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Li X, Shen D, Zhu Z, Lyu D, He C, Sun Y, Li J, Lu Q, Wang G. Dual roles of demethylation in cancer treatment and cardio-function recovery. Redox Biol 2023; 64:102785. [PMID: 37343447 PMCID: PMC10363477 DOI: 10.1016/j.redox.2023.102785] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/07/2023] [Accepted: 06/13/2023] [Indexed: 06/23/2023] Open
Abstract
There are no effective therapeutic targets or strategies that simultaneously inhibit tumour growth and promote cardiac function recovery. Here, we analyzed targets for cancer treatments and cardiac repair, with demethylation emerging as a common factor in these candidate lists. As DNA methyltransferase 1 (DNMT1) majorly responds to methylation, a natural compound library is screened, identifying dioscin as a novel agent targeted at DNMT1, widely used for heart diseases. Dioscin was found to reduce DNMT activities and inhibits growth in breast cancer cells. Combined with analyses of RNA-seq and MeDIP-seq, the promoters of antioxidant genes were demethylated after dioscin, recruiting NRF2 and elevating their expression. In Nrf2 knockout mice, the cardiac protection role of dioscin was blocked by Nrf2-loss. Furthermore, in tumour-bearing mice with hypertrophy, dioscin was observed to inhibit tumour growth and alleviate cardiac injury simultaneously. This study is the first to identify dioscin as a novel demethylation agent with dual functions of anti-cancer and cardio-protection.
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Affiliation(s)
- Xinuo Li
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China; Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, China
| | - Dehong Shen
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, China
| | - Zheying Zhu
- School of Pharmacy, The University of Nottingham, Nottingham, NG7 2RD, UK
| | - Dayin Lyu
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, China
| | - Chang He
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, China
| | - Yuan Sun
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China; Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, China
| | - Jinran Li
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China; Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, China
| | - Qiulun Lu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China; Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, China.
| | - Guangji Wang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China; Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, China.
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Sarvari P, Sarvari P, Ramírez-Díaz I, Mahjoubi F, Rubio K. Advances of Epigenetic Biomarkers and Epigenome Editing for Early Diagnosis in Breast Cancer. Int J Mol Sci 2022; 23:ijms23179521. [PMID: 36076918 PMCID: PMC9455804 DOI: 10.3390/ijms23179521] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 12/02/2022] Open
Abstract
Epigenetic modifications are known to regulate cell phenotype during cancer progression, including breast cancer. Unlike genetic alterations, changes in the epigenome are reversible, thus potentially reversed by epi-drugs. Breast cancer, the most common cause of cancer death worldwide in women, encompasses multiple histopathological and molecular subtypes. Several lines of evidence demonstrated distortion of the epigenetic landscape in breast cancer. Interestingly, mammary cells isolated from breast cancer patients and cultured ex vivo maintained the tumorigenic phenotype and exhibited aberrant epigenetic modifications. Recent studies indicated that the therapeutic efficiency for breast cancer regimens has increased over time, resulting in reduced mortality. Future medical treatment for breast cancer patients, however, will likely depend upon a better understanding of epigenetic modifications. The present review aims to outline different epigenetic mechanisms including DNA methylation, histone modifications, and ncRNAs with their impact on breast cancer, as well as to discuss studies highlighting the central role of epigenetic mechanisms in breast cancer pathogenesis. We propose new research areas that may facilitate locus-specific epigenome editing as breast cancer therapeutics.
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Affiliation(s)
- Pourya Sarvari
- Department of Clinical Genetics, National Institute of Genetic Engineering and Biotechnology, Tehran P.O. Box 14965/161, Iran
| | - Pouya Sarvari
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico
| | - Ivonne Ramírez-Díaz
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico
- Facultad de Biotecnología, Campus Puebla, Universidad Popular Autónoma del Estado de Puebla (UPAEP), Puebla 72410, Mexico
| | - Frouzandeh Mahjoubi
- Department of Clinical Genetics, National Institute of Genetic Engineering and Biotechnology, Tehran P.O. Box 14965/161, Iran
| | - Karla Rubio
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Puebla 72160, Mexico
- Licenciatura en Médico Cirujano, Universidad de la Salud del Estado de Puebla (USEP), Puebla 72000, Mexico
- Correspondence:
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3
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Gadaleta E, Thorn GJ, Ross-Adams H, Jones LJ, Chelala C. Field cancerization in breast cancer. J Pathol 2022; 257:561-574. [PMID: 35362092 PMCID: PMC9322418 DOI: 10.1002/path.5902] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/23/2022] [Accepted: 03/29/2022] [Indexed: 11/30/2022]
Abstract
Breast cancer affects one in seven women worldwide during their lifetime. Widespread mammographic screening programs and education campaigns allow for early detection of the disease, often during its asymptomatic phase. Current practice in treatment and recurrence monitoring is based primarily on pathological evaluations but can also encompass genomic evaluations, both of which focus on the primary tumor. Although breast cancer is one of the most studied cancers, patients still recur at a rate of up to 15% within the first 10 years post‐surgery. Local recurrence was originally attributed to tumor cells contaminating histologically normal (HN) tissues beyond the surgical margin, but advances in technology have allowed for the identification of distinct aberrations that exist in the peri‐tumoral tissues themselves. One leading theory to explain this phenomenon is the field cancerization theory. Under this hypothesis, tumors arise from a field of molecularly altered cells that create a permissive environment for malignant evolution, which can occur with or without morphological changes. The traditional histopathology paradigm dictates that molecular alterations are reflected in the tissue phenotype. However, the spectrum of inter‐patient variability of normal breast tissue may obfuscate recognition of a cancerized field during routine diagnostics. In this review, we explore the concept of field cancerization focusing on HN peri‐tumoral tissues: we present the pathological and molecular features of field cancerization within these tissues and discuss how the use of peri‐tumoral tissues can affect research. Our observations suggest that pathological and molecular evaluations could be used synergistically to assess risk and guide the therapeutic management of patients. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Emanuela Gadaleta
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Graeme J Thorn
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Helen Ross-Adams
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Louise J Jones
- Centre for Tumour Biology Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Claude Chelala
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, UK
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Xu Y, Lin Y, Wang Y, Zhou L, Xu S, Wu Y, Peng J, Zhang J, Yin W, Lu J. Association of Neo-Family History Score with pathological complete response, safety, and survival outcomes in patients with breast cancer receiving neoadjuvant platinum-based chemotherapy: An exploratory analysis of two prospective trials. EClinicalMedicine 2021; 38:101031. [PMID: 34337367 PMCID: PMC8318862 DOI: 10.1016/j.eclinm.2021.101031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 06/28/2021] [Accepted: 06/30/2021] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND Homologous recombination deficiency is associated with platinum-based chemosensitivity, whereas few studies reported the predictive value of family history of cancer for breast cancer in the neoadjuvant setting. This study aimed to construct a novel family history scoring system and to explore its association with clinical outcomes for patients with breast cancer receiving neoadjuvant platinum-based chemotherapy. METHODS This study included 262 patients with locally advanced breast cancer enrolled in the SHPD001 and SHPD002 trials from October 2013 to June 2018. The Neo-Family History Score (NeoFHS) was calculated according to cancer type, age at diagnosis, kinship, and number of affected relatives. FINDINGS Clinical tumor stage (p=0·048), estrogen receptor status (p=0·001), progesterone receptor status (p=0·036), human epidermal growth factor receptor 2 status (p=0·013), and molecular subtype (p=0·016) were significantly related to NeoFHS. NeoFHS could serve as an independent predictive factor of pathological complete response (pCR) (OR=2·262, 95% CI 1·159-4·414, p=0·017) and an independent prognostic factor of relapse-free survival (adjusted HR=0·305, 95% CI 0·102-0·910, p=0·033). Alopecia (p=0·001), nausea (p=0·001), peripheral neuropathy (p=0·018), diarrhea (p=0·026), constipation (p=0·037) of any grade and leukopenia of grade 3 or greater (p=0·005) were more common in patients with higher NeoFHS. INTERPRETATION NeoFHS is a practical and effective biomarker for predicting not only pCR and survival outcomes but also chemotherapy-induced adverse events for neoadjuvant platinum-based chemotherapy in breast cancer. It may help screen candidate responders and guide safety managements. FUNDING Shanghai Natural Science Foundation [grant number 19ZR1431100], Clinical Research Plan of Shanghai Hospital Development Center [grant numbers SHDC2020CR3003A, 16CR3065B, and 12016231], Shanghai "Rising Stars of Medical Talent" Youth Development Program for Youth Medical Talents - Specialist Program [grant number 2018-15], Shanghai "Rising Stars of Medical Talent" Youth Development Program for Outstanding Youth Medical Talents [grant number 2018-16], Shanghai Collaborative Innovation Center for Translational Medicine [grant number TM201908], Multidisciplinary Cross Research Foundation of Shanghai Jiao Tong University [grant numbers YG2017QN49, ZH2018QNA42, and YG2019QNA28], Nurturing Fund of Renji Hospital [grant numbers PYMDT-002, PY2018-IIC-01, PY2018-III-15, and PYIII20-09], Science and Technology Commission of Shanghai Municipality [grant numbers 20DZ2201600 and 15JC1402700], and Shanghai Municipal Key Clinical Specialty.
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Metformin: Sentinel of the Epigenetic Landscapes That Underlie Cell Fate and Identity. Biomolecules 2020; 10:biom10050780. [PMID: 32443566 PMCID: PMC7277648 DOI: 10.3390/biom10050780] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/08/2020] [Accepted: 05/15/2020] [Indexed: 12/14/2022] Open
Abstract
The biguanide metformin is the first drug to be tested as a gerotherapeutic in the clinical trial TAME (Targeting Aging with Metformin). The current consensus is that metformin exerts indirect pleiotropy on core metabolic hallmarks of aging, such as the insulin/insulin-like growth factor 1 and AMP-activated protein kinase/mammalian Target Of Rapamycin signaling pathways, downstream of its primary inhibitory effect on mitochondrial respiratory complex I. Alternatively, but not mutually exclusive, metformin can exert regulatory effects on components of the biologic machinery of aging itself such as chromatin-modifying enzymes. An integrative metabolo-epigenetic outlook supports a new model whereby metformin operates as a guardian of cell identity, capable of retarding cellular aging by preventing the loss of the information-theoretic nature of the epigenome. The ultimate anti-aging mechanism of metformin might involve the global preservation of the epigenome architecture, thereby ensuring cell fate commitment and phenotypic outcomes despite the challenging effects of aging noise. Metformin might therefore inspire the development of new gerotherapeutics capable of preserving the epigenome architecture for cell identity. Such gerotherapeutics should replicate the ability of metformin to halt the erosion of the epigenetic landscape, mitigate the loss of cell fate commitment, delay stochastic/environmental DNA methylation drifts, and alleviate cellular senescence. Yet, it remains a challenge to confirm if regulatory changes in higher-order genomic organizers can connect the capacity of metformin to dynamically regulate the three-dimensional nature of epigenetic landscapes with the 4th dimension, the aging time.
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Gogna P, O'Sullivan DE, King WD. The effect of inflammation-related lifestyle exposures and interactions with gene variants on long interspersed nuclear element-1 DNA methylation. Epigenomics 2018; 10:785-796. [PMID: 29888958 DOI: 10.2217/epi-2017-0164] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM To examine the relationship between inflammation-related lifestyle factors and long interspersed nuclear element-1 (LINE-1) DNA methylation, and test for interaction by gene variants involved in one-carbon metabolism. PATIENTS & METHODS The study population consisted of 280 individuals undergoing colonoscopy screening. Multivariable linear regression was employed to examine associations of physical activity, BMI and NSAID use with LINE-1 DNA methylation and interactions with MTR and MTHFR gene variants. RESULTS The highest quartile of physical activity compared with the lowest was associated with higher LINE-1 DNA methylation (p = 0.005). Long-term NSAID use and a normal BMI were associated with increased LINE-1 DNA methylation among individuals with the variant MTR allele (p = 0.02; p = 0.03). CONCLUSION This study provides evidence that inflammation-related exposures may influence LINE-1 DNA methylation.
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Affiliation(s)
- Priyanka Gogna
- Department of Public Health Sciences, Queen's University, Kingston, Ontario, Canada
| | - Dylan E O'Sullivan
- Department of Public Health Sciences, Queen's University, Kingston, Ontario, Canada
| | - Will D King
- Department of Public Health Sciences, Queen's University, Kingston, Ontario, Canada
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7
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Joo JE, Dowty JG, Milne RL, Wong EM, Dugué PA, English D, Hopper JL, Goldgar DE, Giles GG, Southey MC. Heritable DNA methylation marks associated with susceptibility to breast cancer. Nat Commun 2018; 9:867. [PMID: 29491469 PMCID: PMC5830448 DOI: 10.1038/s41467-018-03058-6] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 01/08/2018] [Indexed: 02/03/2023] Open
Abstract
Mendelian-like inheritance of germline DNA methylation in cancer susceptibility genes has been previously reported. We aimed to scan the genome for heritable methylation marks associated with breast cancer susceptibility by studying 25 Australian multiple-case breast cancer families. Here we report genome-wide DNA methylation measured in 210 peripheral blood DNA samples provided by family members using the Infinium HumanMethylation450. We develop and apply a new statistical method to identify heritable methylation marks based on complex segregation analysis. We estimate carrier probabilities for the 1000 most heritable methylation marks based on family structure, and we use Cox proportional hazards survival analysis to identify 24 methylation marks with corresponding carrier probabilities significantly associated with breast cancer. We replicate an association with breast cancer risk for four of the 24 marks using an independent nested case-control study. Here, we report a novel approach for identifying heritable DNA methylation marks associated with breast cancer risk.
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Affiliation(s)
- Jihoon E Joo
- Department of Pathology, The University of Melbourne, Melbourne, VIC, 3010, Australia.,Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, 3168, Australia
| | - James G Dowty
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, VIC, 3010, Australia.,Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, VIC, 3004, Australia
| | - Ee Ming Wong
- Department of Pathology, The University of Melbourne, Melbourne, VIC, 3010, Australia.,Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, 3168, Australia
| | - Pierre-Antoine Dugué
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, VIC, 3010, Australia.,Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, VIC, 3004, Australia
| | - Dallas English
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, VIC, 3010, Australia.,Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, VIC, 3004, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - David E Goldgar
- Department of Pathology, The University of Melbourne, Melbourne, VIC, 3010, Australia.,Huntsman Cancer Institute, Salt Lake, UT, 84112, USA
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, VIC, 3010, Australia.,Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, VIC, 3004, Australia
| | - Melissa C Southey
- Department of Pathology, The University of Melbourne, Melbourne, VIC, 3010, Australia. .,Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, 3168, Australia.
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8
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Terry MB, Keegan THM, Houghton LC, Goldberg M, Andrulis IL, Daly MB, Buys SS, Wei Y, Whittemore AS, Protacio A, Bradbury AR, Chung WK, Knight JA, John EM. Pubertal development in girls by breast cancer family history: the LEGACY girls cohort. Breast Cancer Res 2017; 19:69. [PMID: 28595647 PMCID: PMC5465536 DOI: 10.1186/s13058-017-0849-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 05/03/2017] [Indexed: 01/29/2023] Open
Abstract
Background Pubertal milestones, such as onset of breast development and menstruation, play an important role in breast cancer etiology. It is unclear if these milestones are different in girls with a first- or second-degree breast cancer family history (BCFH). Methods In the LEGACY Girls Study (n = 1040), we examined whether three mother/guardian-reported pubertal milestones (having reached Tanner Stage 2 or higher (T2+) for breast and pubic hair development, and having started menstruation) differed by BCFH. We also examined whether associations between body size and race/ethnicity and pubertal milestones were modified by BCFH. We used mother/guardian reports as the primary measure of pubertal milestones, but also conducted sensitivity analyses using clinical Tanner measurements available for a subcohort (n = 204). We analyzed cross-sectional baseline data with logistic regression models for the entire cohort, and longitudinal data with Weibull survival models for the subcohort of girls that were aged 5–7 years at baseline (n = 258). Results BCFH was modestly, but not statistically significantly, associated with Breast T2+ (odds ratio (OR) = 1.36, 95% confidence interval (CI) = 0.88–2.10), with a stronger association seen in the subcohort of girls with clinical breast Tanner staging (OR = 2.20, 95% CI = 0.91–5.32). In a longitudinal analysis of girls who were aged 5–7 years at baseline, BCFH was associated with a 50% increased rate of having early breast development (hazard ratio (HR) = 1.49, 95% CI = 1.0–2.21). This association increased to twofold in girls who were not overweight at baseline (HR = 2.04, 95% CI = 1.29–3.21). BCFH was not associated with pubic hair development and post-menarche status. The median interval between onset of breast development and menarche was longer for BCFH+ than BCFH– girls (2.3 versus 1.7 years), suggesting a slower developmental tempo for BCFH+ girls. Associations between pubertal milestones and body size and race/ethnicity were similar in girls with or without a BCFH. For example, weight was positively associated with Breast T2+ in both girls with (OR = 1.06 per 1 kg, 95% CI = 1.03–1.10) and without (OR = 1.14 per 1 kg, 95% CI = 1.04–1.24) a BCFH. Conclusions These results suggest that BCFH may be related to earlier breast development and slower pubertal tempo independent of body size and race/ethnicity. Electronic supplementary material The online version of this article (doi:10.1186/s13058-017-0849-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mary Beth Terry
- Department of Epidemiology, Columbia University Mailman School of Public Health, 722 West 168th Street, New York, NY, 10032, USA. .,Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, USA.
| | - Theresa H M Keegan
- Division of Hematology and Oncology, University of California (UC) Davis School of Medicine, and UC Davis Comprehensive Cancer Center, Sacramento, CA, USA
| | - Lauren C Houghton
- Department of Epidemiology, Columbia University Mailman School of Public Health, 722 West 168th Street, New York, NY, 10032, USA
| | - Mandy Goldberg
- Department of Epidemiology, Columbia University Mailman School of Public Health, 722 West 168th Street, New York, NY, 10032, USA
| | - Irene L Andrulis
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Mary B Daly
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Saundra S Buys
- Department of Medicine, University of Utah Health Sciences Center, Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Ying Wei
- Department of Biostatistics, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Alice S Whittemore
- Departments of Biomedical Data Sciences and Health Research and Policy, and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Angeline Protacio
- Department of Epidemiology, Columbia University Mailman School of Public Health, 722 West 168th Street, New York, NY, 10032, USA
| | - Angela R Bradbury
- Departments of Medicine, Hematology/Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Medical Ethics and Health Policy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Wendy K Chung
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, USA.,Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, NY, USA
| | - Julia A Knight
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada.,Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Esther M John
- Cancer Prevention Institute of California, Fremont, CA, USA.,Department of Health Research and Policy (Epidemiology), and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
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9
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Relationships between Global DNA Methylation in Circulating White Blood Cells and Breast Cancer Risk Factors. J Cancer Epidemiol 2017; 2017:2705860. [PMID: 28484492 PMCID: PMC5397634 DOI: 10.1155/2017/2705860] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 02/26/2017] [Accepted: 03/14/2017] [Indexed: 12/21/2022] Open
Abstract
It is not yet clear whether white blood cell DNA global methylation is associated with breast cancer risk. In this review we examine the relationships between multiple breast cancer risk factors and three markers of global DNA methylation: LINE-1, 5-mdC, and Alu. A literature search was conducted using Pubmed up to April 1, 2016, using combinations of relevant outcomes such as “WBC methylation,” “blood methylation,” “blood LINE-1 methylation,” and a comprehensive list of known and suspected breast cancer risk factors. Overall, the vast majority of reports in the literature have focused on LINE-1. There was reasonably consistent evidence across the studies examined that males have higher levels of LINE-1 methylation in WBC DNA than females. None of the other demographic, lifestyle, dietary, or health condition risk factors were consistently associated with LINE-1 DNA methylation across studies. With the possible exception of sex, there was also little evidence that the wide range of breast cancer risk factors we examined were associated with either of the other two global DNA methylation markers: 5-mdC and Alu. One possible implication of the observed lack of association between global WBC DNA methylation and known breast cancer risk factors is that the association between global WBC DNA methylation and breast cancer, if it exists, is due to a disease effect.
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10
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Kappil M, Terry MB, Delgado-Cruzata L, Liao Y, Santella RM. Mismatch Repair Polymorphisms as Markers of Breast Cancer Prevalence in the Breast Cancer Family Registry. Anticancer Res 2017; 36:4437-41. [PMID: 27630279 DOI: 10.21873/anticanres.10987] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 07/20/2016] [Indexed: 01/17/2023]
Abstract
BACKGROUND Major breast cancer susceptibility genes involved in DNA repair, including BRCA1 and BRCA2, have been identified. However, mutations in these genes account for only 5-10% of identified breast cancer cases. Additional DNA repair pathway genes may also contribute to susceptibility. MATERIALS AND METHODS We investigated the association between 12 single nucleotide polymorphisms (SNPs) in mismatch repair (MMR) genes and breast cancer risk among 313 sister-sets enrolled in the New York site of the Breast Cancer Family Registry (BCFR) (n=744) using conditional logistic regression analysis. RESULTS An increase in breast cancer risk was observed for women with the MUTYH_rs3219489 variant allele (odds ratio (OR)=2.23, 95% confidence interval (CI)=1.10-4.52) and for women with the MSH2_rs2303428 variant allele (OR=1.73, 95% CI=1.00-2.99). CONCLUSION Deficiencies in DNA repair pathways, such as MMR, have implications for the onset of familial breast cancer.
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Affiliation(s)
- Maya Kappil
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, U.S.A.
| | - Mary Beth Terry
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, U.S.A. Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, U.S.A
| | - Lissette Delgado-Cruzata
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, U.S.A
| | - Yuyan Liao
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, U.S.A
| | - Regina M Santella
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, U.S.A. Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, U.S.A
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11
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Terry MB, Phillips KA, Daly MB, John EM, Andrulis IL, Buys SS, Goldgar DE, Knight JA, Whittemore AS, Chung WK, Apicella C, Hopper JL. Cohort Profile: The Breast Cancer Prospective Family Study Cohort (ProF-SC). Int J Epidemiol 2016; 45:683-92. [PMID: 26174520 PMCID: PMC5005937 DOI: 10.1093/ije/dyv118] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- Mary Beth Terry
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY, USA, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, USA,
| | - Kelly-Anne Phillips
- Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, School of Population and Global Health, St Vincent's Hospital, University of Melbourne, Melbourne, VIC, Australia
| | - Mary B Daly
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Esther M John
- Cancer Prevention Institute of California, Fremont, CA, USA, Department of Health Research & Policy, Stanford University School of Medicine, Stanford, CA, USA
| | - Irene L Andrulis
- Lunenfeld-Tanenbaum Research Institute, University of Toronto, Toronto, ON, Canada
| | | | - David E Goldgar
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Julia A Knight
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada and
| | - Alice S Whittemore
- Department of Health Research & Policy, Stanford University School of Medicine, Stanford, CA, USA
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, USA
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12
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Llanos AAM, Marian C, Brasky TM, Dumitrescu RG, Liu Z, Mason JB, Makambi KH, Spear SL, Kallakury BVS, Freudenheim JL, Shields PG. Associations between genetic variation in one-carbon metabolism and LINE-1 DNA methylation in histologically normal breast tissues. Epigenetics 2016; 10:727-35. [PMID: 26090795 DOI: 10.1080/15592294.2015.1062205] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Genome-wide DNA hypomethylation is an early event in the carcinogenic process. Percent methylation of long interspersed nucleotide element-1 (LINE-1) is a biomarker of genome-wide methylation and is a potential biomarker for breast cancer. Understanding factors associated with percent LINE-1 DNA methylation in histologically normal tissues could provide insight into early stages of carcinogenesis. In a cross-sectional study of 121 healthy women with no prior history of cancer who underwent reduction mammoplasty, we examined associations between plasma and breast folate, genetic variation in one-carbon metabolism, and percent LINE-1 methylation using multivariable regression models (adjusting for race, oral contraceptive use, and alcohol use). Results are expressed as the ratio of LINE-1 methylation relative to that of the referent group, with the corresponding 95% confidence intervals (CI). We found no significant associations between plasma or breast folate and percent LINE-1 methylation. Variation in MTHFR, MTR, and MTRR were significantly associated with percent LINE-1 methylation. Variant allele carriers of MTHFR A1289C had 4% lower LINE-1 methylation (Ratio 0.96, 95% CI 0.93-0.98), while variant allele carriers of MTR A2756G (Ratio 1.03, 95% CI 1.01-1.06) and MTRR A66G (Ratio 1.03, 95% CI 1.01-1.06) had 3% higher LINE-1 methylation, compared to those carrying the more common genotypes of these SNPs. DNA methylation of LINE-1 elements in histologically normal breast tissues is influenced by polymorphisms in genes in the one-carbon metabolism pathway. Future studies are needed to investigate the sociodemographic, environmental and additional genetic determinants of DNA methylation in breast tissues and the impact on breast cancer susceptibility.
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Affiliation(s)
- Adana A M Llanos
- a Department of Epidemiology; Rutgers School of Public Health and the Rutgers Cancer Institute of New Jersey ; New Brunswick , NJ USA
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13
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John EM, Terry MB, Keegan TH, Bradbury AR, Knight JA, Chung WK, Frost CJ, Lilge L, Patrick-Miller L, Schwartz LA, Whittemore AS, Buys SS, Daly MB, Andrulis IL. The LEGACY Girls Study: Growth and Development in the Context of Breast Cancer Family History. Epidemiology 2016; 27:438-48. [PMID: 26829160 PMCID: PMC5341739 DOI: 10.1097/ede.0000000000000456] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
BACKGROUND Although the timing of pubertal milestones has been associated with breast cancer risk, few studies of girls' development include girls at increased breast cancer risk due to their family history. METHODS The Lessons in Epidemiology and Genetics of Adult Cancer from Youth (LEGACY) Girls Study was initiated in 2011 in the USA and Canada to assess the relation between early life exposures and intermediate markers of breast cancer risk (e.g., pubertal development, breast tissue characteristics) and to investigate psychosocial well being and health behaviors in the context of family history. We describe the methods used to establish and follow a cohort of 1,040 girls ages 6-13 years at baseline, half with a breast cancer family history, and the collection of questionnaire data (family history, early life exposures, growth and development, psychosocial and behavioral), anthropometry, biospecimens, and breast tissue characteristics using optical spectroscopy. RESULTS During this initial 5-year phase of the study, follow-up visits are conducted every 6 months for repeated data and biospecimen collection. Participation in baseline components was high (98% for urine, 97.5% for blood or saliva, and 98% for anthropometry). At enrollment, 77% of girls were premenarcheal and 49% were at breast Tanner stage T1. CONCLUSIONS This study design allows thorough examination of events affecting girls' growth and development and how they differ across the spectrum of breast cancer risk. A better understanding of early life breast cancer risk factors will be essential to enhance prevention across the lifespan for those with and without a family history of the disease.
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Affiliation(s)
- Esther M. John
- Cancer Prevention Institute of California, Fremont, CA, USA
- Department of Health Research & Policy (Epidemiology), and
Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Mary Beth Terry
- Department of Epidemiology, Columbia University Mailman School of
Public Health, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University
Medical Center, New York, NY, USA
| | - Theresa H.M. Keegan
- Cancer Prevention Institute of California, Fremont, CA, USA
- Department of Health Research & Policy (Epidemiology), and
Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Angela R. Bradbury
- Departments of Medicine and Medical Ethics & Health Policy,
Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA,
USA
| | - Julia A. Knight
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital,
Toronto, Ontario, Canada
- Division of Epidemiology, Dalla Lana School of Public Health,
University of Toronto, Toronto, Ontario, Canada
| | - Wendy K. Chung
- Departments of Pediatrics and Medicine, Columbia University, New
York, NY USA
| | - Caren J. Frost
- College of Social Work, University of Utah, Salt Lake City, UT,
USA
| | - Lothar Lilge
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Linda Patrick-Miller
- Center for Clinical Cancer Genetics and Department of Medicine,
University of Chicago, Chicago, IL, USA
| | - Lisa A. Schwartz
- The Children’s Hospital of Philadelphia and Department of
Pediatrics, Perelman School of Medicine of the University of Pennsylvania,
Philadelphia, PA, USA
| | - Alice S. Whittemore
- Department of Health Research & Policy (Epidemiology), and
Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Saundra S. Buys
- Department of Medicine, Huntsman Cancer Institute, University of
Utah School of Medicine, Salt Lake City, UT, USA
| | - Mary B. Daly
- Department of Clinical Genetics, Fox Chase Cancer Center,
Philadelphia, PA, USA
| | - Irene L. Andrulis
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital,
Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto,
Ontario, Canada
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14
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Agodi A, Barchitta M, Quattrocchi A, Maugeri A, Canto C, Marchese AE, Vinciguerra M. Low fruit consumption and folate deficiency are associated with LINE-1 hypomethylation in women of a cancer-free population. GENES AND NUTRITION 2015; 10:480. [PMID: 26183162 PMCID: PMC4504850 DOI: 10.1007/s12263-015-0480-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 07/02/2015] [Indexed: 01/05/2023]
Abstract
Several dietary agents, such as micronutrient and non-nutrient components, the so-called bioactive food components, have been shown to display anticancer properties and influence genetic processes. The most common epigenetic change is DNA methylation. Hypomethylation of long interspersed elements (LINE-1) has been associated with an increased risk of several cancers, although conflicting findings have also been observed. The aim of the present study was to test the hypothesis that a low adherence to the Mediterranean diet (MD) and folate deficiency may cause LINE-1 hypomethylation in blood leukocytes of healthy women, and thus genomic instability. One hundred and seventy-seven non-pregnant women were enrolled. Mediterranean diet score (MDS) and folate intake were calculated using a food frequency questionnaire. LINE-1 methylation level was measured by pyrosequencing analysis in three CpG sites of LINE-1 promoter. According to MDS, only 9.6 % of subjects achieved a high adherence to MD. Taking into account the use of supplements, there was a high prevalence of folate deficiency (73.4 %). Women whose consumption of fruit was below the median value (i.e., <201 gr/day) were 3.7 times more likely to display LINE-1 hypomethylation than women whose consumption was above the median value (OR 3.7; 95 % CI 1.4–9.5). Similarly, women with folate deficiency were 3.6 times more likely to display LINE-1 hypomethylation than women with no folate deficiency (OR 3.6; 95 % CI 1.1–12.1). A dietary pattern characterized by low fruit consumption and folate deficiency is associated with LINE-1 hypomethylation and with cancer risk.
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Affiliation(s)
- Antonella Agodi
- Department of Medical and Surgical Sciences and Advanced Technologies "GF Ingrassia", University of Catania, Via S. Sofia 87, 95121, Catania, Italy,
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15
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DNA methylation as a promising landscape: A simple blood test for breast cancer prediction. Tumour Biol 2015; 36:4905-12. [PMID: 26076810 DOI: 10.1007/s13277-015-3567-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 05/13/2015] [Indexed: 01/27/2023] Open
Abstract
Breast cancer is the most common malignancy among women worldwide. Risk assessment is one of the main services delivered by cancer clinics. Biomarker analysis on different tissues including the peripheral blood can provide crucial information. One of the potential epigenetic biomarkers (epimarkers) is introduced as the peripheral blood DNA methylation pattern. This study was conducted to evaluate the potential value of peripheral blood epimarkers as an accessible tool to predict the risk of breast cancer development. WBC's DNA was the focus of several case-control studies at both genome wide and candidate gene levels to reveal epigenetic changes accounting for predisposition to breast cancer, leading to suggest that ATM, TITF1, SFRP1, NUP155, NEUROD1, ZNF217, DBC2, DOK7 and ESR1 genes and the LINE1, Alu and Sat2 DNA elements could be considered as the potential epimarkers. To address that by which mechanisms WBC's DNA methylation patterns could be linked to the propensity to breast cancer, several contemplations have been offered. Constitutional epimutation during embryonic life, and methylation changes secondary to either environmental exposures or tumor-mediated immune response, are the two main mechanisms. One can deduce that epimarkers based on their potential properties or regulatory impacts on cancer-related genes may be employed for risk prediction, prognosis, and survival inferences that are highly required for breast cancer management toward personalized medicine.
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16
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Cloud AJ, Thai A, Liao Y, Terry MB. The impact of cancer prevention guideline adherence on overall mortality in a high-risk cohort of women from the New York site of the Breast Cancer Family Registry. Breast Cancer Res Treat 2015; 149:537-46. [PMID: 25604794 PMCID: PMC4308644 DOI: 10.1007/s10549-014-3234-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 12/05/2014] [Indexed: 12/13/2022]
Abstract
The American Cancer Society (ACS) recommends at least 150 min of moderate intensity physical activity per week, alcohol intake of ≤1 drink per day, and maintaining a body mass index (BMI) of <25 kg/m2 for breast cancer prevention. Adherence to these guidelines has been linked to lower overall mortality in average-risk populations, it is not known if mortality reduction extends to women at higher risk given their family history of breast cancer. We followed 2,905 women from a high-risk Breast Cancer Family Registry in New York, of which 77 % were white non-Hispanic and 23 % were Hispanic. We collected information on BMI, physical activity, and alcohol intake at baseline and prospectively followed our cohort for outcomes based on questionnaires and National Death Index linkage. We used Cox regression to examine the relation between adherence to ACS guidelines and overall mortality and examined effect modification by race, age, and BRCA status. There were 312 deaths after an average of 9.2 ± 4.1 years of follow-up. Adherence to all three ACS recommendations was associated with 44–53 % lower mortality in women unaffected with breast cancer at baseline [Hazard Ratio (HR) 0.56, 95 % CI (0.33–0.93)] and in women affected with breast cancer at baseline [HR 0.47, 95 % CI (0.30–0.74)]. These associations remained after stratification by age, race, and BRCA status {e.g., BRCA1 and/or BRCA2 carriers [HR 0.39, 95 % CI (0.16–0.97)]}. These results support that women at high risk, similar to women at average risk, may also have substantial benefits from maintaining the ACS guidelines.
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Affiliation(s)
- Ann J Cloud
- Department of Epidemiology, Mailman School of Public Health, Columbia University, 722 West 168th Street, Rm724A, New York, NY, 10032, USA,
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17
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Anjum S, Fourkala EO, Zikan M, Wong A, Gentry-Maharaj A, Jones A, Hardy R, Cibula D, Kuh D, Jacobs IJ, Teschendorff AE, Menon U, Widschwendter M. A BRCA1-mutation associated DNA methylation signature in blood cells predicts sporadic breast cancer incidence and survival. Genome Med 2014; 6:47. [PMID: 25067956 PMCID: PMC4110671 DOI: 10.1186/gm567] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 06/03/2014] [Indexed: 12/18/2022] Open
Abstract
Background BRCA1 mutation carriers have an 85% risk of developing breast cancer but the risk of developing non-hereditary breast cancer is difficult to assess. Our objective is to test whether a DNA methylation (DNAme) signature derived from BRCA1 mutation carriers is able to predict non-hereditary breast cancer. Methods In a case/control setting (72 BRCA1 mutation carriers and 72 BRCA1/2 wild type controls) blood cell DNA samples were profiled on the Illumina 27 k methylation array. Using the Elastic Net classification algorithm, a BRCA1-mutation DNAme signature was derived and tested in two cohorts: (1) The NSHD (19 breast cancers developed within 12 years after sample donation and 77 controls) and (2) the UKCTOCS trial (119 oestrogen receptor positive breast cancers developed within 5 years after sample donation and 122 controls). Results We found that our blood-based BRCA1-mutation DNAme signature applied to blood cell DNA from women in the NSHD resulted in a receiver operating characteristics (ROC) area under the curve (AUC) of 0.65 (95% CI 0.51 to 0.78, P = 0.02) which did not validate in buccal cells from the same individuals. Applying the signature in blood DNA from UKCTOCS volunteers resulted in AUC of 0.57 (95% CI 0.50 to 0.64; P = 0.03) and is independent of family history or any other known risk factors. Importantly the BRCA1-mutation DNAme signature was able to predict breast cancer mortality (AUC = 0.67; 95% CI 0.51 to 0.83; P = 0.02). We also found that the 1,074 CpGs which are hypermethylated in BRCA1 mutation carriers are significantly enriched for stem cell polycomb group target genes (P <10-20). Conclusions A DNAme signature derived from BRCA1 carriers is able to predict breast cancer risk and death years in advance of diagnosis. Future studies may need to focus on DNAme profiles in epithelial cells in order to reach the AUC thresholds required of preventative measures or early detection strategies.
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Affiliation(s)
- Shahzia Anjum
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, 74 Huntley Street, London WC1E 6 AU, UK
| | - Evangelia-Ourania Fourkala
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, 74 Huntley Street, London WC1E 6 AU, UK
| | - Michal Zikan
- Gynecological Oncology Center, Department of Obstetrics and Gynecology, Charles University in Prague - First Faculty of Medicine and General University Hospital, Apolinarska 18, 128 00 Prague, Czech Republic
| | - Andrew Wong
- MRC Unit for Lifelong Health and Ageing at UCL, 33 Bedford Place, London WC1B 5JU, UK
| | - Aleksandra Gentry-Maharaj
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, 74 Huntley Street, London WC1E 6 AU, UK
| | - Allison Jones
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, 74 Huntley Street, London WC1E 6 AU, UK
| | - Rebecca Hardy
- MRC Unit for Lifelong Health and Ageing at UCL, 33 Bedford Place, London WC1B 5JU, UK
| | - David Cibula
- Gynecological Oncology Center, Department of Obstetrics and Gynecology, Charles University in Prague - First Faculty of Medicine and General University Hospital, Apolinarska 18, 128 00 Prague, Czech Republic
| | - Diana Kuh
- MRC Unit for Lifelong Health and Ageing at UCL, 33 Bedford Place, London WC1B 5JU, UK
| | - Ian J Jacobs
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, 74 Huntley Street, London WC1E 6 AU, UK ; Faculty of Medical and Human Sciences, The University of Manchester, 46 Grafton Street, Manchester M13 9NT, UK
| | - Andrew E Teschendorff
- Statistical Genomics Group, Paul O'Gorman Building, UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK ; CAS-MPG Partner Institute for Computational Biology Chinese Academy of Sciences, Shanghai Institute for Biological Sciences, Shanghai 200031, China
| | - Usha Menon
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, 74 Huntley Street, London WC1E 6 AU, UK
| | - Martin Widschwendter
- Department of Women's Cancer, UCL Elizabeth Garrett Anderson Institute for Women's Health, University College London, 74 Huntley Street, London WC1E 6 AU, UK
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18
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Park SY, Seo AN, Jung HY, Gwak JM, Jung N, Cho NY, Kang GH. Alu and LINE-1 hypomethylation is associated with HER2 enriched subtype of breast cancer. PLoS One 2014; 9:e100429. [PMID: 24971511 PMCID: PMC4074093 DOI: 10.1371/journal.pone.0100429] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Accepted: 05/28/2014] [Indexed: 01/31/2023] Open
Abstract
The changes in DNA methylation status in cancer cells are characterized by hypermethylation of promoter CpG islands and diffuse genomic hypomethylation. Alu and long interspersed nucleotide element-1 (LINE-1) are non-coding genomic repetitive sequences and methylation of these elements can be used as a surrogate marker for genome-wide methylation status. This study was designed to evaluate the changes of Alu and LINE-1 hypomethylation during breast cancer progression from normal to pre-invasive lesions and invasive breast cancer (IBC), and their relationship with characteristics of IBC. We analyzed the methylation status of Alu and LINE-1 in 145 cases of breast samples including normal breast tissue, atypical ductal hyperplasia/flat epithelial atypia (ADH/FEA), ductal carcinoma in situ (DCIS) and IBC, and another set of 129 cases of IBC by pyrosequencing. Alu methylation showed no significant changes during multistep progression of breast cancer, although it tended to decrease during the transition from DCIS to IBC. In contrast, LINE-1 methylation significantly decreased from normal to ADH/FEA, while it was similar in ADH/FEA, DCIS and IBC. In IBC, Alu hypomethylation correlated with negative estrogen receptor (ER) status, and LINE-1 hypomethylation was associated with negative ER status, ERBB2 (HER2) amplification and p53 overexpression. Alu and LINE-1 methylation status was significantly different between breast cancer subtypes, and the HER2 enriched subtype had lowest methylation levels. In survival analyses, low Alu methylation status tended to be associated with poor disease-free survival of the patients. Our findings suggest that LINE-1 hypomethylation is an early event and Alu hypomethylation is probably a late event during breast cancer progression, and prominent hypomethylation of Alu and LINE-1 in HER2 enriched subtype may be related to chromosomal instability of this specific subtype.
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Affiliation(s)
- So Yeon Park
- Department of Pathology, Seoul National University College of Medicine, Jongno-gu, Seoul, Korea
- Department of Pathology, Seoul National University Bundang Hospital, Bundang-gu, Seongnam, Gyeonggi, Korea
| | - An Na Seo
- Department of Pathology, Seoul National University Bundang Hospital, Bundang-gu, Seongnam, Gyeonggi, Korea
| | - Hae Yoen Jung
- Department of Pathology, Seoul National University Bundang Hospital, Bundang-gu, Seongnam, Gyeonggi, Korea
| | - Jae Moon Gwak
- Department of Pathology, Seoul National University College of Medicine, Jongno-gu, Seoul, Korea
| | - Namhee Jung
- Laboratory of Epigenetics, Cancer Research Institute, Seoul National University, Jongno-gu, Seoul, Korea
| | - Nam-Yun Cho
- Laboratory of Epigenetics, Cancer Research Institute, Seoul National University, Jongno-gu, Seoul, Korea
| | - Gyeong Hoon Kang
- Department of Pathology, Seoul National University College of Medicine, Jongno-gu, Seoul, Korea
- Laboratory of Epigenetics, Cancer Research Institute, Seoul National University, Jongno-gu, Seoul, Korea
- * E-mail:
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19
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Identification and comparison of aberrant key regulatory networks in breast, colon, liver, lung, and stomach cancers through methylome database analysis. PLoS One 2014; 9:e97818. [PMID: 24842468 PMCID: PMC4026530 DOI: 10.1371/journal.pone.0097818] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 04/24/2014] [Indexed: 12/29/2022] Open
Abstract
Aberrant methylation of specific CpG sites at the promoter is widely responsible for genesis and development of various cancer types. Even though the microarray-based methylome analyzing techniques have contributed to the elucidation of the methylation change at the genome-wide level, the identification of key methylation markers or top regulatory networks appearing common in highly incident cancers through comparison analysis is still limited. In this study, we in silico performed the genome-wide methylation analysis on each 10 sets of normal and cancer pairs of five tissues: breast, colon, liver, lung, and stomach. The methylation array covers 27,578 CpG sites, corresponding to 14,495 genes, and significantly hypermethylated or hypomethylated genes in the cancer were collected (FDR adjusted p-value <0.05; methylation difference >0.3). Analysis of the dataset confirmed the methylation of previously known methylation markers and further identified novel methylation markers, such as GPX2, CLDN15, and KL. Cluster analysis using the methylome dataset resulted in a diagram with a bipartite mode distinguishing cancer cells from normal cells regardless of tissue types. The analysis further revealed that breast cancer was closest with lung cancer, whereas it was farthest from colon cancer. Pathway analysis identified that either the “cancer” related network or the “cancer” related bio-function appeared as the highest confidence in all the five cancers, whereas each cancer type represents its tissue-specific gene sets. Our results contribute toward understanding the essential abnormal epigenetic pathways involved in carcinogenesis. Further, the novel methylation markers could be applied to establish markers for cancer prognosis.
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