1
|
Maji RK, Czepukojc B, Scherer M, Tierling S, Cadenas C, Gianmoena K, Gasparoni N, Nordström K, Gasparoni G, Laggai S, Yang X, Sinha A, Ebert P, Falk-Paulsen M, Kinkley S, Hoppstädter J, Chung HR, Rosenstiel P, Hengstler JG, Walter J, Schulz MH, Kessler SM, Kiemer AK. Alterations in the hepatocyte epigenetic landscape in steatosis. Epigenetics Chromatin 2023; 16:30. [PMID: 37415213 DOI: 10.1186/s13072-023-00504-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 06/21/2023] [Indexed: 07/08/2023] Open
Abstract
Fatty liver disease or the accumulation of fat in the liver, has been reported to affect the global population. This comes with an increased risk for the development of fibrosis, cirrhosis, and hepatocellular carcinoma. Yet, little is known about the effects of a diet containing high fat and alcohol towards epigenetic aging, with respect to changes in transcriptional and epigenomic profiles. In this study, we took up a multi-omics approach and integrated gene expression, methylation signals, and chromatin signals to study the epigenomic effects of a high-fat and alcohol-containing diet on mouse hepatocytes. We identified four relevant gene network clusters that were associated with relevant pathways that promote steatosis. Using a machine learning approach, we predict specific transcription factors that might be responsible to modulate the functionally relevant clusters. Finally, we discover four additional CpG loci and validate aging-related differential CpG methylation. Differential CpG methylation linked to aging showed minimal overlap with altered methylation in steatosis.
Collapse
Affiliation(s)
- Ranjan Kumar Maji
- Institute for Cardiovascular Regeneration, Goethe-University, 60590, Frankfurt, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main, 60590, Frankfurt, Germany
| | - Beate Czepukojc
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, 66123, Saarbrücken, Germany
| | - Michael Scherer
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain
| | - Sascha Tierling
- Department of Genetics, Saarland University, 66123, Saarbrücken, Germany
| | - Cristina Cadenas
- IfADo: Leibniz Research Centre for Working Environment and Human Factors, Dortmund, Germany
| | - Kathrin Gianmoena
- IfADo: Leibniz Research Centre for Working Environment and Human Factors, Dortmund, Germany
| | - Nina Gasparoni
- Department of Genetics, Saarland University, 66123, Saarbrücken, Germany
| | - Karl Nordström
- Department of Genetics, Saarland University, 66123, Saarbrücken, Germany
| | - Gilles Gasparoni
- Department of Genetics, Saarland University, 66123, Saarbrücken, Germany
| | - Stephan Laggai
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, 66123, Saarbrücken, Germany
| | - Xinyi Yang
- Institute of Medical Bioinformatics and Biostatistics, Philipps University of Marburg, 35032, Marburg, Germany
| | - Anupam Sinha
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105, Kiel, Germany
| | - Peter Ebert
- Core Unit Bioinformatics, Medical Faculty, Heinrich Heine University, 40225, Düsseldorf, Germany
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123, Saarbrücken, Germany
| | - Maren Falk-Paulsen
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105, Kiel, Germany
| | - Sarah Kinkley
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Jessica Hoppstädter
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, 66123, Saarbrücken, Germany
| | - Ho-Ryun Chung
- Institute of Medical Bioinformatics and Biostatistics, Philipps University of Marburg, 35032, Marburg, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105, Kiel, Germany
| | - Jan G Hengstler
- IfADo: Leibniz Research Centre for Working Environment and Human Factors, Dortmund, Germany
| | - Jörn Walter
- Department of Genetics, Saarland University, 66123, Saarbrücken, Germany
| | - Marcel H Schulz
- Institute for Cardiovascular Regeneration, Goethe-University, 60590, Frankfurt, Germany.
- German Centre for Cardiovascular Research (DZHK), Partner Site Rhine-Main, 60590, Frankfurt, Germany.
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123, Saarbrücken, Germany.
- Excellence Cluster on Multimodal Computing and Interaction, Saarland University, 66123, Saarbrücken, Germany.
| | - Sonja M Kessler
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, 66123, Saarbrücken, Germany.
- Institute of Pharmacy, Experimental Pharmacology for Natural Sciences, Martin Luther University Halle-Wittenberg, Halle, Germany.
- Halle Research Centre for Drug Therapy (HRCDT), Halle, Germany.
| | - Alexandra K Kiemer
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, 66123, Saarbrücken, Germany.
| |
Collapse
|
2
|
Cheraghpour M, Askari M, Tierling S, Shojaee S, Sadeghi A, Ketabi Moghadam P, Khazdouz M, Asadzadeh Aghdaei H, Piroozkhah M, Nazemalhosseini-Mojarad E, Fatemi N. A systematic review and meta-analysis for the association of the insulin-like growth factor1 pathway genetic polymorphisms with colorectal cancer susceptibility. Front Oncol 2023; 13:1168942. [PMID: 37284192 PMCID: PMC10240407 DOI: 10.3389/fonc.2023.1168942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/04/2023] [Indexed: 06/08/2023] Open
Abstract
Background The receptors, ligands, and associated proteins of the insulin-like growth factor (IGF) family are involved in cancer development. The IGF1 receptor and its accompanying signaling cascade are a crucial growth-regulatory mechanism that plays an important role in colorectal cancer (CRC) proliferation and differentiation. IRS1 (Insulin receptor substrate-1), a major substrate for the IGF1R, is involved in cell growth and promotes tumorigenesis. There are shreds of evidence from prior research suggesting that IGF system polymorphisms may influence susceptibility to CRC. However, the findings in this area were contradictory. Accordingly, we carried out a systematic literature search to identify all case-control, cross-sectional, and cohort studies on the association between various polymorphisms across four IGF1 pathway genes (IGF1, IGF1R, IRS1, and IRS2) and the risk of CRC. Methods We performed a comprehensive search strategy in PubMed, Scopus, and Web of Science databases for articles available until Aug 30, 2022. A total of 26 eligible studies with IGF1/IGF1R, IRS1 and IRS2 polymorphisms; met the inclusion criteria. All case-control studies for IGF1 rs6214C>T, IRS1 rs1801278G>A, and IRS2 rs1805097G>A comprising 22,084 cases and 29,212 controls were included in the current meta-analysis. The pooled odds ratios (ORs) with 95% confidence intervals (CIs) were used to evaluate relationships between the polymorphisms and CRC susceptibility. All statistical analyses were performed using STATA software version 14.0. Results The meta-analysis of available data for rs6214C>T, rs1801278G>A, and rs1805097G>A showed a significant association between these polymorphisms and an increased CRC risk in some of the comparisons studied (rs6214C>T, pooled OR for CC = 0.43, 95% CI 0.21- 0.87, P = 0.019; rs1801278G>A, OR for GA = 0.74, 95% CI 0.58-0.94, P = 0.016; rs1805097G>A, OR for GA = 0.83, 95% CI 0.71-0.96, P = 0.013). Nevertheless, the meta-analysis did not include other genetic variations in IGF1, IGF1R, IRS1, and IRS2 due to heterogeneity and limited sample size. Conclusions This systematic review and meta-analysis provide evidence that genetic variants in IGF1 rs6214C>T, IRS1 rs1801278G>A, and IRS2 rs1805097G>A are associated with an increased risk of CRC. These findings may contribute to a better understanding of the complex genetic mechanisms involved in CRC development and could inform future research on prevention and treatment strategies for this disease.
Collapse
Affiliation(s)
- Makan Cheraghpour
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masomeh Askari
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sascha Tierling
- Department of Genetics/Epigenetics, Faculty NT, Saarland University, Saarbrücken, Germany
| | - Sajad Shojaee
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amir Sadeghi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Pardis Ketabi Moghadam
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Khazdouz
- Growth and Development Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Moein Piroozkhah
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, 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
| | - Nayeralsadat Fatemi
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| |
Collapse
|
3
|
Kärcher J, Schulze B, Dörr A, Tierling S, Walter J. Transfer of blocker-based qPCR reactions for DNA methylation analysis into a microfluidic LoC system using thermal modeling. Biomicrofluidics 2022; 16:064102. [PMID: 36506005 PMCID: PMC9729016 DOI: 10.1063/5.0108374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 11/11/2022] [Indexed: 06/17/2023]
Abstract
Changes in the DNA methylation landscape are associated with many diseases like cancer. Therefore, DNA methylation analysis is of great interest for molecular diagnostics and can be applied, e.g., for minimally invasive diagnostics in liquid biopsy samples like blood plasma. Sensitive detection of local de novo methylation, which occurs in various cancer types, can be achieved with quantitative HeavyMethyl-PCR using oligonucleotides that block the amplification of unmethylated DNA. A transfer of these quantitative PCRs (qPCRs) into point-of-care (PoC) devices like microfluidic Lab-on-Chip (LoC) cartridges can be challenging as LoC systems show significantly different thermal properties than qPCR cyclers. We demonstrate how an adequate thermal model of the specific LoC system can help us to identify a suitable thermal profile, even for complex HeavyMethyl qPCRs, with reduced experimental effort. Using a simulation-based approach, we demonstrate a proof-of-principle for the successful LoC transfer of colorectal SEPT9/ACTB-qPCR from Epi Procolon® colorectal carcinoma test, by avoidance of oligonucleotide interactions.
Collapse
Affiliation(s)
- Janik Kärcher
- Robert Bosch GmbH, Corporate Research, Robert Bosch Campus 1, 71272 Renninge, Germany
| | - Britta Schulze
- Robert Bosch GmbH, Corporate Research, Robert Bosch Campus 1, 71272 Renninge, Germany
| | - Aaron Dörr
- Robert Bosch GmbH, Corporate Research, Robert Bosch Campus 1, 71272 Renninge, Germany
| | - Sascha Tierling
- University of Saarland, Institute for Genetics and Epigenetics, Campus Saarbrücken, 66123 Saarbrücken, Germany
| | - Jörn Walter
- University of Saarland, Institute for Genetics and Epigenetics, Campus Saarbrücken, 66123 Saarbrücken, Germany
| |
Collapse
|
4
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
5
|
Becker A, Schmartz GP, Gröger L, Grammes N, Galata V, Philippeit H, Weiland J, Ludwig N, Meese E, Tierling S, Walter J, Schwiertz A, Spiegel J, Wagenpfeil G, Faßbender K, Keller A, Unger MM. Effects of Resistant Starch on Symptoms, Fecal Markers, and Gut Microbiota in Parkinson's Disease - The RESISTA-PD Trial. Genomics Proteomics Bioinformatics 2022; 20:274-287. [PMID: 34839011 PMCID: PMC9684155 DOI: 10.1016/j.gpb.2021.08.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 05/31/2021] [Accepted: 11/22/2021] [Indexed: 01/05/2023]
Abstract
The composition of the gut microbiota is linked to multiple diseases, including Parkinson's disease (PD). Abundance of bacteria producing short-chain fatty acids (SCFAs) and fecal SCFA concentrations are reduced in PD. SCFAs exert various beneficial functions in humans. In the interventional, monocentric, open-label clinical trial "Effects of Resistant Starch on Bowel Habits, Short Chain Fatty Acids and Gut Microbiota in Parkinson'sDisease" (RESISTA-PD; ID: NCT02784145), we aimed at altering fecal SCFAs by an 8-week prebiotic intervention with resistant starch (RS). We enrolled 87 subjects in three study-arms: 32 PD patients received RS (PD + RS), 30 control subjects received RS, and 25 PD patients received solely dietary instructions. We performed paired-end 100 bp length metagenomic sequencing of fecal samples using the BGISEQ platform at an average of 9.9 GB. RS was well-tolerated. In the PD + RS group, fecal butyrate concentrations increased significantly, and fecal calprotectin concentrations dropped significantly after 8 weeks of RS intervention. Clinically, we observed a reduction in non-motor symptom load in the PD + RS group. The reference-based analysis of metagenomes highlighted stable alpha-diversity and beta-diversity across the three groups, including bacteria producing SCFAs. Reference-free analysis suggested punctual, yet pronounced differences in the metagenomic signature in the PD + RS group. RESISTA-PD highlights that a prebiotic treatment with RS is safe and well-tolerated in PD. The stable alpha-diversity and beta-diversity alongside altered fecal butyrate and calprotectin concentrations call for long-term studies, also investigating whether RS is able to modify the clinical course of PD.
Collapse
Affiliation(s)
- Anouck Becker
- Department of Neurology, Saarland University, D-66421 Homburg, Germany
| | | | - Laura Gröger
- Department of Human Genetics, Saarland University, D-66421 Homburg, Germany
| | - Nadja Grammes
- Chair for Clinical Bioinformatics, Saarland University, D-66123 Saarbrücken, Germany
| | - Valentina Galata
- Chair for Clinical Bioinformatics, Saarland University, D-66123 Saarbrücken, Germany
| | - Hannah Philippeit
- Department of Neurology, Saarland University, D-66421 Homburg, Germany
| | | | - Nicole Ludwig
- Department of Human Genetics, Saarland University, D-66421 Homburg, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University, D-66421 Homburg, Germany
| | - Sascha Tierling
- Department of Genetics/Epigenetics, Saarland University, D-66123 Saarbrücken, Germany
| | - Jörn Walter
- Department of Genetics/Epigenetics, Saarland University, D-66123 Saarbrücken, Germany
| | | | - Jörg Spiegel
- Department of Neurology, Saarland University, D-66421 Homburg, Germany
| | - Gudrun Wagenpfeil
- Institute of Medical Biometry, Epidemiology and Medical Informatics, Saarland University, D-66421 Homburg, Germany
| | - Klaus Faßbender
- Department of Neurology, Saarland University, D-66421 Homburg, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, D-66123 Saarbrücken, Germany,Department of Neurology, Stanford University, Palo Alto, CA 94305, USA
| | - Marcus M. Unger
- Department of Neurology, Saarland University, D-66421 Homburg, Germany,Corresponding author.
| |
Collapse
|
6
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
7
|
Mattonet K, Nowack-Weyers N, Vogel V, Moser D, Tierling S, Kasper-Sonnenberg M, Wilhelm M, Scherer M, Walter J, Hengstler JG, Schölmerich A, Kumsta R. Prenatal exposure to endocrine disrupting chemicals is associated with altered DNA methylation in cord blood. Epigenetics 2021; 17:935-952. [PMID: 34529553 DOI: 10.1080/15592294.2021.1975917] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Prenatal exposure to endocrine disrupting chemicals can interfere with development, and has been associated with social-cognitive functioning and adverse health outcomes later in life. Exposure-associated changes of DNA methylation (DNAm) patterns have been suggested as a possible mediator of this relationship. This study investigated whether prenatal low-dose exposure to polychlorinated biphenyls (PCBs) and polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) is associated with altered DNAm patterns across the genome in a Western urban-industrial population. In 142 mother-infant pairs from the Duisburg Birth Cohort Study, PCBs and PCDD/Fs levels were quantified from maternal blood during late pregnancy and associated with DNAm levels in cord blood using the Illumina EPIC beadchip. The epigenome-wide association studies (EWAS) identified 32 significantly differentially methylated positions (DMPs) and eight differentially methylated regions (DMRs) associated with six congeners of PCB and PCDD in females or males (FDRs < 0.05). DMPs and DMRs mapped to genes involved in neurodevelopment, gene regulation, and immune functioning. Weighted gene correlation network analysis (WGCNA) showed 31 co-methylated modules (FDRs < 0.05) associated with one congener of PCDF levels in females. Results of both analytical strategies indicate that prenatal exposure to PCBs and PCDD/Fs is associated with altered DNAm of genes involved in neurodevelopment, gene expression and immune functioning. DNAm and gene expression levels of several of these genes were previously associated with EDC exposure in rodent models. Follow-up studies will clarify whether these epigenetic changes might contribute to the origin for adverse mental and health outcomes.
Collapse
Affiliation(s)
- Katharina Mattonet
- Department of Genetic Psychology, Faculty of Psychology, Ruhr-University Bochum, Germany
| | - Nikola Nowack-Weyers
- Department of Genetic Psychology, Faculty of Psychology, Ruhr-University Bochum, Germany.,Department of Developmental Psychology, Faculty of Psychology, Ruhr-University Bochum, Germany
| | - Vanessa Vogel
- Department of Genetic Psychology, Faculty of Psychology, Ruhr-University Bochum, Germany
| | - Dirk Moser
- Department of Genetic Psychology, Faculty of Psychology, Ruhr-University Bochum, Germany
| | - Sascha Tierling
- Department of Genetics/ Epigenetics, Saarland University, Saarbrücken, Germany
| | - Monika Kasper-Sonnenberg
- Department of Hygiene Social and Environmental Medicine, Faculty of Medicine, Ruhr-University Bochum, Germany
| | - Michael Wilhelm
- Department of Hygiene Social and Environmental Medicine, Faculty of Medicine, Ruhr-University Bochum, Germany
| | - Michael Scherer
- Department of Genetics/ Epigenetics, Saarland University, Saarbrücken, Germany.,Research Group Computational Biology, Max-Planck-Institute for Informatics, Saarbrücken, Germany
| | - Jörn Walter
- Department of Genetics/ Epigenetics, Saarland University, Saarbrücken, Germany
| | - Jan G Hengstler
- Leibniz Research Centre for Working Environment and Human Factors, Technical University of Dortmund (IfADo), Dortmund, Germany
| | - Axel Schölmerich
- Department of Developmental Psychology, Faculty of Psychology, Ruhr-University Bochum, Germany
| | - Robert Kumsta
- Department of Genetic Psychology, Faculty of Psychology, Ruhr-University Bochum, Germany
| |
Collapse
|
8
|
Tierling S, Kattler K, Vogelgesang M, Pfuhl T, Lohse S, Lo Porto C, Schmitt B, Nastasja S, Salhab A, Smola S, Walter J. Rapid Base-Specific Calling of SARS-CoV-2 Variants of Concern Using Combined RT-PCR Melting Curve Screening and SIRPH Technology. Open Forum Infect Dis 2021; 8:ofab364. [PMID: 34409122 PMCID: PMC8364759 DOI: 10.1093/ofid/ofab364] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 07/12/2021] [Indexed: 12/01/2022] Open
Abstract
Background The emergence of novel variants of concern of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) demands fast and reliable detection of such variants in local populations. Methods Here we present a cost-efficient and fast workflow combining a prescreening of SARS-CoV-2-positive samples using reverse transcription polymerase chain reaction melting curve analysis with multiplexed IP-RP-HPLC-based single nucleotide primer extensions. Results The entire workflow from positive SARS-CoV-2 testing to base-specific identification of variants requires about 24 hours. Conclusions We applied the sensitive method to monitor local variant of concern outbreaks in SARS-CoV-2-positive samples collected in a confined region of Germany.
Collapse
Affiliation(s)
- Sascha Tierling
- Department of Genetics, Saarland University, Saarbrücken, Saarland, Germany
| | - Kathrin Kattler
- Department of Genetics, Saarland University, Saarbrücken, Saarland, Germany
| | - Markus Vogelgesang
- Institute of Virology, Saarland University Medical Center, Homburg, Saarland, Germany
| | - Thorsten Pfuhl
- Institute of Virology, Saarland University Medical Center, Homburg, Saarland, Germany
| | - Stefan Lohse
- Institute of Virology, Saarland University Medical Center, Homburg, Saarland, Germany
| | - Christina Lo Porto
- Department of Genetics, Saarland University, Saarbrücken, Saarland, Germany
| | - Beate Schmitt
- Department of Genetics, Saarland University, Saarbrücken, Saarland, Germany
| | - Seiwert Nastasja
- Institute of Virology, Saarland University Medical Center, Homburg, Saarland, Germany
| | - Abdulrahman Salhab
- Department of Genetics, Saarland University, Saarbrücken, Saarland, Germany
| | - Sigrun Smola
- Institute of Virology, Saarland University Medical Center, Homburg, Saarland, Germany
| | - Jörn Walter
- Department of Genetics, Saarland University, Saarbrücken, Saarland, Germany
| |
Collapse
|
9
|
Filipski K, Scherer M, Zeiner KN, Bucher A, Kleemann J, Jurmeister P, Hartung TI, Meissner M, Plate KH, Fenton TR, Walter J, Tierling S, Schilling B, Zeiner PS, Harter PN. DNA methylation-based prediction of response to immune checkpoint inhibition in metastatic melanoma. J Immunother Cancer 2021; 9:jitc-2020-002226. [PMID: 34281986 PMCID: PMC8291310 DOI: 10.1136/jitc-2020-002226] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2021] [Indexed: 12/18/2022] Open
Abstract
Background Therapies based on targeting immune checkpoints have revolutionized the treatment of metastatic melanoma in recent years. Still, biomarkers predicting long-term therapy responses are lacking. Methods A novel approach of reference-free deconvolution of large-scale DNA methylation data enabled us to develop a machine learning classifier based on CpG sites, specific for latent methylation components (LMC), that allowed for patient allocation to prognostic clusters. DNA methylation data were processed using reference-free analyses (MeDeCom) and reference-based computational tumor deconvolution (MethylCIBERSORT, LUMP). Results We provide evidence that DNA methylation signatures of tumor tissue from cutaneous metastases are predictive for therapy response to immune checkpoint inhibition in patients with stage IV metastatic melanoma. Conclusions These results demonstrate that LMC-based segregation of large-scale DNA methylation data is a promising tool for classifier development and treatment response estimation in cancer patients under targeted immunotherapy.
Collapse
Affiliation(s)
- Katharina Filipski
- Neurological Institute (Edinger Institute), University Hospital, Frankfurt am Main, Germany.,German Cancer Consortium (DKTK) Heidelberg, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Frankfurt Cancer Institute (FCI), Frankfurt am Main, Germany
| | - Michael Scherer
- Department of Genetics, University of Saarland, Saarbrücken, Germany.,Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany.,Graduate School of Computer Science, Saarland Informatics Campus, Saabrücken, Germany
| | - Kim N Zeiner
- Department of Dermatology, University Hospital, Frankfurt am Main, Germany
| | - Andreas Bucher
- Department of Radiology, University Hospital, Frankfurt am Main, Germany
| | - Johannes Kleemann
- Department of Dermatology, University Hospital, Frankfurt am Main, Germany
| | - Philipp Jurmeister
- Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany.,Institute of Pathology, Ludwig Maximilians University Hospital Munich, Munich, Germany
| | - Tabea I Hartung
- Neurological Institute (Edinger Institute), University Hospital, Frankfurt am Main, Germany
| | - Markus Meissner
- Department of Dermatology, University Hospital, Frankfurt am Main, Germany
| | - Karl H Plate
- Neurological Institute (Edinger Institute), University Hospital, Frankfurt am Main, Germany.,German Cancer Consortium (DKTK) Heidelberg, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Frankfurt Cancer Institute (FCI), Frankfurt am Main, Germany
| | - Tim R Fenton
- School of Biosciences, University of Kent, Kent, UK
| | - Jörn Walter
- Department of Genetics, University of Saarland, Saarbrücken, Germany
| | - Sascha Tierling
- Department of Genetics, University of Saarland, Saarbrücken, Germany
| | - Bastian Schilling
- Department of Dermatology, University Hospital Würzburg, Würzburg, Germany
| | - Pia S Zeiner
- German Cancer Consortium (DKTK) Heidelberg, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Frankfurt Cancer Institute (FCI), Frankfurt am Main, Germany.,Dr. Senckenberg Institute of Neurooncology, University Hospital, Frankfurt am Main, Germany
| | - Patrick N Harter
- Neurological Institute (Edinger Institute), University Hospital, Frankfurt am Main, Germany .,German Cancer Consortium (DKTK) Heidelberg, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Frankfurt Cancer Institute (FCI), Frankfurt am Main, Germany
| |
Collapse
|
10
|
Schunk SJ, Kleber ME, März W, Pang S, Zewinger S, Triem S, Ege P, Reichert MC, Krawczyk M, Weber SN, Jaumann I, Schmit D, Sarakpi T, Wagenpfeil S, Kramann R, Boerwinkle E, Ballantyne CM, Grove ML, Tragante V, Pilbrow AP, Richards AM, Cameron VA, Doughty RN, Dubé MP, Tardif JC, Feroz-Zada Y, Sun M, Liu C, Ko YA, Quyyumi AA, Hartiala JA, Tang WHW, Hazen SL, Allayee H, McDonough CW, Gong Y, Cooper-DeHoff RM, Johnson JA, Scholz M, Teren A, Burkhardt R, Martinsson A, Smith JG, Wallentin L, James SK, Eriksson N, White H, Held C, Waterworth D, Trompet S, Jukema JW, Ford I, Stott DJ, Sattar N, Cresci S, Spertus JA, Campbell H, Tierling S, Walter J, Ampofo E, Niemeyer BA, Lipp P, Schunkert H, Böhm M, Koenig W, Fliser D, Laufs U, Speer T. Genetically determined NLRP3 inflammasome activation associates with systemic inflammation and cardiovascular mortality. Eur Heart J 2021; 42:1742-1756. [PMID: 33748830 PMCID: PMC8244638 DOI: 10.1093/eurheartj/ehab107] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/19/2020] [Accepted: 02/09/2021] [Indexed: 12/12/2022] Open
Abstract
AIMS Inflammation plays an important role in cardiovascular disease (CVD) development. The NOD-like receptor protein-3 (NLRP3) inflammasome contributes to the development of atherosclerosis in animal models. Components of the NLRP3 inflammasome pathway such as interleukin-1β can therapeutically be targeted. Associations of genetically determined inflammasome-mediated systemic inflammation with CVD and mortality in humans are unknown. METHODS AND RESULTS We explored the association of genetic NLRP3 variants with prevalent CVD and cardiovascular mortality in 538 167 subjects on the individual participant level in an explorative gene-centric approach without performing multiple testing. Functional relevance of single-nucleotide polymorphisms on NLRP3 inflammasome activation has been evaluated in monocyte-enriched peripheral blood mononuclear cells (PBMCs). Genetic analyses identified the highly prevalent (minor allele frequency 39.9%) intronic NLRP3 variant rs10754555 to affect NLRP3 gene expression. rs10754555 carriers showed significantly higher C-reactive protein and serum amyloid A plasma levels. Carriers of the G allele showed higher NLRP3 inflammasome activation in isolated human PBMCs. In carriers of the rs10754555 variant, the prevalence of coronary artery disease was significantly higher as compared to non-carriers with a significant interaction between rs10754555 and age. Importantly, rs10754555 carriers had significantly higher risk for cardiovascular mortality during follow-up. Inflammasome inducers (e.g. urate, triglycerides, apolipoprotein C3) modulated the association between rs10754555 and mortality. CONCLUSION The NLRP3 intronic variant rs10754555 is associated with increased systemic inflammation, inflammasome activation, prevalent coronary artery disease, and mortality. This study provides evidence for a substantial role of genetically driven systemic inflammation in CVD and highlights the NLRP3 inflammasome as a therapeutic target.
Collapse
Affiliation(s)
- Stefan J Schunk
- Department of Internal Medicine IV, Nephrology and Hypertension, Saarland University Hospital, Kirrberger Strasse, Building 41, 66424 Homburg/Saar, Germany
| | - Marcus E Kleber
- Vth Department of Medicine, University Heidelberg, Mannheim Medical Faculty, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
- SYNLAB MVZ Humangenetik Mannheim, Harrlachweg 1, 68163 Mannheim, Germany
| | - Winfried März
- Vth Department of Medicine, University Heidelberg, Mannheim Medical Faculty, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
- Clinical Institute of Medical and Laboratory Diagnostics, Medical University Graz, Auenbruggerpl. 2, 8036 Graz, Austria
- Synlab Academy, Synlab Holding GmbH, Harrlachweg 1, 68163 Mannheim, Germany
| | - Shichao Pang
- Kardiologie, Deutsches Herzzentrum München, Technische Universität München, Lazarettstraße 36, 80636 Munich, Germany
| | - Stephen Zewinger
- Department of Internal Medicine IV, Nephrology and Hypertension, Saarland University Hospital, Kirrberger Strasse, Building 41, 66424 Homburg/Saar, Germany
| | - Sarah Triem
- Department of Internal Medicine IV, Nephrology and Hypertension, Saarland University Hospital, Kirrberger Strasse, Building 41, 66424 Homburg/Saar, Germany
| | - Philipp Ege
- Department of Internal Medicine IV, Nephrology and Hypertension, Saarland University Hospital, Kirrberger Strasse, Building 41, 66424 Homburg/Saar, Germany
| | - Matthias C Reichert
- Department of Medicine II, Saarland University Medical Center, Kirrberger Straße, 66424 Homburg, Germany
| | - Marcin Krawczyk
- Department of Medicine II, Saarland University Medical Center, Kirrberger Straße, 66424 Homburg, Germany
- Laboratory of Metabolic Liver Diseases, Centre for Preclinical Research, Department of General, Transplant and Liver Surgery, Medical University of Warsaw, ul. Banacha 1B, CePT, 02-097 Warsaw, Poland
| | - Susanne N Weber
- Department of Medicine II, Saarland University Medical Center, Kirrberger Straße, 66424 Homburg, Germany
| | - Isabella Jaumann
- Department of Internal Medicine IV, Nephrology and Hypertension, Saarland University Hospital, Kirrberger Strasse, Building 41, 66424 Homburg/Saar, Germany
| | - David Schmit
- Department of Internal Medicine IV, Nephrology and Hypertension, Saarland University Hospital, Kirrberger Strasse, Building 41, 66424 Homburg/Saar, Germany
| | - Tamim Sarakpi
- Department of Internal Medicine IV, Nephrology and Hypertension, Saarland University Hospital, Kirrberger Strasse, Building 41, 66424 Homburg/Saar, Germany
| | - Stefan Wagenpfeil
- Institute of Medical Biometry, Epidemiology & Medical Informatics, Saarland University Campus Homburg/Saar, Kirrberger Straße, 66424 Homburg/Saar, Germany
| | - Rafael Kramann
- Division of Nephrology and Clinical Immunology, RWTH Aachen University, Pauwelsstrasse 30 52074 Aachen, Germany
- Institute of Experimental Medicine and Systems Biology, RWTH, Pauwelsstraße 30, 52074 Aachen, Germany
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, 1200 Pressler Street, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, BCM226, Houston, TX 77030, USA
| | - Christie M Ballantyne
- Section of Cardiovascular Research, Department of Medicine, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- Center of Cardiovascular Disease Prevention, Methodist DeBakey Heart and Vascular Center, 6565 Fannin St, Houston, TX 77030, USA
| | - Megan L Grove
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, 1200 Pressler Street, Houston, TX 77030, USA
| | - Vinicius Tragante
- Department of Cardiology, Heart and Lungs Division, UMC Utrecht, Heidelberglaan 100 3584 CX Utrecht, Netherlands
| | - Anna P Pilbrow
- The Christchurch Heart Institute, University of Otago Christchurch, 2 Riccarton Avenue, Christchurch Central City, Christchurch 8011, New Zealand
| | - A Mark Richards
- The Christchurch Heart Institute, University of Otago Christchurch, 2 Riccarton Avenue, Christchurch Central City, Christchurch 8011, New Zealand
| | - Vicky A Cameron
- The Christchurch Heart Institute, University of Otago Christchurch, 2 Riccarton Avenue, Christchurch Central City, Christchurch 8011, New Zealand
| | - Robert N Doughty
- Heart Health Research Group, University of Auckland, Level 2 / 22-30 Park Ave, Grafton, Auckland, New Zealand
| | - Marie-Pierre Dubé
- Montreal Heart Institute, 5000 Rue Bélanger, Montreal QC H1T 1C8, Canada
- Faculty of Medicine, Université der Montréal, Pavillon Roger-Gaudry, 2900 Edouard Montpetit Blvd, Montreal, Quebec H3T 1J4, Canada
| | - Jean-Claude Tardif
- Montreal Heart Institute, 5000 Rue Bélanger, Montreal QC H1T 1C8, Canada
- Faculty of Medicine, Université der Montréal, Pavillon Roger-Gaudry, 2900 Edouard Montpetit Blvd, Montreal, Quebec H3T 1J4, Canada
| | | | - Maxine Sun
- Faculty of Medicine, Université der Montréal, Pavillon Roger-Gaudry, 2900 Edouard Montpetit Blvd, Montreal, Quebec H3T 1J4, Canada
| | - Chang Liu
- Emory Clinical Cardiovascular Research Institute, Division of Cardiology, Emory University School of Medicine, 1462 Clifton Road NE, Atlanta, GA 30322, USA
| | - Yi-An Ko
- Department of Biostatistics and Bioinformatics, Rollins School of Public Healthy, Emory University, 1518 Clifton Road NE, Atlanta, GA 30322, USA
| | - Arshed A Quyyumi
- Emory Clinical Cardiovascular Research Institute, Division of Cardiology, Emory University School of Medicine, 1462 Clifton Road NE, Atlanta, GA 30322, USA
| | - Jaana A Hartiala
- Department of Preventive Medicine, University of Southern California, Keck School of Medicine, 2001 N. Soto St. Los Angeles, CA 90033, USA
| | - W H Wilson Tang
- Department of Cardiovascular Medicine, Cleveland Clinic, 9500 Euclid Ave, Cleveland, OH 44195, USA
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Ave, NB 21, Cleveland, OH 44195, USA
| | - Stanley L Hazen
- Department of Cardiovascular Medicine, Cleveland Clinic, 9500 Euclid Ave, Cleveland, OH 44195, USA
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Ave, NB 21, Cleveland, OH 44195, USA
| | - Hooman Allayee
- Department of Preventive Medicine, University of Southern California, Keck School of Medicine, 2001 N. Soto St. Los Angeles, CA 90033, USA
| | - Caitrin W McDonough
- Department of Pharmacotherapy and Translational Research, University of Florida, College of Pharmacy, 1225 Center Drive, HPNP Building, Gainesville, FL 32610-0486, USA
| | - Yan Gong
- Department of Pharmacotherapy and Translational Research, University of Florida, College of Pharmacy, 1225 Center Drive, HPNP Building, Gainesville, FL 32610-0486, USA
| | - Rhonda M Cooper-DeHoff
- Department of Pharmacotherapy and Translational Research, University of Florida, College of Pharmacy, 1225 Center Drive, HPNP Building, Gainesville, FL 32610-0486, USA
- Division of Cardiovascular Medicine, Department of Medicine, University of Florida, 1600 SW Archer Rd, Gainesville, FL 32610, USA
| | - Julie A Johnson
- Department of Pharmacotherapy and Translational Research, University of Florida, College of Pharmacy, 1225 Center Drive, HPNP Building, Gainesville, FL 32610-0486, USA
- Division of Cardiovascular Medicine, Department of Medicine, University of Florida, 1600 SW Archer Rd, Gainesville, FL 32610, USA
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Härtelstraße 16-18, 04107 Leipzig, Germany
- LIFE Research Center for Civilization Diseases, University of Leipzig, Härtelstraße 16-18, 04107 Leipzig, Germany
| | - Andrej Teren
- LIFE Research Center for Civilization Diseases, University of Leipzig, Härtelstraße 16-18, 04107 Leipzig, Germany
- Heart Center Leipzig, Strümpellstraße 39, 04289 Leipzig, Germany
| | - Ralph Burkhardt
- LIFE Research Center for Civilization Diseases, University of Leipzig, Härtelstraße 16-18, 04107 Leipzig, Germany
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Franz-Josef-Strauß-Allee 11, 93053 Regensburg,Germany
| | - Andreas Martinsson
- Department of Cardiology, Sahlgrenska University Hospital, Blå stråket 5, 413 45 Göteborg, Sweden
| | - J Gustav Smith
- Department of Cardiology, Clinical Sciences, Lund University and Skane University Hospital, BMC F12, 221 84 Lund, Sweden
| | - Lars Wallentin
- Department of Medical Sciences, Cardiology, Uppsala University, Akademiska sjukhuset Entrance 40, 751 85 Uppsala, Sweden
- Uppsala Clinical Research Center, Uppsala University, Dag Hammarskjölds Väg 38, 751 85 Uppsala, Sweden
| | - Stefan K James
- Department of Medical Sciences, Cardiology, Uppsala University, Akademiska sjukhuset Entrance 40, 751 85 Uppsala, Sweden
- Uppsala Clinical Research Center, Uppsala University, Dag Hammarskjölds Väg 38, 751 85 Uppsala, Sweden
| | - Niclas Eriksson
- Department of Medical Sciences, Cardiology, Uppsala University, Akademiska sjukhuset Entrance 40, 751 85 Uppsala, Sweden
- Uppsala Clinical Research Center, Uppsala University, Dag Hammarskjölds Väg 38, 751 85 Uppsala, Sweden
| | - Harvey White
- Green Lane Cardiovascular Service, Auckland City Hospital, 2 Park Road, Grafton, Auckland 1023, New Zealand
| | - Claes Held
- Department of Medical Sciences, Cardiology, Uppsala University, Akademiska sjukhuset Entrance 40, 751 85 Uppsala, Sweden
- Uppsala Clinical Research Center, Uppsala University, Dag Hammarskjölds Väg 38, 751 85 Uppsala, Sweden
| | - Dawn Waterworth
- Genetics, GlaxoSmithKline, 709 Swedeland Rd, King of Prussia, PA 19406, USA
| | - Stella Trompet
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Cernter, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
- Netherlands Heart Institute, Moreelsepark 1, 3511 EP Utrecht, The Netherlands
| | - Ian Ford
- Robertson Centre for Biostatistics, University of Glasgow, Boyd Orr Building University Avenue, Glasgow G12 8QQ, UK
| | - David J Stott
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, 126 University Place, Glasgow G12 8TA, UK
| | - Naveed Sattar
- BHF Glasgow Research Centre, Institute of Cardiovascular and Medical Sciences, University of Glasgow, 126 University Place, Glasgow G12 8TA UK
| | - Sharon Cresci
- Washington University School of Medicine, 2300 I St NW, Washington, DC 20052, USA
- Department of Medicine & Genetics, Campus Box 8232, 4515 McKinley Ave., St. Louis, MO 63110, USA
| | - John A Spertus
- Saint Luke's Mid America Heart Institute and University of Missouri-Kansas City, 4401 Wornall Rd, Kansas City, MO 64111, USA
| | - Hannah Campbell
- Washington University School of Medicine, 2300 I St NW, Washington, DC 20052, USA
- Department of Medicine & Genetics, Campus Box 8232, 4515 McKinley Ave., St. Louis, MO 63110, USA
| | - Sascha Tierling
- Faculty of Natural Sciences and Technology, Department of Genetics/Epigenetics, Saarland University, Postfach 151150, 66041 Saarbrücken, Germany
| | - Jörn Walter
- Faculty of Natural Sciences and Technology, Department of Genetics/Epigenetics, Saarland University, Postfach 151150, 66041 Saarbrücken, Germany
| | - Emmanuel Ampofo
- Institute of Clinical & Experimental Surgery, Saarland University, Kirrberger Straße, 66424 Homburg/Saar, Germany
| | - Barbara A Niemeyer
- Molecular Biophysics, CIPMM, Saarland University, Kirrberger Straße, 66424 Homburg/Saar, Germany
| | - Peter Lipp
- Center for Molecular Signaling (PZMS), Institute for Molecular Cell Biology, Research Center for Molecular Imaging and Screening, Medical Faculty, Saarland University, Kirrberger Straße, 66424 Homburg, Germany
| | - Heribert Schunkert
- Kardiologie, Deutsches Herzzentrum München, Technische Universität München, Lazarettstraße 36, 80636 Munich, Germany
- Partner Site Munich Heart Alliance, German Centre of Cardiovascular Research (DZHK), Ismaninger Straße 22, 81675 Munich, Germany
| | - Michael Böhm
- Department of Internal Medicine III, Cardiology, Angiology, and Intensive Care Medicine, Saarland University Hospital, Kirrberger Strasse, Building 41, 66424 Homburg/Saar, Germany
| | - Wolfgang Koenig
- Kardiologie, Deutsches Herzzentrum München, Technische Universität München, Lazarettstraße 36, 80636 Munich, Germany
- Partner Site Munich Heart Alliance, German Centre of Cardiovascular Research (DZHK), Ismaninger Straße 22, 81675 Munich, Germany
- Institute of Epidemiology and Medical Biometry, University of Ulm, Helmholtzstr. 22, 89081 Ulm, Germany
| | - Danilo Fliser
- Department of Internal Medicine IV, Nephrology and Hypertension, Saarland University Hospital, Kirrberger Strasse, Building 41, 66424 Homburg/Saar, Germany
| | - Ulrich Laufs
- Department of Cardiology, University Medical Center Leipzig, Liebigstraße 20, Leipzig, Germany
| | - Thimoteus Speer
- Department of Internal Medicine IV, Nephrology and Hypertension, Saarland University Hospital, Kirrberger Strasse, Building 41, 66424 Homburg/Saar, Germany
- Translational Cardio-Renal Medicine, Saarland University, Kirrberger Straße, 66424 Homburg/Saar, Germany
| | | | | |
Collapse
|
11
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
12
|
Kressler C, Gasparoni G, Nordström K, Hamo D, Salhab A, Dimitropoulos C, Tierling S, Reinke P, Volk HD, Walter J, Hamann A, Polansky JK. Targeted De-Methylation of the FOXP3-TSDR Is Sufficient to Induce Physiological FOXP3 Expression but Not a Functional Treg Phenotype. Front Immunol 2021; 11:609891. [PMID: 33488615 PMCID: PMC7817622 DOI: 10.3389/fimmu.2020.609891] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 11/20/2020] [Indexed: 12/22/2022] Open
Abstract
CD4+ regulatory T cells (Tregs) are key mediators of immunological tolerance and promising effector cells for immuno-suppressive adoptive cellular therapy to fight autoimmunity and chronic inflammation. Their functional stability is critical for their clinical utility and has been correlated to the demethylated state of the TSDR/CNS2 enhancer element in the Treg lineage transcription factor FOXP3. However, proof for a causal contribution of the TSDR de-methylation to FOXP3 stability and Treg induction is so far lacking. We here established a powerful transient-transfection CRISPR-Cas9-based epigenetic editing method for the selective de-methylation of the TSDR within the endogenous chromatin environment of a living cell. The induced de-methylated state was stable over weeks in clonal T cell proliferation cultures even after expression of the editing complex had ceased. Epigenetic editing of the TSDR resulted in FOXP3 expression, even in its physiological isoform distribution, proving a causal role for the de-methylated TSDR in FOXP3 regulation. However, successful FOXP3 induction was not associated with a switch towards a functional Treg phenotype, in contrast to what has been reported from FOXP3 overexpression approaches. Thus, TSDR de-methylation is required, but not sufficient for a stable Treg phenotype induction. Therefore, targeted demethylation of the TSDR may be a critical addition to published in vitro Treg induction protocols which so far lack FOXP3 stability.
Collapse
Affiliation(s)
- Christopher Kressler
- Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, Berlin, Germany.,Immuno-Epigenetics, German Rheumatism Research Centre (DRFZ), Berlin, Germany
| | | | - Karl Nordström
- Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
| | - Dania Hamo
- Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, Berlin, Germany.,Immuno-Epigenetics, German Rheumatism Research Centre (DRFZ), Berlin, Germany
| | | | | | - Sascha Tierling
- Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
| | - Petra Reinke
- Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, Berlin, Germany.,Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Hans-Dieter Volk
- Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, Berlin, Germany.,Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Jörn Walter
- Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
| | - Alf Hamann
- Immuno-Epigenetics, German Rheumatism Research Centre (DRFZ), Berlin, Germany
| | - Julia K Polansky
- Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, Berlin, Germany.,Immuno-Epigenetics, German Rheumatism Research Centre (DRFZ), Berlin, Germany.,Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, Berlin, Germany
| |
Collapse
|
13
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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.
| |
Collapse
|
14
|
Frach L, Tierling S, Schwaiger M, Moser D, Heinrichs M, Hengstler JG, Walter J, Kumsta R. The mediating role of KITLG DNA methylation in the association between childhood adversity and cortisol stress reactivity does not replicate in monocytes. Psychoneuroendocrinology 2020; 116:104653. [PMID: 32203862 DOI: 10.1016/j.psyneuen.2020.104653] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 01/19/2020] [Accepted: 03/09/2020] [Indexed: 01/01/2023]
Abstract
Adverse childhood experiences such as maltreatment or neglect are associated with mental health problems in adulthood. Changes in the regulation of the psychological and physiological stress reaction, mediated via epigenetic modifications, are discussed as potential mechanisms. This study aimed to replicate the role of DNA methylation of the KITLG gene in mediating the association between childhood adversity and stress-induced cortisol reactivity in a sample of adults reporting childhood adversity and a matched control group (N = 60). DNA was extracted from purified CD14+ monocytes and genome-wide DNA methylation was assessed with the 450k BeadChip for targeted replication and exploratory analyses. As previously reported, childhood adversity was associated with significantly lower cortisol reactivity to stress. We could neither replicate the association between KITLG DNA methylation and cortisol stress reactivity nor the association with childhood adversity. Moreover, DNA methylation of the target CpG (cg27512205) was not associated with KITLG mRNA expression in monocytes. Exploratory analyses of array-wide DNA methylation patterns showed no significant results for individual sites after correction for multiple testing - neither in association with childhood trauma nor with adult cortisol stress reactivity. The analysis of differentially methylated regions (DMRs) revealed two significant regions which both mapped to non-coding genes in the association with cortisol stress reactivity. The mediating role of DNA methylation of the KITLG locus in the association between childhood adversity and cortisol stress reactivity could not be replicated in monocytes. In addition to differences in investigated tissue, reasons for non-replication might include differences between samples in age, ethnicity, trauma severity, and cortisol reactivity.
Collapse
Affiliation(s)
- Leonard Frach
- Department of Genetic Psychology, Faculty of Psychology, Ruhr University Bochum, Bochum, Germany
| | - Sascha Tierling
- Department of Genetics/ Epigenetics, Saarland University, Saarbrücken, Germany
| | - Marion Schwaiger
- Department of Genetic Psychology, Faculty of Psychology, Ruhr University Bochum, Bochum, Germany
| | - Dirk Moser
- Department of Genetic Psychology, Faculty of Psychology, Ruhr University Bochum, Bochum, Germany
| | - Markus Heinrichs
- Department of Psychology, Laboratory for Biological and Personality Psychology, University of Freiburg, Freiburg, Germany; Freiburg Brain Imaging Center, University Medical Center, University of Freiburg, Freiburg, Germany
| | - Jan G Hengstler
- Leibniz Research Centre for Working Environment and Human Factors at the Technical University of Dortmund (IfADo), Dortmund, Germany
| | - Jörn Walter
- Department of Genetics/ Epigenetics, Saarland University, Saarbrücken, Germany
| | - Robert Kumsta
- Department of Genetic Psychology, Faculty of Psychology, Ruhr University Bochum, Bochum, Germany.
| |
Collapse
|
15
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
16
|
Bormann F, Stinzing S, Tierling S, Morkel M, Markelova MR, Walter J, Weichert W, Roßner F, Kuhn N, Perner J, Dietz J, Ispasanie S, Dietel M, Schäfer R, Heinemann V, Sers C. Epigenetic regulation of Amphiregulin and Epiregulin in colorectal cancer. Int J Cancer 2018; 144:569-581. [PMID: 30252132 DOI: 10.1002/ijc.31892] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 08/05/2018] [Accepted: 08/20/2018] [Indexed: 12/23/2022]
Abstract
Expression of the epidermal growth factor ligands amphiregulin (AREG) and epiregulin (EREG) is positively correlated with a response to EGFR-targeted therapies in colorectal cancer. Gene-body methylation sites, which show a strong inverse correlation with AREG and EREG gene expression, were identified in cell lines using targeted 454 FLX-bisulfite sequencing and SIRPH analyses for AREG/EREG promoters and intragenic CpGs. Upon treatment of colorectal cancer cells with 5-aza-2'-desoxycytidine, methylation decreases at specific intragenic CpGs accompanied by upregulation of AREG and EREG gene expression. The same AREG gene-body methylation was also found in human colorectal cancer samples and is independent of KRAS and NRAS mutations. Methylation is specifically decreased in the tumor epithelial compartment as compared to stromal tissue and normal epithelium. Investigation of a promoter/enhancer function of the AREG exon 2 region revealed a potential promoter function in reverse orientation. Retrospective comparison of the predictive power of AREG gene-body methylation versus AREG gene expression using samples from colorectal cancer patients treated with anti-EGFR inhibitors with complete clinical follow-up revealed that AREG expression is superior to AREG gene methylation. AREG and EREG genes undergo a complex regulation involving both intragenic methylation and promoter-dependent control.
Collapse
Affiliation(s)
- Felix Bormann
- Charité Universitätsmedizin Berlin, Institute of Pathology, Laboratory of Molecular Tumor Pathology and Systems Biology, Berlin, Germany
| | - Sebastian Stinzing
- Department of Hematology and Medical Oncology, Klinikum der Universität München (LMU); German Cancer Consortium site Munich (DKTK); German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Sascha Tierling
- Department of Genetics/Epigenetics, FR8.3 Life Sciences, Saarland University, Saarbrücken
| | - Markus Morkel
- Charité Universitätsmedizin Berlin, Institute of Pathology, Laboratory of Molecular Tumor Pathology and Systems Biology, Berlin, Germany.,DKTK, German Consortium for Translational Cancer Research, Partner Site Berlin and DKFZ, German Cancer Research Center, Heidelberg, Germany
| | | | - Jörn Walter
- Department of Genetics/Epigenetics, FR8.3 Life Sciences, Saarland University, Saarbrücken
| | - Wilko Weichert
- DKTK, German Consortium for Translational Cancer Research, Partner Site Berlin and DKFZ, German Cancer Research Center, Heidelberg, Germany.,Institute of Pathology, Technical University Munich, Germany and Munich German Cancer Consortium (DKTK), German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Florian Roßner
- Charité Universitätsmedizin Berlin, Institute of Pathology, Laboratory of Molecular Tumor Pathology and Systems Biology, Berlin, Germany
| | - Natalia Kuhn
- Charité Universitätsmedizin Berlin, Institute of Pathology, Laboratory of Molecular Tumor Pathology and Systems Biology, Berlin, Germany
| | - Juliane Perner
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Johanna Dietz
- Charité Universitätsmedizin Berlin, Institute of Pathology, Laboratory of Molecular Tumor Pathology and Systems Biology, Berlin, Germany
| | - Sylvia Ispasanie
- Charité Universitätsmedizin Berlin, Institute of Pathology, Laboratory of Molecular Tumor Pathology and Systems Biology, Berlin, Germany.,BSIO Berlin School of Integrative Oncology, University Medicine Charité, Berlin, Germany
| | - Manfred Dietel
- Charité Universitätsmedizin Berlin, Institute of Pathology, Laboratory of Molecular Tumor Pathology and Systems Biology, Berlin, Germany.,DKTK, German Consortium for Translational Cancer Research, Partner Site Berlin and DKFZ, German Cancer Research Center, Heidelberg, Germany
| | - Reinhold Schäfer
- Charité Universitätsmedizin Berlin, Institute of Pathology, Laboratory of Molecular Tumor Pathology and Systems Biology, Berlin, Germany.,DKTK, German Consortium for Translational Cancer Research, Partner Site Berlin and DKFZ, German Cancer Research Center, Heidelberg, Germany
| | - Volker Heinemann
- Department of Hematology and Medical Oncology, Klinikum der Universität München (LMU); German Cancer Consortium site Munich (DKTK); German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Christine Sers
- Charité Universitätsmedizin Berlin, Institute of Pathology, Laboratory of Molecular Tumor Pathology and Systems Biology, Berlin, Germany.,DKTK, German Consortium for Translational Cancer Research, Partner Site Berlin and DKFZ, German Cancer Research Center, Heidelberg, Germany
| |
Collapse
|
17
|
Rupf S, Laczny CC, Galata V, Backes C, Keller A, Umanskaya N, Erol A, Tierling S, Lo Porto C, Walter J, Kirsch J, Hannig M, Hannig C. Comparison of initial oral microbiomes of young adults with and without cavitated dentin caries lesions using an in situ biofilm model. Sci Rep 2018; 8:14010. [PMID: 30228377 PMCID: PMC6143549 DOI: 10.1038/s41598-018-32361-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 09/06/2018] [Indexed: 02/06/2023] Open
Abstract
Dental caries is caused by acids released from bacterial biofilms. However, the in vivo formation of initial biofilms in relation to caries remains largely unexplored. The aim of this study was to compare the oral microbiome during the initial phase of bacterial colonization for individuals with (CC) and without (NC) cavitated dentin caries lesions. Bovine enamel slabs on acrylic splints were worn by the volunteers (CC: 14, NC: 13) for in situ biofilm formation (2 h, 4 h, 8 h, 1 ml saliva as reference). Sequencing of the V1/V2 regions of the 16S rRNA gene was performed (MiSeq). The relative abundances of individual operational taxonomic units (OTUs) were compared between samples from the CC group and the NC group. Random forests models were furthermore trained to separate the groups. While the overall heterogeneity did not differ substantially between CC and NC individuals, several individual OTUs were found to have significantly different relative abundances. For the 8 h samples, most of the significant OTUs showed higher relative abundances in the CC group, while the majority of significant OTUs in the saliva samples were more abundant in the NC group. Furthermore, using OTU signatures enabled a separation between both groups, with area-under-the-curve (AUC) values of ~0.8. In summary, the results suggest that initial oral biofilms provide the potential to differentiate between CC and NC individuals.
Collapse
Affiliation(s)
- Stefan Rupf
- Clinic of Operative Dentistry, Periodontology and Preventive Dentistry, Saarland University Medical Center, Homburg, Germany.
| | - Cedric C Laczny
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Valentina Galata
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Natalia Umanskaya
- Clinic of Operative Dentistry, Periodontology and Preventive Dentistry, Saarland University Medical Center, Homburg, Germany
| | - Arzu Erol
- Clinic of Operative Dentistry, Periodontology and Preventive Dentistry, Saarland University Medical Center, Homburg, Germany
| | - Sascha Tierling
- Faculty of Natural Sciences and Technology, Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
| | - Christina Lo Porto
- Faculty of Natural Sciences and Technology, Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
| | - Jörn Walter
- Faculty of Natural Sciences and Technology, Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
| | - Jasmin Kirsch
- Policlinic of Operative and Pediatric Dentistry, Medical Faculty Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Matthias Hannig
- Clinic of Operative Dentistry, Periodontology and Preventive Dentistry, Saarland University Medical Center, Homburg, Germany
| | - Christian Hannig
- Policlinic of Operative and Pediatric Dentistry, Medical Faculty Carl Gustav Carus, TU Dresden, Dresden, Germany
| |
Collapse
|
18
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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
| |
Collapse
|
19
|
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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [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.
Collapse
Affiliation(s)
- Laura de Boni
- 1Department of Neurology, University Hospital of Bonn, Bonn, Germany.,2Institute of Reconstructive Neurobiology, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Gilles Gasparoni
- 3Institute for Genetics/Epigenetics, FR8.3 Life Sciences, Saarland University, Saarbrücken, Germany
| | - Carolin Haubenreich
- 2Institute of Reconstructive Neurobiology, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Sascha Tierling
- 3Institute for Genetics/Epigenetics, FR8.3 Life Sciences, Saarland University, Saarbrücken, Germany
| | - Ina Schmitt
- 1Department of Neurology, University Hospital of Bonn, Bonn, Germany.,4German Center for Neurodegenerative Diseases (DZNE), University of Bonn, Bonn, Germany
| | - Michael Peitz
- 2Institute of Reconstructive Neurobiology, Life & Brain Center, University of Bonn, Bonn, Germany.,4German Center for Neurodegenerative Diseases (DZNE), University of Bonn, Bonn, Germany
| | - Philipp Koch
- 2Institute of Reconstructive Neurobiology, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Jörn Walter
- 3Institute for Genetics/Epigenetics, FR8.3 Life Sciences, Saarland University, Saarbrücken, Germany
| | - Ullrich Wüllner
- 1Department of Neurology, University Hospital of Bonn, Bonn, Germany.,4German Center for Neurodegenerative Diseases (DZNE), University of Bonn, Bonn, Germany
| | - Oliver Brüstle
- 2Institute of Reconstructive Neurobiology, Life & Brain Center, University of Bonn, Bonn, Germany
| |
Collapse
|
20
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
21
|
Tierling S, Schmitt B, Walter J. Comprehensive Evaluation of Commercial Bisulfite-Based DNA Methylation Kits and Development of an Alternative Protocol With Improved Conversion Performance. Genet Epigenet 2018; 10:1179237X18766097. [PMID: 29636635 PMCID: PMC5888801 DOI: 10.1177/1179237x18766097] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 02/01/2018] [Indexed: 04/30/2023]
Abstract
DNA methylation is the most studied epigenetic modification with a wide range of regulatory functions in mammalian genomes. It almost exclusively resides on CpG dinucleotides and, among others, plays important roles in early embryo development, onset, and maintenance of cancer. During the past 3 decades, many approaches have been developed to discriminate methylated from unmethylated DNA including antibody-based enrichment of methylated DNA, restriction enzyme-based, or hybridization-based methods. The conversion of unmethylated cytosines to uracils by sodium or ammonium bisulfite is regarded as golden standard as this approach requires no enzymatic reaction and provides deep and reliable insight in methylation patterns at single-base resolution. Nowadays, there are many commercial kits for bisulfite conversion available but they perform differently and also vary in protocols and chemicals used. Here, we provide the first comprehensive and comparative evaluation of bisulfite conversion kits observing major differences in conversion efficiency and DNA degradation which greatly affect the performance of downstream applications, ie, polymerase chain reactions (PCRs). Moreover, deep sequencing of amplicons containing oxidized derivates of 5'-methylC shows that none of the tested kits efficiently converts 5'-formylC without substantial conversion of 5'-methylC or 5'-hydroxymethylC. Consequently, we developed a robust and easy-to-use protocol that allows maximal discrimination between 5'-formylC and 5'-methylC/5'-hydroxymethylC with low DNA degradation and high PCR efficiency on the bisulfite-treated DNA. We highly recommend to use our time- and cost-efficient protocol for any genome-wide or local high-resolution bisulfite sequencing application to minimize conversion-dependent error rates.
Collapse
Affiliation(s)
- Sascha Tierling
- Sascha Tierling, Faculty of Natural Sciences and Technology, Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany.
| | | | | |
Collapse
|
22
|
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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 10/28/2017] [Accepted: 10/28/2017] [Indexed: 12/12/2022]
|
23
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
24
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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
| |
Collapse
|
25
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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
| |
Collapse
|
26
|
Mamlouk S, Childs LH, Aust D, Heim D, Melching F, Oliveira C, Wolf T, Durek P, Schumacher D, Bläker H, von Winterfeld M, Gastl B, Möhr K, Menne A, Zeugner S, Redmer T, Lenze D, Tierling S, Möbs M, Weichert W, Folprecht G, Blanc E, Beule D, Schäfer R, Morkel M, Klauschen F, Leser U, Sers C. DNA copy number changes define spatial patterns of heterogeneity in colorectal cancer. Nat Commun 2017; 8:14093. [PMID: 28120820 PMCID: PMC5288500 DOI: 10.1038/ncomms14093] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 11/28/2016] [Indexed: 02/06/2023] Open
Abstract
Genetic heterogeneity between and within tumours is a major factor determining cancer progression and therapy response. Here we examined DNA sequence and DNA copy-number heterogeneity in colorectal cancer (CRC) by targeted high-depth sequencing of 100 most frequently altered genes. In 97 samples, with primary tumours and matched metastases from 27 patients, we observe inter-tumour concordance for coding mutations; in contrast, gene copy numbers are highly discordant between primary tumours and metastases as validated by fluorescent in situ hybridization. To further investigate intra-tumour heterogeneity, we dissected a single tumour into 68 spatially defined samples and sequenced them separately. We identify evenly distributed coding mutations in APC and TP53 in all tumour areas, yet highly variable gene copy numbers in numerous genes. 3D morpho-molecular reconstruction reveals two clusters with divergent copy number aberrations along the proximal-distal axis indicating that DNA copy number variations are a major source of tumour heterogeneity in CRC.
Collapse
Affiliation(s)
- Soulafa Mamlouk
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
- German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Liam Harold Childs
- Knowledge Management in Bioinformatics, Humboldt University of Berlin, Berlin 10099, Germany
| | - Daniela Aust
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
- Institute for Pathology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden 01307, Germany
- NCT Biobank Dresden, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden 01307, Germany
| | - Daniel Heim
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Friederike Melching
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Cristiano Oliveira
- Institute of Pathology, University of Heidelberg, Heidelberg 69120, Germany
| | - Thomas Wolf
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
- Institute of Pathology, University of Heidelberg, Heidelberg 69120, Germany
| | - Pawel Durek
- Experimental Rheumatology, German Rheumatism Research Centre, Berlin 10117, Germany
| | - Dirk Schumacher
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
- German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Hendrik Bläker
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
| | | | - Bastian Gastl
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
- BSIO Berlin School of Integrative Oncology, University Medicine Charité, Berlin 13353, Germany
| | - Kerstin Möhr
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Andrea Menne
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
- German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Silke Zeugner
- Institute for Pathology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden 01307, Germany
| | - Torben Redmer
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
- German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Dido Lenze
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Sascha Tierling
- Department of Genetics/Epigenetics, FR8.3 Life Sciences, Saarland University, Saarbrücken 66123, Germany
| | - Markus Möbs
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Wilko Weichert
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
- Institute of Pathology, Technical University Munich, Munich 81675, Germany
| | - Gunnar Folprecht
- University Hospital Carl Gustav Carus, University Cancer Center/Medical Dpt. I, Dresden 01307, Germany
| | - Eric Blanc
- Core Unit Bioinformatics, Berlin Institute of Health, Berlin 10117, Germany
- Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Dieter Beule
- Core Unit Bioinformatics, Berlin Institute of Health, Berlin 10117, Germany
- Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Reinhold Schäfer
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
- German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Markus Morkel
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Frederick Klauschen
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Ulf Leser
- Knowledge Management in Bioinformatics, Humboldt University of Berlin, Berlin 10099, Germany
| | - Christine Sers
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
| |
Collapse
|
27
|
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. J Immunol 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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
28
|
Laqqan M, Alkhaled Y, Tierling S, Walter J, Hammadeh M. Epigenome analysis using Infinium 450K BeadChip arrays identifies aberrant DNA methylation in spermatozoa of males with unexplained infertility. Fertil Steril 2016. [DOI: 10.1016/j.fertnstert.2016.07.658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
29
|
Laqqan M, Walter J, Alkhaled Y, Tierling S, Hammadeh M. Genome-wide DNA methylation analysis of sperm DNA from smoking males suffering from idiopathic infertility. Fertil Steril 2016. [DOI: 10.1016/j.fertnstert.2016.07.1057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
30
|
Qiao S, Nordström K, Muijs L, Gasparoni G, Tierling S, Krause E, Walter J, Boehm U. Molecular Plasticity of Male and Female Murine Gonadotropes Revealed by mRNA Sequencing. Endocrinology 2016; 157:1082-93. [PMID: 26677881 DOI: 10.1210/en.2015-1836] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Gonadotropes in the anterior pituitary gland are of particular importance within the hypothalamic-pituitary-gonadal axis because they provide a means of communication and thus a functional link between the brain and the gonads. Recent results indicate that female gonadotropes may be organized in the form of a network that shows plasticity and adapts to the altered endocrine conditions of different physiological states. However, little is known about functional changes on the molecular level within gonadotropes during these different conditions. In this study we capitalize on a binary genetic strategy in order to fluorescently label murine gonadotrope cells. Using this mouse model allows to produce an enriched gonadotrope population using fluorescence activated cell sorting to perform mRNA sequencing. By using this strategy, we analyze and compare the expression profile of murine gonadotropes in different genders and developmental and hormonal stages. We find that gonadotropes taken from juvenile males and females, from cycling females at diestrus and at proestrus, from lactating females, and from adult males each have unique gene expression patterns with approximately 100 to approximately 500 genes expressed only in one particular stage. We also demonstrate extensive gene-expression profile changes with up to approximately 2200 differentially expressed genes when comparing female and male development, juveniles and adults, and cycling females. Differentially expressed genes were significantly enriched in the GnRH signaling, calcium signaling, and MAPK signaling pathways by Kyoto Encyclopedia of Genes and Genomes analysis. Our data provide an unprecedented molecular view of the primary gonadotropes and reveal a high degree of molecular plasticity within the gonadotrope population.
Collapse
Affiliation(s)
- Sen Qiao
- Department of Pharmacology and Toxicology (S.Q., L.M., U.B.) and Center for Integrative Physiology and Molecular Medicine (E.K.), University of Saarland School of Medicine, Kirrberger Straße D-66421 Homburg, Germany; and Department of Genetics (K.N., G.G., S.T., J.W.), University of Saarland, D-66123 Saarbrücken, Germany
| | - Karl Nordström
- Department of Pharmacology and Toxicology (S.Q., L.M., U.B.) and Center for Integrative Physiology and Molecular Medicine (E.K.), University of Saarland School of Medicine, Kirrberger Straße D-66421 Homburg, Germany; and Department of Genetics (K.N., G.G., S.T., J.W.), University of Saarland, D-66123 Saarbrücken, Germany
| | - Leon Muijs
- Department of Pharmacology and Toxicology (S.Q., L.M., U.B.) and Center for Integrative Physiology and Molecular Medicine (E.K.), University of Saarland School of Medicine, Kirrberger Straße D-66421 Homburg, Germany; and Department of Genetics (K.N., G.G., S.T., J.W.), University of Saarland, D-66123 Saarbrücken, Germany
| | - Gilles Gasparoni
- Department of Pharmacology and Toxicology (S.Q., L.M., U.B.) and Center for Integrative Physiology and Molecular Medicine (E.K.), University of Saarland School of Medicine, Kirrberger Straße D-66421 Homburg, Germany; and Department of Genetics (K.N., G.G., S.T., J.W.), University of Saarland, D-66123 Saarbrücken, Germany
| | - Sascha Tierling
- Department of Pharmacology and Toxicology (S.Q., L.M., U.B.) and Center for Integrative Physiology and Molecular Medicine (E.K.), University of Saarland School of Medicine, Kirrberger Straße D-66421 Homburg, Germany; and Department of Genetics (K.N., G.G., S.T., J.W.), University of Saarland, D-66123 Saarbrücken, Germany
| | - Elmar Krause
- Department of Pharmacology and Toxicology (S.Q., L.M., U.B.) and Center for Integrative Physiology and Molecular Medicine (E.K.), University of Saarland School of Medicine, Kirrberger Straße D-66421 Homburg, Germany; and Department of Genetics (K.N., G.G., S.T., J.W.), University of Saarland, D-66123 Saarbrücken, Germany
| | - Jörn Walter
- Department of Pharmacology and Toxicology (S.Q., L.M., U.B.) and Center for Integrative Physiology and Molecular Medicine (E.K.), University of Saarland School of Medicine, Kirrberger Straße D-66421 Homburg, Germany; and Department of Genetics (K.N., G.G., S.T., J.W.), University of Saarland, D-66123 Saarbrücken, Germany
| | - Ulrich Boehm
- Department of Pharmacology and Toxicology (S.Q., L.M., U.B.) and Center for Integrative Physiology and Molecular Medicine (E.K.), University of Saarland School of Medicine, Kirrberger Straße D-66421 Homburg, Germany; and Department of Genetics (K.N., G.G., S.T., J.W.), University of Saarland, D-66123 Saarbrücken, Germany
| |
Collapse
|
31
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
32
|
Ispasanie S, Bormann F, Kuhn N, Tierling S, Walter J, Sers C. 436: Epigenetic regulation of AREG and EREG expression by ZBTB33/KAISO in colorectal cancer. Eur J Cancer 2014. [DOI: 10.1016/s0959-8049(14)50390-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
33
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
Collapse
|
34
|
Gries J, Schumacher D, Arand J, Lutsik P, Markelova MR, Fichtner I, Walter J, Sers C, Tierling S. Bi-PROF: bisulfite profiling of target regions using 454 GS FLX Titanium technology. Epigenetics 2013; 8:765-71. [PMID: 23803588 DOI: 10.4161/epi.25242] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The use of next generation sequencing has expanded our view on whole mammalian methylome patterns. In particular, it provides a genome-wide insight of local DNA methylation diversity at single nucleotide level and enables the examination of single chromosome sequence sections at a sufficient statistical power. We describe a bisulfite-based sequence profiling pipeline, Bi-PROF, which is based on the 454 GS-FLX Titanium technology that allows to obtain up to one million sequence stretches at single base pair resolution without laborious subcloning. To illustrate the performance of the experimental workflow connected to a bioinformatics program pipeline (BiQ Analyzer HT) we present a test analysis set of 68 different epigenetic marker regions (amplicons) in five individual patient-derived xenograft tissue samples of colorectal cancer and one healthy colon epithelium sample as a control. After the 454 GS-FLX Titanium run, sequence read processing and sample decoding, the obtained alignments are quality controlled and statistically evaluated. Comprehensive methylation pattern interpretation (profiling) assessed by analyzing 10 (2)-10 (4) sequence reads per amplicon allows an unprecedented deep view on pattern formation and methylation marker heterogeneity in tissues concerned by complex diseases like cancer.
Collapse
Affiliation(s)
- Jasmin Gries
- Department of Genetics/Epigenetics, FR8.3 Life Sciences, Saarland University, Saarbrücken, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Souren NYP, Lutsik P, Gasparoni G, Tierling S, Gries J, Riemenschneider M, Fryns JP, Derom C, Zeegers MP, Walter J. Adult monozygotic twins discordant for intra-uterine growth have indistinguishable genome-wide DNA methylation profiles. Genome Biol 2013; 14:R44. [PMID: 23706164 PMCID: PMC4054831 DOI: 10.1186/gb-2013-14-5-r44] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 05/26/2013] [Indexed: 01/21/2023] Open
Abstract
Background Low birth weight is associated with an increased adult metabolic disease risk. It is widely discussed that poor intra-uterine conditions could induce long-lasting epigenetic modifications, leading to systemic changes in regulation of metabolic genes. To address this, we acquire genome-wide DNA methylation profiles from saliva DNA in a unique cohort of 17 monozygotic monochorionic female twins very discordant for birth weight. We examine if adverse prenatal growth conditions experienced by the smaller co-twins lead to long-lasting DNA methylation changes. Results Overall, co-twins show very similar genome-wide DNA methylation profiles. Since observed differences are almost exclusively caused by variable cellular composition, an original marker-based adjustment strategy was developed to eliminate such variation at affected CpGs. Among adjusted and unchanged CpGs 3,153 are differentially methylated between the heavy and light co-twins at nominal significance, of which 45 show sensible absolute mean β-value differences. Deep bisulfite sequencing of eight such loci reveals that differences remain in the range of technical variation, arguing against a reproducible biological effect. Analysis of methylation in repetitive elements using methylation-dependent primer extension assays also indicates no significant intra-pair differences. Conclusions Severe intra-uterine growth differences observed within these monozygotic twins are not associated with long-lasting DNA methylation differences in cells composing saliva, detectable with up-to-date technologies. Additionally, our results indicate that uneven cell type composition can lead to spurious results and should be addressed in epigenomic studies.
Collapse
|
36
|
Classen CF, Riehmer V, Landwehr C, Kosfeld A, Heilmann S, Scholz C, Kabisch S, Engels H, Tierling S, Zivicnjak M, Schacherer F, Haffner D, Weber RG. Dissecting the genotype in syndromic intellectual disability using whole exome sequencing in addition to genome-wide copy number analysis. Hum Genet 2013; 132:825-41. [PMID: 23552953 DOI: 10.1007/s00439-013-1296-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 03/15/2013] [Indexed: 12/31/2022]
Abstract
When a known microimbalance affecting multiple genes is detected in a patient with syndromic intellectual disability, it is usually presumed causative for all observed features. Whole exome sequencing (WES) allows questioning this assumption. In this study of three families with children affected by unexplained syndromic intellectual disability, genome-wide copy number and subsequent analyses revealed a de novo maternal 1.1 Mb microdeletion in the 14q32 imprinted region causing a paternal UPD(14)-like phenotype, and two inherited 22q11.21 microduplications of 2.5 or 2.8 Mb. In patient 1 carrying the 14q32 microdeletion, tall stature and renal malformation were unexplained by paternal UPD(14), and there was no altered DLK1 expression or unexpected methylation status. By WES and filtering with a mining tool, a novel FBN1 missense variant was found in patient 1 and his mother, who both showed clinical features of Marfan syndrome by thorough anthropometric assessment, and a novel EYA1 missense variant as a probable cause of the renal malformation in the patient. In patient 2 with the 22q11.21 microduplication syndrome, skin hypo- and hyperpigmentation and two malignancies were only partially explained. By WES, compound heterozygous BLM stop founder mutations were detected causing Bloom syndrome. In male patient 3 carrying a 22q11.21 microduplication inherited from his unaffected father, WES identified a novel missense variant in the OPHN1 X-linked intellectual disability gene inherited from the unaffected mother as a possible additional cause for developmental delay. Thus, WES seems warranted in patients carrying microdeletions or microduplications, who have unexplained clinical features or microimbalances inherited from an unaffected parent.
Collapse
Affiliation(s)
- Carl Friedrich Classen
- Department of Pediatrics, University Hospital, Ernst-Heydemann-Str. 8, 18057 Rostock, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Grimm C, Chavez L, Vilardell M, Farrall AL, Tierling S, Böhm JW, Grote P, Lienhard M, Dietrich J, Timmermann B, Walter J, Schweiger MR, Lehrach H, Herwig R, Herrmann BG, Morkel M. DNA-methylome analysis of mouse intestinal adenoma identifies a tumour-specific signature that is partly conserved in human colon cancer. PLoS Genet 2013; 9:e1003250. [PMID: 23408899 PMCID: PMC3567140 DOI: 10.1371/journal.pgen.1003250] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 12/02/2012] [Indexed: 12/31/2022] Open
Abstract
Aberrant CpG methylation is a universal epigenetic trait of cancer cell genomes. However, human cancer samples or cell lines preclude the investigation of epigenetic changes occurring early during tumour development. Here, we have used MeDIP-seq to analyse the DNA methylome of APCMin adenoma as a model for intestinal cancer initiation, and we present a list of more than 13,000 recurring differentially methylated regions (DMRs) characterizing intestinal adenoma of the mouse. We show that Polycomb Repressive Complex (PRC) targets are strongly enriched among hypermethylated DMRs, and several PRC2 components and DNA methyltransferases were up-regulated in adenoma. We further demonstrate by bisulfite pyrosequencing of purified cell populations that the DMR signature arises de novo in adenoma cells rather than by expansion of a pre-existing pattern in intestinal stem cells or undifferentiated crypt cells. We found that epigenetic silencing of tumour suppressors, which occurs frequently in colon cancer, was rare in adenoma. Quite strikingly, we identified a core set of DMRs, which is conserved between mouse adenoma and human colon cancer, thus possibly revealing a global panel of epigenetically modified genes for intestinal tumours. Our data allow a distinction between early conserved epigenetic alterations occurring in intestinal adenoma and late stochastic events promoting colon cancer progression, and may facilitate the selection of more specific clinical epigenetic biomarkers. The formation and progression of tumours to metastatic disease is driven by two major mechanisms, i.e. genetic alterations that activate oncogenes or inactivate tumour suppressor genes, and changes in the epigenome that cause variations in the expression of the genetic information. A deeper understanding of the interaction between the genetic and epigenetic mechanisms is critical for the selection of tumour biomarkers and for the future development of therapies. Human tumour specimens and cell lines contain a plethora of genetic and epigenetic changes, which complicate data analysis. In contrast, mouse tumour models such as the APCMin mouse used in this study arise by a single initiating genetic mutation, yet share key traits with human cancer. Here we show that mouse adenomas acquire a multitude of epigenetic alterations, which are recurring in mouse adenoma and in human colon cancer, representing early and advanced tumours, respectively. The use of a mouse model thus allowed us to uncover a sequence of epigenetic changes occurring in tumours, which may facilitate the identification of novel clinical colon cancer biomarkers.
Collapse
Affiliation(s)
- Christina Grimm
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
- Charité Universitätsmedizin Berlin, Department of Rheumatology, Berlin, Germany
| | - Lukas Chavez
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
| | - Mireia Vilardell
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
| | - Alexandra L. Farrall
- Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, Berlin, Germany
| | - Sascha Tierling
- Universität des Saarlandes, FR 8.3 Biowissenschaften, Genetik/Epigenetik Campus, Saarbrücken, Germany
| | - Julia W. Böhm
- Universität des Saarlandes, FR 8.3 Biowissenschaften, Genetik/Epigenetik Campus, Saarbrücken, Germany
| | - Phillip Grote
- Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, Berlin, Germany
| | - Matthias Lienhard
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
| | - Jörn Dietrich
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
| | - Bernd Timmermann
- Max Planck Institute for Molecular Genetics, Next Generation Sequencing Core Facility, Berlin, Germany
| | - Jörn Walter
- Universität des Saarlandes, FR 8.3 Biowissenschaften, Genetik/Epigenetik Campus, Saarbrücken, Germany
| | - Michal R. Schweiger
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
| | - Hans Lehrach
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
| | - Ralf Herwig
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
| | - Bernhard G. Herrmann
- Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, Berlin, Germany
- Charité Universitätsmedizin Berlin, Institute for Medical Genetics, Berlin, Germany
| | - Markus Morkel
- Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, Berlin, Germany
- Charité Universitätsmedizin Berlin, Laboratory of Molecular Tumor Pathology, Berlin, Germany
- * E-mail:
| |
Collapse
|
38
|
Wöhrmann HJP, Gagliardini V, Raissig MT, Wehrle W, Arand J, Schmidt A, Tierling S, Page DR, Schöb H, Walter J, Grossniklaus U. Identification of a DNA methylation-independent imprinting control region at the Arabidopsis MEDEA locus. Genes Dev 2012; 26:1837-50. [PMID: 22855791 DOI: 10.1101/gad.195123.112] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Genomic imprinting is exclusive to mammals and seed plants and refers to parent-of-origin-dependent, differential transcription. As previously shown in mammals, studies in Arabidopsis have implicated DNA methylation as an important hallmark of imprinting. The current model suggests that maternally expressed imprinted genes, such as MEDEA (MEA), are activated by the DNA glycosylase DEMETER (DME), which removes DNA methylation established by the DNA methyltransferase MET1. We report the systematic functional dissection of the MEA cis-regulatory region, resulting in the identification of a 200-bp fragment that is necessary and sufficient to mediate MEA activation and imprinted expression, thus containing the imprinting control region (ICR). Notably, imprinted MEA expression mediated by this ICR is independent of DME and MET1, consistent with the lack of any significant DNA methylation in this region. This is the first example of an ICR without differential DNA methylation, suggesting that factors other than DME and MET1 are required for imprinting at the MEA locus.
Collapse
Affiliation(s)
- Heike J P Wöhrmann
- Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Bormann F, Tierling S, Walter J, Sers C. 569 Epigenetic Regulation of Amphiregulin and Epiregulin and Their Impact on the Outcome of EGFR Targeted Therapeutics in Colorectal Cancer Cell Lines. Eur J Cancer 2012. [DOI: 10.1016/s0959-8049(12)71227-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
40
|
Tierling S, Souren NY, Reither S, Zang KD, Meng-Hentschel J, Leitner D, Oehl-Jaschkowitz B, Walter J. DNA methylation studies on imprinted loci in a male monozygotic twin pair discordant for Beckwith-Wiedemann syndrome. Clin Genet 2011; 79:546-53. [PMID: 20618351 DOI: 10.1111/j.1399-0004.2010.01482.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Beckwith–Wiedemann syndrome (BWS) is one of the most prevalent congenital disorders predominantly caused by epigenetic alterations. Here we present an extensive case study of a monozygotic monochorionic male twin pair discordant for BWS. Our analysis allows to correlate BWS symptoms, like a protruding tongue, indented ears and transient neonatal hypoglycaemia, to an abnormal methylation at the KvDMR1. DNAs extracted from peripheral blood, skin fibroblasts, saliva and buccal swab of both twins, their sister and parents were analysed at 11 differentially methylated regions (DMRs) including all four relevant DMRs of the BWS region. The KvDMR1 was exclusively found to be hypomethylated in all cell types of the affected BWS twin, while the unaffected twin and the relatives showed normal methylation in fibroblasts, buccal swab and saliva DNA. Interestingly, the twins share a common blood-specific hypomethylation phenotype most probably caused by a feto-fetal transfusion between both twins. Because microsatellite analysis furthermore revealed a normal biparental karyotype for chromosome 11, our results point to an exclusive correlation of the observed BWS symptoms to locally restricted epimutations at the KvDMR1 of the maternal chromosome.
Collapse
Affiliation(s)
- S Tierling
- Universität des Saarlandes, FR8.3 Biowissenschaften, Genetik/Epigenetik, Saarbrücken, Germany.
| | | | | | | | | | | | | | | |
Collapse
|
41
|
Diesel B, Ripoche N, Risch RT, Tierling S, Walter J, Kiemer AK. Inflammation-induced up-regulation of TLR2 expression in human endothelial cells is independent of differential methylation in the TLR2 promoter CpG island. Innate Immun 2011; 18:112-23. [PMID: 21768203 DOI: 10.1177/1753425910394888] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Toll-like receptors play an important role in endothelial inflammation; however, little is known on the mechanisms regulating their expression. Differential promoter DNA methylation is an increasingly recognized mechanism that determines a switch between gene silencing and gene transcription. We hypothesized that epigenetic mechanisms are involved in the regulation of endothelial TLR2 expression because of the localization of the TLR2 promoter on a CpG-island. Resting human umbilical vein endothelial cells (HUVECs) displayed rather low TLR2 mRNA expression, while a strong expression increase occurred under inflammatory conditions. We examined the TLR2 promoter methylation pattern in resting HUVECs and compared it to cells treated either with the inflammatory cytokine TNF-α or the DNA-demethylating agent 5-azacytidine. DNA bisulfite conversion was followed by either genomic sequencing or single nucleotide primer extension (SNuPE) HPLC. Results of both techniques showed a low- or non-methylated TLR2 promoter in resting HUVECs and no alteration of the methylation pattern under inflammatory conditions. Whereas 5-azacytidine significantly increased the mRNA expression of the epigenetically regulated gene H19, TLR2 expression was not affected. Taken together, employing different methodological approaches, our data show no implication of methylation pattern changes in inflammatory induction of TLR2 expression in human endothelial cells.
Collapse
Affiliation(s)
- Britta Diesel
- Department of Pharmaceutical Biology, Saarland University, Saarbrücken, Germany
| | | | | | | | | | | |
Collapse
|
42
|
Souren NYP, Tierling S, Fryns JP, Derom C, Walter J, Zeegers MP. DNA methylation variability at growth-related imprints does not contribute to overweight in monozygotic twins discordant for BMI. Obesity (Silver Spring) 2011; 19:1519-22. [PMID: 21273997 DOI: 10.1038/oby.2010.353] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Defective genomic imprinting is often associated with syndromes that include abnormal growth as a clinical phenotype. However, whether differential methylation at imprinted loci also contributes to nonsyndromic abnormal body weight regulation is yet unknown. In this study, we investigated a potential contribution of aberrant DNA methylation at nine differentially methylated regions (DMRs) to the development of nonsyndromic overweight. Sixteen monozygotic (MZ) twins discordant for BMI (BMI difference ranging from 2.9-9.5 kg/m(2)) were recruited from the East Flanders Prospective Twin Survey. DNA extracted from saliva samples was bisulfite-treated followed by PCR amplification of target regions in DMRs most representative for abnormal growth syndromes: KvDMR1, H19 CTCF4, H19 CTCF6, IGF2 DMR0, IGF2 DMR2, GRB10, MEST, SNRPN, GNAS XL-α-s and GNAS Exon1A. At the DMRs analyzed, methylation-dependent primer extension experiments revealed only small intrapair differences in methylation indexes (MI) between the heavy and lean co-twins. In addition, no significant correlations between intrapair BMI differences and intrapair differences in MI were observed. In conclusion, DNA methylation variability at the nine DMRs analyzed does not seem to contribute to the discordancy in BMI observed in these MZ twins.
Collapse
Affiliation(s)
- Nicole Y P Souren
- Department of Complex Genetics, Cluster of Genetics and Cell Biology, Maastricht University Medical Center+, Maastricht, The Netherlands.
| | | | | | | | | | | |
Collapse
|
43
|
Tybl E, Shi FD, Kessler SM, Tierling S, Walter J, Bohle RM, Wieland S, Zhang J, Tan EM, Kiemer AK. Overexpression of the IGF2-mRNA binding protein p62 in transgenic mice induces a steatotic phenotype. J Hepatol 2011; 54:994-1001. [PMID: 21145819 PMCID: PMC3079004 DOI: 10.1016/j.jhep.2010.08.034] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Revised: 08/04/2010] [Accepted: 08/23/2010] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS The insulin-like growth-factor 2 (IGF2) mRNA binding protein p62 is highly expressed in hepatocellular carcinoma tissue. Still, its potential role in liver disease is largely unknown. In this study, we investigated pathophysiological implications of p62 overexpression in mice. METHODS We generated mice overexpressing p62 under a LAP-promotor. mRNA expression levels and stability were examined by real-time RT-PCR. Allele-specific expression of Igf2 and H19 was assessed after crossing mice with SD7 animals. The Igf2 downstream mediators pAKT and PTEN were determined by Western blot. RESULTS Hepatic p62 overexpression neither induced inflammatory processes nor liver damage. However, 2.5week old transgenic animals displayed a steatotic phenotype and improved glucose tolerance. p62 overexpression induced the expression of the imprinted genes Igf2 and H19 and their transcriptional regulator Aire (autoimmune regulator). Neither monoallelic expression nor mRNA stability of Igf2 and H19 was affected. Investigating Igf2 downstream signalling pathways showed increased AKT activation and attenuated PTEN expression. CONCLUSIONS The induction of a steatotic phenotype implies that p62 plays a role in hepatic pathophysiology.
Collapse
Affiliation(s)
- Elisabeth Tybl
- Saarland University, Department of Pharmacy, Pharmaceutical Biology, Saarbrücken, Germany
| | - Fu-Dong Shi
- Barrow Neurological Institute, St. Joseph´ s Hospital and Medical Center, Phoenix, USA
| | - Sonja M. Kessler
- Saarland University, Department of Pharmacy, Pharmaceutical Biology, Saarbrücken, Germany
| | - Sascha Tierling
- Saarland University, Institute of Genetics/Epigenetics, Saarbrücken, Germany
| | - Jörn Walter
- Saarland University, Institute of Genetics/Epigenetics, Saarbrücken, Germany
| | - Rainer M. Bohle
- Department of Pathology, Saarland University, Homburg/Saar, Germany
| | - Stefan Wieland
- The Scripps Research Institute, Department of Molecular and Experimental Medicine, La Jolla, USA
| | - Jianying Zhang
- University of Texas El Paso, Department of Biology, El Paso, Texas, USA
| | - Eng M. Tan
- The Scripps Research Institute, Department of Molecular and Experimental Medicine, La Jolla, USA
| | - Alexandra K. Kiemer
- Saarland University, Department of Pharmacy, Pharmaceutical Biology, Saarbrücken, Germany,To whom correspondence should be addressed, Alexandra K. Kiemer, Ph.D., Saarland University, P.O. box 15 11 50, 66041 Saarbrücken, Germany, phone: +49-681-302 57301, fax: +49-681-302 57302,
| |
Collapse
|
44
|
Tierling S, Sers C, Lehmann A, Walter J. A fast, cost-efficient and sensitive approach for KRAS mutation detection using multiplexed primer extension with IP/RP-HPLC separation. Int J Cancer 2011; 130:567-74. [PMID: 21387306 DOI: 10.1002/ijc.26040] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Accepted: 02/21/2011] [Indexed: 12/17/2022]
Abstract
Mutations in the KRAS gene are very important diagnostic and prognostic markers in cancer. Particularly, KRAS mutations at codons 12 and 13 have a high prognostic value for EGFR-directed antibody therapies. Several methods are available to detect the most common mutations, some of them are commercialized. The most frequently used techniques, allele-specific PCR or direct sequencing, are not standardized and often lack sensitivity to detect low amounts of mutated tumor cells in paraffin-embedded tissue-blocks leading to a high number of false-negatives. Here we present a reliable, fast, cost-effective and sensitive approach for KRAS mutation detection that has a high potential for standardized large scale screening. The method is based on multiplexed primer extension reactions coupled to HPLC separation. The highly sensitive assay gives easily interpretable and reproducible results at affordable costs. We describe the method and an application example for diagnosis in early colorectal cancer screening.
Collapse
Affiliation(s)
- Sascha Tierling
- Saarland University, FR 8.3 Life Sciences, Genetics/Epigenetics, 66041 Saarbrücken, Germany.
| | | | | | | |
Collapse
|
45
|
Tierling S, Schuster M, Tetzner R, Walter J. A combined HM-PCR/SNuPE method for high sensitive detection of rare DNA methylation. Epigenetics Chromatin 2010; 3:12. [PMID: 20525169 PMCID: PMC2887863 DOI: 10.1186/1756-8935-3-12] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Accepted: 06/02/2010] [Indexed: 02/06/2023] Open
Abstract
Background DNA methylation changes are widely used as early molecular markers in cancer detection. Sensitive detection and classification of rare methylation changes in DNA extracted from circulating body fluids or complex tissue samples is crucial for the understanding of tumor etiology, clinical diagnosis and treatment. In this paper, we describe a combined method to monitor the presence of methylated tumor DNA in an excess of unmethylated background DNA of non-tumorous cells. The method combines heavy methyl-PCR, which favors preferential amplification of methylated marker sequence from bisulfite-treated DNA with a methylation-specific single nucleotide primer extension monitored by ion-pair, reversed-phase, high-performance liquid chromatography separation. Results This combined method allows detection of 14 pg (that is, four to five genomic copies) of methylated chromosomal DNA in a 2000-fold excess (that is, 50 ng) of unmethylated chromosomal background, with an analytical sensitivity of > 90%. We outline a detailed protocol for the combined assay on two examples of known cancer markers (SEPT9 and TMEFF2) and discuss general aspects of assay design and data interpretation. Finally, we provide an application example for rapid testing on tumor methylation in plasma DNA derived from a small cohort of patients with colorectal cancer. Conclusion The method allows unambiguous detection of rare DNA methylation, for example in body fluid or DNA isolates from cells or tissues, with very high sensitivity and accuracy. The application combines standard technologies and can easily be adapted to any target region of interest. It does not require costly reagents and can be used for routine screening of many samples.
Collapse
|
46
|
Tierling S, Souren NY, Reither S, Neitzel H, Gillessen-Kaesbach G, Kentenich H, Griesinger G, Meng-Hentschel J, Leitner D, Oehl-Jaschkowitz B, Walter J. Epigenetik und molekulare Mechanismen der Fehlregulation von Genen. Klin Padiatr 2010. [DOI: 10.1055/s-0030-1261386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
47
|
Meng-Hentschel J, Tierling S, Oehl-Jaschkowitz B, Souren N, Walter J. Epigenetic characterization of discordant twins with Beckwith Wiedemann syndrome, with clinical findings at birth and neurodevelopmental follow-up. Klin Padiatr 2010. [DOI: 10.1055/s-0030-1261623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
48
|
Tierling S, Souren NY, Gries J, Loporto C, Groth M, Lutsik P, Neitzel H, Utz-Billing I, Gillessen-Kaesbach G, Kentenich H, Griesinger G, Sperling K, Schwinger E, Walter J. Assisted reproductive technologies do not enhance the variability of DNA methylation imprints in human. J Med Genet 2009; 47:371-6. [PMID: 19948534 DOI: 10.1136/jmg.2009.073189] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Assisted reproductive technologies (ART) such as in vitro fertilisation (IVF) and intracytoplasmic sperm injection (ICSI) are believed to destabilise genomic imprints. An increased frequency of Beckwith-Wiedemann syndrome in children born after ART has been reported. Other, mostly epidemiological, studies argue against this finding. OBJECTIVE To examine the effect of ART on the stability of DNA methylation imprints, DNA was extracted from maternal peripheral blood (MPB), umbilical cord blood (UCB) and amnion/chorion tissue (ACT) of 185 phenotypically normal children (77 ICSI, 35 IVF, and 73 spontaneous conceptions). Using bisulfite based technologies 10 differentially methylated regions (DMRs) were analysed, including KvDMR1, H19, SNRPN, MEST, GRB10, DLK1/MEG3 IG-DMR, GNAS NESP55, GNAS NESPas, GNAS XL-alpha-s and GNAS Exon1A. RESULTS Methylation indices (MI) do not reveal any significant differences at nine DMRs among the conception groups in neither MPB, UCB nor in ACT. The only slightly variable DMR was that of MEST. Here the mean MI was higher in UCB and MPB of IVF cases (mean MI+/-SD: 0.41+/-0.03 (UCB) and 0.40+/-0.03 (MPB)) compared to the ICSI (0.38+/-0.03, p=0.003 (UCB); 0.37+/-0.04, p=0.0007 (MPB)) or spontaneous cases (0.38+/-0.03, p=0.003 (UCB); 0.38+/-0.04, p=0.02 (MPB)). Weak but suggestive correlations between DMRs were, however, found between MPB, UCB and ACT. CONCLUSION This study supports the notion that children conceived by ART do not show a higher degree of imprint variability and hence do not have an a priori higher risk for imprinting disorders.
Collapse
Affiliation(s)
- Sascha Tierling
- Universität des Saarlandes, FR 8.3 Biowissenschaften, Genetik/Epigenetik, Postfach 151150, D-66041 Saarbrücken, Germany.
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Tierling S, Gasparoni G, Youngson N, Paulsen M. The Begain gene marks the centromeric boundary of the imprinted region on mouse chromosome 12. Mamm Genome 2009; 20:699-710. [DOI: 10.1007/s00335-009-9205-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Accepted: 07/01/2009] [Indexed: 11/29/2022]
|
50
|
Zhang Y, Rohde C, Tierling S, Jurkowski TP, Bock C, Santacruz D, Ragozin S, Reinhardt R, Groth M, Walter J, Jeltsch A. DNA methylation analysis of chromosome 21 gene promoters at single base pair and single allele resolution. PLoS Genet 2009; 5:e1000438. [PMID: 19325872 PMCID: PMC2653639 DOI: 10.1371/journal.pgen.1000438] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2008] [Accepted: 02/25/2009] [Indexed: 11/19/2022] Open
Abstract
Differential DNA methylation is an essential epigenetic signal for gene regulation, development, and disease processes. We mapped DNA methylation patterns of 190 gene promoter regions on chromosome 21 using bisulfite conversion and subclone sequencing in five human cell types. A total of 28,626 subclones were sequenced at high accuracy using (long-read) Sanger sequencing resulting in the measurement of the DNA methylation state of 580427 CpG sites. Our results show that average DNA methylation levels are distributed bimodally with enrichment of highly methylated and unmethylated sequences, both for amplicons and individual subclones, which represent single alleles from individual cells. Within CpG-rich sequences, DNA methylation was found to be anti-correlated with CpG dinucleotide density and GC content, and methylated CpGs are more likely to be flanked by AT-rich sequences. We observed over-representation of CpG sites in distances of 9, 18, and 27 bps in highly methylated amplicons. However, DNA sequence alone is not sufficient to predict an amplicon's DNA methylation status, since 43% of all amplicons are differentially methylated between the cell types studied here. DNA methylation in promoter regions is strongly correlated with the absence of gene expression and low levels of activating epigenetic marks like H3K4 methylation and H3K9 and K14 acetylation. Utilizing the single base pair and single allele resolution of our data, we found that i) amplicons from different parts of a CpG island frequently differ in their DNA methylation level, ii) methylation levels of individual cells in one tissue are very similar, and iii) methylation patterns follow a relaxed site-specific distribution. Furthermore, iv) we identified three cases of allele-specific DNA methylation on chromosome 21. Our data shed new light on the nature of methylation patterns in human cells, the sequence dependence of DNA methylation, and its function as epigenetic signal in gene regulation. Further, we illustrate genotype–epigenotype interactions by showing novel examples of allele-specific methylation. Epigenetics is defined as the inheritance of changes in gene function without changing the DNA sequence. Epigenetic signals comprise methylation of cytosine bases of the DNA and chemical modifications of the histone proteins. DNA methylation plays important roles in development and disease processes. To investigate the biological role of DNA methylation, we analyzed DNA methylation patterns of 190 gene promoter regions on chromosome 21 in five human cell types. Our results show that average DNA methylation levels are distributed bimodally with enrichment of highly methylated and unmethylated sequences, indicating that DNA methylation acts in a switch-like manner. Consistent with the well-established role of DNA methylation in gene silencing, we found DNA methylation in promoter regions strongly correlated with absence of gene expression and low levels of additional activating epigenetic marks. Although methylation levels of individual cells in one tissue are very similar, we observed differences in DNA methylation when comparing different cell types in 43% of all regions analyzed. This finding is in agreement with a role of DNA methylation in cellular development. We identified three cases of genes that are differentially methylated in both alleles that illustrate the tight interplay of genetic and epigenetic processes.
Collapse
Affiliation(s)
- Yingying Zhang
- School of Engineering and Science, Jacobs University Bremen, Bremen, Germany
| | - Christian Rohde
- School of Engineering and Science, Jacobs University Bremen, Bremen, Germany
| | - Sascha Tierling
- Institut für Genetik, FB Biowissenschaften, Universität des Saarlandes, Saarbrücken, Germany
| | - Tomasz P. Jurkowski
- School of Engineering and Science, Jacobs University Bremen, Bremen, Germany
| | - Christoph Bock
- Max-Planck-Institut für Informatik, Saarbrücken, Germany
| | - Diana Santacruz
- Institut für Genetik, FB Biowissenschaften, Universität des Saarlandes, Saarbrücken, Germany
| | - Sergey Ragozin
- School of Engineering and Science, Jacobs University Bremen, Bremen, Germany
| | | | - Marco Groth
- Leibniz-Institute for Age Research—Fritz-Lipmann-Institute, Jena, Germany
| | - Jörn Walter
- Institut für Genetik, FB Biowissenschaften, Universität des Saarlandes, Saarbrücken, Germany
- * E-mail: (JW); (AJ)
| | - Albert Jeltsch
- School of Engineering and Science, Jacobs University Bremen, Bremen, Germany
- * E-mail: (JW); (AJ)
| |
Collapse
|