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Sahoo K, Sundararajan V. Methods in DNA methylation array dataset analysis: A review. Comput Struct Biotechnol J 2024; 23:2304-2325. [PMID: 38845821 PMCID: PMC11153885 DOI: 10.1016/j.csbj.2024.05.015] [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: 12/18/2023] [Revised: 04/25/2024] [Accepted: 05/08/2024] [Indexed: 06/09/2024] Open
Abstract
Understanding the intricate relationships between gene expression levels and epigenetic modifications in a genome is crucial to comprehending the pathogenic mechanisms of many diseases. With the advancement of DNA Methylome Profiling techniques, the emphasis on identifying Differentially Methylated Regions (DMRs/DMGs) has become crucial for biomarker discovery, offering new insights into the etiology of illnesses. This review surveys the current state of computational tools/algorithms for the analysis of microarray-based DNA methylation profiling datasets, focusing on key concepts underlying the diagnostic/prognostic CpG site extraction. It addresses methodological frameworks, algorithms, and pipelines employed by various authors, serving as a roadmap to address challenges and understand changing trends in the methodologies for analyzing array-based DNA methylation profiling datasets derived from diseased genomes. Additionally, it highlights the importance of integrating gene expression and methylation datasets for accurate biomarker identification, explores prognostic prediction models, and discusses molecular subtyping for disease classification. The review also emphasizes the contributions of machine learning, neural networks, and data mining to enhance diagnostic workflow development, thereby improving accuracy, precision, and robustness.
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Affiliation(s)
| | - Vino Sundararajan
- Correspondence to: Department of Bio Sciences, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632 014, Tamil Nadu, India.
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Qu Y, Zhang X, Qiao R, Di F, Song Y, Wang J, Ji L, Zhang J, Gu W, Fang Y, Han B, Yang R, Dai L, Ouyang S. Blood FOLR3 methylation dysregulations and heterogeneity in non-small lung cancer highlight its strong associations with lung squamous carcinoma. Respir Res 2024; 25:59. [PMID: 38273401 PMCID: PMC10809478 DOI: 10.1186/s12931-024-02691-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 01/14/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND Non-small cell lung cancer (NSCLC) accounts for the vast majority of lung cancers. Early detection is crucial to reduce lung cancer-related mortality. Aberrant DNA methylation occurs early during carcinogenesis and can be detected in blood. It is essential to investigate the dysregulated blood methylation markers for early diagnosis of NSCLC. METHODS NSCLC-associated methylation gene folate receptor gamma (FOLR3) was selected from an Illumina 850K array analysis of peripheral blood samples. Mass spectrometry was used for validation in two independent case-control studies (validation I: n = 2548; validation II: n = 3866). Patients with lung squamous carcinoma (LUSC) or lung adenocarcinoma (LUAD), normal controls (NCs) and benign pulmonary nodule (BPN) cases were included. FOLR3 methylations were compared among different populations. Their associations with NSCLC clinical features were investigated. Receiver operating characteristic analyses, Kruskal-Wallis test, Wilcoxon test, logistics regression analysis and nomogram analysis were performed. RESULTS Two CpG sites (CpG_1 and CpG_2) of FOLR3 was significantly lower methylated in NSCLC patients than NCs in the discovery round. In the two validations, both LUSC and LUAD patients presented significant FOLR3 hypomethylations. LUSC patients were highlighted to have significantly lower methylation levels of CpG_1 and CpG_2 than BPN cases and LUAD patients. Both in the two validations, CpG_1 methylation and CpG_2 methylation could discriminate LUSC from NCs well, with areas under the curve (AUCs) of 0.818 and 0.832 in validation I, and 0.789 and 0.780 in validation II. They could also differentiate LUAD from NCs, but with lower efficiency. CpG_1 and CpG_2 methylations could also discriminate LUSC from BPNs well individually in the two validations. With the combined dataset of two validations, the independent associations of age, gender, and FOLR3 methylation with LUSC and LUAD risk were shown and the age-gender-CpG_1 signature could discriminate LUSC and LUAD from NCs and BPNs, with higher efficiency for LUSC. CONCLUSIONS Blood-based FOLR3 hypomethylation was shown in LUSC and LUAD. FOLR3 methylation heterogeneity between LUSC and LUAD highlighted its stronger associations with LUSC. FOLR3 methylation and the age-gender-CpG_1 signature might be novel diagnostic markers for the early detection of NSCLC, especially for LUSC.
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Affiliation(s)
- Yunhui Qu
- Department of Clinical Laboratory, the First Affiliated Hospital of Zhengzhou University and the Key Clinical Laboratory of Henan Province, Zhengzhou, 450052, China
| | - Xiuzhi Zhang
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou, 4500001, China
| | - Rong Qiao
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, 200030, China
| | - Feifei Di
- Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, 210000, China
| | - Yakang Song
- Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, 210000, China
| | - Jun Wang
- Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, 210000, China
| | - Longtao Ji
- Henan Institute of Medical and Pharmaceutical Sciences & Henan Key Medical Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, 450052, China
| | - Jie Zhang
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, 210000, China
| | - Wanjian Gu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, 210000, China
| | - Yifei Fang
- Department of Respiratory and Sleep Medicine, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Baohui Han
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, 200030, China
| | - Rongxi Yang
- Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, 210000, China.
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, 210000, China.
| | - Liping Dai
- Henan Institute of Medical and Pharmaceutical Sciences & Henan Key Medical Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, 450052, China.
| | - Songyun Ouyang
- Department of Respiratory and Sleep Medicine, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
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Zhu L, Zhu C, Jin J, Wang J, Zhao X, Yang R. Identification of an association between coronary heart disease and ITGB2 methylation in peripheral blood by a case-control study. Clin Chim Acta 2024; 552:117627. [PMID: 37923103 DOI: 10.1016/j.cca.2023.117627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 10/24/2023] [Accepted: 10/31/2023] [Indexed: 11/07/2023]
Abstract
BACKGROUND Blood DNA methylation was associated with coronary heart disease (CHD) risk in Caucasians. We investigated the association between DNA methylation in peripheral blood at the reported loci and CHD in the Chinese population. METHODS The integrin subunit beta 2 (ITGB2) gene was identified in 196 CHD cases and 184 controls, and its methylation level was determined by mass spectrometry. Logistic regression was used to assess the association. RESULTS Hypomethylation of ITGB2 was significantly associated with heart failure CHD and NYHA Ⅰ&Ⅱ CHD patients with minor to medium cardiac function impairment (ITGB2_CpG_11/cg08422803, OR per -10 % methylation = 1.15 and 1.16; p = 0.012 and 0.018 by Bonferroni correction, respectively). Hypomethylation of ITGB2_CpG_11/cg08422803 was a risk factor for CHD in people < 65 years and males (p < 0.05 after Bonferroni correction). The combination of ITGB2 methylation and conventional CHD risk factors could efficiently discriminate CHD, heart failure CHD, NYHA I&II CHD, and myocardial infarction CHD patients from controls (AUC = 0.78, 0.81, 0.80, and 0.81, respectively). CONCLUSION Blood-based ITGB2 methylation has the potential as a biomarker for CHD. The combination of ITGB2 methylation and conventional CHD risk factors may improve the risk assessment and detection of CHD.
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Affiliation(s)
- Liya Zhu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China; Kunshan Center for Disease Control and Prevention, Kunshan, 215300, China
| | - Chao Zhu
- Department of Cardiology, Beijing Friendship Hospital, Capital Medical University, 95 Yong'an Road, West District, Beijing, 100050, China
| | - Jialie Jin
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Jinxin Wang
- Department of Cardiology, the Second Medical Center, Chinese PLA General Hospital, 100853 Beijing, China
| | - Xiaojing Zhao
- Military translational medicine lab, Medical Innovation Research Division, Chinese PLA General Hospital, Beijing, 100853, China; Beijing Key Laboratory of Chronic Heart Failure Precision Medicine, Medical Innovation Research Division, Chinese PLA General Hospital, Beijing, 100853, China.
| | - Rongxi Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China; Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, 210000, China.
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Qiao R, Di F, Wang J, Wei Y, Xu T, Dai L, Gu W, Han B, Yang R. Identification of FUT7 hypomethylation as the blood biomarker in the prediction of early-stage lung cancer. J Genet Genomics 2023; 50:573-581. [PMID: 36898609 DOI: 10.1016/j.jgg.2023.02.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 02/09/2023] [Accepted: 02/17/2023] [Indexed: 03/12/2023]
Abstract
Early detection of lung cancer (LC) is vital for reducing LC-related mortality. However, noninvasive diagnostic tools remain a great challenge. We aim to identify blood-based biomarkers for the early detection of LC. Here, LC-associated hypomethylation in alpha-1,3-fucosyltransferase VII (FUT7) is identified via the Illumina 850K array in a discovery study and validated by mass spectrometry in two independent case-control studies with blood samples from 1720 LC patients (86.8% LC at stage I, blood is collected before surgery and treatment) and 3143 healthy controls. Compared to the controls, blood-based FUT7 hypomethylation is identified in LC patients at stage I, and even in LC patients with malignant nodules ≤ 1 cm and in patients with adenocarcinoma in situ. Gender plays a role in the LC-associated FUT7 hypomethylation in blood, which is more significant in males than in females. We also reveal that FUT7 hypomethylation in LC could be enhanced by the advanced stage of cancer, involvement of lymph nodes, and larger tumor size. Based on a large sample size and semi-quantitative methods, our study reveals a strong association between blood-based FUT7 hypomethylation and LC, suggesting that methylation signatures in blood may be a group of potential biomarkers for detection of early-stage LC.
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Affiliation(s)
- Rong Qiao
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai 200030, China
| | - Feifei Di
- Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, Jiangsu 210061, China
| | - Jun Wang
- Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, Jiangsu 210061, China
| | - Yujie Wei
- Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, Jiangsu 210061, China
| | - Tian Xu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu 210029, China
| | - Liping Dai
- Henan Institute of Medical and Pharmaceutical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Wanjian Gu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu 210029, China
| | - Baohui Han
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai 200030, China.
| | - Rongxi Yang
- Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, Jiangsu 210061, China; Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China; Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, 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, Jiangsu 211166, China.
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Chung FFL, Maldonado SG, Nemc A, Bouaoun L, Cahais V, Cuenin C, Salle A, Johnson T, Ergüner B, Laplana M, Datlinger P, Jeschke J, Weiderpass E, Kristensen V, Delaloge S, Fuks F, Risch A, Ghantous A, Plass C, Bock C, Kaaks R, Herceg Z. Buffy coat signatures of breast cancer risk in a prospective cohort study. Clin Epigenetics 2023; 15:102. [PMID: 37309009 PMCID: PMC10262593 DOI: 10.1186/s13148-023-01509-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/20/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND Epigenetic alterations are a near-universal feature of human malignancy and have been detected in malignant cells as well as in easily accessible specimens such as blood and urine. These findings offer promising applications in cancer detection, subtyping, and treatment monitoring. However, much of the current evidence is based on findings in retrospective studies and may reflect epigenetic patterns that have already been influenced by the onset of the disease. METHODS Studying breast cancer, we established genome-scale DNA methylation profiles of prospectively collected buffy coat samples (n = 702) from a case-control study nested within the EPIC-Heidelberg cohort using reduced representation bisulphite sequencing (RRBS). RESULTS We observed cancer-specific DNA methylation events in buffy coat samples. Increased DNA methylation in genomic regions associated with SURF6 and REXO1/CTB31O20.3 was linked to the length of time to diagnosis in the prospectively collected buffy coat DNA from individuals who subsequently developed breast cancer. Using machine learning methods, we piloted a DNA methylation-based classifier that predicted case-control status in a held-out validation set with 76.5% accuracy, in some cases up to 15 years before clinical diagnosis of the disease. CONCLUSIONS Taken together, our findings suggest a model of gradual accumulation of cancer-associated DNA methylation patterns in peripheral blood, which may be detected long before clinical manifestation of cancer. Such changes may provide useful markers for risk stratification and, ultimately, personalized cancer prevention.
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Affiliation(s)
- Felicia Fei-Lei Chung
- International Agency for Research On Cancer (IARC), 25 avenue Tony Garnier, CS 90627, 69366, Lyon, France.
- Department of Medical Sciences, School of Medical and Life Sciences, Sunway University, 5, Jalan Universiti, Bandar Sunway, 47500, Subang Jaya, Selangor, Malaysia.
| | | | - Amelie Nemc
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Liacine Bouaoun
- International Agency for Research On Cancer (IARC), 25 avenue Tony Garnier, CS 90627, 69366, Lyon, France
| | - Vincent Cahais
- International Agency for Research On Cancer (IARC), 25 avenue Tony Garnier, CS 90627, 69366, Lyon, France
| | - Cyrille Cuenin
- International Agency for Research On Cancer (IARC), 25 avenue Tony Garnier, CS 90627, 69366, Lyon, France
| | - Aurelie Salle
- International Agency for Research On Cancer (IARC), 25 avenue Tony Garnier, CS 90627, 69366, Lyon, France
| | - Theron Johnson
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bekir Ergüner
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Marina Laplana
- Division of Cancer Epigenomics, German Cancer Research Center, Heidelberg, Germany
- Department of Basic Medical Sciences, University of Lleida, IRBLleida, 25198, Lleida, Spain
| | - Paul Datlinger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Jana Jeschke
- Laboratory of Cancer Epigenetics, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Elisabete Weiderpass
- International Agency for Research On Cancer (IARC), 25 avenue Tony Garnier, CS 90627, 69366, Lyon, France
| | - Vessela Kristensen
- Faculty of Medicine, Institute for Clinical Epidemiology and Molecular Biology, University of Oslo, Oslo, Norway
| | - Suzette Delaloge
- Department of Cancer Medicine, Institut Gustave Roussy, Villejuif, France
| | - François Fuks
- Laboratory of Cancer Epigenetics, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Angela Risch
- Division of Cancer Epigenomics, German Cancer Research Center, Heidelberg, Germany
- Department of Biosciences and Medical Biology, Allergy-Cancer-BioNano Research Centre, University of Salzburg, 5020, Salzburg, Austria
- Cancer Cluster Salzburg, Salzburg, Austria
| | - Akram Ghantous
- International Agency for Research On Cancer (IARC), 25 avenue Tony Garnier, CS 90627, 69366, Lyon, France
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center, Heidelberg, Germany
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Medical University of Vienna, Institute of Artificial Intelligence, Center for Medical Data Science, Vienna, Austria
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Zdenko Herceg
- International Agency for Research On Cancer (IARC), 25 avenue Tony Garnier, CS 90627, 69366, Lyon, France.
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Unlu Yazici M, Marron JS, Bakir-Gungor B, Zou F, Yousef M. Invention of 3Mint for feature grouping and scoring in multi-omics. Front Genet 2023; 14:1093326. [PMID: 37007972 PMCID: PMC10050723 DOI: 10.3389/fgene.2023.1093326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/27/2023] [Indexed: 03/17/2023] Open
Abstract
Advanced genomic and molecular profiling technologies accelerated the enlightenment of the regulatory mechanisms behind cancer development and progression, and the targeted therapies in patients. Along this line, intense studies with immense amounts of biological information have boosted the discovery of molecular biomarkers. Cancer is one of the leading causes of death around the world in recent years. Elucidation of genomic and epigenetic factors in Breast Cancer (BRCA) can provide a roadmap to uncover the disease mechanisms. Accordingly, unraveling the possible systematic connections between-omics data types and their contribution to BRCA tumor progression is crucial. In this study, we have developed a novel machine learning (ML) based integrative approach for multi-omics data analysis. This integrative approach combines information from gene expression (mRNA), microRNA (miRNA) and methylation data. Due to the complexity of cancer, this integrated data is expected to improve the prediction, diagnosis and treatment of disease through patterns only available from the 3-way interactions between these 3-omics datasets. In addition, the proposed method bridges the interpretation gap between the disease mechanisms that drive onset and progression. Our fundamental contribution is the 3 Multi-omics integrative tool (3Mint). This tool aims to perform grouping and scoring of groups using biological knowledge. Another major goal is improved gene selection via detection of novel groups of cross-omics biomarkers. Performance of 3Mint is assessed using different metrics. Our computational performance evaluations showed that the 3Mint classifies the BRCA molecular subtypes with lower number of genes when compared to the miRcorrNet tool which uses miRNA and mRNA gene expression profiles in terms of similar performance metrics (95% Accuracy). The incorporation of methylation data in 3Mint yields a much more focused analysis. The 3Mint tool and all other supplementary files are available at https://github.com/malikyousef/3Mint/.
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Affiliation(s)
- Miray Unlu Yazici
- Department of Bioengineering, Abdullah Gül University, Kayseri, Türkiye
| | - J. S. Marron
- Department of Statistics and Operations Research, University of North Carolina, Chapel Hill, NC, United States
| | - Burcu Bakir-Gungor
- Department of Bioengineering, Abdullah Gül University, Kayseri, Türkiye
- Department of Computer Engineering, Abdullah Gul University, Kayseri, Türkiye
| | - Fei Zou
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Malik Yousef
- Department of Information Systems, Zefat Academic College, Zefat, Israel
- Galilee Digital Health Research Center, Zefat Academic College, Zefat, Israel
- *Correspondence: Malik Yousef,
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DOK7 CpG hypermethylation in blood leukocytes as an epigenetic biomarker for acquired tamoxifen resistant in breast cancer. J Hum Genet 2023; 68:33-38. [PMID: 36372800 DOI: 10.1038/s10038-022-01092-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 09/28/2022] [Accepted: 10/05/2022] [Indexed: 11/15/2022]
Abstract
BACKGROUND Breast cancer (BC) is among the most common cause of cancer 10.4% and one of the leading causes of death among 20-50 years old women in the world. Tamoxifen drug is the first line therapy for BC however tamoxifen resistance (TR) has shown in 30-50% of cases that may face BC recurrence. Hence, TR early detection reduces BC recurrence and fatalities. The epigenetic alteration that happens by hypermethylation of tumor suppressor genes and hypomethylation of oncogenes has been suggested to be useful in early cancer or drug resistance diagnosis. METHODS This is the first study to investigate DOK7 CpG hypermethylation in blood leukocytes of 31 TR (ER+) BC compared to 29 tamoxifen sensitive BC to evaluate DOK7 as a potential TR biomarker. DNA was extracted from blood samples of all participants and MSRE-PCR and real-time PCR were used for quantification of CpG methylation alterations. RESULTS The means of DOK7 CpG hypermethylation were obtained as 85.03%, 29.1% and 57.34% in TR, TS and normal control respectively. Significant hypermethylation were found among TR vs. TS (p < 0.001), TS vs. normal (p < 0.001) and TR vs. normal controls (p < 0.03). Online databases expression and survival analysis of DOK7 showed increasing expression in TS groups vs. TR groups which have consistency with our methylation alteration results. The sensitivity and specificity of the TR epigenetic test were determined using ROC analysis showed 89.66% and 96.77% respectively and showed that 37.5% above hypermethylation is at risk for TR and breast cancer recurrence. CONCLUSION There is a significant difference in the methylation ratio of DOK7 between tamoxifen resistant and tamoxifen sensitive groups that may be useful in the early diagnosis of tamoxifen resistance in BC cases and cancer recurrence prevention.
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Liu C, Li M, Yin Q, Fan Y, Shen C, Yang R. HTRA1 methylation in peripheral blood as a potential marker for the preclinical detection of stroke: a case-control study and a prospective nested case-control study. Clin Epigenetics 2022; 14:191. [PMID: 36581876 PMCID: PMC9801609 DOI: 10.1186/s13148-022-01418-0] [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: 04/12/2022] [Accepted: 12/22/2022] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Stroke is the leading cause of mortality in China. DNA methylation has essential roles in multiple diseases, but its association with stroke was barely studied. We hereby explored the association between blood-based HTRA serine protease 1 (HTRA1) methylation and the risk of stroke. RESULTS The association was discovered in a hospital-based case-control study (cases/controls = 190:190) and further validated in a prospective nested case-control study including 139 cases who developed stroke within 2 years after recruitment and 144 matched stroke-free controls. We observed stroke-related altered HTRA1 methylation and expression in both case-control study and prospective study. This blood-based HTRA1 methylation was associated with stroke independently from the known risk factors and mostly affected the older population. The prospective results further showed that the altered HTRA1 methylation was detectable 2 years before the clinical determination of stroke and became more robust with increased discriminatory power for stroke along with time when combined with other known stroke-related variables [onset time ≤ 1 year: area under the curve (AUC) = 0.76]. CONCLUSIONS In our study, altered HTRA1 methylation was associated with stroke at clinical and preclinical stages and thus may provide a potential biomarker in the blood for the risk evaluation and preclinical detection of stroke.
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Affiliation(s)
- Chunlan Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Jiangning, Nanjing, 211166, China
| | - Mengxia Li
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Jiangning, Nanjing, 211166, China
| | - Qiming Yin
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Jiangning, Nanjing, 211166, China
| | - Yao Fan
- Division of Clinical Epidemiology, Affiliated Geriatric Hospital of Nanjing Medical University, Nanjing, 211166, China
| | - Chong Shen
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Jiangning, Nanjing, 211166, China.
| | - Rongxi Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Jiangning, Nanjing, 211166, China.
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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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10
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Zhu L, Zhu C, Wang J, Yang R, Zhao X. The association between DNA methylation of 6p21.33 and AHRR in blood and coronary heart disease in Chinese population. BMC Cardiovasc Disord 2022; 22:370. [PMID: 35964014 PMCID: PMC9375073 DOI: 10.1186/s12872-022-02766-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 07/13/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Early detection could significantly improve the prognosis of coronary heart disease (CHD). In-invitro diagnostic technique may provide a solution when sufficient biomarkers could be identified. Pertinent associations between blood-based aberrant DNA methylation and smoking, the pathogenesis of atherosclerosis, and CHD have been robustly demonstrated and replicated, but that studies in Chinese populations are rare. The blood-based methylation of aryl-hydrocarbon receptor repressor (AHRR) cg05575921 and 6p21.33 cg06126421 has been associated with cardiovascular mortality in Caucasians. Here, we aim to investigate whether the AHRR and 6p21.33 methylation in the blood is associated with CHD in the Chinese population. METHODS In this case-control study, 180 CHD patients recruited at their first registration in our study center, and 184 controls randomly selected from the people who participated in the annual health examination were enrolled. Methylation intensities of 19 CpG sites, including AHRR cg05575921, 6p21.33 cg06126421, and their flanking CpG sites, were quantified by mass spectrometry. The association between methylation intensities and CHD was estimated by logistic regression analyses adjusted for covariant. RESULTS Compared to the controls, lower methylation of 6p21.33_CpG_4.5/cg06126421 was independently associated with increased odds of being a CHD patient (OR per - 10% methylation = 1.42 after adjustment for age, gender, and batch effect; p = 0.032 by multiple testing corrections). No association between blood-based AHRR methylation and CHD was found. CONCLUSIONS 6p21.33 methylation exhibits a significant association with CHD. The combination of 6p21.33 methylation and conventional risk factors might be an intermediate step towards the early detection of CHD.
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Affiliation(s)
- Liya Zhu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Chao Zhu
- Department of Cardiology, Beijing Friendship Hospital, Capital Medical University, 95 Yong'an Road, West District, Beijing, 100050, China
| | - Jinxin Wang
- Department of Cardiology, The Second Medical Centre, Chinese PLA General Hospital, Beijing, 100853, China
| | - Rongxi Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.
| | - Xiaojing Zhao
- Military Translational Medicine Lab, Medical Innovation Research Division, Chinese PLA General Hospital, Beijing, 100853, China. .,Beijing Key Laboratory of Chronic Heart Failure Precision Medicine, Medical Innovation Research Division, Chinese PLA General Hospital, Beijing, 100853, China.
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Yin Q, Qiao R, Xu T, Dai L, Han B, Gu W, Yang R. The influence of blood sample processing on blood-based DNA methylation signatures. Clin Biochem 2022; 115:116-125. [PMID: 35787405 DOI: 10.1016/j.clinbiochem.2022.06.013] [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: 02/23/2022] [Revised: 06/07/2022] [Accepted: 06/29/2022] [Indexed: 11/03/2022]
Abstract
Stability is crucial for the clinical applicable biomarker such as DNA methylation profiles. However, the influence of various blood processing on the DNA methylation signatures have been barely studied. Here, we systematically evaluated the impact of temporary storage and frozen and thaw on the levels of DNA methylation. The methylation intensities of 13 CpG loci from 53 individuals (42 healthy participants and 11 lung cancer patients) whose blood samples were processed by up to 14 various protocols were quantitatively determined by the mass spectrometry, obtaining more than 8,000 quantitative data. We disclosed a trend of accumulatively increased DNA methylation along with time when the blood from healthy people were stored for up to 96 hours at room temperature (RT), whereas the storage at 4℃ had much weaker effects or no impact. On the contrary, the methylation patterns in the blood of lung cancer patients were more stable at both RT and 4℃ even for 96 hours. Multiple cycles of frozen and thaw could result in demethylation, but was more significant to the blood than to the extracted DNA. Our study indicated that the blood processing in vitro could influence the DNA methylation signatures and introduce unexpected biases.
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Affiliation(s)
- Qiming Yin
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Rong Qiao
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Tian Xu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Liping Dai
- Henan Institute of Medical and Pharmaceutical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Baohui Han
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Wanjian Gu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Rongxi Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China.
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12
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Kashyap D, Pal D, Sharma R, Garg VK, Goel N, Koundal D, Zaguia A, Koundal S, Belay A. Global Increase in Breast Cancer Incidence: Risk Factors and Preventive Measures. BIOMED RESEARCH INTERNATIONAL 2022; 2022:9605439. [PMID: 35480139 PMCID: PMC9038417 DOI: 10.1155/2022/9605439] [Citation(s) in RCA: 150] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/25/2022] [Accepted: 03/21/2022] [Indexed: 02/07/2023]
Abstract
Breast cancer is a global cause for concern owing to its high incidence around the world. The alarming increase in breast cancer cases emphasizes the management of disease at multiple levels. The management should start from the beginning that includes stringent cancer screening or cancer registry to effective diagnostic and treatment strategies. Breast cancer is highly heterogeneous at morphology as well as molecular levels and needs different therapeutic regimens based on the molecular subtype. Breast cancer patients with respective subtype have different clinical outcome prognoses. Breast cancer heterogeneity emphasizes the advanced molecular testing that will help on-time diagnosis and improved survival. Emerging fields such as liquid biopsy and artificial intelligence would help to under the complexity of breast cancer disease and decide the therapeutic regimen that helps in breast cancer management. In this review, we have discussed various risk factors and advanced technology available for breast cancer diagnosis to combat the worst breast cancer status and areas that need to be focused for the better management of breast cancer.
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Affiliation(s)
- Dharambir Kashyap
- Department of Histopathology, Postgraduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Deeksha Pal
- Department of Translational and Regenerative Medicine, Postgraduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Riya Sharma
- Department of Pulmonary Medicine, Postgraduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Vivek Kumar Garg
- Department of Medical Laboratory Technology, University Institute of Applied Health Sciences, Chandigarh University (Gharuan), Mohali 140313, India
| | - Neelam Goel
- Department of Information Technology, University Institute of Engineering & Technology, Panjab University, Chandigarh 160014, India
| | - Deepika Koundal
- Department of Systemics, School of Computer Science, University of Petroleum & Energy Studies, Dehradun, India
| | - Atef Zaguia
- Department of computer science, College of Computers and Information Technology, Taif University, P.O. BOX 11099, Taif 21944, Saudi Arabia
| | - Shubham Koundal
- Department of Medical Laboratory Technology, University Institute of Applied Health Sciences, Chandigarh University (Gharuan), Mohali 140313, India
| | - Assaye Belay
- Department of Statistics, Mizan-Tepi University, Ethiopia
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13
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Zhao X, Zhu L, Yin Q, Xu Z, Jia Q, Yang R, He K. F2RL3 Methylation in the Peripheral Blood as a Potential Marker for the Detection of Coronary Heart Disease: A Case-Control Study. Front Genet 2022; 13:833923. [PMID: 35419024 PMCID: PMC8996303 DOI: 10.3389/fgene.2022.833923] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 02/14/2022] [Indexed: 12/24/2022] Open
Abstract
Background and Aims: Previous work has shown the association between blood-based methylation of coagulation factor II receptor-like 3 gene (F2RL3) and cardiovascular mortality in Caucasians. However, the diagnostic value of F2RL3 methylation for CHD is still unknown. The aim of our study was to evaluate the association between blood-based F2RL3 methylation and the risk of CHD in the Chinese population. Methods: The methylation level of F2RL3 was quantified by mass spectrometry in a case-control study with 180 CHD cases and 184 controls. The association between F2RL3 methylation intensity and CHD was assessed by logistic regression models, controlling confounding factors. Results: The hypomethylation in F2RL3_A amplicon was significantly associated with CHD (odds ratio (ORs) per -10% methylation: 1.22–1.42, p < 0.035 for six out of seven CpG loci). Specifically, this significant association was observed in elderly CHD patients (≥60 years), myocardial infarction (MI) patients, heart failure patients and the patients with minor to medium cardiac function impairment (NYHA Ⅰ&Ⅱ CHD cases) (ORs per -10% methylation: 1.35–1.58, 1.32–2.00, 1.29–1.43, 1.25–1.44; p < 0.024, 0.033, 0.035, 0.025, respectively). However, F2RL3_B CpG sites showed no or very weak association with CHD. The combination of F2RL3_A_CpG_1 and F2RL3_A_CpG_3 methylation levels could efficiently discriminate CHD, MI, heart failure, NYHA I&II CHD, and elderly CHD patients from controls (area under curve (AUC) = 0.75, 0.79, 0.75, 0.76, and 0.82, respectively). Conclusion: We propose blood-based F2RL3 methylation as a potential biomarker for CHD, especially for people with older age or with the status of MI. The combination of F2RL3 methylation and conventional risk factors might be an approach to evaluate CHD at early stage.
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Affiliation(s)
- Xiaojing Zhao
- Military Translational Medicine Lab, Medical Innovation Research Division, Chinese PLA General Hospital, Beijing, China.,Beijing Key Laboratory of Chronic Heart Failure Precision Medicine, Medical Innovation Research Division, Chinese PLA General Hospital, Beijing, China
| | - Liya Zhu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Qiming Yin
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhenguo Xu
- The First Medical Center, Chinese PLA General Hospital, Beijing, China.,The Medical School of Chinese PLA, Beijing, China
| | - Qian Jia
- Military Translational Medicine Lab, Medical Innovation Research Division, Chinese PLA General Hospital, Beijing, China.,Beijing Key Laboratory of Chronic Heart Failure Precision Medicine, Medical Innovation Research Division, Chinese PLA General Hospital, Beijing, China
| | - Rongxi Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Kunlun He
- Military Translational Medicine Lab, Medical Innovation Research Division, Chinese PLA General Hospital, Beijing, China.,Beijing Key Laboratory of Chronic Heart Failure Precision Medicine, Medical Innovation Research Division, Chinese PLA General Hospital, Beijing, China
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14
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Afzal S, Hassan M, Ullah S, Abbas H, Tawakkal F, Khan MA. Breast Cancer; Discovery of Novel Diagnostic Biomarkers, Drug Resistance, and Therapeutic Implications. Front Mol Biosci 2022; 9:783450. [PMID: 35265667 PMCID: PMC8899313 DOI: 10.3389/fmolb.2022.783450] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 02/02/2022] [Indexed: 12/12/2022] Open
Abstract
Breast cancer is the second most reported cancer in women with high mortality causing millions of cancer-related deaths annually. Early detection of breast cancer intensifies the struggle towards discovering, developing, and optimizing diagnostic biomarkers that can improve its prognosis and therapeutic outcomes. Breast cancer-associated biomarkers comprise macromolecules, such as nucleic acid (DNA/RNA), proteins, and intact cells. Advancements in molecular technologies have identified all types of biomarkers that are exclusively studied for diagnostic, prognostic, drug resistance, and therapeutic implications. Identifying biomarkers may solve the problem of drug resistance which is a challenging obstacle in breast cancer treatment. Dysregulation of non-coding RNAs including circular RNAs (circRNAs) and microRNAs (miRNAs) initiates and progresses breast cancer. The circulating multiple miRNA profiles promise better diagnostic and prognostic performance and sensitivity than individual miRNAs. The high stability and existence of circRNAs in body fluids make them a promising new diagnostic biomarker. Many therapeutic-based novels targeting agents have been identified, including ESR1 mutation (DNA mutations), Oligonucleotide analogs and antagonists (miRNA), poly (ADP-ribose) polymerase (PARP) in BRCA mutations, CDK4/6 (cell cycle regulating factor initiates tumor progression), Androgen receptor (a steroid hormone receptor), that have entered clinical validation procedure. In this review, we summarize the role of novel breast cancer diagnostic biomarkers, drug resistance, and therapeutic implications for breast cancer.
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Affiliation(s)
- Samia Afzal
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
- *Correspondence: Samia Afzal,
| | - Muhammad Hassan
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Safi Ullah
- Department of Genetics, Hazara University, Mansehra, Pakistan
| | - Hazrat Abbas
- Department of Genetics, Hazara University, Mansehra, Pakistan
| | - Farah Tawakkal
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Mohsin Ahmad Khan
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
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15
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[Detection of DNA methylation of HYAL2 gene for differentiating malignant from benign thyroid tumors]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2022; 42:123-129. [PMID: 35249879 PMCID: PMC8901399 DOI: 10.12122/j.issn.1673-4254.2022.01.15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
OBJECTIVE To assess the value of DNA methylation level of HYAL2 gene as a molecular marker for differential diagnosis of malignant and benign thyroid tumors. METHODS DNA methylation of HYAL2 gene in tissue specimens of 190 patients with papillary thyroid cancer (PTC) and 190 age- and gender-matched patients with benign thyroid tumors was examined by mass spectrometry, and the protein expression of HYAL2 was detected immunohistochemically for another 55 pairs of patients. Logistic regression analysis was performed to calculate the odds ratio (OR) and evaluate the correlation of per 10% reduction in DNA methylation with PTC. Receiver operating characteristic (ROC) curve analysis was performed and the area under curve (AUC) was calculated to assess the predictive value of alterations in HYAL2 methylation. RESULTS Hypomethylation of HYAL2_CpG_3 was significantly correlated with early-stage PTC (OR=1.51, P=0.001), even in stage I cancer (OR=1.42, P=0.007). Age-stratified analysis revealed a significantly stronger correlation between increased HYAL2_CpG_ 3 methylation and early-stage PTC in patients below 50 years than in those older than 50 years (OR: 1.89 vs 1.37, P < 0.05); ROC analysis also showed a larger AUC of 0.787 in younger patients. The results of immunohistochemistry showed that patients with PTC had significantly higher protein expressions of HYAL2 than patients with benign tumors. CONCLUSION The alterations of DNA methylation level of HYAL2 gene is significantly correlated with early-stage PTC, suggesting the value of DNA methylation level as a potential biomarker for differentiation of malignant from benign thyroid tumors.
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16
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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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17
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Qiao R, Li M, Zhong R, Wei Y, Wang J, Zhang Z, Wang L, Xu T, Wang Y, Dai L, Gu W, Han B, Yang R. The Association Between PNPLA2 Methylation in Peripheral Blood and Early-Stage Lung Cancer in a Case-Control Study. Cancer Manag Res 2021; 13:7919-7927. [PMID: 34703313 PMCID: PMC8526517 DOI: 10.2147/cmar.s329629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/20/2021] [Indexed: 01/06/2023] Open
Abstract
Purpose Lung cancer (LC) brings great burden to the society worldwide. Exploring novel biomarkers in vitro for the early detection of LC would be of great importance. Patients and Methods We measured DNA methylation levels of 21 CpG sites within Patatin-like phospholipase domain containing 2 (PNPLA2) gene in the peripheral blood of 168 early-stage LC cases (94.0% LC at stage I) and 187 age- and gender-matched cancer-free controls. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated using logistic regression adjusted for covariates. Non-parametric tests were applied for the comparisons of stratified groups. Results Hypomethylation of PNPLA2_CpG_8,10 and hypermethylation of PNPLA2_CpG_9 were correlated to the early-stage LC with the ORs of 1.44 (95% CI: 1.06–1.96, P = 0.018) and 0.82 (95% CI: 0.69–0.98, P = 0.029), respectively. The associations were still significant for the very early-stage LC patients (stage I). Further gender- and age-stratified analyses indicated that the association between hypomethylation of PNPLA2_CpG_8,10 and LC existed only in females and in subjects younger than 55 years. In addition, the association between LC and hypermethylation of PNPLA2_CpG_6 and PNPLA2_CpG_9 was also observed in the younger population. Conclusion Taken together, our study has proved the hypothesis that the altered methylation in the peripheral blood may be correlated with the burden of cancer at an early stage. Here, we find a novel association between blood-based aberrant PNPLA2 methylation and LC at a very early stage and particularly for women at a younger age.
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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
| | - Mengxia Li
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 210000, People's Republic of China
| | - Runbo Zhong
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, 200030, People's Republic of China
| | - Yujie Wei
- Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, 210000, People's Republic of China
| | - Jun Wang
- Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, 210000, People's Republic of China
| | - Zheng Zhang
- Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, 210000, People's Republic of China
| | - Ling Wang
- 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
| | - Liping Dai
- Henan Institute of Medical and Pharmaceutical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, 450052, 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 Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 210000, People's Republic of China.,Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, 210000, People's Republic of China
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18
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Zhou X, Lei S, Li L, Xu T, Gu W, Ma F, Yang R. [Peripheral blood EMR3 gene methylation level is correlated with breast cancer in Chinese women]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2021; 41:1456-1463. [PMID: 34755660 DOI: 10.12122/j.issn.1673-4254.2021.10.03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To explore the association of methylation levels of C19orf57, MAP9, EMR3, NEK6 and PCOLCE2 genes in peripheral blood with breast cancer (BC) in Chinese women. METHODS We collected peripheral blood samples from 258 early-stage BC patients and 272 healthy women. Agena matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) was utilized to quantitatively measure the methylation levels of CpG sites in the genes. The association between DNA methylation and BC was analyzed using a logistic regression model adjusted for covariants. Spearman's correlation analysis was performed to analyze the association between the gene methylation levels and age. The methylation levels of the genes in the BC patients with different clinical characteristics were investigated using non-parametric tests. RESULTS In stead of EMR3 gene hypermethylation as found in BC patients as found in the Caucasian population, EMR3 gene hypomethylation was found to correlate with BC in Chinese women, but this correlation was significant only in women beyond the age of 50 years (for every 10% reduction of the methylation level, EMR3_CpG_1: OR=1.40; EMR3_CpG_2: OR=2.31; EMR3_CpG_3: OR=2.76, P < 0.05). EMR3 methylation was not or was only weakly correlated with tumor stage, size, lymphatic metastasis, ER, PR, HER2, or Ki67. Our data did not show a correlation between C19orf57 methylation and BC. CONCLUSION Peripheral blood EMR3 gene hypomethylation is associated with BC in Chinese women, especially in those at an old age and in postmenopausal women.
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Affiliation(s)
- X Zhou
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - S Lei
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - L 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 100021, China
| | - T Xu
- Department of Clinical Laboratory, Jiangsu Provincial Hospital of Chinese Medicine, Nanjing 210029, China
| | - W Gu
- Department of Clinical Laboratory, Jiangsu Provincial Hospital of Chinese Medicine, Nanjing 210029, China
| | - F 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 100021, China
| | - R Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
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19
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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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20
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Wang SC, Liao LM, Ansar M, Lin SY, Hsu WW, Su CM, Chung YM, Liu CC, Hung CS, Lin RK. Automatic Detection of the Circulating Cell-Free Methylated DNA Pattern of GCM2, ITPRIPL1 and CCDC181 for Detection of Early Breast Cancer and Surgical Treatment Response. Cancers (Basel) 2021; 13:cancers13061375. [PMID: 33803633 PMCID: PMC8002961 DOI: 10.3390/cancers13061375] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 12/31/2022] Open
Abstract
The early detection of cancer can reduce cancer-related mortality. There is no clinically useful noninvasive biomarker for early detection of breast cancer. The aim of this study was to develop accurate and precise early detection biomarkers and a dynamic monitoring system following treatment. We analyzed a genome-wide methylation array in Taiwanese and The Cancer Genome Atlas (TCGA) breast cancer (BC) patients. Most breast cancer-specific circulating methylated CCDC181, GCM2 and ITPRIPL1 biomarkers were found in the plasma. An automatic analysis process of methylated ccfDNA was established. A combined analysis of CCDC181, GCM2 and ITPRIPL1 (CGIm) was performed in R using Recursive Partitioning and Regression Trees to establish a new prediction model. Combined analysis of CCDC181, GCM2 and ITPRIPL1 (CGIm) was found to have a sensitivity level of 97% and an area under the curve (AUC) of 0.955 in the training set, and a sensitivity level of 100% and an AUC of 0.961 in the test set. The circulating methylated CCDC181, GCM2 and ITPRIPL1 was also significantly decreased after surgery (all p < 0.001). The aberrant methylation patterns of the CCDC181, GCM2 and ITPRIPL1 genes means that they are potential biomarkers for the detection of early BC and can be combined with breast imaging data to achieve higher accuracy, sensitivity and specificity, facilitating breast cancer detection. They may also be applied to monitor the surgical treatment response.
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Affiliation(s)
- Sheng-Chao Wang
- Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, No. 250, Wuxing Street, Taipei 110, Taiwan;
| | - Li-Min Liao
- Division of General Surgery, Department of Surgery, Taipei Medical University Shuang Ho Hospital, No.291, Zhongzheng Rd., Zhonghe District, New Taipei City 23561, Taiwan; (L.-M.L.); (C.-M.S.)
| | - Muhamad Ansar
- Ph.D. Program in the Clinical Drug Development of Herbal Medicine, Taipei Medical University, 250 Wu-Hsing Street, Taipei 110, Taiwan;
| | - Shih-Yun Lin
- Graduate Institute of Pharmacognosy, Taipei Medical University, 250 Wu-Hsing Street, Taipei 110, Taiwan;
| | - Wei-Wen Hsu
- Department of Statistics, College of Arts and Sciences, Kansas State University, 101 Dickens Hall, 1116 Mid-Campus Drive N, Manhattan, KS 66506-0802, USA;
| | - Chih-Ming Su
- Division of General Surgery, Department of Surgery, Taipei Medical University Shuang Ho Hospital, No.291, Zhongzheng Rd., Zhonghe District, New Taipei City 23561, Taiwan; (L.-M.L.); (C.-M.S.)
- Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, No. 250, Wuxing Street, Taipei 110, Taiwan
| | - Yu-Mei Chung
- Master Program for Clinical Pharmacogenomics and Pharmacoproteomics, Taipei Medical University, 250 Wu-Hsing Street, Taipei 110, Taiwan;
| | - Cai-Cing Liu
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, 250 Wu-Hsing Street, Taipei 110, Taiwan;
| | - Chin-Sheng Hung
- Division of General Surgery, Department of Surgery, Taipei Medical University Shuang Ho Hospital, No.291, Zhongzheng Rd., Zhonghe District, New Taipei City 23561, Taiwan; (L.-M.L.); (C.-M.S.)
- Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, No. 250, Wuxing Street, Taipei 110, Taiwan
- Correspondence: (C.-S.H.); (R.-K.L.); Tel.: +886-970-405-127 (C.-S.H.); +886-2-2736-1661 (ext. 6162) (R.-K.L.)
| | - Ruo-Kai Lin
- Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, No. 250, Wuxing Street, Taipei 110, Taiwan;
- Ph.D. Program in the Clinical Drug Development of Herbal Medicine, Taipei Medical University, 250 Wu-Hsing Street, Taipei 110, Taiwan;
- Graduate Institute of Pharmacognosy, Taipei Medical University, 250 Wu-Hsing Street, Taipei 110, Taiwan;
- Master Program for Clinical Pharmacogenomics and Pharmacoproteomics, Taipei Medical University, 250 Wu-Hsing Street, Taipei 110, Taiwan;
- Clinical trial center, Taipei Medical University Hospital, 252 Wu-Hsing Street, Taipei 110, Taiwan
- Correspondence: (C.-S.H.); (R.-K.L.); Tel.: +886-970-405-127 (C.-S.H.); +886-2-2736-1661 (ext. 6162) (R.-K.L.)
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21
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Wu HJ, Chu PY. Recent Discoveries of Macromolecule- and Cell-Based Biomarkers and Therapeutic Implications in Breast Cancer. Int J Mol Sci 2021; 22:ijms22020636. [PMID: 33435254 PMCID: PMC7827149 DOI: 10.3390/ijms22020636] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/31/2020] [Accepted: 01/08/2021] [Indexed: 12/13/2022] Open
Abstract
Breast cancer is the most commonly diagnosed cancer type and the leading cause of cancer-related mortality in women worldwide. Breast cancer is fairly heterogeneous and reveals six molecular subtypes: luminal A, luminal B, HER2+, basal-like subtype (ER−, PR−, and HER2−), normal breast-like, and claudin-low. Breast cancer screening and early diagnosis play critical roles in improving therapeutic outcomes and prognosis. Mammography is currently the main commercially available detection method for breast cancer; however, it has numerous limitations. Therefore, reliable noninvasive diagnostic and prognostic biomarkers are required. Biomarkers used in cancer range from macromolecules, such as DNA, RNA, and proteins, to whole cells. Biomarkers for cancer risk, diagnosis, proliferation, metastasis, drug resistance, and prognosis have been identified in breast cancer. In addition, there is currently a greater demand for personalized or precise treatments; moreover, the identification of novel biomarkers to further the development of new drugs is urgently needed. In this review, we summarize and focus on the recent discoveries of promising macromolecules and cell-based biomarkers for the diagnosis and prognosis of breast cancer and provide implications for therapeutic strategies.
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Affiliation(s)
- Hsing-Ju Wu
- Department of Biology, National Changhua University of Education, Changhua 500, Taiwan;
- Research Assistant Center, Show Chwan Memorial Hospital, Changhua 500, Taiwan
- Department of Medical Research, Chang Bing Show Chwan Memorial Hospital, Lukang Town, Changhua County 505, Taiwan
| | - Pei-Yi Chu
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei City 231, Taiwan
- Department of Pathology, Show Chwan Memorial Hospital, No. 542, Sec. 1 Chung-Shan Rd., Changhua 500, Taiwan
- Department of Health Food, Chung Chou University of Science and Technology, Changhua 510, Taiwan
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan
- Correspondence: ; Tel.: +886-975-611-855; Fax: +886-4-7227-116
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22
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Yin Q, Yang X, Li L, Xu T, Zhou W, Gu W, Ma F, Yang R. The Association Between Breast Cancer and Blood-Based Methylation of S100P and HYAL2 in the Chinese Population. Front Genet 2020; 11:977. [PMID: 33005177 PMCID: PMC7485126 DOI: 10.3389/fgene.2020.00977] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 08/03/2020] [Indexed: 02/05/2023] Open
Abstract
Previous work has shown that DNA methylation in peripheral blood may be associated with malignancy; however, these studies have mainly been conducted within Caucasian populations. Here, we investigated the association between blood-based methylation of S100 calcium-binding protein P gene (S100P) and hyaluronoglucosaminidase 2 gene (HYAL2) and breast cancer (BC) via mass spectrometry in two independent case-control studies of the Chinese population with a total of 351 BC cases and 427 cancer-free female controls. In Study I, in which subjects had an average of 45 years, hypomethylation of S100P showed a protective effect for women ≤45 years (six out of nine CpG sites, p < 0.05) but not for women >45 years. In contrast, hypomethylation of HAYL2 was not correlated with BC in women ≤45 years but was a risk factor for women >45 years (three out of four CpG sites, p < 0.05). We proposed an age-dependent correlation between BC and methylation of S100P and HYAL2 and performed further validation in Study II with older subjects (average age = 52.5 years), where hypomethylation of both S100P and HYAL2 was a risk factor for BC (p < 0.05 for 10 CpG sites) as reported in Caucasians who develop BC around 55 years old. Together with the observation that Chinese cancer-free females having variant basal methylation levels comparing to Caucasians, we assumed that blood-based methylation might be modified by ethnic background, hormone status, and lifestyle. Here, we highlighted that the epigenetic biomarkers warrant validations when its application in variant ethnic groups is considered.
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Affiliation(s)
- Qiming Yin
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xiaoqin Yang
- Department of Breast Surgery, West China Hospital, Sichuan University, Chengdu, 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
| | - 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
| | - 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 & Peking Union Medical College, Beijing, China
| | - Rongxi Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
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23
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Sher G, Salman NA, Khan AQ, Prabhu KS, Raza A, Kulinski M, Dermime S, Haris M, Junejo K, Uddin S. Epigenetic and breast cancer therapy: Promising diagnostic and therapeutic applications. Semin Cancer Biol 2020; 83:152-165. [PMID: 32858230 DOI: 10.1016/j.semcancer.2020.08.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 08/17/2020] [Accepted: 08/17/2020] [Indexed: 12/24/2022]
Abstract
The global burden of breast cancer (BC) is increasing significantly. This trend is caused by several factors such as late diagnosis, limited treatment options for certain BC subtypes, drug resistance which all lead to poor clinical outcomes. Recent research has reported the role of epigenetic alterations in the mechanism of BC pathogenesis and its hallmarks include drug resistance and stemness features. The understanding of these modifications and their significance in the management of BC carcinogenesis is challenging and requires further attention. Nevertheless, it promises to provide novel insight needed for utilizing these alterations as potential diagnostic, prognostic markers, predict treatment efficacy, as well as therapeutic agents. This highlights the importance of continuing research development to further advance the existing knowledge on epigenetics and BC carcinogenesis to overcome the current challenges. Hence, this review aims to shed light and discuss the current state of epigenetics research in the diagnosis and management of BC.
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Affiliation(s)
- Gulab Sher
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, P.O. Box 3050, Qatar
| | - Nadia Aziz Salman
- Kingston University London, School of Life Science, Pharmacy and Chemistry, SEC Faculty, Kingston, upon Thames, London, KT1 2EE, UK
| | - Abdul Q Khan
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, P.O. Box 3050, Qatar
| | - Kirti S Prabhu
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, P.O. Box 3050, Qatar
| | - Afsheen Raza
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, P.O. Box 3050, Qatar
| | - Michal Kulinski
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, P.O. Box 3050, Qatar
| | - Said Dermime
- National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, P.O. Box 3050, Qatar
| | - Mohammad Haris
- Functional and Molecular Imaging Laboratory, Sidra Medicine, P.O. Box 26999, Qatar; Laboratory Animal Research Center, Qatar University, Doha, P.O. Box 2713, Qatar
| | - Kulsoom Junejo
- General Surgery Department, Hamad General Hospital, Hamad Medical Corporation, Doha, P.O. Box 3050, Qatar
| | - Shahab Uddin
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, P.O. Box 3050, Qatar; Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, P.O. Box 3050, Qatar.
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24
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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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25
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Wang X, Liu Y, Sun H, Ge A, Li D, Fu J, Li Y, Pang D, Zhao Y. DNA Methylation in RARβ Gene as a Mediator of the Association Between Healthy Lifestyle and Breast Cancer: A Case-Control Study. Cancer Manag Res 2020; 12:4677-4684. [PMID: 32606959 PMCID: PMC7308131 DOI: 10.2147/cmar.s244606] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 05/20/2020] [Indexed: 12/12/2022] Open
Abstract
Purpose Lifestyle factors and methylation in the retinoic acid receptor β (RARβ) gene are associated with breast cancer (BC). This study aims to examine the mediation effect of RARβ methylation on the association between healthy lifestyle and BC in Chinese women. Patients and Methods This case–control study consisted of 408 BC patients and 573 controls. A healthy lifestyle score (HLS) was constructed based on diet, alcohol use, physical activity, body mass index and smoking. The mediation effect of RARβ methylation in peripheral blood leukocytes was assessed in a causal mediation model using R package Lavaan. Results A higher HLS was significantly associated with lower risk of BC (P-value<0.001). In mediation analyses, the total effect of HLS on BC measured as a regression coefficient was significant (−0.237). The indirect effects of HLS on RARβ methylation (−0.153) and RARβ methylation on BC (0.220) were both significant. The significant mediation effect of RARβ methylation on the HLS-BC association was estimated at 14.3%. Conclusion The relationship between healthy lifestyle and BC is partly mediated by RARβ methylation, suggesting that epigenetic modifications play a role in the underlying mechanisms in response to lifestyles and contribute to the development of BC.
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Affiliation(s)
- Xuan Wang
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin 150081, Heilong Jiang Province, People's Republic of China
| | - Yupeng Liu
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin 150081, Heilong Jiang Province, People's Republic of China
| | - Hongru Sun
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin 150081, Heilong Jiang Province, People's Republic of China
| | - Anqi Ge
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin 150081, Heilong Jiang Province, People's Republic of China
| | - Dapeng Li
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin 150081, Heilong Jiang Province, People's Republic of China
| | - Jinming Fu
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin 150081, Heilong Jiang Province, People's Republic of China
| | - Yan Li
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin 150081, Heilong Jiang Province, People's Republic of China
| | - Da Pang
- Department of Breast Surgery, The Affiliated Cancer Hospital of Harbin Medical University, Harbin 150081, Heilong Jiang Province, People's Republic of China
| | - Yashuang Zhao
- Department of Epidemiology, College of Public Health, Harbin Medical University, Harbin 150081, Heilong Jiang Province, People's Republic of China
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26
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Zhang S, Huang J, Lu J, Liu M, Li Y, Fang L, Huang H, Huang J, Mo F, Zheng J. A novel fluorescent biosensor based on dendritic DNA nanostructure in combination with ligase reaction for ultrasensitive detection of DNA methylation. J Nanobiotechnology 2019; 17:121. [PMID: 31812164 PMCID: PMC6898925 DOI: 10.1186/s12951-019-0552-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 11/25/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND DNA methylation detection is indispensable for the diagnosis and prognosis of various diseases including malignancies. Hence, it is crucial to develop a simple, sensitive, and specific detection strategy. METHODS A novel fluorescent biosensor was developed based on a simple dual signal amplification strategy using functional dendritic DNA nanostructure and signal-enriching polystyrene microbeads in combination with ligase detection reaction (LDR). Dendritic DNA self-assembled from Y-DNA and X-DNA through enzyme-free DNA catalysis of a hairpin structure, which was prevented from unwinding at high temperature by adding psoralen. Then dendritic DNA polymer labeled with fluorescent dye Cy5 was ligated with reporter probe into a conjugate. Avidin-labeled polystyrene microbeads were specifically bound to biotin-labeled capture probe, and hybridized with target sequence and dendritic DNA. LDR was triggered by adding Taq ligase. When methylated cytosine existed, the capture probe and reporter probe labeled with fluorescent dye perfectly matched the target sequence, forming a stable duplex to generate a fluorescence signal. However, after bisulfite treatment, unmethylated cytosine was converted into uracil, resulting in a single base mismatch. No fluorescence signal was detected due to the absence of duplex. RESULTS The obtained dendritic DNA polymer had a large volume. This method was time-saving and low-cost. Under the optimal experimental conditions using avidin-labeled polystyrene microbeads, the fluorescence signal was amplified more obviously, and DNA methylation was quantified ultrasensitively and selectively. The detection range of this sensor was 10-15 to 10-7 M, and the limit of detection reached as low as 0.4 fM. The constructed biosensor was also successfully used to analyze actual samples. CONCLUSION This strategy has ultrasensitivity and high specificity for DNA methylation quantification, without requiring complex processes such as PCR and enzymatic digestion, which is thus of great value in tumor diagnosis and biomedical research.
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Affiliation(s)
- Shu Zhang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China.,Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory Science, Guizhou Medical University, Guiyang, 550004, China.,Center for Clinical Laboratories, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Jian Huang
- Center for Clinical Laboratories, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Jingrun Lu
- Center for Clinical Laboratories, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Min Liu
- Center for Clinical Laboratories, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Yan Li
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China
| | - Lichao Fang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China
| | - Hui Huang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China
| | - Jianjun Huang
- Department of Breast Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Fei Mo
- Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory Science, Guizhou Medical University, Guiyang, 550004, China. .,Center for Clinical Laboratories, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China.
| | - Junsong Zheng
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China.
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27
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Analysis of methylation datasets identified significantly changed genes and functional pathways in osteoarthritis. Clin Rheumatol 2019; 38:3529-3538. [PMID: 31376087 DOI: 10.1007/s10067-019-04700-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 07/11/2019] [Accepted: 07/15/2019] [Indexed: 01/15/2023]
Abstract
BACKGROUND Researches indicate that epigenetics was involved in osteoarthritis (OA). The purpose of this study was to describe the alterations of DNA methylation in hip and knee OA by comparing DNA methylome of OA cartilage and non-OA samples and to identify novel genes and pathways associated with OA. METHODS We gained two expression profiling datasets (GSE73626 and GSE63695) from the GEO dataset. The RnBeads in R package was used to identify differentially methylated CpG sites. Genes that showed significant differences in DNA methylation between OA and normal control groups underwent functional annotation analysis using the online tool of GeneCodis. Furthermore, we used the Sequenom MassARRAY platform (CapitalBio, Beijing, China) to perform the quantitative methylation analysis. RESULTS A total of 249 hypermethylated sites and 96 hypomethylated sites were obtained from OA samples compared with normal control samples. Functional analysis of differentially methylated genes obtained that embryonic skeletal system morphogenesis, cartilage development, and skeletal system development may be involved in the pathogenesis of OA. Eight genes including HOXB3, HOXB4, HOXB6, HOXC4, HOXC10, HOXD3, TBX3, and TBX5 were identified as potential novel biomarkers for OA. CONCLUSION Taken together, our study found different molecular characteristics between OA patients and normal controls. This may provide new clues to elucidate the pathogenesis of OA.Key Points• Embryonic skeletal system morphogenesis, cartilage development, skeletal system development may be involved in the pathogenesis of OA.• Eight genes are identified as potential novel markers for OA.• Our future in vivo molecular intervention experiments will extend our current findings.
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28
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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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29
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Qi M, Xiong X. Promoter hypermethylation of RARβ2, DAPK, hMLH1, p14, and p15 is associated with progression of breast cancer: A PRISMA-compliant meta-analysis. Medicine (Baltimore) 2018; 97:e13666. [PMID: 30572486 PMCID: PMC6320171 DOI: 10.1097/md.0000000000013666] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Numerous studies have investigated the associations between RARβ2, DAPK, hMLH1, p14, and p15 promoter hypermethylation and clinical progression of patients with breast cancer, however the results remained uncertain due to the small sample size. Therefore, we performed a meta-analysis to explore the role of RARβ2, DAPK, hMLH1, p14, and p15 promoter hypermethylation in the susceptibility and clinical progression of breast cancer. METHODS Eligible studies were obtained by searching Medicine, Embase, Web of knowledge, and Chinese National Knowledge Infrastructure (CNKI) databases. The odds ratios (OR) and 95% confidence intervals (CI) were calculated to evaluate the associations of RARβ2, DAPK, hMLH1, p14, and p15 promoter hypermethylation with breast cancer pathogenesis. Trial sequential analysis (TSA) was applied to observe the reliability of pooled results of RARβ2 gene, and obtain a conservative required information size (RIS). RESULTS In primary screened 445 articles, 39 literatures with 4492 breast cancer patients were finally enrolled in the final meta-analysis. The results indicated that the frequency of RARβ2 promoter hypermethylation in case group was significantly higher than the frequency of control group (OR = 7.21, 95% CI = 1.54-33.80, P < .05). The RARβ2 promoter hypermethylation had a significant association with lymph node metastasis of breast cancer (OR = 2.13, 95% CI = 1.04-4.47, P < .05). And, the RARβ2 promoter hypermethylation was more common in the breast cancer patients of TNM III-IV stage than those patients of TNM I-II stage (OR = 1.85, 95% CI = 1.33-2.57, P < .05). In addition, the promoter hypermethylation of DAPK, hMLH1, and p14 genes were significantly associated with the susceptibility of breast cancer (for DAPK, OR = 4.93, 95% CI = 3.17-7.65; for hMLH1, OR = 1.84, 95% CI = 1.26-1.29; for p14, OR = 22.52, 95% CI = 7.00-72.41; for p15, OR = 2.13, 95% CI = 0.30-15.07). CONCLUSIONS Our findings revealed that the RARβ2 promoter hypermethylation significantly increased the risk of breast cancer. In the meantime, the meta-analysis demonstrated that there were significant associations of RARβ2 promoter hypermethylation with lymph node metastasis and TNM-stage of breast cancer patients. In addition, DAPK, hMLH1, and p14 genes promoter hypermethylation were significantly associated with the susceptibility of breast cancer.
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Affiliation(s)
- Ming Qi
- Department of Breast and Thyroid Surgery, Shandong Provincial Hospital Affiliated to Shandong University
| | - Xiang Xiong
- Department of Burn and Plastic Surgery, the Second Xiangya Hospital, Central South University, Changsha City, Hunan Province, P. R. China
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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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Li SY, Wu HC, Mai HF, Zhen JX, Li GS, Chen SJ. Microarray-based analysis of whole-genome DNA methylation profiling in early detection of breast cancer. J Cell Biochem 2018; 120:658-670. [PMID: 30203578 DOI: 10.1002/jcb.27423] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 07/12/2018] [Indexed: 12/16/2022]
Abstract
Emerging evidence indicated that changes in DNA methylation early in breast cancer (BC) development might be clinically relevant for therapeutic decisions. Through analysis of whole-genome gene expression microarray and DNA methylation microarray, we explored genes with abnormal DNA methylation in BC for early detection. Firstly, human BC tissues and adjacent non-cancerous tissues were collected from nine BC patients. Gene expression microarray sequencing was conducted for identifying differentially expressed genes and DNA methylation microarray sequencing for differentially methylated genes in BC. Differentially expressed genes and methylated genes in BC were further explored using the Cancer Genome Atlas database. The correlation between DNA methylation and gene expression was illustrated by multiple comparisons. In other 60 clinical samples, methylation specific polymerase chain reaction (PCR) and reverse transcription quantitative PCR were applied for the methylation of HOXA4 and IGF1 genes in BC and adjacent non-cancerous tissues. In total, 1680 upregulated genes and 1249 downregulated genes were determined in BC. Chromosome 16 and 17 showed more differentially methylated genes, and DNA methylation level was increased in BC tissues in each gene region. Chromosome 19 showed more differentially methylated genes, and DNA methylation level was increased in BC tissues in the exoniensis 1, untranslated region-5 and transcriptional start site 200 gene regions. In other 60 clinical samples, HOXA4 and IGF1 in BC tissues presented increased DNA methylation and decreased gene expression in BC. MCF7 cells treated with RG108 showed decreased HOXA4 and IGF1 expressions. It was estimated that HOXA4 and IGF1 were identified with increased DNA methylation and decreased gene expression in BC, which may serve as biomarkers in early BC detection.
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Affiliation(s)
- Shao-Ying Li
- Department of Thyroid and Breast Surgery, Baoan Maternal and Child Health Hospital, Jinan University, Sanming Project of Medicine in Shenzhen (SZSM201606088), Shenzhen, China
| | - Hua-Cong Wu
- Department of Thyroid and Breast Surgery, Baoan Maternal and Child Health Hospital, Jinan University, Sanming Project of Medicine in Shenzhen (SZSM201606088), Shenzhen, China
| | - Hui-Fen Mai
- Department of Thyroid and Breast Surgery, Baoan Maternal and Child Health Hospital, Jinan University, Sanming Project of Medicine in Shenzhen (SZSM201606088), Shenzhen, China
| | - Jian-Xin Zhen
- Department of Thyroid and Breast Surgery, Baoan Maternal and Child Health Hospital, Jinan University, Sanming Project of Medicine in Shenzhen (SZSM201606088), Shenzhen, China
| | - Gui-Sen Li
- Department of Thyroid and Breast Surgery, Baoan Maternal and Child Health Hospital, Jinan University, Sanming Project of Medicine in Shenzhen (SZSM201606088), Shenzhen, China
| | - Shao-Jun Chen
- Department of Breast Surgery, Shenzhen Maternal and Child Health Hospital, Shenzhen, China
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He A, Ning Y, Wen Y, Cai Y, Xu K, Cai Y, Han J, Liu L, Du Y, Liang X, Li P, Fan Q, Hao J, Wang X, Guo X, Ma T, Zhang F. Use of integrative epigenetic and mRNA expression analyses to identify significantly changed genes and functional pathways in osteoarthritic cartilage. Bone Joint Res 2018; 7:343-350. [PMID: 29922454 PMCID: PMC5987683 DOI: 10.1302/2046-3758.75.bjr-2017-0284.r1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Aim Osteoarthritis (OA) is caused by complex interactions between genetic and environmental factors. Epigenetic mechanisms control the expression of genes and are likely to regulate the OA transcriptome. We performed integrative genomic analyses to define methylation-gene expression relationships in osteoarthritic cartilage. Patients and Methods Genome-wide DNA methylation profiling of articular cartilage from five patients with OA of the knee and five healthy controls was conducted using the Illumina Infinium HumanMethylation450 BeadChip (Illumina, San Diego, California). Other independent genome-wide mRNA expression profiles of articular cartilage from three patients with OA and three healthy controls were obtained from the Gene Expression Omnibus (GEO) database. Integrative pathway enrichment analysis of DNA methylation and mRNA expression profiles was performed using integrated analysis of cross-platform microarray and pathway software. Gene ontology (GO) analysis was conducted using the Database for Annotation, Visualization and Integrated Discovery (DAVID). Results We identified 1265 differentially methylated genes, of which 145 are associated with significant changes in gene expression, such as DLX5, NCOR2 and AXIN2 (all p-values of both DNA methylation and mRNA expression < 0.05). Pathway enrichment analysis identified 26 OA-associated pathways, such as mitogen-activated protein kinase (MAPK) signalling pathway (p = 6.25 × 10-4), phosphatidylinositol (PI) signalling system (p = 4.38 × 10-3), hypoxia-inducible factor 1 (HIF-1) signalling pathway (p = 8.63 × 10-3 pantothenate and coenzyme A (CoA) biosynthesis (p = 0.017), ErbB signalling pathway (p = 0.024), inositol phosphate (IP) metabolism (p = 0.025), and calcium signalling pathway (p = 0.032). Conclusion We identified a group of genes and biological pathwayswhich were significantly different in both DNA methylation and mRNA expression profiles between patients with OA and controls. These results may provide new clues for clarifying the mechanisms involved in the development of OA. Cite this article: A. He, Y. Ning, Y. Wen, Y. Cai, K. Xu, Y. Cai, J. Han, L. Liu, Y. Du, X. Liang, P. Li, Q. Fan, J. Hao, X. Wang, X. Guo, T. Ma, F. Zhang. Use of integrative epigenetic and mRNA expression analyses to identify significantly changed genes and functional pathways in osteoarthritic cartilage. Bone Joint Res 2018;7:343–350. DOI: 10.1302/2046-3758.75.BJR-2017-0284.R1.
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Affiliation(s)
- A He
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Y Ning
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Y Wen
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Y Cai
- Department of Orthopaedics, The First Affiliated Hospital, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - K Xu
- Department of Joint Surgery, Xi'an Hong-Hui Hospital, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Y Cai
- Department of Joint Surgery, Xi'an Hong-Hui Hospital, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - J Han
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - L Liu
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Y Du
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - X Liang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - P Li
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Q Fan
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - J Hao
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - X Wang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - X Guo
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - T Ma
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - F Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, China
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Loke SY, Lee ASG. The future of blood-based biomarkers for the early detection of breast cancer. Eur J Cancer 2018; 92:54-68. [DOI: 10.1016/j.ejca.2017.12.025] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 12/15/2017] [Accepted: 12/21/2017] [Indexed: 02/06/2023]
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DNA methylation array analysis identifies breast cancer associated RPTOR, MGRN1 and RAPSN hypomethylation in peripheral blood DNA. Oncotarget 2018; 7:64191-64202. [PMID: 27577081 PMCID: PMC5325435 DOI: 10.18632/oncotarget.11640] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 08/13/2016] [Indexed: 11/30/2022] Open
Abstract
DNA methylation changes in peripheral blood DNA have been shown to be associated with solid tumors. We sought to identify methylation alterations in whole blood DNA that are associated with breast cancer (BC). Epigenome-wide DNA methylation profiling on blood DNA from BC cases and healthy controls was performed by applying Infinium HumanMethylation450K BeadChips. Promising CpG sites were selected and validated in three independent larger sample cohorts via MassARRAY EpiTyper assays. CpG sites located in three genes (cg06418238 in RPTOR, cg00736299 in MGRN1 and cg27466532 in RAPSN), which showed significant hypomethylation in BC patients compared to healthy controls in the discovery cohort (p < 1.00 × 10−6) were selected and successfully validated in three independent cohorts (validation I, n =211; validation II, n=378; validation III, n=520). The observed methylation differences are likely not cell-type specific, as the differences were only seen in whole blood, but not in specific sub cell-types of leucocytes. Moreover, we observed in quartile analysis that women in the lower methylation quartiles of these three loci had higher ORs than women in the higher quartiles. The combined AUC of three loci was 0.79 (95%CI 0.73-0.85) in validation cohort I, and was 0.60 (95%CI 0.54-0.66) and 0.62 (95%CI 0.57-0.67) in validation cohort II and III, respectively. Our study suggests that hypomethylation of CpG sites in RPTOR, MGRN1 and RAPSN in blood is associated with BC and might serve as blood-based marker supplements for BC if these could be verified in prospective studies.
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Yang R, Stöcker S, Schott S, Heil J, Marme F, Cuk K, Chen B, Golatta M, Zhou Y, Sutter C, Wappenschmidt B, Schmutzler R, Bugert P, Qu B, Bartram CR, Sohn C, Schneeweiss A, Burwinkel B. The association between breast cancer and S100P methylation in peripheral blood by multicenter case-control studies. Carcinogenesis 2017; 38:312-320. [PMID: 28426874 DOI: 10.1093/carcin/bgx004] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 01/12/2017] [Indexed: 12/15/2022] Open
Abstract
Breast cancer (BC) is the leading cancer in women worldwide. Changes in DNA methylation in peripheral blood could be associated with malignant diseases. Making use of screening results by llumina 27K Methylation Assay, we validated demethylation of five CpG sites of S100P gene in blood cell DNA of BC patients by three independent retrospective studies with subjects from different centers (Validation I: 235 familial BC case and 206 controls, odds ratio per -1% methylation > 1.03, and P < 6.00 × 10-8 for all five CpG sites; Validation II: 189 sporadic BC case and 189 controls, odds ratio per -1% methylation > 1.03, P < 8.0 × 10-5 for four CpG sites; Validation III: 156 sporadic BC case and 151 controls, odds ratio per -1% methylation > 1.03, P < 6.0 × 10-4 for four CpG sites). In addition, the blood-based S100P methylation pattern was similar among BC patients with differential clinical characteristics regardless of stage, receptor status and menopause status. The observed BC-associated decreased S100P methylation in blood mainly originates from the leucocytes subpopulations but not B cells. The methylation levels of most S100P CpG sites were inversely correlated with the expression of S100P in leucocytes (P < 1.2 × 10-4) and in tissue (P < 1.1 × 10-4). This study reveals significant association between blood-based decreased S100P methylation and BC, and provides another proof for the application of altered DNA methylation signatures from blood cells as potential markers for the detection of BC, especially for the early stage.
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Affiliation(s)
- Rongxi Yang
- Molecular Biology of Breast Cancer.,Department of Gynecology and Obstetrics, University Women's Clinic, 69120 Heidelberg, Germany
| | - Sarah Stöcker
- Molecular Biology of Breast Cancer.,Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Sarah Schott
- Department of Gynecology and Obstetrics, University Women's Clinic, 69120 Heidelberg, Germany
| | - Jörg Heil
- Department of Gynecology and Obstetrics, University Women's Clinic, 69120 Heidelberg, Germany
| | - Frederik Marme
- Department of Gynecology and Obstetrics, University Women's Clinic, 69120 Heidelberg, Germany
| | - Katarina Cuk
- Molecular Biology of Breast Cancer.,Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Bowang Chen
- Division of Molecular Genetic Epidemiology (C050), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,Department of Biology, South University of Science and Technology of China, 518055 Shenzhen, China
| | - Michael Golatta
- Department of Gynecology and Obstetrics, University Women's Clinic, 69120 Heidelberg, Germany
| | - Yan Zhou
- Department of Biophysics, Saarland University, 66421 Homburg (Saar), Germany
| | - Christian Sutter
- Institute of Human Genetics, University of Heidelberg, 69120 Heidelberg, Germany
| | - Barbara Wappenschmidt
- Department of Gynecology and Obstetrics, Clinical Center of University of Cologne, 50931 Cologne, Germany
| | - Rita Schmutzler
- Department of Gynecology and Obstetrics, Clinical Center of University of Cologne, 50931 Cologne, 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 and
| | - Bin Qu
- Department of Biophysics, Saarland University, 66421 Homburg (Saar), Germany
| | - Claus R Bartram
- Institute of Human Genetics, University of Heidelberg, 69120 Heidelberg, Germany
| | - Christof Sohn
- Department of Gynecology and Obstetrics, University Women's Clinic, 69120 Heidelberg, Germany
| | - Andreas Schneeweiss
- Department of Gynecology and Obstetrics, University Women's Clinic, 69120 Heidelberg, Germany.,Division Gynecologic Oncology, National Center for Tumor Diseases (NCT) 69120 Heidelberg, Germany
| | - Barbara Burwinkel
- Molecular Biology of Breast Cancer.,Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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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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Tang Q, Cheng J, Cao X, Surowy H, Burwinkel B. Blood-based DNA methylation as biomarker for breast cancer: a systematic review. Clin Epigenetics 2016; 8:115. [PMID: 27895805 PMCID: PMC5109688 DOI: 10.1186/s13148-016-0282-6] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 10/26/2016] [Indexed: 12/19/2022] Open
Abstract
Multiple studies have investigated global DNA methylation profiles and gene-specific DNA methylation in blood-based DNA to develop powerful screening markers for cancer. This systematic review summarizes the current evidence on methylation studies that investigated methylation level of blood-derived DNA of breast cancer (BC) patients in comparison to healthy controls by conducting a systematic literature review in PubMed and Web of Science. Essential results, such as methylation levels of BC cases and healthy controls, p values, and odds ratios, were extracted from these studies by two investigators independently. Overall, 45 publications met the inclusion criteria for this review. DNA from whole blood, as well as cell-free DNA (cfDNA) from serum or plasma, was used in these studies. The most common method used for measuring global DNA methylation was the investigation of repetitive elements as surrogates and the application of array-based genome-wide methylation analysis. For measuring gene-specific methylation level, methylation-specific PCR and pyrosequencing were the most frequently used methods. Epigenome-wide blood DNA hypomethylation in BC patients were reported in several studies; however, the evidence is still not conclusive. The most frequently investigated gene in whole blood was BRCA1, which was found more frequently methylated in patients compared to controls. RASSF1A was the most widely investigated gene in cfDNA of serum or plasma, which was also found more frequently methylated in patients compared to controls. Several of the eligible studies reported the associations of global hypomethylation and increased BC risk. Studies investigated associations between gene-specific methylation and BC risk, while got heterogeneous results. But two studies reported that hypermethylation of ATM gene was associated with increased BC risk, which suggest the potential use of this gene for BC risk stratification. Overall, our review suggests the possibility of using blood-based DNA methylation marker as promising marker for BC risk stratification, as several studies found associations between certain methylation level in blood and BC risk. However, so far, the evidence is still quite limited. Optimal markers are yet to be developed and promising results needed to be validated in prospective study cohorts and tested in large screening populations.
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Affiliation(s)
- Qiuqiong Tang
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, Ruprecht-Karls-Universitaet Heidelberg, Heidelberg, Germany ; Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jie Cheng
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, Ruprecht-Karls-Universitaet Heidelberg, Heidelberg, Germany ; Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Xue Cao
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, Ruprecht-Karls-Universitaet Heidelberg, Heidelberg, Germany ; Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Harald Surowy
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, Ruprecht-Karls-Universitaet Heidelberg, Heidelberg, Germany ; Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Barbara Burwinkel
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, Ruprecht-Karls-Universitaet Heidelberg, Heidelberg, Germany ; Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg, Germany
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Xu Y, Gao X, Zhang L, Chen D, Dai Z, Zou X. Simultaneous detection of double gene-specific methylation loci based on hairpin probes tagged with electrochemical quantum dots barcodes. J Electroanal Chem (Lausanne) 2016. [DOI: 10.1016/j.jelechem.2016.06.042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Henning AN, Haag JD, Smits BMG, Gould MN. The Non-coding Mammary Carcinoma Susceptibility Locus, Mcs5c, Regulates Pappa Expression via Age-Specific Chromatin Folding and Allele-Dependent DNA Methylation. PLoS Genet 2016; 12:e1006261. [PMID: 27537370 PMCID: PMC4990333 DOI: 10.1371/journal.pgen.1006261] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 07/26/2016] [Indexed: 11/19/2022] Open
Abstract
In understanding the etiology of breast cancer, the contributions of both genetic and environmental risk factors are further complicated by the impact of breast developmental stage. Specifically, the time period ranging from childhood to young adulthood represents a critical developmental window in a woman’s life when she is more susceptible to environmental hazards that may affect future breast cancer risk. Although the effects of environmental exposures during particular developmental Windows of Susceptibility (WOS) are well documented, the genetic mechanisms governing these interactions are largely unknown. Functional characterization of the Mammary Carcinoma Susceptibility 5c, Mcs5c, congenic rat model of breast cancer at various stages of mammary gland development was conducted to gain insight into the interplay between genetic risk factors and WOS. Using quantitative real-time PCR, chromosome conformation capture, and bisulfite pyrosequencing we have found that Mcs5c acts within the mammary gland to regulate expression of the neighboring gene Pappa during a critical mammary developmental time period in the rat, corresponding to the human young adult WOS. Pappa has been shown to positively regulate the IGF signaling pathway, which is required for proper mammary gland/breast development and is of increasing interest in breast cancer pathogenesis. Mcs5c-mediated regulation of Pappa appears to occur through age-dependent and mammary gland-specific chromatin looping, as well as genotype-dependent CpG island shore methylation. This represents, to our knowledge, the first insight into cellular mechanisms underlying the WOS phenomenon and demonstrates the influence developmental stage can have on risk locus functionality. Additionally, this work represents a novel model for further investigation into how environmental factors, together with genetic factors, modulate breast cancer risk in the context of breast developmental stage. A woman’s lifetime risk of developing breast cancer is affected by both genetic and environmental risk factors that can be further exacerbated by breast developmental stage. Time periods conferring increased risk are referred to as Windows of Susceptibility (WOS) and, generally speaking, the molecular mechanisms responsible for their effect on breast cancer risk are unknown. Our work presented here on the characterization of the rat Mammary Carcinoma Susceptibility 5c, Mcs5c, locus has identified a region within Mcs5c that interacts with the neighboring gene, Pappa, in an age-dependent manner to influence gene expression via genotype-dependent DNA methylation. Importantly, Mcs5c-mediated gene regulation occurs specifically within a WOS, and these finding represent the first identified molecular mechanisms by which a WOS influences the ability of a locus to affect mammary/breast cancer risk. This work highlights the importance developmental stage can have on genetic risk factor function, and we anticipate that the Mcs5c locus will serve as a model for future studies on WOS in combination with genetic and environmental risk factors.
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Affiliation(s)
- Amanda N. Henning
- Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin–Madison School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Jill D. Haag
- Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin–Madison School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Bart M. G. Smits
- Department of Pathology and Laboratory Medicine, Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Michael N. Gould
- Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin–Madison School of Medicine and Public Health, Madison, Wisconsin, United States of America
- * E-mail:
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Zhang L, Liu Y, Li Y, Zhao Y, Wei W, Liu S. Sensitive electrochemical assaying of DNA methyltransferase activity based on mimic-hybridization chain reaction amplified strategy. Anal Chim Acta 2016; 933:75-81. [DOI: 10.1016/j.aca.2016.05.044] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 05/16/2016] [Accepted: 05/23/2016] [Indexed: 11/29/2022]
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Li Z, Guo X, Tang L, Peng L, Chen M, Luo X, Wang S, Xiao Z, Deng Z, Dai L, Xia K, Wang J. Methylation analysis of plasma cell-free DNA for breast cancer early detection using bisulfite next-generation sequencing. Tumour Biol 2016; 37:13111-13119. [PMID: 27449045 DOI: 10.1007/s13277-016-5190-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 07/13/2016] [Indexed: 12/15/2022] Open
Abstract
Circulating cell-free DNA (cfDNA) has been considered as a potential biomarker for non-invasive cancer detection. To evaluate the methylation levels of six candidate genes (EGFR, GREM1, PDGFRB, PPM1E, SOX17, and WRN) in plasma cfDNA as biomarkers for breast cancer early detection, quantitative analysis of the promoter methylation of these genes from 86 breast cancer patients and 67 healthy controls was performed by using microfluidic-PCR-based target enrichment and next-generation bisulfite sequencing technology. The predictive performance of different logistic models based on methylation status of candidate genes was investigated by means of the area under the ROC curve (AUC) and odds ratio (OR) analysis. Results revealed that EGFR, PPM1E, and 8 gene-specific CpG sites showed significantly hypermethylation in cancer patients' plasma and significantly associated with breast cancer (OR ranging from 2.51 to 9.88). The AUC values for these biomarkers were ranging from 0.66 to 0.75. Combinations of multiple hypermethylated genes or CpG sites substantially improved the predictive performance for breast cancer detection. Our study demonstrated the feasibility of quantitative measurement of candidate gene methylation in cfDNA by using microfluidic-PCR-based target enrichment and bisulfite next-generation sequencing, which is worthy of further validation and potentially benefits a broad range of applications in clinical oncology practice. Quantitative analysis of methylation pattern of plasma cfDNA by next-generation sequencing might be a valuable non-invasive tool for early detection of breast cancer.
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Affiliation(s)
- Zibo Li
- The State Key Laboratory of Medical Genetics and School of Life Sciences, Central South University, 172 Tongzipo Road, Changsha, Hunan, 410013, China
| | - Xinwu Guo
- Sanway Gene Technology Inc., Changsha, Hunan, 410205, China
| | - Lili Tang
- Department of Breast Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Limin Peng
- Sanway Gene Technology Inc., Changsha, Hunan, 410205, China
| | - Ming Chen
- Sanway Gene Technology Inc., Changsha, Hunan, 410205, China
| | - Xipeng Luo
- Sanway Gene Technology Inc., Changsha, Hunan, 410205, China
| | - Shouman Wang
- Department of Breast Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Zhi Xiao
- Department of Breast Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Zhongping Deng
- Sanway Gene Technology Inc., Changsha, Hunan, 410205, China
- Research Center for Technologies in Nucleic Acid-Based Diagnostics, Changsha, Hunan, 410205, China
- Research Center for Technologies in Nucleic Acid-Based Diagnostics and Therapeutics, Changsha, Hunan, 410205, China
| | - Lizhong Dai
- Sanway Gene Technology Inc., Changsha, Hunan, 410205, China
- Research Center for Technologies in Nucleic Acid-Based Diagnostics, Changsha, Hunan, 410205, China
- Research Center for Technologies in Nucleic Acid-Based Diagnostics and Therapeutics, Changsha, Hunan, 410205, China
| | - Kun Xia
- The State Key Laboratory of Medical Genetics and School of Life Sciences, Central South University, 172 Tongzipo Road, Changsha, Hunan, 410013, China
| | - Jun Wang
- The State Key Laboratory of Medical Genetics and School of Life Sciences, Central South University, 172 Tongzipo Road, Changsha, Hunan, 410013, China.
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Pfütze K, Benner A, Hoffmeister M, Jansen L, Yang R, Bläker H, Herpel E, Ulrich A, Ulrich CM, Chang-Claude J, Brenner H, Burwinkel B. Methylation status at HYAL2 predicts overall and progression-free survival of colon cancer patients under 5-FU chemotherapy. Genomics 2015; 106:348-54. [PMID: 26453961 DOI: 10.1016/j.ygeno.2015.10.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 10/05/2015] [Accepted: 10/06/2015] [Indexed: 12/31/2022]
Abstract
DNA methylation variations in gene promoter regions are well documented tumor-specific alterations in human malignancies including colon cancer, which may influence tumor behavior and clinical outcome. As a subset of colon cancer patients does not benefit from adjuvant chemotherapy, predictive biomarkers are desirable. Here, we describe that DNA methylation levels at CpG loci of hyaluronoglucosaminidase 2 (HYLA2) could be used to identify stage II and III colon cancer patients who are most likely to benefit from 5-flourouracil (5-FU) chemotherapy with respect to overall survival and progression-free survival.
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Affiliation(s)
- Katrin Pfütze
- Helmholtz-University Group Molecular Epidemiology, German Cancer Research Center (DKFZ), Germany; Molecular Biology of Breast Cancer, Department of Obstetrics and Gynecology, University of Heidelberg, Germany.
| | - Axel Benner
- Division of Biostatistics, German Cancer Research Center (DKFZ), Germany
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Germany
| | - Lina Jansen
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Germany
| | - Rongxi Yang
- Helmholtz-University Group Molecular Epidemiology, German Cancer Research Center (DKFZ), Germany; Molecular Biology of Breast Cancer, Department of Obstetrics and Gynecology, University of Heidelberg, Germany
| | - Hendrik Bläker
- Department of General Pathology, Institute of Pathology, 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
| | - Alexis Ulrich
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany; Division of Molecular oncology, National Center for Tumor Diseases (NCT), Germany
| | - Cornelia M Ulrich
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT)/German Cancer Research Center (DKFZ), Germany
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, Unit of Genetic Epidemiology, German Cancer Research Center (DKFZ), Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Germany; German Cancer Research Center (DKTk)Germany
| | - Barbara Burwinkel
- Helmholtz-University Group Molecular Epidemiology, German Cancer Research Center (DKFZ), Germany; Molecular Biology of Breast Cancer, Department of Obstetrics and Gynecology, University of Heidelberg, Germany
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Genomic-Wide Analysis with Microarrays in Human Oncology. MICROARRAYS 2015; 4:454-73. [PMID: 27600234 PMCID: PMC4996403 DOI: 10.3390/microarrays4040454] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 10/08/2015] [Accepted: 10/13/2015] [Indexed: 12/19/2022]
Abstract
DNA microarray technologies have advanced rapidly and had a profound impact on examining gene expression on a genomic scale in research. This review discusses the history and development of microarray and DNA chip devices, and specific microarrays are described along with their methods and applications. In particular, microarrays have detected many novel cancer-related genes by comparing cancer tissues and non-cancerous tissues in oncological research. Recently, new methods have been in development, such as the double-combination array and triple-combination array, which allow more effective analysis of gene expression and epigenetic changes. Analysis of gene expression alterations in precancerous regions compared with normal regions and array analysis in drug-resistance cancer tissues are also successfully performed. Compared with next-generation sequencing, a similar method of genome analysis, several important differences distinguish these techniques and their applications. Development of novel microarray technologies is expected to contribute to further cancer research.
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Cava C, Bertoli G, Castiglioni I. Integrating genetics and epigenetics in breast cancer: biological insights, experimental, computational methods and therapeutic potential. BMC SYSTEMS BIOLOGY 2015; 9:62. [PMID: 26391647 PMCID: PMC4578257 DOI: 10.1186/s12918-015-0211-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 09/15/2015] [Indexed: 12/11/2022]
Abstract
BACKGROUND Development of human cancer can proceed through the accumulation of different genetic changes affecting the structure and function of the genome. Combined analyses of molecular data at multiple levels, such as DNA copy-number alteration, mRNA and miRNA expression, can clarify biological functions and pathways deregulated in cancer. The integrative methods that are used to investigate these data involve different fields, including biology, bioinformatics, and statistics. RESULTS These methodologies are presented in this review, and their implementation in breast cancer is discussed with a focus on integration strategies. We report current applications, recent studies and interesting results leading to the identification of candidate biomarkers for diagnosis, prognosis, and therapy in breast cancer by using both individual and combined analyses. CONCLUSION This review presents a state of art of the role of different technologies in breast cancer based on the integration of genetics and epigenetics, and shares some issues related to the new opportunities and challenges offered by the application of such integrative approaches.
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Affiliation(s)
- Claudia Cava
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Milan, Italy.
| | - Gloria Bertoli
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Milan, Italy.
| | - Isabella Castiglioni
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Milan, Italy.
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S100P and HYAL2 as prognostic markers for patients with triple-negative breast cancer. Exp Mol Pathol 2015; 99:180-7. [PMID: 26112095 DOI: 10.1016/j.yexmp.2015.06.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Accepted: 06/18/2015] [Indexed: 01/10/2023]
Abstract
Triple-negative breast cancer (TNBC) is a group of very aggressive breast tumours, characterised by lack of expression of oestrogen receptor (ER), progesterone receptor (PR) and erb-b2 receptor tyrosine kinase 2 (ERBB2/HER2). Nevertheless, TNBCs show different clinical characteristics and are very diverse regarding prognostic outcome. So far, only a few prognostic markers for TNBC have been reported that could be helpful for therapeutic stratification. Here we have analysed the expression of S100P and HYAL2 using immunohistochemistry (IHC) in a TNBC cohort of 98 patients with a follow-up for recurrence and death. TNBC patients with high expression of both proteins showed significantly shorter progression-free survival (PFS) (mean PFS=35.9months, P=0.001) compared to TNBC patients with high expression levels of only one of the proteins (mean PFS=69.4months) and to TNBC patients with low expression of both proteins (mean PFS=83.3months). Moreover, multivariate Cox-regression model showed the combined expression of S100P and HYAL2 as independent prognostic factor for PFS (P=0.001). The expression of S100P and HYAL2 indicated similar prognostic effect to the overall survival (OS) of TNBC patients. In addition, high expression levels of both S100P and HYAL2 showed significant association with different clinicopathological characteristics, such as more recurrence events (P=0.004), and higher occurrence of metastasis (P=0.002). Our study proposes S100P and HYAL2 as potential prognostic markers for TNBC.
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Gentry AE, Jackson-Cook CK, Lyon DE, Archer KJ. Penalized Ordinal Regression Methods for Predicting Stage of Cancer in High-Dimensional Covariate Spaces. Cancer Inform 2015; 14:201-8. [PMID: 26052223 PMCID: PMC4447150 DOI: 10.4137/cin.s17277] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 02/16/2015] [Accepted: 02/17/2015] [Indexed: 12/20/2022] Open
Abstract
The pathological description of the stage of a tumor is an important clinical designation and is considered, like many other forms of biomedical data, an ordinal outcome. Currently, statistical methods for predicting an ordinal outcome using clinical, demographic, and high-dimensional correlated features are lacking. In this paper, we propose a method that fits an ordinal response model to predict an ordinal outcome for high-dimensional covariate spaces. Our method penalizes some covariates (high-throughput genomic features) without penalizing others (such as demographic and/or clinical covariates). We demonstrate the application of our method to predict the stage of breast cancer. In our model, breast cancer subtype is a nonpenalized predictor, and CpG site methylation values from the Illumina Human Methylation 450K assay are penalized predictors. The method has been made available in the ordinalgmifs package in the R programming environment.
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Affiliation(s)
| | | | - Debra E Lyon
- College of Nursing, University of Florida, Gainesville, FL, USA
| | - Kellie J Archer
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA
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Shvetsov YB, Song MA, Cai Q, Tiirikainen M, Xiang YB, Shu XO, Yu H. Intraindividual variation and short-term temporal trend in DNA methylation of human blood. Cancer Epidemiol Biomarkers Prev 2015; 24:490-7. [PMID: 25538225 PMCID: PMC4355238 DOI: 10.1158/1055-9965.epi-14-0853] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Between- and within-person variation in DNA methylation levels are important parameters to be considered in epigenome-wide association studies. Temporal change is one source of within-person variation in DNA methylation that has been linked to aging and disease. METHODS We analyzed CpG-site-specific intraindividual variation and short-term temporal trend in leukocyte DNA methylation among 24 healthy Chinese women, with blood samples drawn at study entry and after 9 months. Illumina HumanMethylation450 BeadChip was used to measure methylation. Intraclass correlation coefficients (ICC) and trend estimates were summarized by genomic location and probe type. RESULTS The median ICC was 0.36 across nonsex chromosomes and 0.80 on the X chromosome. There was little difference in ICC profiles by genomic region and probe type. Among CpG loci with high variability between participants, more than 99% had ICC > 0.8. Statistically significant trend was observed in 10.9% CpG loci before adjustment for cell-type composition and in 3.4% loci after adjustment. CONCLUSIONS For CpG loci differentially methylated across subjects, methylation levels can be reliably assessed with one blood sample. More samples per subject are needed for low-variability and unmethylated loci. Temporal changes are largely driven by changes in cell-type composition of blood samples, but temporal trend unrelated to cell types is detected in a small percentage of CpG sites. IMPACT This study shows that one measurement can reliably assess methylation of differentially methylated CpG loci. Cancer Epidemiol Biomarkers Prev; 24(3); 490-7. ©2014 AACR.
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Affiliation(s)
| | - Min-Ae Song
- Comprehensive Cancer Center, Ohio State University and James Cancer Hospital, Columbus, Ohio
| | - Qiuyin Cai
- Division of Epidemiology and Vanderbilt Epidemiology Center, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee. Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | | | - Yong-Bing Xiang
- Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiao-Ou Shu
- Division of Epidemiology and Vanderbilt Epidemiology Center, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee. Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Herbert Yu
- University of Hawaii Cancer Center, Honolulu, Hawaii
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