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Xu S, Xie B, Liu H, Liu J, Wang M, Zhong L, Zhou J, Wen Z, Zhang L, Chen X, Zhang S. 5 mC modification of steroid hormone biosynthesis-related genes orchestrates feminization of channel catfish induced by high-temperature. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 356:124310. [PMID: 38838810 DOI: 10.1016/j.envpol.2024.124310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 06/01/2024] [Accepted: 06/03/2024] [Indexed: 06/07/2024]
Abstract
To elucidate the mechanism behind channel catfish feminization induced by high temperature, gonad samples were collected from XY pseudo-females and wild-type females and subjected to high-throughput sequencing for Whole-Genome-Bisulfite-Seq (WGBS) and transcriptome sequencing (RNA-Seq). The analysis revealed 50 differentially methylated genes between wild-type females and XY pseudo-females, identified through the analysis of KEGG pathways and GO enrichment in the promoter of the genome and differentially methylated regions (DMRs). Among these genes, multiple differential methylation sites observed within the srd5a2 gene. Repeatability tests confirmed 7 differential methylation sites in the srd5a2 gene in XY pseudo-females compared to normal males, with 1 specific differential methylation site (16608174) distinguishing XY pseudo-females from normal females. Interestingly, the expression of these genes in the transcriptome showed no difference between wild-type females and XY pseudo-females. Our study concluded that methylation of the srd5a2 gene sequence leads to decreased expression, which inhibits testosterone synthesis while promoting the synthesis of 17β-estradiol from testosterone. This underscores the significance of the srd5a2 gene in the sexual differentiation of channel catfish, as indicated by the ipu00140 KEGG pathway analysis.
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Affiliation(s)
- Siqi Xu
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210027, China; Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Fisheries, Southwest University, Chongqing 402460, China
| | - Bingjie Xie
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210027, China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Hongyan Liu
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210027, China; The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Ju Liu
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210027, China
| | - Minghua Wang
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210027, China; The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Liqiang Zhong
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210027, China; The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China
| | - Jian Zhou
- Fisheries Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 611731, China
| | - Zhengyong Wen
- Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, Neijiang Normal University, Neijiang 641100, China
| | - Lu Zhang
- Fisheries Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 611731, China
| | - Xiaohui Chen
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210027, China; The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China; College of Marine Science and Fisheries, Jiangsu Ocean University, Lianyungang 222005, China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Shiyong Zhang
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210027, China; The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing 210014, China; College of Marine Science and Fisheries, Jiangsu Ocean University, Lianyungang 222005, China.
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Schwartz M, Ibadioune S, Chansavang A, Vacher S, Caputo SM, Delhomelle H, Wong J, Abidallah K, Moncoutier V, Becette V, Popova T, Suybeng V, De Pauw A, Stern MH, Colas C, Mouret-Fourme E, Stoppa-Lyonnet D, Golmard L, Bieche I, Masliah-Planchon J. Mosaic BRCA1 promoter methylation contribution in hereditary breast/ovarian cancer pedigrees. J Med Genet 2024; 61:284-288. [PMID: 37748860 DOI: 10.1136/jmg-2023-109325] [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: 04/07/2023] [Accepted: 09/05/2023] [Indexed: 09/27/2023]
Abstract
PURPOSE Mosaic BRCA1 promoter methylation (BRCA1meth) increases the risk of early-onset breast cancer, triple-negative breast cancer and ovarian cancer. As mosaic BRCA1meth are believed to occur de novo, their role in family breast/ovarian cancer has not been assessed. PATIENTS Blood-derived DNA from 20 unrelated affected cases from families with aggregation of breast/ovarian cancer, but with no germline pathogenic variants in BRCA1/2, PALB2 or RAD51C/D, were screened by methylation-sensitive high-resolution melting. CpG analysis was performed by pyrosequencing on blood and buccal swab. Two probands carried a pathogenic variant in a moderate-penetrance gene (ATM and BARD1), and 8 of 18 others (44%) carried BRCA1meth (vs none of the 20 age-matched controls). Involvement of BRCA1 in tumourigenesis in methylated probands was demonstrated in most tested cases by detection of a loss of heterozygosity and a homologous recombination deficiency signature. Among the eight methylated probands, two had relatives with breast cancer with detectable BRCA1meth in blood, including one with high methylation levels in two non-tumour tissues. CONCLUSIONS The high prevalence of mosaic BRCA1meth in patients with breast/ovarian cancer with affected relatives, as well as this first description of a family aggregation of mosaic BRCA1meth, shows how this de novo event can contribute to hereditary breast/ovarian cancer pedigrees.
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Affiliation(s)
- Mathias Schwartz
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
- UMR3244, Curie Institute, Paris, France
| | - Sabrina Ibadioune
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Albain Chansavang
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Sophie Vacher
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Sandrine M Caputo
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Hélène Delhomelle
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Jennifer Wong
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Khadija Abidallah
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Virginie Moncoutier
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Véronique Becette
- Paris Sciences & Lettres Research University, Paris, France
- Department of Pathology, Curie Institute, Saint-Cloud, France
| | - Tatiana Popova
- Paris Sciences & Lettres Research University, Paris, France
- DNA Repair and Uveal Melanoma (D.R.U.M.), Inserm U830, Curie Institute, Paris, France
| | - Voreak Suybeng
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Antoine De Pauw
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Marc-Henri Stern
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
- DNA Repair and Uveal Melanoma (D.R.U.M.), Inserm U830, Curie Institute, Paris, France
| | - Chrystelle Colas
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
- DNA Repair and Uveal Melanoma (D.R.U.M.), Inserm U830, Curie Institute, Paris, France
| | - Emmanuelle Mouret-Fourme
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Dominique Stoppa-Lyonnet
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
- Université de Paris Cité, Paris, France
| | - Lisa Golmard
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
| | - Ivan Bieche
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
- Université de Paris Cité, Paris, France
| | - Julien Masliah-Planchon
- Department of genetics, Curie Institute Hospital Group, Paris, France
- Paris Sciences & Lettres Research University, Paris, France
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Schwartz M, Ibadioune S, Vacher S, Villy MC, Trabelsi-Grati O, Le Gall J, Caputo SM, Delhomelle H, Warcoin M, Moncoutier V, Bourneix C, Boutry-Kryza N, De Pauw A, Stern MH, Buecher B, Mouret-Fourme E, Colas C, Stoppa-Lyonnet D, Masliah-Planchon J, Golmard L, Bieche I. Male breast cancer: No evidence for mosaic BRCA1 promoter methylation involvement. Breast 2024; 73:103620. [PMID: 38096711 PMCID: PMC10761895 DOI: 10.1016/j.breast.2023.103620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 01/06/2024] Open
Abstract
Breast cancers (BC) are rare in men and are often caused by constitutional predisposing factors. In women, mosaic BRCA1 promoter methylations (MBPM) are frequent events, detected in 4-8% of healthy subjects. This constitutional epimutation increases risk of early-onset and triple-negative BC. However, the role of MBPM in male BC predisposition has never been assessed. We screened 40 blood samples from men affected by BC, and performed extensive tumour analysis on MBPM-positive patients. We detected two patients carrying MBPM. Surprisingly, tumour analysis revealed that neither of these two male BCs were caused by the constitutional BRCA1 epimutations carried by the patients.
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Affiliation(s)
- Mathias Schwartz
- Department of genetics, Curie Institute, Paris, France; UMR3244, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France.
| | - Sabrina Ibadioune
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | - Sophie Vacher
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | - Marie-Charlotte Villy
- Department of genetics, Curie Institute, Paris, France; Université Paris Cité, Paris, France
| | - Olfa Trabelsi-Grati
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | - Jessica Le Gall
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | - Sandrine M Caputo
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | - Hélène Delhomelle
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | - Mathilde Warcoin
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | - Virginie Moncoutier
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | - Christine Bourneix
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | | | - Antoine De Pauw
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | - Marc-Henri Stern
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France; DNA Repair and Uveal Melanoma (D.R.U.M.), Inserm U830, Paris, France
| | - Bruno Buecher
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | - Emmanuelle Mouret-Fourme
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | - Chrystelle Colas
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | - Dominique Stoppa-Lyonnet
- Department of genetics, Curie Institute, Paris, France; Université Paris Cité, Paris, France; DNA Repair and Uveal Melanoma (D.R.U.M.), Inserm U830, Paris, France
| | - Julien Masliah-Planchon
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | - Lisa Golmard
- Department of genetics, Curie Institute, Paris, France; Paris Sciences & Lettres Research University, Paris, France
| | - Ivan Bieche
- Department of genetics, Curie Institute, Paris, France; Université Paris Cité, Paris, France
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A Heuristic Machine Learning-Based Optimization Technique to Predict Lung Cancer Patient Survival. COMPUTATIONAL INTELLIGENCE AND NEUROSCIENCE 2023; 2023:4506488. [PMID: 36776617 PMCID: PMC9911240 DOI: 10.1155/2023/4506488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/26/2022] [Accepted: 11/24/2022] [Indexed: 02/05/2023]
Abstract
Cancer has been a significant threat to human health and well-being, posing the biggest obstacle in the history of human sickness. The high death rate in cancer patients is primarily due to the complexity of the disease and the wide range of clinical outcomes. Increasing the accuracy of the prediction is equally crucial as predicting the survival rate of cancer patients, which has become a key issue of cancer research. Many models have been suggested at the moment. However, most of them simply use single genetic data or clinical data to construct prediction models for cancer survival. There is a lot of emphasis in present survival studies on determining whether or not a patient will survive five years. The personal issue of how long a lung cancer patient will survive remains unanswered. The proposed technique Naive Bayes and SSA is estimating the overall survival time with lung cancer. Two machine learning challenges are derived from a single customized query. To begin with, determining whether a patient will survive for more than five years is a simple binary question. The second step is to develop a five-year survival model using regression analysis. When asked to forecast how long a lung cancer patient would survive within five years, the mean absolute error (MAE) of this technique's predictions is accurate within a month. Several biomarker genes have been associated with lung cancers. The accuracy, recall, and precision achieved from this algorithm are 98.78%, 98.4%, and 98.6%, respectively.
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Southey MC, Dugué PA. Improving breast cancer risk prediction with epigenetic risk factors. Nat Rev Clin Oncol 2022; 19:363-364. [PMID: 35351995 DOI: 10.1038/s41571-022-00622-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia. .,Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia. .,Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Parkville, Victoria, Australia.
| | - Pierre-Antoine Dugué
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia.,Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia.,Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
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6
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Čelešnik H, Potočnik U. Peripheral Blood Transcriptome in Breast Cancer Patients as a Source of Less Invasive Immune Biomarkers for Personalized Medicine, and Implications for Triple Negative Breast Cancer. Cancers (Basel) 2022; 14:cancers14030591. [PMID: 35158858 PMCID: PMC8833511 DOI: 10.3390/cancers14030591] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 01/14/2022] [Accepted: 01/19/2022] [Indexed: 12/21/2022] Open
Abstract
Simple Summary Triple-negative breast cancer (TNBC) is an aggressive and heterogeneous breast cancer (BC) type which is difficult to treat and accompanied by disease recurrence. A better understanding of TNBC and the identification of novel biomarkers is needed to facilitate clinical decisions. Immune-related biomarkers are of particular interest, since immune responses play an important role in BC outcome. Transcriptome studies of peripheral blood cells can help us to understand the systemic immune responses to cancer cells and the mechanisms underlying cancer initiation and progression. They enable the identification of novel immune biomarkers for early cancer detection and personalized BC management and may bring forward new immunotherapy options. Recent transcriptome analyses of peripheral blood cells have delineated novel BC-patient immune subgroups. This categorization has implications for cancer prognosis, the identification of patients likely to benefit from immunotherapy, and treatment efficacy monitoring. Additionally, transcriptome studies have identified TNBC-enriched blood transcriptional signatures that can differentiate TNBC from other classical BC subtypes. Abstract Transcriptome studies of peripheral blood cells can advance our understanding of the systemic immune response to the presence of cancer and the mechanisms underlying cancer onset and progression. This enables the identification of novel minimally invasive immune biomarkers for early cancer detection and personalized cancer management and may bring forward new immunotherapy options. Recent blood gene expression analyses in breast cancer (BC) identified distinct patient subtypes that differed in the immune reaction to cancer and were distinct from the clinical BC subtypes, which are categorized based on expression of specific receptors on tumor cells. Introducing new BC subtypes based on peripheral blood gene expression profiles may be appropriate, since it may assist in BC prognosis, the identification of patients likely to benefit from immunotherapy, and treatment efficacy monitoring. Triple-negative breast cancer (TNBC) is an aggressive, heterogeneous, and difficult-to-treat disease, and identification of novel biomarkers for this BC is crucial for clinical decision-making. A few studies have reported TNBC-enriched blood transcriptional signatures, mostly related to strong inflammation and augmentation of altered immune signaling, that can differentiate TNBC from other classical BC subtypes and facilitate diagnosis. Future research is geared toward transitioning from expression signatures in unfractionated blood cells to those in immune cell subpopulations.
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Affiliation(s)
- Helena Čelešnik
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova Ulica 17, 2000 Maribor, Slovenia;
- Center for Human Genetics & Pharmacogenomics, Faculty of Medicine, University of Maribor, Taborska Ulica 8, 2000 Maribor, Slovenia
| | - Uroš Potočnik
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova Ulica 17, 2000 Maribor, Slovenia;
- Center for Human Genetics & Pharmacogenomics, Faculty of Medicine, University of Maribor, Taborska Ulica 8, 2000 Maribor, Slovenia
- Department for Science and Research, University Medical Centre Maribor, Ljubljanska Ulica 5, 2000 Maribor, Slovenia
- Correspondence: ; Tel.: +386-2-330-5874
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Wang T, Ala-Korpela M. Commentary: Polygenic risk for breast cancer: in search for potential clinical utility. Int J Epidemiol 2022; 50:1911-1913. [PMID: 34999886 PMCID: PMC9295014 DOI: 10.1093/ije/dyab230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/12/2021] [Indexed: 11/12/2022] Open
Affiliation(s)
- Tingting Wang
- Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Mika Ala-Korpela
- Computational Medicine, Faculty of Medicine, University of Oulu and Biocenter Oulu, Oulu, Finland
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
- NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio, Finland
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8
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Buha A, Manic L, Maric D, Tinkov A, Skolny A, Antonijevic B, Hayes AW. The effects of endocrine-disrupting chemicals (EDCs) on the epigenome-A short overview. TOXICOLOGY RESEARCH AND APPLICATION 2022. [DOI: 10.1177/23978473221115817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
To understand the effects of endocrine-disrupting chemicals (EDCs), the mechanism(s) by which EDCs exert their harmful effects on humans and their offspring needs careful examination and clarification. Epigenetic modification, including DNA methylation, expression of aberrant microRNA (miRNA), and histone modification, is one mechanism assumed to be a primary pathway leading to the untoward effects of endocrine disruptors. However, it remains unclear whether such epigenetic changes caused by EDCs are truly predicting adverse outcomes. Therefore, it is important to understand the relationship between epigenetic changes and various endocrine endpoints or markers. This paper highlights the possibility that certain chemicals (Cd, As, Pb, bisphenol A, phthalate, polychlorinated biphenyls) reported having ED properties may adversely affect the epigenome. Electronic database sources PubMed, SCOPUS, JSTOR, and the Google Scholar web browser were used to search the literature. The search was based on keywords from existing theories and basic knowledge of endocrine disorders and epigenetic effects, well-known EDCs, and previous search results. Unclear and often conflicting results regarding the effects of EDCs indicate the need for further research to support better risk assessments and management of these chemicals.
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Affiliation(s)
- Aleksandra Buha
- Department of Toxicology “Akademik Danilo Soldatović”, University of Belgrade – Faculty of Pharmacy, Belgrade, Serbia
| | - Luka Manic
- Department of Toxicology “Akademik Danilo Soldatović”, University of Belgrade – Faculty of Pharmacy, Belgrade, Serbia
| | - Djurdjica Maric
- Department of Toxicology “Akademik Danilo Soldatović”, University of Belgrade – Faculty of Pharmacy, Belgrade, Serbia
| | - Alexey Tinkov
- Laboratory of Ecobiomonitoring and Quality Control, Yaroslavl State University, Yaroslavl, Russia
- Laboratory of Molecular Dietetics, IM Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Anatoly Skolny
- Laboratory of Ecobiomonitoring and Quality Control, Yaroslavl State University, Yaroslavl, Russia
- Laboratory of Molecular Dietetics, IM Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Biljana Antonijevic
- Department of Toxicology “Akademik Danilo Soldatović”, University of Belgrade – Faculty of Pharmacy, Belgrade, Serbia
| | - A. Wallace Hayes
- Center for Environmental Occupational Risk Analysis and Management, College of Public Health, University of South Florida, Tampa, FL, USA
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI, USA
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9
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Yu C, Dugué PA, Dowty JG, Hammet F, Joo JE, Wong EM, Hosseinpour M, Giles GG, Hopper JL, Nguyen-Dumont T, MacInnis RJ, Southey MC. Repeatability of methylation measures using a QIAseq targeted methyl panel and comparison with the Illumina HumanMethylation450 assay. BMC Res Notes 2021; 14:394. [PMID: 34689793 PMCID: PMC8543877 DOI: 10.1186/s13104-021-05809-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/11/2021] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVE In previous studies using Illumina Infinium methylation arrays, we have identified DNA methylation marks associated with cancer predisposition and progression. In the present study, we have sought to find appropriate technology to both technically validate our data and expand our understanding of DNA methylation in these genomic regions. Here, we aimed to assess the repeatability of methylation measures made using QIAseq targeted methyl panel and to compare them with those obtained from the Illumina HumanMethylation450 (HM450K) assay. We included in the analysis high molecular weight DNA extracted from whole blood (WB) and DNA extracted from formalin-fixed paraffin-embedded tissues (FFPE). RESULTS The repeatability of QIAseq-methylation measures was assessed at 40 CpGs, using the Intraclass Correlation Coefficient (ICC). The mean ICCs and 95% confidence intervals (CI) were 0.72 (0.62-0.81), 0.59 (0.47-0.71) and 0.80 (0.73-0.88) for WB, FFPE and both sample types combined, respectively. For technical replicates measured using QIAseq and HM450K, the mean ICCs (95% CI) were 0.53 (0.39-0.68), 0.43 (0.31-0.56) and 0.70 (0.59-0.80), respectively. Bland-Altman plots indicated good agreement between QIAseq and HM450K measurements. These results demonstrate that the QIAseq targeted methyl panel produces reliable and reproducible methylation measurements across the 40 CpGs that were examined.
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Affiliation(s)
- Chenglong Yu
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Victoria, Australia
| | - Pierre-Antoine Dugué
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Victoria, Australia
- Cancer Council Victoria, Cancer Epidemiology Division, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - James G Dowty
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - Fleur Hammet
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Victoria, Australia
| | - JiHoon E Joo
- Department of Clinical Pathology, The Melbourne Medical School, The University of Melbourne, Melbourne, VIC, Australia
| | - Ee Ming Wong
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Victoria, Australia
| | - Mahnaz Hosseinpour
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Victoria, Australia
| | - Graham G Giles
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Victoria, Australia
- Cancer Council Victoria, Cancer Epidemiology Division, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - Tu Nguyen-Dumont
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Victoria, Australia
- Department of Clinical Pathology, The Melbourne Medical School, The University of Melbourne, Melbourne, VIC, Australia
| | - Robert J MacInnis
- Cancer Council Victoria, Cancer Epidemiology Division, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Victoria, Australia.
- Cancer Council Victoria, Cancer Epidemiology Division, Melbourne, Australia.
- Department of Clinical Pathology, The Melbourne Medical School, The University of Melbourne, Melbourne, VIC, Australia.
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10
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Kresovich JK, Xu Z, O'Brien KM, Shi M, Weinberg CR, Sandler DP, Taylor JA. Blood DNA methylation profiles improve breast cancer prediction. Mol Oncol 2021; 16:42-53. [PMID: 34411412 PMCID: PMC8732352 DOI: 10.1002/1878-0261.13087] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 06/24/2021] [Accepted: 08/18/2021] [Indexed: 12/21/2022] Open
Abstract
Although blood DNA methylation (DNAm) profiles are reported to be associated with breast cancer incidence, they have not been widely used in breast cancer risk assessment. Among a breast cancer case–cohort of 2774 women (1551 cases) in the Sister Study, we used candidate CpGs and DNAm estimators of physiologic characteristics to derive a methylation‐based breast cancer risk score, mBCRS. Overall, 19 CpGs and five DNAm estimators were selected using elastic net regularization to comprise mBCRS. In a test set, higher mBCRS was positively associated with breast cancer incidence, showing similar strength to the polygenic risk score (PRS) based on 313 single nucleotide polymorphisms (313 SNPs). Area under the curve for breast cancer prediction was 0.60 for self‐reported risk factors (RFs), 0.63 for PRS, and 0.63 for mBCRS. Adding mBCRS to PRS and RFs improved breast cancer prediction from 0.66 to 0.71. mBCRS findings were replicated in a nested case–control study within the EPIC‐Italy cohort. These results suggest that mBCRS, a risk score derived using blood DNAm, can be used to enhance breast cancer prediction.
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Affiliation(s)
- Jacob K Kresovich
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Zongli Xu
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Katie M O'Brien
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Min Shi
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Clarice R Weinberg
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Jack A Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA.,Epigenetic and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
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11
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Franchet C, Hoffmann JS, Dalenc F. Recent Advances in Enhancing the Therapeutic Index of PARP Inhibitors in Breast Cancer. Cancers (Basel) 2021; 13:cancers13164132. [PMID: 34439286 PMCID: PMC8392832 DOI: 10.3390/cancers13164132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 12/27/2022] Open
Abstract
Simple Summary Two to three percent of breast cancer patients harbor germline mutation of either BRCA1 or BRCA2 genes. Their tumor cells are deficient in homologous recombination, a BRCA-dependent DNA repair machinery. These deficient cells survive thanks to the PARP-mediated alternative pathway. Therefore, PARP inhibitors have already shown some level of efficiency in the treatment of metastatic breast cancer patients. Unfortunately, some tumor cells inevitably resist PARP inhibitors by different mechanisms. In this review, we (i) present the notion of homologous recombination deficiency and its evaluation methods, (ii) detail the PARP inhibitor clinical trials in breast cancer, (iii) briefly describe the mechanisms to PARP inhibitors resistance, and (iv) discuss some strategies currently under evaluation to enhance the therapeutic index of PARP inhibitors in breast cancer. Abstract As poly-(ADP)-ribose polymerase (PARP) inhibition is synthetic lethal with the deficiency of DNA double-strand (DSB) break repair by homologous recombination (HR), PARP inhibitors (PARPi) are currently used to treat breast cancers with mutated BRCA1/2 HR factors. Unfortunately, the increasingly high rate of PARPi resistance in clinical practice has dented initial hopes. Multiple resistance mechanisms and acquired vulnerabilities revealed in vitro might explain this setback. We describe the mechanisms and vulnerabilities involved, including newly identified modes of regulation of DSB repair that are now being tested in large cohorts of patients and discuss how they could lead to novel treatment strategies to improve the therapeutic index of PARPi.
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Affiliation(s)
- Camille Franchet
- Laboratoire de Pathologie and Institut Claudius Regaud, Institut Universitaire du Cancer de Toulouse-Oncopole, 1 Av. Irène Joliot-Curie, 31100 Toulouse, France;
| | - Jean-Sébastien Hoffmann
- Laboratoire d’Excellence Toulouse Cancer (TOUCAN), Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, 31037 Toulouse, France;
| | - Florence Dalenc
- Institut Claudius Regaud, Institut Universitaire du Cancer de Toulouse-Oncopole, 1 Av. Irène Joliot-Curie, 31100 Toulouse, France
- Correspondence:
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Nikolaienko O, Lønning PE, Knappskog S. ramr: an R/Bioconductor package for detection of rare aberrantly methylated regions. Bioinformatics 2021; 38:133-140. [PMID: 34383893 PMCID: PMC8696093 DOI: 10.1093/bioinformatics/btab586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 06/26/2021] [Accepted: 08/11/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION With recent advances in the field of epigenetics, the focus is widening from large and frequent disease- or phenotype-related methylation signatures to rare alterations transmitted mitotically or transgenerationally (constitutional epimutations). Merging evidence indicate that such constitutional alterations, albeit occurring at a low mosaic level, may confer risk of disease later in life. Given their inherently low incidence rate and mosaic nature, there is a need for bioinformatic tools specifically designed to analyze such events. RESULTS We have developed a method (ramr) to identify aberrantly methylated DNA regions (AMRs). ramr can be applied to methylation data obtained by array or next-generation sequencing techniques to discover AMRs being associated with elevated risk of cancer as well as other diseases. We assessed accuracy and performance metrics of ramr and confirmed its applicability for analysis of large public datasets. Using ramr we identified aberrantly methylated regions that are known or may potentially be associated with development of colorectal cancer and provided functional annotation of AMRs that arise at early developmental stages. AVAILABILITY AND IMPLEMENTATION The R package is freely available at https://github.com/BBCG/ramr and https://bioconductor.org/packages/ramr. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Per Eystein Lønning
- K. G. Jebsen Center for Genome-Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen, Norway,Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Stian Knappskog
- K. G. Jebsen Center for Genome-Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen, Norway,Department of Oncology, Haukeland University Hospital, Bergen, Norway
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Sturgeon SR, Sela DA, Browne EP, Einson J, Rani A, Halabi M, Kania T, Keezer A, Balasubramanian R, Ziegler RG, Schairer C, Kelsey KT, Arcaro KF. Prediagnostic White Blood Cell DNA Methylation and Risk of Breast Cancer in the Prostate Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO) Cohort. Cancer Epidemiol Biomarkers Prev 2021; 30:1575-1581. [PMID: 34108140 PMCID: PMC10825794 DOI: 10.1158/1055-9965.epi-20-1717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/11/2021] [Accepted: 05/21/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND White blood cell (WBC) DNA may contain methylation patterns that are associated with subsequent breast cancer risk. Using a high-throughput array and samples collected, on average, 1.3 years prior to diagnosis, a case-cohort analysis nested in the prospective Sister Study identified 250 individual CpG sites that were differentially methylated between breast cancer cases and noncases. We examined five of the top 40 CpG sites in a case-control study nested in the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO) Cohort. METHODS We investigated the associations between prediagnostic WBC DNA methylation in 297 breast cancer cases and 297 frequency-matched controls. Two WBC DNA specimens from each participant were used: a proximate sample collected 1 to 2.9 years and a distant sample collected 4.2-7.3 years prior to diagnosis in cases or the comparable timepoints in controls. WBC DNA methylation level was measured using targeted bisulfite amplification sequencing. We used logistic regression to obtain ORs and 95% confidence intervals (CI). RESULTS A one-unit increase in percent methylation in ERCC1 in proximate WBC DNA was associated with increased breast cancer risk (adjusted OR = 1.29; 95% CI, 1.06-1.57). However, a one-unit increase in percent methylation in ERCC1 in distant WBC DNA was inversely associated with breast cancer risk (adjusted OR = 0.83; 95% CI, 0.69-0.98). None of the other ORs met the threshold for statistical significance. CONCLUSIONS There was no convincing pattern between percent methylation in the five CpG sites and breast cancer risk. IMPACT The link between prediagnostic WBC DNA methylation marks and breast cancer, if any, is poorly understood.
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Affiliation(s)
- Susan R Sturgeon
- Department of Biostatistics and Epidemiology, University of Massachusetts, Amherst, Massachusetts.
| | - David A Sela
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts
| | - Eva P Browne
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts
| | - Jonah Einson
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts
| | - Asha Rani
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts
| | - Mohamed Halabi
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts
| | - Thomas Kania
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts
| | - Andrew Keezer
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts
| | - Raji Balasubramanian
- Department of Biostatistics and Epidemiology, University of Massachusetts, Amherst, Massachusetts
| | - Regina G Ziegler
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Catherine Schairer
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Karl T Kelsey
- Department of Epidemiology, Department of Pathology, and Department of Laboratory Medicine, Brown University, Providence, Rhode Island
| | - Kathleen F Arcaro
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts
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15
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Houghton SC, Hankinson SE. Cancer Progress and Priorities: Breast Cancer. Cancer Epidemiol Biomarkers Prev 2021; 30:822-844. [PMID: 33947744 DOI: 10.1158/1055-9965.epi-20-1193] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/13/2020] [Accepted: 02/19/2021] [Indexed: 12/24/2022] Open
Affiliation(s)
- Serena C Houghton
- Department of Biostatistics and Epidemiology, University of Massachusetts Amherst, Amherst, Massachusetts.
| | - Susan E Hankinson
- Department of Biostatistics and Epidemiology, University of Massachusetts Amherst, Amherst, Massachusetts
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Understanding breast cancer heterogeneity through non-genetic heterogeneity. Breast Cancer 2021; 28:777-791. [PMID: 33723745 DOI: 10.1007/s12282-021-01237-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 03/04/2021] [Indexed: 01/01/2023]
Abstract
Intricacy in treatment and diagnosis of breast cancer has been an obstacle due to genotype and phenotype heterogeneity. Understanding of non-genetic heterogeneity mechanisms along with considering role of genetic heterogeneity may fill the gaps in landscape painting of heterogeneity. The main factors contribute to non-genetic heterogeneity including: transcriptional pulsing/bursting or discontinuous transcriptions, stochastic partitioning of components at cell division and various signal transduction from tumor ecosystem. Throughout this review, we desired to provide a conceptual framework focused on non-genetic heterogeneity, which has been intended to offer insight into prediction, diagnosis and treatment of breast cancer.
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