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Hubens W, Kluge L, Seitz A, Verjans E, Rink L, Wagner W. Epigenetic Leukocyte Counts from Dried Blood Spots of Pediatric Patients. Clin Chem 2024; 70:997-999. [PMID: 38712654 DOI: 10.1093/clinchem/hvae066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/15/2024] [Indexed: 05/08/2024]
Affiliation(s)
- Wouter Hubens
- Institute of Stem Cell Biology, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Lara Kluge
- Institute of Stem Cell Biology, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Alexander Seitz
- Institute of Stem Cell Biology, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Eva Verjans
- Institute for Pediatrics, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Lothar Rink
- Institute of Immunology, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Wolfgang Wagner
- Institute of Stem Cell Biology, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany
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2
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Hubens WHG, Maié T, Schnitker M, Bocova L, Puri D, Wessiepe M, Kramer J, Rink L, Koschmieder S, Costa IG, Wagner W. Targeted DNA Methylation Analysis Facilitates Leukocyte Counts in Dried Blood Samples. Clin Chem 2023; 69:1283-1294. [PMID: 37708296 DOI: 10.1093/clinchem/hvad143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/10/2023] [Indexed: 09/16/2023]
Abstract
BACKGROUND Cell-type specific DNA methylation (DNAm) can be employed to determine the numbers of leukocyte subsets in blood. In contrast to conventional methods for leukocyte counts, which are based on cellular morphology or surface marker protein expression, the cellular deconvolution based on DNAm levels is applicable for frozen or dried blood. Here, we further enhanced targeted DNAm assays for leukocyte counts in clinical application. METHODS DNAm profiles of 40 different studies were compiled to identify CG dinucleotides (CpGs) with cell-type specific DNAm using a computational framework, CimpleG. DNAm levels at these CpGs were then measured with digital droplet PCR in venous blood from 160 healthy donors and 150 patients with various hematological disorders. Deconvolution was further validated with venous blood (n = 75) and capillary blood (n = 31) that was dried on Whatman paper or on Mitra microsampling devices. RESULTS In venous blood, automated cell counting or flow cytometry correlated well with epigenetic estimates of relative leukocyte counts for granulocytes (r = 0.95), lymphocytes (r = 0.97), monocytes (r = 0.82), CD4 T cells (r = 0.84), CD8 T cells (r = 0.94), B cells (r = 0.96), and NK cells (r = 0.72). Similar correlations and precisions were achieved for dried blood samples. Spike-in with a reference plasmid enabled accurate epigenetic estimation of absolute leukocyte counts from dried blood samples, correlating with conventional venous (r = 0.86) and capillary (r = 0.80) blood measurements. CONCLUSIONS The advanced selection of cell-type specific CpGs and utilization of digital droplet PCR analysis provided accurate epigenetic blood counts. Analysis of dried blood facilitates self-sampling with a finger prick, thereby enabling easier accessibility to testing.
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Affiliation(s)
- Wouter H G Hubens
- Institute for Stem Cell Biology, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Tiago Maié
- Institute for Computational Genomics, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Matthis Schnitker
- Institute for Stem Cell Biology, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Ledio Bocova
- Institute for Stem Cell Biology, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Deepika Puri
- Institute for Stem Cell Biology, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Martina Wessiepe
- Institute for Transfusion Medicine, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Jan Kramer
- Division of Nephrology and Transplantation Unit, Department of Internal Medicine I, University of Lübeck, Lübeck, Germany
- LADR Laboratory Group Dr. Kramer & Colleagues, Geesthacht, Germany
| | - Lothar Rink
- Institute of Immunology, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Steffen Koschmieder
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany
| | - Ivan G Costa
- Institute for Computational Genomics, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Wolfgang Wagner
- Institute for Stem Cell Biology, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany
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3
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Maié T, Schmidt M, Erz M, Wagner W, G Costa I. CimpleG: finding simple CpG methylation signatures. Genome Biol 2023; 24:161. [PMID: 37430364 DOI: 10.1186/s13059-023-03000-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 06/28/2023] [Indexed: 07/12/2023] Open
Abstract
DNA methylation signatures are usually based on multivariate approaches that require hundreds of sites for predictions. Here, we propose a computational framework named CimpleG for the detection of small CpG methylation signatures used for cell-type classification and deconvolution. We show that CimpleG is both time efficient and performs as well as top performing methods for cell-type classification of blood cells and other somatic cells, while basing its prediction on a single DNA methylation site per cell type. Altogether, CimpleG provides a complete computational framework for the delineation of DNAm signatures and cellular deconvolution.
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Affiliation(s)
- Tiago Maié
- Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School, Pauwelsstr. 19, Aachen, 52074, NRW, Germany.
| | - Marco Schmidt
- Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Pauwelsstr. 19, Aachen, 52074, NRW, Germany
- Institute for Stem Cell Biology, RWTH Aachen University Medical School, Pauwelsstr. 19, Aachen, 52074, NRW, Germany
| | - Myriam Erz
- Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School, Pauwelsstr. 19, Aachen, 52074, NRW, Germany
| | - Wolfgang Wagner
- Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Pauwelsstr. 19, Aachen, 52074, NRW, Germany
- Institute for Stem Cell Biology, RWTH Aachen University Medical School, Pauwelsstr. 19, Aachen, 52074, NRW, Germany
| | - Ivan G Costa
- Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School, Pauwelsstr. 19, Aachen, 52074, NRW, Germany.
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4
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Bocova L, Hubens W, Engel C, Koschmieder S, Jost E, Wagner W. Quantification of hematopoietic stem and progenitor cells by targeted DNA methylation analysis. Clin Epigenetics 2023; 15:105. [PMID: 37370186 DOI: 10.1186/s13148-023-01521-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Hematopoietic stem and progenitor cells (HSPCs) are quantified in daily clinical practice by flow cytometry. In this study, we provide proof of concept that HSPCs can also be estimated by targeted DNA methylation (DNAm) analysis. The DNAm levels at three individual CG dinucleotides (CpG sites) in the genes MYO1D, STK17A, and SP140 correlated with CD34+ cell numbers in mobilized peripheral blood and with blast counts in leukemia. In the future, such epigenetic biomarkers can support the evaluation of stem cell mobilization, HSPC harvesting, or blast count in leukemia.
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Affiliation(s)
- Ledio Bocova
- Institute for Stem Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
- Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Wouter Hubens
- Institute for Stem Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
- Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Cordula Engel
- Department of Gynecology and Obstetrics, University Hospital of RWTH Aachen, Aachen, Germany
| | - Steffen Koschmieder
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, University Hospital of RWTH Aachen, Aachen, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany
| | - Edgar Jost
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, University Hospital of RWTH Aachen, Aachen, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany
| | - Wolfgang Wagner
- Institute for Stem Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany.
- Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany.
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany.
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Apsley AT, Etzel L, Hastings WJ, Heim CC, Noll JG, O'Donnell KJ, Schreier HMC, Shenk CE, Ye Q, Shalev I. Investigating the effects of maltreatment and acute stress on the concordance of blood and DNA methylation methods of estimating immune cell proportions. Clin Epigenetics 2023; 15:33. [PMID: 36855187 PMCID: PMC9976543 DOI: 10.1186/s13148-023-01437-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 02/05/2023] [Indexed: 03/02/2023] Open
Abstract
BACKGROUND Immune cell proportions can be used to detect pathophysiological states and are also critical covariates in genomic analyses. The complete blood count (CBC) is the most common method of immune cell proportion estimation, but immune cell proportions can also be estimated using whole-genome DNA methylation (DNAm). Although the concordance of CBC and DNAm estimations has been validated in various adult and clinical populations, less is known about the concordance of existing estimators among stress-exposed individuals. As early life adversity and acute psychosocial stress have both been associated with unique DNAm alterations, the concordance of CBC and DNAm immune cell proportion needs to be validated in various states of stress. RESULTS We report the correlation and concordance between CBC and DNAm estimates of immune cell proportions using the Illumina EPIC DNAm array within two unique studies: Study 1, a high-risk pediatric cohort of children oversampled for exposure to maltreatment (N = 365, age 8 to 14 years), and Study 2, a sample of young adults who have participated in an acute laboratory stressor with four pre- and post-stress measurements (N = 28, number of observations = 100). Comparing CBC and DNAm proportions across both studies, estimates of neutrophils (r = 0.948, p < 0.001), lymphocytes (r = 0.916, p < 0.001), and eosinophils (r = 0.933, p < 0.001) were highly correlated, while monocyte estimates were moderately correlated (r = 0.766, p < 0.001) and basophil estimates were weakly correlated (r = 0.189, p < 0.001). In Study 1, we observed significant deviations in raw values between the two approaches for some immune cell subtypes; however, the observed differences were not significantly predicted by exposure to child maltreatment. In Study 2, while significant changes in immune cell proportions were observed in response to acute psychosocial stress for both CBC and DNAm estimates, the observed changes were similar for both approaches. CONCLUSIONS Although significant differences in immune cell proportion estimates between CBC and DNAm exist, as well as stress-induced changes in immune cell proportions, neither child maltreatment nor acute psychosocial stress alters the concordance of CBC and DNAm estimation methods. These results suggest that the agreement between CBC and DNAm estimators of immune cell proportions is robust to exposure to child maltreatment and acute psychosocial stress.
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Affiliation(s)
- Abner T Apsley
- Department of Biobehavioral Health, The Pennsylvania State University, 219 Biobehavioral Health Building, University Park, PA, 16802, USA
- Department of Molecular, Cellular, and Integrated Biosciences, The Pennsylvania State University, University Park, PA, USA
| | - Laura Etzel
- Department of Biobehavioral Health, The Pennsylvania State University, 219 Biobehavioral Health Building, University Park, PA, 16802, USA
| | - Waylon J Hastings
- Department of Biobehavioral Health, The Pennsylvania State University, 219 Biobehavioral Health Building, University Park, PA, 16802, USA
| | - Christine C Heim
- Department of Biobehavioral Health, The Pennsylvania State University, 219 Biobehavioral Health Building, University Park, PA, 16802, USA
- Corporate Member of Freie Universität Berlin, and Humboldt-Universität Zu Berlin, Berlin Institute of Health (BIH), Institute of Medical Psychology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Jennie G Noll
- Department of Human Development and Family Studies, The Pennsylvania State University, University Park, PA, USA
| | - Kieran J O'Donnell
- Yale Child Study Center, Yale School of Medicine, Yale University, New Haven, CT, USA
- Department of Obstetrics Gynecology and Reproductive Sciences, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Hannah M C Schreier
- Department of Biobehavioral Health, The Pennsylvania State University, 219 Biobehavioral Health Building, University Park, PA, 16802, USA
| | - Chad E Shenk
- Department of Human Development and Family Studies, The Pennsylvania State University, University Park, PA, USA
- Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Qiaofeng Ye
- Department of Biobehavioral Health, The Pennsylvania State University, 219 Biobehavioral Health Building, University Park, PA, 16802, USA
| | - Idan Shalev
- Department of Biobehavioral Health, The Pennsylvania State University, 219 Biobehavioral Health Building, University Park, PA, 16802, USA.
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Schmidt M, Zeevaert K, Elsafi Mabrouk MH, Goetzke R, Wagner W. Epigenetic biomarkers to track differentiation of pluripotent stem cells. Stem Cell Reports 2022; 18:145-158. [PMID: 36460001 PMCID: PMC9860076 DOI: 10.1016/j.stemcr.2022.11.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/31/2022] [Accepted: 11/01/2022] [Indexed: 12/03/2022] Open
Abstract
Quality control of induced pluripotent stem cells remains a challenge. For validation of the pluripotent state, it is crucial to determine trilineage differentiation potential toward endoderm, mesoderm, and ectoderm. Here, we report GermLayerTracker, a combination of site-specific DNA methylation (DNAm) assays that serve as biomarker for early germ layer specification. CG dinucleotides (CpGs) were identified with characteristic DNAm at pluripotent state and after differentiation into endoderm, mesoderm, and ectoderm. Based on this, a pluripotency score was derived that tracks reprogramming and may indicate differentiation capacity, as well as lineage-specific scores to monitor either directed differentiation or self-organized multilineage differentiation in embryoid bodies. Furthermore, we established pyrosequencing assays for fast and cost-effective analysis. In the future, the GermLayerTracker could be used for quality control of pluripotent cells and to estimate lineage-specific commitment during initial differentiation events.
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Affiliation(s)
- Marco Schmidt
- Institute for Stem Cell Biology, RWTH Aachen University Medical School, 52074 Aachen, Germany,Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, 52074 Aachen, Germany
| | - Kira Zeevaert
- Institute for Stem Cell Biology, RWTH Aachen University Medical School, 52074 Aachen, Germany,Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, 52074 Aachen, Germany
| | - Mohamed H. Elsafi Mabrouk
- Institute for Stem Cell Biology, RWTH Aachen University Medical School, 52074 Aachen, Germany,Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, 52074 Aachen, Germany
| | - Roman Goetzke
- Institute for Stem Cell Biology, RWTH Aachen University Medical School, 52074 Aachen, Germany,Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, 52074 Aachen, Germany
| | - Wolfgang Wagner
- Institute for Stem Cell Biology, RWTH Aachen University Medical School, 52074 Aachen, Germany; Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, 52074 Aachen, Germany.
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7
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Cypris O, Franzen J, Frobel J, Glück P, Kuo CC, Schmitz S, Nüchtern S, Zenke M, Wagner W. Hematopoietic differentiation persists in human iPSCs defective in de novo DNA methylation. BMC Biol 2022; 20:141. [PMID: 35705990 PMCID: PMC9202186 DOI: 10.1186/s12915-022-01343-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 06/07/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DNA methylation is involved in the epigenetic regulation of gene expression during developmental processes and is primarily established by the DNA methyltransferase 3A (DNMT3A) and 3B (DNMT3B). DNMT3A is one of the most frequently mutated genes in clonal hematopoiesis and leukemia, indicating that it plays a crucial role for hematopoietic differentiation. However, the functional relevance of Dnmt3a for hematopoietic differentiation and hematological malignancies has mostly been analyzed in mice, with the specific role for human hematopoiesis remaining elusive. In this study, we therefore investigated if DNMT3A is essential for hematopoietic differentiation of human induced pluripotent stem cells (iPSCs). RESULTS We generated iPSC lines with knockout of either exon 2, 19, or 23 and analyzed the impact of different DNMT3A exon knockouts on directed differentiation toward mesenchymal and hematopoietic lineages. Exon 19-/- and 23-/- lines displayed an almost entire absence of de novo DNA methylation during mesenchymal and hematopoietic differentiation. Yet, differentiation efficiency was only slightly reduced in exon 19-/- and rather increased in exon 23-/- lines, while there was no significant impact on gene expression in hematopoietic progenitors (iHPCs). Notably, DNMT3A-/- iHPCs recapitulate some DNA methylation patterns of acute myeloid leukemia (AML) with DNMT3A mutations. Furthermore, multicolor genetic barcoding revealed growth advantage of exon 23-/- iHPCs in a syngeneic competitive differentiation assay. CONCLUSIONS Our results demonstrate that iPSCs with homozygous knockout of different exons of DNMT3A remain capable of mesenchymal and hematopoietic differentiation-and exon 23-/- iHPCs even gained growth advantage-despite loss of almost the entire de novo DNA methylation. Partial recapitulation of DNA methylation patterns of AML with DNMT3A mutations by our DNMT3A knockout iHPCs indicates that our model system can help to elucidate mechanisms of clonal hematopoiesis.
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Affiliation(s)
- Olivia Cypris
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, North-Rhine Westphalia, Germany.,Institute for Stem Cell Biology, RWTH Aachen University Medical School, 52074, Aachen, North-Rhine Westphalia, Germany
| | - Julia Franzen
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, North-Rhine Westphalia, Germany.,Institute for Stem Cell Biology, RWTH Aachen University Medical School, 52074, Aachen, North-Rhine Westphalia, Germany
| | - Joana Frobel
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, North-Rhine Westphalia, Germany.,Institute for Stem Cell Biology, RWTH Aachen University Medical School, 52074, Aachen, North-Rhine Westphalia, Germany
| | - Philipp Glück
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, North-Rhine Westphalia, Germany.,Institute for Stem Cell Biology, RWTH Aachen University Medical School, 52074, Aachen, North-Rhine Westphalia, Germany
| | - Chao-Chung Kuo
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, North-Rhine Westphalia, Germany.,Institute for Stem Cell Biology, RWTH Aachen University Medical School, 52074, Aachen, North-Rhine Westphalia, Germany
| | - Stephani Schmitz
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, North-Rhine Westphalia, Germany.,Institute for Stem Cell Biology, RWTH Aachen University Medical School, 52074, Aachen, North-Rhine Westphalia, Germany
| | - Selina Nüchtern
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, North-Rhine Westphalia, Germany.,Institute for Stem Cell Biology, RWTH Aachen University Medical School, 52074, Aachen, North-Rhine Westphalia, Germany
| | - Martin Zenke
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, North-Rhine Westphalia, Germany.,Institute for Stem Cell Biology, RWTH Aachen University Medical School, 52074, Aachen, North-Rhine Westphalia, Germany
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, North-Rhine Westphalia, Germany. .,Institute for Stem Cell Biology, RWTH Aachen University Medical School, 52074, Aachen, North-Rhine Westphalia, Germany. .,Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), 52074, Aachen, North-Rhine Westphalia, Germany.
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Wagner W. How to Translate DNA Methylation Biomarkers Into Clinical Practice. Front Cell Dev Biol 2022; 10:854797. [PMID: 35281115 PMCID: PMC8905294 DOI: 10.3389/fcell.2022.854797] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 02/04/2022] [Indexed: 12/14/2022] Open
Abstract
Recent advances in sequencing technologies provide unprecedented opportunities for epigenetic biomarker development. Particularly the DNA methylation pattern—which is modified at specific sites in the genome during cellular differentiation, aging, and disease—holds high hopes for a wide variety of diagnostic applications. While many epigenetic biomarkers have been described, only very few of them have so far been successfully translated into clinical practice and almost exclusively in the field of oncology. This discrepancy might be attributed to the different demands of either publishing a new finding or establishing a standardized and approved diagnostic procedure. This is exemplified for epigenetic leukocyte counts and epigenetic age-predictions. To ease later clinical translation, the following hallmarks should already be taken into consideration when designing epigenetic biomarkers: 1) Identification of best genomic regions, 2) pre-analytical processing, 3) accuracy of DNA methylation measurements, 4) identification of confounding parameters, 5) accreditation as diagnostic procedure, 6) standardized data analysis, 7) turnaround time, and 8) costs and customer requirements. While the initial selection of relevant genomic regions is usually performed on genome wide DNA methylation profiles, it might be advantageous to subsequently establish targeted assays that focus on specific genomic regions. Development of an epigenetic biomarker for clinical application is a long and cumbersome process that is only initiated with the identification of an epigenetic signature.
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Affiliation(s)
- Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany
- *Correspondence: Wolfgang Wagner,
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9
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Neuberger EWI, Sontag S, Brahmer A, Philippi KFA, Radsak MP, Wagner W, Simon P. Physical activity specifically evokes release of cell-free DNA from granulocytes thereby affecting liquid biopsy. Clin Epigenetics 2022; 14:29. [PMID: 35193681 PMCID: PMC8864902 DOI: 10.1186/s13148-022-01245-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 02/07/2022] [Indexed: 11/28/2022] Open
Abstract
Physical activity impacts immune homeostasis and leads to rapid and marked increase in cell-free DNA (cfDNA). However, the origin of cfDNA during exercise remains elusive and it is unknown if physical activity could improve or interfere with methylation based liquid biopsy. We analyzed the methylation levels of four validated CpGs representing cfDNA from granulocytes, lymphocytes, monocytes, and non-hematopoietic cells, in healthy individuals in response to exercise, and in patients with hematological malignancies under resting conditions. The analysis revealed that physical activity almost exclusively triggered DNA release from granulocytes, highlighting the relevance as a pre-analytical variable which could compromise diagnostic accuracy.
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Affiliation(s)
- Elmo W I Neuberger
- Department of Sports Medicine, Rehabilitation and Disease Prevention, Faculty of Social Science, Media and Sport, Johannes Gutenberg-University Mainz, Albert-Schweitzerstr. 22, 55128, Mainz, Germany
| | - Stephanie Sontag
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Alexandra Brahmer
- Department of Sports Medicine, Rehabilitation and Disease Prevention, Faculty of Social Science, Media and Sport, Johannes Gutenberg-University Mainz, Albert-Schweitzerstr. 22, 55128, Mainz, Germany
| | - Keito F A Philippi
- Department of Sports Medicine, Rehabilitation and Disease Prevention, Faculty of Social Science, Media and Sport, Johannes Gutenberg-University Mainz, Albert-Schweitzerstr. 22, 55128, Mainz, Germany
| | - Markus P Radsak
- Department of Medicine III, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Perikles Simon
- Department of Sports Medicine, Rehabilitation and Disease Prevention, Faculty of Social Science, Media and Sport, Johannes Gutenberg-University Mainz, Albert-Schweitzerstr. 22, 55128, Mainz, Germany.
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11
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OUP accepted manuscript. Clin Chem 2022; 68:613-615. [DOI: 10.1093/clinchem/hvac035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 02/15/2022] [Indexed: 11/14/2022]
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Schmidt M, Maixner F, Hotz G, Pap I, Szikossy I, Pálfi G, Zink A, Wagner W. DNA methylation profiling in mummified human remains from the eighteenth-century. Sci Rep 2021; 11:15493. [PMID: 34326450 PMCID: PMC8322318 DOI: 10.1038/s41598-021-95021-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 07/19/2021] [Indexed: 12/19/2022] Open
Abstract
Reconstruction of ancient epigenomes by DNA methylation (DNAm) can shed light into the composition of cell types, disease states, and age at death. However, such analysis is hampered by impaired DNA quality and little is known how decomposition affects DNAm. In this study, we determined if EPIC Illumina BeadChip technology is applicable for specimens from mummies of the eighteenth century CE. Overall, the signal intensity on the microarray was extremely low, but for one of two samples we were able to detect characteristic DNAm signals in a subset of CG dinucleotides (CpGs), which were selected with a stringent processing pipeline. Using only these CpGs we could train epigenetic signatures with reference DNAm profiles of multiple tissues and our predictions matched the fact that the specimen was lung tissue from a 28-year-old woman. Thus, we provide proof of principle that Illumina BeadChips are applicable for DNAm profiling in ancient samples.
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Affiliation(s)
- Marco Schmidt
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstrasse 20, 52074, Aachen, Germany
| | - Frank Maixner
- Institute for Mummy Studies, Eurac Research, Viale Druso, 1, 39100, Bolzano, Italy
| | - Gerhard Hotz
- Anthropological Collection, Natural History Museum of Basel, 4051, Basel, Switzerland.,Integrative Prehistory and Archaeological Science (IPAS), University of Basel, 4051, Basel, Switzerland
| | - Ildikó Pap
- Department of Biological Anthropology, Faculty of Science and Informatics, University of Szeged, 6726, Szeged, Hungary.,Department of Anthropology, Hungarian Natural History Museum, 1083, Budapest, Hungary.,Department of Biological Anthropology, Eötvös University, 1117, Budapest, Hungary
| | - Ildikó Szikossy
- Department of Biological Anthropology, Faculty of Science and Informatics, University of Szeged, 6726, Szeged, Hungary.,Department of Anthropology, Hungarian Natural History Museum, 1083, Budapest, Hungary
| | - György Pálfi
- Department of Biological Anthropology, Faculty of Science and Informatics, University of Szeged, 6726, Szeged, Hungary
| | - Albert Zink
- Institute for Mummy Studies, Eurac Research, Viale Druso, 1, 39100, Bolzano, Italy
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstrasse 20, 52074, Aachen, Germany.
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13
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Schmidt M, Maié T, Dahl E, Costa IG, Wagner W. Deconvolution of cellular subsets in human tissue based on targeted DNA methylation analysis at individual CpG sites. BMC Biol 2020; 18:178. [PMID: 33234153 PMCID: PMC7687708 DOI: 10.1186/s12915-020-00910-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 10/28/2020] [Indexed: 12/12/2022] Open
Abstract
Background The complex composition of different cell types within a tissue can be estimated by deconvolution of bulk gene expression profiles or with various single-cell sequencing approaches. Alternatively, DNA methylation (DNAm) profiles have been used to establish an atlas for multiple human tissues and cell types. DNAm is particularly suitable for deconvolution of cell types because each CG dinucleotide (CpG site) has only two states per DNA strand—methylated or non-methylated—and these epigenetic modifications are very consistent during cellular differentiation. So far, deconvolution of DNAm profiles implies complex signatures of many CpGs that are often measured by genome-wide analysis with Illumina BeadChip microarrays. In this study, we investigated if the characterization of cell types in tissue is also feasible with individual cell type-specific CpG sites, which can be addressed by targeted analysis, such as pyrosequencing. Results We compiled and curated 579 Illumina 450k BeadChip DNAm profiles of 14 different non-malignant human cell types. A training and validation strategy was applied to identify and test for cell type-specific CpGs. We initially focused on estimating the relative amount of fibroblasts using two CpGs that were either hypermethylated or hypomethylated in fibroblasts. The combination of these two DNAm levels into a “FibroScore” correlated with the state of fibrosis and was associated with overall survival in various types of cancer. Furthermore, we identified hypomethylated CpGs for leukocytes, endothelial cells, epithelial cells, hepatocytes, glia, neurons, fibroblasts, and induced pluripotent stem cells. The accuracy of this eight CpG signature was tested in additional BeadChip datasets of defined cell mixtures and the results were comparable to previously published signatures based on several thousand CpGs. Finally, we established and validated pyrosequencing assays for the relevant CpGs that can be utilized for classification and deconvolution of cell types. Conclusion This proof of concept study demonstrates that DNAm analysis at individual CpGs reflects the cellular composition of cellular mixtures and different tissues. Targeted analysis of these genomic regions facilitates robust methods for application in basic research and clinical settings.
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Affiliation(s)
- Marco Schmidt
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, 52074, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, 52074, Aachen, Germany
| | - Tiago Maié
- Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School, 52074, Aachen, Germany
| | - Edgar Dahl
- RWTH centralized Biomaterial Bank (RWTH cBMB), Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Ivan G Costa
- Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School, 52074, Aachen, Germany
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, 52074, Aachen, Germany. .,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, 52074, Aachen, Germany.
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Abstract
The remarkable success of cancer immunotherapies, especially the checkpoint blocking antibodies, in a subset of patients has reinvigorated the study of tumor-immune crosstalk and its role in heterogeneity of response. High-throughput sequencing and imaging technologies can help recapitulate various aspects of the tumor ecosystem. Computational approaches provide an arsenal of tools to efficiently analyze, quantify and integrate multiple parameters of tumor immunity mined from these diverse but complementary high-throughput datasets. This chapter describes numerous such computational approaches in tumor immunology that leverage high-throughput data from diverse sources (genomic, transcriptomics, epigenomics and digitized histopathology images) to systematically interrogate tumor immunity in context of its microenvironment, and to identify mechanisms that confer resistance or sensitivity to cancer therapies, in particular immunotherapy.
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Goetzke R, Keijdener H, Franzen J, Ostrowska A, Nüchtern S, Mela P, Wagner W. Differentiation of Induced Pluripotent Stem Cells towards Mesenchymal Stromal Cells is Hampered by Culture in 3D Hydrogels. Sci Rep 2019; 9:15578. [PMID: 31666572 PMCID: PMC6821810 DOI: 10.1038/s41598-019-51911-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 10/10/2019] [Indexed: 01/08/2023] Open
Abstract
Directed differentiation of induced pluripotent stem cells (iPSCs) towards specific lineages remains a major challenge in regenerative medicine, while there is a growing perception that this process can be influenced by the three-dimensional environment. In this study, we investigated whether iPSCs can differentiate towards mesenchymal stromal cells (MSCs) when embedded into fibrin hydrogels to enable a one-step differentiation procedure within a scaffold. Differentiation of iPSCs on tissue culture plastic or on top of fibrin hydrogels resulted in a typical MSC-like phenotype. In contrast, iPSCs embedded into fibrin gel gave rise to much smaller cells with heterogeneous growth patterns, absence of fibronectin, faint expression of CD73 and CD105, and reduced differentiation potential towards osteogenic and adipogenic lineage. Transcriptomic analysis demonstrated that characteristic genes for MSCs and extracellular matrix were upregulated on flat substrates, whereas genes of neural development were upregulated in 3D culture. Furthermore, the 3D culture had major effects on DNA methylation profiles, particularly within genes for neuronal and cardiovascular development, while there was no evidence for epigenetic maturation towards MSCs. Taken together, iPSCs could be differentiated towards MSCs on tissue culture plastic or on a flat fibrin hydrogel. In contrast, the differentiation process was heterogeneous and not directed towards MSCs when iPSCs were embedded into the hydrogel.
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Affiliation(s)
- Roman Goetzke
- Helmholtz Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Hans Keijdener
- Department of Biohybrid & Medical Textiles (BioTex), AME-Institute of Applied Medical Engineering, Helmholtz Institute, RWTH Aachen University, Aachen, Germany
| | - Julia Franzen
- Helmholtz Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Alina Ostrowska
- Helmholtz Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Selina Nüchtern
- Helmholtz Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany
| | - Petra Mela
- Department of Biohybrid & Medical Textiles (BioTex), AME-Institute of Applied Medical Engineering, Helmholtz Institute, RWTH Aachen University, Aachen, Germany. .,Medical Materials and Implants, Department of Mechanical Engineering and Munich School of BioEngineering, Technical University of Munich, Garching, Germany.
| | - Wolfgang Wagner
- Helmholtz Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany. .,Institute for Biomedical Engineering - Cell Biology, RWTH Aachen University Medical School, Aachen, Germany.
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16
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Cypris O, Frobel J, Rai S, Franzen J, Sontag S, Goetzke R, Szymanski de Toledo MA, Zenke M, Wagner W. Tracking of epigenetic changes during hematopoietic differentiation of induced pluripotent stem cells. Clin Epigenetics 2019; 11:19. [PMID: 30717806 PMCID: PMC6360658 DOI: 10.1186/s13148-019-0617-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 01/17/2019] [Indexed: 01/09/2023] Open
Abstract
Background Differentiation of induced pluripotent stem cells (iPSCs) toward hematopoietic progenitor cells (HPCs) raises high hopes for disease modeling, drug screening, and cellular therapy. Various differentiation protocols have been established to generate iPSC-derived HPCs (iHPCs) that resemble their primary counterparts in morphology and immunophenotype, whereas a systematic epigenetic comparison was yet elusive. Results In this study, we compared genome-wide DNA methylation (DNAm) patterns of iHPCs with various different hematopoietic subsets. After 20 days of in vitro differentiation, cells revealed typical hematopoietic morphology, CD45 expression, and colony-forming unit (CFU) potential. DNAm changes were particularly observed in genes that are associated with hematopoietic differentiation. On the other hand, the epigenetic profiles of iHPCs remained overall distinct from natural HPCs. Furthermore, we analyzed if additional co-culture for 2 weeks with syngenic primary mesenchymal stromal cells (MSCs) or iPSC-derived MSCs (iMSCs) further supports epigenetic maturation toward the hematopoietic lineage. Proliferation of iHPCs and maintenance of CFU potential was enhanced upon co-culture. However, DNAm profiles support the notion that additional culture expansion with stromal support did not increase epigenetic maturation of iHPCs toward natural HPCs. Conclusion Differentiation of iPSCs toward the hematopoietic lineage remains epigenetically incomplete. These results substantiate the need to elaborate advanced differentiation regimen while DNAm profiles provide a suitable measure to track this process. Electronic supplementary material The online version of this article (10.1186/s13148-019-0617-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Olivia Cypris
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany
| | - Joana Frobel
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany
| | - Shivam Rai
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany
| | - Julia Franzen
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany
| | - Stephanie Sontag
- Institute for Biomedical Engineering - Cell Biology, RWTH Aachen University Medical School, Aachen, Germany.,Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Roman Goetzke
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany
| | - Marcelo A Szymanski de Toledo
- Institute for Biomedical Engineering - Cell Biology, RWTH Aachen University Medical School, Aachen, Germany.,Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Martin Zenke
- Institute for Biomedical Engineering - Cell Biology, RWTH Aachen University Medical School, Aachen, Germany.,Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany. .,Institute for Biomedical Engineering - Cell Biology, RWTH Aachen University Medical School, Aachen, Germany.
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Han Y, Eipel M, Franzen J, Sakk V, Dethmers-Ausema B, Yndriago L, Izeta A, de Haan G, Geiger H, Wagner W. Epigenetic age-predictor for mice based on three CpG sites. eLife 2018; 7:37462. [PMID: 30142075 PMCID: PMC6156076 DOI: 10.7554/elife.37462] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 08/23/2018] [Indexed: 11/25/2022] Open
Abstract
Epigenetic clocks for mice were generated based on deep-sequencing analysis of the methylome. Here, we demonstrate that site-specific analysis of DNA methylation levels by pyrosequencing at only three CG dinucleotides (CpGs) in the genes Prima1, Hsf4, and Kcns1 facilitates precise estimation of chronological age in murine blood samples, too. DBA/2 mice revealed accelerated epigenetic aging as compared to C57BL6 mice, which is in line with their shorter life-expectancy. The three-CpG-predictor provides a simple and cost-effective biomarker to determine biological age in large intervention studies with mice. Epigenetic marks are chemical modifications found throughout the genome – the DNA within cells. By influencing the activity of nearby genes, the marks govern developmental processes and help cells to adapt to changes in their surroundings. Some epigenetic marks can be gained or lost with age. A lot of aging research focuses on one type of mark, called “DNA methylation”. By measuring the presence or absence of specific methyl groups, scientists can estimate biological age – which may differ from calendar age. Recent studies have developed computer models called epigenetic aging clocks to predict the biological age of mouse cells. These clocks use epigenetic data collected from the entire genomes of mice, and are useful for understanding how the aging process is affected by genetic parameters, diet, or other environmental factors. Yet, the genome sequencing methods used to construct most existing epigenetic clocks are expensive, labor-intensive, and cannot be easily applied to large groups of mice. Han et al. have developed a new way to predict biological aging in mice that needs methylation information from just three particular sections of the genome. Even though this approach is much faster and less expensive than other epigenetic approaches to measuring aging, it has a similar level of accuracy to existing models. Han et al. use the new method to show that cells from different strains of laboratory mice age at different rates. Furthermore, in a strain that has a shorter life expectancy, aging seems to be accelerated. The new approach developed by Han et al. will make it easier to study how aging in mice is affected by different interventions. Further studies will also be needed to better understand how epigenetic marks relate to biological aging.
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Affiliation(s)
- Yang Han
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital RWTH Aachen, Aachen, Germany
| | - Monika Eipel
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital RWTH Aachen, Aachen, Germany
| | - Julia Franzen
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital RWTH Aachen, Aachen, Germany
| | - Vadim Sakk
- Institute of Molecular Medicine, Ulm University, Ulm, Germany
| | - Bertien Dethmers-Ausema
- Laboratory of Ageing Biology and Stem Cells, European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, Netherlands
| | - Laura Yndriago
- Tissue Engineering Laboratory, Instituto Biodonostia, San Sebastian, Spain
| | - Ander Izeta
- Tissue Engineering Laboratory, Instituto Biodonostia, San Sebastian, Spain.,Department of Biomedical Engineering, School of Engineering, Tecnun-University of Navarra, San Sebastian, Spain
| | - Gerald de Haan
- Laboratory of Ageing Biology and Stem Cells, European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, Netherlands
| | - Hartmut Geiger
- Institute of Molecular Medicine, Ulm University, Ulm, Germany.,Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Burnet Campus, Cincinnati, United States
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital RWTH Aachen, Aachen, Germany
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18
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Frobel J, Rahmig S, Franzen J, Waskow C, Wagner W. Epigenetic aging of human hematopoietic cells is not accelerated upon transplantation into mice. Clin Epigenetics 2018; 10:67. [PMID: 29796118 PMCID: PMC5964682 DOI: 10.1186/s13148-018-0499-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 05/09/2018] [Indexed: 12/12/2022] Open
Abstract
Background Transplantation of human hematopoietic stem cells into immunodeficient mice provides a powerful in vivo model system to gain functional insights into hematopoietic differentiation. So far, it remains unclear if epigenetic changes of normal human hematopoiesis are recapitulated upon engraftment into such “humanized mice.” Mice have a much shorter life expectancy than men, and therefore, we hypothesized that the xenogeneic environment might greatly accelerate the epigenetic clock. Results We demonstrate that genome-wide DNA methylation patterns of normal human hematopoietic development are indeed recapitulated upon engraftment in mice—particularly those of normal early B cell progenitor cells. Furthermore, we tested three epigenetic aging signatures, and none of them indicated that the murine environment accelerated age-associated DNA methylation changes. Conclusions Epigenetic changes of human hematopoietic development are recapitulated in the murine transplantation model, whereas epigenetic aging is not accelerated by the faster aging environment and seems to occur in the cell intrinsically.
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Affiliation(s)
- Joana Frobel
- 1Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074 Aachen, Germany
| | - Susann Rahmig
- 2Regeneration in Hematopoiesis, Institute for Immunology, Technical University Dresden, Dresden, Germany
| | - Julia Franzen
- 1Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074 Aachen, Germany
| | - Claudia Waskow
- 2Regeneration in Hematopoiesis, Institute for Immunology, Technical University Dresden, Dresden, Germany
| | - Wolfgang Wagner
- 1Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074 Aachen, Germany
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