS3, the hyaluronidase HYAL-1 and CD44, the major HA cell membrane receptor. By controlling this pathway, ∆Np63 contributes to maintain the self-renewal of breast cancer stem cells. Importantly, high HAS3 expression is a negative prognostic factor of TNBC patients. Our data suggest that in basal-type breast carcinoma ∆Np63 might favor a HA-rich microenviroment, which can sustain tumor proliferation and stemness.
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Affiliation(s)
- Veronica Gatti
- National Research Council of Italy, (CNR), Institute of Cell Biology and Neurobiology (IBCN), CNR, Monterotondo, Rome, Italy
| | - Claudia Fierro
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
| | - Mirco Compagnone
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy.,Paediatric Haematology/Oncology Department, Bambino Gesù Children's Hospital IRCCS, Piazza S. Onofrio 4, 00165, Rome, Italy
| | - Federica Giangrazi
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy.,Molecular Cell Biology Laboratory, Department of Genetics, The Smurfit Institute, Trinity College, The University of Dublin, Dublin 2, Ireland
| | - Elke Katrin Markert
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - Lucilla Bongiorno-Borbone
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
| | - Gerry Melino
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy. .,Medical Research Council, Toxicology Unit, Hodgkin Building, Leicester University, Lancaster Road, P.O. Box 138, Leicester, LE1 9HN, UK.
| | - Angelo Peschiaroli
- National Research Council of Italy, (CNR), Institute of Translational Pharmacology (IFT), Via Fosso del Cavaliere 100, Rome, 00133, Italy.
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19
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Nasif D, Campoy E, Laurito S, Branham R, Urrutia G, Roqué M, Branham MT. Epigenetic regulation of ID4 in breast cancer: tumor suppressor or oncogene? Clin Epigenetics 2018; 10:111. [PMID: 30139383 PMCID: PMC6108146 DOI: 10.1186/s13148-018-0542-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 08/06/2018] [Indexed: 12/11/2022] Open
Abstract
Background Inhibitor of differentiation protein 4 (ID4) is a dominant negative regulator of the basic helix-loop-helix (bHLH) family of transcription factors. During tumorigenesis, ID4 may act as a tumor suppressor or as an oncogene in different tumor types. However, the role of ID4 in breast cancer is not clear where both an oncogenic and a tumor suppressor function have been attributed. Here, we hypothesize that ID4 behaves as both, but its role in breast differs according to the estrogen receptor (ER) status of the tumor. Methods ID4 expression was retrieved from TCGA database using UCSC Xena. Association between overall survival (OS) and ID4 was assessed using Kaplan–Meier plotter. Correlation between methylation and expression was analyzed using the MEXPRESS tool. In vitro experiments involved ectopic expression of ID4 in MCF-7, T47D, and MDA-MB231 breast cancer cell lines. Migration and colony formation capacity were assessed after transfection treatments. Gene expression was analyzed by ddPCR and methylation by MSP, MS-MLPA, or ddMSP. Results Data mining analysis revealed that ID4 expression is significantly lower in ER+ tumors with respect to ER− tumors or normal tissue. We also demonstrate that ID4 is significantly methylated in ER+ tumors. Kaplan–Meier analysis indicated that low ID4 expression levels were associated with poor overall survival in patients with ER+ tumors. In silico expression analysis indicated that ID4 was associated with the expression of key genes of the ER pathway only in ER+ tumors. In vitro experiments revealed that ID4 overexpression in ER+ cell lines resulted in decreased migration capacity and reduced number of colonies. ID4 overexpression induced a reduction in ER levels in ER+ cell lines, while estrogen deprivation with fulvestrant did not induce changes neither in ID4 methylation nor in ID4 expression. Conclusions We propose that ID4 is frequently silenced by promoter methylation in ER+ breast cancers and functions as a tumor suppressor gene in these tumors, probably due to its interaction with key genes of the ER pathway. Our present study contributes to the knowledge of the role of ID4 in breast cancer. Electronic supplementary material The online version of this article (10.1186/s13148-018-0542-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniela Nasif
- IHEM, National University of Cuyo, CONICET, Mendoza, Argentina
| | - Emanuel Campoy
- IHEM, CONICET, Facultad de Ciencias Médicas, National University of Cuyo, Mendoza, Argentina
| | - Sergio Laurito
- IHEM, Faculty of Exact and Natural Sciences, National University of Cuyo, CONICET, Mendoza, Argentina
| | | | | | - María Roqué
- IHEM, Faculty of Exact and Natural Sciences, National University of Cuyo, CONICET, Mendoza, Argentina
| | - María T Branham
- IHEM, National University of Cuyo, CONICET, Mendoza, Argentina.
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20
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Graff-Baker AN, Orozco JIJ, Marzese DM, Salomon MP, Hoon DSB, Goldfarb M. Epigenomic and Transcriptomic Characterization of Secondary Breast Cancers. Ann Surg Oncol 2018; 25:3082-3087. [PMID: 29956094 DOI: 10.1245/s10434-018-6582-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND Molecular alterations impact tumor prognosis and response to treatment. This study was designed to identify transcriptomic and epigenomic signatures of breast cancer (BC) tumors from patients with any prior malignancy. METHODS RNA-sequencing and genome-wide DNA methylation profiles from BCs were generated in the Cancer Genome Atlas project. Patients with secondary breast cancer (SBC) were separated by histological subtype and matched to primary breast cancer controls to create two independent cohorts of invasive ductal (IDC, n = 36) and invasive lobular (ILC, n = 40) carcinoma. Differentially expressed genes, as well as differentially methylated genomic regions, were integrated to identify epigenetically regulated abnormal gene pathways in SBCs. RESULTS Differentially expressed genes were identified in IDC SBCs (n = 727) and in ILC SBCs (n = 261; Wilcoxon's test; P < 0.05). In IDC SBCs, 105 genes were upregulated and hypomethylated, including an estrogen receptor gene, and 73 genes were downregulated and hypermethylated, including genes involved in antigen presentation and interferon response pathways (HLA-E, IRF8, and RELA). In ILC SBCs, however, only 17 genes were synchronously hypomethylated and upregulated, whereas 46 genes hypermethylated and downregulated. Interestingly, the SBC gene expression signatures closely corresponded with each histological subtype with only 1.51% of genes overlapping between the two histological subtypes. CONCLUSIONS Differential gene expression and DNA methylation signatures are seen in both IDC and ILC SBCs, including genes that are relevant to tumor growth and proliferation. Differences in gene expression signatures corresponding with each histological subtype emphasize the importance of disease subtype-specific evaluations of molecular alterations.
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Affiliation(s)
- Amanda N Graff-Baker
- Center for Endocrine Tumors and Disorders, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Javier I J Orozco
- Center for Endocrine Tumors and Disorders, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Diego M Marzese
- Center for Endocrine Tumors and Disorders, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Matthew P Salomon
- Center for Endocrine Tumors and Disorders, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Dave S B Hoon
- Center for Endocrine Tumors and Disorders, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, USA
| | - Melanie Goldfarb
- Center for Endocrine Tumors and Disorders, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, USA.
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21
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Identification of differentially expressed genes regulated by molecular signature in breast cancer-associated fibroblasts by bioinformatics analysis. Arch Gynecol Obstet 2017; 297:161-183. [PMID: 29063236 DOI: 10.1007/s00404-017-4562-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 09/21/2017] [Indexed: 12/18/2022]
Abstract
OBJECTIVE Breast cancer is a severe risk to public health and has adequately convoluted pathogenesis. Therefore, the description of key molecular markers and pathways is of much importance for clarifying the molecular mechanism of breast cancer-associated fibroblasts initiation and progression. Breast cancer-associated fibroblasts gene expression dataset was downloaded from Gene Expression Omnibus database. METHODS A total of nine samples, including three normal fibroblasts, three granulin-stimulated fibroblasts and three cancer-associated fibroblasts samples, were used to identify differentially expressed genes (DEGs) between normal fibroblasts, granulin-stimulated fibroblasts and cancer-associated fibroblasts samples. The gene ontology (GO) and pathway enrichment analysis was performed, and protein-protein interaction (PPI) network of the DEGs was constructed by NetworkAnalyst software. RESULTS Totally, 190 DEGs were identified, including 66 up-regulated and 124 down-regulated genes. GO analysis results showed that up-regulated DEGs were significantly enriched in biological processes (BP), including cell-cell signalling and negative regulation of cell proliferation; molecular function (MF), including insulin-like growth factor II binding and insulin-like growth factor I binding; cellular component (CC), including insulin-like growth factor binding protein complex and integral component of plasma membrane; the down-regulated DEGs were significantly enriched in BP, including cell adhesion and extracellular matrix organization; MF, including N-acetylgalactosamine 4-sulfate 6-O-sulfotransferase activity and calcium ion binding; CC, including extracellular space and extracellular matrix. WIKIPATHWAYS analysis showed the up-regulated DEGs were enriched in myometrial relaxation and contraction pathways. WIKIPATHWAYS, REACTOME, PID_NCI and KEGG pathway analysis showed the down-regulated DEGs were enriched endochondral ossification, TGF beta signalling pathway, integrin cell surface interactions, beta1 integrin cell surface interactions, malaria and glycosaminoglycan biosynthesis-chondroitin sulfate/dermatan sulphate. The top 5 up-regulated hub genes, CDKN2A, MME, PBX1, IGFBP3, and TFAP2C and top 5 down-regulated hub genes VCAM1, KRT18, TGM2, ACTA2, and STAMBP were identified from the PPI network, and subnetworks revealed these genes were involved in significant pathways, including myometrial relaxation and contraction pathways, integrin cell surface interactions, beta1 integrin cell surface interaction. Besides, the target hsa-mirs for DEGs were identified. hsa-mir-759, hsa-mir-4446-5p, hsa-mir-219a-1-3p and hsa-mir-26a-5p were important miRNAs in this study. CONCLUSIONS We pinpoint important key genes and pathways closely related with breast cancer-associated fibroblasts initiation and progression by a series of bioinformatics analysis on DEGs. These screened genes and pathways provided for a more detailed molecular mechanism underlying breast cancer-associated fibroblasts occurrence and progression, holding promise for acting as molecular markers and probable therapeutic targets.
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Gomez LC, Sottile ML, Guerrero-Gimenez ME, Zoppino FCM, Redondo AL, Gago FE, Orozco JI, Tello OM, Roqué M, Nadin SB, Marzese DM, Vargas-Roig LM. TP73 DNA methylation and upregulation of ΔNp73 are associated with an adverse prognosis in breast cancer. J Clin Pathol 2017; 71:52-58. [PMID: 28743687 DOI: 10.1136/jclinpath-2017-204499] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 05/12/2017] [Accepted: 05/12/2017] [Indexed: 12/14/2022]
Abstract
AIM Accumulated evidence suggests that aberrant methylation of the TP73 gene and increased levels of ΔNp73 in primary tumours correlate with poor prognosis. However, little is known regarding the transcriptional and functional regulation of the TP73 gene in breast cancer. The aim of the present study was to determine the expression of the ΔNp73 isoform, its relationship with DNA methylation of TP73 and their clinical prognostic significance in breast cancer patients. METHODS TP73 gene methylation was studied in TCGA datasets and in 70 invasive ductal breast carcinomas (IDCs). The expression of p73 isoforms was evaluated by immunohistochemistry (IHC) and Western blot and correlated with clinicopathological variables and clinical outcome. RESULTS We observed that the methylation of diverse CpG islands of TP73 differed significantly between molecular subtypes. An inverse correlation was found between p73 protein expression and the methylation status of the TP73 gene. The expression of exon 3' of p73 (only expressed in ΔNp73) was significantly higher in patients with wild-type p53. Immunohistochemical analysis revealed that all p73 isoforms were localised in both the nuclear and cytoplasmic compartments. We confirmed a positive association between the expression of ∆Np73 and high histological grade. CONCLUSIONS Our findings suggest that high expression of ΔNp73 could be used to determine the aggressiveness of IDCs and could be incorporated in the pathologist's report.
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Affiliation(s)
- Laura C Gomez
- Tumor Biology Laboratory, Institute of Medicine and Experimental Biology of Cuyo (IMBECU), National Scientific and Technical Research Council (CONICET), Mendoza, Argentina.,Faculty of Exact Sciences, National University of Cuyo, Mendoza, Argentina
| | - Mayra L Sottile
- Tumor Biology Laboratory, Institute of Medicine and Experimental Biology of Cuyo (IMBECU), National Scientific and Technical Research Council (CONICET), Mendoza, Argentina
| | - Martin E Guerrero-Gimenez
- Oncology Laboratory, IMBECU-CONICET, Mendoza, Argentina.,Medical School, National University of Cuyo, Mendoza, Argentina
| | - Felipe C M Zoppino
- Oncology Laboratory, IMBECU-CONICET, Mendoza, Argentina.,Medical School, National University of Cuyo, Mendoza, Argentina
| | - Analia L Redondo
- Tumor Biology Laboratory, Institute of Medicine and Experimental Biology of Cuyo (IMBECU), National Scientific and Technical Research Council (CONICET), Mendoza, Argentina.,Medical School, National University of Cuyo, Mendoza, Argentina
| | | | - Javier I Orozco
- Medical School, National University of Cuyo, Mendoza, Argentina.,Gineco-Mamario Institute, San Lorenzo, Mendoza, Argentina.,Department of Translational Molecular Medicine, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, USA
| | - Olga M Tello
- Gineco-Mamario Institute, San Lorenzo, Mendoza, Argentina
| | - Maria Roqué
- Faculty of Exact Sciences, National University of Cuyo, Mendoza, Argentina.,IHEM-CONICET, Mendoza, Argentina
| | - Silvina B Nadin
- Tumor Biology Laboratory, Institute of Medicine and Experimental Biology of Cuyo (IMBECU), National Scientific and Technical Research Council (CONICET), Mendoza, Argentina
| | - Diego M Marzese
- Department of Translational Molecular Medicine, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, USA
| | - Laura M Vargas-Roig
- Tumor Biology Laboratory, Institute of Medicine and Experimental Biology of Cuyo (IMBECU), National Scientific and Technical Research Council (CONICET), Mendoza, Argentina.,Medical School, National University of Cuyo, Mendoza, Argentina
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23
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Spitzwieser M, Entfellner E, Werner B, Pulverer W, Pfeiler G, Hacker S, Cichna-Markl M. Hypermethylation of CDKN2A exon 2 in tumor, tumor-adjacent and tumor-distant tissues from breast cancer patients. BMC Cancer 2017; 17:260. [PMID: 28403857 PMCID: PMC5389179 DOI: 10.1186/s12885-017-3244-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 03/29/2017] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Breast carcinogenesis is a multistep process involving genetic and epigenetic changes. Tumor tissues are frequently characterized by gene-specific hypermethylation and global DNA hypomethylation. Aberrant DNA methylation levels have, however, not only been found in tumors, but also in tumor-surrounding tissue appearing histologically normal. This phenomenon is called field cancerization. Knowledge of the existence of a cancer field and its spread are of clinical relevance. If the tissue showing pre-neoplastic lesions is not removed by surgery, it may develop into invasive carcinoma. METHODS We investigated the prevalence of gene-specific and global DNA methylation changes in tumor-adjacent and tumor-distant tissues in comparison to tumor tissues from the same breast cancer patients (n = 18) and normal breast tissues from healthy women (n = 4). Methylation-sensitive high resolution melting (MS-HRM) analysis was applied to determine methylation levels in the promoters of APC, BRCA1, CDKN2A (p16), ESR1, HER2/neu and PTEN, in CDKN2A exon 2 and in LINE-1, as indicator for the global DNA methylation extent. The methylation status of the ESR2 promoter was determined by pyrosequencing. RESULTS Tumor-adjacent and tumor-distant tissues frequently showed pre-neoplastic gene-specific and global DNA methylation changes. The APC promoter (p = 0.003) and exon 2 of CDKN2A (p < 0.001) were significantly higher methylated in tumors than in normal breast tissues from healthy women. For both regions, significant differences were also found between tumor and tumor-adjacent tissues (p = 0.001 and p < 0.001, respectively) and tumor and tumor-distant tissues (p = 0.001 and p < 0.001, respectively) from breast cancer patients. In addition, tumor-adjacent (p = 0.002) and tumor-distant tissues (p = 0.005) showed significantly higher methylation levels of CDKN2A exon 2 than normal breast tissues serving as control. Significant correlations were found between the proliferative activity and the methylation status of CDKN2A exon 2 in tumor (r = -0.485, p = 0.041) and tumor-distant tissues (r = -0.498, p = 0.036). CONCLUSIONS From our results we can conclude that methylation changes in CDKN2A exon 2 are associated with breast carcinogenesis. Further investigations are, however, necessary to confirm that hypermethylation of CDKN2A exon 2 is associated with tumor proliferative activity.
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Affiliation(s)
- Melanie Spitzwieser
- Department of Analytical Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria
| | - Elisabeth Entfellner
- Department of Analytical Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria
| | - Bettina Werner
- Department of Analytical Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria
| | - Walter Pulverer
- Molecular Diagnostics, Austrian Institute of Technology, Muthgasse 11, 1190, Vienna, Austria
| | - Georg Pfeiler
- Department of Obstetrics and Gynecology, Division of Gynecology and Gynecological Oncology, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Stefan Hacker
- Department of Plastic and Reconstructive Surgery, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Margit Cichna-Markl
- Department of Analytical Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria.
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Zhang Y, Zhang LX, Liu XQ, Zhao FY, Ge C, Chen TY, Yao M, Li JJ. Id4 promotes cell proliferation in hepatocellular carcinoma. CHINESE JOURNAL OF CANCER 2017; 36:19. [PMID: 28143562 PMCID: PMC5286768 DOI: 10.1186/s40880-017-0186-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 01/14/2017] [Indexed: 11/29/2022]
Abstract
Background Hepatocellular carcinoma (HCC) is a common malignant tumor in the world, especially in China. As a member of the inhibitor of differentiation (Id) family, Id4 has been reported to function in many cancer types, but relatively little is known about its role in HCC. The purpose of this study was to investigate the potential relationship between Id4 and HCC development and the underlying mechanism involving the function of Id4 in HCC. Methods We used quantitative real-time polymerase chain reaction and Western blotting to examine the RNA and protein expression of Id4. In addition, we used Cell Counting Kit-8 assay and colony formation assay to identify the function of Id4 in the regulation of cell proliferation in human HCC. Results We found that the expression of Id4 protein was up-regulated in tumor tissues from HCC patients. Overexpression of Id4 promoted HCC cell proliferation, clonogenicity in vitro, and tumorigenicity in vivo. Id4 knockdown experiments showed that silencing Id4 blocked the proliferation and colony formation ability of HCC cells in vitro. Furthermore, overexpression of CCAAT/enhancer-binding protein β inhibited Id4 expression in HCC cells. Conclusion Id4 may be developed as a potent therapeutic agent for the treatment of HCC, but more details about the underlying mechanisms of action are needed.
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Affiliation(s)
- Yang Zhang
- Shanghai Medical College, Fudan University, Shanghai, 200032, P. R. China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, 25/Ln 2200, Xietu Road, Shanghai, 200032, P. R. China
| | - Li-Xing Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, 25/Ln 2200, Xietu Road, Shanghai, 200032, P. R. China
| | - Xiao-Qin Liu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, 25/Ln 2200, Xietu Road, Shanghai, 200032, P. R. China
| | - Fang-Yu Zhao
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, 25/Ln 2200, Xietu Road, Shanghai, 200032, P. R. China
| | - Chao Ge
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, 25/Ln 2200, Xietu Road, Shanghai, 200032, P. R. China
| | - Tao-Yang Chen
- Qidong Liver Cancer Institute, Qidong, 226200, Jiangsu, P. R. China
| | - Ming Yao
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, 25/Ln 2200, Xietu Road, Shanghai, 200032, P. R. China
| | - Jin-Jun Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, 25/Ln 2200, Xietu Road, Shanghai, 200032, P. R. China.
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25
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A CpG island methylator phenotype in acute myeloid leukemia independent of IDH mutations and associated with a favorable outcome. Leukemia 2017; 31:2011-2019. [PMID: 28074068 PMCID: PMC5537054 DOI: 10.1038/leu.2017.12] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 12/09/2016] [Accepted: 12/13/2016] [Indexed: 12/12/2022]
Abstract
Genetic changes are infrequent in acute myeloid leukemia (AML) compared to other malignancies and often involve epigenetic regulators, suggesting that an altered epigenome may underlie AML biology and outcomes. In 96 AML cases including 65 pilot samples selected for cured/not-cured, we found higher CpG island (CGI) promoter methylation in cured patients. Expanded genome-wide digital restriction enzyme analysis of methylation (DREAM) data revealed a CGI methylator phenotype independent of IDH1/2 mutations we term AML-CIMP (A-CIMP+). A-CIMP was associated with longer overall survival (OS) in this dataset (median OS, years: A-CIMP+ = Not reached, A-CIMP− =1.17; P=0.08). For validation we used 194 samples from The Cancer Genome Atlas interrogated with Illumina 450k methylation arrays where we confirmed longer OS in A-CIMP (median OS, years: A-CIMP+ =2.34, A-CIMP− =1.00; P=0.01). Hypermethylation in A-CIMP favored CGIs (OR: CGI/non-CGI=5.21), and while A-CIMP was enriched in CEBPA (P=0.002) and WT1 mutations (P=0.02), 70% of cases lacked either mutation. Hypermethylated genes in A-CIMP function in pluripotency maintenance, and a gene expression signature of A-CIMP was associated with outcomes in multiple datasets. We conclude that CIMP in AML cannot be explained solely by gene mutations (e.g. IDH1/2, TET2), and that curability in A-CIMP+ AML should be validated prospectively.
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26
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Eyüpoglu IY, Savaskan NE. Epigenetics in Brain Tumors: HDACs Take Center Stage. Curr Neuropharmacol 2016; 14:48-54. [PMID: 26521944 PMCID: PMC4787285 DOI: 10.2174/1570159x13666151030162457] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 06/22/2015] [Accepted: 10/12/2015] [Indexed: 12/14/2022] Open
Abstract
Primary tumors of the brain account for 2 % of all cancers with malignant gliomas taking the lion’s share at 70 %. Malignant gliomas (high grade gliomas WHO° III and °IV) belong to one of the most threatening tumor entities known for their disappointingly short median survival time of just 14 months despite maximum therapy according to current gold standards. Malignant gliomas manifest various factors, through which they adapt and manipulate the tumor microenvironment to their advantage. Epigenetic mechanisms operate on the tumor microenvironment by de- and methylation processes and imbalances between the histone deacetylases (HDAC) and histone acetylases (HAT). Many compounds have been discovered modulating epigenetically controlled signals. Recent studies indicate that xCT (system xc-, SLC7a11) and CD44 (H-CAM, ECM-III, HUTCH-1) functions as a bridge between these epigenetic regulatory mechanisms and malignant glioma progression. The question that ensues is the extent to which therapeutic intervention on these signaling pathways would exert influence on the treatment of malignant gliomas as well as the extent to which manipulation of HDAC activity can sensitize tumor cells for chemotherapeutics through ‘epigenetic priming’. In light of considering the current stagnation in the development of therapeutic options, the need for new strategies in the treatment of gliomas has never been so pressing. In this context the possibility of pharmacological intervention on tumor-associated genes by epigenetic priming opens a novel path in the treatment of primary brain tumors.
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Affiliation(s)
- Ilker Y Eyüpoglu
- Department of Neurosurgery, Universitätsklinikum Erlangen, University of Erlangen- Nürnberg, Schwabachanlage 6, 91054 Erlangen, Germany.
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27
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Fleisher B, Clarke C, Ait-Oudhia S. Current advances in biomarkers for targeted therapy in triple-negative breast cancer. BREAST CANCER (DOVE MEDICAL PRESS) 2016; 8:183-197. [PMID: 27785100 PMCID: PMC5063595 DOI: 10.2147/bctt.s114659] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Triple-negative breast cancer (TNBC) is a complex heterogeneous disease characterized by the absence of three hallmark receptors: human epidermal growth factor receptor 2, estrogen receptor, and progesterone receptor. Compared to other breast cancer subtypes, TNBC is more aggressive, has a higher prevalence in African-Americans, and more frequently affects younger patients. Currently, TNBC lacks clinically accepted targets for tailored therapy, warranting the need for candidate biomarkers. BiomarkerBase, an online platform used to find biomarkers reported in clinical trials, was utilized to screen all potential biomarkers for TNBC and select only the ones registered in completed TNBC trials through clinicaltrials.gov. The selected candidate biomarkers were classified as surrogate, prognostic, predictive, or pharmacodynamic (PD) and organized by location in the blood, on the cell surface, in the cytoplasm, or in the nucleus. Blood biomarkers include vascular endothelial growth factor/vascular endothelial growth factor receptor and interleukin-8 (IL-8); cell surface biomarkers include EGFR, insulin-like growth factor binding protein, c-Kit, c-Met, and PD-L1; cytoplasm biomarkers include PIK3CA, pAKT/S6/p4E-BP1, PTEN, ALDH1, and the PIK3CA/AKT/mTOR-related metabolites; and nucleus biomarkers include BRCA1, the gluco-corticoid receptor, TP53, and Ki67. Candidate biomarkers were further organized into a "cellular protein network" that demonstrates potential connectivity. This review provides an inventory and reference point for promising biomarkers for breakthrough targeted therapies in TNBC.
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Affiliation(s)
- Brett Fleisher
- Department of Pharmaceutics, Center for Pharmacometrics and Systems Pharmacology, College of Pharmacy, University of Florida, Orlando, FL
| | - Charlotte Clarke
- Department of Translational Research, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Sihem Ait-Oudhia
- Department of Pharmaceutics, Center for Pharmacometrics and Systems Pharmacology, College of Pharmacy, University of Florida, Orlando, FL
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28
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DNA methylation profile of triple negative breast cancer-specific genes comparing lymph node positive patients to lymph node negative patients. Sci Rep 2016; 6:33435. [PMID: 27671774 PMCID: PMC5037364 DOI: 10.1038/srep33435] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 08/26/2016] [Indexed: 01/01/2023] Open
Abstract
Triple negative breast cancer (TNBC) is the most aggressive breast cancer subtype with no targeted treatment available. Our previous study identified 38 TNBC-specific genes with altered expression comparing tumour to normal samples. This study aimed to establish whether DNA methylation contributed to these expression changes in the same cohort as well as disease progression from primary breast tumour to lymph node metastasis associated with changes in the epigenome. We obtained DNA from 23 primary TNBC samples, 12 matched lymph node metastases, and 11 matched normal adjacent tissues and assayed for differential methylation profiles using Illumina HumanMethylation450 BeadChips. The results were validated in an independent cohort of 70 primary TNBC samples. The expression of 16/38 TNBC-specific genes was associated with alteration in DNA methylation. Novel methylation changes between primary tumours and lymph node metastases, as well as those associated with survival were identified. Altered methylation of 18 genes associated with lymph node metastasis were identified and validated. This study reveals the important role DNA methylation plays in altered gene expression of TNBC-specific genes and lymph node metastases. The novel insights into progression of TNBC to secondary disease may provide potential prognostic indicators for this hard-to-treat breast cancer subtype.
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Baker LA, Holliday H, Swarbrick A. ID4 controls luminal lineage commitment in normal mammary epithelium and inhibits BRCA1 function in basal-like breast cancer. Endocr Relat Cancer 2016; 23:R381-92. [PMID: 27412917 DOI: 10.1530/erc-16-0196] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 07/13/2016] [Indexed: 12/21/2022]
Abstract
Inhibitor of differentiation (ID) proteins are key regulators of development and tumorigenesis. One member of this family, ID4, controls lineage commitment during mammary gland development by acting upstream of key developmental pathways. Recent evidence suggests an emerging role for ID4 as a lineage-dependent proto-oncogene that is overexpressed and amplified in a subset of basal-like breast cancers (BLBCs), conferring poor prognosis. Several lines of evidence suggest ID4 may suppress BRCA1 function in BLBC and in doing so, define a subset of BLBC patients who may respond to therapies traditionally used in BRCA1-mutant cancers. This review highlights recent advances in our understanding of the requirement for ID4 in mammary lineage commitment and the role for ID4 in BLBC. We address current shortfalls in this field and identify important areas of future research.
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Affiliation(s)
- Laura A Baker
- The Kinghorn Cancer Centre and Cancer Research DivisionGarvan Institute of Medical Research, Darlinghurst, New South Wales, Australia St Vincent's Clinical SchoolFaculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Holly Holliday
- The Kinghorn Cancer Centre and Cancer Research DivisionGarvan Institute of Medical Research, Darlinghurst, New South Wales, Australia St Vincent's Clinical SchoolFaculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Alexander Swarbrick
- The Kinghorn Cancer Centre and Cancer Research DivisionGarvan Institute of Medical Research, Darlinghurst, New South Wales, Australia St Vincent's Clinical SchoolFaculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
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Asymmetric Cancer Hallmarks in Breast Tumors on Different Sides of the Body. PLoS One 2016; 11:e0157416. [PMID: 27383829 PMCID: PMC4934783 DOI: 10.1371/journal.pone.0157416] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 05/31/2016] [Indexed: 02/06/2023] Open
Abstract
During the last decades it has been established that breast cancer arises through the accumulation of genetic and epigenetic alterations in different cancer related genes. These alterations confer the tumor oncogenic abilities, which can be resumed as cancer hallmarks (CH). The purpose of this study was to establish the methylation profile of CpG sites located in cancer genes in breast tumors so as to infer their potential impact on 6 CH: i.e. sustained proliferative signaling, evasion of growth suppressors, resistance to cell death, induction of angiogenesis, genome instability and invasion and metastasis. For 51 breast carcinomas, MS-MLPA derived-methylation profiles of 81 CpG sites were converted into 6 CH profiles. CH profiles distribution was tested by different statistical methods and correlated with clinical-pathological data. Unsupervised Hierarchical Cluster Analysis revealed that CH profiles segregate in two main groups (bootstrapping 90–100%), which correlate with breast laterality (p = 0.05). For validating these observations, gene expression data was obtained by RealTime-PCR in a different cohort of 25 tumors and converted into CH profiles. This analyses confirmed the same clustering and a tendency of association with breast laterality (p = 0.15). In silico analyses on gene expression data from TCGA Breast dataset from left and right breast tumors showed that they differed significantly when data was previously converted into CH profiles (p = 0.033). We show here for the first time, that breast carcinomas arising on different sides of the body present differential cancer traits inferred from methylation and expression profiles. Our results indicate that by converting methylation or expression profiles in terms of Cancer Hallmarks, it would allow to uncover veiled associations with clinical features. These results contribute with a new finding to the better understanding of breast tumor behavior, and can moreover serve as proof of principle for other bilateral cancers like lung, testes or kidney.
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Callegari CC, Cavalli IJ, Lima RS, Jucoski TS, Torresan C, Urban CA, Kuroda F, Anselmi KF, Cavalli LR, Ribeiro EM. Copy number and expression analysis of FOSL1, GSTP1, NTSR1, FADD and CCND1 genes in primary breast tumors with axillary lymph node metastasis. Cancer Genet 2016; 209:331-9. [DOI: 10.1016/j.cancergen.2016.06.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 05/02/2016] [Accepted: 06/06/2016] [Indexed: 12/20/2022]
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Buchanan PJ, McCloskey KD. Ca V channels and cancer: canonical functions indicate benefits of repurposed drugs as cancer therapeutics. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2016; 45:621-633. [PMID: 27342111 PMCID: PMC5045480 DOI: 10.1007/s00249-016-1144-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 05/17/2016] [Accepted: 05/23/2016] [Indexed: 01/19/2023]
Abstract
The importance of ion channels in the hallmarks of many cancers is increasingly recognised. This article reviews current knowledge of the expression of members of the voltage-gated calcium channel family (CaV) in cancer at the gene and protein level and discusses their potential functional roles. The ten members of the CaV channel family are classified according to expression of their pore-forming α-subunit; moreover, co-expression of accessory α2δ, β and γ confers a spectrum of biophysical characteristics including voltage dependence of activation and inactivation, current amplitude and activation/inactivation kinetics. CaV channels have traditionally been studied in excitable cells including neurones, smooth muscle, skeletal muscle and cardiac cells, and drugs targeting the channels are used in the treatment of hypertension and epilepsy. There is emerging evidence that several CaV channels are differentially expressed in cancer cells compared to their normal counterparts. Interestingly, a number of CaV channels also have non-canonical functions and are involved in transcriptional regulation of the expression of other proteins including potassium channels. Pharmacological studies show that CaV canonical function contributes to the fundamental biology of proliferation, cell-cycle progression and apoptosis. This raises the intriguing possibility that calcium channel blockers, approved for the treatment of other conditions, could be repurposed to treat particular cancers. Further research will reveal the full extent of both the canonical and non-canonical functions of CaV channels in cancer and whether calcium channel blockers are beneficial in cancer treatment.
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Affiliation(s)
- Paul J Buchanan
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, Northern Ireland, BT9 7AE, UK.,National Institute of Cellular Biotechnology, School of Nursing and Human Science, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Karen D McCloskey
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, Northern Ireland, BT9 7AE, UK.
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33
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Branham MT, Campoy E, Laurito S, Branham R, Urrutia G, Orozco J, Gago F, Urrutia R, Roqué M. Epigenetic regulation of ID4 in the determination of the BRCAness phenotype in breast cancer. Breast Cancer Res Treat 2016; 155:13-23. [PMID: 26610810 PMCID: PMC6036618 DOI: 10.1007/s10549-015-3648-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 11/18/2015] [Indexed: 01/15/2023]
Abstract
BRCAness breast tumors represent a group of sporadic tumors characterized by a reduction in BRCA1 gene expression. As BRCA1 is involved in double-strand breaks (DSBs) repair, dysfunctional BRCA pathway could make a tumor sensitive to DNA damaging drugs (e.g., platinum agents). Thus, accurately identifying BRCAness could contribute to therapeutic decision making in patients harboring these tumors. The purpose of this study was to identify if BRCAness tumors present a characteristic methylation profile and/or were related to specific clinico-pathological features. BRCAness was measured by MLPA in 63 breast tumors; methylation status of 98 CpG sites within 84 cancer-related genes was analyzed by MS-MLPA. Protein and mRNA expressions of the selected genes were measured by quantitative real-time PCR and Western Blot. BRCAness was associated with younger age, higher nuclear pleomorphism, and triple-negative (TN) status. Epigenetically, we found that the strongest predictors for BRCAness tumors were the methylations of MLH1 and PAX5 plus the unmethylations of CCND2 and ID4. We determined that ID4 unmethylation correlated with the expression levels of both its mRNA and protein. We observed an inverse relation between the expressions of ID4 and BRCA1. To the best of our knowledge, this is the first report suggesting an epigenetic regulation of ID4 in BRCAness tumors. Our findings give new information of BRCAness etiology and encourage future studies on potential drug targets for BRCAness breast tumors.
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Affiliation(s)
- M T Branham
- IHEM-CCT-CONICET Mendoza and National University of Cuyo, Mendoza, Argentina.
| | - E Campoy
- IHEM-CCT-CONICET Mendoza and National University of Cuyo, Mendoza, Argentina
| | - S Laurito
- IHEM-CCT-CONICET Mendoza and National University of Cuyo, Mendoza, Argentina
| | - R Branham
- IANIGLA-CCT-CONICET Mendoza, Mendoza, Argentina
| | - G Urrutia
- IHEM-CCT-CONICET Mendoza and National University of Cuyo, Mendoza, Argentina
| | - J Orozco
- Gineco-Mamario Institute of Mendoza, Mendoza, Argentina
| | - F Gago
- Gineco-Mamario Institute of Mendoza, Mendoza, Argentina
| | - R Urrutia
- GI Research Unit, Division of Gastroenterology and Hepatology, Epigenomics Translational Program, Center for Individualized Medicine, Mayo Clinic, Rochester, USA
| | - M Roqué
- IHEM-CCT-CONICET Mendoza and National University of Cuyo, Mendoza, Argentina
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Sheng Y, Wang H, Liu D, Zhang C, Deng Y, Yang F, Zhang T, Zhang C. Methylation of tumor suppressor gene CDH13 and SHP1 promoters and their epigenetic regulation by the UHRF1/PRMT5 complex in endometrial carcinoma. Gynecol Oncol 2015; 140:145-51. [PMID: 26597461 DOI: 10.1016/j.ygyno.2015.11.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 10/24/2015] [Accepted: 11/17/2015] [Indexed: 12/19/2022]
Abstract
OBJECTIVE Epigenetic changes in cancer and precancerous lesions could be utilized as biomarkers for cancer early detection. This study aims to investigate the novel biomarkers in endometrial carcinoma, and explore their epigenetic regulation. METHODS Methylation of six tumor suppressor genes (CDH13, SHP1, HIN1, DKK3, CTNNA1 and PCDH8) was evaluated in 155 endometrium samples. Changes of methylation and mRNA expression after treatment with 5-Aza-2'-deoxycytidine (5-Aza-CdR) or/and trichostatin A (TSA) were investigated by MSP and qRT-PCR respectively. Co-immunoprecipitation was used to detect the interactions between UHRF1 and PRMT5 proteins. RESULTS CDH13 and SHP1 promoters were highly methylated (81.36% and 86.44%, respectively) in endometrial carcinoma, while CDH13 promoter methylation was also present in complex hyperplasia and atypical hyperplasia (51.72% and 50.00%, respectively). Methylation of CDH13 and SHP1 promoters was associated with age and tumor differentiation or muscular infiltration depth. CDH13 and SHP1 promoters were completely methylated in endometrial carcinoma cell lines and were partially reversed by 5-Aza-CdR or TSA to induce mRNA levels (P<0.01). After combined treatment with these two agents, methylation of CDH13 and SHP1 promoters was completely reversed and expression of their mRNA was significantly increased (P<0.01). Moreover, PRMT5 could bind to UHRF1 and down-regulated by 5-Aza-CdR and/or TSA treatment (P<0.05). CONCLUSIONS Our data demonstrate for the first time that SHP1 methylation has high specificity for diagnosis of endometrial carcinoma, while CDH13 promoter methylation plays a role in the earlier stage. Furthermore, UHRF1 could form a complex with PRMT5 to contribute to the endometrial carcinogenesis.
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Affiliation(s)
- Yan Sheng
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan 250012, China; Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, China
| | - Hongtao Wang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research for Cancer, The Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, China
| | - Dongchen Liu
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan 250012, China
| | - Cheng Zhang
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan 250012, China
| | - Yupeng Deng
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan 250012, China
| | - Fan Yang
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan 250012, China
| | - Tingguo Zhang
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan 250012, China.
| | - Cuijuan Zhang
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan 250012, China.
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Abstract
Most recent investigations into cancer etiology have identified a key role played by epigenetics. Specifically, aberrant DNA and histone modifications which silence tumor suppressor genes or promote oncogenes have been demonstrated in multiple cancer models. While the role of epigenetics in several solid tumor cancers such as colorectal cancer are well established, there is emerging evidence that epigenetics also plays a critical role in breast and prostate cancer. In breast cancer, DNA methylation profiles have been linked to hormone receptor status and tumor progression. Similarly in prostate cancer, epigenetic patterns have been associated with androgen receptor status and response to therapy. The regulation of key receptor pathways and activities which affect clinical therapy treatment options by epigenetics renders this field high priority for elucidating mechanisms and potential targets. A new set of methylation arrays are now available to screen epigenetic changes and provide the cutting-edge tools needed to perform such investigations. The role of nutritional interventions affecting epigenetic changes particularly holds promise. Ultimately, determining the causes and outcomes from epigenetic changes will inform translational applications for utilization as biomarkers for risk and prognosis as well as candidates for therapy.
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Affiliation(s)
- Yanyuan Wu
- Division of Cancer Research and Training, Center to Eliminate Cancer Health Disparities, Department of Internal Medicine, Charles Drew University of Medicine and Science, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, CA, USA
| | - Marianna Sarkissyan
- Division of Cancer Research and Training, Center to Eliminate Cancer Health Disparities, Department of Internal Medicine, Charles Drew University of Medicine and Science, Los Angeles, CA, USA
| | - Jaydutt V. Vadgama
- Division of Cancer Research and Training, Center to Eliminate Cancer Health Disparities, Department of Internal Medicine, Charles Drew University of Medicine and Science, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, University of California at Los Angeles, Los Angeles, CA, USA
- Corresponding Author Contact Information: Division of Cancer Research and Training, Center to Eliminate Cancer Health Disparities, Department of Internal Medicine, Charles R. Drew University of Medicine and Science, 1731 East 120th Street, Los Angeles, CA 90059, USA. Tele: 323-563-4853. Fax: 323-563-4859 ;
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Patel D, Morton DJ, Carey J, Havrda MC, Chaudhary J. Inhibitor of differentiation 4 (ID4): From development to cancer. Biochim Biophys Acta Rev Cancer 2014; 1855:92-103. [PMID: 25512197 DOI: 10.1016/j.bbcan.2014.12.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 11/25/2014] [Accepted: 12/06/2014] [Indexed: 01/25/2023]
Abstract
Highly conserved Inhibitors of DNA-Binding (ID1-ID4) genes encode multi-functional proteins whose transcriptional activity is based on dominant negative inhibition of basic helix-loop-helix (bHLH) transcription factors. Initial animal models indicated a degree of compensatory overlap between ID genes such that deletion of multiple ID genes was required to generate easily recognizable phenotypes. More recently, new model systems have revealed alterations in mice harboring deletions in single ID genes suggesting complex gene and tissue specific functions for members of the ID gene family. Because ID genes are highly expressed during development and their function is associated with a primitive, proliferative cellular phenotype there has been significant interest in understanding their potential roles in neoplasia. Indeed, numerous studies indicate an oncogenic function for ID1, ID2 and ID3. In contrast, the inhibitor of differentiation 4 (ID4) presents a paradigm shift in context of well-established role of ID1, ID2 and ID3 in development and cancer. Apart from some degree of functional redundancy such as HLH dependent interactions with bHLH protein E2A, many of the functions of ID4 are distinct from ID1, ID2 and ID3: ID4 proteins a) regulate distinct developmental processes and tissue expression in the adult, b) promote stem cell survival, differentiation and/or timing of differentiation, c) epigenetic inactivation/loss of expression in several advanced stage cancers and d) increased expression in some cancers such as those arising in the breast and ovary. Thus, in spite of sharing the conserved HLH domain, ID4 defies the established model of ID protein function and expression. The underlying molecular mechanism responsible for the unique role of ID4 as compared to other ID proteins still remains largely un-explored. This review will focus on the current understanding of ID4 in context of development and cancer.
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Affiliation(s)
- Divya Patel
- Department of Biological Sciences, Center for Cancer Research and Therapeutics Development, Clark Atlanta University, Atlanta, GA 30314, USA
| | - Derrick J Morton
- Department of Biological Sciences, Center for Cancer Research and Therapeutics Development, Clark Atlanta University, Atlanta, GA 30314, USA
| | - Jason Carey
- Department of Experimental Radiation Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Mathew C Havrda
- Norris Cotton Cancer Center and Geisel Medical School at Dartmouth, Lebanon, NH, USA
| | - Jaideep Chaudhary
- Department of Biological Sciences, Center for Cancer Research and Therapeutics Development, Clark Atlanta University, Atlanta, GA 30314, USA.
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Epigenetic alterations in a gastric leiomyoma. Case Rep Gastrointest Med 2014; 2014:371638. [PMID: 25544907 PMCID: PMC4273588 DOI: 10.1155/2014/371638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 11/17/2014] [Accepted: 11/17/2014] [Indexed: 01/17/2023] Open
Abstract
Leiomyomas constitute 2.5% of all resected neoplasms of the stomach. They are usually asymptomatic, but may present mucosal ulceration. Aberrant DNA methylation is a well-defined epigenetic change in human neoplasms; however, gene-acquired methylation may not necessarily be related with a malignant phenotype. In this report we analyzed in a gastric leiomyoma, the methylation status of 84 CpGI in tumor suppressor and DNA repair genes. We analyzed the tumor center (TC) and tumor periphery (TP) separately. We found aberrant methylation in 2/84 CpGI in the TC portion, that is, MLH1 and MSH3, and 5/84 CpGI in the TP, that is, MLH1, MSH3, APC, MSH6, and MGMT. The gene with the highest methylation percentage in the TC and TP was MLH1. Given that MLH1 methylation has been associated with microsatellite instability, we analyzed the status of the microsatellite Bat-26. We found that neither the TC nor the TP presented instability. The methylation of MLH1, MGMT, and APC has been described in GISTs, but to the best of our knowledge this is the first time that the methylation of these genes has been associated with gastric leiomyoma. Further research should be conducted to identify reliable molecular markers that could differentiate between GISTs and gastric leiomyomas.
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Wolf IML, Fan Z, Rauh M, Seufert S, Hore N, Buchfelder M, Savaskan NE, Eyüpoglu IY. Histone deacetylases inhibition by SAHA/Vorinostat normalizes the glioma microenvironment via xCT equilibration. Sci Rep 2014; 4:6226. [PMID: 25228443 PMCID: PMC4165982 DOI: 10.1038/srep06226] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 08/04/2014] [Indexed: 12/13/2022] Open
Abstract
Malignant gliomas are characterized by neurodegenerative actions leading to the destruction of surrounding brain parenchyma. The disturbance in glutamate homeostasis caused by increased expression of the glutamate transporter xCT plays a key role in glioma progression. We demonstrate that the HDAC-inhibitor SAHA specifically inhibits the xCT-transporter expression. Thereby, tumor cell stress is engendered, marked by increase in ROS. Moreover, SAHA dependent xCT-reduction correlates with the inhibition of ATF4-expression, a factor known to foster xCT expression. Since xCT/system Xc- is pivotal for the brain tumor microenvironment, normalization of this system is a key in the management of malignant gliomas. To date, the problem lay in the inability to specifically target xCT due to the ubiquitous expression of the xCT-transporter—i.e. in non-cancerously transformed cells too—as well as its essential role in physiological CNS processes. Here, we show xCT-transporter equilibration through SAHA is specific for malignant brain tumors whereas SAHA does not affect the physiological xCT levels in healthy brain parenchyma. Our data indicate that SAHA operates on gliomas specifically via normalizing xCT expression which in consequence leads to reduced extracellular glutamate levels. This in turn causes a marked reduction in neuronal cell death and normalized tumor microenvironment.
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Affiliation(s)
- Ines M L Wolf
- 1] Department of Neurosurgery, Universitätsklinikum Erlangen, Friedrich Alexander Universität Erlangen-Nürnberg (FAU) [2]
| | - Zheng Fan
- 1] Department of Neurosurgery, Universitätsklinikum Erlangen, Friedrich Alexander Universität Erlangen-Nürnberg (FAU) [2]
| | - Manfred Rauh
- Department of Pediatrics and Adolescent Medicine, University of Erlangen-Nuremberg
| | | | - Nirjhar Hore
- Department of Neurosurgery, Universitätsklinikum Erlangen, Friedrich Alexander Universität Erlangen-Nürnberg (FAU)
| | - Michael Buchfelder
- Department of Neurosurgery, Universitätsklinikum Erlangen, Friedrich Alexander Universität Erlangen-Nürnberg (FAU)
| | - Nic E Savaskan
- 1] Department of Neurosurgery, Universitätsklinikum Erlangen, Friedrich Alexander Universität Erlangen-Nürnberg (FAU) [2]
| | - Ilker Y Eyüpoglu
- 1] Department of Neurosurgery, Universitätsklinikum Erlangen, Friedrich Alexander Universität Erlangen-Nürnberg (FAU) [2]
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Marzese DM, Scolyer RA, Roqué M, Vargas-Roig LM, Huynh JL, Wilmott JS, Murali R, Buckland ME, Barkhoudarian G, Thompson JF, Morton DL, Kelly DF, Hoon DSB. DNA methylation and gene deletion analysis of brain metastases in melanoma patients identifies mutually exclusive molecular alterations. Neuro Oncol 2014; 16:1499-509. [PMID: 24968695 DOI: 10.1093/neuonc/nou107] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND The brain is a common target of metastases for melanoma patients. Little is known about the genetic and epigenetic alterations in melanoma brain metastases (MBMs). Unraveling these molecular alterations is a key step in understanding their aggressive nature and identifying novel therapeutic targets. METHODS Genome-wide DNA methylation analyses of MBMs (n = 15) and normal brain tissues (n = 91) and simultaneous multigene DNA methylation and gene deletion analyses of metastatic melanoma tissues (99 MBMs and 43 extracranial metastases) were performed. BRAF and NRAS mutations were evaluated in MBMs by targeted sequencing. RESULTS MBMs showed significant epigenetic heterogeneity. RARB, RASSF1, ESR1, APC, PTEN, and CDH13 genes were frequently hypermethylated. Deletions were frequently detected in the CDKN2A/B locus. Of MBMs, 46.1% and 28.8% had BRAF and NRAS missense mutations, respectively. Compared with lung and liver metastases, MBMs exhibited higher frequency of CDH13 hypermethylation and CDKN2A/B locus deletion. Mutual exclusivity between hypermethylated genes and CDKN2A/B locus deletion identified 2 clinically relevant molecular subtypes of MBMs. CDKN2A/B deletions were associated with multiple MBMs and frequently hypermethylated genes with shorter time to brain metastasis. CONCLUSIONS Melanoma cells that colonize the brain harbor numerous genetically and epigenetically altered genes. This study presents an integrated genomic and epigenomic analysis that reveals MBM-specific molecular alterations and mutually exclusive molecular subtypes.
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Affiliation(s)
- Diego M Marzese
- Department of Molecular Oncology, John Wayne Cancer Institute, Santa Monica, California (D.M.M., J.L.H., D.S.B.H.); Department of Tissue Oncology and Diagnostic Pathology (R.A.S., M.E.B., J.F.T.) and Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, Australia (J.F.T.); Sydney Medical School, The University of Sydney, Sydney, Australia (R.A.S., J.S.W., M.E.B., J.F.T.); Melanoma Institute Australia, Sydney, Australia (R.A.S., J.S.W.); Cellular and Molecular Biology Laboratory, Institute of Histology and Embryology, Mendoza, Argentina (M.R.); Tumor Biology Laboratory, Institute of Medicine and Experimental Biology of Cuyo, Mendoza, Argentina (L.M.V.-R.); Department of Pathology (R.M.), Center for Molecular Oncology (R.M.), and Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York (R.M.); Division of Surgical Oncology, John Wayne Cancer Institute, Santa Monica, California (D.L.M.); Brain Tumor Center, Saint John's Health Center, Santa Monica, California (G.B., D.F.K.)
| | - Richard A Scolyer
- Department of Molecular Oncology, John Wayne Cancer Institute, Santa Monica, California (D.M.M., J.L.H., D.S.B.H.); Department of Tissue Oncology and Diagnostic Pathology (R.A.S., M.E.B., J.F.T.) and Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, Australia (J.F.T.); Sydney Medical School, The University of Sydney, Sydney, Australia (R.A.S., J.S.W., M.E.B., J.F.T.); Melanoma Institute Australia, Sydney, Australia (R.A.S., J.S.W.); Cellular and Molecular Biology Laboratory, Institute of Histology and Embryology, Mendoza, Argentina (M.R.); Tumor Biology Laboratory, Institute of Medicine and Experimental Biology of Cuyo, Mendoza, Argentina (L.M.V.-R.); Department of Pathology (R.M.), Center for Molecular Oncology (R.M.), and Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York (R.M.); Division of Surgical Oncology, John Wayne Cancer Institute, Santa Monica, California (D.L.M.); Brain Tumor Center, Saint John's Health Center, Santa Monica, California (G.B., D.F.K.)
| | - Maria Roqué
- Department of Molecular Oncology, John Wayne Cancer Institute, Santa Monica, California (D.M.M., J.L.H., D.S.B.H.); Department of Tissue Oncology and Diagnostic Pathology (R.A.S., M.E.B., J.F.T.) and Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, Australia (J.F.T.); Sydney Medical School, The University of Sydney, Sydney, Australia (R.A.S., J.S.W., M.E.B., J.F.T.); Melanoma Institute Australia, Sydney, Australia (R.A.S., J.S.W.); Cellular and Molecular Biology Laboratory, Institute of Histology and Embryology, Mendoza, Argentina (M.R.); Tumor Biology Laboratory, Institute of Medicine and Experimental Biology of Cuyo, Mendoza, Argentina (L.M.V.-R.); Department of Pathology (R.M.), Center for Molecular Oncology (R.M.), and Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York (R.M.); Division of Surgical Oncology, John Wayne Cancer Institute, Santa Monica, California (D.L.M.); Brain Tumor Center, Saint John's Health Center, Santa Monica, California (G.B., D.F.K.)
| | - Laura M Vargas-Roig
- Department of Molecular Oncology, John Wayne Cancer Institute, Santa Monica, California (D.M.M., J.L.H., D.S.B.H.); Department of Tissue Oncology and Diagnostic Pathology (R.A.S., M.E.B., J.F.T.) and Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, Australia (J.F.T.); Sydney Medical School, The University of Sydney, Sydney, Australia (R.A.S., J.S.W., M.E.B., J.F.T.); Melanoma Institute Australia, Sydney, Australia (R.A.S., J.S.W.); Cellular and Molecular Biology Laboratory, Institute of Histology and Embryology, Mendoza, Argentina (M.R.); Tumor Biology Laboratory, Institute of Medicine and Experimental Biology of Cuyo, Mendoza, Argentina (L.M.V.-R.); Department of Pathology (R.M.), Center for Molecular Oncology (R.M.), and Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York (R.M.); Division of Surgical Oncology, John Wayne Cancer Institute, Santa Monica, California (D.L.M.); Brain Tumor Center, Saint John's Health Center, Santa Monica, California (G.B., D.F.K.)
| | - Jamie L Huynh
- Department of Molecular Oncology, John Wayne Cancer Institute, Santa Monica, California (D.M.M., J.L.H., D.S.B.H.); Department of Tissue Oncology and Diagnostic Pathology (R.A.S., M.E.B., J.F.T.) and Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, Australia (J.F.T.); Sydney Medical School, The University of Sydney, Sydney, Australia (R.A.S., J.S.W., M.E.B., J.F.T.); Melanoma Institute Australia, Sydney, Australia (R.A.S., J.S.W.); Cellular and Molecular Biology Laboratory, Institute of Histology and Embryology, Mendoza, Argentina (M.R.); Tumor Biology Laboratory, Institute of Medicine and Experimental Biology of Cuyo, Mendoza, Argentina (L.M.V.-R.); Department of Pathology (R.M.), Center for Molecular Oncology (R.M.), and Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York (R.M.); Division of Surgical Oncology, John Wayne Cancer Institute, Santa Monica, California (D.L.M.); Brain Tumor Center, Saint John's Health Center, Santa Monica, California (G.B., D.F.K.)
| | - James S Wilmott
- Department of Molecular Oncology, John Wayne Cancer Institute, Santa Monica, California (D.M.M., J.L.H., D.S.B.H.); Department of Tissue Oncology and Diagnostic Pathology (R.A.S., M.E.B., J.F.T.) and Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, Australia (J.F.T.); Sydney Medical School, The University of Sydney, Sydney, Australia (R.A.S., J.S.W., M.E.B., J.F.T.); Melanoma Institute Australia, Sydney, Australia (R.A.S., J.S.W.); Cellular and Molecular Biology Laboratory, Institute of Histology and Embryology, Mendoza, Argentina (M.R.); Tumor Biology Laboratory, Institute of Medicine and Experimental Biology of Cuyo, Mendoza, Argentina (L.M.V.-R.); Department of Pathology (R.M.), Center for Molecular Oncology (R.M.), and Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York (R.M.); Division of Surgical Oncology, John Wayne Cancer Institute, Santa Monica, California (D.L.M.); Brain Tumor Center, Saint John's Health Center, Santa Monica, California (G.B., D.F.K.)
| | - Rajmohan Murali
- Department of Molecular Oncology, John Wayne Cancer Institute, Santa Monica, California (D.M.M., J.L.H., D.S.B.H.); Department of Tissue Oncology and Diagnostic Pathology (R.A.S., M.E.B., J.F.T.) and Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, Australia (J.F.T.); Sydney Medical School, The University of Sydney, Sydney, Australia (R.A.S., J.S.W., M.E.B., J.F.T.); Melanoma Institute Australia, Sydney, Australia (R.A.S., J.S.W.); Cellular and Molecular Biology Laboratory, Institute of Histology and Embryology, Mendoza, Argentina (M.R.); Tumor Biology Laboratory, Institute of Medicine and Experimental Biology of Cuyo, Mendoza, Argentina (L.M.V.-R.); Department of Pathology (R.M.), Center for Molecular Oncology (R.M.), and Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York (R.M.); Division of Surgical Oncology, John Wayne Cancer Institute, Santa Monica, California (D.L.M.); Brain Tumor Center, Saint John's Health Center, Santa Monica, California (G.B., D.F.K.)
| | - Michael E Buckland
- Department of Molecular Oncology, John Wayne Cancer Institute, Santa Monica, California (D.M.M., J.L.H., D.S.B.H.); Department of Tissue Oncology and Diagnostic Pathology (R.A.S., M.E.B., J.F.T.) and Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, Australia (J.F.T.); Sydney Medical School, The University of Sydney, Sydney, Australia (R.A.S., J.S.W., M.E.B., J.F.T.); Melanoma Institute Australia, Sydney, Australia (R.A.S., J.S.W.); Cellular and Molecular Biology Laboratory, Institute of Histology and Embryology, Mendoza, Argentina (M.R.); Tumor Biology Laboratory, Institute of Medicine and Experimental Biology of Cuyo, Mendoza, Argentina (L.M.V.-R.); Department of Pathology (R.M.), Center for Molecular Oncology (R.M.), and Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York (R.M.); Division of Surgical Oncology, John Wayne Cancer Institute, Santa Monica, California (D.L.M.); Brain Tumor Center, Saint John's Health Center, Santa Monica, California (G.B., D.F.K.)
| | - Garni Barkhoudarian
- Department of Molecular Oncology, John Wayne Cancer Institute, Santa Monica, California (D.M.M., J.L.H., D.S.B.H.); Department of Tissue Oncology and Diagnostic Pathology (R.A.S., M.E.B., J.F.T.) and Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, Australia (J.F.T.); Sydney Medical School, The University of Sydney, Sydney, Australia (R.A.S., J.S.W., M.E.B., J.F.T.); Melanoma Institute Australia, Sydney, Australia (R.A.S., J.S.W.); Cellular and Molecular Biology Laboratory, Institute of Histology and Embryology, Mendoza, Argentina (M.R.); Tumor Biology Laboratory, Institute of Medicine and Experimental Biology of Cuyo, Mendoza, Argentina (L.M.V.-R.); Department of Pathology (R.M.), Center for Molecular Oncology (R.M.), and Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York (R.M.); Division of Surgical Oncology, John Wayne Cancer Institute, Santa Monica, California (D.L.M.); Brain Tumor Center, Saint John's Health Center, Santa Monica, California (G.B., D.F.K.)
| | - John F Thompson
- Department of Molecular Oncology, John Wayne Cancer Institute, Santa Monica, California (D.M.M., J.L.H., D.S.B.H.); Department of Tissue Oncology and Diagnostic Pathology (R.A.S., M.E.B., J.F.T.) and Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, Australia (J.F.T.); Sydney Medical School, The University of Sydney, Sydney, Australia (R.A.S., J.S.W., M.E.B., J.F.T.); Melanoma Institute Australia, Sydney, Australia (R.A.S., J.S.W.); Cellular and Molecular Biology Laboratory, Institute of Histology and Embryology, Mendoza, Argentina (M.R.); Tumor Biology Laboratory, Institute of Medicine and Experimental Biology of Cuyo, Mendoza, Argentina (L.M.V.-R.); Department of Pathology (R.M.), Center for Molecular Oncology (R.M.), and Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York (R.M.); Division of Surgical Oncology, John Wayne Cancer Institute, Santa Monica, California (D.L.M.); Brain Tumor Center, Saint John's Health Center, Santa Monica, California (G.B., D.F.K.)
| | - Donald L Morton
- Department of Molecular Oncology, John Wayne Cancer Institute, Santa Monica, California (D.M.M., J.L.H., D.S.B.H.); Department of Tissue Oncology and Diagnostic Pathology (R.A.S., M.E.B., J.F.T.) and Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, Australia (J.F.T.); Sydney Medical School, The University of Sydney, Sydney, Australia (R.A.S., J.S.W., M.E.B., J.F.T.); Melanoma Institute Australia, Sydney, Australia (R.A.S., J.S.W.); Cellular and Molecular Biology Laboratory, Institute of Histology and Embryology, Mendoza, Argentina (M.R.); Tumor Biology Laboratory, Institute of Medicine and Experimental Biology of Cuyo, Mendoza, Argentina (L.M.V.-R.); Department of Pathology (R.M.), Center for Molecular Oncology (R.M.), and Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York (R.M.); Division of Surgical Oncology, John Wayne Cancer Institute, Santa Monica, California (D.L.M.); Brain Tumor Center, Saint John's Health Center, Santa Monica, California (G.B., D.F.K.)
| | - Daniel F Kelly
- Department of Molecular Oncology, John Wayne Cancer Institute, Santa Monica, California (D.M.M., J.L.H., D.S.B.H.); Department of Tissue Oncology and Diagnostic Pathology (R.A.S., M.E.B., J.F.T.) and Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, Australia (J.F.T.); Sydney Medical School, The University of Sydney, Sydney, Australia (R.A.S., J.S.W., M.E.B., J.F.T.); Melanoma Institute Australia, Sydney, Australia (R.A.S., J.S.W.); Cellular and Molecular Biology Laboratory, Institute of Histology and Embryology, Mendoza, Argentina (M.R.); Tumor Biology Laboratory, Institute of Medicine and Experimental Biology of Cuyo, Mendoza, Argentina (L.M.V.-R.); Department of Pathology (R.M.), Center for Molecular Oncology (R.M.), and Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York (R.M.); Division of Surgical Oncology, John Wayne Cancer Institute, Santa Monica, California (D.L.M.); Brain Tumor Center, Saint John's Health Center, Santa Monica, California (G.B., D.F.K.)
| | - Dave S B Hoon
- Department of Molecular Oncology, John Wayne Cancer Institute, Santa Monica, California (D.M.M., J.L.H., D.S.B.H.); Department of Tissue Oncology and Diagnostic Pathology (R.A.S., M.E.B., J.F.T.) and Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, Australia (J.F.T.); Sydney Medical School, The University of Sydney, Sydney, Australia (R.A.S., J.S.W., M.E.B., J.F.T.); Melanoma Institute Australia, Sydney, Australia (R.A.S., J.S.W.); Cellular and Molecular Biology Laboratory, Institute of Histology and Embryology, Mendoza, Argentina (M.R.); Tumor Biology Laboratory, Institute of Medicine and Experimental Biology of Cuyo, Mendoza, Argentina (L.M.V.-R.); Department of Pathology (R.M.), Center for Molecular Oncology (R.M.), and Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York (R.M.); Division of Surgical Oncology, John Wayne Cancer Institute, Santa Monica, California (D.L.M.); Brain Tumor Center, Saint John's Health Center, Santa Monica, California (G.B., D.F.K.)
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Vogelsang M, Paccez JD, Schäfer G, Dzobo K, Zerbini LF, Parker MI. Aberrant methylation of the MSH3 promoter and distal enhancer in esophageal cancer patients exposed to first-hand tobacco smoke. J Cancer Res Clin Oncol 2014; 140:1825-33. [PMID: 24934723 DOI: 10.1007/s00432-014-1736-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 06/04/2014] [Indexed: 12/15/2022]
Abstract
PURPOSE Polymorphisms in MSH3 gene confer risk of esophageal cancer when in combination with tobacco smoke exposure. The purpose of this study was to investigate the methylation status of MSH3 gene in esophageal cancer patients in order to further elucidate possible role of MSH3 in esophageal tumorigenesis. METHODS We applied nested methylation-specific polymerase chain reaction to investigate the methylation status of the MSH3 promoter in tumors and matching adjacent normal-looking tissues of 84 esophageal cancer patients from a high-risk South African population. The Cancer Genome Atlas data were used to examine DNA methylation profiles at 17 CpG sites located in the MSH3 locus. RESULTS Overall, promoter methylation was detected in 91.9 % of tumors, which was significantly higher compared to 76.0 % in adjacent normal-looking esophageal tissues (P = 0.008). When samples were grouped according to different demographics (including age, gender and ethnicity) and smoking status of patients, methylation frequencies were found to be significantly higher in tumor tissues of Black subjects (P = 0.024), patients of 55-65 years of age (P = 0.032), males (P = 0.037) and tobacco smokers (P = 0.015). Furthermore, methylation of the MSH3 promoter was significantly more frequent in tumor samples from smokers compared to tumor samples from non-smokers [odds ratio (OR) = 31.9, P = 0.031]. The TCGA data confirmed significantly higher DNA methylation level at the MSH3 promoter region in tumors (P = 0.0024). In addition, we found evidence of an aberrantly methylated putative MSH3-associated distal enhancer element. CONCLUSION Our results suggest that methylation of MSH3 together with exposure to tobacco smoke is involved in esophageal carcinogenesis. Due to the active role of the MSH3 protein in modulating chemosensitivity of cells, methylation of MSH3 should further be examined in association with the outcome of esophageal cancer treatment using anticancer drugs.
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Affiliation(s)
- Matjaz Vogelsang
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town Component, UCT Medical Campus, Anzio Road, Observatory, Cape Town, 7925, South Africa
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Fumagalli C, Della Pasqua S, Bagnardi V, Cardillo A, Sporchia A, Colleoni M, Viale G, Barberis M, Pruneri G. Prevalence and clinicopathologic correlates of O⁶-methylguanine-DNA methyltransferase methylation status in patients with triple-negative breast cancer treated preoperatively by alkylating drugs. Clin Breast Cancer 2014; 14:285-90. [PMID: 24709436 DOI: 10.1016/j.clbc.2014.02.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 02/14/2014] [Accepted: 02/24/2014] [Indexed: 11/17/2022]
Abstract
BACKGROUND Predictive factors of benefit from specific chemotherapy regimens are not currently available in triple-negative breast cancer (TNBC). MGMT (O(6)-methylguanine-DNA methyltransferase) controls DNA repair pathways, and its epigenetic silencing is used for predicting the response to the alkylating drug temozolomide in patients with glioma. MATERIALS AND METHODS The study population was composed of 84 patients with TNBC treated with alkylating agents and evaluated for clinicopathologic parameters (tumor shrinkage and pathologic complete response [pCR]). MGMT methylation status was assessed in formalin-fixed, paraffin-embedded tumor specimens by pyrosequencing. The samples were categorized as methylated (mean methylation value > 5%), indeterminate (4%-5%), and unmethylated (≤ 3%). RESULTS MGMT methylation status was successfully evaluated in all the cases: 58.3% were methylated; 27.4%, unmethylated; and 14.3%, indeterminate. MGMT methylation was observed in 80%, 62%, and 29% of patients showing a 100%, 99% to 30%, and < 30% tumor reduction, respectively, a trend not achieving statistical significance (P = .23). There was no association between MGMT methylation status and pCR. CONCLUSION The present study provided evidence that pyrosequencing performs well for the evaluation of MGMT methylation even in small bioptic samples, suggesting that it could be reliably used in translational studies of preoperative clinical trials. Although there was an association trend between high methylation levels and clinical response to therapy, no statistically significant association with the pCR was found. Further studies in larger series of patients are warranted for ascertaining the putative clinical role of MGMT in patients with TNBC.
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Affiliation(s)
| | | | - Vincenzo Bagnardi
- Division of Epidemiology and Biostatistics, European Institute of Oncology, Milan, Italy
| | - Anna Cardillo
- Division of Medical Senology, European Institute of Oncology, Milan, Italy
| | - Andrea Sporchia
- Division of Medical Senology, European Institute of Oncology, Milan, Italy
| | - Marco Colleoni
- Division of Medical Senology, European Institute of Oncology, Milan, Italy
| | - Giuseppe Viale
- Division of Pathology, European Institute of Oncology, Milan, Italy; University of Milan School of Medicine; Department of Statistics and Quantitative Methods, University of Milan-Bicocca, Milan, Italy
| | - Massimo Barberis
- Division of Pathology, European Institute of Oncology, Milan, Italy
| | - Giancarlo Pruneri
- Division of Pathology, European Institute of Oncology, Milan, Italy; University of Milan School of Medicine; Department of Statistics and Quantitative Methods, University of Milan-Bicocca, Milan, Italy.
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Watanabe Y, Maeda I, Oikawa R, Wu W, Tsuchiya K, Miyoshi Y, Itoh F, Tsugawa KI, Ohta T. Aberrant DNA methylation status of DNA repair genes in breast cancer treated with neoadjuvant chemotherapy. Genes Cells 2013; 18:1120-30. [PMID: 24581343 DOI: 10.1111/gtc.12100] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 09/06/2013] [Indexed: 12/14/2022]
Abstract
Dysregulation of homologous recombination (HR) DNA repair has been implicated in breast carcinogenesis and chemosensitivity. Here, we investigated the methylation status of sixteen HR genes and analyzed their association with tumor subtypes and responses to neoadjuvant chemotherapy. Core specimens were obtained before neoadjuvant chemotherapy from sixty cases of primary breast cancer of the following four subgroups: luminal breast cancer (LBC) with pathological complete response (pCR), LBC with stable disease, triple-negative breast cancer (TNBC) with pCR and TNBC with poor response. The aberrant DNA methylation status of the following HR related-genes was analyzed using bisulfite-pyrosequencing: BRCA1, BRCA2, BARD1, MDC1, RNF8, RNF168, UBC13, ABRA1, PALB2, RAD50, RAD51, RAD51C, MRE11, NBS1, CtIP and ATM. Among the genes analyzed, only the incidence of BRCA1 and RNF8 methylation was significantly higher in TNBC than that in LBC. Whereas the incidence of BRCA1 methylation was tended to be higher in pCR cases than in poor-response cases in TNBC, that of RNF8 was significantly lower in pCR cases than in poor-response cases. Our results indicate that the methylation status of HR genes was not generally associated with TNBC subtype or chemosensitivity although hypermethylation of BRCA1 is associated with TNBC subtype and may impact chemosensitivity.
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Affiliation(s)
- Yoshiyuki Watanabe
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, 216-8511, Japan
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