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Kim DH, Binder AM, Zhou H, Jung SY. DNA methylation patterns associated with breast cancer prognosis that are specific to tumor subtype and menopausal status. Front Genet 2023; 14:1133443. [PMID: 36936429 PMCID: PMC10018014 DOI: 10.3389/fgene.2023.1133443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
Tumor subtype and menopausal status are strong predictors of breast cancer (BC) prognosis. We aimed to find and validate subtype- or menopausal-status-specific changes in tumor DNA methylation (DNAm) associated with all-cause mortality or BC progression. Associations between site-specific tumor DNAm and BC prognosis were estimated among The Cancer Genome Atlas participants (n = 692) with Illumina Infinium HumanMethylation450 BeadChip array data. All-cause mortality and BC progression were modeled using Cox proportional hazards models stratified by tumor subtypes, adjusting for age, race, stage, menopausal status, tumor purity, and cell type proportion. Effect measure modification by subtype and menopausal status were evaluated by incorporating a product term with DNAm. Site-specific inference was used to identify subtype- or menopausal-status-specific differentially methylated regions (DMRs) and functional pathways. The validation of the results was carried out on an independent dataset (GSE72308; n = 180). We identified a total of fifteen unique CpG probes that were significantly associated ( P ≤ 1 × 10 - 7 with survival outcomes in subtype- or menopausal-status-specific manner. Seven probes were associated with overall survival (OS) or progression-free interval (PFI) for women with luminal A subtype, and four probes were associated with PFI for women with luminal B subtype. Five probes were associated with PFI for post-menopausal women. A majority of significant probes showed a lower risk of OS or BC progression with higher DNAm. We identified subtype- or menopausal-status-specific DMRs and functional pathways of which top associated pathways differed across subtypes or menopausal status. None of significant probes from site-specific analyses met genome-wide significant level in validation analyses while directions and magnitudes of coefficients showed consistent pattern. We have identified subtype- or menopausal-status-specific DNAm biomarkers, DMRs and functional pathways associated with all-cause mortality or BC progression, albeit with limited validation. Future studies with larger independent cohort of non-post-menopausal women with non-luminal A subtypes are warranted for identifying subtype- and menopausal-status-specific DNAm biomarkers for BC prognosis.
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Affiliation(s)
- Do Hyun Kim
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, United States
| | - Alexandra M. Binder
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, United States
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, United States
- *Correspondence: Alexandra M. Binder,
| | - Hua Zhou
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Su Yon Jung
- Translational Sciences Section, School of Nursing, University of California, Los Angeles, Los Angeles, CA, United States
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, United States
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Chiang CC, Lin GL, Yang SY, Tu CW, Huang WL, Wei CF, Wang FC, Lin PJ, Huang WH, Chuang YM, Lee YT, Yeh CC, Chan M, Hsu YC. PCDHB15 as a potential tumor suppressor and epigenetic biomarker for breast cancer. Oncol Lett 2022; 23:117. [PMID: 35261631 PMCID: PMC8855166 DOI: 10.3892/ol.2022.13237] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 01/07/2022] [Indexed: 11/05/2022] Open
Abstract
Breast cancer is among the most frequently diagnosed cancer types and the leading cause of cancer-related death in women. The mortality rate of patients with breast cancer is currently increasing, perhaps due to a lack of early screening tools. In the present study, using The Cancer Genome Atlas (TCGA) breast cancer dataset (n=883), it was determined that methylation of the protocadherin β15 (PCDHB15) promoter was higher in breast cancer samples than that in normal tissues. A negative association between promoter methylation and expression of PCDHB15 was observed in the TCGA dataset and breast cancer cell lines. In TCGA cohort, lower PCDHB15 expression was associated with shorter relapse-free survival times. Treatment with the DNA methyltransferase inhibitor restored PCDHB15 expression in a breast cancer cell line; however, overexpression of PCDHB15 was shown to suppress colony formation. PCDHB15 methylation detected in circulating cell-free DNA (cfDNA) isolated from serum samples was higher in patients with breast cancer (40.8%) compared with that in patients with benign tumors (22.4%). PCDHB15 methylation was not correlated with any clinical parameters. Taken together, PCDHB15 is a potential tumor suppressor in cases of breast cancer, which can be epigenetically silenced via promoter methylation. PCDHB15 methylation using cfDNA is a novel minimally invasive epigenetic biomarker for the diagnosis and prognosis of breast cancer.
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Affiliation(s)
- Ching-Chung Chiang
- Department of Surgery, Ditmanson Medical Foundation Chiayi Christian Hospital, Chiayi 60002, Taiwan, R.O.C
| | - Guan-Ling Lin
- Department of Biomedical Sciences, National Chung Cheng University, Chiayi 62101, Taiwan, R.O.C
| | - Shu-Yi Yang
- Department of Biomedical Sciences, National Chung Cheng University, Chiayi 62101, Taiwan, R.O.C
| | - Chi-Wen Tu
- Department of Surgery, Ditmanson Medical Foundation Chiayi Christian Hospital, Chiayi 60002, Taiwan, R.O.C
| | - Wen-Long Huang
- Department of Chinese Medicine, Dalin Tzuchi Hospital, The Buddhist Tzuchi Medical Foundation, Chiayi 62247, Taiwan, R.O.C
| | - Chun-Feng Wei
- Department of Surgery, Ditmanson Medical Foundation Chiayi Christian Hospital, Chiayi 60002, Taiwan, R.O.C
| | - Feng-Chi Wang
- Department of Biomedical Sciences, National Chung Cheng University, Chiayi 62101, Taiwan, R.O.C
| | - Pin-Ju Lin
- Department of Biomedical Sciences, National Chung Cheng University, Chiayi 62101, Taiwan, R.O.C
| | - Wan-Hong Huang
- Department of Biomedical Sciences, National Chung Cheng University, Chiayi 62101, Taiwan, R.O.C
| | - Yu-Ming Chuang
- Department of Biomedical Sciences, National Chung Cheng University, Chiayi 62101, Taiwan, R.O.C
| | - Yu-Ting Lee
- Department of Biomedical Sciences, National Chung Cheng University, Chiayi 62101, Taiwan, R.O.C
| | - Chia-Chou Yeh
- Department of Chinese Medicine, Dalin Tzuchi Hospital, The Buddhist Tzuchi Medical Foundation, Chiayi 62247, Taiwan, R.O.C
| | - Michael Chan
- Department of Biomedical Sciences, National Chung Cheng University, Chiayi 62101, Taiwan, R.O.C
| | - Yu-Chen Hsu
- Department of Surgery, Ditmanson Medical Foundation Chiayi Christian Hospital, Chiayi 60002, Taiwan, R.O.C
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Chen Y, Xia F, Jiang B, Wang W, Li X. Role of Immune Cell-Specific Hypermethylation Signatures in Classification and Risk Stratification of Breast Cancer. Front Med (Lausanne) 2021; 8:674338. [PMID: 34513864 PMCID: PMC8426625 DOI: 10.3389/fmed.2021.674338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 08/06/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Epigenetic regulation, including DNA methylation, plays a major role in shaping the identity and function of immune cells. Innate and adaptive immune cells recruited into tumor tissues contribute to the formation of the tumor immune microenvironment (TIME), which is closely involved in tumor progression in breast cancer (BC). However, the specific methylation signatures of immune cells have not been thoroughly investigated yet. Additionally, it remains unknown whether immune cells-specific methylation signatures can identify subgroups and stratify the prognosis of BC patients. Methods: DNA methylation profiles of six immune cell types from eight datasets downloaded from the Gene Expression Omnibus were collected to identify immune cell-specific hypermethylation signatures (IC-SHMSs). Univariate and multivariate cox regression analyses were performed using BC data obtained from The Cancer Genome Atlas to identify the prognostic value of these IC-SHMSs. An unsupervised clustering analysis of the IC-SHMSs with prognostic value was performed to categorize BC patients into subgroups. Multiple Cox proportional hazard models were constructed to explore the role of IC-SHMSs and their relationship to clinical characteristics in the risk stratification of BC patients. Integrated discrimination improvement (IDI) was performed to determine whether the improvement of IC-SHMSs on clinical characteristics in risk stratification was statistically significant. Results: A total of 655 IC-SHMSs of six immune cell types were identified. Thirty of them had prognostic value, and 10 showed independent prognostic value. Four subgroups of BC patients, which showed significant heterogeneity in terms of survival prognosis and immune landscape, were identified. The model incorporating nine IC-SHMSs showed similar survival prediction accuracy as the clinical model incorporating age and TNM stage [3-year area under the curve (AUC): 0.793 vs. 0.785; 5-year AUC: 0.735 vs. 0.761]. Adding the IC-SHMSs to the clinical model significantly improved its prediction accuracy in risk stratification (3-year AUC: 0.897; 5-year AUC: 0.856). The results of IDI validated the statistical significance of the improvement (p < 0.05). Conclusions: Our study suggests that IC-SHMSs may serve as signatures of classification and risk stratification in BC. Our findings provide new insights into epigenetic signatures, which may help improve subgroup identification, risk stratification, and treatment management.
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Affiliation(s)
- Yong Chen
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Fada Xia
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Bo Jiang
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Wenlong Wang
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Xinying Li
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
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Zhang D, Wang Y, Yang Q. A High Epigenetic Risk Score Shapes the Non-Inflamed Tumor Microenvironment in Breast Cancer. Front Mol Biosci 2021; 8:675198. [PMID: 34381812 PMCID: PMC8350480 DOI: 10.3389/fmolb.2021.675198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 07/14/2021] [Indexed: 11/18/2022] Open
Abstract
Background: Epigenetic dysregulation via aberrant DNA methylation has gradually become recognized as an efficacious signature for predicting tumor prognosis and response to therapeutic targets. However, reliable DNA methylation biomarkers describing tumorigenesis remain to be comprehensively explored regarding their prognostic and therapeutic potential in breast cancer (BC). Methods: Whole-genome methylation datasets integrated from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database were profiled (n = 1,268). A three-stage selection procedure (discovery, training, and external validation) was utilized to screen out the prominent biomarkers and establish a robust risk score from more than 300,000 CpG sites after quality control, rigorous filtering, and reducing dimension. Moreover, gene set enrichment analyses guided us to systematically correlate this epigenetic risk score with immunological characteristics, including immunomodulators, anti-cancer immunity cycle, immune checkpoints, tumor-infiltrating immune cells and a series of signatures upon modulating components within BC tumor microenvironment (TME). Multi-omics data analyses were performed to decipher specific genomic alterations in low- and high-risk patients. Additionally, we also analyzed the role of risk score in predicting response to several treatment options. Results: A 10-CpG-based prognostic signature which could significantly and independently categorize BC patients into distinct prognoses was established and sufficiently validated. And we hypothesize that this signature designs a non-inflamed TME in BC based on the evidence that the derived risk score is negatively correlated with tumor-associated infiltrating immune cells, anti-cancer immunity cycle, immune checkpoints, immune cytolytic activity, T cell inflamed score, immunophenoscore, and the vast majority of immunomodulators. The identified high-risk patients were characterized by upregulation of immune inhibited oncogenic pathways, higher TP53 mutation and copy number burden, but lower response to cancer immunotherapy and chemotherapy. Conclusion: Our work highlights the complementary roles of 10-CpG-based signature in estimating overall survival in BC patients, shedding new light on investigating failed events concerning immunotherapy at present.
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Affiliation(s)
- Dong Zhang
- Department of Breast Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Department of Clinical Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yingnan Wang
- Department of Breast Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Department of Clinical Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Qifeng Yang
- Department of Breast Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Department of Pathology Tissue Bank, Qilu Hospital, Shandong University, Jinan, China
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Schröder R, Illert AL, Erbes T, Flotho C, Lübbert M, Duque-Afonso J. The epigenetics of breast cancer - Opportunities for diagnostics, risk stratification and therapy. Epigenetics 2021; 17:612-624. [PMID: 34159881 PMCID: PMC9235902 DOI: 10.1080/15592294.2021.1940644] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The stage and molecular pathology-dependent prognosis of breast cancer, the limited treatment options for triple-negative carcinomas, as well as the development of resistance to therapies illustrate the need for improved early diagnosis and the development of new therapeutic approaches. Increasing data suggests that some answers to these challenges could be found in the area of epigenetics. In this study, we focus on the current research of the epigenetics of breast cancer, especially on the potential of epigenetics for clinical application in diagnostics, risk stratification and therapy. The differential DNA methylation status of specific gene regions has been used in the past to differentiate breast cancer cells from normal tissue. New technologies as detection of circulating nucleic acids including microRNAs to early detect breast cancer are emerging. Pattern of DNA methylation and expression of histone-modifying enzymes have been successfully used for risk stratification. However, all these epigenetic biomarkers should be validated in larger clinical studies. Recent preclinical and clinical studies show a therapeutic benefit of epigenetically active drugs for breast cancer entities that are still difficult to treat (triple negative, UICC stage IV). Remarkably, epigenetic therapies combined with chemotherapies or hormone-based therapies represent the most promising strategy. At the current stage, the integration of epigenetic substances into established breast cancer therapy protocols seems to hold the greatest potential for a clinical application of epigenetic research.
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Affiliation(s)
- Rieke Schröder
- Department for Pediatric Hematology and Oncology, Faculty of Medicine and University of Freiburg Medical Center, University of Freiburg, Freiburg, Germany
| | - Anna-Lena Illert
- Department of Hematology/Oncology/Stem Cell Transplantation, University of Freiburg, Freiburg, Germany
| | - Thalia Erbes
- Department of Gynecology, Faculty of Medicine and University of Freiburg Medical Center, University of Freiburg, Freiburg, Germany
| | - Christian Flotho
- Department for Pediatric Hematology and Oncology, Faculty of Medicine and University of Freiburg Medical Center, University of Freiburg, Freiburg, Germany.,German Cancer Consortium (Deutsches Konsortium Für Translationale Krebsforschung, DKTK), Freiburg, Germany
| | - Michael Lübbert
- Department of Hematology/Oncology/Stem Cell Transplantation, University of Freiburg, Freiburg, Germany.,German Cancer Consortium (Deutsches Konsortium Für Translationale Krebsforschung, DKTK), Freiburg, Germany
| | - Jesús Duque-Afonso
- Department of Hematology/Oncology/Stem Cell Transplantation, University of Freiburg, Freiburg, Germany
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Emerging Precision Oncology Applications of Liquid Biopsy using Circulating Tumour DNA and Methylome Profiling. Clin Oncol (R Coll Radiol) 2020; 32:626-631. [PMID: 32586654 DOI: 10.1016/j.clon.2020.05.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 05/13/2020] [Accepted: 05/29/2020] [Indexed: 01/13/2023]
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7
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Kuang Y, Wang Y, Zhai W, Wang X, Zhang B, Xu M, Guo S, Ke M, Jia B, Liu H. Genome-Wide Analysis of Methylation-Driven Genes and Identification of an Eight-Gene Panel for Prognosis Prediction in Breast Cancer. Front Genet 2020; 11:301. [PMID: 32373154 PMCID: PMC7186397 DOI: 10.3389/fgene.2020.00301] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/13/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Aberrant DNA methylation is a crucial epigenetic regulator that is closely related to the occurrence and development of various cancers, including breast cancer (BC). The present study aimed to identify a novel methylation-based prognosis biomarker panel by integrally analyzing gene expression and methylation patterns in BC patients. METHODS DNA methylation and gene expression data of breast cancer (BRCA) were downloaded from The Cancer Genome Atlas (TCGA). R packages, including ChAMP, SVA, and MethylMix, were applied to identify the unique methylation-driven genes. Subsequently, these genes were subjected to Metascape for GO analysis. Univariant Cox regression was used to identify survival-related genes among the methylation-driven genes. Robust likelihood-based survival modeling was applied to define the prognosis markers. An independent data set (GSE72308) was used for further validation of our risk score system. RESULTS A total of 879 DNA methylation-driven genes were identified from 765 BC patients. In the discovery cohort, we identified 50 survival-related methylation-driven genes. Finally, we built an eight-methylation-driven gene panel that serves as prognostic predictors. CONCLUSIONS Our analysis of transcriptome and methylome variations associated with the survival status of BC patients provides a further understanding of basic biological processes and a basis for the genetic etiology in BC.
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Affiliation(s)
- Yanshen Kuang
- Department of General Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Ying Wang
- State Key Laboratory of Membrane Biology, School of Medicine, Tsinghua University, Beijing, China
| | - Wanli Zhai
- State Key Laboratory of Membrane Biology, School of Medicine, Tsinghua University, Beijing, China
| | - Xuning Wang
- Department of General Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Bingdong Zhang
- Department of General Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Maolin Xu
- Department of General Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Shaohua Guo
- Department of General Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Mu Ke
- Department of General Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Baoqing Jia
- Department of General Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Hongyi Liu
- Department of General Surgery, The First Medical Center, Chinese PLA General Hospital, Beijing, China
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Chen HL, Du L, Li XM. Re: Association of depression and anxiety disorder with the risk of mortality in breast cancer. Breast Cancer Res Treat 2019; 179:767-768. [PMID: 31858319 DOI: 10.1007/s10549-019-05510-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 12/08/2019] [Indexed: 10/25/2022]
Affiliation(s)
- Hong-Lin Chen
- School of Public Health, Nantong University, Nantong City, 226001, Jiangsu Province, People's Republic of China.
| | - Lin Du
- School of Medicine, Nantong University, Nantong City, 226001, Jiangsu Province, People's Republic of China
| | - Xiao-Min Li
- Surgical Department, Affiliated Hospital 2 of Nantong University, No. 6, Hai'er'xian North Road, Nantong, People's Republic of China
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