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Kang H, Yang M, Zhang F, Xu H, Ren S, Li J, Chen D, Wang F, Li D, Chen X. Identification lymph node metastasis in esophageal squamous cell carcinoma using whole slide images and a hybrid network of multiple instance and transfer learning. Biomed Signal Process Control 2023. [DOI: 10.1016/j.bspc.2023.104577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Gohar J, Do WL, Miller-Kleinhenz J, Conneely K, Krishnamurti U, D'Angelo O, Gogineni K, Torres M, Gabram-Mendola S, McCullough LE. Neighborhood characteristics and breast tumor methylation: using epigenomics to explore cancer outcome disparities. Breast Cancer Res Treat 2022; 191:653-663. [PMID: 34978015 DOI: 10.1007/s10549-021-06430-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 10/15/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND Social exposures may drive epigenetic alterations that affect racial disparities in breast cancer outcomes. This study examined the association between neighborhood-level factors and DNA methylation in non-Hispanic Black and White women diagnosed with breast cancer. METHODS Genome-wide DNA methylation was measured using the EPIC array in the tumor tissue of 96 women. Linear regression models were used to examine the association between nine neighborhood-level factors and methylation, regressing β values for each cytosine-phosphate guanine dinucleotide (CpG) site on neighborhood-level factors while adjusting for covariates. Neighborhood data were obtained from the Opportunity Atlas. We used a false discovery rate (FDR) threshold < 0.05, and for CpGs below this threshold, we examined interactions with race. We employed multivariable Cox proportional-hazards models to estimate whether aberrant methylation was associated with all-cause mortality. RESULTS 26 of the CpG sites were associated with job density or college education (FDR < 0.05). Further exploration of these 26 CpG sites revealed no interactions by race, but a single probe in TMEM204 was associated with all-cause mortality. CONCLUSION We identified novel associations between neighborhood-level factors and the breast tumor DNA methylome. Our data are the first to show that dysregulation in neighborhood associated CpG sites may be associated with all-cause mortality. Neighborhood-level factors may contribute to differential tumor methylation in genes related to tumor progression and metastasis. This contributes to the increasing body of evidence that area-level factors (such as neighborhood characteristics) may play an important role in cancer disparities through modulation of the breast tumor epigenome.
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Affiliation(s)
- Jazib Gohar
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, 30322, USA
| | - Whitney L Do
- Department of Global Health, Emory University Rollins School of Public Health, Atlanta, GA, 30322, USA
| | - Jasmine Miller-Kleinhenz
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, 30322, USA
| | - Karen Conneely
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Uma Krishnamurti
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Olivia D'Angelo
- Department of Surgery, Jackson Memorial Hospital/University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Keerthi Gogineni
- Department of Medical Oncology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Mylin Torres
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | | | - Lauren E McCullough
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, 30322, USA.
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Ratna MG, Nugrahaningsih DAA, Sholikhah EN, Dwianingsih EK, Malueka RG. The association between PON1 and GSTM1 genetic variation with methylation of p16 gene promoter among Javanese farmers exposed to pesticides at Magelang Regency, Central Java, Indonesia. Heliyon 2020; 6:e03993. [PMID: 32478190 PMCID: PMC7248662 DOI: 10.1016/j.heliyon.2020.e03993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 12/11/2019] [Accepted: 05/12/2020] [Indexed: 12/08/2022] Open
Abstract
Occupational exposure to pesticides leads to the development of cancer. Aberrant DNA methylation plays a crucial role in cancer. The manifestation of the carcinogenic effect of pesticides could be determined by the variation of genes encoding enzyme, including PON1 Q192R and GSTM1. The goal of this study was to find out polymorphism of PON1 Q192R and methylation of p16 gene promoter, and their correlation on Javanese farmers in the agricultural area of Ngablak Subdistrict, Magelang Regency, Central Java. Seventy-eight pesticide-exposed farmers enrolled in the study. Polymorphism of PON Q192R was determined using PCR-RFLP and variation of GSTM1 was examined using conventional PCR. The methylation of the p16 gene promoter was determined using methylation-specific PCR. The result revealed 94.9% polymorphism of PON1 Q192R, which was higher in the R/R (Arg/Arg) genotypes than Q/R (Gln/Arg) and lowest in Q/Q (Gln/Gln) genotypes. We also found 82.1% GSTM1 null genotype among the farmers enrolled in the study. As many as 26.9% methylations of p16 gene promoter were found among farmers. Genetic variation of PON1 Q192R and GSTM1 were not found to be correlated to the methylation status of p16 gene promoter in the Javanese population.
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Affiliation(s)
- Maya G Ratna
- Master of Biomedical Science Program, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Dwi A A Nugrahaningsih
- Department of Pharmacology and Therapy, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia.,Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Indonesia
| | - Eti N Sholikhah
- Department of Pharmacology and Therapy, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Ery K Dwianingsih
- Department of Anatomical Pathology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia.,Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Indonesia
| | - Rusdy G Malueka
- Department of Neurology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia.,Genetics Working Group, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Indonesia
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Lu T, Chen D, Wang Y, Sun X, Li S, Miao S, Wo Y, Dong Y, Leng X, Du W, Jiao W. Identification of DNA methylation-driven genes in esophageal squamous cell carcinoma: a study based on The Cancer Genome Atlas. Cancer Cell Int 2019; 19:52. [PMID: 30886542 PMCID: PMC6404309 DOI: 10.1186/s12935-019-0770-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 02/28/2019] [Indexed: 02/06/2023] Open
Abstract
Background Aberrant DNA methylations are significantly associated with esophageal squamous cell carcinoma (ESCC). In this study, we aimed to investigate the DNA methylation-driven genes in ESCC by integrative bioinformatics analysis. Methods Data of DNA methylation and transcriptome profiling were downloaded from TCGA database. DNA methylation-driven genes were obtained by methylmix R package. David database and ConsensusPathDB were used to perform gene ontology (GO) analysis and pathway analysis, respectively. Survival R package was used to analyze overall survival analysis of methylation-driven genes. Results Totally 26 DNA methylation-driven genes were identified by the methylmix, which were enriched in molecular function of DNA binding and transcription factor activity. Then, ABCD1, SLC5A10, SPIN3, ZNF69, and ZNF608 were recognized as significant independent prognostic biomarkers from 26 methylation-driven genes. Additionally, a further integrative survival analysis, which combined methylation and gene expression data, was identified that ABCD1, CCDC8, FBXO17 were significantly associated with patients’ survival. Also, multiple aberrant methylation sites were found to be correlated with gene expression. Conclusion In summary, we studied the DNA methylation-driven genes in ESCC by bioinformatics analysis, offering better understand of molecular mechanisms of ESCC and providing potential biomarkers precision treatment and prognosis detection. Electronic supplementary material The online version of this article (10.1186/s12935-019-0770-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tong Lu
- 1Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, No. 16 Jiangsu Road, Shinan District, Qingdao, 266003 China
| | - Di Chen
- 2Department of Gastroenterology, Affiliated Hospital of Qingdao University, No 16 Jiangsu Road, Shinan District, Qingdao, 266003 China
| | - Yuanyong Wang
- 1Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, No. 16 Jiangsu Road, Shinan District, Qingdao, 266003 China
| | - Xiao Sun
- 1Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, No. 16 Jiangsu Road, Shinan District, Qingdao, 266003 China
| | - Shicheng Li
- 1Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, No. 16 Jiangsu Road, Shinan District, Qingdao, 266003 China
| | - Shuncheng Miao
- 1Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, No. 16 Jiangsu Road, Shinan District, Qingdao, 266003 China
| | - Yang Wo
- 1Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, No. 16 Jiangsu Road, Shinan District, Qingdao, 266003 China
| | - Yanting Dong
- 1Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, No. 16 Jiangsu Road, Shinan District, Qingdao, 266003 China
| | - Xiaoliang Leng
- 1Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, No. 16 Jiangsu Road, Shinan District, Qingdao, 266003 China
| | - Wenxing Du
- 1Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, No. 16 Jiangsu Road, Shinan District, Qingdao, 266003 China
| | - Wenjie Jiao
- 1Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, No. 16 Jiangsu Road, Shinan District, Qingdao, 266003 China
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Ma K, Cao B, Guo M. The detective, prognostic, and predictive value of DNA methylation in human esophageal squamous cell carcinoma. Clin Epigenetics 2016; 8:43. [PMID: 27110300 PMCID: PMC4840959 DOI: 10.1186/s13148-016-0210-9] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 04/14/2016] [Indexed: 12/17/2022] Open
Abstract
Esophageal cancer is one of the most common malignancies in the world. Squamous cell carcinoma accounts for approximately 90 % of esophageal cancer cases. Genetic and epigenetic changes have been found to accumulate during the development of various cancers, including esophageal squamous carcinoma (ESCC). Tobacco smoking and alcohol consumption are two major risk factors for ESCC, and both tobacco and alcohol were found to induce methylation changes in ESCC. Growing evidence demonstrates that aberrant epigenetic changes play important roles in the multiple-step processes of carcinogenesis and tumor progression. DNA methylation may occur in the key components of cancer-related signaling pathways. Aberrant DNA methylation affects genes involved in cell cycle, DNA damage repair, Wnt, TGF-β, and NF-κB signaling pathways, including P16, MGMT, SFRP2, DACH1, and ZNF382. Certain genes methylated in precursor lesions of the esophagus demonstrate that DNA methylation may serve as esophageal cancer early detection marker, such as methylation of HIN1, TFPI-2, DACH1, and SOX17. CHFR methylation is a late stage event in ESCC and is a sensitive marker for taxanes in human ESCC. FHIT methylation is associated with poor prognosis in ESCC. Aberrant DNA methylation changes may serve as diagnostic, prognostic, and chemo-sensitive markers. Characterization of the DNA methylome in ESCC will help to better understand its mechanisms and develop improved therapies.
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Affiliation(s)
- Kai Ma
- />Department of Thoracic Surgery, the Affiliated Hospital of Qingdao University, Qingdao, China
| | - Baoping Cao
- />Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
| | - Mingzhou Guo
- />Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
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Baba Y, Watanabe M, Baba H. A review of the alterations in DNA methylation in esophageal squamous cell carcinoma. Surg Today 2013; 43:1355-64. [DOI: 10.1007/s00595-012-0451-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Accepted: 10/26/2012] [Indexed: 12/20/2022]
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[Chromosomal and genomic aberrations in esophageal squamous cell carcinoma]. YI CHUAN = HEREDITAS 2012; 34:519-25. [PMID: 22659423 DOI: 10.3724/sp.j.1005.2012.00519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Esophageal squamous cell carcinoma (ESCC) is one of the most common malignancies with poor prognosis in China. Patients with ESCC may present with vague symptoms in early stage and most of the cases are diagnosed at advanced stage, without the chance of optimal therapy. In the development and progression of ESCC, cytogenetic and molecular aberrations are frequently observed. This review is to summarize the advances in the chromosomal and genomic alterations of ESCC reported recently.
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Tao MH, Marian C, Nie J, Ambrosone C, Krishnan SS, Edge SB, Trevisan M, Shields PG, Freudenheim JL. Body mass and DNA promoter methylation in breast tumors in the Western New York Exposures and Breast Cancer Study. Am J Clin Nutr 2011; 94:831-8. [PMID: 21775555 PMCID: PMC3155934 DOI: 10.3945/ajcn.110.009365] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The mechanism of the observed association between body mass, particularly centralized body fat, and postmenopausal breast cancer risk is not well understood. OBJECTIVE We hypothesized that body mass may affect DNA methylation through increased estrogen and chronic inflammation. The association between body mass and promoter methylation in breast tumors was investigated in a population-based, case-control study. DESIGN The promoter methylation of E-cadherin, p16, and RAR-β(2) genes was assessed in breast tumor blocks from 803 pre- and postmenopausal cases by using real-time methylation-specific polymerase chain reaction. Unconditional logistic regression was used to derive the adjusted OR and 95% CI for case-case comparisons of tumors with and without promoter methylation of the genes. RESULTS The frequency of promoter methylation was 20% for E-cadherin, 25.9% for p16, and 27.5% for RAR-β(2). There was no difference in the prevalence of the DNA methylation of individual genes by BMI, waist-to-hip ratio (WHR), or lifetime weight change between the age of 20 y and the present. However, in a case-case comparison of postmenopausal breast cancer, a greater WHR was associated with an increased likelihood of ≥1 of the 3 genes being methylated (OR: 1.85; 95% CI: 1.10, 3.11; P-trend < 0.02). CONCLUSIONS We showed that WHR was associated with DNA promoter methylation of ≥1 of 3 genes in postmenopausal breast tumors. It may be that the association of body fat composition and postmenopausal breast cancer is related to altered DNA methylation. However, future studies in other populations and with an examination of the methylation of more genes are needed.
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Affiliation(s)
- Meng-Hua Tao
- Department of Social and Preventive Medicine, School of Public Health and Health Professions, University at Buffalo, NY, USA.
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Zare M, Jazii FR, Soheili ZS, Moghanibashi MM. Downregulation of tropomyosin-1 in squamous cell carcinoma of esophagus, the role of Ras signaling and methylation. Mol Carcinog 2011; 51:796-806. [DOI: 10.1002/mc.20847] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Revised: 07/08/2011] [Accepted: 07/27/2011] [Indexed: 12/16/2022]
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