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Erenpreisa J, Vainshelbaum NM, Lazovska M, Karklins R, Salmina K, Zayakin P, Rumnieks F, Inashkina I, Pjanova D, Erenpreiss J. The Price of Human Evolution: Cancer-Testis Antigens, the Decline in Male Fertility and the Increase in Cancer. Int J Mol Sci 2023; 24:11660. [PMID: 37511419 PMCID: PMC10380301 DOI: 10.3390/ijms241411660] [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: 06/08/2023] [Revised: 07/15/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
The increasing frequency of general and particularly male cancer coupled with the reduction in male fertility seen worldwide motivated us to seek a potential evolutionary link between these two phenomena, concerning the reproductive transcriptional modules observed in cancer and the expression of cancer-testis antigens (CTA). The phylostratigraphy analysis of the human genome allowed us to link the early evolutionary origin of cancer via the reproductive life cycles of the unicellulars and early multicellulars, potentially driving soma-germ transition, female meiosis, and the parthenogenesis of polyploid giant cancer cells (PGCCs), with the expansion of the CTA multi-families, very late during their evolution. CTA adaptation was aided by retrovirus domestication in the unstable genomes of mammals, for protecting male fertility in stress conditions, particularly that of humans, as compensation for the energy consumption of a large complex brain which also exploited retrotransposition. We found that the early and late evolutionary branches of human cancer are united by the immunity-proto-placental network, which evolved in the Cambrian and shares stress regulators with the finely-tuned sex determination system. We further propose that social stress and endocrine disruption caused by environmental pollution with organic materials, which alter sex determination in male foetuses and further spermatogenesis in adults, bias the development of PGCC-parthenogenetic cancer by default.
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Affiliation(s)
| | | | - Marija Lazovska
- Molecular Genetics Scientific Laboratory, Riga Stradins University, Dzirciema 16, LV-1007 Riga, Latvia
| | - Roberts Karklins
- Molecular Genetics Scientific Laboratory, Riga Stradins University, Dzirciema 16, LV-1007 Riga, Latvia
| | - Kristine Salmina
- Latvian Biomedical Research and Study Centre, Ratsupites 1-1k, LV-1067 Riga, Latvia
| | - Pawel Zayakin
- Latvian Biomedical Research and Study Centre, Ratsupites 1-1k, LV-1067 Riga, Latvia
| | - Felikss Rumnieks
- Latvian Biomedical Research and Study Centre, Ratsupites 1-1k, LV-1067 Riga, Latvia
| | - Inna Inashkina
- Latvian Biomedical Research and Study Centre, Ratsupites 1-1k, LV-1067 Riga, Latvia
| | - Dace Pjanova
- Latvian Biomedical Research and Study Centre, Ratsupites 1-1k, LV-1067 Riga, Latvia
- Molecular Genetics Scientific Laboratory, Riga Stradins University, Dzirciema 16, LV-1007 Riga, Latvia
| | - Juris Erenpreiss
- Molecular Genetics Scientific Laboratory, Riga Stradins University, Dzirciema 16, LV-1007 Riga, Latvia
- Clinic iVF-Riga, Zala 1, LV-1010 Riga, Latvia
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Sun S, Dammann J, Lai P, Tian C. Thorough statistical analyses of breast cancer co-methylation patterns. BMC Genom Data 2022; 23:29. [PMID: 35428183 PMCID: PMC9011975 DOI: 10.1186/s12863-022-01046-w] [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: 11/27/2021] [Accepted: 04/01/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Breast cancer is one of the most commonly diagnosed cancers. It is associated with DNA methylation, an epigenetic event with a methyl group added to a cytosine paired with a guanine, i.e., a CG site. The methylation levels of different genes in a genome are correlated in certain ways that affect gene functions. This correlation pattern is known as co-methylation. It is still not clear how different genes co-methylate in the whole genome of breast cancer samples. Previous studies are conducted using relatively small datasets (Illumina 27K data). In this study, we analyze much larger datasets (Illumina 450K data).
Results
Our key findings are summarized below. First, normal samples have more highly correlated, or co-methylated, CG pairs than tumor samples. Both tumor and normal samples have more than 93% positive co-methylation, but normal samples have significantly more negatively correlated CG sites than tumor samples (6.6% vs. 2.8%). Second, both tumor and normal samples have about 94% of co-methylated CG pairs on different chromosomes, but normal samples have 470 million more CG pairs. Highly co-methylated pairs on the same chromosome tend to be close to each other. Third, a small proportion of CG sites’ co-methylation patterns change dramatically from normal to tumor. The percentage of differentially methylated (DM) sites among them is larger than the overall DM rate. Fourth, certain CG sites are highly correlated with many CG sites. The top 100 of such super-connector CG sites in tumor and normal samples have no overlaps. Fifth, both highly changing sites and super-connector sites’ locations are significantly different from the genome-wide CG sites’ locations. Sixth, chromosome X co-methylation patterns are very different from other chromosomes. Finally, the network analyses of genes associated with several sets of co-methylated CG sites identified above show that tumor and normal samples have different patterns.
Conclusions
Our findings will provide researchers with a new understanding of co-methylation patterns in breast cancer. Our ability to thoroughly analyze co-methylation of large datasets will allow researchers to study relationships and associations between different genes in breast cancer.
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Foschini MP, Morandi L, Sanchez AM, Santoro A, Mulè A, Zannoni GF, Varga Z, Moskovszky L, Cucchi MC, Moelans CB, Giove G, van Diest PJ, Masetti R. Methylation Profile of X-Chromosome-Related Genes in Male Breast Cancer. Front Oncol 2020; 10:784. [PMID: 32626651 PMCID: PMC7313421 DOI: 10.3389/fonc.2020.00784] [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: 01/20/2020] [Accepted: 04/22/2020] [Indexed: 12/19/2022] Open
Abstract
Background: Androgen receptor (AR) has been described to play a prominent role in male breast cancer (MBC). It maps on chromosome X, and recent reports indicate that X-chromosome polysomy is frequent in MBC. Since the response to anti-androgen therapy may depend on AR polysomy and on its overexpression similarly to prostate cancer, the aim of the present study was to investigate the DNA methylation level of AR and its coregulators, especially those mapped on the X-chromosome, that may influence the activity of AR in MBC. Methods: The DNA methylation level of AR, MAGEA2, MAGEA11, MAGEC1, MAGEC2, FLNA, HDAC6, and UXT, mapped on the X-chromosome, was evaluated by quantitative bisulfite-NGS. Bioinformatic analysis was performed in a Galaxy Project environment using BWA-METH, MethylDackel, and Methylation Plotter tools. The study population consisted of MBC (41 cases) compared with gynecomastia (17 cases). Results:MAGEA family members, especially MAGEA2, MAGEA11, MAGEC, and UXT and HDAC6 showed hypomethylation of several CpGs, reaching statistical significance by the Kruskal–Wallis test (p < 0.01) in MBC when compared to gynecomastia. AR showed almost no methylation at all. Conclusions: Our study demonstrated for the first time that MAGEA family members mapped on the X-chromosome and coregulators of AR are hypomethylated in MBC. This may lead to their overexpression, enhancing AR activity.
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Affiliation(s)
- Maria P Foschini
- Anatomic Pathology Section "M. Malpighi", Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Luca Morandi
- Functional MR Unit, Department of Biomedical and Neuromotor Sciences, IRCCS Istituto delle Scienze Neurologiche di Bologna, University of Bologna, Bologna, Italy
| | - Alejandro M Sanchez
- Dipartimento Scienze della Salute della donna e del Bambino e di Sanità Pubblica, Multidisciplinary Breast Center, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Angela Santoro
- Pathology Unit, Dipartimento Scienze della Salute della donna e del Bambino e di Sanità Pubblica, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Antonino Mulè
- Pathology Unit, Dipartimento Scienze della Salute della donna e del Bambino e di Sanità Pubblica, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Gian Franco Zannoni
- Pathology Unit, Dipartimento Scienze della Salute della donna e del Bambino e di Sanità Pubblica, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Zsuzsanna Varga
- Institute of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Linda Moskovszky
- Institute of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Maria C Cucchi
- Unit of Breast Surgery, Department of Oncology, Bellaria Hospital, AUSL Bologna, Bologna, Italy
| | - Cathy B Moelans
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Gianluca Giove
- Anatomic Pathology Section "M. Malpighi", Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Paul J van Diest
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Riccardo Masetti
- Dipartimento Scienze della Salute della donna e del Bambino e di Sanità Pubblica, Multidisciplinary Breast Center, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
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Toropov AA, Toropova AP, Raitano G, Benfenati E. CORAL: Building up QSAR models for the chromosome aberration test. Saudi J Biol Sci 2018; 26:1101-1106. [PMID: 31516335 PMCID: PMC6734133 DOI: 10.1016/j.sjbs.2018.05.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 04/23/2018] [Accepted: 05/06/2018] [Indexed: 12/13/2022] Open
Abstract
A high level of chromosomal aberrations in peripheral blood lymphocytes may be an early marker of cancer risk, but data on risk of specific cancers and types of chromosomal aberrations are limited. Consequently, the development of predictive models for chromosomal aberrations test is important task. Majority of models for chromosomal aberrations test are so-called knowledge-based rules system. The CORAL software (http://www.insilico.eu/coral, abbreviation of “CORrelation And Logic”) is an alternative for knowledge-based rules system. In contrast to knowledge-based rules system, the CORAL software gives possibility to estimate the influence upon the predictive potential of a model of different molecular alerts as well as different splits into the training set and validation set. This possibility is not available for the approaches based on the knowledge-based rules system. Quantitative Structure–Activity Relationships (QSAR) for chromosome aberration test are established for five random splits into the training, calibration, and validation sets. The QSAR approach is based on representation of the molecular structure by simplified molecular input-line entry system (SMILES) without data on physicochemical and/or biochemical parameters. In spite of this limitation, the statistical quality of these models is quite good.
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Affiliation(s)
| | - Alla P. Toropova
- Corresponding author at: Laboratory of Environmental Chemistry and Toxicology, IRCCS – Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa 19, 20156 Milano, Italy.
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Zhou W, Laird PW, Shen H. Comprehensive characterization, annotation and innovative use of Infinium DNA methylation BeadChip probes. Nucleic Acids Res 2017; 45:e22. [PMID: 27924034 PMCID: PMC5389466 DOI: 10.1093/nar/gkw967] [Citation(s) in RCA: 308] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 10/12/2016] [Indexed: 12/13/2022] Open
Abstract
Illumina Infinium DNA Methylation BeadChips represent the most widely used genome-scale DNA methylation assays. Existing strategies for masking Infinium probes overlapping repeats or single nucleotide polymorphisms (SNPs) are based largely on ad hoc assumptions and subjective criteria. In addition, the recently introduced MethylationEPIC (EPIC) array expands on the utility of this platform, but has not yet been well characterized. We present in this paper an extensive characterization of probes on the EPIC and HM450 microarrays, including mappability to the latest genome build, genomic copy number of the 3΄ nested subsequence and influence of polymorphisms including a previously unrecognized color channel switch for Type I probes. We show empirical evidence for exclusion criteria for underperforming probes, providing a sounder basis than current ad hoc criteria for exclusion. In addition, we describe novel probe uses, exemplified by the addition of a total of 1052 SNP probes to the existing 59 explicit SNP probes on the EPIC array and the use of these probes to predict ethnicity. Finally, we present an innovative out-of-band color channel application for the dual use of 62 371 probes as internal bisulfite conversion controls.
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Affiliation(s)
- Wanding Zhou
- Center for Epigenetics, Van Andel Research Institute, 333 Bostwick Ave NE, Grand Rapids, MI 49503, USA
| | - Peter W Laird
- Center for Epigenetics, Van Andel Research Institute, 333 Bostwick Ave NE, Grand Rapids, MI 49503, USA
| | - Hui Shen
- Center for Epigenetics, Van Andel Research Institute, 333 Bostwick Ave NE, Grand Rapids, MI 49503, USA
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Abstract
X-chromosome inactivation, which was discovered by Mary Lyon in 1961 results in random silencing of one X chromosome in female mammals. This review is dedicated to Mary Lyon, who passed away last year. She predicted many of the features of X inactivation, for e.g., the existence of an X inactivation center, the role of L1 elements in spreading of silencing and the existence of genes that escape X inactivation. Starting from her published work here we summarize advances in the field.
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Sticca T, Caberg JH, Wenric S, Poulet C, Herens C, Jamar M, Josse C, El Guendi S, Max S, Beguin Y, Gothot A, Caers J, Bours V. Genomic studies of multiple myeloma reveal an association between X chromosome alterations and genomic profile complexity. Genes Chromosomes Cancer 2016; 56:18-27. [DOI: 10.1002/gcc.22397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 07/20/2016] [Accepted: 07/20/2016] [Indexed: 01/29/2023] Open
Affiliation(s)
- Tiberio Sticca
- Laboratory of Human Genetics; University of Liège, GIGA-Research; Liège Belgium
| | | | - Stephane Wenric
- Laboratory of Human Genetics; University of Liège, GIGA-Research; Liège Belgium
| | - Christophe Poulet
- Laboratory of Human Genetics; University of Liège, GIGA-Research; Liège Belgium
| | - Christian Herens
- Department of Human Genetics; University Hospital (CHU); Liège Belgium
| | - Mauricette Jamar
- Department of Human Genetics; University Hospital (CHU); Liège Belgium
| | - Claire Josse
- Laboratory of Human Genetics; University of Liège, GIGA-Research; Liège Belgium
| | - Sonia El Guendi
- Laboratory of Human Genetics; University of Liège, GIGA-Research; Liège Belgium
| | - Stéphanie Max
- Department of Hematology and Immuno-Hematology; University Hospital (CHU); Liège Belgium
| | - Yves Beguin
- Laboratory of Hematology; University of Liège, GIGA-Research; Liège Belgium
- Department of Clinical Hematology; University Hospital (CHU); Liège Belgium
| | - André Gothot
- Department of Hematology and Immuno-Hematology; University Hospital (CHU); Liège Belgium
| | - Jo Caers
- Laboratory of Hematology; University of Liège, GIGA-Research; Liège Belgium
- Department of Clinical Hematology; University Hospital (CHU); Liège Belgium
| | - Vincent Bours
- Laboratory of Human Genetics; University of Liège, GIGA-Research; Liège Belgium
- Department of Human Genetics; University Hospital (CHU); Liège Belgium
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Wu C, Sun Z. X chromosome abnormal inactivation: a unique factor for women's diseases? Epigenomics 2016; 8:447-50. [DOI: 10.2217/epi.16.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Cuijiao Wu
- Department of Histology & Embryology, Qingdao University Medical School, Qingdao, Shandong, China
| | - Zhifu Sun
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
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