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Cellular and Molecular Mechanisms Involved in Hematopoietic Stem Cell Aging as a Clinical Prospect. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:2713483. [PMID: 35401928 PMCID: PMC8993567 DOI: 10.1155/2022/2713483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 02/28/2022] [Accepted: 03/22/2022] [Indexed: 11/17/2022]
Abstract
There is a hot topic in stem cell research to investigate the process of hematopoietic stem cell (HSC) aging characterized by decreased self-renewal ability, myeloid-biased differentiation, impaired homing, and other abnormalities related to hematopoietic repair function. It is of crucial importance that HSCs preserve self-renewal and differentiation ability to maintain hematopoiesis under homeostatic states over time. Although HSC numbers increase with age in both mice and humans, this cannot compensate for functional defects of aged HSCs. The underlying mechanisms regarding HSC aging have been studied from various perspectives, but the exact molecular events remain unclear. Several cell-intrinsic and cell-extrinsic factors contribute to HSC aging including DNA damage responses, reactive oxygen species (ROS), altered epigenetic profiling, polarity, metabolic alterations, impaired autophagy, Janus kinase/signal transducer and activator of transcription (JAK/STAT) pathway, nuclear factor- (NF-) κB pathway, mTOR pathway, transforming growth factor-beta (TGF-β) pathway, and wingless-related integration site (Wnt) pathway. To determine how deficient HSCs develop during aging, we provide an overview of different hallmarks, age-related signaling pathways, and epigenetic modifications in young and aged HSCs. Knowing how such changes occur and progress will help researchers to develop medications and promote the quality of life for the elderly and possibly alleviate age-associated hematopoietic disorders. The present review is aimed at discussing the latest advancements of HSC aging and the role of HSC-intrinsic factors and related events of a bone marrow niche during HSC aging.
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Poisa-Beiro L, Landry JJM, Raffel S, Tanaka M, Zaugg J, Gavin AC, Ho AD. Glucose Metabolism and Aging of Hematopoietic Stem and Progenitor Cells. Int J Mol Sci 2022; 23:ijms23063028. [PMID: 35328449 PMCID: PMC8955027 DOI: 10.3390/ijms23063028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/26/2022] [Accepted: 03/02/2022] [Indexed: 12/13/2022] Open
Abstract
Comprehensive proteomics studies of human hematopoietic stem and progenitor cells (HSPC) have revealed that aging of the HSPC compartment is characterized by elevated glycolysis. This is in addition to deregulations found in murine transcriptomics studies, such as an increased differentiation bias towards the myeloid lineage, alterations in DNA repair, and a decrease in lymphoid development. The increase in glycolytic enzyme activity is caused by the expansion of a more glycolytic HSPC subset. We therefore developed a method to isolate HSPC into three distinct categories according to their glucose uptake (GU) levels, namely the GUhigh, GUinter and GUlow subsets. Single-cell transcriptomics studies showed that the GUhigh subset is highly enriched for HSPC with a differentiation bias towards myeloid lineages. Gene set enrichment analysis (GSEA) demonstrated that the gene sets for cell cycle arrest, senescence-associated secretory phenotype, and the anti-apoptosis and P53 pathways are significantly upregulated in the GUhigh population. With this series of studies, we have produced a comprehensive proteomics and single-cell transcriptomics atlas of molecular changes in human HSPC upon aging. Although many of the molecular deregulations are similar to those found in mice, there are significant differences. The most unique finding is the association of elevated central carbon metabolism with senescence. Due to the lack of specific markers, the isolation and collection of senescent cells have yet to be developed, especially for human HSPC. The GUhigh subset from the human HSPC compartment possesses all the transcriptome characteristics of senescence. This property may be exploited to accurately enrich, visualize, and trace senescence development in human bone marrow.
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Affiliation(s)
- Laura Poisa-Beiro
- Department of Medicine V, University of Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany; (L.P.-B.); (S.R.)
- Molecular Medicine Partnership Unit Heidelberg, European Molecular Biology Laboratory (EMBL) & Heidelberg University, 69120 Heidelberg, Germany; (J.Z.); (A.-C.G.)
| | - Jonathan J. M. Landry
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, 69117 Heidelberg, Germany;
| | - Simon Raffel
- Department of Medicine V, University of Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany; (L.P.-B.); (S.R.)
| | - Motomu Tanaka
- Physical Chemistry of Biosystems, Inst, Heidelberg University, Im Neuenheimer Feld 253, 69120 Heidelberg, Germany;
| | - Judith Zaugg
- Molecular Medicine Partnership Unit Heidelberg, European Molecular Biology Laboratory (EMBL) & Heidelberg University, 69120 Heidelberg, Germany; (J.Z.); (A.-C.G.)
- European Molecular Biology Laboratory, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Anne-Claude Gavin
- Molecular Medicine Partnership Unit Heidelberg, European Molecular Biology Laboratory (EMBL) & Heidelberg University, 69120 Heidelberg, Germany; (J.Z.); (A.-C.G.)
- Department for Cell Physiology and Metabolism, Centre Medical Universitaire, University of Geneva, Rue Michel-Servet 1, 1211 Geneva, Switzerland
| | - Anthony D. Ho
- Department of Medicine V, University of Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany; (L.P.-B.); (S.R.)
- Molecular Medicine Partnership Unit Heidelberg, European Molecular Biology Laboratory (EMBL) & Heidelberg University, 69120 Heidelberg, Germany; (J.Z.); (A.-C.G.)
- Correspondence:
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Chondronasiou D, Gill D, Mosteiro L, Urdinguio RG, Berenguer‐Llergo A, Aguilera M, Durand S, Aprahamian F, Nirmalathasan N, Abad M, Martin‐Herranz DE, Stephan‐Otto Attolini C, Prats N, Kroemer G, Fraga MF, Reik W, Serrano M. Multi-omic rejuvenation of naturally aged tissues by a single cycle of transient reprogramming. Aging Cell 2022; 21:e13578. [PMID: 35235716 PMCID: PMC8920440 DOI: 10.1111/acel.13578] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 12/01/2022] Open
Abstract
The expression of the pluripotency factors OCT4, SOX2, KLF4, and MYC (OSKM) can convert somatic differentiated cells into pluripotent stem cells in a process known as reprogramming. Notably, partial and reversible reprogramming does not change cell identity but can reverse markers of aging in cells, improve the capacity of aged mice to repair tissue injuries, and extend longevity in progeroid mice. However, little is known about the mechanisms involved. Here, we have studied changes in the DNA methylome, transcriptome, and metabolome in naturally aged mice subject to a single period of transient OSKM expression. We found that this is sufficient to reverse DNA methylation changes that occur upon aging in the pancreas, liver, spleen, and blood. Similarly, we observed reversion of transcriptional changes, especially regarding biological processes known to change during aging. Finally, some serum metabolites and biomarkers altered with aging were also restored to young levels upon transient reprogramming. These observations indicate that a single period of OSKM expression can drive epigenetic, transcriptomic, and metabolomic changes toward a younger configuration in multiple tissues and in the serum.
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Affiliation(s)
- Dafni Chondronasiou
- Institute for Research in Biomedicine (IRB Barcelona) Barcelona Institute of Science and Technology (BIST) Barcelona Spain
| | - Diljeet Gill
- Epigenetics Programme Babraham Institute Cambridge UK
| | | | - Rocio G. Urdinguio
- Cancer Epigenetics and Nanomedicine Laboratory Nanomaterials and Nanotechnology Research Center (CINN CSIC) Oviedo Spain
- Health Research Institute of Asturias (ISPA) Oviedo Spain
- Institute of Oncology of Asturias (IUOPA) University of Oviedo Oviedo Spain
- Department of Organisms and Systems Biology (BOS) University of Oviedo Oviedo Spain
- CIBER of Rare Diseases (CIBERER) Oviedo Spain
| | - Antonio Berenguer‐Llergo
- Institute for Research in Biomedicine (IRB Barcelona) Barcelona Institute of Science and Technology (BIST) Barcelona Spain
| | - Mònica Aguilera
- Institute for Research in Biomedicine (IRB Barcelona) Barcelona Institute of Science and Technology (BIST) Barcelona Spain
| | - Sylvere Durand
- Metabolomics and Cell Biology Platforms Institut Gustave Roussy Villejuif France
- Centre de Recherche des Cordeliers Equipe Labellisée par la Ligue Contre le Cancer Université de Paris Sorbonne Université Paris France
- Inserm U1138 Institut Universitaire de France Paris France
| | - Fanny Aprahamian
- Metabolomics and Cell Biology Platforms Institut Gustave Roussy Villejuif France
- Centre de Recherche des Cordeliers Equipe Labellisée par la Ligue Contre le Cancer Université de Paris Sorbonne Université Paris France
- Inserm U1138 Institut Universitaire de France Paris France
| | - Nitharsshini Nirmalathasan
- Metabolomics and Cell Biology Platforms Institut Gustave Roussy Villejuif France
- Centre de Recherche des Cordeliers Equipe Labellisée par la Ligue Contre le Cancer Université de Paris Sorbonne Université Paris France
- Inserm U1138 Institut Universitaire de France Paris France
| | - Maria Abad
- Vall d'Hebron Institute of Oncology (VHIO) Barcelona Spain
| | | | - Camille Stephan‐Otto Attolini
- Institute for Research in Biomedicine (IRB Barcelona) Barcelona Institute of Science and Technology (BIST) Barcelona Spain
| | - Neus Prats
- Institute for Research in Biomedicine (IRB Barcelona) Barcelona Institute of Science and Technology (BIST) Barcelona Spain
| | - Guido Kroemer
- Metabolomics and Cell Biology Platforms Institut Gustave Roussy Villejuif France
- Centre de Recherche des Cordeliers Equipe Labellisée par la Ligue Contre le Cancer Université de Paris Sorbonne Université Paris France
- Inserm U1138 Institut Universitaire de France Paris France
- Pôle de Biologie Hôpital Européen Georges Pompidou AP‐HP Paris France
- Suzhou Institute for Systems Medicine Chinese Academy of Medical Sciences Suzhou China
| | - Mario F. Fraga
- Cancer Epigenetics and Nanomedicine Laboratory Nanomaterials and Nanotechnology Research Center (CINN CSIC) Oviedo Spain
- Health Research Institute of Asturias (ISPA) Oviedo Spain
- Institute of Oncology of Asturias (IUOPA) University of Oviedo Oviedo Spain
- Department of Organisms and Systems Biology (BOS) University of Oviedo Oviedo Spain
- CIBER of Rare Diseases (CIBERER) Oviedo Spain
| | - Wolf Reik
- Epigenetics Programme Babraham Institute Cambridge UK
- Centre for Trophoblast Research University of Cambridge Cambridge UK
- Wellcome Trust Sanger Institute Cambridge UK
- Altos Labs Cambridge Institute Cambridge UK
| | - Manuel Serrano
- Institute for Research in Biomedicine (IRB Barcelona) Barcelona Institute of Science and Technology (BIST) Barcelona Spain
- Catalan Institution for Research and Advanced Studies (ICREA) Barcelona Spain
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Aging and Clonal Behavior of Hematopoietic Stem Cells. Int J Mol Sci 2022; 23:ijms23041948. [PMID: 35216063 PMCID: PMC8878540 DOI: 10.3390/ijms23041948] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/04/2022] [Accepted: 02/08/2022] [Indexed: 12/19/2022] Open
Abstract
Hematopoietic stem cells (HSCs) are the only cell population that possesses both a self-renewing capacity and multipotency, and can give rise to all lineages of blood cells throughout an organism’s life. However, the self-renewal capacity of HSCs is not infinite, and cumulative evidence suggests that HSCs alter their function and become less active during organismal aging, leading ultimately to the disruption of hematopoietic homeostasis, such as anemia, perturbed immunity and increased propensity to hematological malignancies. Thus, understanding how HSCs alter their function during aging is a matter of critical importance to prevent or overcome these age-related changes in the blood system. Recent advances in clonal analysis have revealed the functional heterogeneity of murine HSC pools that is established upon development and skewed toward the clonal expansion of functionally poised HSCs during aging. In humans, next-generation sequencing has revealed age-related clonal hematopoiesis that originates from HSC subsets with acquired somatic mutations, and has highlighted it as a significant risk factor for hematological malignancies and cardiovascular diseases. In this review, we summarize the current fate-mapping strategies that are used to track and visualize HSC clonal behavior during development or after stress. We then review the age-related changes in HSCs that can be inherited by daughter cells and act as a cellular memory to form functionally distinct clones. Altogether, we link aging of the hematopoietic system to HSC clonal evolution and discuss how HSC clones with myeloid skewing and low regenerative potential can be expanded during aging.
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55
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Hematopoiesis, Inflammation and Aging-The Biological Background and Clinical Impact of Anemia and Increased C-Reactive Protein Levels on Elderly Individuals. J Clin Med 2022; 11:jcm11030706. [PMID: 35160156 PMCID: PMC8836692 DOI: 10.3390/jcm11030706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 01/27/2023] Open
Abstract
Anemia and systemic signs of inflammation are common in elderly individuals and are associated with decreased survival. The common biological context for these two states is then the hallmarks of aging, i.e., genomic instability, telomere shortening, epigenetic alterations, loss of proteostasis, deregulated nutrient sensing, mitochondrial dysfunction, cellular senescence, stem cell exhaustion and altered intercellular communication. Such aging-associated alterations of hematopoietic stem cells are probably caused by complex mechanisms and depend on both the aging of hematopoietic (stem) cells and on the supporting stromal cells. The function of inflammatory or immunocompetent cells is also altered by aging. The intracellular signaling initiated by soluble proinflammatory mediators (e.g., IL1, IL6 and TNFα) is altered during aging and contributes to the development of both the inhibition of erythropoiesis with anemia as well as to the development of the acute-phase reaction as a systemic sign of inflammation with increased CRP levels. Both anemia and increased CRP levels are associated with decreased overall survival and increased cardiovascular mortality. The handling of elderly patients with inflammation and/or anemia should in our opinion be individualized; all of them should have a limited evaluation with regard to the cause of the abnormalities, but the extent of additional and especially invasive diagnostic evaluation should be based on an overall clinical evaluation and the possible therapeutic consequences.
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56
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Temporal Gene Expression Profiles Reflect the Dynamics of Lymphoid Differentiation. Int J Mol Sci 2022; 23:ijms23031115. [PMID: 35163045 PMCID: PMC8834919 DOI: 10.3390/ijms23031115] [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: 12/14/2021] [Revised: 01/10/2022] [Accepted: 01/16/2022] [Indexed: 02/01/2023] Open
Abstract
Understanding the emergence of lymphoid committed cells from multipotent progenitors (MPP) is a great challenge in hematopoiesis. To gain deeper insight into the dynamic expression changes associated with these transitions, we report the quantitative transcriptome of two MPP subsets and the common lymphoid progenitor (CLP). While the transcriptome is rather stable between MPP2 and MPP3, expression changes increase with differentiation. Among those, we found that pioneer lymphoid genes such as Rag1, Mpeg1, and Dntt are expressed continuously from MPP2. Others, such as CD93, are CLP specific, suggesting their potential use as new markers to improve purification of lymphoid populations. Notably, a six-transcription factor network orchestrates the lymphoid differentiation program. Additionally, we pinpointed 24 long intergenic-non-coding RNA (lincRNA) differentially expressed through commitment and further identified seven novel forms. Collectively, our approach provides a comprehensive landscape of coding and non-coding transcriptomes expressed during lymphoid commitment.
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57
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Mi L, Hu J, Li N, Gao J, Huo R, Peng X, Zhang N, Liu Y, Zhao H, Liu R, Zhang L, Xu K. The Mechanism of Stem Cell Aging. Stem Cell Rev Rep 2022; 18:1281-1293. [PMID: 35000109 PMCID: PMC9033730 DOI: 10.1007/s12015-021-10317-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2021] [Indexed: 12/22/2022]
Abstract
Stem cells have self-renewal ability and multi-directional differentiation potential. They have tissue repair capabilities and are essential for maintaining the tissue homeostasis. The depletion of stem cells is closely related to the occurrence of body aging and aging-related diseases. Therefore, revealing the molecular mechanisms of stem cell aging will set new directions for the therapeutic application of stem cells, the study of aging mechanisms, and the prevention and treatment of aging-related diseases. This review comprehensively describes the molecular mechanisms related to stem cell aging and provides the basis for further investigations aimed at developing new anti-stem cell aging strategies and promoting the clinical application of stem cells.
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Affiliation(s)
- Liangyu Mi
- Department of Rheumatology, Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, 030032, China
| | - Junping Hu
- Department of Rheumatology, Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, 030032, China
- Department of Immunology, Shanxi Medical University, Taiyuan, 030000, Shanxi, China
| | - Na Li
- Department of Rheumatology, Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, 030032, China
| | - Jinfang Gao
- Department of Rheumatology, Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, 030032, China
| | - Rongxiu Huo
- Department of Rheumatology, Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, 030032, China
| | - Xinyue Peng
- Department of Rheumatology, Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, 030032, China
| | - Na Zhang
- Department of Rheumatology, Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, 030032, China
| | - Ying Liu
- Department of Rheumatology, Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, 030032, China
| | - Hanxi Zhao
- Silc Business School, Shanghai University, Shanghai, 200444, China
| | - Ruiling Liu
- Department of Rheumatology, Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, 030032, China
- Department of Immunology, Shanxi Medical University, Taiyuan, 030000, Shanxi, China
| | - Liyun Zhang
- Department of Rheumatology, Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, 030032, China
| | - Ke Xu
- Department of Rheumatology, Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, 030032, China.
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D Palmer R, Papa V, Vaccarezza M. The Ability of Nutrition to Mitigate Epigenetic Drift: A Novel Look at Regulating Gene Expression. J Nutr Sci Vitaminol (Tokyo) 2022; 67:359-365. [PMID: 34980713 DOI: 10.3177/jnsv.67.359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Epigenetic drift causes modification in gene expression during aging and a myriad of physiological changes that are mostly undesirable, remove youthful phenotype and are related to biological decay and disease onset. The epigenome is considered a stable regulator of genetic expression. Moreover, evidence is now accumulating that commonly available compounds found in foods can influence the epigenome to embrace a more youthful and therefore, more disease resistant state. Here we explore the correlation between nutriment and the epigenetic regulation through various types of alimentation. The aim is not to discuss specific chemicals involved in disease onset. Instead, we offer a brief glance at pathogens and offer a practical pathway into epigenetic regulation, hypothesizing that epigenetic drift might be attenuated by several foods able to drive a more youthful and disease resistant phenotype.
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Affiliation(s)
| | - Veronica Papa
- Department of Motor Sciences and Wellness, University of Naples "Parthenope".,FABAP Research Center
| | - Mauro Vaccarezza
- Curtin Medical School, Faculty of Health Sciences, Curtin Health Innovation Research Institute (CHIRI), Curtin University.,Department of Translational Medicine, University of Ferrara
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Investigation of measurable residual disease in acute myeloid leukemia by DNA methylation patterns. Leukemia 2022; 36:80-89. [PMID: 34131280 PMCID: PMC8727289 DOI: 10.1038/s41375-021-01316-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 05/25/2021] [Accepted: 05/28/2021] [Indexed: 02/05/2023]
Abstract
Assessment of measurable residual disease (MRD) upon treatment of acute myeloid leukemia (AML) remains challenging. It is usually addressed by highly sensitive PCR- or sequencing-based screening of specific mutations, or by multiparametric flow cytometry. However, not all patients have suitable mutations and heterogeneity of surface markers hampers standardization in clinical routine. In this study, we propose an alternative approach to estimate MRD based on AML-associated DNA methylation (DNAm) patterns. We identified four CG dinucleotides (CpGs) that commonly reveal aberrant DNAm in AML and their combination could reliably discern healthy and AML samples. Interestingly, bisulfite amplicon sequencing demonstrated that aberrant DNAm patterns were symmetric on both alleles, indicating that there is epigenetic crosstalk between homologous chromosomes. We trained shallow-learning and deep-learning algorithms to identify anomalous DNAm patterns. The method was then tested on follow-up samples with and without MRD. Notably, even samples that were classified as MRD negative often revealed higher anomaly ratios than healthy controls, which may reflect clonal hematopoiesis. Our results demonstrate that targeted DNAm analysis facilitates reliable discrimination of malignant and healthy samples. However, since healthy samples also comprise few abnormal-classified DNAm reads the approach does not yet reliably discriminate MRD positive and negative samples.
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Wu G, Zhang X, Gao F. The epigenetic landscape of exercise in cardiac health and disease. JOURNAL OF SPORT AND HEALTH SCIENCE 2021; 10:648-659. [PMID: 33333247 PMCID: PMC8724625 DOI: 10.1016/j.jshs.2020.12.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/16/2020] [Accepted: 11/16/2020] [Indexed: 05/02/2023]
Abstract
With the rising incidence of cardiovascular diseases, the concomitant mortality and morbidity impose huge burdens on quality of life and societal costs. It is generally accepted that physical inactivity is one of the major risk factors for cardiac disease and that exercise benefits the heart in both physiological and pathologic conditions. However, the molecular mechanisms governing the cardioprotective effects exerted by exercise remain incompletely understood. Most recently, an increasing number of studies indicate the involvement of epigenetic modifications in the promotion of cardiac health and prevention of cardiac disease. Exercise and other lifestyle factors extensively induce epigenetic modifications, including DNA/RNA methylation, histone post-translational modifications, and non-coding RNAs in multiple tissues, which may contribute to their positive effects in human health and diseases. In addition, several studies have shown that maternal or paternal exercise prevents age-associated or high-fat diet-induced metabolic dysfunction in the offspring, reinforcing the importance of epigenetics in mediating the beneficial effects of exercise. It has been shown that exercise can directly modify cardiac epigenetics to promote cardiac health and protect the heart against various pathological processes, or it can modify epigenetics in other tissues, which reduces the risk of cardiac disease and affords cardioprotection through exerkines. An in-depth understanding of the epigenetic landscape of cardioprotective response to exercise will provide new therapeutic targets for cardiac diseases. This review, therefore, aimed to acquaint the cardiac community with the rapidly advancing and evolving field of exercise and epigenetics.
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Affiliation(s)
- Guiling Wu
- School of Aerospace Medicine, Fourth Military Medical University, Xi'an 710032, China
| | - Xing Zhang
- School of Aerospace Medicine, Fourth Military Medical University, Xi'an 710032, China.
| | - Feng Gao
- School of Aerospace Medicine, Fourth Military Medical University, Xi'an 710032, China.
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Ageing and Obesity Shared Patterns: From Molecular Pathogenesis to Epigenetics. Diseases 2021; 9:diseases9040087. [PMID: 34940025 PMCID: PMC8700721 DOI: 10.3390/diseases9040087] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/23/2021] [Accepted: 11/28/2021] [Indexed: 12/22/2022] Open
Abstract
In modern societies, ageing and obesity represent medical challenges for healthcare professionals and caregivers. Obesity and ageing share common features including the related cellular and molecular pathways as well as the impacts they have as risk factors for a variety of diseases and health problems. Both of these health problems also share exercise and a healthy lifestyle as the best therapeutic options. Importantly, ageing and obesity also have common epigenetic changes (histone modification, DNA methylation, noncoding RNAs, and chromatin remodeling) that are also impacted by exercise. This suggests that epigenetic pathways are among the mechanisms via which exercise induces its benefits, including ageing and obesity improvements. Exploring these interrelations and based on the fact that both ageing and obesity represent risk factors for each other, would lead to optimizing the available therapeutic approaches towards improved obesity management and healthy ageing.
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62
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Samoilova EM, Belopasov VV, Ekusheva EV, Zhang C, Troitskiy AV, Baklaushev VP. Epigenetic Clock and Circadian Rhythms in Stem Cell Aging and Rejuvenation. J Pers Med 2021; 11:1050. [PMID: 34834402 PMCID: PMC8620936 DOI: 10.3390/jpm11111050] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/12/2021] [Accepted: 10/14/2021] [Indexed: 12/12/2022] Open
Abstract
This review summarizes the current understanding of the interaction between circadian rhythms of gene expression and epigenetic clocks characterized by the specific profile of DNA methylation in CpG-islands which mirror the senescence of all somatic cells and stem cells in particular. Basic mechanisms of regulation for circadian genes CLOCK-BMAL1 as well as downstream clock-controlled genes (ССG) are also discussed here. It has been shown that circadian rhythms operate by the finely tuned regulation of transcription and rely on various epigenetic mechanisms including the activation of enhancers/suppressors, acetylation/deacetylation of histones and other proteins as well as DNA methylation. Overall, up to 20% of all genes expressed by the cell are subject to expression oscillations associated with circadian rhythms. Additionally included in the review is a brief list of genes involved in the regulation of circadian rhythms, along with genes important for cell aging, and oncogenesis. Eliminating some of them (for example, Sirt1) accelerates the aging process, while the overexpression of Sirt1, on the contrary, protects against age-related changes. Circadian regulators control a number of genes that activate the cell cycle (Wee1, c-Myc, p20, p21, and Cyclin D1) and regulate histone modification and DNA methylation. Approaches for determining the epigenetic age from methylation profiles across CpG islands in individual cells are described. DNA methylation, which characterizes the function of the epigenetic clock, appears to link together such key biological processes as regeneration and functioning of stem cells, aging and malignant transformation. Finally, the main features of adult stem cell aging in stem cell niches and current possibilities for modulating the epigenetic clock and stem cells rejuvenation as part of antiaging therapy are discussed.
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Affiliation(s)
- Ekaterina M. Samoilova
- Federal Research and Clinical Center of Specialized Medical Care and Medical Technologies, FMBA of Russia, 115682 Moscow, Russia; (A.V.T.); (V.P.B.)
| | | | - Evgenia V. Ekusheva
- Academy of Postgraduate Education of the Federal Scientific and Clinical Center for Specialized Types of Medical Care and Medical Technologies, FMBA of Russia, 125371 Moscow, Russia;
| | - Chao Zhang
- Tianjin’s Clinical Research Center for Cancer, Tianjin 300060, China;
| | - Alexander V. Troitskiy
- Federal Research and Clinical Center of Specialized Medical Care and Medical Technologies, FMBA of Russia, 115682 Moscow, Russia; (A.V.T.); (V.P.B.)
| | - Vladimir P. Baklaushev
- Federal Research and Clinical Center of Specialized Medical Care and Medical Technologies, FMBA of Russia, 115682 Moscow, Russia; (A.V.T.); (V.P.B.)
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63
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Borgoni S, Kudryashova KS, Burka K, de Magalhães JP. Targeting immune dysfunction in aging. Ageing Res Rev 2021; 70:101410. [PMID: 34280555 DOI: 10.1016/j.arr.2021.101410] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/28/2021] [Accepted: 07/14/2021] [Indexed: 12/23/2022]
Abstract
Human aging is a multifactorial phenomenon that affects numerous organ systems and cellular processes, with the immune system being one of the most dysregulated. Immunosenescence, the gradual deterioration of the immune system, and inflammaging, a chronic inflammatory state that persists in the elderly, are among the plethora of immune changes that occur during aging. Almost all populations of immune cells change with age in terms of numbers and/or activity. These alterations are in general highly detrimental, resulting in an increased susceptibility to infections, reduced healing abilities, and altered homeostasis that promote the emergence of age-associated diseases such as cancer, diabetes, and other diseases associated with inflammation. Thanks to recent developments, several strategies have been proposed to target central immunological processes or specific immune subpopulations affected by aging. These therapeutic approaches could soon be applied in the clinic to slow down or even reverse specific age-induced immune changes in order to rejuvenate the immune system and prevent or reduce the impact of various diseases. Due to its systemic nature and interconnection with all the other systems in the body, the immune system is an attractive target for aging intervention because relatively targeted modifications to a small set of cells have the potential to improve the health of multiple organ systems. Therefore, anti-aging immune targeting therapies could represent a potent approach for improving healthspan. Here, we review aging changes in the major components of the immune system, we summarize the current immune-targeting therapeutic approaches in the context of aging and discuss the future directions in the field of immune rejuvenation.
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64
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Mejia-Ramirez E, Geiger H, Florian MC. Loss of epigenetic polarity is a hallmark of hematopoietic stem cell aging. Hum Mol Genet 2021; 29:R248-R254. [PMID: 32821941 DOI: 10.1093/hmg/ddaa189] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 01/01/2023] Open
Abstract
Changes of polarity in somatic stem cells upon aging or disease lead to a functional deterioration of stem cells and consequently loss of tissue homeostasis, likely due to changes in the mode (symmetry versus asymmetry) of stem cell divisions. Changes in polarity of epigenetic markers (or 'epi-polarity') in stem cells, which are linked to alterations in chromatin architecture, might explain how a decline in the frequency of epipolar stem cells can have a long-lasting impact on the function of especially aging stem cells. The drift in epipolarity might represent a novel therapeutic target to improve stem cell function upon aging or disease. Here we review basic biological principles of epigenetic polarity, with a special focus on epipolarity and aging of hematopoietic stem cells.
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Affiliation(s)
- Eva Mejia-Ramirez
- Program of Regenerative Medicine, IDIBELL and Program for Clinical Translation of Regenerative Medicine in Catalonia (P-CMRC), Av. Granvia 199, 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Hartmut Geiger
- Institute of Molecular Medicine, University of Ulm, James-Franck-Ring 11c, 89081, Ulm, Germany
| | - M Carolina Florian
- Program of Regenerative Medicine, IDIBELL and Program for Clinical Translation of Regenerative Medicine in Catalonia (P-CMRC), Av. Granvia 199, 08908 L'Hospitalet de Llobregat, Barcelona, Spain.,Institute of Molecular Medicine, University of Ulm, James-Franck-Ring 11c, 89081, Ulm, Germany
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65
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Belyavsky A, Petinati N, Drize N. Hematopoiesis during Ontogenesis, Adult Life, and Aging. Int J Mol Sci 2021; 22:ijms22179231. [PMID: 34502137 PMCID: PMC8430730 DOI: 10.3390/ijms22179231] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/13/2021] [Accepted: 08/24/2021] [Indexed: 12/17/2022] Open
Abstract
In the bone marrow of vertebrates, two types of stem cells coexist-hematopoietic stem cells (HSCs) and mesenchymal stem cells (MSCs). Hematopoiesis only occurs when these two stem cell types and their descendants interact. The descendants of HSCs supply the body with all the mature blood cells, while MSCs give rise to stromal cells that form a niche for HSCs and regulate the process of hematopoiesis. The studies of hematopoiesis were initially based on morphological observations, later extended by the use of physiological methods, and were subsequently augmented by massive application of sophisticated molecular techniques. The combination of these methods produced a wealth of new data on the organization and functional features of hematopoiesis in the ontogenesis of mammals and humans. This review summarizes the current views on hematopoiesis in mice and humans, discusses the development of blood elements and hematopoiesis in the embryo, and describes how the hematopoietic system works in the adult organism and how it changes during aging.
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Affiliation(s)
- Alexander Belyavsky
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia;
| | | | - Nina Drize
- National Research Center for Hematology, 125167 Moscow, Russia;
- Correspondence:
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66
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Orjuela S, Parker HR, Sajibu S, Cereatti F, Sauter M, Buffoli F, Robinson MD, Marra G. Disentangling tumorigenesis-associated DNA methylation changes in colorectal tissues from those associated with ageing. Epigenetics 2021; 17:677-694. [PMID: 34369258 DOI: 10.1080/15592294.2021.1952375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Physiological ageing and tumorigenesis are both associated with epigenomic alterations in human tissue cells, the most extensively investigated of which entails de novo cytosine methylation (i.e., hypermethylation) within the CpG dinucleotides of CpG islands. Genomic regions that become hypermethylated during tumorigenesis are generally believed to overlap regions that acquire methylation in normal tissues as an effect of ageing. To define the extension of this overlap, we analysed the DNA methylomes of 48 large-bowel tissue samples taken from women of different ages during screening colonoscopy: 18 paired samples of normal and lesional tissues from donors harbouring a precancerous lesion and 12 samples of normal mucosa from tumour-free donors. Each sample was subjected to targeted, genome-wide bisulphite sequencing of ~2.5% of the genome, including all CpG islands. In terms of both its magnitude and extension along the chromatin, tumour-associated DNA hypermethylation in these regions was much more conspicuous than that observed in the normal mucosal samples from older (vs. younger) tumour-free donors. 83% of the ageing-associated hypermethylated regions (n = 2501) coincided with hypermethylated regions observed in tumour samples. However, 86% of the regions displaying hypermethylation in precancerous lesions (n = 16,772) showed no methylation changes in the ageing normal mucosa. The tumour-specificity of this latter hypermethylation was validated using published sets of data on DNA methylation in normal and neoplastic colon tissues. This extensive set of genomic regions displaying tumour-specific hypermethylation represents a rich vein of putative biomarkers for the early, non-invasive detection of colorectal tumours in women of all ages.
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Affiliation(s)
- Stephany Orjuela
- Institute of Molecular Cancer Research, University of Zurich, Switzerland.,Department of Molecular Life Sciences, University of Zurich and SIB Swiss Institute of Bioinformatics, Switzerland
| | - Hannah R Parker
- Institute of Molecular Cancer Research, University of Zurich, Switzerland.,Department of Molecular Life Sciences, University of Zurich and SIB Swiss Institute of Bioinformatics, Switzerland
| | - Sija Sajibu
- Institute of Molecular Cancer Research, University of Zurich, Switzerland
| | | | - Matthias Sauter
- Division of Gastroenterology, Triemli Hospital Zurich, Switzerland
| | | | - Mark D Robinson
- Department of Molecular Life Sciences, University of Zurich and SIB Swiss Institute of Bioinformatics, Switzerland
| | - Giancarlo Marra
- Institute of Molecular Cancer Research, University of Zurich, Switzerland
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67
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Inflammation, epigenetics, and metabolism converge to cell senescence and ageing: the regulation and intervention. Signal Transduct Target Ther 2021; 6:245. [PMID: 34176928 PMCID: PMC8236488 DOI: 10.1038/s41392-021-00646-9] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 05/09/2021] [Accepted: 05/13/2021] [Indexed: 02/05/2023] Open
Abstract
Remarkable progress in ageing research has been achieved over the past decades. General perceptions and experimental evidence pinpoint that the decline of physical function often initiates by cell senescence and organ ageing. Epigenetic dynamics and immunometabolic reprogramming link to the alterations of cellular response to intrinsic and extrinsic stimuli, representing current hotspots as they not only (re-)shape the individual cell identity, but also involve in cell fate decision. This review focuses on the present findings and emerging concepts in epigenetic, inflammatory, and metabolic regulations and the consequences of the ageing process. Potential therapeutic interventions targeting cell senescence and regulatory mechanisms, using state-of-the-art techniques are also discussed.
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68
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Udroiu I, Sgura A. Growing and aging of hematopoietic stem cells. World J Stem Cells 2021; 13:594-604. [PMID: 34249229 PMCID: PMC8246248 DOI: 10.4252/wjsc.v13.i6.594] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/22/2020] [Accepted: 02/02/2021] [Indexed: 02/06/2023] Open
Abstract
In the hematopoietic system, a small number of stem cells produce a progeny of several distinct lineages. During ontogeny, they arise in the aorta-gonad-mesonephros region of the embryo and the placenta, afterwards colonise the liver and finally the bone marrow. After this fetal phase of rapid expansion, the number of hematopoietic stem cells continues to grow, in order to sustain the increasing blood volume of the developing newborn, and eventually reaches a steady-state. The kinetics of this growth are mirrored by the rates of telomere shortening in leukocytes. During adulthood, hematopoietic stem cells undergo a very small number of cell divisions. Nonetheless, they are subjected to aging, eventually reducing their potential to produce differentiated progeny. The causal relationships between telomere shortening, DNA damage, epigenetic changes, and aging have still to be elucidated.
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Affiliation(s)
- Ion Udroiu
- Department of Science, Roma Tre University, Rome 00146, Italy
| | - Antonella Sgura
- Department of Science, Roma Tre University, Rome 00146, Italy
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69
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Abstract
[Figure: see text].
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70
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Ho TT, Dellorusso PV, Verovskaya EV, Bakker ST, Flach J, Smith LK, Ventura PB, Lansinger OM, Hérault A, Zhang SY, Kang YA, Mitchell CA, Villeda SA, Passegué E. Aged hematopoietic stem cells are refractory to bloodborne systemic rejuvenation interventions. J Exp Med 2021; 218:212183. [PMID: 34032859 PMCID: PMC8155813 DOI: 10.1084/jem.20210223] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/24/2021] [Accepted: 04/15/2021] [Indexed: 01/13/2023] Open
Abstract
While young blood can restore many aged tissues, its effects on the aged blood system itself and old hematopoietic stem cells (HSCs) have not been determined. Here, we used transplantation, parabiosis, plasma transfer, exercise, calorie restriction, and aging mutant mice to understand the effects of age-regulated systemic factors on HSCs and their bone marrow (BM) niche. We found that neither exposure to young blood, nor long-term residence in young niches after parabiont separation, nor direct heterochronic transplantation had any observable rejuvenating effects on old HSCs. Likewise, exercise and calorie restriction did not improve old HSC function, nor old BM niches. Conversely, young HSCs were not affected by systemic pro-aging conditions, and HSC function was not impacted by mutations influencing organismal aging in established long-lived or progeroid genetic models. Therefore, the blood system that carries factors with either rejuvenating or pro-aging properties for many other tissues is itself refractory to those factors.
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Affiliation(s)
- Theodore T Ho
- The Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Department of Medicine, Hematology/Oncology Division, University of California, San Francisco, San Francisco, CA
| | - Paul V Dellorusso
- Columbia Stem Cell Initiative, Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY
| | - Evgenia V Verovskaya
- The Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Department of Medicine, Hematology/Oncology Division, University of California, San Francisco, San Francisco, CA.,Columbia Stem Cell Initiative, Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY
| | - Sietske T Bakker
- The Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Department of Medicine, Hematology/Oncology Division, University of California, San Francisco, San Francisco, CA
| | - Johanna Flach
- The Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Department of Medicine, Hematology/Oncology Division, University of California, San Francisco, San Francisco, CA
| | - Lucas K Smith
- Department of Anatomy, University of California, San Francisco, San Francisco, CA
| | - Patrick B Ventura
- Department of Anatomy, University of California, San Francisco, San Francisco, CA
| | - Olivia M Lansinger
- The Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Department of Medicine, Hematology/Oncology Division, University of California, San Francisco, San Francisco, CA
| | - Aurélie Hérault
- The Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Department of Medicine, Hematology/Oncology Division, University of California, San Francisco, San Francisco, CA
| | - Si Yi Zhang
- The Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Department of Medicine, Hematology/Oncology Division, University of California, San Francisco, San Francisco, CA
| | - Yoon-A Kang
- The Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Department of Medicine, Hematology/Oncology Division, University of California, San Francisco, San Francisco, CA.,Columbia Stem Cell Initiative, Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY
| | - Carl A Mitchell
- Columbia Stem Cell Initiative, Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY
| | - Saul A Villeda
- Department of Anatomy, University of California, San Francisco, San Francisco, CA
| | - Emmanuelle Passegué
- The Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Department of Medicine, Hematology/Oncology Division, University of California, San Francisco, San Francisco, CA.,Columbia Stem Cell Initiative, Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY
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71
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Masi S, Ambrosini S, Mohammed SA, Sciarretta S, Lüscher TF, Paneni F, Costantino S. Epigenetic Remodeling in Obesity-Related Vascular Disease. Antioxid Redox Signal 2021; 34:1165-1199. [PMID: 32808539 DOI: 10.1089/ars.2020.8040] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Significance: The prevalence of obesity and cardiometabolic phenotypes is alarmingly increasing across the globe and is associated with atherosclerotic vascular complications and high mortality. In spite of multifactorial interventions, vascular residual risk remains high in this patient population, suggesting the need for breakthrough therapies. The mechanisms underpinning obesity-related vascular disease remain elusive and represent an intense area of investigation. Recent Advances: Epigenetic modifications-defined as environmentally induced chemical changes of DNA and histones that do not affect DNA sequence-are emerging as a potent modulator of gene transcription in the vasculature and might significantly contribute to the development of obesity-induced endothelial dysfunction. DNA methylation and histone post-translational modifications cooperate to build complex epigenetic signals, altering transcriptional networks that are implicated in redox homeostasis, mitochondrial function, vascular inflammation, and perivascular fat homeostasis in patients with cardiometabolic disturbances. Critical Issues: Deciphering the epigenetic landscape in the vasculature is extremely challenging due to the complexity of epigenetic signals and their function in regulating transcription. An overview of the most important epigenetic pathways is required to identify potential molecular targets to treat or prevent obesity-related endothelial dysfunction and atherosclerotic disease. This would enable the employment of precision medicine approaches in this setting. Future Directions: Current and future research efforts in this field entail a better definition of the vascular epigenome in obese patients as well as the unveiling of novel, cell-specific chromatin-modifying drugs that are able to erase specific epigenetic signals that are responsible for maladaptive transcriptional alterations and vascular dysfunction in obese patients. Antioxid. Redox Signal. 34, 1165-1199.
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Affiliation(s)
- Stefano Masi
- Dipartimento di Medicina Clinica e Sperimentale, Università di Pisa, Pisa, Italy
| | - Samuele Ambrosini
- Center for Molecular Cardiology, University of Zürich, Zurich, Switzerland
| | - Shafeeq A Mohammed
- Center for Molecular Cardiology, University of Zürich, Zurich, Switzerland
| | - Sebastiano Sciarretta
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Latina, Italy.,Department of AngioCardioNeurology, IRCCS Neuromed, Pozzilli, Italy
| | - Thomas F Lüscher
- Center for Molecular Cardiology, University of Zürich, Zurich, Switzerland.,Heart Division, Royal Brompton and Harefield Hospital Trust, National Heart & Lung Institute, Imperial College, London, United Kingdom
| | - Francesco Paneni
- Center for Molecular Cardiology, University of Zürich, Zurich, Switzerland.,Department of Cardiology, University Heart Center, University Hospital Zurich, Switzerland.,Department of Research and Education, University Hospital Zurich, Zurich, Switzerland
| | - Sarah Costantino
- Center for Molecular Cardiology, University of Zürich, Zurich, Switzerland
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72
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Heterochromatin and Polycomb as regulators of haematopoiesis. Biochem Soc Trans 2021; 49:805-814. [PMID: 33929498 PMCID: PMC8106494 DOI: 10.1042/bst20200737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 12/23/2022]
Abstract
Haematopoiesis is the process by which multipotent haematopoietic stem cells are transformed into each and every type of terminally differentiated blood cell. Epigenetic silencing is critical for this process by regulating the transcription of cell-cycle genes critical for self-renewal and differentiation, as well as restricting alternative fate genes to allow lineage commitment and appropriate differentiation. There are two distinct forms of transcriptionally repressed chromatin: H3K9me3-marked heterochromatin and H3K27me3/H2AK119ub1-marked Polycomb (often referred to as facultative heterochromatin). This review will discuss the role of these distinct epigenetic silencing mechanisms in regulating normal haematopoiesis, how these contribute to age-related haematopoietic dysfunction, and the rationale for therapeutic targeting of these pathways in the treatment of haematological malignancies.
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73
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Newell LF, Williams T, Liu J, Yu Y, Chen Y, Booth GC, Knight RJ, Goslee KR, Cook RJ, Leonard J, Meyers G, Traer E, Press RD, Fan G, Wang Y, Raess PW, Maziarz RT, Dunlap J. Engrafted Donor-Derived Clonal Hematopoiesis after Allogenic Hematopoietic Cell Transplantation is Associated with Chronic Graft-versus-Host Disease Requiring Immunosuppressive Therapy, but no Adverse Impact on Overall Survival or Relapse. Transplant Cell Ther 2021; 27:662.e1-662.e9. [PMID: 33901720 DOI: 10.1016/j.jtct.2021.04.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 11/19/2022]
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP) is an age-associated condition defined by the presence of a somatic mutation in a leukemia-associated gene in individuals who otherwise have no evidence of a hematologic malignancy. In the allogeneic hematopoietic cell transplantation (HCT) setting, clonal hematopoiesis (CH) mutations present in donor stem cells can be transferred to recipients at the time of HCT. Given that the consequences of donor-derived CH in HCT recipients are not entirely clear, we sought to investigate clinical outcomes in patients with engrafted donor-derived CH using a matched cohort analysis of both related and unrelated donors. Of 209 patients with next-generation sequencing performed before and after HCT, donor-derived CH mutations were detected in 15 (5.2%). DNMT3A was the most commonly mutated gene (9 of 15; 60%); mutations in SF3B1, CSF3R, STAT3, CBLB, TET2, and ASXL1 were also identified. Donor-derived CH was not associated with delayed neutrophil or platelet engraftment, and there was no impact on conversion to full donor chimerism. No patients with donor-derived CH experienced relapse, in contrast to 15.6% (7 of 45) in the matched control cohort without CH (P = .176). Donor-derived CH was not associated with worse overall survival; however, patients with donor-derived CH were more likely to develop chronic graft-versus-host disease (GVHD) necessitating systemic immunosuppressive therapy (IST) (P = .045) and less likely to discontinue IST (P = .03) compared with controls without donor-derived CH. We conclude that donor-derived CH does not have an adverse impact on relapse, survival, or engraftment outcomes but may potentiate a graft-versus-leukemia effect, as reflected by increased chronic GVHD necessitating IST.
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Affiliation(s)
- Laura F Newell
- Knight Cancer Institute, Hematology and Medical Oncology, Oregon Health & Science University, Portland, Oregon
| | - Todd Williams
- Department of Pathology, Oregon Health & Science University, Portland, Oregon
| | - James Liu
- Department of Pathology, Oregon Health & Science University, Portland, Oregon
| | - Yun Yu
- Biostatistics Shared Resources, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Yiyi Chen
- Biostatistics Shared Resources, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Georgeann C Booth
- Knight Cancer Institute, Hematology and Medical Oncology, Oregon Health & Science University, Portland, Oregon
| | - Rebekah J Knight
- Cellular Therapy Laboratory, Hospital and Clinics, Oregon Health & Science University, Portland, Oregon
| | - Kelli R Goslee
- Knight Cancer Institute, Hematology and Medical Oncology, Oregon Health & Science University, Portland, Oregon
| | - Rachel J Cook
- Knight Cancer Institute, Hematology and Medical Oncology, Oregon Health & Science University, Portland, Oregon
| | - Jessica Leonard
- Knight Cancer Institute, Hematology and Medical Oncology, Oregon Health & Science University, Portland, Oregon
| | - Gabrielle Meyers
- Knight Cancer Institute, Hematology and Medical Oncology, Oregon Health & Science University, Portland, Oregon
| | - Elie Traer
- Knight Cancer Institute, Hematology and Medical Oncology, Oregon Health & Science University, Portland, Oregon
| | - Richard D Press
- Knight Cancer Institute, Hematology and Medical Oncology, Oregon Health & Science University, Portland, Oregon; Department of Pathology, Oregon Health & Science University, Portland, Oregon
| | - Guang Fan
- Department of Pathology, Oregon Health & Science University, Portland, Oregon
| | - Ying Wang
- Department of Pathology, Oregon Health & Science University, Portland, Oregon
| | - Philipp W Raess
- Department of Pathology, Oregon Health & Science University, Portland, Oregon
| | - Richard T Maziarz
- Knight Cancer Institute, Hematology and Medical Oncology, Oregon Health & Science University, Portland, Oregon
| | - Jennifer Dunlap
- Department of Pathology, Oregon Health & Science University, Portland, Oregon.
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74
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A comprehensive transcriptome signature of murine hematopoietic stem cell aging. Blood 2021; 138:439-451. [PMID: 33876187 DOI: 10.1182/blood.2020009729] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 04/02/2021] [Indexed: 01/11/2023] Open
Abstract
We surveyed 16 published and unpublished data sets to determine whether a consistent pattern of transcriptional deregulation in aging murine hematopoietic stem cells (HSC) exists. Despite substantial heterogeneity between individual studies, we uncovered a core and robust HSC aging signature. We detected increased transcriptional activation in aged HSCs, further confirmed by chromatin accessibility analysis. Unexpectedly, using two independent computational approaches, we established that deregulated aging genes consist largely of membrane-associated transcripts, including many cell surface molecules previously not associated with HSC biology. We show that Selp, the most consistent deregulated gene, is not merely a marker for aged HSCs but is associated with HSC functional decline. Additionally, single-cell transcriptomics analysis revealed increased heterogeneity of the aged HSC pool. We identify the presence of transcriptionally "young-like" HSCs in aged bone marrow. We share our results as an online resource and demonstrate its utility by confirming that exposure to sympathomimetics, and deletion of Dnmt3a/b, molecularly resembles HSC rejuvenation or aging, respectively.
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75
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Guidi N, Marka G, Sakk V, Zheng Y, Florian MC, Geiger H. An aged bone marrow niche restrains rejuvenated hematopoietic stem cells. STEM CELLS (DAYTON, OHIO) 2021; 39:1101-1106. [PMID: 33847429 DOI: 10.1002/stem.3372] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 02/19/2021] [Indexed: 11/11/2022]
Abstract
Aging-associated leukemia and aging-associated immune remodeling are in part caused by aging of hematopoietic stem cells (HSCs). An increase in the activity of the small RhoGTPase cell division control protein 42 (Cdc42) within HSCs causes aging of HSCs. Old HSCs, treated ex vivo with a specific inhibitor of Cdc42 activity termed CASIN, stay rejuvenated upon transplantation into young recipients. We determined in this study the influence of an aged niche on the function of ex vivo rejuvenated old HSCs, as the relative contribution of HSCs intrinsic mechanisms vs extrinsic mechanisms (niche) for aging of HSCs still remain unknown. Our results show that an aged niche restrains the function of ex vivo rejuvenated HSCs, which is at least in part linked to a low level of the cytokine osteopontin found in aged niches. The data imply that sustainable rejuvenation of the function of aged HSCs in vivo will need to address the influence of an aged niche on rejuvenated HSCs.
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Affiliation(s)
- Novella Guidi
- Institute of Molecular Medicine, Ulm University, Ulm, Germany
| | - Gina Marka
- Institute of Molecular Medicine, Ulm University, Ulm, Germany
| | - Vadim Sakk
- Institute of Molecular Medicine, Ulm University, Ulm, Germany
| | - Yi Zheng
- Experimental Hematology and Cancer Biology, CCHMC, Cincinnati, Ohio, USA
| | | | - Hartmut Geiger
- Institute of Molecular Medicine, Ulm University, Ulm, Germany
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76
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Grigoryan A, Pospiech J, Krämer S, Lipka D, Liehr T, Geiger H, Kimura H, Mulaw MA, Florian MC. Attrition of X Chromosome Inactivation in Aged Hematopoietic Stem Cells. Stem Cell Reports 2021; 16:708-716. [PMID: 33798450 PMCID: PMC8072063 DOI: 10.1016/j.stemcr.2021.03.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 01/03/2023] Open
Abstract
During X chromosome inactivation (XCI), the inactive X chromosome (Xi) is recruited to the nuclear lamina at the nuclear periphery. Beside X chromosome reactivation resulting in a highly penetrant aging-like hematopoietic malignancy, little is known about XCI in aged hematopoietic stem cells (HSCs). Here, we demonstrate that LaminA/C defines a distinct repressive nuclear compartment for XCI in young HSCs, and its reduction in aged HSCs correlates with an impairment in the overall control of XCI. Integrated omics analyses reveal higher variation in gene expression, global hypomethylation, and significantly increased chromatin accessibility on the X chromosome (Chr X) in aged HSCs. In summary, our data support the role of LaminA/C in the establishment of a special repressive compartment for XCI in HSCs, which is impaired upon aging.
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Affiliation(s)
- Ani Grigoryan
- Institute of Molecular Medicine and Stem Cell Aging, University of Ulm, Albert-Einstein-Allee 11c, 89081 Ulm, Germany
| | - Johannes Pospiech
- Institute of Molecular Medicine and Stem Cell Aging, University of Ulm, Albert-Einstein-Allee 11c, 89081 Ulm, Germany
| | - Stephen Krämer
- Section Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) & National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany; Bioinformatics and Omics Data Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany; Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany; Biomedical Informatics, Data Mining and Data Analytics, Faculty of Applied Computer Science and Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Daniel Lipka
- Section Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) & National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Am Klinikum 1, 07747 Jena, Germany
| | - Hartmut Geiger
- Institute of Molecular Medicine and Stem Cell Aging, University of Ulm, Albert-Einstein-Allee 11c, 89081 Ulm, Germany
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Medhanie A Mulaw
- Institute of Molecular Medicine and Stem Cell Aging, University of Ulm, Albert-Einstein-Allee 11c, 89081 Ulm, Germany; Department of Internal Medicine I, University Hospital Ulm, Ulm, Germany.
| | - Maria Carolina Florian
- Institute of Molecular Medicine and Stem Cell Aging, University of Ulm, Albert-Einstein-Allee 11c, 89081 Ulm, Germany; Stem Cell Aging Group, Regenerative Medicine Program, Bellvitge Institute for Biomedical Research (IDIBELL) and Program for advancing the Clinical Translation of Regenerative Medicine of Catalonia, P-CMR[C], Av. Gran Via 199-203, 08908, L'Hospitalet de Llobregat, Barcelona, Spain; Center for Networked Biomedical Research on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain.
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Sun J, Zheng W, Liu W, Kou X, Zhao Y, Liang Z, Wang L, Zhang Z, Xiao J, Gao R, Gao S, Jiang C. Differential Transcriptomes and Methylomes of Trophoblast Stem Cells From Naturally-Fertilized and Somatic Cell Nuclear-Transferred Embryos. Front Cell Dev Biol 2021; 9:664178. [PMID: 33869230 PMCID: PMC8047118 DOI: 10.3389/fcell.2021.664178] [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: 02/04/2021] [Accepted: 02/25/2021] [Indexed: 12/05/2022] Open
Abstract
Trophoblast stem cells (TSCs) are critical to mammalian embryogenesis by providing the cell source of the placenta. TSCs can be derived from trophoblast cells. However, the efficiency of TSC derivation from somatic cell nuclear transfer (NT) blastocysts is low. The regulatory mechanisms underlying transcription dynamics and epigenetic landscape remodeling during TSC derivation remain elusive. Here, we derived TSCs from the blastocysts by natural fertilization (NF), NT, and a histone deacetylase inhibitor Scriptaid-treated NT (SNT). Profiling of the transcriptomes across the stages of TSC derivation revealed that fibroblast growth factor 4 (FGF4) treatment resulted in many differentially expressed genes (DEGs) at outgrowth and initiated transcription program for TSC formation. We identified 75 transcription factors (TFs) that are continuously upregulated during NF TSC derivation, whose transcription profiles can infer the time course of NF not NT TSC derivation. Most DEGs in NT outgrowth are rescued in SNT outgrowth. The correct time course of SNT TSC derivation is inferred accordingly. Moreover, these TFs comprise an interaction network important to TSC stemness. Profiling of DNA methylation dynamics showed an extremely low level before FGF4 treatment and gradual increases afterward. FGF4 treatment results in a distinct DNA methylation remodeling process committed to TSC formation. We further identified 1,293 CpG islands (CGIs) whose DNA methylation difference is more than 0.25 during NF TSC derivation. The majority of these CGIs become highly methylated upon FGF4 treatment and remain in high levels. This may create a barrier for lineage commitment to restrict embryonic development, and ensure TSC formation. There exist hundreds of aberrantly methylated CGIs during NT TSC derivation, most of which are corrected during SNT TSC derivation. More than half of the aberrantly methylated CGIs before NT TSC formation are inherited from the donor genome. In contrast, the aberrantly methylated CGIs upon TSC formation are mainly from the highly methylated CGIs induced by FGF4 treatment. Functional annotation indicates that the aberrantly highly methylated CGIs play a role in repressing placenta development genes, etc., related to post-implantation development and maintaining TSC pluripotency. Collectively, our findings provide novel insights into the transcription dynamics, DNA methylation remodeling, and the role of FGF4 during TSC derivation.
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Affiliation(s)
- Jin Sun
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Weisheng Zheng
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Wenqiang Liu
- Clinical and Translation Research Center of Shanghai First Maternity and Infant Hospital, Tongji University, Shanghai, China.,Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, China
| | - Xiaochen Kou
- Clinical and Translation Research Center of Shanghai First Maternity and Infant Hospital, Tongji University, Shanghai, China.,Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, China
| | - Yanhong Zhao
- Clinical and Translation Research Center of Shanghai First Maternity and Infant Hospital, Tongji University, Shanghai, China.,Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, China
| | - Zehang Liang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Lu Wang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Zihao Zhang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jing Xiao
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Rui Gao
- Clinical and Translation Research Center of Shanghai First Maternity and Infant Hospital, Tongji University, Shanghai, China.,Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, China
| | - Shaorong Gao
- Clinical and Translation Research Center of Shanghai First Maternity and Infant Hospital, Tongji University, Shanghai, China.,Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, China
| | - Cizhong Jiang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
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78
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Pouikli A, Tessarz P. Epigenetic alterations in stem cell ageing-a promising target for age-reversing interventions? Brief Funct Genomics 2021; 21:35-42. [PMID: 33738480 PMCID: PMC8789308 DOI: 10.1093/bfgp/elab010] [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] [Indexed: 11/17/2022] Open
Abstract
Ageing is accompanied by loss of tissue integrity and organismal homeostasis partly due to decline in stem cell function. The age-associated decrease in stem cell abundance and activity is often referred to as stem cell exhaustion and is considered one major hallmark of ageing. Importantly, stem cell proliferation and differentiation potential are tightly coupled to the cellular epigenetic state. Thus, research during the last years has started to investigate how the epigenome regulates stem cell function upon ageing. Here, we summarize the role of epigenetic regulation in stem cell fate decisions and we review the impact of age-related changes of the epigenome on stem cell activity. Finally, we discuss how targeted interventions on the epigenetic landscape might delay ageing and extend health-span.
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Affiliation(s)
- Andromachi Pouikli
- Max Planck Research Group Chromatin and Ageing, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany
| | - Peter Tessarz
- Max Planck Research Group Chromatin and Ageing, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany.,Cologne Excellence Cluster on Stress Responses in ageing-associated Diseases (CECAD), Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
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79
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Kelsey MMG. Reconsidering LINE-1's role in cancer: does LINE-1 function as a reporter detecting early cancer-associated epigenetic signatures? EVOLUTION MEDICINE AND PUBLIC HEALTH 2021; 9:78-82. [PMID: 33717489 PMCID: PMC7937435 DOI: 10.1093/emph/eoab004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 01/17/2021] [Indexed: 11/24/2022]
Abstract
Long interspersed nuclear element-1 (LINE-1 or L1) is the only autonomously active retrotransposon in humans. While L1 has been implicated in several pathologies and the aging process, I present a model which challenges an understanding of L1 as predominantly antagonistic to human health. I hypothesize that L1 serves as a reporter in an early cancer alert system: a tripwire strung throughout the genome poised to trigger p53 and a type I interferon (IFN-1) response when the epigenetic landscape portends cancer. Cell proliferation and a shift to aerobic glycolysis cause dramatic changes in the epigenome which are permissive to L1’s escape from suppression. L1 has several properties which make it particularly apt to fulfill this hypothesized sentinel function. Being present in many copies spread throughout the genome allows it to monitor many regions for epigenetic instability and renders it robust to deactivation by mutation. This proposed cancer alert system would alter the cancer cell fitness landscape discouraging the use of growth-favoring aerobic glycolysis by threatening the activation of tumor-suppressive mechanisms. It also imposes costs on a strategy of non-specific global transcriptional derepression aimed at activating oncogenes. Erroneous activations of this system are predicted to increase the rate of aging, suggesting this represents a case of antagonistic pleiotropy trading prolonged youth for cancer prevention. More research is needed to assess this model. Lay summary: During carcinogenesis the epigenome is remodeled by the Warburg effect and cellular proliferation. These processes globally relax chromatin. This epigenetic environment is permissive to the retrotransposon long interspersed nuclear element-1’s (LINE-1 or L1) escape from suppression. I hypothesize and present evidence for the notion that L1 has been co-opted to serve as a reporter in an early cancer alert system, poised to trigger tumor suppressive mechanisms when the epigenetic landscape portends cancer. This hypothesis describes a potentially major means by which transformation is thwarted early on.
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Affiliation(s)
- Maxfield M G Kelsey
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
- Corresponding author. Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA. Tel: 1-818-397-5181; E-mail:
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80
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Cordes S, Wu C, Dunbar CE. Clonal tracking of haematopoietic cells: insights and clinical implications. Br J Haematol 2021; 192:819-831. [PMID: 33216985 PMCID: PMC9927566 DOI: 10.1111/bjh.17175] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 09/16/2020] [Indexed: 01/03/2023]
Abstract
Recent advances in high-throughput genomics have enabled the direct tracking of outputs from many cell types, greatly accelerating the study of developmental processes and tissue regeneration. The capacity for long-term self-renewal with multilineage differentiation potential characterises the cellular dynamics of a special set of developmental states that are critical for maintaining homeostasis. In haematopoiesis, the archetypal model for development, lineage-tracing experiments have elucidated the roles of haematopoietic stem cells to ongoing blood production and the importance of long-lived immune cells to immunological memory. An understanding of the biology and clonal dynamics of these cellular fates and states can provide clues to the response of haematopoiesis to ageing, the process of malignant transformation, and are key to designing more efficacious and durable clinical gene and cellular therapies.
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Affiliation(s)
- Stefan Cordes
- Translational Stem Cell Biology Branch National Heart, Lung, and Blood Institute Bethesda MD USA
| | - Chuanfeng Wu
- Translational Stem Cell Biology Branch National Heart, Lung, and Blood Institute Bethesda MD USA
| | - Cynthia E. Dunbar
- Translational Stem Cell Biology Branch National Heart, Lung, and Blood Institute Bethesda MD USA
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81
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Kuribayashi W, Oshima M, Itokawa N, Koide S, Nakajima-Takagi Y, Yamashita M, Yamazaki S, Rahmutulla B, Miura F, Ito T, Kaneda A, Iwama A. Limited rejuvenation of aged hematopoietic stem cells in young bone marrow niche. J Exp Med 2021; 218:e20192283. [PMID: 33231616 PMCID: PMC7690939 DOI: 10.1084/jem.20192283] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 09/17/2020] [Accepted: 10/19/2020] [Indexed: 12/19/2022] Open
Abstract
Hematopoietic stem cells (HSCs) exhibit functional alterations, such as reduced regenerative capacity and myeloid-biased differentiation, with age. The HSC niche, which is essential for the maintenance of HSCs, also undergoes marked changes with aging. However, it has been technically challenging to directly evaluate the contribution of niche aging to age-associated HSC alterations without niche-damaging myeloablation in HSC transplantation assays. We herein transplanted an excess of aged HSCs into young mice without preconditioning. Although aged HSCs successfully engrafted in the intact young bone marrow niche, they poorly regenerated downstream progenitors and exhibited persistent myeloid-biased differentiation, resulting in no significant functional rejuvenation. Transcriptome and methylome analyses revealed that the young niche largely restored the transcriptional profile of aged HSCs, but not their DNA methylation profiles. Therefore, the restoration of the young niche is insufficient for rejuvenating HSC functions, highlighting a key role for age-associated cell-intrinsic defects in HSC aging.
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Affiliation(s)
- Wakako Kuribayashi
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
- Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Motohiko Oshima
- Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Naoki Itokawa
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
- Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Shuhei Koide
- Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yaeko Nakajima-Takagi
- Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Masayuki Yamashita
- Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Satoshi Yamazaki
- Division of Stem Cell Biology, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, University of Tokyo, Tokyo, Japan
- Laboratory of Stem Cell Therapy, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Bahityar Rahmutulla
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Fumihito Miura
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Takashi Ito
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Atsushi Iwama
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
- Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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82
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Tharakan R, Ubaida-Mohien C, Moore AZ, Hernandez D, Tanaka T, Ferrucci L. Blood DNA Methylation and Aging: A Cross-Sectional Analysis and Longitudinal Validation in the InCHIANTI Study. J Gerontol A Biol Sci Med Sci 2021; 75:2051-2055. [PMID: 32147700 DOI: 10.1093/gerona/glaa052] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Indexed: 12/18/2022] Open
Abstract
Changes in DNA methylation have been found to be highly correlated with aging in humans, but causes or consequences of these changes are not understood. We characterized the DNA methylomes of several hundred people in the Invecchiare in Chianti study to identify DNA sites in which percent methylation was systematically different with age. Then, we tested the hypothesis that changes of percent methylation in the same DNA sites occur longitudinally for the same DNA sites in the same subjects. We identified six differentially methylated regions in which percent methylation showed robust longitudinal changes in the same direction. We then describe functions of the genes near these differentially methylated regions and their potential relationship with aging, noting that the genes appear to regulate metabolism or cell type specificity. The nature of transcription factor binding sites in the vicinity of these differentially methylated regions suggest that these age-associated methylation changes reflect modulation of two biological mechanisms: the polycomb repressive complex 2, a protein complex that trimethylates histone H3 on lysine 27, and the transcriptional repressor CCCTC-binding factor or CTCF, both of which are regulators of chromatin architecture. These findings are consistent with the idea that changes in methylation with aging are of adaptive nature.
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Affiliation(s)
- Ravi Tharakan
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland
| | - Ceereena Ubaida-Mohien
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland
| | - Ann Zenobia Moore
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland
| | - Dena Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland
| | - Toshiko Tanaka
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland
| | - Luigi Ferrucci
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland
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83
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Yokomizo-Nakano T, Sashida G. Two faces of RUNX3 in myeloid transformation. Exp Hematol 2021; 97:14-20. [PMID: 33600870 DOI: 10.1016/j.exphem.2021.02.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 02/01/2021] [Accepted: 02/10/2021] [Indexed: 01/09/2023]
Abstract
RUNX3, a transcription factor, has been implicated as a tumor suppressor in various cancers, including hematological malignancies; however, recent studies revealed an oncogenic function of RUNX3 in the pathogenesis of myeloid malignancies, such as myelodysplastic syndrome and acute myeloid leukemia. In contrast to the high frequency of mutations in the RUNX1 gene, deletion of and loss-of-function mutations in RUNX3 are rarely detected in patients with hematopoietic malignancies. Although RUNX3 is expressed in normal hematopoietic stem and progenitor cells, its expression decreases with aging in humans. The loss of Runx3 did not result in the development of lethal hematological diseases in mice despite the expansion of myeloid cells. Therefore, RUNX3 does not appear to initiate the transformation of normal hematopoietic stem cells. However, the overexpression of RUNX3 inhibits the expression and transcriptional function of the RUNX1 gene, but activates the expression of key oncogenic pathways, such as MYC, resulting in the transformation of premalignant stem cells harboring a driver genetic mutation. We herein discuss the mechanisms by which RUNX3 is activated and how RUNX3 exerts oncogenic effects on the cellular function of and transcriptional program in premalignant stem cells to drive myeloid transformation.
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Affiliation(s)
- Takako Yokomizo-Nakano
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan
| | - Goro Sashida
- Laboratory of Transcriptional Regulation in Leukemogenesis, International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan.
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84
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Chen R, Okeyo-Owuor T, Patel RM, Casey EB, Cluster AS, Yang W, Magee JA. Kmt2c mutations enhance HSC self-renewal capacity and convey a selective advantage after chemotherapy. Cell Rep 2021; 34:108751. [PMID: 33596429 PMCID: PMC7951951 DOI: 10.1016/j.celrep.2021.108751] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/16/2020] [Accepted: 01/25/2021] [Indexed: 12/17/2022] Open
Abstract
The myeloid tumor suppressor KMT2C is recurrently deleted in myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML), particularly therapy-related MDS/AML (t-MDS/t-AML), as part of larger chromosome 7 deletions. Here, we show that KMT2C deletions convey a selective advantage to hematopoietic stem cells (HSCs) after chemotherapy treatment that may precipitate t-MDS/t-AML. Kmt2c deletions markedly enhance murine HSC self-renewal capacity without altering proliferation rates. Haploid Kmt2c deletions convey a selective advantage only when HSCs are driven into cycle by a strong proliferative stimulus, such as chemotherapy. Cycling Kmt2c-deficient HSCs fail to differentiate appropriately, particularly in response to interleukin-1. Kmt2c deletions mitigate histone methylation/acetylation changes that accrue as HSCs cycle after chemotherapy, and they impair enhancer recruitment during HSC differentiation. These findings help explain why Kmt2c deletions are more common in t-MDS/t-AML than in de novo AML or clonal hematopoiesis: they selectively protect cycling HSCs from differentiation without inducing HSC proliferation themselves.
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Affiliation(s)
- Ran Chen
- Department of Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Theresa Okeyo-Owuor
- Department of Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Riddhi M Patel
- Department of Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Emily B Casey
- Department of Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Andrew S Cluster
- Department of Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Wei Yang
- Department of Genetics, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Jeffrey A Magee
- Department of Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO 63110, USA.
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85
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Lasigliè D. Sirtuins and the prevention of immunosenescence. VITAMINS AND HORMONES 2021; 115:221-264. [PMID: 33706950 DOI: 10.1016/bs.vh.2020.12.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Aging of hematopoietic stem cells (HSCs) has been largely described as one underlying cause of senescence of the immune-hematopoietic system (immunosenescence). A set of well-defined hallmarks characterizes aged HSCs contributing to unbalanced hematopoiesis and aging-associated functional alterations of both branches of the immune system. In this chapter, the contribution of sirtuins, a family of conserved NAD+ dependent deacetylases with key roles in metabolism, genome integrity, aging and lifespan, to immunosenescence, will be addressed. In particular, the role of SIRT6 will be deeply analyzed highlighting a multifaceted part of this deacetylase in HSCs aging as well as in the immunosenescence of dendritic cells (DCs). These and other emerging data are currently paving the way for future design and development of rejuvenation means aiming at rescuing age-related changes in immune function in the elderly and combating age-associated hematopoietic diseases.
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Affiliation(s)
- Denise Lasigliè
- Istituto Comprensivo "Franco Marro", Ministero dell'Istruzione Ministero dell'Università e della Ricerca (M.I.U.R), Villar Perosa, TO, Italy.
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86
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Lehmann U, Stark H, Bartels S, Schlue J, Büsche G, Kreipe H. Genome-wide DNA methylation profiling is able to identify prefibrotic PMF cases at risk for progression to myelofibrosis. Clin Epigenetics 2021; 13:28. [PMID: 33541399 PMCID: PMC7860011 DOI: 10.1186/s13148-021-01010-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 01/11/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Patients suffering from the BCR-ABL1-negative myeloproliferative disease prefibrotic primary myelofibrosis (pre-PMF) have a certain risk for progression to myelofibrosis. Accurate risk estimation for this fibrotic progression is of prognostic importance and clinically relevant. Commonly applied risk scores are based on clinical, cytogenetic, and genetic data but do not include epigenetic modifications. Therefore, we evaluated the assessment of genome-wide DNA methylation patterns for their ability to predict fibrotic progression in PMF patients. RESULTS For this purpose, the DNA methylation profile was analyzed genome-wide in a training set of 22 bone marrow trephines from patients with either fibrotic progression (n = 12) or stable disease over several years (n = 10) using the 850 k EPIC array from Illumina. The DNA methylation classifier constructed from this data set was validated in an independently measured test set of additional 11 bone marrow trephines (7 with stable disease, 4 with fibrotic progress). Hierarchical clustering of methylation β-values and linear discriminant classification yielded very good discrimination between both patient groups. By gene ontology analysis, the most differentially methylated CpG sites are primarily associated with genes involved in cell-cell and cell-matrix interactions. CONCLUSIONS In conclusion, we could show that genome-wide DNA methylation profiling of bone marrow trephines is feasible under routine diagnostic conditions and, more importantly, is able to predict fibrotic progression in pre-fibrotic primary myelofibrosis with high accuracy.
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Affiliation(s)
- Ulrich Lehmann
- Institute of Pathology, Medical School Hannover, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
| | - Helge Stark
- Institute of Pathology, Medical School Hannover, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Stephan Bartels
- Institute of Pathology, Medical School Hannover, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Jerome Schlue
- Institute of Pathology, Medical School Hannover, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Guntram Büsche
- Institute of Pathology, Medical School Hannover, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Hans Kreipe
- Institute of Pathology, Medical School Hannover, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
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87
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Renders S, Svendsen AF, Panten J, Rama N, Maryanovich M, Sommerkamp P, Ladel L, Redavid AR, Gibert B, Lazare S, Ducarouge B, Schönberger K, Narr A, Tourbez M, Dethmers-Ausema B, Zwart E, Hotz-Wagenblatt A, Zhang D, Korn C, Zeisberger P, Przybylla A, Sohn M, Mendez-Ferrer S, Heikenwälder M, Brune M, Klimmeck D, Bystrykh L, Frenette PS, Mehlen P, de Haan G, Cabezas-Wallscheid N, Trumpp A. Niche derived netrin-1 regulates hematopoietic stem cell dormancy via its receptor neogenin-1. Nat Commun 2021; 12:608. [PMID: 33504783 PMCID: PMC7840807 DOI: 10.1038/s41467-020-20801-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Accepted: 12/14/2020] [Indexed: 01/30/2023] Open
Abstract
Haematopoietic stem cells (HSCs) are characterized by their self-renewal potential associated to dormancy. Here we identify the cell surface receptor neogenin-1 as specifically expressed in dormant HSCs. Loss of neogenin-1 initially leads to increased HSC expansion but subsequently to loss of self-renewal and premature exhaustion in vivo. Its ligand netrin-1 induces Egr1 expression and maintains quiescence and function of cultured HSCs in a Neo1 dependent manner. Produced by arteriolar endothelial and periarteriolar stromal cells, conditional netrin-1 deletion in the bone marrow niche reduces HSC numbers, quiescence and self-renewal, while overexpression increases quiescence in vivo. Ageing associated bone marrow remodelling leads to the decline of netrin-1 expression in niches and a compensatory but reversible upregulation of neogenin-1 on HSCs. Our study suggests that niche produced netrin-1 preserves HSC quiescence and self-renewal via neogenin-1 function. Decline of netrin-1 production during ageing leads to the gradual decrease of Neo1 mediated HSC self-renewal.
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Affiliation(s)
- Simon Renders
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120, Heidelberg, Germany
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Arthur Flohr Svendsen
- Laboratory of Ageing Biology and Stem Cells, European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jasper Panten
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Nicolas Rama
- Apoptosis, Cancer and Development Laboratory, Equipe labellisée "La Ligue," LabEx DEVweCAN, Institut Convergence Rabelais, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Université de Lyon1, Centre Léon Bérard, 69008, Lyon, France
| | - Maria Maryanovich
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Pia Sommerkamp
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Luisa Ladel
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120, Heidelberg, Germany
| | - Anna Rita Redavid
- Apoptosis, Cancer and Development Laboratory, Equipe labellisée "La Ligue," LabEx DEVweCAN, Institut Convergence Rabelais, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Université de Lyon1, Centre Léon Bérard, 69008, Lyon, France
| | - Benjamin Gibert
- Apoptosis, Cancer and Development Laboratory, Equipe labellisée "La Ligue," LabEx DEVweCAN, Institut Convergence Rabelais, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Université de Lyon1, Centre Léon Bérard, 69008, Lyon, France
| | - Seka Lazare
- Laboratory of Ageing Biology and Stem Cells, European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Benjamin Ducarouge
- Apoptosis, Cancer and Development Laboratory, Equipe labellisée "La Ligue," LabEx DEVweCAN, Institut Convergence Rabelais, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Université de Lyon1, Centre Léon Bérard, 69008, Lyon, France
| | | | - Andreas Narr
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Manon Tourbez
- Laboratory of Ageing Biology and Stem Cells, European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Bertien Dethmers-Ausema
- Laboratory of Ageing Biology and Stem Cells, European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Erik Zwart
- Laboratory of Ageing Biology and Stem Cells, European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Agnes Hotz-Wagenblatt
- Core Facility Omics IT and Data Management, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dachuan Zhang
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Claudia Korn
- Wellcome Trust/MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AH, UK
- Department of Haematology, University of Cambridge, Cambridge, CB2 0AH, UK
- NHS Blood and Transplant, Cambridge, CB2 0PT, UK
| | - Petra Zeisberger
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120, Heidelberg, Germany
| | - Adriana Przybylla
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120, Heidelberg, Germany
| | - Markus Sohn
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120, Heidelberg, Germany
| | - Simon Mendez-Ferrer
- Wellcome Trust/MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AH, UK
- Department of Haematology, University of Cambridge, Cambridge, CB2 0AH, UK
- NHS Blood and Transplant, Cambridge, CB2 0PT, UK
| | - Mathias Heikenwälder
- Division of Chronic Inflammation and Cancer, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany
| | - Maik Brune
- Department of Internal Medicine I and Clinical Chemistry, Heidelberg University Hospital, Heidelberg, Germany
| | - Daniel Klimmeck
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120, Heidelberg, Germany
| | - Leonid Bystrykh
- Laboratory of Ageing Biology and Stem Cells, European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Paul S Frenette
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Patrick Mehlen
- Apoptosis, Cancer and Development Laboratory, Equipe labellisée "La Ligue," LabEx DEVweCAN, Institut Convergence Rabelais, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Université de Lyon1, Centre Léon Bérard, 69008, Lyon, France
| | - Gerald de Haan
- Laboratory of Ageing Biology and Stem Cells, European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | - Andreas Trumpp
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany.
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120, Heidelberg, Germany.
- German Cancer Consortium (DKTK), 69120, Heidelberg, Germany.
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Abstract
Human lifespan is now longer than ever and, as a result, modern society is getting older. Despite that, the detailed mechanisms behind the ageing process and its impact on various tissues and organs remain obscure. In general, changes in DNA, RNA and protein structure throughout life impair their function. Haematopoietic ageing refers to the age-related changes affecting a haematopoietic system. Aged blood cells display different functional aberrations depending on their cell type, which might lead to the development of haematologic disorders, including leukaemias, anaemia or declining immunity. In contrast to traditional bulk assays, which are not suitable to dissect cell-to-cell variation, single-cell-level analysis provides unprecedented insight into the dynamics of age-associated changes in blood. In this Review, we summarise recent studies that dissect haematopoietic ageing at the single-cell level. We discuss what cellular changes occur during haematopoietic ageing at the genomic, transcriptomic, epigenomic and metabolomic level, and provide an overview of the benefits of investigating those changes with single-cell precision. We conclude by considering the potential clinical applications of single-cell techniques in geriatric haematology, focusing on the impact on haematopoietic stem cell transplantation in the elderly and infection studies, including recent COVID-19 research.
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Affiliation(s)
- Paulina M Strzelecka
- Department of Hematology, Oncology, and Tumor Immunology, Charité - Universitätsmedizin Berlin, 13353 Berlin, Germany
- German Consortium for Translational Cancer Research (DKTK), 69120 Heidelberg, Germany
| | - Frederik Damm
- Department of Hematology, Oncology, and Tumor Immunology, Charité - Universitätsmedizin Berlin, 13353 Berlin, Germany
- German Consortium for Translational Cancer Research (DKTK), 69120 Heidelberg, Germany
- Berlin Institute of Health, 10178 Berlin, Germany
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Abstract
PURPOSE OF REVIEW Our understanding of the effects of aging on human hematopoiesis has advanced significantly in recent years, yet the full ramifications of these findings are not fully understood. This review summarizes these findings and discusses their implication as they relate to malignant hematopoiesis. RECENT FINDINGS With human aging there is an impaired immune response, loss of hematopoietic stem cell (HSC) function, increase in clonal hematopoiesis, and higher frequency of myeloid malignancies. Although murine models have implicated abnormalities in DNA damage repair, autophagy, metabolism, and epigenetics, studies in primary human specimens are more limited. The development of age-related clonal hematopoiesis and the risk associated with this is one of the major findings in the field of recent years. This is accompanied by changes in bone marrow stem and progenitor composition, changes in the epigenetic program of stem cells and an inflammatory milieu in the bone marrow. The precise consequences of these changes for the development of age-related malignancies are still unclear. SUMMARY Advances in the field have begun to reveal the mechanisms driving human HSC loss of function with age. It will be critical to delineate between normal and malignant aging in order to better prevent age-associated myeloid malignancies.
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Affiliation(s)
- Emmalee R. Adelman
- Dept of Human Genetics, Miller School of Medicine, University of Miami
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami
| | - Maria E. Figueroa
- Dept of Human Genetics, Miller School of Medicine, University of Miami
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami
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90
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Shchukina I, Bagaitkar J, Shpynov O, Loginicheva E, Porter S, Mogilenko DA, Wolin E, Collins P, Demidov G, Artomov M, Zaitsev K, Sidorov S, Camell C, Bambouskova M, Arthur L, Swain A, Panteleeva A, Dievskii A, Kurbatsky E, Tsurinov P, Chernyatchik R, Dixit VD, Jovanovic M, Stewart SA, Daly MJ, Dmitriev S, Oltz EM, Artyomov MN. Enhanced epigenetic profiling of classical human monocytes reveals a specific signature of healthy aging in the DNA methylome. NATURE AGING 2021; 1:124-141. [PMID: 34796338 PMCID: PMC8597198 DOI: 10.1038/s43587-020-00002-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 10/06/2020] [Indexed: 12/20/2022]
Abstract
The impact of healthy aging on molecular programming of immune cells is poorly understood. Here, we report comprehensive characterization of healthy aging in human classical monocytes, with a focus on epigenomic, transcriptomic, and proteomic alterations, as well as the corresponding proteomic and metabolomic data for plasma, using healthy cohorts of 20 young and 20 older males (~27 and ~64 years old on average). For each individual, we performed eRRBS-based DNA methylation profiling, which allowed us to identify a set of age-associated differentially methylated regions (DMRs) - a novel, cell-type specific signature of aging in DNA methylome. Hypermethylation events were associated with H3K27me3 in the CpG islands near promoters of lowly-expressed genes, while hypomethylated DMRs were enriched in H3K4me1 marked regions and associated with age-related increase of expression of the corresponding genes, providing a link between DNA methylation and age-associated transcriptional changes in primary human cells.
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Affiliation(s)
- Irina Shchukina
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
- These authors contributed equally: Irina Shchukina, Juhi Bagaitkar, Oleg Shpynov
| | - Juhi Bagaitkar
- Department of Oral Immunology and Infectious Diseases, University of Louisville, Louisville, KY, USA
- These authors contributed equally: Irina Shchukina, Juhi Bagaitkar, Oleg Shpynov
| | - Oleg Shpynov
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
- JetBrains Research, St. Petersburg, Russia
- These authors contributed equally: Irina Shchukina, Juhi Bagaitkar, Oleg Shpynov
| | - Ekaterina Loginicheva
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Sofia Porter
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Denis A. Mogilenko
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Erica Wolin
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Patrick Collins
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | - German Demidov
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Mykyta Artomov
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Konstantin Zaitsev
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
- Present address: Computer Technologies Department, ITMO University, St. Petersburg, Russia
| | - Sviatoslav Sidorov
- Yale Center for Research on Aging, Yale School of Medicine, New Haven, CT, USA
| | - Christina Camell
- Yale Center for Research on Aging, Yale School of Medicine, New Haven, CT, USA
| | - Monika Bambouskova
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Laura Arthur
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Amanda Swain
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Alexandra Panteleeva
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | | | | | - Petr Tsurinov
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
- JetBrains Research, St. Petersburg, Russia
| | - Roman Chernyatchik
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
- JetBrains Research, St. Petersburg, Russia
| | - Vishwa Deep Dixit
- Yale Center for Research on Aging, Yale School of Medicine, New Haven, CT, USA
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Sheila A. Stewart
- Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Mark J. Daly
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
- Institute for Molecular Medicine, Helsinki, Finland
| | | | - Eugene M. Oltz
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Maxim N. Artyomov
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
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Broxmeyer HE, Liu Y, Kapur R, Orschell CM, Aljoufi A, Ropa JP, Trinh T, Burns S, Capitano ML. Fate of Hematopoiesis During Aging. What Do We Really Know, and What are its Implications? Stem Cell Rev Rep 2020; 16:1020-1048. [PMID: 33145673 PMCID: PMC7609374 DOI: 10.1007/s12015-020-10065-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2020] [Indexed: 12/11/2022]
Abstract
There is an ongoing shift in demographics such that older persons will outnumber young persons in the coming years, and with it age-associated tissue attrition and increased diseases and disorders. There has been increased information on the association of the aging process with dysregulation of hematopoietic stem (HSC) and progenitor (HPC) cells, and hematopoiesis. This review provides an extensive up-to date summary on the literature of aged hematopoiesis and HSCs placed in context of potential artifacts of the collection and processing procedure, that may not be totally representative of the status of HSCs in their in vivo bone marrow microenvironment, and what the implications of this are for understanding aged hematopoiesis. This review covers a number of interactive areas, many of which have not been adequately explored. There are still many unknowns and mechanistic insights to be elucidated to better understand effects of aging on the hematopoietic system, efforts that will take multidisciplinary approaches, and that could lead to means to ameliorate at least some of the dysregulation of HSCs and HPCs associated with the aging process. Graphical Abstract.
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Affiliation(s)
- Hal E Broxmeyer
- Department of Microbiology and Immunology, Indiana University School of Medicine, 950 West Walnut Street, R2-302, Indianapolis, IN, 46202-5181, USA.
| | - Yan Liu
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Reuben Kapur
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Christie M Orschell
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Arafat Aljoufi
- Department of Microbiology and Immunology, Indiana University School of Medicine, 950 West Walnut Street, R2-302, Indianapolis, IN, 46202-5181, USA
| | - James P Ropa
- Department of Microbiology and Immunology, Indiana University School of Medicine, 950 West Walnut Street, R2-302, Indianapolis, IN, 46202-5181, USA
| | - Thao Trinh
- Department of Microbiology and Immunology, Indiana University School of Medicine, 950 West Walnut Street, R2-302, Indianapolis, IN, 46202-5181, USA
| | - Sarah Burns
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Maegan L Capitano
- Department of Microbiology and Immunology, Indiana University School of Medicine, 950 West Walnut Street, R2-302, Indianapolis, IN, 46202-5181, USA.
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93
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Zhang L, Mack R, Breslin P, Zhang J. Molecular and cellular mechanisms of aging in hematopoietic stem cells and their niches. J Hematol Oncol 2020; 13:157. [PMID: 33228751 PMCID: PMC7686726 DOI: 10.1186/s13045-020-00994-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 11/09/2020] [Indexed: 02/08/2023] Open
Abstract
Aging drives the genetic and epigenetic changes that result in a decline in hematopoietic stem cell (HSC) functioning. Such changes lead to aging-related hematopoietic/immune impairments and hematopoietic disorders. Understanding how such changes are initiated and how they progress will help in the development of medications that could improve the quality life for the elderly and to treat and possibly prevent aging-related hematopoietic diseases. Here, we review the most recent advances in research into HSC aging and discuss the role of HSC-intrinsic events, as well as those that relate to the aging bone marrow niche microenvironment in the overall processes of HSC aging. In addition, we discuss the potential mechanisms by which HSC aging is regulated.
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Affiliation(s)
- Lei Zhang
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, IL, 60153, USA
| | - Ryan Mack
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, IL, 60153, USA
| | - Peter Breslin
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, IL, 60153, USA.,Departments of Molecular/Cellular Physiology and Department of Biology, Loyola University Medical Center and Loyola University Chicago, Chicago, IL, 60660, USA
| | - Jiwang Zhang
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, IL, 60153, USA. .,Department of Pathology, Loyola University Medical Center, Maywood, IL, 60153, USA.
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94
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He X, Liu J, Liu B, Shi J. The use of DNA methylation clock in aging research. Exp Biol Med (Maywood) 2020; 246:436-446. [PMID: 33175612 DOI: 10.1177/1535370220968802] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
One of the key characteristics of aging is a progressive loss of physiological integrity, which weakens bodily functions and increases the risk of death. A robust biomarker is important for the assessment of biological age, the rate of aging, and a person's health status. DNA methylation clocks, novel biomarkers of aging, are composed of a group of cytosine-phosphate-guanine dinucleotides, the DNA methylation status of which can be used to accurately measure subjective age. These clocks are considered accurate biomarkers of chronological age for humans and other vertebrates. Numerous studies have demonstrated these clocks to quantify the rate of biological aging and the effects of longevity and anti-aging interventions. In this review, we describe the purpose and use of DNA methylation clocks in aging research.
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Affiliation(s)
- Xi He
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, 66367Zunyi Medical University, Zunyi 563003, China
| | - Jiaojiao Liu
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, 66367Zunyi Medical University, Zunyi 563003, China
| | - Bo Liu
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, 66367Zunyi Medical University, Zunyi 563003, China
| | - Jingshan Shi
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, 66367Zunyi Medical University, Zunyi 563003, China
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95
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The proliferative history shapes the DNA methylome of B-cell tumors and predicts clinical outcome. ACTA ACUST UNITED AC 2020; 1:1066-1081. [PMID: 34079956 DOI: 10.1038/s43018-020-00131-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We report a systematic analysis of the DNA methylation variability in 1,595 samples of normal cell subpopulations and 14 tumor subtypes spanning the entire human B-cell lineage. Differential methylation among tumor entities relates to differences in cellular origin and to de novo epigenetic alterations, which allowed us to build an accurate machine learning-based diagnostic algorithm. We identify extensive patient-specific methylation variability in silenced chromatin associated with the proliferative history of normal and neoplastic B cells. Mitotic activity generally leaves both hyper- and hypomethylation imprints, but some B-cell neoplasms preferentially gain or lose DNA methylation. Subsequently, we construct a DNA methylation-based mitotic clock called epiCMIT, whose lapse magnitude represents a strong independent prognostic variable in B-cell tumors and is associated with particular driver genetic alterations. Our findings reveal DNA methylation as a holistic tracer of B-cell tumor developmental history, with implications in the differential diagnosis and prediction of clinical outcome.
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96
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Roels J, Thénoz M, Szarzyńska B, Landfors M, De Coninck S, Demoen L, Provez L, Kuchmiy A, Strubbe S, Reunes L, Pieters T, Matthijssens F, Van Loocke W, Erarslan-Uysal B, Richter-Pechańska P, Declerck K, Lammens T, De Moerloose B, Deforce D, Van Nieuwerburgh F, Cheung LC, Kotecha RS, Mansour MR, Ghesquière B, Van Camp G, Berghe WV, Kowalczyk JR, Szczepański T, Davé UP, Kulozik AE, Goossens S, Curtis DJ, Taghon T, Dawidowska M, Degerman S, Van Vlierberghe P. Aging of preleukemic thymocytes drives CpG island hypermethylation in T-cell acute lymphoblastic leukemia. Blood Cancer Discov 2020; 1:274-289. [PMID: 33179015 PMCID: PMC7116343 DOI: 10.1158/2643-3230.bcd-20-0059] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 08/06/2020] [Accepted: 09/15/2020] [Indexed: 12/20/2022] Open
Abstract
Cancer cells display DNA hypermethylation at specific CpG islands in comparison to their normal healthy counterparts, but the mechanism that drives this so-called CpG island methylator phenotype (CIMP) remains poorly understood. Here, we show that CpG island methylation in human T-cell acute lymphoblastic leukemia (T-ALL) mainly occurs at promoters of Polycomb Repressor Complex 2 (PRC2) target genes that are not expressed in normal or malignant T-cells and which display a reciprocal association with H3K27me3 binding. In addition, we revealed that this aberrant methylation profile reflects the epigenetic history of T-ALL and is established already in pre-leukemic, self-renewing thymocytes that precede T-ALL development. Finally, we unexpectedly uncover that this age-related CpG island hypermethylation signature in T-ALL is completely resistant to the FDA-approved hypomethylating agent Decitabine. Altogether, we here provide conceptual evidence for the involvement of a pre-leukemic phase characterized by self-renewing thymocytes in the pathogenesis of human T-ALL.
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Affiliation(s)
- Juliette Roels
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Morgan Thénoz
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | | | - Mattias Landfors
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | - Stien De Coninck
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Lisa Demoen
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Lien Provez
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Anna Kuchmiy
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Steven Strubbe
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Lindy Reunes
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Tim Pieters
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Filip Matthijssens
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Wouter Van Loocke
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Büşra Erarslan-Uysal
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, and Hopp Children's Cancer Center at NCT Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany
| | - Paulina Richter-Pechańska
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, and Hopp Children's Cancer Center at NCT Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany
| | - Ken Declerck
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES) and Integrated Personalized and Precision Oncology Network (IPPON), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Tim Lammens
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Barbara De Moerloose
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | | | - Laurence C Cheung
- Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, Western Australia
- School of Pharmacy and Biomedical Sciences, Curtin University, Perth, Western Australia
| | - Rishi S Kotecha
- Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, Western Australia
- School of Pharmacy and Biomedical Sciences, Curtin University, Perth, Western Australia
| | - Marc R Mansour
- Department of Haematology, University College London Cancer Institute, London, England
| | - Bart Ghesquière
- Metabolomics Expertise Center, VIB Center for Cancer Biology, Leuven, Belgium
| | - Guy Van Camp
- Center of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Wim Vanden Berghe
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES) and Integrated Personalized and Precision Oncology Network (IPPON), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Jerzy R Kowalczyk
- Department of Pediatric Hematology, Oncology and Transplantology, Medical University of Lublin, Lublin, Poland
| | - Tomasz Szczepański
- Department of Pediatric Hematology and Oncology, Zabrze, Medical University of Silesia, Katowice, Poland
| | - Utpal P Davé
- Roudebush Veterans Affairs Medical Center and Indiana University School of Medicine, Indianapolis, Indiana
| | - Andreas E Kulozik
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, and Hopp Children's Cancer Center at NCT Heidelberg, Heidelberg, Germany
- Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory (EMBL), University of Heidelberg, Heidelberg, Germany
| | - Steven Goossens
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - David J Curtis
- Australian Centre for Blood Diseases (ACBD), Monash University, Melbourne, Australia
| | - Tom Taghon
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | | | - Sofie Degerman
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Pieter Van Vlierberghe
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
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Yu C, Ding S. Therapeutic strategies targeting somatic stem cells: Chemical approaches. Bioorg Med Chem 2020; 28:115824. [PMID: 33126088 DOI: 10.1016/j.bmc.2020.115824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 10/15/2020] [Accepted: 10/17/2020] [Indexed: 02/08/2023]
Abstract
Therapeutic modulation of fate and behavior of somatic stem cells can generate safe and functional cells ex vivo for cell-based therapy, or to repair and regenerate damaged tissues in vivo. Chemical approaches involving small molecules have provided promising approaches for modulating cellular fate and function. These strategies offer opportunities that support regenerative medicine. Here, we discuss strategies targeting somatic stem cells through chemical approaches, highlighting their progression as well as future prospects.
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Affiliation(s)
- Chen Yu
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Sheng Ding
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China.
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98
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Ambrosini S, Mohammed SA, Costantino S, Paneni F. Disentangling the epigenetic landscape in cardiovascular patients: a path toward personalized medicine. Minerva Cardiol Angiol 2020; 69:331-345. [PMID: 32996305 DOI: 10.23736/s2724-5683.20.05326-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Despite significant advances in our understanding of cardiovascular disease (CVD) we are still far from having developed breakthrough strategies to combat coronary atherosclerosis and heart failure, which account for most of CV deaths worldwide. Available cardiovascular therapies have failed to show to be equally effective in all patients, suggesting that inter-individual diversity is an important factor when it comes to conceive and deliver effective personalized treatments. Genome mapping has proved useful in identifying patients who could benefit more from specific drugs depending on genetic variances; however, our genetic make-up determines only a limited part of an individual's risk profile. Recent studies have demonstrated that epigenetic changes - defined as dynamic changes of DNA and histones which do not affect DNA sequence - are key players in the pathophysiology of cardiovascular disease and may participate to delineate cardiovascular risk trajectories over the lifetime. Epigenetic modifications include changes in DNA methylation, histone modifications and non-coding RNAs and these epigenetic signals have shown to cooperate in modulating chromatin accessibility to transcription factors and gene expression. Environmental factors such as air pollution, smoking, psychosocial context, and unhealthy diet regimens have shown to significantly modify the epigenome thus leading to altered transcriptional programs and CVD phenotypes. Therefore, the integration of genetic and epigenetic information might be invaluable to build individual maps of cardiovascular risk and hence, could be employed for the design of customized diagnostic and therapeutic strategies. In the present review, we discuss the growing importance of epigenetic information and its putative implications in cardiovascular precision medicine.
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Affiliation(s)
- Samuele Ambrosini
- Center for Molecular Cardiology, University of Zürich, Zurich, Switzerland
| | - Shafeeq A Mohammed
- Center for Molecular Cardiology, University of Zürich, Zurich, Switzerland
| | - Sarah Costantino
- Center for Molecular Cardiology, University of Zürich, Zurich, Switzerland
| | - Francesco Paneni
- Center for Molecular Cardiology, University of Zürich, Zurich, Switzerland - .,Department of Cardiology, University Heart Center, University Hospital Zurich, Zurich, Switzerland.,Department of Research and Education, University Hospital Zurich, Zurich, Switzerland
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99
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He Y, Zhou D. Can molecular targeting the TNFα-ERK-ETS1-IL27Rα pathway keep us young and healthy by protecting HSCs from aging? BLOOD SCIENCE 2020; 2:148-149. [PMID: 35400025 PMCID: PMC8975103 DOI: 10.1097/bs9.0000000000000060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 08/31/2020] [Indexed: 11/25/2022] Open
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100
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Yanai H, Beerman I. Proliferation: Driver of HSC aging phenotypes? Mech Ageing Dev 2020; 191:111331. [PMID: 32798509 PMCID: PMC7541746 DOI: 10.1016/j.mad.2020.111331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 08/02/2020] [Accepted: 08/07/2020] [Indexed: 01/09/2023]
Abstract
The decline of stem cell performance with age is a potential paramount mechanism of aging. Hematopoietic stem cells (HSCs) are perhaps the most studied and best characterized tissue-specific somatic stem cells. As such, HSCs offer an excellent research model of how aging affects stem cell performance, and vice versa. Studies from recent years have elucidated major aging phenotypes of HSCs including a decline in reconstitution potential, altered differentiation predisposition, an increase in number, accumulation of DNA damage/mutations and several others. However, what drives these changes, and exactly how they translate to pathology is poorly understood. Recent studies point to proliferative stress of HSCs as a potential driver of their aging and the resulting pathologies. Here we discuss the recent discoveries and suggest the context in which aging phenotypes could be driven, and the relevant mechanisms by which HSCs could be affected.
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Affiliation(s)
- Hagai Yanai
- Epigenetics and Stem Cell Unit, Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA.
| | - Isabel Beerman
- Epigenetics and Stem Cell Unit, Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA
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