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Fatemi N, Tierling S, Es HA, Varkiani M, Nazemalhosseini Mojarad E, Asadzadeh Aghdaei H, Walter J, Totonchi M. DNA Methylation Biomarkers in Colorectal Cancer: Clinical Applications for Precision Medicine. Int J Cancer 2022; 151:2068-2081. [PMID: 35730647 DOI: 10.1002/ijc.34186] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/29/2022] [Accepted: 06/08/2022] [Indexed: 11/06/2022]
Abstract
Colorectal cancer (CRC) is the second leading cause of cancer death worldwide that is attributed to gradual long-term accumulation of both genetic and epigenetic changes. To reduce the mortality rate of CRC and to improve treatment efficacy, it will be important to develop accurate noninvasive diagnostic tests for screening, acute, and personalized diagnosis. Epigenetic changes such as DNA methylation play an important role in the development and progression of CRC. Over the last decade, a panel of DNA methylation markers has been reported showing a high accuracy and reproducibility in various semi-invasive or noninvasive biosamples. Research to obtain comprehensive panels of markers allowing a highly sensitive and differentiating diagnosis of CRC is ongoing. Moreover, the epigenetic alterations for cancer therapy, as a precision medicine strategy will increase their therapeutic potential over time. Here, we discuss the current state of DNA methylation-based biomarkers and their impact on CRC diagnosis. We emphasize the need to further identify and stratify methylation-biomarkers and to develop robust and effective detection methods that are applicable for a routine clinical setting of CRC diagnostics particularly at the early stage of the disease.
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Affiliation(s)
- Nayeralsadat Fatemi
- Basic & Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology & Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sascha Tierling
- Department of Genetics/Epigenetics, Faculty NT, Life Sciences, Saarland University, Saarbrücken, Germany
| | | | - Maryam Varkiani
- Department of Molecular Genetics, Faculty of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran
| | - Ehsan Nazemalhosseini Mojarad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic & Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology & Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Jörn Walter
- Department of Genetics/Epigenetics, Faculty NT, Life Sciences, Saarland University, Saarbrücken, Germany
| | - Mehdi Totonchi
- Basic & Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology & Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
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2
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Laqqan MM, Yassin MM. Cigarette heavy smoking alters DNA methylation patterns and gene transcription levels in humans spermatozoa. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:26835-26849. [PMID: 34855177 DOI: 10.1007/s11356-021-17786-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/23/2021] [Indexed: 05/27/2023]
Abstract
Tobacco smoking is considered the most common reason of death and infertility around the world. This study was designed to assess the impact of tobacco heavy smoking on sperm DNA methylation patterns and to determine whether the transcription level of ALDH3B2, PTGIR, PRICKLE2, and ALS2CR12 genes is different in heavy smokers compared to non-smokers. As a screening study, the 450 K array was used to assess the alteration in DNA methylation patterns between heavy smokers (n = 15) and non-smokers (n = 15). Then, four CpGs that have the highest difference in methylation level (cg16338278, cg08408433, cg05799088, and cg07227024) were selected for validation using deep bisulfite sequencing in an independent cohort of heavy smokers (n = 200) and non-smokers (n = 100). A significant variation was found between heavy smokers and non-smokers in the methylation level at all CpGs within the PRICKLE2 and ALS2CR12 gene amplicon (P < 0.001). Similarly, a significant variation was found in the methylation level at nine out of thirteen CpGs within the ALDH3B2 gene amplicon (P < 0.01). Additionally, eighteen CpGs out of the twenty-six within the PTGIR gene amplicon have a significant difference in the methylation level between heavy smokers and non-smokers (P < 0.01). The study showed a significant difference in sperm global DNA methylation, chromatin non-condensation, and DNA fragmentation (P < 0.001) between heavy smokers and non-smokers. A significant decline was shown in the transcription level of ALDH3B2, PTGIR, PRICKLE2, and ALS2CR12 genes (P < 0.001) in heavy smokers. In conclusion, heavy smoking influences DNA methylation at several CpGs, sperm global DNA methylation, and transcription level of the PRICKLE2, ALS2CR12, ALDH3B2, and PTGIR genes, which affects negatively the semen parameters of heavy smokers.
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Affiliation(s)
- Mohammed M Laqqan
- Department of Medical Laboratory Sciences, Faculty of Health Sciences, Islamic University, Gaza, Palestinian Territories, Palestine.
| | - Maged M Yassin
- Department of Human Physiology, Faculty of Medicine, Islamic University, Gaza, Palestinian Territories, Palestine
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3
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Tierling S, Jürgens-Wemheuer WM, Leismann A, Becker-Kettern J, Scherer M, Wrede A, Breuskin D, Urbschat S, Sippl C, Oertel J, Schulz-Schaeffer WJ, Walter J. Bisulfite profiling of the MGMT promoter and comparison with routine testing in glioblastoma diagnostics. Clin Epigenetics 2022; 14:26. [PMID: 35180887 PMCID: PMC8857788 DOI: 10.1186/s13148-022-01244-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 02/07/2022] [Indexed: 11/26/2022] Open
Abstract
Background Promoter methylation of the DNA repair gene O6-methylguanine-DNA methyltransferase (MGMT) is an acknowledged predictive epigenetic marker in glioblastoma multiforme and anaplastic astrocytoma. Patients with methylated CpGs in the MGMT promoter benefit from treatment with alkylating agents, such as temozolomide, and show an improved overall survival and progression-free interval. A precise determination of MGMT promoter methylation is of importance for diagnostic decisions. We experienced that different methods show partially divergent results in a daily routine. For an integrated neuropathological diagnosis of malignant gliomas, we therefore currently apply a combination of methylation-specific PCR assays and pyrosequencing. Results To better rationalize the variation across assays, we compared these standard techniques and assays to deep bisulfite sequencing results in a cohort of 80 malignant astrocytomas. Our deep analysis covers 49 CpG sites of the expanded MGMT promoter, including exon 1, parts of intron 1 and a region upstream of the transcription start site (TSS). We observed that deep sequencing data are in general in agreement with CpG-specific pyrosequencing, while the most widely used MSP assays published by Esteller et al. (N Engl J Med 343(19):1350–1354, 2000. 10.1056/NEJM200011093431901) and Felsberg et al. (Clin Cancer Res 15(21):6683–6693, 2009. 10.1158/1078-0432.CCR-08-2801) resulted in partially discordant results in 22 tumors (27.5%). Local deep bisulfite sequencing (LDBS) revealed that CpGs located in exon 1 are suited best to discriminate methylated from unmethylated samples. Based on LDBS data, we propose an optimized MSP primer pair with 83% and 85% concordance to pyrosequencing and LDBS data. A hitherto neglected region upstream of the TSS, with an overall higher methylation compared to exon 1 and intron 1 of MGMT, is also able to discriminate the methylation status. Conclusion Our integrated analysis allows to evaluate and redefine co-methylation domains within the MGMT promoter and to rationalize the practical impact on assays used in daily routine diagnostics. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-022-01244-4.
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Affiliation(s)
- Sascha Tierling
- Fak.NT Life Sciences, Department of Genetics/Epigenetics, Saarland University, Campus, Building A2 4, 66041, Saarbrücken, Germany.
| | | | - Alea Leismann
- Fak.NT Life Sciences, Department of Genetics/Epigenetics, Saarland University, Campus, Building A2 4, 66041, Saarbrücken, Germany
| | - Julia Becker-Kettern
- Institute of Neuropathology, Medical Faculty of the Saarland University, Homburg, Germany
| | - Michael Scherer
- Fak.NT Life Sciences, Department of Genetics/Epigenetics, Saarland University, Campus, Building A2 4, 66041, Saarbrücken, Germany.,Department of Bioinformatics and Genomics, Centre for Genomic Regulation, Barcelona, Spain
| | - Arne Wrede
- Institute of Neuropathology, Medical Faculty of the Saarland University, Homburg, Germany
| | - David Breuskin
- Institute for Neurosurgery, Medical Faculty of the Saarland University, Homburg, Germany
| | - Steffi Urbschat
- Institute for Neurosurgery, Medical Faculty of the Saarland University, Homburg, Germany
| | - Christoph Sippl
- Institute for Neurosurgery, Medical Faculty of the Saarland University, Homburg, Germany
| | - Joachim Oertel
- Institute for Neurosurgery, Medical Faculty of the Saarland University, Homburg, Germany
| | | | - Jörn Walter
- Fak.NT Life Sciences, Department of Genetics/Epigenetics, Saarland University, Campus, Building A2 4, 66041, Saarbrücken, Germany
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Laqqan MM, Yassin MM. Influence of tobacco cigarette heavy smoking on DNA methylation patterns and transcription levels of MAPK8IP3, GAA, ANXA2, PRRC2A, and PDE11A genes in human spermatozoa. MIDDLE EAST FERTILITY SOCIETY JOURNAL 2021. [DOI: 10.1186/s43043-021-00084-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Abstract
Background
Tobacco smoking is considered as one of the lifestyles factors that influence the sperm DNA methylation and global sperm DNA methylation and that may affect the sperm phenotype. This study was performed to investigate whether tobacco cigarette heavy smoking influences sperm DNA methylation patterns and semen parameters and to determine whether there is an alteration in the transcription level of MAPK8IP3, GAA, ANXA2, PRRC2A, and PDE11A genes in heavy smokers compared to non-smokers. Thirty samples were subjected to 450K arrays as a screening study to assess the variation in sperm DNA methylation levels between heavy smokers and non-smokers. Five CpG sites have the highest difference in methylation levels (cg07869343, cg05813498, cg09785377, cg06833981, and cg02745784), which are located in the MAPK8IP3, GAA, ANXA2, PRRC2A, and PDE11A genes, respectively, and were selected for further analysis using deep bisulfite sequencing in 280 independent samples (120 proven non-smokers and 160 heavy smokers) with a mean age of 33.8 ± 8.4 years. The global sperm DNA methylation, sperm DNA fragmentation, and chromatin non-condensation were evaluated also.
Results
A significant increase was found in the methylation level at seven, three, and seventeen CpGs within the GAA, ANXA2, and MAPK8IP3 genes amplicon, respectively (P< 0.01) in heavy smokers compared to non-smokers. Additionally, a significant increase was found in the methylation levels at all CpGs within PRRC2A and PDE11A gene amplicon (P< 0.01). A significant increase was found in the level of sperm chromatin non-condensation, DNA fragmentation, and global DNA methylation (P < 0.001) in heavy smokers compared to non-smokers.
Conclusion
These results indicate that tobacco cigarette smoking can alter the DNA methylation level at several CpGs, the status of global DNA methylation, and transcription level of the following genes “MAPK8IP3, GAA, ANXA2, PRRC2A, and PDE11A” in human spermatozoa. These findings may affect negatively semen parameters and men’s fertility.
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Epigenetic Modifications Associated with Maternal Anxiety during Pregnancy and Children's Behavioral Measures. Cells 2021; 10:cells10092421. [PMID: 34572069 PMCID: PMC8469633 DOI: 10.3390/cells10092421] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 09/03/2021] [Accepted: 09/08/2021] [Indexed: 12/15/2022] Open
Abstract
Epigenetic changes are associated with altered behavior and neuropsychiatric disorders and they modify the trajectory of aging. Maternal anxiety during pregnancy is a common environmental challenge for the fetus, causing changes in DNA methylation. Here, we determined the mediating role of DNA methylation and the moderating role of offspring sex on the association between maternal anxiety and children's behavioral measures. In 83 mother-child dyads, maternal anxiety was assessed in each trimester of pregnancy when the child was four years of age. Children's behavioral measures and children's buccal DNA methylation levels (NR3C1, IGF2/H19 ICR, and LINE1) were examined. Higher maternal anxiety during the third trimester was associated with more methylation levels of the NR3C1. Moderating effects of sex on the association between maternal anxiety and methylation were found for IGF2/H19 and LINE1 CpGs. Mediation analysis showed that methylation of NR3C1 could buffer the effects of maternal anxiety on children's behavioral measures, but this effect did not remain significant after controlling for covariates. In conclusion, our data support an association between maternal anxiety during pregnancy and DNA methylation. The results also underscore the importance of sex differences and timing effects. However, DNA methylation as underlying mechanism of the effect of maternal anxiety during pregnancy on offspring's behavioral measures was not supported.
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Feiner LK, Tierling S, Holländer S, Glanemann M, Rubie C. An aging and p53 related marker: HOXA5 promoter methylation negatively correlates with mRNA and protein expression in old age. Aging (Albany NY) 2021; 13:4831-4849. [PMID: 33547267 PMCID: PMC7950283 DOI: 10.18632/aging.202621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/04/2021] [Indexed: 12/02/2022]
Abstract
The process of aging has been associated with differential patterns of DNA methylation which relate to changes in gene expression. Hence, we aimed to identify genes with significant age-related methylation differences and to study their mRNA and protein expression profile. Genome-wide DNA methylation analysis was performed with the Illumina Infinium Methylation EPIC BeadChip Microarray on bisulfite-converted DNA prepared from monocytes derived from young (average age: 23.8 yrs) and old (average age: 81.5 yrs) volunteers that are separated by at least 50 years of age difference, n=4, respectively. Differentially methylated CpG sites were assigned to the associated genes and validated by deep sequencing analysis (n=20). Demonstrating an age-associated significant increase of methylation in the promoter region (p=1x10-8), Homeobox A5 (HOXA5), also known to activate p53, emerged as an interesting candidate for further expression analyses by Realtime PCR, ELISA and Western Blot Analysis (n=30, respectively). Consistent with its hypermethylation we observed significant HOXA5 mRNA downregulation (p=0.0053) correlating with significant p53 downregulation (p=0.0431) in the old cohort. Moreover, we observed a significant change in HOXA5 protein expression (p=3x10-5) negatively correlating with age and promoter methylation thus qualifying HOXA5 for an eligible p53-related aging marker.
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Affiliation(s)
- Laura-Kim Feiner
- Department of General-, Visceral-, Vascular- and Pediatric Surgery, University of Saarland Medical Center, Homburg 66421, Saar, Germany
| | - Sascha Tierling
- Department of Genetics and Epigenetics, Saarland University, Saarbrücken 66123, Germany
| | - Sebastian Holländer
- Department of General-, Visceral-, Vascular- and Pediatric Surgery, University of Saarland Medical Center, Homburg 66421, Saar, Germany
| | - Matthias Glanemann
- Department of General-, Visceral-, Vascular- and Pediatric Surgery, University of Saarland Medical Center, Homburg 66421, Saar, Germany
| | - Claudia Rubie
- Department of General-, Visceral-, Vascular- and Pediatric Surgery, University of Saarland Medical Center, Homburg 66421, Saar, Germany
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7
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Berg JL, Perfler B, Hatzl S, Mayer MC, Wurm S, Uhl B, Reinisch A, Klymiuk I, Tierling S, Pregartner G, Bachmaier G, Berghold A, Geissler K, Pichler M, Hoefler G, Strobl H, Wölfler A, Sill H, Zebisch A. Micro-RNA-125a mediates the effects of hypomethylating agents in chronic myelomonocytic leukemia. Clin Epigenetics 2021; 13:1. [PMID: 33407852 PMCID: PMC7789782 DOI: 10.1186/s13148-020-00979-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 11/17/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Chronic myelomonocytic leukemia (CMML) is an aggressive hematopoietic malignancy that arises from hematopoietic stem and progenitor cells (HSPCs). Patients with CMML are frequently treated with epigenetic therapeutic approaches, in particular the hypomethylating agents (HMAs), azacitidine (Aza) and decitabine (Dec). Although HMAs are believed to mediate their efficacy via re-expression of hypermethylated tumor suppressors, knowledge about relevant HMA targets is scarce. As silencing of tumor-suppressive micro-RNAs (miRs) by promoter hypermethylation is a crucial step in malignant transformation, we asked for a role of miRs in HMA efficacy in CMML. RESULTS Initially, we performed genome-wide miR-expression profiling in a KrasG12D-induced CMML mouse model. Selected candidates with prominently decreased expression were validated by qPCR in CMML mice and human CMML patients. These experiments revealed the consistent decrease in miR-125a, a miR with previously described tumor-suppressive function in myeloid neoplasias. Furthermore, we show that miR-125a downregulation is caused by hypermethylation of its upstream region and can be reversed by HMA treatment. By employing both lentiviral and CRISPR/Cas9-based miR-125a modification, we demonstrate that HMA-induced miR-125a upregulation indeed contributes to mediating the anti-leukemic effects of these drugs. These data were validated in a clinical context, as miR-125a expression increased after HMA treatment in CMML patients, a phenomenon that was particularly pronounced in cases showing clinical response to these drugs. CONCLUSIONS Taken together, we report decreased expression of miR-125a in CMML and delineate its relevance as mediator of HMA efficacy within this neoplasia.
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Affiliation(s)
- Johannes Lorenz Berg
- Division of Hematology, Medical University of Graz, Auenbruggerplatz 38, 8036, Graz, Austria
| | - Bianca Perfler
- Division of Hematology, Medical University of Graz, Auenbruggerplatz 38, 8036, Graz, Austria
| | - Stefan Hatzl
- Division of Hematology, Medical University of Graz, Auenbruggerplatz 38, 8036, Graz, Austria
| | - Marie-Christina Mayer
- Division of Hematology, Medical University of Graz, Auenbruggerplatz 38, 8036, Graz, Austria
| | - Sonja Wurm
- Division of Hematology, Medical University of Graz, Auenbruggerplatz 38, 8036, Graz, Austria
| | - Barbara Uhl
- Division of Hematology, Medical University of Graz, Auenbruggerplatz 38, 8036, Graz, Austria
| | - Andreas Reinisch
- Division of Hematology, Medical University of Graz, Auenbruggerplatz 38, 8036, Graz, Austria
| | - Ingeborg Klymiuk
- Core Facility Molecular Biology, Medical University of Graz, Graz, Austria
| | - Sascha Tierling
- Department of Genetics, University of Saarland, Saarbrücken, Germany
| | - Gudrun Pregartner
- Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria
| | - Gerhard Bachmaier
- Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria
| | - Andrea Berghold
- Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria
| | - Klaus Geissler
- 5th Medical Department with Hematology, Oncology and Palliative Medicine, Hospital Hietzing, Vienna, Austria.,Sigmund Freud University, Vienna, Austria
| | - Martin Pichler
- Division of Oncology, Medical University of Graz, Graz, Austria.,Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Centre, Houston, TX, USA
| | - Gerald Hoefler
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Herbert Strobl
- Otto Loewi Research Centre, Immunology and Pathophysiology, Medical University of Graz, Graz, Austria
| | - Albert Wölfler
- Division of Hematology, Medical University of Graz, Auenbruggerplatz 38, 8036, Graz, Austria
| | - Heinz Sill
- Division of Hematology, Medical University of Graz, Auenbruggerplatz 38, 8036, Graz, Austria
| | - Armin Zebisch
- Division of Hematology, Medical University of Graz, Auenbruggerplatz 38, 8036, Graz, Austria. .,Otto-Loewi Research Centre for Vascular Biology, Immunology and Inflammation, Division of Pharmacology, Medical University of Graz, Universitätsplatz 4, 8010, Graz, Austria.
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8
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Scherer M, Nebel A, Franke A, Walter J, Lengauer T, Bock C, Müller F, List M. Quantitative comparison of within-sample heterogeneity scores for DNA methylation data. Nucleic Acids Res 2020; 48:e46. [PMID: 32103242 PMCID: PMC7192612 DOI: 10.1093/nar/gkaa120] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 02/14/2020] [Indexed: 12/13/2022] Open
Abstract
DNA methylation is an epigenetic mark with important regulatory roles in cellular identity and can be quantified at base resolution using bisulfite sequencing. Most studies are limited to the average DNA methylation levels of individual CpGs and thus neglect heterogeneity within the profiled cell populations. To assess this within-sample heterogeneity (WSH) several window-based scores that quantify variability in DNA methylation in sequencing reads have been proposed. We performed the first systematic comparison of four published WSH scores based on simulated and publicly available datasets. Moreover, we propose two new scores and provide guidelines for selecting appropriate scores to address cell-type heterogeneity, cellular contamination and allele-specific methylation. Most of the measures were sensitive in detecting DNA methylation heterogeneity in these scenarios, while we detected differences in susceptibility to technical bias. Using recently published DNA methylation profiles of Ewing sarcoma samples, we show that DNA methylation heterogeneity provides information complementary to the DNA methylation level. WSH scores are powerful tools for estimating variance in DNA methylation patterns and have the potential for detecting novel disease-associated genomic loci not captured by established statistics. We provide an R-package implementing the WSH scores for integration into analysis workflows.
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Affiliation(s)
- Michael Scherer
- Computational Biology, Max Planck Institute for Informatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Graduate School of Computer Science, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Department of Genetics/Epigenetics, Saarland University, 66123 Saarbrücken, Germany
| | - Almut Nebel
- Institute of Clinical Molecular Biology, Kiel University, 24105 Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, 24105 Kiel, Germany
| | - Jörn Walter
- Department of Genetics/Epigenetics, Saarland University, 66123 Saarbrücken, Germany
| | - Thomas Lengauer
- Computational Biology, Max Planck Institute for Informatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Fabian Müller
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Markus List
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
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Czepukojc B, Abuhaliema A, Barghash A, Tierling S, Naß N, Simon Y, Körbel C, Cadenas C, van Hul N, Sachinidis A, Hengstler JG, Helms V, Laschke MW, Walter J, Haybaeck J, Leclercq I, Kiemer AK, Kessler SM. IGF2 mRNA Binding Protein 2 Transgenic Mice Are More Prone to Develop a Ductular Reaction and to Progress Toward Cirrhosis. Front Med (Lausanne) 2019; 6:179. [PMID: 31555647 PMCID: PMC6737005 DOI: 10.3389/fmed.2019.00179] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 07/23/2019] [Indexed: 12/21/2022] Open
Abstract
The insulin-like growth factor 2 (IGF2) mRNA binding proteins (IMPs/IGF2BPs) IMP1 and 3 are regarded as oncofetal proteins, whereas the hepatic IMP2 expression in adults is controversially discussed. The splice variant IMP2-2/p62 promotes steatohepatitis and hepatocellular carcinoma. Aim of this study was to clarify whether IMP2 is expressed in the adult liver and influences progression toward cirrhosis. IMP2 was expressed at higher levels in embryonic compared to adult tissues as quantified in embryonic, newborn, and adult C57BL/6J mouse livers and suggested by analysis of publicly available human data. In an IMP2-2 transgenic mouse model microarray and qPCR analyses revealed increased expression of liver progenitor cell (LPC) markers Bex1, Prom1, Spp1, and Cdh1 indicating a de-differentiated liver cell phenotype. Induction of these LPC markers was confirmed in human cirrhotic tissue datasets. The LPC marker SPP1 has been described to play a major role in fibrogenesis. Thus, DNA methylation was investigated in order to decipher the regulatory mechanism of Spp1 induction. In IMP2-2 transgenic mouse livers single CpG sites were differentially methylated, as quantified by amplicon sequencing, whereas human HCC samples of a human publicly available dataset showed promoter hypomethylation. In order to study the impact of IMP2 on fibrogenesis in the context of steatohepatitis wild-type or IMP2-2 transgenic mice were fed either a methionine-choline deficient (MCD) or a control diet for 2-12 weeks. MCD-fed IMP2-2 transgenic mice showed a higher incidence of ductular reaction (DR), accompanied by hepatic stellate cell activation, extracellular matrix (ECM) deposition, and induction of the LPC markers Spp1, Cdh1, and Afp suggesting the occurrence of de-differentiated cells in transgenic livers. In human cirrhotic samples IMP2 overexpression correlated with LPC marker and ECM component expression. Progression of liver disease was induced by combined MCD and diethylnitrosamine (DEN) treatment. Combined MCD-DEN treatment resulted in shorter survival of IMP2-2 transgenic compared to wild-type mice. Only IMP2-2 transgenic livers progressed to cirrhosis, which was accompanied by strong DR. In conclusion, IMP2 is an oncofetal protein in the liver that promotes DR characterized by de-differentiated cells toward steatohepatitis-associated cirrhosis development with poor survival.
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Affiliation(s)
- Beate Czepukojc
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Saarbrücken, Germany
| | - Ali Abuhaliema
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Saarbrücken, Germany
| | - Ahmad Barghash
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany.,Department of Computer Science, German Jordanian University, Amman, Jordan
| | - Sascha Tierling
- Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
| | - Norbert Naß
- Department of Pathology, Medical Faculty, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Yvette Simon
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Saarbrücken, Germany
| | - Christina Körbel
- Institute of Clinical-Experimental Surgery, Saarland University Hospital, Homburg, Germany
| | - Cristina Cadenas
- Systems Toxicology, Leibniz Research Centre for Working Environment and Human Factors (IfADo) at the TU Dortmund, Dortmund, Germany
| | - Noemi van Hul
- Laboratory of Hepato-Gastroenterology, Institut de Recherche Expérimentale et Clinique, Université Catholique de Louvain, Brussels, Belgium.,Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Agapios Sachinidis
- Center for Molecular Medicine Cologne (CMMC), Institute of Neurophysiology, University of Cologne, Cologne, Germany
| | - Jan G Hengstler
- Systems Toxicology, Leibniz Research Centre for Working Environment and Human Factors (IfADo) at the TU Dortmund, Dortmund, Germany
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Matthias W Laschke
- Institute of Clinical-Experimental Surgery, Saarland University Hospital, Homburg, Germany
| | - Jörn Walter
- Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
| | - Johannes Haybaeck
- Department of Pathology, Medical Faculty, Otto von Guericke University Magdeburg, Magdeburg, Germany.,Institute of Pathology, Medical University of Graz, Graz, Austria.,Department of Pathology, Medical University Innsbruck, Innsbruck, Austria
| | - Isabelle Leclercq
- Laboratory of Hepato-Gastroenterology, Institut de Recherche Expérimentale et Clinique, Université Catholique de Louvain, Brussels, Belgium
| | - Alexandra K Kiemer
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Saarbrücken, Germany
| | - Sonja M Kessler
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Saarbrücken, Germany.,Laboratory of Hepato-Gastroenterology, Institut de Recherche Expérimentale et Clinique, Université Catholique de Louvain, Brussels, Belgium.,Institute of Pathology, Medical University of Graz, Graz, Austria
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10
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McSwiggin HM, O'Doherty AM. Epigenetic reprogramming during spermatogenesis and male factor infertility. Reproduction 2018; 156:R9-R21. [PMID: 29717022 DOI: 10.1530/rep-18-0009] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 05/01/2018] [Indexed: 12/11/2022]
Abstract
Infertility is an often devastating diagnosis encountered by around one in six couples who are trying to conceive. Moving away from the long-held belief that infertility is primarily a female issue, it is now recognised that half, if not more, of these cases may be due to male factors. Recent evidence has suggested that epigenetic abnormalities in chromatin dynamics, DNA methylation or sperm-borne RNAs may contribute to male infertility. In light of advances in deep sequencing technologies, researchers have been able to increase the coverage and depth of sequencing results, which in turn has allowed more comprehensive analyses of spermatozoa chromatin dynamics and methylomes and enabled the discovery of new subsets of sperm RNAs. This review examines the most current literature related to epigenetic processes in the male germline and the associations of aberrant modifications with fertility and development.
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Affiliation(s)
- H M McSwiggin
- Department of Physiology and Cell BiologyUniversity of Nevada, Reno School of Medicine, Center for Molecular Medicine, Reno, North Virginia, USA
| | - A M O'Doherty
- Animal Genomics LaboratoryUCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
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11
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Alkhaled Y, Laqqan M, Tierling S, Lo Porto C, Hammadeh ME. DNA methylation level of spermatozoa from subfertile and proven fertile and its relation to standard sperm parameters. Andrologia 2018; 50:e13011. [DOI: 10.1111/and.13011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2018] [Indexed: 02/06/2023] Open
Affiliation(s)
- Y. Alkhaled
- Department of Obstetrics; Gynecology & Assisted Reproduction Laboratory; University of Saarland; Homburg Germany
| | - M. Laqqan
- Department of Obstetrics; Gynecology & Assisted Reproduction Laboratory; University of Saarland; Homburg Germany
| | - S. Tierling
- FR8.3 Life Science; Department of Genetics& Epigenetics; Saarland University; Homburg Germany
| | - C. Lo Porto
- FR8.3 Life Science; Department of Genetics& Epigenetics; Saarland University; Homburg Germany
| | - M. E. Hammadeh
- Department of Obstetrics; Gynecology & Assisted Reproduction Laboratory; University of Saarland; Homburg Germany
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12
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de Boni L, Gasparoni G, Haubenreich C, Tierling S, Schmitt I, Peitz M, Koch P, Walter J, Wüllner U, Brüstle O. DNA methylation alterations in iPSC- and hESC-derived neurons: potential implications for neurological disease modeling. Clin Epigenetics 2018; 10:13. [PMID: 29422978 PMCID: PMC5789607 DOI: 10.1186/s13148-018-0440-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 01/04/2018] [Indexed: 12/21/2022] Open
Abstract
Background Genetic predisposition and epigenetic alterations are both considered to contribute to sporadic neurodegenerative diseases (NDDs) such as Parkinson's disease (PD). Since cell reprogramming and the generation of induced pluripotent stem cells (iPSCs) are themselves associated with major epigenetic remodeling, it remains unclear to what extent iPSC-derived neurons lend themselves to model epigenetic disease-associated changes. A key question to be addressed in this context is whether iPSC-derived neurons exhibit epigenetic signatures typically observed in neurons derived from non-reprogrammed human embryonic stem cells (hESCs). Results Here, we compare mature neurons derived from hESC and isogenic human iPSC generated from hESC-derived neural stem cells. Genome-wide 450 K-based DNA methylation and HT12v4 gene array expression analyses were complemented by a deep analysis of selected genes known to be involved in NDD. Our studies show that DNA methylation and gene expression patterns of isogenic hESC- and iPSC-derived neurons are markedly preserved on a genome-wide and single gene level. Conclusions Overall, iPSC-derived neurons exhibit similar DNA methylation patterns compared to isogenic hESC-derived neurons. Further studies will be required to explore whether the epigenetic patterns observed in iPSC-derived neurons correspond to those detectable in native brain neurons.
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Affiliation(s)
- Laura de Boni
- Department of Neurology, University Hospital of Bonn, Bonn, Germany
- Institute of Reconstructive Neurobiology, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Gilles Gasparoni
- Institute for Genetics/Epigenetics, FR8.3 Life Sciences, Saarland University, Saarbrücken, Germany
| | - Carolin Haubenreich
- Institute of Reconstructive Neurobiology, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Sascha Tierling
- Institute for Genetics/Epigenetics, FR8.3 Life Sciences, Saarland University, Saarbrücken, Germany
| | - Ina Schmitt
- Department of Neurology, University Hospital of Bonn, Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE), University of Bonn, Bonn, Germany
| | - Michael Peitz
- Institute of Reconstructive Neurobiology, Life & Brain Center, University of Bonn, Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE), University of Bonn, Bonn, Germany
| | - Philipp Koch
- Institute of Reconstructive Neurobiology, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Jörn Walter
- Institute for Genetics/Epigenetics, FR8.3 Life Sciences, Saarland University, Saarbrücken, Germany
| | - Ullrich Wüllner
- Department of Neurology, University Hospital of Bonn, Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE), University of Bonn, Bonn, Germany
| | - Oliver Brüstle
- Institute of Reconstructive Neurobiology, Life & Brain Center, University of Bonn, Bonn, Germany
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13
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Alkhaled Y, Laqqan M, Tierling S, Lo Porto C, Amor H, Hammadeh ME. Impact of cigarette-smoking on sperm DNA methylation and its effect on sperm parameters. Andrologia 2018; 50:e12950. [PMID: 29315717 DOI: 10.1111/and.12950] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2017] [Indexed: 12/15/2022] Open
Abstract
DNA methylation is an epigenetic modification of the genome. The purpose of this study was to determine the influence of cigarette-smoking on sperm DNA methylation from a genomewide survey of sperm samples and to ascertain its effect on sperm parameters. Twenty-eight sperm DNA samples (from 14 fertile smokers as a case study and 14 proven fertile nonsmokers as controls) were subjected to Infinium 450K BeadChip arrays to identify the changes in the DNA methylation level between the two groups. Then, deep bisulphite sequencing was used to validate five CpGs on 78 samples. The results from the Infinium 450K found that only 11 CpGs showed a significant difference in DNA methylation between the case and the control groups. Five CpGs of the eleven (cg00648582, cg0932376, cg19169023, cg23841288 and cg27391564) underwent deep bisulphite sequencing where cg00648582, related to the PGAM5 gene, and the cg23841288 CpGs, related to the PTPRN2 gene amplicons, showed a significant increase in their DNA methylation level in more than one CpG in the case group. In contrast, a significant decrease was found at cg19169023 and at its various neighbouring CpGs in the TYRO3 gene-related amplicons. Furthermore, this study demonstrated a significant correlation between the variation in sperm DNA methylation level and standard sperm parameters in the case group.
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Affiliation(s)
- Y Alkhaled
- Department of Obstetrics & Gynecology, University of Saarland, Saarbrucken, Germany
| | - M Laqqan
- Department of Obstetrics & Gynecology, University of Saarland, Saarbrucken, Germany
| | - S Tierling
- FR8.3 Life Science, Department of Genetics & Epigenetics, Saarland University, Saarbrucken, Germany
| | - C Lo Porto
- FR8.3 Life Science, Department of Genetics & Epigenetics, Saarland University, Saarbrucken, Germany
| | - H Amor
- Department of Obstetrics & Gynecology, University of Saarland, Saarbrucken, Germany
| | - M E Hammadeh
- Department of Obstetrics & Gynecology, University of Saarland, Saarbrucken, Germany
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14
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Laqqan M, Hammadeh ME. Alterations in DNA methylation patterns and gene expression in spermatozoa of subfertile males. Andrologia 2017; 50. [DOI: 10.1111/and.12934] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2017] [Indexed: 02/06/2023] Open
Affiliation(s)
- M. Laqqan
- Department of Obstetrics & Gynecology; Assisted Reproduction Laboratory; Saarland University; Homburg Germany
| | - M. E. Hammadeh
- Department of Obstetrics & Gynecology; Assisted Reproduction Laboratory; Saarland University; Homburg Germany
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15
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Laqqan M, Tierling S, Alkhaled Y, LoPorto C, Hammadeh ME. Alterations in sperm DNA methylation patterns of oligospermic males. Reprod Biol 2017; 17:396-400. [DOI: 10.1016/j.repbio.2017.10.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 10/28/2017] [Accepted: 10/28/2017] [Indexed: 12/12/2022]
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16
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Gut memories do not fade: epigenetic regulation of lasting gut homing receptor expression in CD4 + memory T cells. Mucosal Immunol 2017; 10:1443-1454. [PMID: 28198363 DOI: 10.1038/mi.2017.7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 01/17/2017] [Indexed: 02/04/2023]
Abstract
The concept of a "topographical memory" in lymphocytes implies a stable expression of homing receptors mediating trafficking of lymphocytes back to the tissue of initial activation. However, a significant plasticity of the gut-homing receptor α4β7 was found in CD8+ T cells, questioning the concept. We now demonstrate that α4β7 expression in murine CD4+ memory T cells is, in contrast, imprinted and remains stable in the absence of the inducing factor retinoic acid (RA) or other stimuli from mucosal environments. Repetitive rounds of RA treatment enhanced the stability of de novo induced α4β7. A novel enhancer element in the murine Itga4 locus was identified that showed, correlating to stability, selective DNA demethylation in mucosa-seeking memory cells and methylation-dependent transcriptional activity in a reporter gene assay. This implies that epigenetic mechanisms contribute to the stabilization of α4β7 expression. Analogous DNA methylation patterns could be observed in the human ITGA4 locus, suggesting that its epigenetic regulation is conserved between mice and men. These data prove that mucosa-specific homing mediated by α4β7 is imprinted in CD4+ memory T cells, reinstating the validity of the concept of "topographical memory" for mucosal tissues, and imply a critical role of epigenetic mechanisms.
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17
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Laqqan M, Hammadeh ME. Aberrations in sperm DNA methylation patterns of males suffering from reduced fecundity. Andrologia 2017; 50. [PMID: 29072328 DOI: 10.1111/and.12913] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2017] [Indexed: 01/06/2023] Open
Abstract
The purpose of this study was to evaluate the aberrations in sperm DNA methylation patterns of males suffering from reduced fecundity. A total of 108 males (65 males suffering from reduced fecundity as cases and 43 proven fertile males as a control) were included in the study. Thirty samples were subjected to 450K arrays as a screening phase, and then, three CpG sites located in the following genes: TYRO3, CGβ and FAM189A1 were selected to validate on 78 samples using deep bisulphite sequencing. A significant difference in the methylation level was found between cases and controls at all CpGs in TYRO3 gene-related amplicon (CpG1, p ≤ .003, CpG2, p ≤ .0001, CpG3, p ≤ .003 and CpG4, p ≤ .030) and CpG1 in CGβ gene-related amplicon (p ≤ .0001). Besides, a significant difference was found at two CpGs (CpG1, p ≤ .004 and CpG2, p ≤ .002) tested in the FAM189A1 gene-related amplicon. A significant correlation was found between the methylation level at CpG1 in the FAM189A1 gene and the different types of sperm motility. In conclusion, an alteration in the methylation levels of sperm DNA from males with reduced fecundity was showed. In addition, a relationship between variations in the methylation level of these CpGs and sperm motility has been observed.
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Affiliation(s)
- M Laqqan
- Department of Obstetrics & Gynecology, Assisted Reproduction Laboratory, Saarland University, Homburg, Germany
| | - M E Hammadeh
- Department of Obstetrics & Gynecology, Assisted Reproduction Laboratory, Saarland University, Homburg, Germany
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18
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Laqqan M, Solomayer EF, Hammadeh M. Aberrations in sperm DNA methylation patterns are associated with abnormalities in semen parameters of subfertile males. Reprod Biol 2017; 17:246-251. [DOI: 10.1016/j.repbio.2017.05.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 05/15/2017] [Accepted: 05/18/2017] [Indexed: 01/07/2023]
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19
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Schultheiss CS, Laggai S, Czepukojc B, Hussein UK, List M, Barghash A, Tierling S, Hosseini K, Golob-Schwarzl N, Pokorny J, Hachenthal N, Schulz M, Helms V, Walter J, Zimmer V, Lammert F, Bohle RM, Dandolo L, Haybaeck J, Kiemer AK, Kessler SM. The long non-coding RNA H19 suppresses carcinogenesis and chemoresistance in hepatocellular carcinoma. Cell Stress 2017; 1:37-54. [PMID: 31225433 PMCID: PMC6551655 DOI: 10.15698/cst2017.10.105] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The long non-coding RNA (lncRNA) H19 represents a maternally expressed and epigenetically regulated imprinted gene product and is discussed to have either tumor-promoting or tumor-suppressive actions. Recently, H19 was shown to be regulated under inflammatory conditions. Therefore, aim of this study was to determine the function of H19 in hepatocellular carcinoma (HCC), an inflammation-associated type of tumor. In four different human HCC patient cohorts H19 was distinctly downregulated in tumor tissue compared to normal or non-tumorous adjacent tissue. We therefore determined the action of H19 in three different human hepatoma cell lines (HepG2, Plc/Prf5, and Huh7). Clonogenicity and proliferation assays showed that H19 overexpression could suppress tumor cell survival and proliferation after treatment with either sorafenib or doxorubicin, suggesting chemosensitizing actions of H19. Since HCC displays a highly chemoresistant tumor entity, cell lines resistant to doxorubicin or sorafenib were established. In all six chemoresistant cell lines H19 expression was significantly downregulated. The promoter methylation of the H19 gene was significantly different in chemoresistant cell lines compared to their sensitive counterparts. Chemoresistant cells were sensitized after H19 overexpression by either increasing the cytotoxic action of doxorubicin or decreasing cell proliferation upon sorafenib treatment. An H19 knockout mouse model (H19Δ3) showed increased tumor development and tumor cell proliferation after treatment with the carcinogen diethylnitrosamine (DEN) independent of the reciprocally imprinted insulin-like growth factor 2 (IGF2). In conclusion, H19 suppresses hepatocarcinogenesis, hepatoma cell growth, and HCC chemoresistance. Thus, mimicking H19 action might be a potential target to overcome chemoresistance in future HCC therapy.
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Affiliation(s)
| | - Stephan Laggai
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Saarbrücken, Germany
| | - Beate Czepukojc
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Saarbrücken, Germany
| | - Usama K Hussein
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Saarbrücken, Germany.,Faculty of Science, Beni-Suef University, Bani Suwaif, Egypt
| | - Markus List
- Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany
| | - Ahmad Barghash
- School of Electrical Engineering and Information Technology, German Jordanian University, Amman, Jordan
| | - Sascha Tierling
- Department of Genetics and Epigenetics, Saarland University, Saarbrücken, Germany
| | - Kevan Hosseini
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Saarbrücken, Germany
| | | | - Juliane Pokorny
- Institute of Pathology, Saarland University, Campus Homburg, Homburg (Saar), Germany
| | - Nina Hachenthal
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Saarbrücken, Germany
| | - Marcel Schulz
- Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany.,Cluster of Excellence in Multimodal Computing and Interaction, Saarland Informatics Campus, Saarbrücken, Germany
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Jörn Walter
- Department of Genetics and Epigenetics, Saarland University, Saarbrücken, Germany
| | - Vincent Zimmer
- Department of Medicine II, Saarland University Medical Center, Saarland University, Homburg (Saar), Germany
| | - Frank Lammert
- Department of Medicine II, Saarland University Medical Center, Saarland University, Homburg (Saar), Germany
| | - Rainer M Bohle
- Institute of Pathology, Saarland University, Campus Homburg, Homburg (Saar), Germany
| | - Luisa Dandolo
- Institut Cochin, Inserm U1016, CNRS UMR 8104, Paris, France
| | - Johannes Haybaeck
- Institute of Pathology, Medical University of Graz, Graz, Austria.,Department of Pharmacy, Pharmaceutical Biology, Saarland University, Saarbrücken, Germany
| | - Alexandra K Kiemer
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Saarbrücken, Germany
| | - Sonja M Kessler
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, Saarbrücken, Germany.,Institute of Pathology, Medical University of Graz, Graz, Austria
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20
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Aberrant DNA methylation patterns of human spermatozoa in current smoker males. Reprod Toxicol 2017; 71:126-133. [DOI: 10.1016/j.reprotox.2017.05.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 03/21/2017] [Accepted: 05/23/2017] [Indexed: 12/11/2022]
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21
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Laqqan M, Solomayer EF, Hammadeh M. Association between alterations in DNA methylation level of spermatozoa at CpGs dinucleotide and male subfertility problems. Andrologia 2017; 50. [DOI: 10.1111/and.12832] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/15/2017] [Indexed: 01/01/2023] Open
Affiliation(s)
- M. Laqqan
- Gynecology & Assisted Reproduction Laboratory; Department of Obstetrics; Saarland University; Saarland Germany
| | - E. F. Solomayer
- Gynecology & Assisted Reproduction Laboratory; Department of Obstetrics; Saarland University; Saarland Germany
| | - M. Hammadeh
- Gynecology & Assisted Reproduction Laboratory; Department of Obstetrics; Saarland University; Saarland Germany
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22
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Laqqan M, Tierling S, Alkhaled Y, Lo Porto C, Solomayer EF, Hammadeh M. Spermatozoa from males with reduced fecundity exhibit differential DNA methylation patterns. Andrology 2017; 5:971-978. [DOI: 10.1111/andr.12362] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 03/06/2017] [Accepted: 03/09/2017] [Indexed: 01/30/2023]
Affiliation(s)
- M. Laqqan
- Department of Obstetrics & Gynecology; Assisted Reproduction Laboratory; Saarland University; Homburg/Saar Germany
| | - S. Tierling
- Life Science; Department of Genetics & Epigenetics; Saarland University; Saarbrücken Germany
| | - Y. Alkhaled
- Department of Obstetrics & Gynecology; Assisted Reproduction Laboratory; Saarland University; Homburg/Saar Germany
| | - C. Lo Porto
- Life Science; Department of Genetics & Epigenetics; Saarland University; Saarbrücken Germany
| | - E. F. Solomayer
- Department of Obstetrics & Gynecology; Assisted Reproduction Laboratory; Saarland University; Homburg/Saar Germany
| | - M. Hammadeh
- Department of Obstetrics & Gynecology; Assisted Reproduction Laboratory; Saarland University; Homburg/Saar Germany
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23
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Al Khaled Y, Tierling S, Laqqan M, Lo Porto C, Hammadeh ME. Cigarette smoking induces only marginal changes in sperm DNA methylation levels of patients undergoing intracytoplasmic sperm injection treatment. Andrologia 2017; 50. [DOI: 10.1111/and.12818] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2017] [Indexed: 12/19/2022] Open
Affiliation(s)
- Y. Al Khaled
- Gynecology & Assisted Reproduction Laboratory; Department of Obstetrics; University of Saarland; Homburg Germany
| | - S. Tierling
- FR8.3 Life Science; Department of Genetics & Epigenetics; Saarland University; Saarbrücken Germany
| | - M. Laqqan
- Gynecology & Assisted Reproduction Laboratory; Department of Obstetrics; University of Saarland; Homburg Germany
| | - C. Lo Porto
- FR8.3 Life Science; Department of Genetics & Epigenetics; Saarland University; Saarbrücken Germany
| | - M. E. Hammadeh
- Gynecology & Assisted Reproduction Laboratory; Department of Obstetrics; University of Saarland; Homburg Germany
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24
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Pink M, Ratsch BA, Mardahl M, Durek P, Polansky JK, Karl M, Baumgrass R, Wallner S, Cadenas C, Gianmoena K, Floess S, Chen W, Nordstroem K, Tierling S, Olek S, Walter J, Hamann A, Syrbe U. Imprinting of Skin/Inflammation Homing in CD4+ T Cells Is Controlled by DNA Methylation within the Fucosyltransferase 7 Gene. THE JOURNAL OF IMMUNOLOGY 2016; 197:3406-3414. [PMID: 27591321 DOI: 10.4049/jimmunol.1502434] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 08/08/2016] [Indexed: 11/19/2022]
Abstract
E- and P-selectin ligands (E- and P-ligs) guide effector memory T cells into skin and inflamed regions, mediate the inflammatory recruitment of leukocytes, and contribute to the localization of hematopoietic precursor cells. A better understanding of their molecular regulation is therefore of significant interest with regard to therapeutic approaches targeting these pathways. In this study, we examined the transcriptional regulation of fucosyltransferase 7 (FUT7), an enzyme crucial for generation of the glycosylated E- and P-ligs. We found that high expression of the coding gene fut7 in murine CD4+ T cells correlates with DNA demethylation within a minimal promoter in skin/inflammation-seeking effector memory T cells. Retinoic acid, a known inducer of the gut-homing phenotype, abrogated the activation-induced demethylation of this region, which contains a cAMP responsive element. Methylation of the promoter or mutation of the cAMP responsive element abolished promoter activity and the binding of CREB, confirming the importance of this region and of its demethylation for fut7 transcription in T cells. Furthermore, studies on human CD4+ effector memory T cells confirmed demethylation within FUT7 corresponding to high FUT7 expression. Monocytes showed an even more extensive demethylation of the FUT7 gene whereas hepatocytes, which lack selectin ligand expression, exhibited extensive methylation. In conclusion, we show that DNA demethylation within the fut7 gene controls selectin ligand expression in mice and humans, including the inducible topographic commitment of T cells for skin and inflamed sites.
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Affiliation(s)
- Matthias Pink
- Experimental Rheumatology, German Rheumatism Research Center, 10117 Berlin, Germany
| | - Boris A Ratsch
- Experimental Rheumatology, German Rheumatism Research Center, 10117 Berlin, Germany
| | - Maibritt Mardahl
- Experimental Rheumatology, German Rheumatism Research Center, 10117 Berlin, Germany
| | - Pawel Durek
- Experimental Rheumatology, German Rheumatism Research Center, 10117 Berlin, Germany
| | - Julia K Polansky
- Experimental Rheumatology, German Rheumatism Research Center, 10117 Berlin, Germany
| | - Martin Karl
- Signal Transduction, German Rheumatism Research Center, 10117 Berlin, Germany
| | - Ria Baumgrass
- Signal Transduction, German Rheumatism Research Center, 10117 Berlin, Germany
| | - Stefan Wallner
- Institute of Clinical and Laboratory Medicine, University Hospital Regensburg, 93042 Regensburg, Germany
| | - Cristina Cadenas
- Leibniz Research Center for Working Environment and Human Factors, 44139 Dortmund, Germany
| | - Kathrin Gianmoena
- Leibniz Research Center for Working Environment and Human Factors, 44139 Dortmund, Germany
| | - Stefan Floess
- Experimental Immunology, Helmholz Center for Infection Research, 38124 Braunschweig, Germany
| | - Wei Chen
- Max Delbrück Center for Molecular Medicine, 13092 Berlin, Germany
| | - Karl Nordstroem
- Laboratory of Epigenetics, Saarland University, 66123 Saarbrücken, Germany
| | - Sascha Tierling
- Laboratory of Epigenetics, Saarland University, 66123 Saarbrücken, Germany
| | - Sven Olek
- Epiontis GmbH, 12489 Berlin, Germany; and
| | - Jörn Walter
- Laboratory of Epigenetics, Saarland University, 66123 Saarbrücken, Germany
| | - Alf Hamann
- Experimental Rheumatology, German Rheumatism Research Center, 10117 Berlin, Germany
| | - Uta Syrbe
- Medical Clinic for Gastroenterology, Infectious Diseases, and Rheumatology, Charité University Hospital, 12200 Berlin, Germany
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25
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Quantitative comparison of DNA methylation assays for biomarker development and clinical applications. Nat Biotechnol 2016; 34:726-37. [PMID: 27347756 DOI: 10.1038/nbt.3605] [Citation(s) in RCA: 218] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 05/10/2016] [Indexed: 02/08/2023]
Abstract
DNA methylation patterns are altered in numerous diseases and often correlate with clinically relevant information such as disease subtypes, prognosis and drug response. With suitable assays and after validation in large cohorts, such associations can be exploited for clinical diagnostics and personalized treatment decisions. Here we describe the results of a community-wide benchmarking study comparing the performance of all widely used methods for DNA methylation analysis that are compatible with routine clinical use. We shipped 32 reference samples to 18 laboratories in seven different countries. Researchers in those laboratories collectively contributed 21 locus-specific assays for an average of 27 predefined genomic regions, as well as six global assays. We evaluated assay sensitivity on low-input samples and assessed the assays' ability to discriminate between cell types. Good agreement was observed across all tested methods, with amplicon bisulfite sequencing and bisulfite pyrosequencing showing the best all-round performance. Our technology comparison can inform the selection, optimization and use of DNA methylation assays in large-scale validation studies, biomarker development and clinical diagnostics.
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Laurentino S, Borgmann J, Gromoll J. On the origin of sperm epigenetic heterogeneity. Reproduction 2016; 151:R71-8. [PMID: 26884419 DOI: 10.1530/rep-15-0436] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 02/15/2016] [Indexed: 01/05/2023]
Abstract
The influence of epigenetic modifications on reproduction and on the function of male germ cells has been thoroughly demonstrated. In particular, aberrant DNA methylation levels in sperm have been associated with abnormal sperm parameters, lower fertilization rates and impaired embryo development. Recent reports have indicated that human sperm might be epigenetically heterogeneous and that abnormal DNA methylation levels found in the sperm of infertile men could be due to the presence of sperm populations with different epigenetic quality. However, the origin and the contribution of different germ cell types to this suspected heterogeneity remain unclear. In this review, we focus on sperm epigenetics at the DNA methylation level and its importance in reproduction. We take into account the latest developments and hypotheses concerning the functional significance of epigenetic heterogeneity coming from the field of stem cell and cancer biology and discuss the potential importance and consequences of sperm epigenetic heterogeneity for reproduction, male (in)fertility and assisted reproductive technologies (ART). Based on the current information, we propose a model in which spermatogonial stem cell variability, either intrinsic or due to external factors (such as endocrine action and environmental stimuli), can lead to epigenetic sperm heterogeneity, sperm epimutations and male infertility. The elucidation of the precise causes for epimutations, the conception of adequate therapeutic options and the development of sperm selection technologies based on epigenetic quality should be regarded as crucial to the improvement of ART outcome in the near future.
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Affiliation(s)
- Sandra Laurentino
- Centre of Reproductive Medicine and AndrologyAlbert-Schweitzer Campus, Münster, Germany
| | - Jennifer Borgmann
- Centre of Reproductive Medicine and AndrologyAlbert-Schweitzer Campus, Münster, Germany
| | - Jörg Gromoll
- Centre of Reproductive Medicine and AndrologyAlbert-Schweitzer Campus, Münster, Germany
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Current and Emerging Technologies for the Analysis of the Genome-Wide and Locus-Specific DNA Methylation Patterns. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 945:343-430. [DOI: 10.1007/978-3-319-43624-1_15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Noehammer C, Pulverer W, Hassler MR, Hofner M, Wielscher M, Vierlinger K, Liloglou T, McCarthy D, Jensen TJ, Nygren A, Gohlke H, Trooskens G, Braspenning M, Van Criekinge W, Egger G, Weinhaeusel A. Strategies for validation and testing of DNA methylation biomarkers. Epigenomics 2015; 6:603-22. [PMID: 25531255 DOI: 10.2217/epi.14.43] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
DNA methylation is a stable covalent epigenetic modification of primarily CpG dinucleotides that has recently gained considerable attention for its use as a biomarker in different clinical settings, including disease diagnosis, prognosis and therapeutic response prediction. Although the advent of genome-wide DNA methylation profiling in primary disease tissue has provided a manifold resource for biomarker development, only a tiny fraction of DNA methylation-based assays have reached clinical testing. Here, we provide a critical overview of different analytical methods that are suitable for biomarker validation, including general study design considerations, which might help to streamline epigenetic marker development. Furthermore, we highlight some of the recent marker validation studies and established markers that are currently commercially available for assisting in clinical management of different cancers.
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Affiliation(s)
- Christa Noehammer
- Health & Environment Department, Molecular Diagnostics, AIT Austrian Institute of Technology, Vienna, Austria
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Drogan D, Boeing H, Janke J, Schmitt B, Zhou Y, Walter J, Pischon T, Tierling S. Regional distribution of body fat in relation to DNA methylation within the LPL, ADIPOQ and PPARγ promoters in subcutaneous adipose tissue. Nutr Diabetes 2015; 5:e168. [PMID: 26148147 PMCID: PMC4521174 DOI: 10.1038/nutd.2015.19] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 05/28/2015] [Indexed: 12/25/2022] Open
Abstract
Obesity may be related to differential DNA methylation and thus to differential expression of key genes in adipose tissue metabolism, such as LPL, ADIPOQ and PPARγ. Using subcutaneous adipose tissue (SAT) from 59 individuals of the European Prospective Investigation into Cancer and Nutrition–Potsdam study, we performed quantitative DNA methylation analysis within the promoters of LPL (LPL-CG1 and -CG2), ADIPOQ (ADIPOQ-CG1 and-CG2) and PPARγ (PPARγ-CG1). We then studied DNA methylation in relation to SAT gene expression, body composition measured using whole-body magnetic resonance imaging, body mass index (BMI), waist circumference (WC) and long-term changes in BMI and WC. For LPL-CG1 and LPL-CG2, higher methylation levels were associated with lower LPL expression, but with higher past WC gain. LPL-CG1 was also positively associated with BMI, WC, and visceral and subcutaneous fat mass. ADIPOQ-CG1 or -CG2 methylation exhibited no association with ADIPOQ expression or with anthropometric parameters. PPARγ-CG1 methylation was significantly higher in individuals with higher visceral fat mass. Among the investigated sites, LPL-CG1 methylation showed the strongest association with gene expression and regional body fat distribution, thereby possibly linking the degree of obesity with major metabolic processes in SAT.
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Affiliation(s)
- D Drogan
- 1] Department of Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Nuthetal, Germany [2] AOK Research Institute (WIdO), AOK Bundesverband, Berlin, Germany
| | - H Boeing
- Department of Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Nuthetal, Germany
| | - J Janke
- Molecular Epidemiology Group, Max Delbrueck Center for Molecular Medicine (MDC), Berlin-Buch, Germany
| | - B Schmitt
- Department of Genetics/Epigenetics, FR8.3 Life Sciences, Saarland University, Saarbrücken, Germany
| | - Y Zhou
- 1] Department of Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Nuthetal, Germany [2] Institute of Sociology and Demography, University of Rostock, Rostock, Germany
| | - J Walter
- Department of Genetics/Epigenetics, FR8.3 Life Sciences, Saarland University, Saarbrücken, Germany
| | - T Pischon
- 1] Department of Epidemiology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Nuthetal, Germany [2] Molecular Epidemiology Group, Max Delbrueck Center for Molecular Medicine (MDC), Berlin-Buch, Germany
| | - S Tierling
- Department of Genetics/Epigenetics, FR8.3 Life Sciences, Saarland University, Saarbrücken, Germany
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Redshaw N, Huggett JF, Taylor MS, Foy CA, Devonshire AS. Quantification of epigenetic biomarkers: an evaluation of established and emerging methods for DNA methylation analysis. BMC Genomics 2014; 15:1174. [PMID: 25539843 PMCID: PMC4523014 DOI: 10.1186/1471-2164-15-1174] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 12/10/2014] [Indexed: 02/06/2023] Open
Abstract
Background DNA methylation is an important epigenetic mechanism in several human diseases, most notably cancer. The quantitative analysis of DNA methylation patterns has the potential to serve as diagnostic and prognostic biomarkers, however, there is currently a lack of consensus regarding the optimal methodologies to quantify methylation status. To address this issue we compared five analytical methods: (i) MethyLight qPCR, (ii) MethyLight digital PCR (dPCR), methylation-sensitive and -dependent restriction enzyme (MSRE/MDRE) digestion followed by (iii) qPCR or (iv) dPCR, and (v) bisulfite amplicon next generation sequencing (NGS). The techniques were evaluated for linearity, accuracy and precision. Results MethyLight qPCR displayed the best linearity across the range of tested samples. Observed methylation measured by MethyLight- and MSRE/MDRE-qPCR and -dPCR were not significantly different to expected values whilst bisulfite amplicon NGS analysis over-estimated methylation content. Bisulfite amplicon NGS showed good precision, whilst the lower precision of qPCR and dPCR analysis precluded discrimination of differences of < 25% in methylation status. A novel dPCR MethyLight assay is also described as a potential method for absolute quantification that simultaneously measures both sense and antisense DNA strands following bisulfite treatment. Conclusions Our findings comprise a comprehensive benchmark for the quantitative accuracy of key methods for methylation analysis and demonstrate their applicability to the quantification of circulating tumour DNA biomarkers by using sample concentrations that are representative of typical clinical isolates. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1174) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Jim F Huggett
- LGC, Queens Road, Teddington, Middlesex, TW11 0LY, UK.
| | - Martin S Taylor
- Medical and Developmental Genetics Section, MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK.
| | - Carole A Foy
- LGC, Queens Road, Teddington, Middlesex, TW11 0LY, UK.
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Deutsch AJA, Rinner B, Wenzl K, Pichler M, Troppan K, Steinbauer E, Schwarzenbacher D, Reitter S, Feichtinger J, Tierling S, Prokesch A, Scheideler M, Krogsdam A, Thallinger GG, Schaider H, Beham-Schmid C, Neumeister P. NR4A1-mediated apoptosis suppresses lymphomagenesis and is associated with a favorable cancer-specific survival in patients with aggressive B-cell lymphomas. Blood 2014; 123:2367-77. [PMID: 24553175 DOI: 10.1182/blood-2013-08-518878] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
NR4A1 (Nur77) and NR4A3 (Nor-1) function as tumor suppressor genes as demonstrated by the rapid development of acute myeloid leukemia in the NR4A1 and NR4A3 knockout mouse. The aim of our study was to investigate NR4A1 and NR4A3 expression and function in lymphoid malignancies. We found a vastly reduced expression of NR4A1 and NR4A3 in chronic lymphocytic B-cell leukemia (71%), in follicular lymphoma (FL, 70%), and in diffuse large B-cell lymphoma (DLBCL, 74%). In aggressive lymphomas (DLBCL and FL grade 3), low NR4A1 expression was significantly associated with a non-germinal center B-cell subtype and with poor overall survival. To investigate the function of NR4A1 in lymphomas, we overexpressed NR4A1 in several lymphoma cell lines. Overexpression of NR4A1 led to a higher proportion of lymphoma cells undergoing apoptosis. To test the tumor suppressor function of NR4A1 in vivo, the stable lentiviral-transduced SuDHL4 lymphoma cell line harboring an inducible NR4A1 construct was further investigated in xenografts. Induction of NR4A1 abrogated tumor growth in the NSG mice, in contrast to vector controls, which formed massive tumors. Our data suggest that NR4A1 has proapoptotic functions in aggressive lymphoma cells and define NR4A1 as a novel gene with tumor suppressor properties involved in lymphomagenesis.
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MESH Headings
- Animals
- Apoptosis/genetics
- Blotting, Western
- Cell Line, Tumor
- DNA-Binding Proteins/genetics
- Heterografts
- Humans
- Immunohistochemistry
- Kaplan-Meier Estimate
- Lymphoma, B-Cell/genetics
- Lymphoma, B-Cell/mortality
- Mice
- Mice, Inbred NOD
- Mice, SCID
- Nuclear Receptor Subfamily 4, Group A, Member 1/genetics
- Proportional Hazards Models
- Receptors, Steroid/genetics
- Receptors, Thyroid Hormone/genetics
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