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Inkster AM, Konwar C, Peñaherrera MS, Brain U, Khan A, Price EM, Schuetz JM, Portales-Casamar É, Burt A, Marsit CJ, Vaillancourt C, Oberlander TF, Robinson WP. Profiling placental DNA methylation associated with maternal SSRI treatment during pregnancy. Sci Rep 2022; 12:22576. [PMID: 36585414 PMCID: PMC9803674 DOI: 10.1038/s41598-022-26071-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 12/08/2022] [Indexed: 12/31/2022] Open
Abstract
Selective serotonin reuptake inhibitors (SSRIs) for treatment of prenatal maternal depression have been associated with neonatal neurobehavioral disturbances, though the molecular mechanisms remain poorly understood. In utero exposure to SSRIs may affect DNA methylation (DNAme) in the human placenta, an epigenetic mark that is established during development and is associated with gene expression. Chorionic villus samples from 64 human placentas were profiled with the Illumina MethylationEPIC BeadChip; clinical assessments of maternal mood and SSRI treatment records were collected at multiple time points during pregnancy. Case distribution was 20 SSRI-exposed cases and 44 SSRI non-exposed cases. Maternal depression was defined using a mean maternal Hamilton Depression score > 8 to indicate symptomatic depressed mood ("maternally-depressed"), and we further classified cases into SSRI-exposed, maternally-depressed (n = 14); SSRI-exposed, not maternally-depressed (n = 6); SSRI non-exposed, maternally-depressed (n = 20); and SSRI non-exposed, not maternally-depressed (n = 24). For replication, Illumina 450K DNAme profiles were obtained from 34 additional cases from an independent cohort (n = 17 SSRI-exposed, n = 17 SSRI non-exposed). No CpGs were differentially methylated at FDR < 0.05 comparing SSRI-exposed to non-exposed placentas, in a model adjusted for mean maternal Hamilton Depression score, or in a model restricted to maternally-depressed cases with and without SSRI exposure. However, at a relaxed threshold of FDR < 0.25, five CpGs were differentially methylated (|Δβ| > 0.03) by SSRI exposure status. Four were covered by the replication cohort measured by the 450K array, but none replicated. No CpGs were differentially methylated (FDR < 0.25) comparing maternally depressed to not depressed cases. In sex-stratified analyses for SSRI-exposed versus non-exposed cases (females n = 31; males n = 33), three additional CpGs in females, but none in males, were differentially methylated at the relaxed FDR < 0.25 cut-off. We did not observe large-scale alterations of DNAme in placentas exposed to maternal SSRI treatment, as compared to placentas with no SSRI exposure. We also found no evidence for altered DNAme in maternal depression-exposed versus depression non-exposed placentas. This novel work in a prospectively-recruited cohort with clinician-ascertained SSRI exposure and mood assessments would benefit from future replication.
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Affiliation(s)
- Amy M. Inkster
- grid.414137.40000 0001 0684 7788BC Children’s Hospital Research Institute (BCCHR), 950 W 28th Ave, Vancouver, BC V5Z 4H4 Canada ,grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3 Canada
| | - Chaini Konwar
- grid.414137.40000 0001 0684 7788BC Children’s Hospital Research Institute (BCCHR), 950 W 28th Ave, Vancouver, BC V5Z 4H4 Canada ,grid.17091.3e0000 0001 2288 9830Centre for Molecular Medicine and Therapeutics, Vancouver, BC V6H 0B3 Canada
| | - Maria S. Peñaherrera
- grid.414137.40000 0001 0684 7788BC Children’s Hospital Research Institute (BCCHR), 950 W 28th Ave, Vancouver, BC V5Z 4H4 Canada ,grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3 Canada
| | - Ursula Brain
- grid.414137.40000 0001 0684 7788BC Children’s Hospital Research Institute (BCCHR), 950 W 28th Ave, Vancouver, BC V5Z 4H4 Canada
| | - Almas Khan
- grid.414137.40000 0001 0684 7788BC Children’s Hospital Research Institute (BCCHR), 950 W 28th Ave, Vancouver, BC V5Z 4H4 Canada ,grid.17091.3e0000 0001 2288 9830Department of Pediatrics, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - E. Magda Price
- grid.414137.40000 0001 0684 7788BC Children’s Hospital Research Institute (BCCHR), 950 W 28th Ave, Vancouver, BC V5Z 4H4 Canada ,grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3 Canada ,grid.28046.380000 0001 2182 2255Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 5B2 Canada
| | - Johanna M. Schuetz
- grid.414137.40000 0001 0684 7788BC Children’s Hospital Research Institute (BCCHR), 950 W 28th Ave, Vancouver, BC V5Z 4H4 Canada ,grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3 Canada
| | - Élodie Portales-Casamar
- grid.414137.40000 0001 0684 7788BC Children’s Hospital Research Institute (BCCHR), 950 W 28th Ave, Vancouver, BC V5Z 4H4 Canada ,grid.17091.3e0000 0001 2288 9830Department of Pediatrics, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Amber Burt
- grid.189967.80000 0001 0941 6502Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322 USA
| | - Carmen J. Marsit
- grid.189967.80000 0001 0941 6502Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322 USA
| | - Cathy Vaillancourt
- grid.418084.10000 0000 9582 2314INRS-Centre Armand Frappier and Réseau intersectoriel de recherche en santé de l’Université du Québec, Laval, QC H7V 1B7 Canada
| | - Tim F. Oberlander
- grid.414137.40000 0001 0684 7788BC Children’s Hospital Research Institute (BCCHR), 950 W 28th Ave, Vancouver, BC V5Z 4H4 Canada ,grid.17091.3e0000 0001 2288 9830School of Population and Public Health, University of British Columbia, Vancouver, BC V6T 1Z3 Canada
| | - Wendy P. Robinson
- grid.414137.40000 0001 0684 7788BC Children’s Hospital Research Institute (BCCHR), 950 W 28th Ave, Vancouver, BC V5Z 4H4 Canada ,grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3 Canada
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Abstract
Changes in DNA methylation in cancer have been heralded as promising targets for the development of powerful diagnostic, prognostic, and predictive biomarkers. Despite the existence of more than 14,000 scientific publications describing DNA methylation-based biomarkers and their clinical associations in cancer, only 14 of these biomarkers have been translated into a commercially available clinical test. Methodological and experimental obstacles are both major causes of this disparity, but the genomic location of a DNA methylation-based biomarker is an intrinsic and essential property that also has an important and often overlooked role. Here, we examine the importance of the location of DNA methylation for the development of cancer biomarkers, and take a detailed look at the genomic location and other relevant characteristics of the various biomarkers with commercially available tests. We also emphasize the value of publicly available databases for the development of DNA methylation-based biomarkers and the importance of accurate reporting of the full methodological details of research findings.
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Aberrant GATA2 epigenetic dysregulation induces a GATA2/GATA6 switch in human gastric cancer. Oncogene 2017; 37:993-1004. [PMID: 29106391 DOI: 10.1038/onc.2017.397] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 08/08/2017] [Accepted: 09/15/2017] [Indexed: 02/07/2023]
Abstract
Six GATA transcription factors play important roles in eukaryotic development. Among these, GATA2, an essential factor for the hematopoietic cell lineage, exhibits low expression in human gastric tissues, whereas GATA6, which is crucial for gastrointestinal development and differentiation, is frequently amplified and/or overexpressed in human gastric cancer. Interestingly, we found that GATA6 was overexpressed in human gastric cancer cells only when GATA2 expression was completely absent, thereby showing an inverse correlation between GATA2 and GATA6. In gastric cancer cells that express high GATA6 levels, a GATA2 CpG island is hypermethylated, repressing expression in these cells. In contrast, GATA6 expression is undetectable in GATA2-overexpressing gastric cancer cells, which lack GATA2 DNA methylation. Furthermore, PRC2 complex-mediated transcriptional silencing of GATA6 was observed in the GATA2-overexpressing cells. We also show that the GATA2 and PRC2 complexes are enriched within the GATA6 locus, and that the recruitment of the PRC2 complex is impaired by disrupting GATA2 expression, resulting in GATA6 upregulation. In addition, ectopic GATA2 expression significantly downregulates GATA6 expression, suggesting GATA2 directly represses GATA6. Furthermore, GATA6 downregulation showed antitumor activity by inducing growth arrest. Finally, we show that aberrant GATA2 methylation occurs early during the multistep process of gastric carcinogenesis regardless of Helicobacter pylori infection. Taken together, GATA2 dysregulation by epigenetic modification is associated with unfavorable phenotypes in human gastric cancer cells by allowing GATA6 expression.
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Chernyavskaya Y, Kent B, Sadler KC. Zebrafish Discoveries in Cancer Epigenetics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 916:169-97. [PMID: 27165354 DOI: 10.1007/978-3-319-30654-4_8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The cancer epigenome is fundamentally different than that of normal cells. How these differences arise in and contribute to carcinogenesis is not known, and studies using model organisms such as zebrafish provide an opportunity to address these important questions. Modifications of histones and DNA comprise the complex epigenome, and these influence chromatin structure, genome stability and gene expression, all of which are fundamental to the cellular changes that cause cancer. The cancer genome atlas covers the wide spectrum of genetic changes associated with nearly every cancer type, however, this catalog is currently uni-dimensional. As the pattern of epigenetic marks and chromatin structure in cancer cells is described and overlaid on the mutational landscape, the map of the cancer genome becomes multi-dimensional and highly complex. Two major questions remain in the field: (1) how the epigenome becomes repatterned in cancer and (2) which of these changes are cancer-causing. Zebrafish provide a tractable in vivo system to monitor the epigenome during transformation and to identify epigenetic drivers of cancer. In this chapter, we review principles of cancer epigenetics and discuss recent work using zebrafish whereby epigenetic modifiers were established as cancer driver genes, thus providing novel insights into the mechanisms of epigenetic reprogramming in cancer.
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Affiliation(s)
- Yelena Chernyavskaya
- Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1020, 1 Gustave L. Levy Place, New York, NY, 10029, USA
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, 1020, 1 Gustave L. Levy Place, New York, NY, 10029, USA
| | - Brandon Kent
- Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1020, 1 Gustave L. Levy Place, New York, NY, 10029, USA
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, 1020, 1 Gustave L. Levy Place, New York, NY, 10029, USA
- School of Biomedical Science, Icahn School of Medicine at Mount Sinai, 1020, 1 Gustave L. Levy Place, New York, NY, 10029, USA
| | - Kirsten C Sadler
- Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, 1020, 1 Gustave L. Levy Place, New York, NY, 10029, USA.
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, 1020, 1 Gustave L. Levy Place, New York, NY, 10029, USA.
- School of Biomedical Science, Icahn School of Medicine at Mount Sinai, 1020, 1 Gustave L. Levy Place, New York, NY, 10029, USA.
- Biology Program, New York University Abu Dhabi, Saadiyat Campus, 129188, Abu Dhabi, United Arab Emirates.
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Mansoori AA, Jain SK. Molecular Links between Alcohol and Tobacco Induced DNA Damage, Gene Polymorphisms and Patho-physiological Consequences: A Systematic Review of Hepatic Carcinogenesis. Asian Pac J Cancer Prev 2015; 16:4803-12. [PMID: 26163595 DOI: 10.7314/apjcp.2015.16.12.4803] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Chronic alcohol and tobacco abuse plays a crucial role in the development of different liver associated disorders. Intake promotes the generation of reactive oxygen species within hepatic cells exposing their DNA to continuous oxidative stress which finally leads to DNA damage. However in response to such damage an entangled protective repair machinery comprising different repair proteins like ATM, ATR, H2AX, MRN complex becomes activated. Under abnormal conditions the excessive reactive oxygen species generation results in genetic predisposition of various genes (as ADH, ALDH, CYP2E1, GSTT1, GSTP1 and GSTM1) involved in xenobiotic metabolic pathways, associated with susceptibility to different liver related diseases such as fibrosis, cirrhosis and hepatocellular carcinoma. There is increasing evidence that the inflammatory process is inherently associated with many different cancer types, including hepatocellular carcinomas. The generated reactive oxygen species can also activate or repress epigenetic elements such as chromatin remodeling, non-coding RNAs (micro-RNAs), DNA (de) methylation and histone modification that affect gene expression, hence leading to various disorders. The present review provides comprehensive knowledge of different molecular mechanisms involved in gene polymorphism and their possible association with alcohol and tobacco consumption. The article also showcases the necessity of identifying novel diagnostic biomarkers for early cancer risk assessment among alcohol and tobacco users.
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Affiliation(s)
- Abdul Anvesh Mansoori
- Molecular Biology Laboratory, Department of Biotechnology, Dr. Hari Singh Gour Central University, Sagar, M.P. India E-mail :
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