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Huerne K, Jackson SS, Lall R, Palmour N, Berner AM, Dupras C, Joly Y. Studies in Cancer Epigenetics through a Sex and Gendered Lens: A Comprehensive Scoping Review. Cancers (Basel) 2023; 15:4207. [PMID: 37686484 PMCID: PMC10486657 DOI: 10.3390/cancers15174207] [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: 06/30/2023] [Revised: 08/18/2023] [Accepted: 08/20/2023] [Indexed: 09/10/2023] Open
Abstract
Background: Sex and gender are vitally important in the study of epigenetic mechanisms for various types of cancer. However, little has been done to assess the state of sex and gender-based analyses (SGBA) in this field. The aim was to undertake a critical evaluation of sex and gender representation, discussion, and data analysis within the cancer epigenetics field since 2010. Methods: A PRISMA-ScR scoping review was conducted with 111 peer-reviewed studies comprising of colorectal, gastric, head and neck, hepatocellular carcinoma, and lung cancers. Data extraction and a quality appraisal were performed by a team of epidemiologists and bioethicists. Results: Of the 111 included studies, only 17 studies (15.3%) explicitly stated sex and gender analysis to be their primary aim. A total of 103 studies (92.8%) provided a detailed analysis of sex/gender as a biological or social variable, while the remaining 8 studies (7.2%) only stratified results by sex/gender. Although sex and gender were a key facet in all the eligible studies, only 7 studies (6.3%) provided an explicit definition of the terms "sex" or "gender", while the remaining 104 studies (93.7%) used the words "sex" or "gender" without providing a definition. A total of 84 studies (75.7%) conflated the concepts of "sex" and "gender", while 44 studies (39.6%) were inconsistent with their usage of the "sex" and "gender" terms. Conclusions: Very few studies offered a robust analysis of sex/gender data according to SAGER guidelines. We call for clear and directed guidelines regarding the use of sex/gender as a variable in epigenetics research.
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Affiliation(s)
- Katherine Huerne
- Center of Genomics and Policy, Department of Human Genetics, McGill University, Montreal, QC H3A 0G1, Canada
| | - Sarah S. Jackson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, USA
| | - Rina Lall
- Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, QC H3A 0G1, Canada
| | - Nicole Palmour
- Center of Genomics and Policy, Department of Human Genetics, McGill University, Montreal, QC H3A 0G1, Canada
| | - Alison May Berner
- Department of Genomics & Computational Biology, Barts Cancer Institute, Queen Mary University of London, London E1 4NS, UK
| | - Charles Dupras
- Department of Social and Preventive Medicine, School of Public Health, University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Yann Joly
- Center of Genomics and Policy, Department of Human Genetics, McGill University, Montreal, QC H3A 0G1, Canada
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Wang B, Li R, Cai Y, Li B, Qin S, Zheng K, Zeng M, Xiao F, Zhang Z, Xu X. Alteration of DNA methylation induced by PM 2.5 in human bronchial epithelial cells. Toxicol Res (Camb) 2020; 9:552-560. [PMID: 32905279 PMCID: PMC7467236 DOI: 10.1093/toxres/tfaa061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 07/14/2020] [Accepted: 07/19/2020] [Indexed: 12/26/2022] Open
Abstract
This current study explored the effects of fine particulate matter (PM2.5) on deoxyribonucleic acid methylation in human bronchial epithelial cells. Human bronchial epithelial cells were exposed to PM2.5 for 24 h after which, deoxyribonucleic acid samples were extracted, and the differences between methylation sites were detected using methylation chips. Subsequent gene ontology functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed for the differential methylation sites. Functional epigenetic modules analysis of the overall differential methylation site interactions was also conducted. A total of 127 differential methylation sites in 89 genes were screened in the PM2.5 10 μg/ml group, of which 55 sites demonstrated increased methylation, with methylation levels decreasing in a further 72 sites. Following an exposure of 50 μg/ml PM2.5, a total of 238 differentially methylated sites were screened in 168 genes, of which methylation levels increased in 127 sites, and decreased in 111. KEGG analysis showed that the top 10 enrichment pathways predominantly involve hepatocellular carcinoma pathways and endometrial cancer pathways, whereas functional epigenetic modules analysis screened eight genes (A2M, IL23A, TPIP6, IL27, MYD88, ILE2B, NLRC4, TNF) with the most interactions. Our results indicate that exposure to PM2.5 for 24 h in human bronchial epithelial cells induces marked changes in deoxyribonucleic acid methylation of multiple genes involved in apoptosis and carcinogenesis pathways, these findings can provide a new direction for further study of PM2.5 carcinogenic biomarkers.
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Affiliation(s)
- Bingyu Wang
- Department of Environmental Toxicology, Institute of Environment and Health, Shenzhen Center for Disease Control and Prevention, 8 Longyuan Road, Shenzhen, Guangdong 518055, China
- Department of Preventive Medicine, School of Public Health, University of South China, 28 Changsheng West Road, Hengyang, Hunan 421001, China
| | - Runbing Li
- Department of Environmental Toxicology, Institute of Environment and Health, Shenzhen Center for Disease Control and Prevention, 8 Longyuan Road, Shenzhen, Guangdong 518055, China
- Department of Preventive Medicine, School of Public Health, University of South China, 28 Changsheng West Road, Hengyang, Hunan 421001, China
| | - Ying Cai
- Department of Environmental Toxicology, Institute of Environment and Health, Shenzhen Center for Disease Control and Prevention, 8 Longyuan Road, Shenzhen, Guangdong 518055, China
- Department of Preventive Medicine, School of Public Health, University of South China, 28 Changsheng West Road, Hengyang, Hunan 421001, China
| | - Boru Li
- Department of Preventive Medicine, School of Public Health, University of South China, 28 Changsheng West Road, Hengyang, Hunan 421001, China
- Department of Health Toxicology, Xiangya School of Public Health, Central South University, 238 Shangmayuanling Lane, Changsha, Hunan 410078, China
| | - Shuangjian Qin
- Department of Preventive Medicine, School of Public Health, University of South China, 28 Changsheng West Road, Hengyang, Hunan 421001, China
- Department of Health Toxicology, Xiangya School of Public Health, Central South University, 238 Shangmayuanling Lane, Changsha, Hunan 410078, China
| | - Kai Zheng
- Department of Environmental Toxicology, Institute of Environment and Health, Shenzhen Center for Disease Control and Prevention, 8 Longyuan Road, Shenzhen, Guangdong 518055, China
- Department of Preventive Medicine, School of Public Health, University of South China, 28 Changsheng West Road, Hengyang, Hunan 421001, China
| | - Ming Zeng
- Department of Health Toxicology, Xiangya School of Public Health, Central South University, 238 Shangmayuanling Lane, Changsha, Hunan 410078, China
| | - Fang Xiao
- Department of Health Toxicology, Xiangya School of Public Health, Central South University, 238 Shangmayuanling Lane, Changsha, Hunan 410078, China
| | - Zhaohui Zhang
- Department of Preventive Medicine, School of Public Health, University of South China, 28 Changsheng West Road, Hengyang, Hunan 421001, China
| | - Xinyun Xu
- Department of Environmental Toxicology, Institute of Environment and Health, Shenzhen Center for Disease Control and Prevention, 8 Longyuan Road, Shenzhen, Guangdong 518055, China
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Li J, Chen N, Gong X. Prognostic implications of aberrantly expressed methylation‑driven genes in hepatocellular carcinoma: A study based on The Cancer Genome Atlas. Mol Med Rep 2019; 20:5304-5314. [PMID: 31661127 DOI: 10.3892/mmr.2019.10771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 08/30/2019] [Indexed: 11/06/2022] Open
Abstract
RNA‑Sequencing and methylation data for hepatocellular carcinoma (HCC) were downloaded from The Cancer Genome Atlas (TCGA). The aberrantly expressed methylation‑driven genes in HCC and normal tissues were identified using the Limma package and the MethylMix algorithm. The Database for Annotation, Visualization and Integrated Discovery and ConsensusPathDB were used for Gene Ontology (GO) enrichment and pathway analysis. Univariate and multivariate Cox regression analyses were used to construct a prognostic risk model of HCC. Survival curve and receiver operating characteristic (ROC) curves were applied to evaluate the clinical utility of the risk model. A total of 238 methylation‑driven genes were successfully identified from cancer and normal tissues. GO enrichment analysis indicated that these genes functioned in the extracellular space, interfering with lipid metabolism in hepatocytes and regulating adaptive immune responses. In total, 14 relevant pathways were identified. The following prognostic risk model was generated: Risk score=CALML3 (degree of methylation) x (‑4.860) + CCNI2 x (2.071) + TNFRSF12A x (‑3.369) + IFITM1 x (1.203) + ENPP7P13 x (‑1.366) + DDT x (2.139) + RASAL2‑AS1 x (‑1.384) + ANKRD22 x (‑3.215). The median risk score (0.970) derived from this model was set as cutoff value for assigning patients to high‑ or low‑risk group. The 5‑year survival rate was 35.8% [95% confidence interval (CI)=27.1‑47.4%] in the high‑risk group and 61.7% (95% CI=51.4‑74.2%) in the low‑risk group (P<0.0001). The ROC curve showed an area under the curve of 0.742, indicating that this model is appropriate for predicting the survival rate of patients. Furthermore, the methylation and expression levels of two key genes, tumor necrosis factor superfamily member 12A and D‑dopachrome decarboxylase, were significantly associated with prognosis and were correlated with cg00510447, cg26808293, cg11060661 and cg16132339 methylation. In conclusion, a prognostic risk model for HCC is proposed based on the bioinformatic analysis of methylation‑driven genes. The findings of the present study may improve understanding of the pathogenesis and prognosis of HCC.
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Affiliation(s)
- Jinzhong Li
- Department of Gastroenterology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 510000, P.R. China
| | - Ning Chen
- Department of General Medicine, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 510000, P.R. China
| | - Xiaobing Gong
- Department of Gastroenterology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 510000, P.R. China
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Ferreira RG, Cardoso MV, de Souza Furtado KM, Espíndola KMM, Amorim RP, Monteiro MC. Epigenetic alterations caused by aflatoxin b1: a public health risk in the induction of hepatocellular carcinoma. Transl Res 2019; 204:51-71. [PMID: 30304666 DOI: 10.1016/j.trsl.2018.09.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 08/27/2018] [Accepted: 09/02/2018] [Indexed: 02/07/2023]
Abstract
Aflatoxin B1 (AFB1) is currently the most commonly studied mycotoxin due to its great toxicity, its distribution in a wide variety of foods such as grains and cereals and its involvement in the development of + (hepatocellular carcinoma; HCC). HCC is one of the main types of liver cancer, and has become a serious public health problem, due to its high incidence mainly in Southeast Asia and Africa. Studies show that AFB1 acts in synergy with other risk factors such as hepatitis B and C virus leading to the development of HCC through genetic and epigenetic modifications. The genetic modifications begin in the liver through the biomorphic AFB1, the AFB1-exo-8.9-Epoxy active, which interacts with DNA to form adducts of AFB1-DNA. These adducts induce mutation in codon 249, mediated by a transversion of G-T in the p53 tumor suppressor gene, causing HCC. Thus, this review provides an overview of the evidence for AFB1-induced epigenetic alterations and the potential mechanisms involved in the development of HCC, focusing on a critical analysis of the importance of severe legislation in the detection of aflatoxins.
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Affiliation(s)
- Roseane Guimarães Ferreira
- Neurosciences and Cell Biology Post-Graduation Program, Biological Sciences Institute, Federal University of Pará/UFPA, Belém, Pará, Brazil.
| | - Magda Vieira Cardoso
- Pharmaceutical Science Post-Graduation Program, Health Science Institute, Federal University of Pará/UFPA, Belém, Pará, Brazil.
| | | | | | | | - Marta Chagas Monteiro
- Neurosciences and Cell Biology Post-Graduation Program, Pharmaceutical Science Post-Graduation Program, Health Science Institute, Federal University of Pará/UFPA, Belém, Pará, Brazil.
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Xiao Y, Liu G, Gong L. Systematic Review and Meta-Analysis on the Association between Polymorphisms in Genes of IL-12 Signaling Pathway and Hepatocellular Carcinoma Risk. J Cancer 2018; 9:3583-3592. [PMID: 30310516 PMCID: PMC6171029 DOI: 10.7150/jca.26419] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 08/02/2018] [Indexed: 02/07/2023] Open
Abstract
We performed an updated meta-analysis and systematic review to explore the associations between polymorphisms in genes of IL-12 signaling pathway and hepatocellular carcinoma (HCC) risk. Diverse databases were retrieved to identify entire available studies, and odds ratios (ORs) correspondence with 95% confidence intervals (CIs) were performed to assess their associations. Finally, 6 polymorphisms in five genes of the IL-12 signaling pathway were extracted from 39 case-control studies, 26 publications. We identified that STAT4-rs7574865 polymorphism was significantly associated with an increased risk of HCC in allelic contrast, dominant, homozygote and recessive models. However, we failed to uncover any significant association between other polymorphisms in genes of IL-12 signaling pathway and HCC risk, including IL18-rs1946518 and -rs187238, IFN-γ-rs2430561, IL12A-rs568408, IL12B-rs3212227 and STAT4-rs7574865. When the subgroup analysis was conducted based on Hardy-Weinberg Equilibrium (HWE) status, we identified that IFN-γ-rs2430561 polymorphism was significantly associated with an increased risk of HCC in homozygote and recessive models of these studies whose control groups were conformed to HWE. To sum up, our study suggests that STAT4-rs7574865 is a risk factor for HCC. Further well-designed large sample size studies are warranted to shed new light on these findings.
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Affiliation(s)
- Yao Xiao
- Department of Hepatobiliary and Pancreatic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan
| | - Guodong Liu
- Department of Pancreatic Biliary Surgery, Xiangya Hospital, Central South University, Changsha, Hunan
| | - Liansheng Gong
- Department of Hepatobiliary and Pancreatic Surgery, Xiangya Hospital, Central South University, Changsha, Hunan
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