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Mendonça V, Soares-Lima SC, Moreira MAM. Exploring cross-tissue DNA methylation patterns: blood-brain CpGs as potential neurodegenerative disease biomarkers. Commun Biol 2024; 7:904. [PMID: 39060467 PMCID: PMC11282059 DOI: 10.1038/s42003-024-06591-x] [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: 11/02/2023] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
The difficulty of obtaining samples from certain human tissues has led to efforts to find accessible sources to analyze molecular markers derived from DNA. In this study, we look for DNA methylation patterns in blood samples and its association with the brain methylation pattern in neurodegenerative disorders. Using data from methylation databases, we selected 18,293 CpGs presenting correlated methylation levels between blood and brain (bb-CpGs) and compare their methylation level between blood samples from patients with neurodegenerative diseases (Alzheimer's disease, Parkinson's disease, Multiple Sclerosis, and X Fragile Syndrome) and healthy controls. Sixty-four bb-CpGs presented significant distinct methylation levels in patients, being: nine for Alzheimer's disease, nine for Parkinson's disease, 28 for Multiple Sclerosis, and 18 for Fragile X Syndrome. Similar differences in methylation pattern for the nine Alzheimer's bb-CpGs was also observed when comparing brain tissue from patients vs. controls. The genomic regions of some of these 64 bb-CpGs are placed close to or inside genes previously associated with the respective condition. Our findings support the rationale of using blood DNA as a surrogate of brain tissue to analyze changes in CpG methylation level in patients with neurodegenerative diseases, opening the possibility for characterizing new biomarkers.
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Affiliation(s)
- Vanessa Mendonça
- Genetic Graduation Program, Genetics Deparment, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Tumoral Genetics and Virology Program, Instituto Nacional de Cancer, Rio de Janeiro, Brazil
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Ruiz-De La Cruz M, Martínez-Gregorio H, Estela Díaz-Velásquez C, Ambriz-Barrera F, Resendiz-Flores NG, Gitler-Weingarten R, Rojo-Castillo MP, Pradda D, Oliver J, Perdomo S, Gómez-García EM, De La Cruz-Montoya AH, Terrazas LI, Torres-Mejía G, Hernández-Hernández FDLC, Vaca-Paniagua F. Methylation marks in blood DNA reveal breast cancer risk in patients fulfilling hereditary disease criteria. NPJ Precis Oncol 2024; 8:136. [PMID: 38898118 PMCID: PMC11187128 DOI: 10.1038/s41698-024-00611-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 05/10/2024] [Indexed: 06/21/2024] Open
Abstract
Less than 15-20% of patients who meet the criteria for hereditary breast and ovarian cancer (HBOC) carry pathogenic coding genetic mutations, implying that other molecular mechanisms may contribute to the increased risk of this condition. DNA methylation in peripheral blood has been suggested as a potential epigenetic marker for the risk of breast cancer (BC). We aimed to discover methylation marks in peripheral blood associated with BC in 231 pre-treatment BC patients meeting HBOC criteria, testing negative for coding pathogenic variants, and 156 healthy controls, through methylation analysis by targeted bisulfite sequencing on 18 tumor suppressor gene promoters (330 CpG sites). We found i) hypermethylation in EPCAM (17 CpG sites; p = 0.017) and RAD51C (27 CpG sites; p = 0.048); ii) hypermethylation in 36 CpG-specific sites (FDR q < 0.05) in the BC patients; iii) four specific CpG sites were associated with a higher risk of BC (FDR q < 0.01, Bonferroni p < 0.001): cg89786999-FANCI (OR = 1.65; 95% CI:1.2-2.2), cg23652916-PALB2 (OR = 2.83; 95% CI:1.7-4.7), cg47630224-MSH2 (OR = 4.17; 95% CI:2.1-8.5), and cg47596828-EPCAM (OR = 1.84; 95% CI:1.5-2.3). Validation of cg47630224-MSH2 methylation in one Australian cohort showed an association with 3-fold increased BC risk (AUC: 0.929; 95% CI: 0.904-0.955). Our findings suggest that four DNA methylation CpG sites may be associated with a higher risk of BC, potentially serving as biomarkers in patients without detectable coding mutations.
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Affiliation(s)
- Miguel Ruiz-De La Cruz
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, 54090, Mexico
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla, 54090, Mexico
- Centro de Investigación y de Estudios Avanzados IPN (CINVESTAV). Avenida Instituto Politécnico Nacional #2508, Colonia San Pedro Zacatenco, Delegación Gustavo A. Madero, Departamento de Infectómica y Patogénesis Molecular, Ciudad de México, Mexico
| | - Héctor Martínez-Gregorio
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, 54090, Mexico
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla, 54090, Mexico
| | - Clara Estela Díaz-Velásquez
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, 54090, Mexico
| | - Fernando Ambriz-Barrera
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, 54090, Mexico
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla, 54090, Mexico
| | - Norma Gabriela Resendiz-Flores
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, 54090, Mexico
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla, 54090, Mexico
| | | | | | - Didier Pradda
- Institute for Health Equity Research, Department of Health Science and Policy and Department of Environmental Medicine and Public Health at the Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Javier Oliver
- Medical Oncology Service, Hospitales Universitarios Regional y Virgen de la Victoria, Institute of Biomedical Research in Malaga, CIMES, University of Málaga, 29010, Málaga, Spain
| | - Sandra Perdomo
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), 150 Cours Albert Thomas, 69372, Lyon, France
| | | | | | - Luis Ignacio Terrazas
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, 54090, Mexico
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla, 54090, Mexico
| | | | - Fidel de la Cruz Hernández-Hernández
- Centro de Investigación y de Estudios Avanzados IPN (CINVESTAV). Avenida Instituto Politécnico Nacional #2508, Colonia San Pedro Zacatenco, Delegación Gustavo A. Madero, Departamento de Infectómica y Patogénesis Molecular, Ciudad de México, Mexico.
| | - Felipe Vaca-Paniagua
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla, 54090, Mexico.
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla, 54090, Mexico.
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Xu J, Gao H, Guan X, Meng J, Ding S, Long Q, Yi W. Circulating tumor DNA: from discovery to clinical application in breast cancer. Front Immunol 2024; 15:1355887. [PMID: 38745646 PMCID: PMC11091288 DOI: 10.3389/fimmu.2024.1355887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 04/16/2024] [Indexed: 05/16/2024] Open
Abstract
Breast cancer (BC) stands out as the cancer with the highest incidence of morbidity and mortality among women worldwide, and its incidence rate is currently trending upwards. Improving the efficiency of breast cancer diagnosis and treatment is crucial, as it can effectively reduce the disease burden. Circulating tumor DNA (ctDNA) originates from the release of tumor cells and plays a pivotal role in the occurrence, development, and metastasis of breast cancer. In recent years, the widespread application of high-throughput analytical technology has made ctDNA a promising biomarker for early cancer detection, monitoring minimal residual disease, early recurrence monitoring, and predicting treatment outcomes. ctDNA-based approaches can effectively compensate for the shortcomings of traditional screening and monitoring methods, which fail to provide real-time information and prospective guidance for breast cancer diagnosis and treatment. This review summarizes the applications of ctDNA in various aspects of breast cancer, including screening, diagnosis, prognosis, treatment, and follow-up. It highlights the current research status in this field and emphasizes the potential for future large-scale clinical applications of ctDNA-based approaches.
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Affiliation(s)
- Jiachi Xu
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center For Breast Disease In Hunan Province, Changsha, China
| | - Hongyu Gao
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center For Breast Disease In Hunan Province, Changsha, China
| | - Xinyu Guan
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center For Breast Disease In Hunan Province, Changsha, China
| | - Jiahao Meng
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center For Breast Disease In Hunan Province, Changsha, China
| | - Shirong Ding
- Department of Oncology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Qian Long
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center For Breast Disease In Hunan Province, Changsha, China
| | - Wenjun Yi
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center For Breast Disease In Hunan Province, Changsha, China
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Herzog C, Jones A, Evans I, Zikan M, Cibula D, Harbeck N, Colombo N, Rådestad AF, Gemzell-Danielsson K, Pashayan N, Widschwendter M. DNA methylation at quantitative trait loci (mQTLs) varies with cell type and nonheritable factors and may improve breast cancer risk assessment. NPJ Precis Oncol 2023; 7:99. [PMID: 37758816 PMCID: PMC10533818 DOI: 10.1038/s41698-023-00452-2] [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: 03/27/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
To individualise breast cancer (BC) prevention, markers to follow a person's changing environment and health extending beyond static genetic risk scores are required. Here, we analysed cervical and breast DNA methylation (n = 1848) and single nucleotide polymorphisms (n = 1442) and demonstrate that a linear combination of methylation levels at 104 BC-associated methylation quantitative trait loci (mQTL) CpGs, termed the WID™-qtBC index, can identify women with breast cancer in hormone-sensitive tissues (AUC = 0.71 [95% CI: 0.65-0.77] in cervical samples). Women in the highest combined risk group (high polygenic risk score and WID™-qtBC) had a 9.6-fold increased risk for BC [95% CI: 4.7-21] compared to the low-risk group and tended to present at more advanced stages. Importantly, the WID™-qtBC is influenced by non-genetic BC risk factors, including age and body mass index, and can be modified by a preventive pharmacological intervention, indicating an interaction between genome and environment recorded at the level of the epigenome. Our findings indicate that methylation levels at mQTLs in relevant surrogate tissues could enable integration of heritable and non-heritable factors for improved disease risk stratification.
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Affiliation(s)
- Chiara Herzog
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, Milser Str. 10, 6060, Hall in Tirol, Austria
- Research Institute for Biomedical Aging Research, Universität Innsbruck, 6020, Innsbruck, Austria
| | - Allison Jones
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, WC1E 6AU, London, UK
| | - Iona Evans
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, WC1E 6AU, London, UK
| | - Michal Zikan
- Department of Gynecology and Obstetrics, Charles University in Prague, First Faculty of Medicine and Hospital Na Bulovce, Prague, Czech Republic
| | - David Cibula
- Gynaecologic Oncology Center, Department of Obstetrics and Gynecology, First Faculty of Medicine, Charles University in Prague, General University Hospital in Prague, Prague, Czech Republic
| | - Nadia Harbeck
- Breast Center, Department of Obstetrics and Gynecology and CCC Munich, LMU University Hospital, Munich, Germany
| | - Nicoletta Colombo
- Istituto Europeo di Oncologia, Milan, Italy
- University of Milano-Bicocca, Milan, Italy
| | | | | | - Nora Pashayan
- Department of Applied Health Research, University College London, London, UK
| | - Martin Widschwendter
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, Milser Str. 10, 6060, Hall in Tirol, Austria.
- Research Institute for Biomedical Aging Research, Universität Innsbruck, 6020, Innsbruck, Austria.
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, Medical School Building, Room 340, 74 Huntley Street, WC1E 6AU, London, UK.
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.
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Machaj F, Sokolowska KE, Borowski K, Retfiński S, Strapagiel D, Sobalska-Kwapis M, Huzarski T, Lubiński J, Wojdacz TK. Analytical sensitivity of a method is critical in detection of low-level BRCA1 constitutional epimutation. Sci Rep 2023; 13:16102. [PMID: 37752189 PMCID: PMC10522570 DOI: 10.1038/s41598-023-43276-7] [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: 08/16/2023] [Accepted: 09/21/2023] [Indexed: 09/28/2023] Open
Abstract
Recent reports based on a substantial number of cases, warrant need for population-based research to determine implications of constitutional methylation of tumor suppressor genes such as BRCA1 occurring in healthy tissue in the prediction of cancer. However, the detection of the constitutional methylation in DNA extracted from blood has already been shown to be technologically challenging, mainly because epimutations appear to be present in blood at a very low level. The analytical sensitivity required for low-level methylation detection can be provided by NGS, but this technique is still labor and cost-intensive. We assessed if PCR-based MS-HRM and BeadChip microarray technologies, which are standardized and cost-effective technologies for methylation changes screening, provide a sufficient level of analytical sensitivity for constitutional BRCA1 methylation detection in blood samples. The study included whole blood samples from 67 healthy women, 35 with previously confirmed and 32 with no detectable BRCA1 promoter methylation for which we performed both MS-HRM based BRCA1 gene methylation screening and genome wide methylation profiling with EPIC microarray. Our results shown, that low-level BRCA1 methylation can be effectively detected in DNA extracted from blood by PCR-based MS-HRM. At the same time, EPIC microarray does not provide conclusive results to unambiguously determine the presence of BRCA1 constitutional methylation in MS-HRM epimutation positive samples. The analytical sensitivity of MS-HRM is sufficient to detect low level BRCA1 constitutional epimutation in DNA extracted from blood and BeadChip technology-based microarrays appear not to provide that level of analytical sensitivity.
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Affiliation(s)
- Filip Machaj
- Independent Clinical Epigenetics Laboratory, Pomeranian Medical University in Szczecin, Unii Lubelskiej 1, 71-252, Szczecin, Poland
| | - Katarzyna Ewa Sokolowska
- Independent Clinical Epigenetics Laboratory, Pomeranian Medical University in Szczecin, Unii Lubelskiej 1, 71-252, Szczecin, Poland
| | - Konrad Borowski
- Independent Clinical Epigenetics Laboratory, Pomeranian Medical University in Szczecin, Unii Lubelskiej 1, 71-252, Szczecin, Poland
| | - Szymon Retfiński
- Independent Clinical Epigenetics Laboratory, Pomeranian Medical University in Szczecin, Unii Lubelskiej 1, 71-252, Szczecin, Poland
| | - Dominik Strapagiel
- Biobank Laboratory, Department of Oncobiology and Epigenetics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 139, 90-237, Lodz, Poland
| | - Marta Sobalska-Kwapis
- Biobank Laboratory, Department of Oncobiology and Epigenetics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 139, 90-237, Lodz, Poland
| | - Tomasz Huzarski
- Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Unii Lubelskiej 1, 71-252, Szczecin, Poland
| | - Jan Lubiński
- Department of Genetics and Pathology, Pomeranian Medical University in Szczecin, Unii Lubelskiej 1, 71-252, Szczecin, Poland
| | - Tomasz Kazimierz Wojdacz
- Independent Clinical Epigenetics Laboratory, Pomeranian Medical University in Szczecin, Unii Lubelskiej 1, 71-252, Szczecin, Poland.
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Liu F, Zhou H, Peng Y, Qiao Y, Wang P, Si C, Wang X, Gong J, Chen K, Song F. Plasma One-Carbon Metabolism-Related Micronutrients and the Risk of Breast Cancer: Involvement of DNA Methylation. Nutrients 2023; 15:3621. [PMID: 37630812 PMCID: PMC10458034 DOI: 10.3390/nu15163621] [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: 06/30/2023] [Revised: 08/05/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Findings of epidemiologic studies focusing on the association between one-carbon metabolism-related micronutrients and breast cancer risk, along with the involvement of DNA methylation, have been inconsistent and incomprehensive. We conducted a case-control study in China including 107 paired participants and comprehensively detected 12 plasma one-carbon metabolism-related micronutrients. Genomic DNA methylation was measured using an 850 K chip and differential methylation probes (DMPs) were identified. Multivariate logistic regression was performed to estimate the associations between plasma micronutrients and the odds of breast cancer. The mediation of selected DMPs in micronutrient breast cancer associations was examined using mediation analyses. An inverse association of plasma folate, methionine cycling-related micronutrients (methionine, S-adenosylmethionine, and S-adenosylhomocysteine), and all micronutrients in the choline metabolism and enzymatic factor groups, and a positive association of methionine cycling-related cysteine with breast cancer risk were observed. Nine micronutrients (methionine, cysteine, SAM, folate, choline, betaine, P5P, vitamins B2, and B12) were related to global or probe-specific methylation levels (p < 0.05). The selected DMPs mediated the micronutrient breast cancer associations with an average mediation proportion of 36.43%. This study depicted comprehensive associations between circulating one-carbon metabolism-related micronutrients and breast cancer risk mediated by DNA methylation.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Kexin Chen
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Major Diseases in the Population, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China; (F.L.); (H.Z.); (Y.P.); (Y.Q.); (P.W.); (C.S.); (X.W.); (J.G.)
| | - Fangfang Song
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Major Diseases in the Population, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China; (F.L.); (H.Z.); (Y.P.); (Y.Q.); (P.W.); (C.S.); (X.W.); (J.G.)
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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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Li J, Zhou X, Li L, Ji L, Li J, Qu Y, Wang Z, Zhao Y, Zhang J, Liang F, Liu J, Gu W, Yang R, Ma F, Dai L. The association between CTSZ methylation in peripheral blood and breast cancer in Chinese women. Front Oncol 2023; 13:1148635. [PMID: 37274256 PMCID: PMC10233099 DOI: 10.3389/fonc.2023.1148635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/02/2023] [Indexed: 06/06/2023] Open
Abstract
Purpose Previous studies have shown that DNA methylation in peripheral blood may be associated with breast cancer (BC). To explore the association between the methylation level of the Cathepsin Z (CTSZ) gene in peripheral blood and BC, we conducted a case-control study in the Chinese population. Methods Peripheral blood samples were collected from 567 BC cases, 635 healthy controls, and 303 benign breast disease (BBD) cases. DNA extraction and bisulfite-specific PCR amplification were performed for all samples. The methylation levels of seven sites of the CTSZ gene were quantitatively determined by Mass spectrometry. The odds ratios (ORs) of CpG sites were evaluated for BC risk using per 10% reduction and quartiles analyses by logistic regression. Results Our analysis showed that five out of the seven CpG sites exhibited significant associations with hypomethylation of CTSZ and BC, compared to healthy controls. The highest OR was for Q2 of CTSZ_CpG_1 (OR: 1.62, P=0.006), particularly for early-stage breast cancer in the case of per 10% reduction of CTSZ_CpG_1 (OR: 1.20, P=0.003). We also found that per 10% reduction of CTSZ_CpG_5 (OR: 1.39, P=0.004) and CTSZ_CpG_7,8 (OR: 1.35, P=0.005) were associated with increased BC risk. Our study also revealed that four out of seven CpG sites were linked to increased BC risk in women under 50 years of age, compared to healthy controls. The highest OR was for per 10% reduction of CTSZ_CpG_1 (OR: 1.47, P<0.001). Additionally, we found that BC exhibited lower methylation levels than BBD at CTSZ_CpG_4 (OR for Q1: 2.18, P<0.001) and CTSZ_CpG_7,8 (OR for Q1: 2.01, P=0.001). Furthermore, we observed a correlation between methylation levels and tumor stage, ER, and HER2 status in BC patients. Conclusion Overall, our findings suggest that altered CTSZ methylation levels in peripheral blood may be associated with breast cancer, particularly in young women, and may serve as a potential biomarker for early-stage BC.
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Affiliation(s)
- Jinyu Li
- School of Basic Medical Sciences & The First Affiliated Hospital, Zhengzhou University, Zhengzhou, Henan, China
| | - Xiajie Zhou
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Lixi Li
- Department of Medical Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Longtao Ji
- BGI College, Zhengzhou University, Zhengzhou, Henan, China
- Henan Institute of Medical and Pharmaceutical Sciences & Henan Key Medical Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, Henan, China
| | - Jiaqi Li
- Henan Institute of Medical and Pharmaceutical Sciences & Henan Key Medical Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, Henan, China
| | - Yunhui Qu
- Department of Clinical Laboratory in the First Affiliated Hospital & Key Clinical Laboratory of Henan Province, Zhengzhou University, Zhengzhou, Henan, China
| | - Zhi Wang
- BGI College, Zhengzhou University, Zhengzhou, Henan, China
- Henan Institute of Medical and Pharmaceutical Sciences & Henan Key Medical Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, Henan, China
| | - Yutong Zhao
- Henan Institute of Medical and Pharmaceutical Sciences & Henan Key Medical Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, Henan, China
| | - Jie Zhang
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, China
| | - Feifei Liang
- BGI College, Zhengzhou University, Zhengzhou, Henan, China
- Henan Institute of Medical and Pharmaceutical Sciences & Henan Key Medical Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, Henan, China
| | - Jingjing Liu
- Henan Institute of Medical and Pharmaceutical Sciences & Henan Key Medical Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, Henan, China
| | - Wanjian Gu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu, China
| | - Rongxi Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Fei Ma
- Department of Medical Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Liping Dai
- School of Basic Medical Sciences & The First Affiliated Hospital, Zhengzhou University, Zhengzhou, Henan, China
- Henan Institute of Medical and Pharmaceutical Sciences & Henan Key Medical Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, Henan, China
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9
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Pham TMQ, Phan TH, Jasmine TX, Tran TTT, Huynh LAK, Vo TL, Nai THT, Tran TT, Truong MH, Tran NC, Nguyen VTC, Nguyen TH, Nguyen THH, Le NDK, Nguyen TD, Nguyen DS, Truong DK, Do TTT, Phan MD, Giang H, Nguyen HN, Tran LS. Multimodal analysis of genome-wide methylation, copy number aberrations, and end motif signatures enhances detection of early-stage breast cancer. Front Oncol 2023; 13:1127086. [PMID: 37223690 PMCID: PMC10200909 DOI: 10.3389/fonc.2023.1127086] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 04/24/2023] [Indexed: 05/25/2023] Open
Abstract
Introduction Breast cancer causes the most cancer-related death in women and is the costliest cancer in the US regarding medical service and prescription drug expenses. Breast cancer screening is recommended by health authorities in the US, but current screening efforts are often compromised by high false positive rates. Liquid biopsy based on circulating tumor DNA (ctDNA) has emerged as a potential approach to screen for cancer. However, the detection of breast cancer, particularly in early stages, is challenging due to the low amount of ctDNA and heterogeneity of molecular subtypes. Methods Here, we employed a multimodal approach, namely Screen for the Presence of Tumor by DNA Methylation and Size (SPOT-MAS), to simultaneously analyze multiple signatures of cell free DNA (cfDNA) in plasma samples of 239 nonmetastatic breast cancer patients and 278 healthy subjects. Results We identified distinct profiles of genome-wide methylation changes (GWM), copy number alterations (CNA), and 4-nucleotide oligomer (4-mer) end motifs (EM) in cfDNA of breast cancer patients. We further used all three signatures to construct a multi-featured machine learning model and showed that the combination model outperformed base models built from individual features, achieving an AUC of 0.91 (95% CI: 0.87-0.95), a sensitivity of 65% at 96% specificity. Discussion Our findings showed that a multimodal liquid biopsy assay based on analysis of cfDNA methylation, CNA and EM could enhance the accuracy for the detection of early- stage breast cancer.
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Affiliation(s)
- Thi Mong Quynh Pham
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Research and Development Department Gene Solutions, Ho Chi Minh, Vietnam
| | - Thanh Hai Phan
- Ultrasound Department Medic Medical Center, Ho Chi Minh, Vietnam
| | | | - Thuy Thi Thu Tran
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Research and Development Department Gene Solutions, Ho Chi Minh, Vietnam
| | - Le Anh Khoa Huynh
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Department of Biostatistics, School of Medicine, Virginia Commonwealth University, Richmond, VA, United States
| | - Thi Loan Vo
- Ultrasound Department Medic Medical Center, Ho Chi Minh, Vietnam
| | | | - Thuy Trang Tran
- Ultrasound Department Medic Medical Center, Ho Chi Minh, Vietnam
| | - My Hoang Truong
- Ultrasound Department Medic Medical Center, Ho Chi Minh, Vietnam
| | - Ngan Chau Tran
- Ultrasound Department Medic Medical Center, Ho Chi Minh, Vietnam
| | - Van Thien Chi Nguyen
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Research and Development Department Gene Solutions, Ho Chi Minh, Vietnam
| | - Trong Hieu Nguyen
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Research and Development Department Gene Solutions, Ho Chi Minh, Vietnam
| | - Thi Hue Hanh Nguyen
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Research and Development Department Gene Solutions, Ho Chi Minh, Vietnam
| | - Nguyen Duy Khang Le
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Research and Development Department Gene Solutions, Ho Chi Minh, Vietnam
| | - Thanh Dat Nguyen
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Research and Development Department Gene Solutions, Ho Chi Minh, Vietnam
| | - Duy Sinh Nguyen
- Research and Development Department Gene Solutions, Ho Chi Minh, Vietnam
- Faculty of Medicine Nguyen Tat Thanh University, Ho Chi Minh, Vietnam
| | | | | | - Minh-Duy Phan
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Research and Development Department Gene Solutions, Ho Chi Minh, Vietnam
| | - Hoa Giang
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Research and Development Department Gene Solutions, Ho Chi Minh, Vietnam
| | - Hoai-Nghia Nguyen
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Research and Development Department Gene Solutions, Ho Chi Minh, Vietnam
| | - Le Son Tran
- Medical Genetics Institute, Ho Chi Minh, Vietnam
- Research and Development Department Gene Solutions, Ho Chi Minh, Vietnam
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10
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Wang Z, Lu Y, Fornage M, Jiao L, Shen J, Li D, Wei P. Identification of novel susceptibility methylation loci for pancreatic cancer in a two-phase epigenome-wide association study. Epigenetics 2022; 17:1357-1372. [PMID: 35030986 PMCID: PMC9586592 DOI: 10.1080/15592294.2022.2026591] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 12/31/2021] [Accepted: 01/04/2022] [Indexed: 02/07/2023] Open
Abstract
The role of DNA methylation and its interplay with gene expression in the susceptibility to pancreatic cancer (PanC) remains largely unexplored. To fill in this gap, we conducted an integrative two-phase epigenome-wide association study (EWAS) of PanC using genomic DNA from 44 cases and 556 controls (20 local controls and 536 public controls in the Framingham Heart Study) in phase 1 and 23 cases and 22 controls in phase 2. We validated the findings using pre-diagnostic blood samples from 13 cases and 26 controls in the Women's Health Initiative (WHI) Study. We further examined gene expression in peripheral leukocytes of 47 cases and 31 controls involved in the methylation study using RNA sequencing and performed bidirectional Mendelian randomization (MR) analysis using existing single nucleotide polymorphism (SNP) data. In phase 1, we identified 2776 significantly differentially methylated CpG sites (DMPs) and 154 significantly differentially methylated regions (DMRs). In phase 2, we validated six DMPs (in or near AIM2, DGKA, STK39, and TNFSF8) and three DMRs (in or near nc886, LY6G5C, and HLA-DPB1). The DMR near nc886 was further validated in the WHI samples (P = 6.69 × 10-5). MR analysis suggested that the CpG sites cg00308130 and cg16684184 for nc886 and cg16875057 for STK39 were causally related to PanC susceptibility and that PanC influenced methylation of cg15354065 for DGKA. This first integrative EWAS of PanC provides novel insights into the role of DNA methylation and its interplay with SNPs and gene expression in the disease susceptibility.
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Affiliation(s)
- Ziqiao Wang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, The Virginia Harris Cockrell Cancer Research Center at the University of Texas MD Anderson Cancer Center, Science Park, Smithville, TX, USA
| | - Myriam Fornage
- IBrown Foundation Institute of Molecular Medicine, McGovern Medical School, the University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Li Jiao
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Jianjun Shen
- Department of Epigenetics and Molecular Carcinogenesis, The Virginia Harris Cockrell Cancer Research Center at the University of Texas MD Anderson Cancer Center, Science Park, Smithville, TX, USA
| | - Donghui Li
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Peng Wei
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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11
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Massi MC, Dominoni L, Ieva F, Fiorito G. A Deep Survival EWAS approach estimating risk profile based on pre-diagnostic DNA methylation: An application to breast cancer time to diagnosis. PLoS Comput Biol 2022; 18:e1009959. [PMID: 36155971 PMCID: PMC9536632 DOI: 10.1371/journal.pcbi.1009959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 10/06/2022] [Accepted: 09/10/2022] [Indexed: 11/19/2022] Open
Abstract
Previous studies for cancer biomarker discovery based on pre-diagnostic blood DNA methylation (DNAm) profiles, either ignore the explicit modeling of the Time To Diagnosis (TTD), or provide inconsistent results. This lack of consistency is likely due to the limitations of standard EWAS approaches, that model the effect of DNAm at CpG sites on TTD independently. In this work, we aim to identify blood DNAm profiles associated with TTD, with the aim to improve the reliability of the results, as well as their biological meaningfulness. We argue that a global approach to estimate CpG sites effect profile should capture the complex (potentially non-linear) relationships interplaying between sites. To prove our concept, we develop a new Deep Learning-based approach assessing the relevance of individual CpG Islands (i.e., assigning a weight to each site) in determining TTD while modeling their combined effect in a survival analysis scenario. The algorithm combines a tailored sampling procedure with DNAm sites agglomeration, deep non-linear survival modeling and SHapley Additive exPlanations (SHAP) values estimation to aid robustness of the derived effects profile. The proposed approach deals with the common complexities arising from epidemiological studies, such as small sample size, noise, and low signal-to-noise ratio of blood-derived DNAm. We apply our approach to a prospective case-control study on breast cancer nested in the EPIC Italy cohort and we perform weighted gene-set enrichment analyses to demonstrate the biological meaningfulness of the obtained results. We compared the results of Deep Survival EWAS with those of a traditional EWAS approach, demonstrating that our method performs better than the standard approach in identifying biologically relevant pathways. Blood-derived DNAm profiles could be exploited as new biomarkers for cancer risk stratification and possibly, early detection. This is of particular interest since blood is a convenient tissue to assay for constitutional methylation and its collection is non-invasive. Exploiting pre-diagnostic blood DNAm data opens the further opportunity to investigate the association of DNAm at baseline on cancer risk, modeling the relationship between sites’ methylation and the Time to Diagnosis. Previous studies mostly provide inconsistent results likely due to the limitations of standard EWAS approaches, that model the effect of DNAm at CpG sites on TTD independently. In this work we argue that an approach to estimate single CpG sites’ effect while modeling their combined effect on the survival outcome is needed, and we claim that such approach should capture the complex (potentially non-linear) relationships interplaying between sites. We prove this concept by developing a novel approach to analyze a prospective case-control study on breast cancer nested in the EPIC Italy cohort. A weighted gene set enrichment analysis confirms that our approach outperforms standard EWAS in identifying biologically meaningful pathways.
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Affiliation(s)
- Michela Carlotta Massi
- Health Data Science Centre, Human Technopole Foundation, Milan, Italy
- MOX Laboratory for Modeling and Scientific Computing, Dept. of Mathematics, Politecnico di Milano, Milan, Italy
- * E-mail:
| | - Lorenzo Dominoni
- MOX Laboratory for Modeling and Scientific Computing, Dept. of Mathematics, Politecnico di Milano, Milan, Italy
| | - Francesca Ieva
- Health Data Science Centre, Human Technopole Foundation, Milan, Italy
- MOX Laboratory for Modeling and Scientific Computing, Dept. of Mathematics, Politecnico di Milano, Milan, Italy
| | - Giovanni Fiorito
- Laboratory of Biostatistics, Dept. of Biomedical Sciences, University of Sassari, Sassari, Italy
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12
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Faltus C, Lahnsteiner A, Barrdahl M, Assenov Y, Hüsing A, Bogatyrova O, Laplana M, Johnson T, Muley T, Meister M, Warth A, Thomas M, Plass C, Kaaks R, Risch A. Identification of NHLRC1 as a Novel AKT Activator from a Lung Cancer Epigenome-Wide Association Study (EWAS). Int J Mol Sci 2022; 23:ijms231810699. [PMID: 36142605 PMCID: PMC9505874 DOI: 10.3390/ijms231810699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 11/16/2022] Open
Abstract
Changes in DNA methylation identified by epigenome-wide association studies (EWAS) have been recently linked to increased lung cancer risk. However, the cellular effects of these differentially methylated positions (DMPs) are often unclear. Therefore, we investigated top differentially methylated positions identified from an EWAS study. This included a putative regulatory region of NHLRC1. Hypomethylation of this gene was recently linked with decreased survival rates in lung cancer patients. HumanMethylation450 BeadChip array (450K) analysis was performed on 66 lung cancer case-control pairs from the European Prospective Investigation into Cancer and Nutrition Heidelberg lung cancer EWAS (EPIC HD) cohort. DMPs identified in these pre-diagnostic blood samples were then investigated for differential DNA methylation in lung tumor versus adjacent normal lung tissue from The Cancer Genome Atlas (TCGA) and replicated in two independent lung tumor versus adjacent normal tissue replication sets with MassARRAY. The EPIC HD top hypermethylated DMP cg06646708 was found to be a hypomethylated region in multiple data sets of lung tumor versus adjacent normal tissue. Hypomethylation within this region caused increased mRNA transcription of the closest gene NHLRC1 in lung tumors. In functional assays, we demonstrate attenuated proliferation, viability, migration, and invasion upon NHLRC1 knock-down in lung cancer cells. Furthermore, diminished AKT phosphorylation at serine 473 causing expression of pro-apoptotic AKT-repressed genes was detected in these knock-down experiments. In conclusion, this study demonstrates the powerful potential for discovery of novel functional mechanisms in oncogenesis based on EWAS DNA methylation data. NHLRC1 holds promise as a new prognostic biomarker for lung cancer survival and prognosis, as well as a target for novel treatment strategies in lung cancer patients.
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Affiliation(s)
- Christian Faltus
- Division of Cancer Epigenomics, DKFZ–German Cancer Research Center, 69120 Heidelberg, Germany
- Division of Cancer (Epi-)Genetics, Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
| | - Angelika Lahnsteiner
- Division of Cancer (Epi-)Genetics, Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
- Cancer Cluster Salzburg, 5020 Salzburg, Austria
| | - Myrto Barrdahl
- Division of Cancer Epidemiology, DKFZ-German Cancer Research Center, 69120 Heidelberg, Germany
| | - Yassen Assenov
- Division of Cancer Epigenomics, DKFZ–German Cancer Research Center, 69120 Heidelberg, Germany
| | - Anika Hüsing
- Division of Cancer Epidemiology, DKFZ-German Cancer Research Center, 69120 Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), 69120 Heidelberg, Germany
| | - Olga Bogatyrova
- Division of Cancer Epigenomics, DKFZ–German Cancer Research Center, 69120 Heidelberg, Germany
| | - Marina Laplana
- Division of Cancer Epigenomics, DKFZ–German Cancer Research Center, 69120 Heidelberg, Germany
- Departament de Ciències Mèdiques Bàsiques, Universitat de Lleida, 25198 Lleida, Spain
| | - Theron Johnson
- Division of Cancer Epidemiology, DKFZ-German Cancer Research Center, 69120 Heidelberg, Germany
| | - Thomas Muley
- Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), 69120 Heidelberg, Germany
- Thoraxklinik at University Hospital Heidelberg, University of Heidelberg, 69126 Heidelberg, Germany
| | - Michael Meister
- Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), 69120 Heidelberg, Germany
- Thoraxklinik at University Hospital Heidelberg, University of Heidelberg, 69126 Heidelberg, Germany
| | - Arne Warth
- Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), 69120 Heidelberg, Germany
- Institute of Pathology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Michael Thomas
- Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), 69120 Heidelberg, Germany
- Thoraxklinik at University Hospital Heidelberg, University of Heidelberg, 69126 Heidelberg, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, DKFZ–German Cancer Research Center, 69120 Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), 69120 Heidelberg, Germany
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, DKFZ-German Cancer Research Center, 69120 Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), 69120 Heidelberg, Germany
| | - Angela Risch
- Division of Cancer Epigenomics, DKFZ–German Cancer Research Center, 69120 Heidelberg, Germany
- Division of Cancer (Epi-)Genetics, Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
- Cancer Cluster Salzburg, 5020 Salzburg, Austria
- Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), 69120 Heidelberg, Germany
- Correspondence: ; Tel.: +43-662-8044-7220
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13
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Dugué PA, Bodelon C, Chung FF, Brewer HR, Ambatipudi S, Sampson JN, Cuenin C, Chajès V, Romieu I, Fiorito G, Sacerdote C, Krogh V, Panico S, Tumino R, Vineis P, Polidoro S, Baglietto L, English D, Severi G, Giles GG, Milne RL, Herceg Z, Garcia-Closas M, Flanagan JM, Southey MC. Methylation-based markers of aging and lifestyle-related factors and risk of breast cancer: a pooled analysis of four prospective studies. Breast Cancer Res 2022; 24:59. [PMID: 36068634 PMCID: PMC9446544 DOI: 10.1186/s13058-022-01554-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/12/2022] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND DNA methylation in blood may reflect adverse exposures accumulated over the lifetime and could therefore provide potential improvements in the prediction of cancer risk. A substantial body of research has shown associations between epigenetic aging and risk of disease, including cancer. Here we aimed to study epigenetic measures of aging and lifestyle-related factors in association with risk of breast cancer. METHODS Using data from four prospective case-control studies nested in three cohorts of European ancestry participants, including a total of 1,655 breast cancer cases, we calculated three methylation-based measures of lifestyle factors (body mass index [BMI], tobacco smoking and alcohol consumption) and seven measures of epigenetic aging (Horvath-based, Hannum-based, PhenoAge and GrimAge). All measures were regression-adjusted for their respective risk factors and expressed per standard deviation (SD). Odds ratios (OR) and 95% confidence intervals (CI) were calculated using conditional or unconditional logistic regression and pooled using fixed-effects meta-analysis. Subgroup analyses were conducted by age at blood draw, time from blood sample to diagnosis, oestrogen receptor-positivity status and tumour stage. RESULTS None of the measures of epigenetic aging were associated with risk of breast cancer in the pooled analysis: Horvath 'age acceleration' (AA): OR per SD = 1.02, 95%CI: 0.95-1.10; AA-Hannum: OR = 1.03, 95%CI:0.95-1.12; PhenoAge: OR = 1.01, 95%CI: 0.94-1.09 and GrimAge: OR = 1.03, 95%CI: 0.94-1.12, in models adjusting for white blood cell proportions, body mass index, smoking and alcohol consumption. The BMI-adjusted predictor of BMI was associated with breast cancer risk, OR per SD = 1.09, 95%CI: 1.01-1.17. The results for the alcohol and smoking methylation-based predictors were consistent with a null association. Risk did not appear to substantially vary by age at blood draw, time to diagnosis or tumour characteristics. CONCLUSION We found no evidence that methylation-based measures of aging, smoking or alcohol consumption were associated with risk of breast cancer. A methylation-based marker of BMI was associated with risk and may provide insights into the underlying associations between BMI and breast cancer.
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Affiliation(s)
- Pierre-Antoine Dugué
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia.
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia.
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia.
| | - Clara Bodelon
- Divison of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, USA
| | - Felicia F Chung
- International Agency for Research On Cancer (IARC), Lyon, France
- Department of Medical Sciences, School of Medical and Life Sciences, Sunway University, Bandar Sunway, Malaysia
| | - Hannah R Brewer
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Srikant Ambatipudi
- International Agency for Research On Cancer (IARC), Lyon, France
- AMCHSS, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala, India
| | - Joshua N Sampson
- Divison of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, USA
| | - Cyrille Cuenin
- International Agency for Research On Cancer (IARC), Lyon, France
| | - Veronique Chajès
- International Agency for Research On Cancer (IARC), Lyon, France
| | - Isabelle Romieu
- International Agency for Research On Cancer (IARC), Lyon, France
| | - Giovanni Fiorito
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - Carlotta Sacerdote
- Unit of Cancer Epidemiology, Città della Salute e Della Scienza University-Hospital, Turin, Italy
| | - Vittorio Krogh
- Department of Research, Epidemiology and Prevention Unit, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, MI, Italy
| | - Salvatore Panico
- Dipartimento di Medicina Clinica e Chirurgia Federico II University, Naples, Italy
| | - Rosario Tumino
- Hyblean Association for Epidemiological Research AIRE-ONLUS, Ragusa, Italy
| | - Paolo Vineis
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | | | - Laura Baglietto
- Department of Clinical and Experimental Medicine, University of Pisa, 56126, Pisa, Italy
| | - Dallas English
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - Gianluca Severi
- CESP UMR1018, Paris-Saclay University, UVSQ, Inserm, Gustave Roussy, Villejuif, France
| | - Graham G Giles
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - Roger L Milne
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - Zdenko Herceg
- International Agency for Research On Cancer (IARC), Lyon, France
| | | | - James M Flanagan
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Parkville, VIC, Australia
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14
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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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15
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Page CM, Nøst TH, Djordjilović V, Thoresen M, Frigessi A, Sandanger TM, Veierød MB. Pre-diagnostic DNA methylation in blood leucocytes in cutaneous melanoma; a nested case–control study within the Norwegian Women and Cancer cohort. Sci Rep 2022; 12:14200. [PMID: 35987900 PMCID: PMC9392730 DOI: 10.1038/s41598-022-18585-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 08/16/2022] [Indexed: 12/03/2022] Open
Abstract
The prognosis of cutaneous melanoma depends on early detection, and good biomarkers for melanoma risk may provide a valuable tool to detect melanoma development at a pre-clinical stage. By studying the epigenetic profile in pre-diagnostic blood samples of melanoma cases and cancer free controls, we aimed to identify DNA methylation sites conferring melanoma risk. DNA methylation was measured at 775,528 CpG sites using the Illumina EPIC array in whole blood in incident melanoma cases (n = 183) and matched cancer-free controls (n = 183) in the Norwegian Women and Cancer cohort. Phenotypic information and ultraviolet radiation exposure were obtained from questionnaires. Epigenome wide association (EWAS) was analyzed in future melanoma cases and controls with conditional logistic regression, with correction for multiple testing using the false discovery rate (FDR). We extended the analysis by including a public data set on melanoma (GSE120878), and combining these different data sets using a version of covariate modulated FDR (AdaPT). The analysis on future melanoma cases and controls did not identify any genome wide significant CpG sites (0.85 ≤ padj ≤ 0.99). In the restricted AdaPT analysis, 7 CpG sites were suggestive at the FDR level of 0.15. These CpG sites may potentially be used as pre-diagnostic biomarkers of melanoma risk.
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16
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Wanowska E, Samorowska K, Szcześniak MW. Emerging Roles of Long Noncoding RNAs in Breast Cancer Epigenetics and Epitranscriptomics. Front Cell Dev Biol 2022; 10:922351. [PMID: 35865634 PMCID: PMC9294602 DOI: 10.3389/fcell.2022.922351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Breast carcinogenesis is a multistep process that involves both genetic and epigenetic changes. Epigenetics refers to reversible changes in gene expression that are not accompanied by changes in gene sequence. In breast cancer (BC), dysregulated epigenetic changes, such as DNA methylation and histone modifications, are accompanied by epitranscriptomic changes, in particular adenine to inosine modifications within RNA molecules. Factors that trigger these phenomena are largely unknown, but there is evidence for widespread participation of long noncoding RNAs (lncRNAs) that already have been linked to virtually any aspect of BC biology, making them promising biomarkers and therapeutic targets in BC patients. Here, we provide a systematic review of known and possible roles of lncRNAs in epigenetic and epitranscriptomic processes, along with methods and tools to study them, followed by a brief overview of current challenges regarding the use of lncRNAs in medical applications.
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Affiliation(s)
- Elżbieta Wanowska
- Department of Biological Sciences, Auburn University, Auburn, AL, United States
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznań, Poland
- *Correspondence: Elżbieta Wanowska, ; Michał Wojciech Szcześniak,
| | - Klaudia Samorowska
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznań, Poland
| | - Michał Wojciech Szcześniak
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznań, Poland
- *Correspondence: Elżbieta Wanowska, ; Michał Wojciech Szcześniak,
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17
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Switzer CH, Cho HJ, Eykyn TR, Lavender P, Eaton P. NOS2 and S-nitrosothiol signaling induces DNA hypomethylation and LINE-1 retrotransposon expression. Proc Natl Acad Sci U S A 2022; 119:e2200022119. [PMID: 35584114 PMCID: PMC9173756 DOI: 10.1073/pnas.2200022119] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 03/29/2022] [Indexed: 12/31/2022] Open
Abstract
Inducible nitric oxide synthase (NOS2) produces high local concentrations of nitric oxide (NO), and its expression is associated with inflammation, cellular stress signals, and cellular transformation. Additionally, NOS2 expression results in aggressive cancer cell phenotypes and is correlated with poor outcomes in patients with breast cancer. DNA hypomethylation, especially of noncoding repeat elements, is an early event in carcinogenesis and is a common feature of cancer cells. In addition to altered gene expression, DNA hypomethylation results in genomic instability via retrotransposon activation. Here, we show that NOS2 expression and associated NO signaling results in substantial DNA hypomethylation in human cell lines by inducing the degradation of DNA (cytosine-5)–methyltransferase 1 (DNMT1) protein. Similarly, NOS2 expression levels were correlated with decreased DNA methylation in human breast tumors. NOS2 expression and NO signaling also resulted in long interspersed noncoding element 1 (LINE-1) retrotransposon hypomethylation, expression, and DNA damage. DNMT1 degradation was mediated by an NO/p38-MAPK/lysine acetyltransferase 5–dependent mechanism. Furthermore, we show that this mechanism is required for NO-mediated epithelial transformation. Therefore, we conclude that NOS2 and NO signaling results in DNA damage and malignant cellular transformation via an epigenetic mechanism.
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Affiliation(s)
- Christopher H. Switzer
- William Harvey Research Institute, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, United Kingdom
| | - Hyun-Ju Cho
- William Harvey Research Institute, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, United Kingdom
| | - Thomas R. Eykyn
- School of Biomedical Engineering & Imaging Sciences, King’s College London, St. Thomas’ Hospital, London, SE1 7EH, United Kingdom
| | - Paul Lavender
- AsthmaUK Centre in Allergic Mechanisms of Asthma, School of Immunology and Microbial Science, King’s College London, Guy’s Hospital, London, SE1 9RT, United Kingdom
| | - Philip Eaton
- William Harvey Research Institute, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, United Kingdom
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18
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Qi L, Teschendorff AE. Cell-type heterogeneity: Why we should adjust for it in epigenome and biomarker studies. Clin Epigenetics 2022; 14:31. [PMID: 35227298 PMCID: PMC8887190 DOI: 10.1186/s13148-022-01253-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 02/21/2022] [Indexed: 12/18/2022] Open
Abstract
Most studies aiming to identify epigenetic biomarkers do so from complex tissues that are composed of many different cell-types. By definition, these cell-types vary substantially in terms of their epigenetic profiles. This cell-type specific variation among healthy cells is completely independent of the variation associated with disease, yet it dominates the epigenetic variability landscape. While cell-type composition of tissues can change in disease and this may provide accurate and reproducible biomarkers, not adjusting for the underlying cell-type heterogeneity may seriously limit the sensitivity and precision to detect disease-relevant biomarkers or hamper our understanding of such biomarkers. Given that computational and experimental tools for tackling cell-type heterogeneity are available, we here stress that future epigenetic biomarker studies should aim to provide estimates of underlying cell-type fractions for all samples in the study, and to identify biomarkers before and after adjustment for cell-type heterogeneity, in order to obtain a more complete and unbiased picture of the biomarker-landscape. This is critical, not only to improve reproducibility and for the eventual clinical application of such biomarkers, but importantly, to also improve our molecular understanding of disease itself.
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Affiliation(s)
- Luo Qi
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China. .,UCL Cancer Institute, University College London, London, WC1E 8BT, UK.
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19
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The WID-BC-index identifies women with primary poor prognostic breast cancer based on DNA methylation in cervical samples. Nat Commun 2022; 13:449. [PMID: 35105882 PMCID: PMC8807602 DOI: 10.1038/s41467-021-27918-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 12/02/2021] [Indexed: 02/07/2023] Open
Abstract
Genetic and non-genetic factors contribute to breast cancer development. An epigenome-based signature capturing these components in easily accessible samples could identify women at risk. Here, we analyse the DNA methylome in 2,818 cervical, 357 and 227 matched buccal and blood samples respectively, and 42 breast tissue samples from women with and without breast cancer. Utilising cervical liquid-based cytology samples, we develop the DNA methylation-based Women’s risk IDentification for Breast Cancer index (WID-BC-index) that identifies women with breast cancer with an AUROC (Area Under the Receiver Operator Characteristic) of 0.84 (95% CI: 0.80–0.88) and 0.81 (95% CI: 0.76–0.86) in internal and external validation sets, respectively. CpGs at progesterone receptor binding sites hypomethylated in normal breast tissue of women with breast cancer or in BRCA mutation carriers are also hypomethylated in cervical samples of women with poor prognostic breast cancer. Our data indicate that a systemic epigenetic programming defect is highly prevalent in women who develop breast cancer. Further studies validating the WID-BC-index may enable clinical implementation for monitoring breast cancer risk. Breast cancer is most commonly diagnosed via a needle biopsy. In this study, the authors show that cervical samples from women with breast cancer have a methylation signature different to that of healthy controls.
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20
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Rykov SV, Filippova EA, Loginov VI, Braga EA. Gene Methylation in Circulating Cell-Free DNA from the Blood Plasma as Prognostic and Predictive Factor in Breast Cancer. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421110120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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21
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Ding YC, Hurley S, Park JS, Steele L, Rakoff M, Zhu Y, Zhao J, LaBarge M, Bernstein L, Chen S, Reynolds P, Neuhausen SL. Methylation biomarkers of polybrominated diphenyl ethers (PBDEs) and association with breast cancer risk at the time of menopause. ENVIRONMENT INTERNATIONAL 2021; 156:106772. [PMID: 34425644 PMCID: PMC8385228 DOI: 10.1016/j.envint.2021.106772] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 07/09/2021] [Accepted: 07/12/2021] [Indexed: 05/27/2023]
Abstract
BACKGROUND Exposure to polybrominated diphenyl ethers (PBDEs) may influence risk of developing post-menopausal breast cancer. Although mechanisms are poorly understood, epigenetic regulation of gene expression may play a role. OBJECTIVES To identify DNA methylation (DNAm) changes associated with PBDE serum levels and test the association of these biomarkers with breast cancer risk. METHODS We studied 397 healthy women (controls) and 133 women diagnosed with breast cancer (cases) between ages 40 and 58 years who participated in the California Teachers Study. PBDE levels were measured in blood. Infinium Human Methylation EPIC Bead Chips were used to measure DNAm. Using multivariable linear regression models, differentially methylated CpG sites (DMSs) and regions (DMRs) associated with serum PBDE levels were identified using controls. For top-ranked DMSs and DMRs, targeted next-generation bisulfite sequencing was used to measure DNAm for 133 invasive breast cancer cases and 301 age-matched controls. Conditional logistic regression was used to evaluate associations between DMSs and DMRs and breast cancer risk. RESULTS We identified 15 DMSs and 10 DMRs statistically significantly associated with PBDE levels (FDR < 0.05). Methylation changes in a DMS at BMP8B and DMRs at TP53 and A2M-AS1 were statistically significantly (FDR < 0.05) associated with breast cancer risk. CONCLUSION We show for the first time that serum PBDE levels are associated with differential methylation and that PBDE-associated DNAm changes in blood are associated with breast cancer risk.
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Affiliation(s)
- Yuan Chun Ding
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Susan Hurley
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA; Office of Environmental Health Hazard Assessment, California Environmental Protection Agency, Oakland, CA, USA
| | - June-Soo Park
- Environmental Chemistry Laboratory, Department of Toxic Substances Control, Berkeley, CA, USA
| | - Linda Steele
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Michele Rakoff
- Breast Cancer Care and Research Fund, Los Angeles, CA, USA
| | - Yun Zhu
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, FL, USA
| | - Jinying Zhao
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, FL, USA
| | - Mark LaBarge
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Leslie Bernstein
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Shiuan Chen
- Department of Cancer Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Peggy Reynolds
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA.
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22
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Lemarchand C, Gabet S, Cénée S, Tvardik N, Slama R, Guénel P. Breast cancer risk in relation to ambient concentrations of nitrogen dioxide and particulate matter: results of a population-based case-control study corrected for potential selection bias (the CECILE study). ENVIRONMENT INTERNATIONAL 2021; 155:106604. [PMID: 34030067 DOI: 10.1016/j.envint.2021.106604] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/20/2021] [Accepted: 04/24/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND There is only scant evidence that air pollution increases the risk of breast cancer. OBJECTIVES We investigated this relationship for three air pollutants: nitrogen dioxide (NO2) and particulate matter with an aerodynamical diameter below 10 µm (PM10) and 2.5 µm (PM2.5). METHODS We conducted a population-based case-control study on breast cancer in two French départements, including 1,229 women diagnosed with breast cancer in 2005-2007 and 1,316 control women frequency-matched on age. Concentrations of NO2, PM10 and PM2.5 at participants' addresses occupied during the last 10 years were assessed using a chemistry transport model. Odds ratios (OR) and 95% confidence intervals (95% CI) were estimated using multivariable logistic regression models where each woman was assigned a weight depending on her probability of selection into the study. RESULTS The OR for breast cancer per 10-µg/m3 increase in NO2 was 1.11 (95% CI, 0.98, 1.26), and 1.41 (95% CI 1.07, 1.86) in the highest exposure quintile (Q5), compared to the first. The ORs per 10-µg/m3 NO2 did not markedly differ between pre- (OR 1.09, 95% CI 0.89, 1.35)) and post-menopausal women (OR 1.14, 95% CI 0.97, 1.33)), but the OR was substantially higher for hormone-receptor positive (ER+/PR+) breast tumor subtypes (OR 1.15, 95% CI 1.00, 1.31) than for ER-/PR- tumors (OR 0.95, 95% CI 0.72, 1.26). Breast cancer risk was not associated with either PM10 (OR per 1 µg/m3 1.01, 95% CI, 0.96, 1.06) or PM2.5 (OR per 1 µg/m3 1.02, 95% CI 0.95, 1.08), regardless of the menopausal status or of the breast tumor subtype. DISCUSSION Our study provides evidence that NO2 exposure, a marker of traffic-related air pollutants, may be associated with an increased risk of breast cancer, particularly ER+/PR+ tumors.
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Affiliation(s)
- Clémentine Lemarchand
- University Paris-Saclay, UVSQ, Gustave Roussy, Inserm, CESP, Team Exposome and Heredity, 94800 Villejuif, France
| | - Stephan Gabet
- Univ. Grenoble Alpes, Inserm, CNRS, Team of Environmental Epidemiology Applied to Reproduction and Respiratory Health, IAB, 38000 Grenoble, France
| | - Sylvie Cénée
- University Paris-Saclay, UVSQ, Gustave Roussy, Inserm, CESP, Team Exposome and Heredity, 94800 Villejuif, France
| | - Nastassia Tvardik
- University Paris-Saclay, UVSQ, Gustave Roussy, Inserm, CESP, Team Exposome and Heredity, 94800 Villejuif, France
| | - Rémy Slama
- Univ. Grenoble Alpes, Inserm, CNRS, Team of Environmental Epidemiology Applied to Reproduction and Respiratory Health, IAB, 38000 Grenoble, France
| | - Pascal Guénel
- University Paris-Saclay, UVSQ, Gustave Roussy, Inserm, CESP, Team Exposome and Heredity, 94800 Villejuif, France.
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23
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Suhre K, Zaghlool S. Connecting the epigenome, metabolome and proteome for a deeper understanding of disease. J Intern Med 2021; 290:527-548. [PMID: 33904619 DOI: 10.1111/joim.13306] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 12/26/2022]
Abstract
Epigenome-wide association studies (EWAS) identify genes that are dysregulated by the studied clinical endpoints, thereby indicating potential new diagnostic biomarkers, drug targets and therapy options. Combining EWAS with deep molecular phenotyping, such as approaches enabled by metabolomics and proteomics, allows further probing of the underlying disease-associated pathways. For instance, methylation of the TXNIP gene is associated robustly with prevalent type 2 diabetes and further with metabolites that are short-term markers of glycaemic control. These associations reflect TXNIP's function as a glucose uptake regulator by interaction with the major glucose transporter GLUT1 and suggest that TXNIP methylation can be used as a read-out for the organism's exposure to glucose stress. Another case is the association between DNA methylation of the AHRR and F2RL3 genes with smoking and a protein that is involved in the reprogramming of the bronchial epithelium. These examples show that associations between DNA methylation and intermediate molecular traits can open new windows into how the body copes with physiological challenges. This knowledge, if carefully interpreted, may indicate novel therapy options and, together with monitoring of the methylation state of specific methylation sites, may in the future allow the early diagnosis of impending disease. It is essential for medical practitioners to recognize the potential that this field holds in translating basic research findings to clinical practice. In this review, we present recent advances in the field of EWAS with metabolomics and proteomics and discuss both the potential and the challenges of translating epigenetic associations, with deep molecular phenotypes, to biomedical applications.
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Affiliation(s)
- K Suhre
- From the, Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar.,Department of Biophysics and Physiology, Weill Cornell Medicine, New York, USA
| | - S Zaghlool
- From the, Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar.,Department of Biophysics and Physiology, Weill Cornell Medicine, New York, USA
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24
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Dai YH, Wang YF, Shen PC, Lo CH, Yang JF, Lin CS, Chao HL, Huang WY. Gene-associated methylation status of ST14 as a predictor of survival and hormone receptor positivity in breast Cancer. BMC Cancer 2021; 21:945. [PMID: 34418985 PMCID: PMC8380334 DOI: 10.1186/s12885-021-08645-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 07/20/2021] [Indexed: 12/14/2022] Open
Abstract
Background Genomic profiles of specific gene sets have been established to guide personalized treatment and prognosis for patients with breast cancer (BC). However, epigenomic information has not yet been applied in a clinical setting. ST14 encodes matriptase, a proteinase that is widely expressed in BC with reported prognostic value. Methods In this present study, we evaluated the effect of ST14 DNA methylation (DNAm) on overall survival (OS) of patients with BC as a representative example to promote the use of the epigenome in clinical decisions. We analyzed publicly available genomic and epigenomic data from 1361 BC patients. Methylation was characterized by the β-value from CpG probes based on sequencing with the Illumina Human 450 K platform. Results A high mean DNAm (β > 0.6779) across 34 CpG probes for ST14, as the gene-associated methylation (GAM) pattern, was associated with a longer OS after adjusting age, stage, histology and molecular features in Cox model (p value < 0.001). A high GAM status was also associated with a higher XBP1 expression level and higher proportion of hormone-positive BC (p value < 0.001). Pathway analysis revealed that altered GAM was related to matrisome-associated pathway. Conclusions Here we show the potential role of ST14 DNAm in BC prognosis and warrant further study. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08645-3.
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Affiliation(s)
- Yang-Hong Dai
- Department of Radiation Oncology, Tri-Service General Hospital, National Defense Medical Center, No. 325, Chengong Rd., Sec. 2, Neihu, Taipei, 114, Taiwan
| | - Ying-Fu Wang
- Department of Radiation Oncology, Tri-Service General Hospital, National Defense Medical Center, No. 325, Chengong Rd., Sec. 2, Neihu, Taipei, 114, Taiwan
| | - Po-Chien Shen
- Department of Radiation Oncology, Tri-Service General Hospital, National Defense Medical Center, No. 325, Chengong Rd., Sec. 2, Neihu, Taipei, 114, Taiwan
| | - Cheng-Hsiang Lo
- Department of Radiation Oncology, Tri-Service General Hospital, National Defense Medical Center, No. 325, Chengong Rd., Sec. 2, Neihu, Taipei, 114, Taiwan
| | - Jen-Fu Yang
- Department of Radiation Oncology, Tri-Service General Hospital, National Defense Medical Center, No. 325, Chengong Rd., Sec. 2, Neihu, Taipei, 114, Taiwan
| | - Chun-Shu Lin
- Department of Radiation Oncology, Tri-Service General Hospital, National Defense Medical Center, No. 325, Chengong Rd., Sec. 2, Neihu, Taipei, 114, Taiwan
| | - Hsing-Lung Chao
- Department of Radiation Oncology, Tri-Service General Hospital, National Defense Medical Center, No. 325, Chengong Rd., Sec. 2, Neihu, Taipei, 114, Taiwan.,Department of Radiation Oncology, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Wen-Yen Huang
- Department of Radiation Oncology, Tri-Service General Hospital, National Defense Medical Center, No. 325, Chengong Rd., Sec. 2, Neihu, Taipei, 114, Taiwan. .,Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.
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25
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Kresovich JK, Xu Z, O'Brien KM, Shi M, Weinberg CR, Sandler DP, Taylor JA. Blood DNA methylation profiles improve breast cancer prediction. Mol Oncol 2021; 16:42-53. [PMID: 34411412 PMCID: PMC8732352 DOI: 10.1002/1878-0261.13087] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 06/24/2021] [Accepted: 08/18/2021] [Indexed: 12/21/2022] Open
Abstract
Although blood DNA methylation (DNAm) profiles are reported to be associated with breast cancer incidence, they have not been widely used in breast cancer risk assessment. Among a breast cancer case–cohort of 2774 women (1551 cases) in the Sister Study, we used candidate CpGs and DNAm estimators of physiologic characteristics to derive a methylation‐based breast cancer risk score, mBCRS. Overall, 19 CpGs and five DNAm estimators were selected using elastic net regularization to comprise mBCRS. In a test set, higher mBCRS was positively associated with breast cancer incidence, showing similar strength to the polygenic risk score (PRS) based on 313 single nucleotide polymorphisms (313 SNPs). Area under the curve for breast cancer prediction was 0.60 for self‐reported risk factors (RFs), 0.63 for PRS, and 0.63 for mBCRS. Adding mBCRS to PRS and RFs improved breast cancer prediction from 0.66 to 0.71. mBCRS findings were replicated in a nested case–control study within the EPIC‐Italy cohort. These results suggest that mBCRS, a risk score derived using blood DNAm, can be used to enhance breast cancer prediction.
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Affiliation(s)
- Jacob K Kresovich
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Zongli Xu
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Katie M O'Brien
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Min Shi
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Clarice R Weinberg
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Jack A Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA.,Epigenetic and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
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26
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Zhang X, Zhao D, Yin Y, Yang T, You Z, Li D, Chen Y, Jiang Y, Xu S, Geng J, Zhao Y, Wang J, Li H, Tao J, Lei S, Jiang Z, Chen Z, Yu S, Fan JB, Pang D. Circulating cell-free DNA-based methylation patterns for breast cancer diagnosis. NPJ Breast Cancer 2021; 7:106. [PMID: 34400642 PMCID: PMC8367945 DOI: 10.1038/s41523-021-00316-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 07/26/2021] [Indexed: 01/02/2023] Open
Abstract
Mammography is used to detect breast cancer (BC), but its sensitivity is limited, especially for dense breasts. Circulating cell-free DNA (cfDNA) methylation tests is expected to compensate for the deficiency of mammography. We derived a specific panel of markers based on computational analysis of the DNA methylation profiles from The Cancer Genome Atlas (TCGA). Through training (n = 160) and validation set (n = 69), we developed a diagnostic prediction model with 26 markers, which yielded a sensitivity of 89.37% and a specificity of 100% for differentiating malignant disease from normal lesions [AUROC = 0.9816 (95% CI: 96.09-100%), and AUPRC = 0.9704 (95% CI: 94.54–99.46%)]. A simplified 4-marker model including cg23035715, cg16304215, cg20072171, and cg21501525 had a similar diagnostic power [AUROC = 0.9796 (95% CI: 95.56–100%), and AUPRC = 0.9220 (95% CI: 91.02–94.37%)]. We found that a single cfDNA methylation marker, cg23035715, has a high diagnostic power [AUROC = 0.9395 (95% CI: 89.72–99.27%), and AUPRC = 0.9111 (95% CI: 88.45–93.76%)], with a sensitivity of 84.90% and a specificity of 93.88%. In an independent testing dataset (n = 104), the obtained diagnostic prediction model discriminated BC patients from normal controls with high accuracy [AUROC = 0.9449 (95% CI: 90.07–98.91%), and AUPRC = 0.8640 (95% CI: 82.82–89.98%)]. We compared the diagnostic power of cfDNA methylation and mammography. Our model yielded a sensitivity of 94.79% (95% CI: 78.72–97.87%) and a specificity of 98.70% (95% CI: 86.36–100%) for differentiating malignant disease from normal lesions [AUROC = 0.9815 (95% CI: 96.75–99.55%), and AUPRC = 0.9800 (95% CI: 96.6–99.4%)], with better diagnostic power and had better diagnostic power than that of using mammography [AUROC = 0.9315 (95% CI: 89.95–96.34%), and AUPRC = 0.9490 (95% CI: 91.7–98.1%)]. In addition, hypermethylation profiling provided insights into lymph node metastasis stratifications (p < 0.05). In conclusion, we developed and tested a cfDNA methylation model for BC diagnosis with better performance than mammography.
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Affiliation(s)
- Xianyu Zhang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Dezhi Zhao
- Department of Research and Development, AnchorDx Medical Co., Ltd., Guangzhou, China
| | - Yanling Yin
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Ting Yang
- Department of Research and Development, AnchorDx Medical Co., Ltd., Guangzhou, China
| | - Zilong You
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Dalin Li
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yanbo Chen
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yongdong Jiang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Shouping Xu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jingshu Geng
- Department of Pathology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yashuang Zhao
- Department of Epidemiology, Harbin Medical University, Harbin, China
| | - Jun Wang
- Department of Research and Development, AnchorDx Medical Co., Ltd., Guangzhou, China
| | - Hui Li
- Department of Research and Development, AnchorDx Medical Co., Ltd., Guangzhou, China
| | - Jinsheng Tao
- Department of Research and Development, AnchorDx Medical Co., Ltd., Guangzhou, China
| | - Shan Lei
- Department of Research and Development, AnchorDx Medical Co., Ltd., Guangzhou, China
| | - Zeyu Jiang
- Department of Research and Development, AnchorDx Medical Co., Ltd., Guangzhou, China
| | - Zhiwei Chen
- Department of Research and Development, AnchorDx Medical Co., Ltd., Guangzhou, China.,AnchorDx, Inc., Fremont, California, USA
| | - Shihui Yu
- Guangzhou Kingmed Center for Clinical Laboratory Co., Ltd., Guangzhou, China
| | - Jian-Bing Fan
- Department of Research and Development, AnchorDx Medical Co., Ltd., Guangzhou, China. .,Department of Pathology, School of Basic Medical Science, Southern Medical University, Guangzhou, China.
| | - Da Pang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China.
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Sturgeon SR, Sela DA, Browne EP, Einson J, Rani A, Halabi M, Kania T, Keezer A, Balasubramanian R, Ziegler RG, Schairer C, Kelsey KT, Arcaro KF. Prediagnostic White Blood Cell DNA Methylation and Risk of Breast Cancer in the Prostate Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO) Cohort. Cancer Epidemiol Biomarkers Prev 2021; 30:1575-1581. [PMID: 34108140 PMCID: PMC10825794 DOI: 10.1158/1055-9965.epi-20-1717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/11/2021] [Accepted: 05/21/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND White blood cell (WBC) DNA may contain methylation patterns that are associated with subsequent breast cancer risk. Using a high-throughput array and samples collected, on average, 1.3 years prior to diagnosis, a case-cohort analysis nested in the prospective Sister Study identified 250 individual CpG sites that were differentially methylated between breast cancer cases and noncases. We examined five of the top 40 CpG sites in a case-control study nested in the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO) Cohort. METHODS We investigated the associations between prediagnostic WBC DNA methylation in 297 breast cancer cases and 297 frequency-matched controls. Two WBC DNA specimens from each participant were used: a proximate sample collected 1 to 2.9 years and a distant sample collected 4.2-7.3 years prior to diagnosis in cases or the comparable timepoints in controls. WBC DNA methylation level was measured using targeted bisulfite amplification sequencing. We used logistic regression to obtain ORs and 95% confidence intervals (CI). RESULTS A one-unit increase in percent methylation in ERCC1 in proximate WBC DNA was associated with increased breast cancer risk (adjusted OR = 1.29; 95% CI, 1.06-1.57). However, a one-unit increase in percent methylation in ERCC1 in distant WBC DNA was inversely associated with breast cancer risk (adjusted OR = 0.83; 95% CI, 0.69-0.98). None of the other ORs met the threshold for statistical significance. CONCLUSIONS There was no convincing pattern between percent methylation in the five CpG sites and breast cancer risk. IMPACT The link between prediagnostic WBC DNA methylation marks and breast cancer, if any, is poorly understood.
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Affiliation(s)
- Susan R Sturgeon
- Department of Biostatistics and Epidemiology, University of Massachusetts, Amherst, Massachusetts.
| | - David A Sela
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts
| | - Eva P Browne
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts
| | - Jonah Einson
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts
| | - Asha Rani
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts
| | - Mohamed Halabi
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts
| | - Thomas Kania
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts
| | - Andrew Keezer
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts
| | - Raji Balasubramanian
- Department of Biostatistics and Epidemiology, University of Massachusetts, Amherst, Massachusetts
| | - Regina G Ziegler
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Catherine Schairer
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Karl T Kelsey
- Department of Epidemiology, Department of Pathology, and Department of Laboratory Medicine, Brown University, Providence, Rhode Island
| | - Kathleen F Arcaro
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts
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28
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Lucia RM, Huang WL, Alvarez A, Masunaka I, Ziogas A, Goodman D, Odegaard AO, Norden-Krichmar TM, Park HL. Association of mammographic density with blood DNA methylation. Epigenetics 2021; 17:531-546. [PMID: 34116608 PMCID: PMC9067527 DOI: 10.1080/15592294.2021.1928994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Background: Altered DNA methylation may be an intermediate phenotype between breast cancer risk factors and disease. Mammographic density is a strong risk factor for breast cancer. However, no studies to date have identified an epigenetic signature of mammographic density. We performed an epigenome-wide association study of mammographic density. Methods: White blood cell DNA methylation was measured for 385 postmenopausal women using the Illumina Infinium MethylationEPIC BeadChip array. Differential methylation was assessed using genome-wide, probe-level, and regional analyses. We implemented a resampling-based approach to improve the stability of our findings. Results: On average, women with elevated mammographic density exhibited DNA hypermethylation within CpG islands and gene promoters compared to women with lower mammographic density. We identified 250 CpG sites for which DNA methylation was significantly associated with mammographic density. The top sites were located within genes associated with cancer, including HDLBP, TGFB2, CCT4, and PAX8, and were more likely to be located in regulatory regions of the genome. We also identified differential DNA methylation in 37 regions, including within the promoters of PAX8 and PF4, a gene involved in the regulation of angiogenesis. Overall, our results paint a picture of epigenetic dysregulation associated with mammographic density. Conclusion: Mammographic density is associated with differential DNA methylation throughout the genome, including within genes associated with cancer. Our results suggest the potential involvement of several genes in the biological mechanisms behind differences in breast density between women. Further studies are warranted to explore these potential mechanisms and potential links to breast cancer risk.
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Affiliation(s)
- Rachel M Lucia
- Department of Epidemiology, University of California, Irvine, USA
| | - Wei-Lin Huang
- Department of Epidemiology, University of California, Irvine, USA
| | - Andrea Alvarez
- Department of Medicine, University of California, Irvine, USA
| | - Irene Masunaka
- Department of Medicine, University of California, Irvine, USA
| | - Argyrios Ziogas
- Department of Medicine, University of California, Irvine, USA
| | - Deborah Goodman
- Department of Epidemiology, University of California, Irvine, USA
| | | | | | - Hannah Lui Park
- Department of Epidemiology, University of California, Irvine, USA.,Department of Pathology and Laboratory Medicine, University of California, Irvine, USA
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29
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Cappetta M, Fernandez L, Brignoni L, Artagaveytia N, Bonilla C, López M, Esteller M, Bertoni B, Berdasco M. Discovery of novel DNA methylation biomarkers for non-invasive sporadic breast cancer detection in the Latino population. Mol Oncol 2021; 15:473-486. [PMID: 33145876 PMCID: PMC7858097 DOI: 10.1002/1878-0261.12842] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/19/2020] [Accepted: 10/23/2020] [Indexed: 01/06/2023] Open
Abstract
Human diversity is one of the main pitfalls in the development of robust worldwide biomarkers in oncology. Epigenetic variability across human populations is associated with different genetic backgrounds, as well as variable lifestyles and environmental exposures, each of which should be investigated. To identify potential non-invasive biomarkers of sporadic breast cancer in the Uruguayan population, we studied genome-wide DNA methylation using Illumina methylation arrays in leukocytes of 22 women with sporadic breast cancer and 10 healthy women in a case-control study. We described a panel of 38 differentially methylated CpG positions that was able to cluster breast cancer patients (BCP) and controls, and that also recapitulated methylation differences in 12 primary breast tumors and their matched normal breast tissue. Moving forward, we simplified the detection method to improve its applicability in a clinical setting and used an independent well-characterized cohort of 80 leukocyte DNA samples from BCP and 80 healthy controls to validate methylation results at specific cancer-related genes. Our investigations identified methylation at CYFIP1 as a novel epigenetic biomarker candidate for sporadic breast cancer in the Uruguayan population. These results provide a proof-of-concept for the design of larger studies aimed at validating biomarker panels for the Latin American population.
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Affiliation(s)
- Mónica Cappetta
- Departamento de GenéticaFacultad de MedicinaUniversidad de la RepúblicaMontevideoUruguay
| | - Lucía Fernandez
- Departamento de GenéticaFacultad de MedicinaUniversidad de la RepúblicaMontevideoUruguay
| | - Lucía Brignoni
- Departamento de GenéticaFacultad de MedicinaUniversidad de la RepúblicaMontevideoUruguay
| | - Nora Artagaveytia
- Departamento Básico de MedicinaFacultad de MedicinaUniversidad de la RepúblicaMontevideoUruguay
| | - Carolina Bonilla
- Departamento de Medicina PreventivaFacultad de MedicinaUniversidad de São PauloBrazil
- Population Health SciencesBristol Medical SchoolUniversity of BristolUK
| | - Miguel López
- Cancer Epigenetics and Biology Program (PEBC)Bellvitge Biomedical Research Institute (IDIBELL)BarcelonaSpain
- Epigenetic Therapies Group, Experimental and Clinical Hematology Program (PHEC)Josep Carreras Leukaemia Research Institute (IJC)BadalonaSpain
| | - Manel Esteller
- Cancer Epigenetics Group, Cancer and Leukemia Epigenetics and Biology Program (PEBCL)Josep Carreras Leukaemia Research Institute (IJC)BadalonaSpain
- Physiological Sciences DepartmentSchool of Medicine and Health SciencesUniversity of BarcelonaSpain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC)MadridSpain
- Institució Catalana de Recerca i Estudis Avançats (ICREA)BarcelonaSpain
| | - Bernardo Bertoni
- Departamento de GenéticaFacultad de MedicinaUniversidad de la RepúblicaMontevideoUruguay
| | - María Berdasco
- Cancer Epigenetics and Biology Program (PEBC)Bellvitge Biomedical Research Institute (IDIBELL)BarcelonaSpain
- Epigenetic Therapies Group, Experimental and Clinical Hematology Program (PHEC)Josep Carreras Leukaemia Research Institute (IJC)BadalonaSpain
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30
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Pubertal mammary gland development is a key determinant of adult mammographic density. Semin Cell Dev Biol 2020; 114:143-158. [PMID: 33309487 DOI: 10.1016/j.semcdb.2020.11.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 11/25/2020] [Accepted: 11/28/2020] [Indexed: 01/04/2023]
Abstract
Mammographic density refers to the radiological appearance of fibroglandular and adipose tissue on a mammogram of the breast. Women with relatively high mammographic density for their age and body mass index are at significantly higher risk for breast cancer. The association between mammographic density and breast cancer risk is well-established, however the molecular and cellular events that lead to the development of high mammographic density are yet to be elucidated. Puberty is a critical time for breast development, where endocrine and paracrine signalling drive development of the mammary gland epithelium, stroma, and adipose tissue. As the relative abundance of these cell types determines the radiological appearance of the adult breast, puberty should be considered as a key developmental stage in the establishment of mammographic density. Epidemiological studies have pointed to the significance of pubertal adipose tissue deposition, as well as timing of menarche and thelarche, on adult mammographic density and breast cancer risk. Activation of hypothalamic-pituitary axes during puberty combined with genetic and epigenetic molecular determinants, together with stromal fibroblasts, extracellular matrix, and immune signalling factors in the mammary gland, act in concert to drive breast development and the relative abundance of different cell types in the adult breast. Here, we discuss the key cellular and molecular mechanisms through which pubertal mammary gland development may affect adult mammographic density and cancer risk.
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31
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Ennour-Idrissi K, Dragic D, Durocher F, Diorio C. Epigenome-wide DNA methylation and risk of breast cancer: a systematic review. BMC Cancer 2020; 20:1048. [PMID: 33129307 PMCID: PMC7603741 DOI: 10.1186/s12885-020-07543-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 10/20/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND DNA methylation is a potential biomarker for early detection of breast cancer. However, robust evidence of a prospective relationship between DNA methylation patterns and breast cancer risk is still lacking. The objective of this study is to provide a systematic analysis of the findings of epigenome-wide DNA methylation studies on breast cancer risk, in light of their methodological strengths and weaknesses. METHODS We searched major databases (MEDLINE, EMBASE, Web of Science, CENTRAL) from inception up to 30th June 2019, for observational or intervention studies investigating the association between epigenome-wide DNA methylation (using the HM450k or EPIC BeadChip), measured in any type of human sample, and breast cancer risk. A pre-established protocol was drawn up following the Cochrane Reviews rigorous methodology. Study selection, data abstraction, and risk of bias assessment were performed by at least two investigators. A qualitative synthesis and systematic comparison of the strengths and weaknesses of studies was performed. RESULTS Overall, 20 studies using the HM450k BeadChip were included, 17 of which had measured blood-derived DNA methylation. There was a consistent trend toward an association of global blood-derived DNA hypomethylation and higher epigenetic age with higher risk of breast cancer. The strength of associations was modest for global hypomethylation and relatively weak for most of epigenetic age algorithms. Differences in length of follow-up periods may have influenced the ability to detect associations, as studies reporting follow-up periods shorter than 10 years were more likely to observe an association with global DNA methylation. Probe-wise differential methylation analyses identified between one and 806 differentially methylated CpGs positions in 10 studies. None of the identified differentially methylated sites overlapped between studies. Three studies used breast tissue DNA and suffered major methodological issues that precludes any conclusion. Overall risk of bias was critical mainly because of incomplete control of confounding. Important issues relative to data preprocessing could have limited the consistency of results. CONCLUSIONS Global DNA methylation may be a short-term predictor of breast cancer risk. Further studies with rigorous methodology are needed to determine spatial distribution of DNA hypomethylation and identify differentially methylated sites associated with risk of breast cancer. PROSPERO REGISTRATION NUMBER CRD42020147244.
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Affiliation(s)
- Kaoutar Ennour-Idrissi
- Department of Social and Preventive Medicine, Faculty of Medicine, Laval University, Quebec, QC, Canada
- Laval University Cancer Research Center, Quebec, QC, Canada
- Axe Oncologie, Centre de recherche du CHU de Québec-Université Laval, 1050 chemin Sainte-Foy, Quebec City, QC, G1S 4L8, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec, QC, Canada
| | - Dzevka Dragic
- Department of Social and Preventive Medicine, Faculty of Medicine, Laval University, Quebec, QC, Canada
- Laval University Cancer Research Center, Quebec, QC, Canada
- Axe Oncologie, Centre de recherche du CHU de Québec-Université Laval, 1050 chemin Sainte-Foy, Quebec City, QC, G1S 4L8, Canada
| | - Francine Durocher
- Laval University Cancer Research Center, Quebec, QC, Canada
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Quebec, QC, Canada
| | - Caroline Diorio
- Department of Social and Preventive Medicine, Faculty of Medicine, Laval University, Quebec, QC, Canada.
- Laval University Cancer Research Center, Quebec, QC, Canada.
- Axe Oncologie, Centre de recherche du CHU de Québec-Université Laval, 1050 chemin Sainte-Foy, Quebec City, QC, G1S 4L8, Canada.
- Deschênes-Fabia Center for Breast Diseases, Saint-Sacrement Hospital, Quebec, QC, Canada.
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32
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Brägelmann J, Lorenzo Bermejo J. A comparative analysis of cell-type adjustment methods for epigenome-wide association studies based on simulated and real data sets. Brief Bioinform 2020; 20:2055-2065. [PMID: 30099476 PMCID: PMC6954449 DOI: 10.1093/bib/bby068] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 06/11/2018] [Accepted: 07/06/2018] [Indexed: 12/26/2022] Open
Abstract
Technological advances and reduced costs of high-density methylation arrays have led to an increasing number of association studies on the possible relationship between human disease and epigenetic variability. DNA samples from peripheral blood or other tissue types are analyzed in epigenome-wide association studies (EWAS) to detect methylation differences related to a particular phenotype. Since information on the cell-type composition of the sample is generally not available and methylation profiles are cell-type specific, statistical methods have been developed for adjustment of cell-type heterogeneity in EWAS. In this study we systematically compared five popular adjustment methods: the factored spectrally transformed linear mixed model (FaST-LMM-EWASher), the sparse principal component analysis algorithm ReFACTor, surrogate variable analysis (SVA), independent SVA (ISVA) and an optimized version of SVA (SmartSVA). We used real data and applied a multilayered simulation framework to assess the type I error rate, the statistical power and the quality of estimated methylation differences according to major study characteristics. While all five adjustment methods improved false-positive rates compared with unadjusted analyses, FaST-LMM-EWASher resulted in the lowest type I error rate at the expense of low statistical power. SVA efficiently corrected for cell-type heterogeneity in EWAS up to 200 cases and 200 controls, but did not control type I error rates in larger studies. Results based on real data sets confirmed simulation findings with the strongest control of type I error rates by FaST-LMM-EWASher and SmartSVA. Overall, ReFACTor, ISVA and SmartSVA showed the best comparable statistical power, quality of estimated methylation differences and runtime.
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Affiliation(s)
- Johannes Brägelmann
- University Hospital of Cologne, Germany.,Departement of medical biometry and biostatistics, University of Heidelberg, Germany
| | - Justo Lorenzo Bermejo
- Statistical Genetics Group, Institute of Medical Biometry and Informatics, University of Heidelberg, Germany
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33
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Gagliardi A, Dugué PA, Nøst TH, Southey MC, Buchanan DD, Schmidt DF, Makalic E, Hodge AM, English DR, Doo NW, Hopper JL, Severi G, Baglietto L, Naccarati A, Tarallo S, Pace L, Krogh V, Palli D, Panico S, Sacerdote C, Tumino R, Lund E, Giles GG, Pardini B, Sandanger TM, Milne RL, Vineis P, Polidoro S, Fiorito G. Stochastic Epigenetic Mutations Are Associated with Risk of Breast Cancer, Lung Cancer, and Mature B-cell Neoplasms. Cancer Epidemiol Biomarkers Prev 2020; 29:2026-2037. [PMID: 32788174 DOI: 10.1158/1055-9965.epi-20-0451] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/18/2020] [Accepted: 07/29/2020] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Age-related epigenetic dysregulations are associated with several diseases, including cancer. The number of stochastic epigenetic mutations (SEM) has been suggested as a biomarker of life-course accumulation of exposure-related DNA damage; however, the predictive role of SEMs in cancer has seldom been investigated. METHODS A SEM, at a given CpG site, was defined as an extreme outlier of DNA methylation value distribution across individuals. We investigated the association of the total number of SEMs with the risk of eight cancers in 4,497 case-control pairs nested in three prospective cohorts. Furthermore, we investigated whether SEMs were randomly distributed across the genome or enriched in functional genomic regions. RESULTS In the three-study meta-analysis, the estimated ORs per one-unit increase in log(SEM) from logistic regression models adjusted for age and cancer risk factors were 1.25; 95% confidence interval (CI), 1.11-1.41 for breast cancer, and 1.23; 95% CI, 1.07-1.42 for lung cancer. In the Melbourne Collaborative Cohort Study, the OR for mature B-cell neoplasm was 1.46; 95% CI, 1.25-1.71. Enrichment analyses indicated that SEMs frequently occur in silenced genomic regions and in transcription factor binding sites regulated by EZH2 and SUZ12 (P < 0.0001 and P = 0.0005, respectively): two components of the polycomb repressive complex 2 (PCR2). Finally, we showed that PCR2-specific SEMs are generally more stable over time compared with SEMs occurring in the whole genome. CONCLUSIONS The number of SEMs is associated with a higher risk of different cancers in prediagnostic blood samples. IMPACT We identified a candidate biomarker for cancer early detection, and we described a carcinogenesis mechanism involving PCR2 complex proteins worthy of further investigations.
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Affiliation(s)
- Amedeo Gagliardi
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Candiolo, Torino, Italy.
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Torino, Italy
| | - Pierre-Antoine Dugué
- Cancer Epidemiology Division, Cancer Council of Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Therese H Nøst
- Department of Community Medicine, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Melissa C Southey
- Cancer Epidemiology Division, Cancer Council of Victoria, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
- Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Daniel D Buchanan
- Department of Clinical Pathology | Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne Centre for Cancer Research Level 10, Victorian Comprehensive Cancer Centre, Melbourne, Victoria, Australia
| | - Daniel F Schmidt
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
- Faculty of Information Technology, Monash University, Melbourne, Victoria, Australia
| | - Enes Makalic
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Allison M Hodge
- Cancer Epidemiology Division, Cancer Council of Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Dallas R English
- Cancer Epidemiology Division, Cancer Council of Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Nicole W Doo
- Cancer Epidemiology Division, Cancer Council of Victoria, Melbourne, Victoria, Australia
- Concord Repatriation General Hospital, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
- Concord Clinical School, University of Sydney, Concord, New South Wales, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Gianluca Severi
- Centre de Recherche en Épidémiologie et Santé des Populations (CESP, Inserm U1018), Université Paris-Saclay, UPS, USQ, Gustave Roussy, Villejuif, France
| | - Laura Baglietto
- Centre de Recherche en Épidémiologie et Santé des Populations (CESP, Inserm U1018), Université Paris-Saclay, UPS, USQ, Gustave Roussy, Villejuif, France
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Alessio Naccarati
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Candiolo, Torino, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Torino, Italy
| | - Sonia Tarallo
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Candiolo, Torino, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Torino, Italy
| | - Luigia Pace
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Candiolo, Torino, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Torino, Italy
| | - Vittorio Krogh
- Fondazione IRCCS - Istituto Nazionale dei Tumori, Milan, Italy
| | - Domenico Palli
- Institute for Cancer Research, Prevention and Clinical Network - ISPRO, Villa delle Rose, Via Cosimo il Vecchio, Florence, Italy
| | - Salvatore Panico
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Corso Umberto I, Naples, Italy
| | - Carlotta Sacerdote
- Piedmont Reference Centre for Epidemiology and Cancer Prevention (CPO Piemonte), Turin, Italy
| | - Rosario Tumino
- Department of Cancer Registry and Histopathology, Provincial Health Authority (ASP 7) Ragusa, Piazza Igea, Ragusa, Italy
| | - Eiliv Lund
- Department of Community Medicine, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
- The Cancer Registry of Norway, Oslo, Norway
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council of Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Barbara Pardini
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Candiolo, Torino, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Torino, Italy
| | - Torkjel M Sandanger
- Department of Community Medicine, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council of Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Paolo Vineis
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Candiolo, Torino, Italy
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, United Kingdom
| | - Silvia Polidoro
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Candiolo, Torino, Italy
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, United Kingdom
| | - Giovanni Fiorito
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, United Kingdom
- Department of Biomedical Sciences, Laboratory of Biostatistics, University of Sassari, Sassari, Italy
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34
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Xu Z, Sandler DP, Taylor JA. Blood DNA Methylation and Breast Cancer: A Prospective Case-Cohort Analysis in the Sister Study. J Natl Cancer Inst 2020; 112:87-94. [PMID: 30989176 DOI: 10.1093/jnci/djz065] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 02/14/2019] [Accepted: 04/09/2019] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Peripheral blood DNA methylation may be associated with breast cancer, but studies of candidate genes and global and genome-wide DNA methylation have been inconsistent. METHODS We performed an epigenome-wide study using Infinium HumanMethylation450 BeadChips with prospectively collected blood DNA samples from the Sister Study (1552 cases, 1224 subcohort). Differentially methylated cytosine-phosphate-guanine sites (dmCpGs) were identified using case-cohort proportional hazard models and replicated using deposited data from European Prospective Investigation into Cancer and Nutrition in Italy (EPIC-Italy) (n = 329). The correlation between methylation and time to diagnosis was examined using robust linear regression. Causal or consequential relationships of methylation to breast cancer were examined by Mendelian randomization using OncoArray 500 K single-nucleotide polymorphism data. All statistical tests were two-sided. RESULTS We identified 9601 CpG markers associated with invasive breast cancer (false discovery rate = q < 0.01), with 510 meeting a strict Bonferroni correction threshold (10-7). A total of 2095 of these CpGs replicated in the independent EPIC-Italy dataset, including 144 meeting the Bonferroni threshold. Sister Study women who developed ductal carcinoma in situ had methylation similar to noncases. Most (1501, 71.6%) dmCpGs showed lower methylation in invasive cases. In case-only analysis, methylation was statistically significantly associated (false discovery rate = q < 0.05) with time to diagnosis for 892 (42.6%) of the dmCpGs. Analyses based on genetic association suggest that methylation differences are likely a consequence rather than a cause of breast cancer. Pathway analysis shows enrichment of breast cancer-related gene pathways, and dmCpGs are overrepresented in known breast cancer susceptibility genes. CONCLUSIONS Our findings suggest that the DNA methylation profile of blood starts to change in response to invasive breast cancer years before the tumor is clinically detected.
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Affiliation(s)
- Zongli Xu
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC
| | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC
| | - Jack A Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC.,Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC
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35
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Page CM, Djordjilović V, Nøst TH, Ghiasvand R, Sandanger TM, Frigessi A, Thoresen M, Veierød MB. Lifetime Ultraviolet Radiation Exposure and DNA Methylation in Blood Leukocytes: The Norwegian Women and Cancer Study. Sci Rep 2020; 10:4521. [PMID: 32161338 PMCID: PMC7066249 DOI: 10.1038/s41598-020-61430-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 02/26/2020] [Indexed: 12/04/2022] Open
Abstract
Ultraviolet radiation (UVR) exposure is a leading cause of skin cancers and an ubiquitous environmental exposure. However, the molecular mechanisms relating UVR exposure to melanoma is not fully understood. We aimed to investigate if lifetime UVR exposure could be robustly associated to DNA methylation (DNAm). We assessed DNAm in whole blood in three data sets (n = 183, 191, and 125) from the Norwegian Woman and Cancer cohort, using Illumina platforms. We studied genome-wide DNAm, targeted analyses of CpG sites indicated in the literature, global methylation, and accelerated aging. Lifetime history of UVR exposure (residential ambient UVR, sunburns, sunbathing vacations and indoor tanning) was collected by questionnaires. We used one data set for discovery and the other two for replication. One CpG site showed a genome-wide significant association to cumulative UVR exposure (cg01884057) (pnominal = 3.96e-08), but was not replicated in any of the two replication sets (pnominal ≥ 0.42). Two CpG sites (cg05860019, cg00033666) showed suggestive associations with the other UVR exposures. We performed extensive analyses of the association between long-term UVR exposure and DNAm. There was no indication of a robust effect of past UVR exposure on DNAm.
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Affiliation(s)
- Christian M Page
- Oslo Centre for Biostatistics and Epidemiology, Oslo University Hospital, Oslo, Norway
- Centre for Fertility and Health, Norwegian Institute of Public health, Oslo, Norway
| | - Vera Djordjilović
- Oslo Centre for Biostatistics and Epidemiology, Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Therese H Nøst
- Department of Community Medicine, UiT - the Arctic University of Norway, Tromsø, Norway
| | - Reza Ghiasvand
- Oslo Centre for Biostatistics and Epidemiology, Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
- Department of Research, Cancer Registry of Norway, Oslo, Norway
| | - Torkjel M Sandanger
- Department of Community Medicine, UiT - the Arctic University of Norway, Tromsø, Norway
| | - Arnoldo Frigessi
- Oslo Centre for Biostatistics and Epidemiology, Oslo University Hospital, Oslo, Norway
- Oslo Centre for Biostatistics and Epidemiology, Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Magne Thoresen
- Oslo Centre for Biostatistics and Epidemiology, Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Marit B Veierød
- Oslo Centre for Biostatistics and Epidemiology, Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.
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36
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Yang Y, Wu L, Shu XO, Cai Q, Shu X, Li B, Guo X, Ye F, Michailidou K, Bolla MK, Wang Q, Dennis J, Andrulis IL, Brenner H, Chenevix-Trench G, Campa D, Castelao JE, Gago-Dominguez M, Dörk T, Hollestelle A, Lophatananon A, Muir K, Neuhausen SL, Olsson H, Sandler DP, Simard J, Kraft P, Pharoah PDP, Easton DF, Zheng W, Long J. Genetically Predicted Levels of DNA Methylation Biomarkers and Breast Cancer Risk: Data From 228 951 Women of European Descent. J Natl Cancer Inst 2020; 112:295-304. [PMID: 31143935 PMCID: PMC7073907 DOI: 10.1093/jnci/djz109] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 05/08/2019] [Accepted: 05/22/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND DNA methylation plays a critical role in breast cancer development. Previous studies have identified DNA methylation marks in white blood cells as promising biomarkers for breast cancer. However, these studies were limited by low statistical power and potential biases. Using a new methodology, we investigated DNA methylation marks for their associations with breast cancer risk. METHODS Statistical models were built to predict levels of DNA methylation marks using genetic data and DNA methylation data from HumanMethylation450 BeadChip from the Framingham Heart Study (n = 1595). The prediction models were validated using data from the Women's Health Initiative (n = 883). We applied these models to genomewide association study (GWAS) data of 122 977 breast cancer patients and 105 974 controls to evaluate if the genetically predicted DNA methylation levels at CpG sites (CpGs) are associated with breast cancer risk. All statistical tests were two-sided. RESULTS Of the 62 938 CpG sites CpGs investigated, statistically significant associations with breast cancer risk were observed for 450 CpGs at a Bonferroni-corrected threshold of P less than 7.94 × 10-7, including 45 CpGs residing in 18 genomic regions, that have not previously been associated with breast cancer risk. Of the remaining 405 CpGs located within 500 kilobase flaking regions of 70 GWAS-identified breast cancer risk variants, the associations for 11 CpGs were independent of GWAS-identified variants. Integrative analyses of genetic, DNA methylation, and gene expression data found that 38 CpGs may affect breast cancer risk through regulating expression of 21 genes. CONCLUSION Our new methodology can identify novel DNA methylation biomarkers for breast cancer risk and can be applied to other diseases.
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Affiliation(s)
- Yaohua Yang
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Lang Wu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Xiang Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Bingshan Li
- Department of Molecular Physiology and Biophysics, Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Fei Ye
- Division of Cancer Biostatistics, Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN
| | - Kyriaki Michailidou
- Center for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Manjeet K Bolla
- Center for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Qin Wang
- Center for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | | | - Irene L Andrulis
- Center for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research (HB) and German Cancer Consortium (HB), German Cancer Research Center, Heidelberg, Germany; Division of Preventive Oncology, German Cancer Research Center and National Center for Tumor Diseases, Heidelberg, Germany
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Daniele Campa
- Department of Biology, University of Pisa, Pisa, Italy
| | - Jose E Castelao
- Oncology and Genetics Unit, Instituto de Investigación Biomedica Orense-Pontevedra-Vigo, Xerencia de Xestión Integrada de Vigo-SERGAS, Vigo, Spain
| | - Manuela Gago-Dominguez
- Genomic Medicine Group, Galician Foundation of Genomic Medicine, Instituto de Investigación Sanitaria de Santiago de Compostela, Complejo Hospitalario Universitario de Santiago, SERGAS, Santiago De Compostela, Spain
- Moores Cancer Center, University of California San Diego, La Jolla, CA
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Antoinette Hollestelle
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Artitaya Lophatananon
- Division of Health Sciences, Warwick Medical School, Warwick University, Coventry, UK
- Institute of Population Health, University of Manchester, Manchester, UK
| | - Kenneth Muir
- Division of Health Sciences, Warwick Medical School, Warwick University, Coventry, UK
- Institute of Population Health, University of Manchester, Manchester, UK
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA
| | - Håkan Olsson
- Department of Cancer Epidemiology, Clinical Sciences, Lund University, Lund, Sweden
| | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC
| | - Jacques Simard
- Genomics Center, Centre Hospitalier Universitaire de Québec Research Center, Laval University, Québec City, QC, Canada
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T. H. Chan School of Public Health (PK) and Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA
| | - Paul D P Pharoah
- Center for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Douglas F Easton
- Center for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
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37
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Wong EM, Southey MC, Terry MB. Integrating DNA methylation measures to improve clinical risk assessment: are we there yet? The case of BRCA1 methylation marks to improve clinical risk assessment of breast cancer. Br J Cancer 2020; 122:1133-1140. [PMID: 32066913 PMCID: PMC7156506 DOI: 10.1038/s41416-019-0720-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 12/11/2019] [Accepted: 12/19/2019] [Indexed: 12/13/2022] Open
Abstract
Current risk prediction models estimate the probability of developing breast cancer over a defined period based on information such as family history, non-genetic breast cancer risk factors, genetic information from high and moderate risk breast cancer susceptibility genes and, over the past several years, polygenic risk scores (PRS) from more than 300 common variants. The inclusion of additional data such as PRS improves risk stratification, but it is anticipated that the inclusion of epigenetic marks could further improve model performance accuracy. Here, we present the case for including information on DNA methylation marks to improve the accuracy of these risk prediction models, and consider how this approach contrasts genetic information, as identifying DNA methylation marks associated with breast cancer risk differs inherently according to the source of DNA, approaches to the measurement of DNA methylation, and the timing of measurement. We highlight several DNA-methylation-specific challenges that should be considered when incorporating information on DNA methylation marks into risk prediction models, using BRCA1, a highly penetrant breast cancer susceptibility gene, as an example. Only after careful consideration of study design and DNA methylation measurement will prospective performance of the incorporation of information regarding DNA methylation marks into risk prediction models be valid.
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Affiliation(s)
- Ee Ming Wong
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia.,Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, Australia
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia.,Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, Australia.,Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
| | - Mary Beth Terry
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA. .,Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA.
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38
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Nikas JB, Mitanis NT, Nikas EG. Whole Exome and Transcriptome RNA-Sequencing Model for the Diagnosis of Prostate Cancer. ACS OMEGA 2020; 5:481-486. [PMID: 31956794 PMCID: PMC6964263 DOI: 10.1021/acsomega.9b02995] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 12/18/2019] [Indexed: 06/02/2023]
Abstract
In our previous study, we developed a genome-wide DNA methylation model for the diagnosis of prostate cancer, and we pointed out that a considerable average error is associated with the current method for the diagnosis of prostate cancer, which is predicated on pathological assessment of biopsied tissue. In this study, we utilized whole exome and transcriptome RNA-sequencing (RNA-seq) data that were derived from 468 tumor samples and 51 normal samples of prostatic tissue, and we analyzed over 20,000 genes per sample. We were able to develop a mathematical model that classified tumor tissue versus normal tissue with a high accuracy. The overall sensitivity was 97.01%, and the overall specificity was 94.12%. The input variables to the model were the mRNA expression values of the following nine genes: ANGPT1, MED21, AOX1, PLP2, HPN, HPN-AS1, EPHA10, NKX2-3, and LRFN1. The model was validated with unknown samples, with a 10-fold cross-validation, and a leave-one-out cross-validation. We present here a genomic model, based on a whole exome and transcriptome RNA-seq analysis of biopsied prostatic tissue, that could be utilized in the diagnosis of prostate cancer.
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Affiliation(s)
- Jason B. Nikas
- Research
& Development, Genomix Inc., Minneapolis, Minnesota 55364, United States
| | - Nikos T. Mitanis
- Department
of Mathematics, University of the Aegean, Samos 83200, Greece
| | - Emily G. Nikas
- School
of Mathematics, University of Minnesota, Minneapolis, Minnesota 55455, United States
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39
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Guan Z, Raut JR, Weigl K, Schöttker B, Holleczek B, Zhang Y, Brenner H. Individual and joint performance of DNA methylation profiles, genetic risk score and environmental risk scores for predicting breast cancer risk. Mol Oncol 2019; 14:42-53. [PMID: 31677238 PMCID: PMC6944111 DOI: 10.1002/1878-0261.12594] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 08/30/2019] [Accepted: 10/24/2019] [Indexed: 12/24/2022] Open
Abstract
DNA methylation patterns in the blood, genetic risk scores (GRSs), and environmental risk factors can potentially improve breast cancer (BC) risk prediction. We assessed the individual and joint predictive performance of methylation, GRS, and environmental risk factors for BC incidence in a prospective cohort study. In a cohort of 5462 women aged 50–75 from Germany, 101 BC cases were identified during 14 years of follow‐up and were compared to 263 BC‐free controls in a nested case–control design. Three previously suggested methylation risk scores (MRSs) based on methylation of 423, 248, and 131 cytosine‐phosphate‐guanine (CpG) loci, and a GRS based on the risk alleles from 269 recently identified single nucleotide polymorphisms were constructed. Additionally, multiple previously proposed environmental risk scores (ERSs) were built based on environmental variables. Areas under the receiver operating characteristic curves (AUCs) were estimated for evaluating BC risk prediction performance. MRS and ERS showed limited accuracy in predicting BC incidence, with AUCs ranging from 0.52 to 0.56 and from 0.52 to 0.59, respectively. The GRS predicted BC incidence with a higher accuracy (AUC = 0.61). Adjusted odds ratios per standard deviation increase (95% confidence interval) were 1.07 (0.84–1.36) and 1.40 (1.09–1.80) for the best performing MRS and ERS, respectively, and 1.48 (1.16–1.90) for the GRS. A full risk model combining the MRS, GRS, and ERS predicted BC incidence with the highest accuracy (AUC = 0.64) and might be useful for identifying high‐risk populations for BC screening.
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Affiliation(s)
- Zhong Guan
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Medical Faculty Heidelberg, University of Heidelberg, Germany
| | - Janhavi R Raut
- Medical Faculty Heidelberg, University of Heidelberg, Germany.,Division of Preventive Oncology, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Korbinian Weigl
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ben Schöttker
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Network Aging Research, University of Heidelberg, Germany
| | | | - Yan Zhang
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Division of Preventive Oncology, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), Heidelberg, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
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40
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DNA methylation-based biological age, genome-wide average DNA methylation, and conventional breast cancer risk factors. Sci Rep 2019; 9:15055. [PMID: 31636290 PMCID: PMC6803691 DOI: 10.1038/s41598-019-51475-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 09/25/2019] [Indexed: 12/12/2022] Open
Abstract
DNA methylation-based biological age (DNAm age), as well as genome-wide average DNA methylation, have been reported to predict breast cancer risk. We aimed to investigate the associations between these DNA methylation-based risk factors and 18 conventional breast cancer risk factors for disease-free women. A sample of 479 individuals from the Australian Mammographic Density Twins and Sisters was used for discovery, a sample of 3354 individuals from the Melbourne Collaborative Cohort Study was used for replication, and meta-analyses pooling results from the two studies were conducted. DNAm age based on three epigenetic clocks (Hannum, Horvath and Levine) and genome-wide average DNA methylation were calculated using the HumanMethylation 450 K BeadChip assay data. The DNAm age measures were positively associated with body mass index (BMI), smoking, alcohol drinking and age at menarche (all nominal P < 0.05). Genome-wide average DNA methylation was negatively associated with smoking and number of live births, and positively associated with age at first live birth (all nominal P < 0.05). The association of DNAm age with BMI was also evident in within-twin-pair analyses that control for familial factors. This study suggests that some lifestyle and hormonal risk factors are associated with these DNA methylation-based breast cancer risk factors, and the observed associations are unlikely to be due to familial confounding but are likely causal. DNA methylation-based risk factors could interplay with conventional risk factors in modifying breast cancer risk.
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41
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Acceleration in the DNA methylation age in breast cancer tumours from very young women. Sci Rep 2019; 9:14991. [PMID: 31628391 PMCID: PMC6800453 DOI: 10.1038/s41598-019-51457-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 09/20/2019] [Indexed: 12/13/2022] Open
Abstract
Breast cancer in very young women (≤35 years; BCVY) presents more aggressive and complex biological features than their older counterparts (BCO). Our aim was to evaluate methylation differences between BCVY and BCO and their DNA epigenetic age. EPIC and 450k Illumina methylation arrays were used in 67 breast cancer tumours, including 32 from BCVY, for methylation study and additionally we analysed their epigenetic age. We identified 2 219 CpG sites differently-methylated in BCVY vs. BCO (FDR < 0.05; β-value difference ± 0.1). The signature showed a general hypomethylation profile with a selective small hypermethylation profile located in open-sea regions in BCVY against BCO and normal tissue. Strikingly, BCVY presented a significant increased epigenetic age-acceleration compared with older women. The affected genes were enriched for pathways in neuronal-system pathways, cell communication, and matrix organisation. Validation in an independent sample highlighted consistent higher expression of HOXD9, and PCDH10 genes in BCVY. Regions implicated in the hypermethylation profile were involved in Notch signalling pathways, the immune system or DNA repair. We further validated HDAC5 expression in BCVY. We have identified a DNA methylation signature that is specific to BCVY and have shown that epigenetic age-acceleration is increased in BCVY.
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42
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Prajzendanc K, Domagała P, Hybiak J, Ryś J, Huzarski T, Szwiec M, Tomiczek-Szwiec J, Redelbach W, Sejda A, Gronwald J, Kluz T, Wiśniowski R, Cybulski C, Łukomska A, Białkowska K, Sukiennicki G, Kulczycka K, Narod SA, Wojdacz TK, Lubiński J, Jakubowska A. BRCA1 promoter methylation in peripheral blood is associated with the risk of triple-negative breast cancer. Int J Cancer 2019; 146:1293-1298. [PMID: 31469414 DOI: 10.1002/ijc.32655] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 07/19/2019] [Accepted: 08/16/2019] [Indexed: 12/16/2022]
Abstract
Methylation of the promoter of the BRCA1 gene in DNA derived from peripheral blood cells is a possible risk factor for breast cancer. It is not clear if this association is restricted to certain types of breast cancer or is a general phenomenon. We evaluated BRCA1 methylation status in peripheral blood cells from 942 breast cancer patients and from 500 controls. We also assessed methylation status in 262 paraffin-embedded breast cancer tissues. Methylation status was assessed using methylation-sensitive high-resolution melting and was categorized as positive or negative. BRCA1 methylation in peripheral blood cells was strongly associated with the risk of triple-negative breast cancer (TNBC) (odds ratio [OR] 4.70; 95% confidence interval [CI]: 3.13-7.07; p < 0.001), but not of estrogen-receptor positive breast cancer (OR 0.80; 95% CI: 0.46-1.42; p = 0.46). Methylation was also overrepresented among patients with high-grade cancers (OR 4.53; 95% CI: 2.91-7.05; p < 0.001) and medullary cancers (OR 3.08; 95% CI: 1.38-6.88; p = 0.006). Moreover, we detected a significant concordance of BRCA1 promoter methylation in peripheral blood and paired tumor tissue (p < 0.001). We found that BRCA1 promoter methylation in peripheral blood cells is associated with approximately five times greater risk of TNBC. We propose that BRCA1 methylation in blood-derived DNA could be a novel biomarker of increased breast cancer susceptibility, in particular for triple-negative tumors.
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Affiliation(s)
- Karolina Prajzendanc
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Paweł Domagała
- Department of Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Jolanta Hybiak
- Department of Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Janusz Ryś
- Department of Tumor Pathology, Maria Skłodowska-Curie Memorial Centre and Institute of Oncology, Cracow, Poland
| | - Tomasz Huzarski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland.,Department of Clinical Genetics and Pathology, University of Zielona Góra, Zielona Góra, Poland
| | - Marek Szwiec
- Department of Surgery and Oncology, University of Zielona Góra, Zielona Góra, Poland.,Department of Clinical Oncology, University Hospital in Zielona Góra, Zielona Góra, Poland
| | - Joanna Tomiczek-Szwiec
- Department of Histology, Institute of Medicine, University of Opole, Opole, Poland.,Regional Oncology Centre, Opole, Poland
| | - Wojciech Redelbach
- Department of Anatomy, Institute of Medicine, University of Opole, Opole, Poland
| | - Aleksandra Sejda
- Department of Pathology, Provincial Specialist Hospital, Olsztyn, Poland.,Patomorphology Department, University of Warmia and Mazury, Olsztyn, Poland
| | - Jacek Gronwald
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Tomasz Kluz
- Institute of Obstetric and Emergency Medicine, Faculty of Medicine, University of Rzeszow, Rzeszow, Poland
| | - Rafał Wiśniowski
- Department of Clinical Oncology, Regional Oncology Centre, Bielsko-Biala, Poland
| | - Cezary Cybulski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Alicja Łukomska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Katarzyna Białkowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Grzegorz Sukiennicki
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Katarzyna Kulczycka
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Steven A Narod
- Women's College Research Institute, Women's College Hospital, Toronto, ON, Canada
| | - Tomasz K Wojdacz
- Independent Clinical Epigenetics Laboratory, Pomeranian Medical University, Szczecin, Poland
| | - Jan Lubiński
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland.,Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University, Szczecin, Poland
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43
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Nikas JB, Nikas EG. Genome-Wide DNA Methylation Model for the Diagnosis of Prostate Cancer. ACS OMEGA 2019; 4:14895-14901. [PMID: 31552329 PMCID: PMC6751714 DOI: 10.1021/acsomega.9b01613] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Accepted: 08/22/2019] [Indexed: 06/02/2023]
Abstract
Prostate cancer is the most prevalent and the second most lethal malignancy among males in the United States of America. Its diagnosis is almost entirely predicated upon histopathological analysis of the biopsied tissue, and it is associated with a substantial average error. Using genome-wide DNA methylation data derived from 469 prostatic tumor tissue samples and 50 normal prostatic tissue samples and interrogating over 485 000 CpG sites per sample (spanning across gene promoters, CpG islands, shores, shelves, gene bodies, and intergenic and other areas), we were able to develop a mathematical model that classified with a high accuracy (overall sensitivity = 95.31% and overall specificity = 94.00%) tumor tissue versus normal tissue. The methylation β values of five CpG sites, corresponding to the genes LINC01091, RPS15, SNORA10, and two unknown DNA areas in chromosome 1, provided the input to the model. The model was validated with unknown samples, as well as with a sixfold cross-validation and a leave-one-out cross-validation. This study presents a novel genomic model based on genome-wide DNA methylation analysis of biopsied prostatic tissue that could aid in the diagnosis of prostate cancer and help advance the transition to genomic medicine.
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Affiliation(s)
- Jason B. Nikas
- Research &
Development, Genomix Incorporation, Minneapolis, Minnesota 55364, United States
| | - Emily G. Nikas
- School
of Mathematics, University of Minnesota, Minneapolis, Minnesota 55455, United States
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Sayols-Baixeras S, Fernández-Sanlés A, Prats-Uribe A, Subirana I, Plusquin M, Künzli N, Marrugat J, Basagaña X, Elosua R. Association between long-term air pollution exposure and DNA methylation: The REGICOR study. ENVIRONMENTAL RESEARCH 2019; 176:108550. [PMID: 31260916 DOI: 10.1016/j.envres.2019.108550] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 06/14/2019] [Accepted: 06/18/2019] [Indexed: 05/17/2023]
Abstract
INTRODUCTION Limited evidence suggests that epigenetic mechanisms may partially mediate the adverse effects of air pollution on health. Our aims were to identify new genomic loci showing differential DNA methylation associated with long-term exposure to air pollution and to replicate loci previously identified in other studies. METHODS A two-stage epigenome-wide association study was designed: 630 individuals from the REGICOR study were included in the discovery and 454 participants of the EPIC-Italy study in the validation stage. DNA methylation was assessed using the Infinium HumanMethylation450 BeadChip. NOX, NO2, PM10, PM2.5, PMcoarse, traffic intensity and traffic load exposure were measured according to the ESCAPE protocol. A systematic review was undertaken to identify those cytosine-phosphate-guanine (CpGs) associated with air pollution in previous studies and we screened for them in the discovery study. RESULTS In the discovery stage of the epigenome-wide association study, 81 unique CpGs were associated with air pollution (p-value <10-5) but none of them were validated in the replication sample. Furthermore, we identified 15 CpGs in the systematic review showing differential methylation with a p-value fulfilling the Bonferroni criteria and 1673 CpGs fulfilling the false discovery rate criteria, all of which were related to PM2.5 or NO2. None of them was replicated in the discovery study, in which the top hits were located in an intergenic region on chromosome 1 (cg10893043, p-value = 6.79·10-5) and in the LRRC45 and PXK genes (cg05088605, p-value = 2.15·10-04; cg16560256, p-value = 2.23·10-04). CONCLUSIONS Neither new genomic loci associated with long-term air pollution were identified, nor previously identified loci were replicated. Continued efforts to test this potential association are warranted.
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Affiliation(s)
- Sergi Sayols-Baixeras
- Cardiovascular Epidemiology and Genetics Research Group, IMIM (Hospital del Mar Medical Research Institute), Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain; Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain; CIBER Cardiovascular Diseases (CIBERCV), Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain
| | - Alba Fernández-Sanlés
- Cardiovascular Epidemiology and Genetics Research Group, IMIM (Hospital del Mar Medical Research Institute), Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain; Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain
| | - Albert Prats-Uribe
- Cardiovascular Epidemiology and Genetics Research Group, IMIM (Hospital del Mar Medical Research Institute), Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain; Preventive Medicine and Public Health Training Unit, Parc de Salut Mar-Universitat Pompeu Fabra-Agència de Salut Pública de Barcelona (UDMPiSP PSMar-UPF-ASPB), Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain
| | - Isaac Subirana
- CIBER Epidemiology and Public Health (CIBERESP), Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain; Cardiovascular Epidemiology and Genetics Research Group, IMIM (Hospital del Mar Medical Research Institute), Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain
| | - Michelle Plusquin
- Department of Epidemiology and Biostatics, The School of Public Health, Imperial College London, Medical School Building, St Mary's Hospital, Norfolk Place, London, W2 1PG, United Kingdom; Medical Research Council-Health Protection Agency Centre for Environment and Health, Imperial College London, St Mary's Campus, Imperial College, Paddington, London, W2 1PG, United Kingdom; Centre for Environmental Sciences, Hasselt University, Campus Hasselt, Martelarenlaan 42, BE3500, Hasselt, Belgium
| | - Nino Künzli
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051, Basel, Switzerland; University of Basel, Klingelbergstrasse 61, 4056, Basel, Switzerland
| | - Jaume Marrugat
- REGICOR Research Group, IMIM (Hospital del Mar Medical Research Institute), DR Aiguader 88, 08003 Barcelona, Catalonia, Spain; CIBER Cardiovascular Diseases (CIBERCV), Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain
| | - Xavier Basagaña
- ISGlobal (Institute for Global Health), Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain; CIBER Epidemiology and Public Health (CIBERESP), Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain
| | - Roberto Elosua
- Cardiovascular Epidemiology and Genetics Research Group, IMIM (Hospital del Mar Medical Research Institute), Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain; CIBER Cardiovascular Diseases (CIBERCV), Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain; Faculty of Medicine, University of Vic-Central University of Catalonia (UVic-UCC), Carretera de Roda 70, 08500 Vic, Catalonia, Spain.
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Abstract
Over the last years, epigenetic changes, including DNA methylation and histone modifications detected in early tumorigenesis and cancer progression, have been proposed as biomarkers for cancer detection, tumor prognosis, and prediction to treatment response. Importantly for the clinical use of DNA methylation biomarkers, specific methylation signatures can be detected in many body fluids including serum/plasma samples. Several of these potential epigenetic biomarkers detected in women's cancers, colorectal cancers, prostate, pancreatic, gastric, and lung cancers are discussed. Studies conducted in breast cancer, for example, found that aberrant methylation detection of several genes in serum DNA and genome-wide epigenetic change could be used for early breast cancer diagnosis and prediction of breast cancer risk. In colorectal cancers, numerous studies have been conducted to identify specific methylation markers important for CRC detection and in fact clinical assays evaluating the methylation status of SEPT19 gene and vimentin, became commercially available. Furthermore, some epigenetic changes detected in gastric washes have been suggested as potential circulating noninvasive biomarkers for the early detection of gastric cancers. For the early detection of prostate cancer, few epigenetic markers have shown a better sensitivity and specificity than serum PSA, indicating that the inclusion of these markers together with current screening tools, could improve early diagnosis and may reduce unnecessary repeat biopsies. Similarly, in pancreatic cancers, abnormal DNA methylation of several genes including NPTX2, have been suggested as a diagnostic biomarker. Epigenetic dysregulation was also observed in several tumor suppressor genes and miRNAs in lung cancer patients, suggesting the important role of these changes in cancer initiation and progression. In conclusion, epigenetic changes detected in biological fluids could play an essential role in the early detection of several cancer types and this may have a great impact for the cancer precision medicine field.
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Bodelon C, Ambatipudi S, Dugué PA, Johansson A, Sampson JN, Hicks B, Karlins E, Hutchinson A, Cuenin C, Chajès V, Southey MC, Romieu I, Giles GG, English D, Polidoro S, Assumma M, Baglietto L, Vineis P, Severi G, Herceg Z, Flanagan JM, Milne RL, Garcia-Closas M. Blood DNA methylation and breast cancer risk: a meta-analysis of four prospective cohort studies. Breast Cancer Res 2019; 21:62. [PMID: 31101124 PMCID: PMC6525390 DOI: 10.1186/s13058-019-1145-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/23/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Environmental and genetic factors play an important role in the etiology of breast cancer. Several small blood-based DNA methylation studies have reported risk associations with methylation at individual CpGs and average methylation levels; however, these findings require validation in larger prospective cohort studies. To investigate the role of blood DNA methylation on breast cancer risk, we conducted a meta-analysis of four prospective cohort studies, including a total of 1663 incident cases and 1885 controls, the largest study of blood DNA methylation and breast cancer risk to date. METHODS We assessed associations with methylation at 365,145 CpGs present in the HumanMethylation450 (HM450K) Beadchip, after excluding CpGs that did not pass quality controls in all studies. Each of the four cohorts estimated odds ratios (ORs) and 95% confidence intervals (CI) for the association between each individual CpG and breast cancer risk. In addition, each study assessed the association between average methylation measures and breast cancer risk, adjusted and unadjusted for cell-type composition. Study-specific ORs were combined using fixed-effect meta-analysis with inverse variance weights. Stratified analyses were conducted by age at diagnosis (< 50, ≥ 50), estrogen receptor (ER) status (+/-), and time since blood collection (< 5, 5-10, > 10 years). The false discovery rate (q value) was used to account for multiple testing. RESULTS The average age at blood draw ranged from 52.2 to 62.2 years across the four cohorts. Median follow-up time ranged from 6.6 to 8.4 years. The methylation measured at individual CpGs was not associated with breast cancer risk (q value > 0.59). In addition, higher average methylation level was not associated with risk of breast cancer (OR = 0.94, 95% CI = 0.85, 1.05; P = 0.26; P for study heterogeneity = 0.86). We found no evidence of modification of this association by age at diagnosis (P = 0.17), ER status (P = 0.88), time since blood collection (P = 0.98), or CpG location (P = 0.98). CONCLUSIONS Our data indicate that DNA methylation measured in the blood prior to breast cancer diagnosis in predominantly postmenopausal women is unlikely to be associated with substantial breast cancer risk on the HM450K array. Larger studies or with greater methylation coverage are needed to determine if associations exist between blood DNA methylation and breast cancer risk.
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Affiliation(s)
- Clara Bodelon
- Divison of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, USA
| | - Srikant Ambatipudi
- International Agency for Research on Cancer (IARC), Lyon, France
- AMCHSS, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Trivandrum, India
| | - Pierre-Antoine Dugué
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria Australia
| | | | - Joshua N. Sampson
- Divison of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, USA
| | - Belynda Hicks
- Divison of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, USA
| | - Eric Karlins
- Divison of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, USA
| | - Amy Hutchinson
- Divison of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, USA
| | - Cyrille Cuenin
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Veronique Chajès
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Melissa C. Southey
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, Australia
| | - Isabelle Romieu
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Graham G. Giles
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria Australia
| | - Dallas English
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria Australia
| | - Silvia Polidoro
- IIGM (Italian Institute for Genomic Medicine), Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Manuela Assumma
- IIGM (Italian Institute for Genomic Medicine), Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Laura Baglietto
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Paolo Vineis
- MRC-PHE Center for Environment and Health, School of Public Health, Imperial College, London, UK
| | - Gianluca Severi
- CESP (U1018 INSERM, Équipe Générations et Santé), Facultés de médecine Université Paris-Sud, UVSQ, Université Paris-Saclay, Villejuif, France
| | - Zdenko Herceg
- International Agency for Research on Cancer (IARC), Lyon, France
| | | | - Roger L. Milne
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Victoria Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria Australia
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Johansson A, Palli D, Masala G, Grioni S, Agnoli C, Tumino R, Giurdanella MC, Fasanelli F, Sacerdote C, Panico S, Mattiello A, Polidoro S, Jones ME, Schoemaker MJ, Orr N, Tomczyk K, Johnson N, Fletcher O, Perduca V, Baglietto L, Dugué PA, Southey MC, Giles GG, English DR, Milne RL, Severi G, Ambatipudi S, Cuenin C, Chajès V, Romieu I, Herceg Z, Swerdlow AJ, Vineis P, Flanagan JM. Epigenome-wide association study for lifetime estrogen exposure identifies an epigenetic signature associated with breast cancer risk. Clin Epigenetics 2019; 11:66. [PMID: 31039828 PMCID: PMC6492393 DOI: 10.1186/s13148-019-0664-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 04/09/2019] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND It is well established that estrogens and other hormonal factors influence breast cancer susceptibility. We hypothesized that a woman's total lifetime estrogen exposure accumulates changes in DNA methylation, detectable in the blood, which could be used in risk assessment for breast cancer. METHODS An estimated lifetime estrogen exposure (ELEE) model was defined using epidemiological data from EPIC-Italy (n = 31,864). An epigenome-wide association study (EWAS) of ELEE was performed using existing Illumina HumanMethylation450K Beadchip (HM450K) methylation data obtained from EPIC-Italy blood DNA samples (n = 216). A methylation index (MI) of ELEE based on 31 CpG sites was developed using HM450K data from EPIC-Italy and the Generations Study and evaluated for association with breast cancer risk in an independent dataset from the Generations Study (n = 440 incident breast cancer cases matched to 440 healthy controls) using targeted bisulfite sequencing. Lastly, a meta-analysis was conducted including three additional cohorts, consisting of 1187 case-control pairs. RESULTS We observed an estimated 5% increase in breast cancer risk per 1-year longer ELEE (OR = 1.05, 95% CI 1.04-1.07, P = 3 × 10-12) in EPIC-Italy. The EWAS identified 694 CpG sites associated with ELEE (FDR Q < 0.05). We report a DNA methylation index (MI) associated with breast cancer risk that is validated in the Generations Study targeted bisulfite sequencing data (ORQ4_vs_Q1 = 1.77, 95% CI 1.07-2.93, P = 0.027) and in the meta-analysis (ORQ4_vs_Q1 = 1.43, 95% CI 1.05-2.00, P = 0.024); however, the correlation between the MI and ELEE was not validated across study cohorts. CONCLUSION We have identified a blood DNA methylation signature associated with breast cancer risk in this study. Further investigation is required to confirm the interaction between estrogen exposure and DNA methylation in the blood.
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Affiliation(s)
- Annelie Johansson
- Division of Cancer, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, 4th Floor IRDB, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK
| | - Domenico Palli
- Cancer Risk Factors and Lifestyle Epidemiology Unit, Institute for Cancer Research Prevention and Clinical Network-ISPRO, Florence, Italy
| | - Giovanna Masala
- Cancer Risk Factors and Lifestyle Epidemiology Unit, Institute for Cancer Research Prevention and Clinical Network-ISPRO, Florence, Italy
| | - Sara Grioni
- Epidemiology and Prevention Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Claudia Agnoli
- Epidemiology and Prevention Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | | | - Francesca Fasanelli
- Unit of Cancer Epidemiology, Città della Salute e della Scienza University-Hospital and Center for Cancer Prevention (CPO), Turin, Italy
| | - Carlotta Sacerdote
- Unit of Cancer Epidemiology, Città della Salute e della Scienza University-Hospital and Center for Cancer Prevention (CPO), Turin, Italy
| | - Salvatore Panico
- Dipartimento di Medicina Clinica e Chirurgia, University of Naples Frederico II, Naples, Italy
| | - Amalia Mattiello
- Dipartimento di Medicina Clinica e Chirurgia, University of Naples Frederico II, Naples, Italy
| | | | | | | | - Nick Orr
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Katarzyna Tomczyk
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Nichola Johnson
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Olivia Fletcher
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | | | - Laura Baglietto
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Pierre-Antoine Dugué
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, Australia
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, Australia
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, Australia
| | - Graham G Giles
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Dallas R English
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Roger L Milne
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, Australia
| | - Gianluca Severi
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
- Centre de Recherche en Épidémiologie et Santé des Populations (CESP, Inserm U1018), Université Paris-Saclay, UPS, UVSQ, Gustave Roussy, Villejuif, France
| | - Srikant Ambatipudi
- International Agency for Research on Cancer (IARC), Lyon, France
- AMCHSS, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Trivandrum, Kerala, 695011, India
| | - Cyrille Cuenin
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Veronique Chajès
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Isabelle Romieu
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Zdenko Herceg
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Anthony J Swerdlow
- The Institute of Cancer Research, London, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Paolo Vineis
- Italian Institute for Genomic Medicine, Turin, Italy
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - James M Flanagan
- Division of Cancer, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, 4th Floor IRDB, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK.
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Cheng I, Tseng C, Wu J, Yang J, Conroy SM, Shariff-Marco S, Li L, Hertz A, Gomez SL, Le Marchand L, Whittemore AS, Stram DO, Ritz B, Wu AH. Association between ambient air pollution and breast cancer risk: The multiethnic cohort study. Int J Cancer 2019; 146:699-711. [PMID: 30924138 DOI: 10.1002/ijc.32308] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 01/23/2019] [Accepted: 02/06/2019] [Indexed: 12/30/2022]
Abstract
Previous studies using different exposure methods to assess air pollution and breast cancer risk among primarily whites have been inconclusive. Air pollutant exposures of particulate matter and oxides of nitrogen were estimated by kriging (NOx , NO2 , PM10 , PM2.5 ), land use regression (LUR, NOx , NO2 ) and California Line Source Dispersion model (CALINE4, NOx , PM2.5 ) for 57,589 females from the Multiethnic Cohort, residing largely in Los Angeles County from recruitment (1993-1996) through 2010. Cox proportional hazards models were used to examine the associations between time-varying air pollution and breast cancer incidence adjusting for confounding factors. Stratified analyses were conducted by race/ethnicity and distance to major roads. Among all women, breast cancer risk was positively but not significantly associated with NOx (per 50 parts per billion [ppb]) and NO2 (per 20 ppb) determined by kriging and LUR and with PM2.5 and PM10 (per 10 μg/m3 ) determined by kriging. However, among women who lived within 500 m of major roads, significantly increased risks were observed with NOx (hazard ratio [HR] = 1.35, 95% confidence interval [95% CI]: 1.02-1.79), NO2 (HR = 1.44, 95% CI: 1.04-1.99), PM10 (HR = 1.29, 95% CI: 1.07-1.55) and PM2.5 (HR = 1.85, 95% CI: 1.15-2.99) determined by kriging and NOx (HR = 1.21, 95% CI:1.01-1.45) and NO2 (HR = 1.26, 95% CI: 1.00-1.59) determined by LUR. No overall associations were observed with exposures assessed by CALINE4. Subgroup analyses suggested stronger associations of NOx and NO2 among African Americans and Japanese Americans. Further studies of multiethnic populations to confirm the effects of air pollution, particularly near-roadway exposures, on the risk of breast cancer is warranted.
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Affiliation(s)
- Iona Cheng
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Chiuchen Tseng
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jun Wu
- Program in Public Health, Susan and Henry Samueli College of Health Sciences, University of Irvine, Irvine, CA, USA
| | - Juan Yang
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Shannon M Conroy
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Salma Shariff-Marco
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Lianfa Li
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Andrew Hertz
- Cancer Prevention Institute of California, Fremont, CA, USA
| | - Scarlett Lin Gomez
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.,Cancer Prevention Institute of California, Fremont, CA, USA
| | - Loïc Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | | | - Daniel O Stram
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Beate Ritz
- Department of Epidemiology, School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - Anna H Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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DNA Methylation Contributes to the Differential Expression Levels of Mecp2 in Male Mice Neurons and Astrocytes. Int J Mol Sci 2019; 20:ijms20081845. [PMID: 31013990 PMCID: PMC6514911 DOI: 10.3390/ijms20081845] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 04/09/2019] [Accepted: 04/11/2019] [Indexed: 02/01/2023] Open
Abstract
Methyl CpG binding protein-2 (MeCP2) isoforms (E1 and E2) are important epigenetic regulators in brain cells. Accordingly, MeCP2 loss- or gain-of-function mutation causes neurodevelopmental disorders, including Rett syndrome (RTT), MECP2 duplication syndrome (MDS), and autism spectrum disorders (ASD). Within different types of brain cells, highest MeCP2 levels are detected in neurons and the lowest in astrocytes. However, our current knowledge of Mecp2/MeCP2 regulatory mechanisms remains largely elusive. It appears that there is a sex-dependent effect in X-linked MeCP2-associated disorders, as RTT primarily affects females, whereas MDS is found almost exclusively in males. This suggests that Mecp2 expression levels in brain cells might be sex-dependent. Here, we investigated the sex- and cell type-specific expression of Mecp2 isoforms in male and female primary neurons and astrocytes isolated from the murine forebrain. Previously, we reported that DNA methylation of six Mecp2 regulatory elements correlated with Mecp2 levels in the brain. We now show that in male brain cells, DNA methylation is significantly correlated with the transcript expression of these two isoforms. We show that both Mecp2 isoforms are highly expressed in male neurons compared to male astrocytes, with Mecp2e1 expressed at higher levels than Mecp2e2. Our data indicate that higher DNA methylation at the Mecp2 regulatory element(s) is associated with lower levels of Mecp2 isoforms in male astrocytes compared to male neurons.
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