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Mak JKL, Skovgaard AC, Nygaard M, Kananen L, Reynolds CA, Wang Y, Kuja‐Halkola R, Karlsson IK, Pedersen NL, Hägg S, Soerensen M, Jylhävä J. Epigenome-wide analysis of frailty: Results from two European twin cohorts. Aging Cell 2024; 23:e14135. [PMID: 38414347 PMCID: PMC11166364 DOI: 10.1111/acel.14135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 02/11/2024] [Accepted: 02/17/2024] [Indexed: 02/29/2024] Open
Abstract
Epigenetics plays an important role in the aging process, but it is unclear whether epigenetic factors also influence frailty, an age-related state of physiological decline. In this study, we performed a meta-analysis of epigenome-wide association studies in four samples drawn from the Swedish Adoption/Twin Study of Aging (SATSA) and the Longitudinal Study of Aging Danish Twins (LSADT) to explore the association between DNA methylation and frailty. Frailty was defined using the frailty index (FI), and DNA methylation levels were measured in whole blood using Illumina's Infinium HumanMethylation450K and MethylationEPIC arrays. In the meta-analysis consisting of a total of 829 participants, we identified 589 CpG sites that were statistically significantly associated with either the continuous or categorical FI (false discovery rate <0.05). Many of these CpGs have previously been associated with age and age-related diseases. The identified sites were also largely directionally consistent in a longitudinal analysis using mixed-effects models in SATSA, where the participants were followed up to a maximum of 20 years. Moreover, we identified three differentially methylated regions within the MGRN1, MIR596, and TAPBP genes that have been linked to neuronal aging, tumor growth, and immune functions. Furthermore, our meta-analysis results replicated 34 of the 77 previously reported frailty-associated CpGs at p < 0.05. In conclusion, our findings demonstrate robust associations between frailty and DNA methylation levels in 589 novel CpGs, previously unidentified for frailty, and strengthen the role of neuronal/brain pathways in frailty.
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Affiliation(s)
- Jonathan K. L. Mak
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
- Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
| | - Asmus Cosmos Skovgaard
- The Danish Twin Registry and Epidemiology, Biostatistics and Biodemography, Department of Public HealthUniversity of Southern DenmarkOdense MDenmark
| | - Marianne Nygaard
- The Danish Twin Registry and Epidemiology, Biostatistics and Biodemography, Department of Public HealthUniversity of Southern DenmarkOdense MDenmark
| | - Laura Kananen
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
- Faculty of Social Sciences (Health Sciences) and Gerontology Research Center (GEREC)University of TampereTampereFinland
| | - Chandra A. Reynolds
- Institute for Behavioral Genetics, University of ColoradoBoulderColoradoUSA
- Department of PsychologyUniversity of CaliforniaRiversideCaliforniaUSA
| | - Yunzhang Wang
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
- Department of Clinical Sciences, Danderyd HospitalKarolinska InstitutetStockholmSweden
| | - Ralf Kuja‐Halkola
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
| | - Ida K. Karlsson
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
| | - Nancy L. Pedersen
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
| | - Sara Hägg
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
| | - Mette Soerensen
- The Danish Twin Registry and Epidemiology, Biostatistics and Biodemography, Department of Public HealthUniversity of Southern DenmarkOdense MDenmark
- Department of Clinical GeneticsOdense University HospitalOdense CDenmark
| | - Juulia Jylhävä
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
- Faculty of Social Sciences (Health Sciences) and Gerontology Research Center (GEREC)University of TampereTampereFinland
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2
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Wang T, Li P, Qi Q, Zhang S, Xie Y, Wang J, Liu S, Ma S, Li S, Gong T, Xu H, Xiong M, Li G, You C, Luo Z, Li J, Du L, Wang C. A multiplex blood-based assay targeting DNA methylation in PBMCs enables early detection of breast cancer. Nat Commun 2023; 14:4724. [PMID: 37550304 PMCID: PMC10406825 DOI: 10.1038/s41467-023-40389-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 07/21/2023] [Indexed: 08/09/2023] Open
Abstract
The immune system can monitor tumor development, and DNA methylation is involved in the body's immune response to tumors. In this work, we investigate whether DNA methylation alterations in peripheral blood mononuclear cells (PBMCs) could be used as markers for early detection of breast cancer (BC) from the perspective of tumor immune alterations. We identify four BC-specific methylation markers by combining Infinium 850 K BeadChips, pyrosequencing and targeted bisulfite sequencing. Based on the four methylation markers in PBMCs of BC, we develop an efficient and convenient multiplex methylation-specific quantitative PCR assay for the detection of BC and validate its diagnostic performance in a multicenter cohort. This assay was able to distinguish early-stage BC patients from normal controls, with an AUC of 0.940, sensitivity of 93.2%, and specificity of 90.4%. More importantly, this assay outperformed existing clinical diagnostic methods, especially in the detection of early-stage and minimal tumors.
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Affiliation(s)
- Tiantian Wang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, 247 Beiyuan Street, Jinan, 250033, Shandong, China
| | - Peilong Li
- Department of Clinical Laboratory, The Second Hospital of Shandong University, 247 Beiyuan Street, Jinan, 250033, Shandong, China
| | - Qiuchen Qi
- Department of Clinical Laboratory, The Second Hospital of Shandong University, 247 Beiyuan Street, Jinan, 250033, Shandong, China
| | - Shujun Zhang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, 247 Beiyuan Street, Jinan, 250033, Shandong, China
| | - Yan Xie
- Department of Clinical Laboratory, The Second Hospital of Shandong University, 247 Beiyuan Street, Jinan, 250033, Shandong, China
| | - Jing Wang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, 247 Beiyuan Street, Jinan, 250033, Shandong, China
| | - Shibiao Liu
- Department of Clinical Laboratory, The Second Hospital of Shandong University, 247 Beiyuan Street, Jinan, 250033, Shandong, China
| | - Suhong Ma
- Department of Clinical Laboratory, The Second Hospital of Shandong University, 247 Beiyuan Street, Jinan, 250033, Shandong, China
| | - Shijun Li
- Clinical Laboratory, The First Hospital of Dalian Medical University, Dalian, 116011, P. R. China
| | - Tingting Gong
- Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, P. R. China
| | - Huiting Xu
- Departmemt of Clinical Laboratory Medicine, Affiliated Tumor Hospital of Nantong University, 226361, Jiangsu, China; Medical School of Nantong University, Nantong, 226001, P. R. China
| | - Mengqiu Xiong
- Clinical Laboratory, Nanjing First Hospital, Nanjing Medical University, Nanjing, 210006, P. R. China
| | - Guanghua Li
- Department of clinical laboratory, Guangdong Provincial People's Hospital/Guangdong Academy of Medical Sciences, Guangzhou, 510000, P. R. China
| | - Chongge You
- Laboratory Medicine Center, Lanzhou University Second Hospital, the Second Clinical Medical College of Lanzhou University, Lanzhou, 730000, P. R. China
| | - Zhaofan Luo
- Department of Clinical Laboratory, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, 518107, P. R. China
| | - Juan Li
- Department of Clinical Laboratory, The Second Hospital of Shandong University, 247 Beiyuan Street, Jinan, 250033, Shandong, China.
| | - Lutao Du
- Department of Clinical Laboratory, The Second Hospital of Shandong University, 247 Beiyuan Street, Jinan, 250033, Shandong, China.
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Shandong Provincial Key Laboratory of Innovation Technology in Laboratory Medicine, Jinan, 250012, P. R. China.
| | - Chuanxin Wang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, 247 Beiyuan Street, Jinan, 250033, Shandong, China.
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, 250033, China.
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, 250033, China.
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3
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Zhu Y, Chen J, Li J, Zhou C, Huang X, Chen B. Ginsenoside Rg1 as a promising adjuvant agent for enhancing the anti-cancer functions of granulocytes inhibited by noradrenaline. Front Immunol 2023; 14:1070679. [PMID: 36817446 PMCID: PMC9929943 DOI: 10.3389/fimmu.2023.1070679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 01/16/2023] [Indexed: 02/04/2023] Open
Abstract
Introduction In recent years, numerous studies have confirmed that chronic stress is closely related to the development of cancer. Our previous research showed that high levels of stress hormones secreted in the body during chronic stress could inhibit the cancer-killing activity of granulocytes, which could further promote the development of cancer. Therefore, reversing the immunosuppressive effect of stress hormones on granulocytes is an urgent problem in clinical cancer treatment. Here, we selected noradrenaline (NA) as a representative stress hormone. Methods and results After screening many traditional Chinese herbal medicine active ingredients, a promising compound, ginsenoside Rg1, attracted our attention. We verified the immunoprotective effect of ginsenoside Rg1 on granulocytes in vitro and ex vivo, and attempted to understand its potential immunoprotective mechanism. We confirmed the immunoprotective effect of ginsenoside Rg1 on granulocytes using cell and animal experiments. Cell counting kit-8 (CCK-8) and ex vivo experiments were performed to investigate the immunoprotective effects of ginsenoside Rg1 on the anti-cancer function of granulocytes inhibited by NA. Transcriptome sequencing analysis and qRT-PCR showed that NA elevated the mRNA expression of ARG2, MMP1, S100A4, and RAPSN in granulocytes, thereby reducing the anti-cancer function of granulocytes. In contrast, ginsenoside Rg1 downregulated the mRNA expression of ARG2, MMP1, S100A4, and RAPSN, and upregulated the mRNA expression of LAMC2, DSC2, KRT6A, and FOSB, thereby enhancing the anti-cancer function of granulocytes inhibited by NA. Transwell cell migration experiments were performed to verify that ginsenoside Rg1 significantly enhanced the migration capability of granulocytes inhibited by NA. Tumor-bearing model mice were used to verify the significant immunoprotective effects in vivo. Finally, CCK-8 and hematoxylin and eosin staining experiments indicated that ginsenoside Rg1 exhibited high biosafety in vitro and in vivo. Discussion In future clinical treatments, ginsenoside Rg1 may be used as an adjuvant agent for cancer treatment to alleviate chronic stress-induced adverse events in cancer patients.
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Affiliation(s)
| | | | | | | | - Xin Huang
- Shanghai East Hospital, The Institute for Biomedical Engineering & Nano Science, Tongji University School of Medicine, Shanghai, China
| | - Bingdi Chen
- Shanghai East Hospital, The Institute for Biomedical Engineering & Nano Science, Tongji University School of Medicine, Shanghai, China
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4
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Hypomethylation of RPTOR in peripheral blood is associated with very early-stage lung cancer. Clin Chim Acta 2022; 537:173-180. [DOI: 10.1016/j.cca.2022.10.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/07/2022] [Accepted: 10/17/2022] [Indexed: 11/05/2022]
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Potential of blood-based biomarker approaches in endometrium and breast cancer: a case-control comparison study. Arch Gynecol Obstet 2022; 306:1623-1632. [PMID: 35284957 PMCID: PMC9519681 DOI: 10.1007/s00404-022-06482-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 02/18/2022] [Indexed: 02/08/2023]
Abstract
Purpose Endometrial carcinoma is the second most common gynecological malignancy. Until today lacking a screening tool. A blood-based biomarker could help address this need. Methods The expression levels of 30 acylcarnitines, 18 amino acids, 6 miRNAs, and 7 DNA methylation sites were measured in blood samples from 331 women (20 EC, 14 benign uterine lesions (benign), 140 breast cancers (BC), 157 controls). Areas under the ROC curves (AUC), sensitivity (sens.) and specificity (spec.) were computed to identify the variables best distinguishing. Results The best top ten markers for the four comparisons (cancer vs. cancer-free; EC vs. BC, EC vs. controls; EC vs. benign), were identified via AUC. Malonylcarnitine distinguished best patients with EC from controls (AUC: 0.827, sens. 80%, spec. 73.1%) or BC (AUC: 0.819, sens. 84.3%, spec. 80%) being most notable. Tryptophan best differentiated benign from EC (AUC: 0.846, sens. 70%, spec. 92.9%). Conclusions The levels of the analyzed blood markers yielded promising results in the detection of EC and warrant further evaluation. Supplementary Information The online version contains supplementary material available at 10.1007/s00404-022-06482-8.
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Mc Auley MT. DNA methylation in genes associated with the evolution of ageing and disease: A critical review. Ageing Res Rev 2021; 72:101488. [PMID: 34662746 DOI: 10.1016/j.arr.2021.101488] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/30/2021] [Accepted: 10/12/2021] [Indexed: 12/28/2022]
Abstract
Ageing is characterised by a physical decline in biological functioning which results in a progressive risk of mortality with time. As a biological phenomenon, it is underpinned by the dysregulation of a myriad of complex processes. Recently, however, ever-increasing evidence has associated epigenetic mechanisms, such as DNA methylation (DNAm) with age-onset pathologies, including cancer, cardiovascular disease, and Alzheimer's disease. These diseases compromise healthspan. Consequently, there is a medical imperative to understand the link between epigenetic ageing, and healthspan. Evolutionary theory provides a unique way to gain new insights into epigenetic ageing and health. This review will: (1) provide a brief overview of the main evolutionary theories of ageing; (2) discuss recent genetic evidence which has revealed alleles that have pleiotropic effects on fitness at different ages in humans; (3) consider the effects of DNAm on pleiotropic alleles, which are associated with age related disease; (4) discuss how age related DNAm changes resonate with the mutation accumulation, disposable soma and programmed theories of ageing; (5) discuss how DNAm changes associated with caloric restriction intersect with the evolution of ageing; and (6) conclude by discussing how evolutionary theory can be used to inform investigations which quantify age-related DNAm changes which are linked to age onset pathology.
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Affiliation(s)
- Mark Tomás Mc Auley
- Faculty of Science and Engineering, University of Chester, Exton Park, Chester CH1 4BJ, UK.
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7
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Yin Y, Lei S, Li L, Yang X, Yin Q, Xu T, Zhou W, Li H, Gu W, Ma F, Yang R, Zhang Z. RPTOR methylation in the peripheral blood and breast cancer in the Chinese population. Genes Genomics 2021; 44:435-443. [PMID: 34767153 DOI: 10.1007/s13258-021-01182-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/26/2021] [Indexed: 02/05/2023]
Abstract
BACKGROUND Altered regulatory-associated protein of mTOR, complex 1 (RPTOR) methylation levels in peripheral blood was originally discovered as breast cancer (BC)-associated risk factor in Caucasians. OBJECTIVE To explore the relationship between RPTOR methylation and BC in the Chinese population, we conducted two independent case-control studies. METHODS Peripheral blood samples were collected from a total of 333 sporadic BC cases and 378 healthy female controls for the DNA extraction and bisulfite-specific PCR amplification. Mass spectrometry was applied to quantitatively measure the levels of methylation. The logistic regression, Spearman's rank correlation, and Non-parametric tests were used for the statistical analyses. RESULTS In our study, we found an association between BC and RPTOR_CpG_4 hypomethylation in the general population (per-10% of methylation, OR 1.29, P = 0.012), and a weak association between BC and RPTOR_CpG_8 hypomethylation in the women with older age (per-10% of methylation, OR 2.34, P = 0.006). We also identified age as a confounder for the change of RPTOR methylation patterns, especially at RPTOR_CpG_4, which represented differential methylation comparing age groups especially in the BC cases (age < 50 years vs age ≥ 50 years by Mann-Whitney U test, P < 0.0001 for BC cases and P = 0.079 for controls). CONCLUSION Our study validated the association between hypomethylation of RPTOR and BC risk in the Chinese population also with weak effect and mostly for postmenopausal women. In addition, our findings provided novel insight for the regulation of DNA methylation upon aging or the change of hormone levels.
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Affiliation(s)
- Yifei Yin
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China.,Department of Thyroid and Breast Surgery, The Affiliated Huai'an Hospital of Xuzhou Medical University and The Second People's Hospital of Huai'an, Huai'an, China
| | - Shuifang Lei
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Lixi Li
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaoqin Yang
- Department of Breast Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Qiming Yin
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Tian Xu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Wenjie Zhou
- Chengdu Shang Jin Nan Fu Hospital, West China Hospital, Sichuan University, Chengdu, China
| | - Hong Li
- Department of Pathology, The Affiliated Huai'an Hospital of Xuzhou Medical University and The Second People's Hospital of Huai'an, Huai'an, China
| | - Wanjian Gu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Fei Ma
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Rongxi Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China.
| | - Zhengdong Zhang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China. .,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.
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8
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Wei S, Tao J, Xu J, Chen X, Wang Z, Zhang N, Zuo L, Jia Z, Chen H, Sun H, Yan Y, Zhang M, Lv H, Kong F, Duan L, Ma Y, Liao M, Xu L, Feng R, Liu G, Project TEWAS, Jiang Y. Ten Years of EWAS. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2100727. [PMID: 34382344 PMCID: PMC8529436 DOI: 10.1002/advs.202100727] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/11/2021] [Indexed: 06/13/2023]
Abstract
Epigenome-wide association study (EWAS) has been applied to analyze DNA methylation variation in complex diseases for a decade, and epigenome as a research target has gradually become a hot topic of current studies. The DNA methylation microarrays, next-generation, and third-generation sequencing technologies have prepared a high-quality platform for EWAS. Here, the progress of EWAS research is reviewed, its contributions to clinical applications, and mainly describe the achievements of four typical diseases. Finally, the challenges encountered by EWAS and make bold predictions for its future development are presented.
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Affiliation(s)
- Siyu Wei
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
| | - Junxian Tao
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
| | - Jing Xu
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
| | - Xingyu Chen
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Zhaoyang Wang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Nan Zhang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Lijiao Zuo
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Zhe Jia
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Haiyan Chen
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Hongmei Sun
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Yubo Yan
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Mingming Zhang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Hongchao Lv
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Fanwu Kong
- The EWAS ProjectHarbinChina
- Department of NephrologyThe Second Affiliated HospitalHarbin Medical UniversityHarbin150001China
| | - Lian Duan
- The EWAS ProjectHarbinChina
- The First Affiliated Hospital of Wenzhou Medical UniversityWenzhou325000China
| | - Ye Ma
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
| | - Mingzhi Liao
- The EWAS ProjectHarbinChina
- College of Life SciencesNorthwest A&F UniversityYanglingShanxi712100China
| | - Liangde Xu
- The EWAS ProjectHarbinChina
- School of Biomedical EngineeringWenzhou Medical UniversityWenzhou325035China
| | - Rennan Feng
- The EWAS ProjectHarbinChina
- Department of Nutrition and Food HygienePublic Health CollegeHarbin Medical UniversityHarbin150081China
| | - Guiyou Liu
- The EWAS ProjectHarbinChina
- Beijing Institute for Brain DisordersCapital Medical UniversityBeijing100069China
| | | | - Yongshuai Jiang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
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9
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Salas LA, Lundgren SN, Browne EP, Punska EC, Anderton DL, Karagas MR, Arcaro KF, Christensen BC. Prediagnostic breast milk DNA methylation alterations in women who develop breast cancer. Hum Mol Genet 2021; 29:662-673. [PMID: 31943067 PMCID: PMC7068171 DOI: 10.1093/hmg/ddz301] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 11/30/2019] [Accepted: 12/06/2019] [Indexed: 12/16/2022] Open
Abstract
Prior candidate gene studies have shown tumor suppressor DNA methylation in breast milk related with history of breast biopsy, an established risk factor for breast cancer. To further establish the utility of breast milk as a tissue-specific biospecimen for investigations of breast carcinogenesis, we measured genome-wide DNA methylation in breast milk from women with and without a diagnosis of breast cancer in two independent cohorts. DNA methylation was assessed using Illumina HumanMethylation450k in 87 breast milk samples. Through an epigenome-wide association study we explored CpG sites associated with a breast cancer diagnosis in the prospectively collected milk samples from the breast that would develop cancer compared with women without a diagnosis of breast cancer using linear mixed effects models adjusted for history of breast biopsy, age, RefFreeCellMix cell estimates, time of delivery, array chip and subject as random effect. We identified 58 differentially methylated CpG sites associated with a subsequent breast cancer diagnosis (q-value <0.05). Nearly all CpG sites associated with a breast cancer diagnosis were hypomethylated in cases compared with controls and were enriched for CpG islands. In addition, inferred repeat element methylation was lower in breast milk DNA from cases compared to controls, and cases exhibited increased estimated epigenetic mitotic tick rate as well as DNA methylation age compared with controls. Breast milk has utility as a biospecimen for prospective assessment of disease risk, for understanding the underlying molecular basis of breast cancer risk factors and improving primary and secondary prevention of breast cancer.
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Affiliation(s)
- Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH 03766, USA.,The Children's Environmental Health and Disease Prevention Research Center at Dartmouth, Hanover, NH 03766, USA
| | - Sara N Lundgren
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH 03766, USA.,The Children's Environmental Health and Disease Prevention Research Center at Dartmouth, Hanover, NH 03766, USA
| | - Eva P Browne
- Department of Veterinary & Animal Sciences, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Elizabeth C Punska
- Department of Veterinary & Animal Sciences, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Douglas L Anderton
- Department of Sociology, University of South Carolina, Columbus, SC 29208, USA
| | - Margaret R Karagas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH 03766, USA.,The Children's Environmental Health and Disease Prevention Research Center at Dartmouth, Hanover, NH 03766, USA
| | - Kathleen F Arcaro
- Department of Veterinary & Animal Sciences, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH 03766, USA.,Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03766, USA.,Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Hanover, NH 03766, USA
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10
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The association between RAPSN methylation in peripheral blood and breast cancer in the Chinese population. J Hum Genet 2021; 66:1069-1078. [PMID: 33958711 DOI: 10.1038/s10038-021-00933-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/15/2021] [Accepted: 04/17/2021] [Indexed: 02/05/2023]
Abstract
DNA methylation in peripheral blood is associated with breast cancer (BC) but has mainly been studied in Caucasian populations. We investigated the association between blood-based methylation of receptor-associated protein of the synapse (RAPSN) and BC in Chinese population. The methylation levels of 12 RAPSN CpG sites were quantitatively evaluated by mass spectrometry in two case-control studies with 283 sporadic BC cases and 331 controls totally. The association was analyzed by logistic regression adjusted for covariants. The RAPSN methylation levels in patients with variant clinical characteristics were investigated by non-parametric tests. We found a significant association between BC and altered RAPSN methylation in blood in women at premenopausal and perimenopausal (age < 50 years old), but not in the elder women. This was approved by two independent case-control studies as well as by combining the subjects of the two studies (taken all subjects together, age < 50 years old, per 5% of methylation, odds ratio (OR) range from 1.17 to 1.30 for two CpG sites; OR = 0.75 for one CpG site; all p values < 0.02). This age-related RAPSN methylation was further modified by human epidermal growth factor receptor 2 (HER2) status (age < 50 years old, HER2 negative, per 5% of methylation, OR range from 1.27 to 1.48 for two CpG sites; OR = 0.76 for one CpG site; all p values < 0.02). We elucidated an association between BC and blood-based RAPSN methylation influenced by age and the status of HER2 in Chinese population.
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11
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Qiao R, Di F, Wang J, Wei Y, Zhang Y, Xu T, Wang Y, Gu W, Han B, Yang R. The Association Between RAPSN Methylation in Peripheral Blood and Early Stage Lung Cancer Detected in Case-Control Cohort. Cancer Manag Res 2020; 12:11063-11075. [PMID: 33173339 PMCID: PMC7646459 DOI: 10.2147/cmar.s275321] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/03/2020] [Indexed: 12/24/2022] Open
Abstract
Background Early detection is essential to improve the survival and life quality of lung cancer (LC) patients. Changes of peripheral blood DNA methylation could be associated with malignancy but were mostly studied in Caucasians. Methods Here, in a Chinese population, we performed mass spectrometry assays to investigate the association between very early stage LC and methylation levels of RAPSN in the peripheral blood by a case–control cohort using of 221 LC patients (93.2% LC at stage I) and 285 unrelated cancer free control individuals. Results The odds ratios (ORs) of all CpG sites were evaluated for their risk to LC using inter-quartile analyses by logistic regression. In general, we observed an association between very early LC and decreased methylation of RAPSN_CpG_1.15 and RAPSN_CpG_3.4 (referring to Q4, OR range from 1.64 to 1.81, p<0.05). Stratified by gender, while hypomethylation of RAPSN_CpG_1.15, RAPSN_CpG_3.4 and RAPSN_CpG_7.14 were associated with LC in males (referring to Q4, ORs range from 1.94 to 2.31, p<0.05), RAPSN_CpG_2 and RAPSN_CpG_5 showed significantly lower methylation in female LC patients comparing to controls (referring to Q4, ORs range from 2.49 to 3.60, p<0.05). The risk of RAPSN hypomethylation to LC was enhanced by aging, and typically for people older than 55 years (referring to Q4, ORs range from 2.17 to 3.61 in six out of all 10 analyzed CpG groups, p<0.05). Conclusion Our study reveals an association between RAPSN hypomethylation in peripheral blood and LC and suggests the occurrence of altered blood-based methylation at the early stage of cancer.
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Affiliation(s)
- Rong Qiao
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai 200030, People's Republic of China
| | - Feifei Di
- Department of Research and Academic, Nanjing TANTICA Biotechnology Co. Ltd, Nanjing 210000, People's Republic of China
| | - Jun Wang
- Department of Research and Academic, Nanjing TANTICA Biotechnology Co. Ltd, Nanjing 210000, People's Republic of China
| | - Yujie Wei
- Department of Research and Academic, Nanjing TANTICA Biotechnology Co. Ltd, Nanjing 210000, People's Republic of China
| | - Yanman Zhang
- Department of Research and Academic, Nanjing TANTICA Biotechnology Co. Ltd, Nanjing 210000, People's Republic of China
| | - Tian Xu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210000, People's Republic of China
| | - Yue Wang
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai 200030, People's Republic of China
| | - Wanjian Gu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210000, People's Republic of China
| | - Baohui Han
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai 200030, People's Republic of China
| | - Rongxi Yang
- Department of Research and Academic, Nanjing TANTICA Biotechnology Co. Ltd, Nanjing 210000, People's Republic of China.,Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 210000, People's Republic of China
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12
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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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13
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Mahogunin Ring Finger 1 Is Required for Genomic Stability and Modulates the Malignant Phenotype of Melanoma Cells. Cancers (Basel) 2020; 12:cancers12102840. [PMID: 33019669 PMCID: PMC7599452 DOI: 10.3390/cancers12102840] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/25/2020] [Accepted: 09/29/2020] [Indexed: 01/20/2023] Open
Abstract
Simple Summary Melanoma, the most aggressive skin cancer, accounts for the majority of deaths due to this disease. Therefore, identification of genes/proteins involved in melanoma genesis and/or progression is urgent. Mutations abrogating expression of Mahogunin Ring Finger 1 (MGRN1) in mice cause complex phenotypes with hyperpigmentation, and known MGRN1 interactors are important regulators of cell shape and movement. This suggests that MGRN1 may modulate the malignant phenotype of melanoma cells. Analysis of MGRN1-KO mouse melanocytes and melanoma cells showed that lack of MGRN1 leads to cell cycle defects and to a more differentiated, less aggressive phenotype, with increased adhesion to various matrices, decreased motility and high genomic instability. The higher aggressivity of MGRN1-expressing melanoma cells was confirmed in an in vivo mouse melanoma model and is consistent with higher survival of human melanoma patients expressing low levels of MGRN1. Therefore, MGRN1 appears an important determinant of the malignant phenotype of melanoma. Abstract The mouse mahoganoid mutation abrogating Mahogunin Ring Finger-1 (MGRN1) E3 ubiquitin ligase expression causes hyperpigmentation, congenital heart defects and neurodegeneration. To study the pathophysiology of MGRN1 loss, we compared Mgrn1-knockout melanocytes with genetically matched controls and melan-md1 (mahoganoid) melanocytes. MGRN1 knockout induced a more differentiated and adherent phenotype, decreased motility, increased the percentage of cells in the S phase of the cell cycle and promoted genomic instability, as shown by stronger γH2AX labelling, increased burden of DNA breaks and higher abundance of aneuploid cells. Lack of MGRN1 expression decreased the ability of melanocytes to cope with DNA breaks generated by oxidizing agents or hydroxyurea-induced replicative stress, suggesting a contribution of genomic instability to the mahoganoid phenotype. MGRN1 knockout in B16-F10 melanoma cells also augmented pigmentation, increased cell adhesion to collagen, impaired 2D and 3D motility and caused genomic instability. Tumors formed by Mgrn1-KO B16-F10 cells had lower mitotic indices, fewer Ki67-positive cells and showed a trend towards smaller size. In short-term lung colonization assays Mgrn1-KO cells showed impaired colonization potential. Moreover, lower expression of MGRN1 is significantly associated with better survival of human melanoma patients. Therefore, MGRN1 might be an important phenotypic determinant of melanoma cells.
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14
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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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15
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Bartlett AH, Liang JW, Sandoval-Sierra JV, Fowke JH, Simonsick EM, Johnson KC, Mozhui K. Longitudinal study of leukocyte DNA methylation and biomarkers for cancer risk in older adults. Biomark Res 2019; 7:10. [PMID: 31149338 PMCID: PMC6537435 DOI: 10.1186/s40364-019-0161-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/29/2019] [Indexed: 12/14/2022] Open
Abstract
Background Changes in DNA methylation over the course of life may provide an indicator of risk for cancer. We explored longitudinal changes in CpG methylation from blood leukocytes, and likelihood of future cancer diagnosis. Methods Peripheral blood samples were obtained at baseline and at follow-up visit from 20 participants in the Health, Aging and Body Composition prospective cohort study. Genome-wide CpG methylation was assayed using the Illumina Infinium Human MethylationEPIC (HM850K) microarray. Results Global patterns in DNA methylation from CpG-based analyses showed extensive changes in cell composition over time in participants who developed cancer. By visit year 6, the proportion of CD8+ T-cells decreased (p-value = 0.02), while granulocytes cell levels increased (p-value = 0.04) among participants diagnosed with cancer compared to those who remained cancer-free (cancer-free vs. cancer-present: 0.03 ± 0.02 vs. 0.003 ± 0.005 for CD8+ T-cells; 0.52 ± 0.14 vs. 0.66 ± 0.09 for granulocytes). Epigenome-wide analysis identified three CpGs with suggestive p-values ≤10− 5 for differential methylation between cancer-free and cancer-present groups, including a CpG located in MTA3, a gene linked with metastasis. At a lenient statistical threshold (p-value ≤3 × 10− 5), the top 10 cancer-associated CpGs included a site near RPTOR that is involved in the mTOR pathway, and the candidate tumor suppressor genes REC8, KCNQ1, and ZSWIM5. However, only the CpG in RPTOR (cg08129331) was replicated in an independent data set. Analysis of within-individual change from baseline to Year 6 found significant correlations between the rates of change in methylation in RPTOR, REC8 and ZSWIM5, and time to cancer diagnosis. Conclusion The results show that changes in cellular composition explains much of the cross-sectional and longitudinal variation in CpG methylation. Additionally, differential methylation and longitudinal dynamics at specific CpGs could provide powerful indicators of cancer development and/or progression. In particular, we highlight CpG methylation in the RPTOR gene as a potential biomarker of cancer that awaits further validation. Electronic supplementary material The online version of this article (10.1186/s40364-019-0161-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexandra H Bartlett
- 1Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN USA
| | - Jane W Liang
- 1Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN USA
| | | | - Jay H Fowke
- 1Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN USA
| | - Eleanor M Simonsick
- 2Intramural Research Program, National Institute on Aging, Baltimore, MD USA
| | - Karen C Johnson
- 1Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN USA
| | - Khyobeni Mozhui
- 1Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN USA
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16
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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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17
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Sahay D, Terry MB, Miller R. Is breast cancer a result of epigenetic responses to traffic-related air pollution? A review of the latest evidence. Epigenomics 2019; 11:701-714. [PMID: 31070457 DOI: 10.2217/epi-2018-0158] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Environmental toxicants can exert adverse health effects via epigenetic regulation. We conducted a review of studies assessing traffic-related air pollution (TRAP) exposure and breast cancer (BC) risk, and the evidence for epigenetic mediation. 14 epidemiological studies demonstrated associations between TRAP exposure and BC risk, in which a total of 26 comparisons were assessed. 11 of these comparisons reported a positive association; whereas 15 comparisons were negative. Five publications linked TRAP exposure to epigenetic alterations in genes that may be related to BC risk. One animal study provided evidence of TRAP-treatment inducing breast tumorigenesis. Associations between TRAP components polycyclic aromatic hydrocarbons (PAH) and nitrogen dioxide (NO2) and BC risk were more consistent. While evidence for epigenetic regulation remains limited, polycyclic aromatic hydrocarbons (PAH) and nitrogen dioxide (NO2) exposures may alter methylation of breast tumorigenic genes (e.g., EPHB2, LONP1). Future epigenomic studies with environmental measures are needed to interrogate the relationship between TRAP and BC risk.
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Affiliation(s)
- Debashish Sahay
- Division of Pulmonary, Allergy & Critical Care of Medicine, Department of Medicine, College of Physicians & Surgeons, Columbia University, New York City 10032, NY, USA
| | - Mary B Terry
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York City 10032, NY, USA.,Herbert Irving Comprehensive Cancer Center, Columbia University, New York City 10032, NY, USA
| | - Rachel Miller
- Division of Pulmonary, Allergy & Critical Care of Medicine, Department of Medicine, College of Physicians & Surgeons, Columbia University, New York City 10032, NY, USA.,Herbert Irving Comprehensive Cancer Center, Columbia University, New York City 10032, NY, USA.,Division of Pediatric Allergy, Immunology, & Rheumatology, Department of Pediatrics, College of Physicians & Surgeons, Columbia University, New York City 10032, NY, USA.,Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York City 10032, NY, USA
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18
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Gào X, Zhang Y, Burwinkel B, Xuan Y, Holleczek B, Brenner H, Schöttker B. The associations of DNA methylation alterations in oxidative stress-related genes with cancer incidence and mortality outcomes: a population-based cohort study. Clin Epigenetics 2019; 11:14. [PMID: 30678711 PMCID: PMC6346508 DOI: 10.1186/s13148-018-0604-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 12/20/2018] [Indexed: 12/20/2022] Open
Abstract
Background Reactive oxygen species may be involved in epigenetic gene activation or silencing. We aimed to identify CpG sites, at which DNA methylation is related to urinary 8-isoprostane levels (biomarker of lipid peroxidation) and cancer or mortality outcomes. This investigation was based on a German, population-based cohort with linkage to cancer and mortality registry data (2000–2016). Results Blood DNA methylation in promoter regions of 519 genes, known to be involved in pathways from oxidative stress (OS) to cancer, was obtained at the cohort's baseline examination. Inverse associations of DNA methylation at cg25365794 (ALOXE3) and cg08862778 (MTOR) with 8-isoprostane levels were observed in a derivation set (n = 1000) and validated in two independent subsets of the cohort (n = 548 and n = 741). Multivariate regression models were used to evaluate the associations of DNA methylation at the two CpG sites with lung, colorectal, prostate, breast, and overall cancer incidence as well as CVD, cancer, and all-cause mortality. DNA methylation at cg25365794 (ALOXE3) was inversely associated with lung and prostate cancer incidence. DNA methylation at cg08862778 (MTOR) was associated with a 43% lower breast cancer incidence in the top vs. bottom tertile. Conclusion The finding for ALOXE3 may not be causal. As ALOXE3 is mainly expressed in skin tissue, the observed association might reflect the fact that both DNA methylation at the ALOXE3 gene and urinary 8-isoprostane concentrations depend on the level of OS in tissues. Contrarily, the finding for the MTOR gene and breast cancer is biologically plausible because the MTOR protein plays an important role in PI3K/Akt signaling, which is a pathway related to cancer development and cell senescence. Electronic supplementary material The online version of this article (10.1186/s13148-018-0604-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xīn Gào
- Division of Clinical Epidemiology and Ageing Research, German Cancer Research Center, Im Neuenheimer Feld 581, 69120, Heidelberg, Germany.,Network Aging Research, University of Heidelberg, Bergheimer Straße 20, 69115, Heidelberg, Germany
| | - Yan Zhang
- Division of Clinical Epidemiology and Ageing Research, German Cancer Research Center, Im Neuenheimer Feld 581, 69120, Heidelberg, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
| | - Barbara Burwinkel
- Division of Molecular Epidemiology, German Cancer Research Center, Im Neuenheimer Feld 581, 69120, Heidelberg, Germany.,Division Molecular Biology of Breast Cancer, University Women's Clinic, Heidelberg University, Voßstraße 9, 69115, Heidelberg, Germany
| | - Yang Xuan
- Division of Clinical Epidemiology and Ageing Research, German Cancer Research Center, Im Neuenheimer Feld 581, 69120, Heidelberg, Germany.,Network Aging Research, University of Heidelberg, Bergheimer Straße 20, 69115, Heidelberg, Germany
| | - Bernd Holleczek
- Saarland Cancer Registry, Krebsregister Saarland, Präsident-Baltz-Straße 5, 66119, Saarbrücken, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Ageing Research, German Cancer Research Center, Im Neuenheimer Feld 581, 69120, Heidelberg, Germany.,Network Aging Research, University of Heidelberg, Bergheimer Straße 20, 69115, Heidelberg, Germany.,Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 410, 69120, Heidelberg, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
| | - Ben Schöttker
- Division of Clinical Epidemiology and Ageing Research, German Cancer Research Center, Im Neuenheimer Feld 581, 69120, Heidelberg, Germany. .,Network Aging Research, University of Heidelberg, Bergheimer Straße 20, 69115, Heidelberg, Germany.
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19
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Yuan B, Schafferer S, Tang Q, Scheffler M, Nees J, Heil J, Schott S, Golatta M, Wallwiener M, Sohn C, Koal T, Wolf B, Schneeweiß A, Burwinkel B. A plasma metabolite panel as biomarkers for early primary breast cancer detection. Int J Cancer 2019; 144:2833-2842. [PMID: 30426507 DOI: 10.1002/ijc.31996] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 09/19/2018] [Accepted: 10/16/2018] [Indexed: 01/14/2023]
Abstract
In recent years, metabolites have attracted substantial attention as promising novel biomarkers of various diseases. However, breast cancer plasma metabolite studies are still in their infancy. Here, we investigated the potential of metabolites to serve as minimally invasive, early detection markers of primary breast cancer. We profiled metabolites extracted from the plasma of primary breast cancer patients and healthy controls using tandem mass spectrometry (UHPLC-MS/MS and FIA-MS/MS). Two metabolites were found to be upregulated, while 16 metabolites were downregulated in primary breast cancer patients compared to healthy controls in both the training and validation cohorts. A panel of seven metabolites was selected by LASSO regression analysis. This panel could differentiate primary breast cancer patients from healthy controls, with an AUC of 0.87 (95% CI: 0.81 ~ 0.92) in the training cohort and an AUC of 0.80 (95% CI: 0.71 ~ 0.87) in the validation cohort. These significantly differentiated metabolites are mainly involved in the amino acid metabolism and breast cancer cell growth pathways. In conclusion, using a metabolomics approach, we identified metabolites that have potential value for development of a multimarker blood-based test to complement and improve early breast cancer detection. The panel identified herein might be part of a prescreening tool, especially for younger women or for closely observing women with certain risks, to facilitate decision making regarding which individuals should undergo further diagnostic tests. In the future, the combination of metabolites and other blood-based molecular marker sets, such as DNA methylation, microRNA, and cell-free DNA mutation markers, will be an attractive option.
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Affiliation(s)
- Baowen Yuan
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg, Germany.,Division of Molecular Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Qiuqiong Tang
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg, Germany.,Division of Molecular Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Juliane Nees
- National Center for Tumor Diseases (NCT), Heidelberg, Germany.,Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg, Germany
| | - Jörg Heil
- Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg, Germany
| | - Sarah Schott
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg, Germany
| | - Michael Golatta
- Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg, Germany
| | - Markus Wallwiener
- National Center for Tumor Diseases (NCT), Heidelberg, Germany.,Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg, Germany
| | - Christof Sohn
- Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg, Germany
| | | | | | - Andreas Schneeweiß
- National Center for Tumor Diseases (NCT), Heidelberg, Germany.,Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg, Germany
| | - Barbara Burwinkel
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg, Germany.,Division of Molecular Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
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20
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Gündert M, Edelmann D, Benner A, Jansen L, Jia M, Walter V, Knebel P, Herpel E, Chang-Claude J, Hoffmeister M, Brenner H, Burwinkel B. Genome-wide DNA methylation analysis reveals a prognostic classifier for non-metastatic colorectal cancer (ProMCol classifier). Gut 2019; 68:101-110. [PMID: 29101262 DOI: 10.1136/gutjnl-2017-314711] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 09/21/2017] [Accepted: 09/30/2017] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Pathological staging used for the prediction of patient survival in colorectal cancer (CRC) provides only limited information. DESIGN Here, a genome-wide study of DNA methylation was conducted for two cohorts of patients with non-metastatic CRC (screening cohort (n=572) and validation cohort (n=274)). A variable screening for prognostic CpG sites was performed in the screening cohort using marginal testing based on a Cox model and subsequent adjustment of the p-values via independent hypothesis weighting using the methylation difference between 34 pairs of tumour and normal mucosa tissue as auxiliary covariate. From the 1000 CpG sites with the smallest adjusted p-value, 20 CpG sites with the smallest Brier score for overall survival (OS) were selected. Applying principal component analysis, we derived a prognostic methylation-based classifier for patients with non-metastatic CRC (ProMCol classifier). RESULTS This classifier was associated with OS in the screening (HR 0.51, 95% CI 0.41 to 0.63, p=6.2E-10) and the validation cohort (HR 0.61, 95% CI 0.45 to 0.82, p=0.001). The independent validation of the ProMCol classifier revealed a reduction of the prediction error for 3-year OS from 0.127, calculated only with standard clinical variables, to 0.120 combining the clinical variables with the classifier and for 4-year OS from 0.153 to 0.140. All results were confirmed for disease-specific survival. CONCLUSION The ProMCol classifier could improve the prognostic accuracy for patients with non-metastatic CRC.
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Affiliation(s)
- Melanie Gündert
- Division of Molecular Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg, Germany
| | - Dominic Edelmann
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Axel Benner
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lina Jansen
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Min Jia
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Viola Walter
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Phillip Knebel
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Esther Herpel
- Department of General Pathology, Institute of Pathology, University of Heidelberg, Heidelberg, Germany.,NCT Tissue Bank, National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, Unit of Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Genetic Tumour Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, 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) and National Center for Tumor Diseases (NCT), Heidelberg, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Barbara Burwinkel
- Division of Molecular Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg, Germany
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21
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Guan Z, Yu H, Cuk K, Zhang Y, Brenner H. Whole-Blood DNA Methylation Markers in Early Detection of Breast Cancer: A Systematic Literature Review. Cancer Epidemiol Biomarkers Prev 2018; 28:496-505. [DOI: 10.1158/1055-9965.epi-18-0378] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 07/09/2018] [Accepted: 11/20/2018] [Indexed: 11/16/2022] Open
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22
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Fang X, Chen C, Cai J, Xiang E, Li J, Chen P. Genome-wide methylation study of whole blood cells DNA in men with congenital hypopituitarism disease. Int J Mol Med 2018; 43:155-166. [PMID: 30365064 PMCID: PMC6257856 DOI: 10.3892/ijmm.2018.3945] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 10/10/2018] [Indexed: 11/20/2022] Open
Abstract
Congenital hypopituitarism (CH) is a relatively rare disease that is characterized by the deficiency of one or more hormones secreted by the pituitary gland, which leads to metabolic disorders, amenorrhea and infertility. However, the underlying molecular mechanisms of CH have not yet been fully elucidated. The present study evaluated the genome-wide methylation level of whole blood DNA in 12 patients with CH and 12 age-matched controls using Illumina Human Methylation 450 array, in order to determine the roles of epigenetic regulation in the pathogenesis of CH. The results demonstrated that the methylation levels of 51 CpG sites were significantly different between the patients with CH and the controls. Functional enrichment analysis identified that the aberrant methylated genes were enriched in gene sets associated with metabolic or cellular process, immune system process and reproduction. In addition, two CpG sites on genes LIM domain kinase 2 (LIMK2) and piwi-like RNA-mediated gene silencing 2 (PIWIL2), which are involved in spermatogenesis and/or testicular development, were identified to be hypermethylated in male patients with CH. The hypermethylation of these sites was further validated in another 40 patients with CH and 40 matched controls with a quantitative bisulfite pyrosequencing method, and the methylation levels of these two loci demonstrated promising diagnostic capacities for CH. The present results suggested that aberrant methylation of genes may be involved in the pathogenesis of CH, and hypermethylation of LIMK2 and PIWIL2 may contribute to the infertility of male patients with CH. Further studies are required to elucidate the underlying mechanisms of the epigenetic regulation of these genes.
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Affiliation(s)
- Xuqian Fang
- Department of Pathology, Ruijin Hospital North, Shanghai Jiao Tong University School of Medicine, Shanghai 201821, P.R. China
| | - Changqiang Chen
- Department of Clinical Medicine, Ruijin Hospital North, Shanghai Jiao Tong University School of Medicine, Shanghai 201821, P.R. China
| | - Jialin Cai
- Clinical Research Center, Ruijin Hospital North, Shanghai Jiao Tong University School of Medicine, Shanghai 201821, P.R. China
| | - Enfei Xiang
- Clinical Research Center, Ruijin Hospital North, Shanghai Jiao Tong University School of Medicine, Shanghai 201821, P.R. China
| | - Jingquan Li
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P.R. China
| | - Peizhan Chen
- Clinical Research Center, Ruijin Hospital North, Shanghai Jiao Tong University School of Medicine, Shanghai 201821, P.R. China
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23
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Cao X, Tang Q, Holland-Letz T, Gündert M, Cuk K, Schott S, Heil J, Golatta M, Sohn C, Schneeweiss A, Burwinkel B. Evaluation of Promoter Methylation of RASSF1A and ATM in Peripheral Blood of Breast Cancer Patients and Healthy Control Individuals. Int J Mol Sci 2018; 19:ijms19030900. [PMID: 29562656 PMCID: PMC5877761 DOI: 10.3390/ijms19030900] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 03/11/2018] [Accepted: 03/12/2018] [Indexed: 01/26/2023] Open
Abstract
Breast cancer (BC) is the most common cancer among women and has high mortality rates. Early detection is supposed to be critical for the patient’s prognosis. In recent years, several studies have investigated global DNA methylation profiles and gene-specific DNA methylation in blood-based DNA to develop putative screening markers for cancer. However, most of the studies have not yet been validated. In our study, we analyzed the promoter methylation of RASSF1A and ATM in peripheral blood DNA of 229 sporadic patients and 151 healthy controls by the MassARRAY EpiTYPER assay. There were no significant differences in DNA methylation levels of RASSF1A and ATM between the sporadic BC cases and the healthy controls. Furthermore, we performed the Infinium HumanMethylation450 BeadChip (450K) array analysis using 48 sporadic BC cases and 48 healthy controls (cases and controls are the same from those of the MassARRAY EpiTYPER assay) and made a comparison with the published data. No significant differences were presented in DNA methylation levels of RASSF1A and ATM between the sporadic BC cases and the healthy controls. So far, the evidence for powerful blood-based methylation markers is still limited and the identified markers need to be further validated.
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Affiliation(s)
- Xue Cao
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg 69120, Germany.
- Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.
| | - Qiuqiong Tang
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg 69120, Germany.
- Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.
| | - Tim Holland-Letz
- Division of Biostatistics (C060), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.
| | - Melanie Gündert
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg 69120, Germany.
- Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.
| | - Katarina Cuk
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg 69120, Germany.
- Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.
| | - Sarah Schott
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg 69120, Germany.
| | - Jörg Heil
- Department of Gynecology and Obstetrics, University Women's Clinic, Heidelberg 69120, Germany.
| | - Michael Golatta
- Department of Gynecology and Obstetrics, University Women's Clinic, Heidelberg 69120, Germany.
| | - Christof Sohn
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg 69120, Germany.
| | - Andreas Schneeweiss
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg 69120, Germany.
- National Centre for Tumor Diseases, Heidelberg 69120, Germany.
| | - Barbara Burwinkel
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg 69120, Germany.
- Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.
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24
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Zhang C, Wang X, Li X, Zhao N, Wang Y, Han X, Ci C, Zhang J, Li M, Zhang Y. The landscape of DNA methylation-mediated regulation of long non-coding RNAs in breast cancer. Oncotarget 2017; 8:51134-51150. [PMID: 28881636 PMCID: PMC5584237 DOI: 10.18632/oncotarget.17705] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/24/2017] [Indexed: 12/22/2022] Open
Abstract
Although systematic studies have identified a host of long non-coding RNAs (lncRNAs) which are involved in breast cancer, the knowledge about the methyla-tion-mediated dysregulation of those lncRNAs remains limited. Here, we integrated multi-omics data to analyze the methylated alteration of lncRNAs in breast invasive carcinoma (BRCA). We found that lncRNAs showed diverse methylation patterns on promoter regions in BRCA. LncRNAs were divided into two categories and four subcategories based on their promoter methylation patterns and expression levels be-tween tumor and normal samples. Through cis-regulatory analysis and gene ontology network, abnormally methylated lncRNAs were identified to be associated with can-cer regulation, proliferation or expression of transcription factors. Competing endog-enous RNA network and functional enrichment analysis of abnormally methylated lncRNAs showed that lncRNAs with different methylation patterns were involved in several hallmarks and KEGG pathways of cancers significantly. Finally, survival analysis based on mRNA modules in networks revealed that lncRNAs silenced by high methylation were associated with prognosis significantly in BRCA. This study enhances the understanding of aberrantly methylated patterns of lncRNAs and pro-vides a novel insight for identifying cancer biomarkers and potential therapeutic tar-gets in breast cancer.
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Affiliation(s)
- Chunlong Zhang
- Department of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163000, China
| | - Xinyu Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Xuecang Li
- Department of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163000, China
| | - Ning Zhao
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150081, China
| | - Yihan Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Xiaole Han
- Department of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163000, China
| | - Ce Ci
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Jian Zhang
- Department of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163000, China
| | - Meng Li
- Department of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163000, China
| | - Yan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
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25
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Schott S, Yang R, Stöcker S, Canzian F, Giese N, Bugert P, Bergmann F, Strobel O, Hackert T, Sohn C, Burwinkel B. HYAL2 methylation in peripheral blood as a potential marker for the detection of pancreatic cancer: a case control study. Oncotarget 2017; 8:67614-67625. [PMID: 28978057 PMCID: PMC5620197 DOI: 10.18632/oncotarget.18757] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 05/23/2017] [Indexed: 12/27/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal malignancy which is mostly diagnosed in advanced and inoperable stages though surgery remains the only curable therapeutic approach. Early detection markers are urgently needed to improve diagnosis. Altered hyaluronoglucosaminidase 2 gene (HYAL2) DNA methylation in peripheral blood is known to be associated with malignancy at early stage but has not been evaluated in PDAC patients. This study evaluates the association between blood-based HYAL2 methylation and PDAC by a case-control study with 191 controls and 82 PDAC patients. Decreased methylation of all four investigated HYAL2 methylation sites showed highly significant association with PDAC (odds ratio (ORs) per −10% methylation ranging from 2.03 to 12.74, depending on the specific CpG site, p < 0.0001 for all). HYAL2 methylation sites were also distinguishable between stage I&II PDAC (61 subjects) and controls (ORs per-10% methylation from 3.17 - 23.04, p < 0.0001 for all). Thus, HYAL2 methylation level enabled a very good discrimination of PDAC cases from healthy controls (area under curve (AUC) = 0.92, 95% Confidence interval (C.I.): 0.88 - 0.96), and was also powerful for the detection of PDAC at stage I&II (AUC = 0.93, 95% C.I.: 0.89 - 0.98). Moreover, the blood-based HYAL2 methylation pattern was similar among PDAC patients with differential clinical characteristics, and showed no correlation with the overall survival of PDAC patients. Our study reveals a strong association between decreased HYAL2 methylation in peripheral blood and PDAC, and provides a promising blood-based marker for the detection of PDAC.
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Affiliation(s)
- Sarah Schott
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, 69120 Heidelberg, Germany.,Department of Gynecology and Obstetrics, University Women's Clinic, 69120 Heidelberg, Germany.,German Cancer Consortium (DKTK), NCT Heidelberg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Rongxi Yang
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, 69120 Heidelberg, Germany.,Department of Gynecology and Obstetrics, University Women's Clinic, 69120 Heidelberg, Germany.,Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Sarah Stöcker
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, 69120 Heidelberg, Germany.,Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Federico Canzian
- Genomic Epidemiology Group (C055), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Nathalia Giese
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Peter Bugert
- Institute of Transfusion Medicine and Immunology, Medical Faculty Mannheim, University of Heidelberg, German Red Cross Blood Service Baden-Württemberg - Hessen, 68167 Mannheim, Germany
| | - Frank Bergmann
- Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Oliver Strobel
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Thilo Hackert
- Department of General, Visceral and Transplantation Surgery, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Christof Sohn
- Department of Gynecology and Obstetrics, University Women's Clinic, 69120 Heidelberg, Germany
| | - Barbara Burwinkel
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, 69120 Heidelberg, Germany.,Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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26
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A prospective study of peripheral blood DNA methylation at RPTOR, MGRN1 and RAPSN and risk of breast cancer. Breast Cancer Res Treat 2016; 161:181-183. [PMID: 27778206 DOI: 10.1007/s10549-016-4032-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 10/19/2016] [Indexed: 10/20/2022]
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