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Yanai H, Park B, Koh H, Jang HJ, Vaughan KL, Tanaka-Yano M, Aon M, Blanton M, Messaoudi I, Diaz-Ruiz A, Mattison JA, Beerman I. Short-term periodic restricted feeding elicits metabolome-microbiome signatures with sex dimorphic persistence in primate intervention. Nat Commun 2024; 15:1088. [PMID: 38316796 PMCID: PMC10844192 DOI: 10.1038/s41467-024-45359-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 01/18/2024] [Indexed: 02/07/2024] Open
Abstract
Dietary restriction has shown benefits in physiological, metabolic, and molecular signatures associated with aging but is a difficult lifestyle to maintain for most individuals. In mice, a less restrictive diet that allows for cyclical periods of reduced calories mitigates aging phenotypes, yet the effects of such an intervention in a genetically heterogenous, higher-order mammal has not been examined. Here, using middle-aged rhesus macaques matched for age and sex, we show that a regimen of 4 days of low-calorie intake followed by 10 days of ad libitum feeding (4:10 diet) performed in repeating cycles over 12 weeks led to significant loss of weight and fat percentage, despite the free access to food for most of the study duration. We show the 4-day restriction period is sufficient to drive alterations to the serum metabolome characterized by substantial differences in lipid classes. These phenotypes were paralleled by changes in the gut microbiome of restricted monkeys that highlight the involvement of a microbiome-metabolome axis. This regimen shows promising phenotypes, with some sex-dimorphic responses, including residual memory of the diet. As many calorie restriction interventions are difficult to sustain, we propose that this short-term diet may be easier to adhere to and have benefits directly relevant to human aging.
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Affiliation(s)
- Hagai Yanai
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Bongsoo Park
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Hyunwook Koh
- Department of Applied Mathematics & Statistics, The State University of New York, Korea (SUNY Korea), Incheon, South Korea
| | - Hyo Jung Jang
- Department of Applied Mathematics & Statistics, The State University of New York, Korea (SUNY Korea), Incheon, South Korea
| | - Kelli L Vaughan
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Mayuri Tanaka-Yano
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Miguel Aon
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Madison Blanton
- Department of Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Ilhem Messaoudi
- Department of Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Alberto Diaz-Ruiz
- Laboratory of Cellular and Molecular Gerontology, Precision Nutrition and Aging Program, Institute IMDEA Food (CEI UAM+CSIC), Madrid, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), Madrid, Spain
| | - Julie A Mattison
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Isabel Beerman
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA.
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2
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Tanaka-Yano M, Zong L, Park B, Yanai H, Tekin-Turhan F, Blackshear PJ, Beerman I. Tristetraprolin overexpression drives hematopoietic changes in young and middle-aged mice generating dominant mitigating effects on induced inflammation in murine models. GeroScience 2024; 46:1271-1284. [PMID: 37535204 PMCID: PMC10828162 DOI: 10.1007/s11357-023-00879-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/17/2023] [Indexed: 08/04/2023] Open
Abstract
Tristetraprolin (TTP), encoded by Zfp36 in mice, is one of the best-characterized tandem zinc-finger mRNA binding proteins involved in mRNA deadenylation and decay. TTPΔARE mice lack an AU-rich motif in the 3'-untranslated regions of TTP mRNA, leading to increased TTP mRNA stability and more TTP protein, resulting in elevated mRNA decay rates of TTP targets. We examined the effect of TTP overexpression on the hematopoietic system in both young and middle-aged mice using TTPΔARE mice and found alterations in blood cell frequencies, with loss of platelets and B220 cells and gains of eosinophils and T cells. TTPΔARE mice also have skewed primitive populations in the bone marrow, with increases in myeloid-biased hematopoietic stem cells (HSCs) but decreases in granulocyte/macrophage-biased multipotent progenitors (MPP3) in both young and middle-aged mice. Changes in the primitive cells' frequencies were associated with transcriptional alterations in the TTP overexpression cells specific to age as well as cell type. Regardless of age, there was a consistent elevation of transcripts regulated by TNFα and TGFβ signaling pathways in both the stem and multipotent progenitor populations. HSCs with TTP overexpression had decreased reconstitution potential in murine transplants but generated hematopoietic environments that mitigated the inflammatory response to the collagen antibody-induced arthritis (CAIA) challenge, which models rheumatoid arthritis and other autoimmune disorders. This dampening of the inflammatory response was even present when there was only a small frequency of TTP overexpressing cells present in the middle-aged mice. We provide an analysis of the early hematopoietic compartments with elevated TTP expression in both young and middle-aged mice which inhibits the reconstitution potential of the HSCs but generates a hematopoietic system that provides dominant repression of induced inflammation.
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Affiliation(s)
- Mayuri Tanaka-Yano
- Epigenetics and Stem Cell Unit, Translational Gerontology Branch, National Institute On Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD, 21224, USA
| | - Le Zong
- Epigenetics and Stem Cell Unit, Translational Gerontology Branch, National Institute On Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD, 21224, USA
| | - Bongsoo Park
- Epigenetics and Stem Cell Unit, Translational Gerontology Branch, National Institute On Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD, 21224, USA
| | - Hagai Yanai
- Epigenetics and Stem Cell Unit, Translational Gerontology Branch, National Institute On Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD, 21224, USA
| | - Ferda Tekin-Turhan
- Epigenetics and Stem Cell Unit, Translational Gerontology Branch, National Institute On Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD, 21224, USA
| | - Perry J Blackshear
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, 27709, USA
| | - Isabel Beerman
- Epigenetics and Stem Cell Unit, Translational Gerontology Branch, National Institute On Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD, 21224, USA.
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3
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Arao Y, Stumpo DJ, Hoenerhoff MJ, Tighe RM, Yu YR, Sutton D, Kashyap A, Beerman I, Blackshear PJ. Lethal eosinophilic crystalline pneumonia in mice expressing a stabilized Csf2 mRNA. FASEB J 2023; 37:e23100. [PMID: 37462673 DOI: 10.1096/fj.202300757r] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/29/2023] [Accepted: 07/05/2023] [Indexed: 07/21/2023]
Abstract
Granulocyte-macrophage colony-stimulating factor (GM-CSF) is a cytokine that stimulates the proliferation and differentiation of granulocyte and macrophage precursors. The mouse gene-encoding GM-CSF, Csf2, is regulated at both transcriptional and post-transcriptional levels. An adenine-uridine-rich element (ARE) within the 3'-untranslated region of Csf2 mRNA was shown in cell transfection studies to confer instability on this transcript. To explore the physiological importance of this element in an intact animal, we generated mice with a knock-in deletion of the 75-nucleotide ARE. Mice heterozygous for this ARE deletion developed severe respiratory distress and death within about 12 weeks of age. There was dense infiltration of lung alveolar spaces by crystal-containing macrophages. Increased stability of Csf2 mRNA was confirmed in bone marrow-derived macrophages, and elevated GM-CSF levels were observed in serum and lung. These mice did not exhibit notable abnormalities in blood or bone marrow, and transplantation of bone marrow from mutant mice into lethally irradiated WT mice did not confer the pulmonary phenotype. Mice with a conditional deletion of the ARE restricted to lung type II alveolar cells exhibited an essentially identical lethal lung phenotype at the same ages as the mice with the whole-body deletion. In contrast, mice with the same conditional ARE deletion in myeloid cells, including macrophages, exhibited lesser degrees of macrophage infiltration into alveolar spaces much later in life, at approximately 9 months of age. Post-transcriptional Csf2 mRNA stability regulation in pulmonary alveolar epithelial cells appears to be essential for normal physiological GM-CSF secretion and pulmonary macrophage homeostasis.
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Affiliation(s)
- Yukitomo Arao
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences/NIH, Durham, North Carolina, USA
| | - Deborah J Stumpo
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences/NIH, Durham, North Carolina, USA
| | - Mark J Hoenerhoff
- In Vivo Animal Core, Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Robert M Tighe
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Yen-Rei Yu
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Deloris Sutton
- Cellular & Molecular Pathology Branch, National Institute of Environmental Health Sciences/NIH, Durham, North Carolina, USA
| | - Amogh Kashyap
- Epigenetics and Stem Cell Aging Unit, National Institute on Aging/NIH, Baltimore, Maryland, USA
| | - Isabel Beerman
- Epigenetics and Stem Cell Aging Unit, National Institute on Aging/NIH, Baltimore, Maryland, USA
| | - Perry J Blackshear
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences/NIH, Durham, North Carolina, USA
- Departments of Medicine and Biochemistry, Duke University Medical Center, Durham, North Carolina, USA
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Stock AJ, Ayyar S, Kashyap A, Wang Y, Yanai H, Starost MF, Tanaka-Yano M, Bodogai M, Sun C, Wang Y, Gong Y, Puligilla C, Fang EF, Bohr VA, Liu Y, Beerman I. Boosting NAD ameliorates hematopoietic impairment linked to short telomeres in vivo. GeroScience 2023; 45:2213-2228. [PMID: 36826621 PMCID: PMC10651621 DOI: 10.1007/s11357-023-00752-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 02/03/2023] [Indexed: 02/25/2023] Open
Abstract
Short telomeres are a defining feature of telomere biology disorders (TBDs), including dyskeratosis congenita (DC), for which there is no effective general cure. Patients with TBDs often experience bone marrow failure. NAD, an essential metabolic coenzyme, is decreased in models of DC. Herein, using telomerase reverse transcriptase null (Tert-/-) mice with critically short telomeres, we investigated the effect of NAD supplementation with the NAD precursor, nicotinamide riboside (NR), on features of health span disrupted by telomere impairment. Our results revealed that NR ameliorated body weight loss in Tert-/- mice and improved telomere integrity and telomere dysfunction-induced systemic inflammation. NR supplementation also mitigated myeloid skewing of Tert-/- hematopoietic stem cells. Furthermore, NR alleviated villous atrophy and inflammation in the small intestine of Tert-/- transplant recipient mice. Altogether, our findings support NAD intervention as a potential therapeutic strategy to enhance aspects of health span compromised by telomere attrition.
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Affiliation(s)
- Amanda J Stock
- Laboratory of Genetics and Genomics, Biomedical Research Center, National Institute On Aging/National Institutes of Health, 251 Bayview Blvd., Baltimore, MD, USA
| | - Saipriya Ayyar
- Translational Gerontology Branch, Biomedical Research Center, National Institute On Aging/National Institutes of Health, 251 Bayview Blvd., Baltimore, MD, USA
| | - Amogh Kashyap
- Translational Gerontology Branch, Biomedical Research Center, National Institute On Aging/National Institutes of Health, 251 Bayview Blvd., Baltimore, MD, USA
| | - Yunong Wang
- Laboratory of Genetics and Genomics, Biomedical Research Center, National Institute On Aging/National Institutes of Health, 251 Bayview Blvd., Baltimore, MD, USA
| | - Hagai Yanai
- Translational Gerontology Branch, Biomedical Research Center, National Institute On Aging/National Institutes of Health, 251 Bayview Blvd., Baltimore, MD, USA
| | - Matthew F Starost
- Division of Veterinary Resources, Building 14E, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, USA
| | - Mayuri Tanaka-Yano
- Translational Gerontology Branch, Biomedical Research Center, National Institute On Aging/National Institutes of Health, 251 Bayview Blvd., Baltimore, MD, USA
| | - Monica Bodogai
- Laboratory of Molecular Biology and Immunology, Biomedical Research Center, National Institute On Aging/National Institutes of Health, 251 Bayview Blvd., Baltimore, MD, USA
| | - Chongkui Sun
- Laboratory of Genetics and Genomics, Biomedical Research Center, National Institute On Aging/National Institutes of Health, 251 Bayview Blvd., Baltimore, MD, USA
| | - Yajun Wang
- Laboratory of Genetics and Genomics, Biomedical Research Center, National Institute On Aging/National Institutes of Health, 251 Bayview Blvd., Baltimore, MD, USA
| | - Yi Gong
- Laboratory of Genetics and Genomics, Biomedical Research Center, National Institute On Aging/National Institutes of Health, 251 Bayview Blvd., Baltimore, MD, USA
| | - Chandrakala Puligilla
- Laboratory of Genetics and Genomics, Biomedical Research Center, National Institute On Aging/National Institutes of Health, 251 Bayview Blvd., Baltimore, MD, USA
| | - Evandro F Fang
- DNA Repair Section, Biomedical Research Center, National Institute On Aging/National Institutes of Health, 251 Bayview Blvd., Baltimore, MD, USA
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, 1478, Lørenskog, Norway
| | - Vilhelm A Bohr
- DNA Repair Section, Biomedical Research Center, National Institute On Aging/National Institutes of Health, 251 Bayview Blvd., Baltimore, MD, USA
| | - Yie Liu
- Laboratory of Genetics and Genomics, Biomedical Research Center, National Institute On Aging/National Institutes of Health, 251 Bayview Blvd., Baltimore, MD, USA.
| | - Isabel Beerman
- Translational Gerontology Branch, Biomedical Research Center, National Institute On Aging/National Institutes of Health, 251 Bayview Blvd., Baltimore, MD, USA.
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5
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Schaffer ED, Beerman I, de Cabo R, Brosh RM. Frontiers in aging special issue: DNA repair and interventions in aging perspective on "loss of epigenetic information as a cause of mammalian aging". Front Aging 2023; 4:1199596. [PMID: 37475956 PMCID: PMC10354253 DOI: 10.3389/fragi.2023.1199596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/23/2023] [Indexed: 07/22/2023]
Abstract
The recently published article in Cell by the Sinclair lab and collaborators entitled "Loss of Epigenetic Information as a Cause of Mammalian Aging" [1] implicates heritable changes in gene expression as the basis for aging, a postulate consistent with the emerging information theory of aging. Sinclair's group and colleagues induced epigenetic changes, i.e., DNA and histone modifications, via double-strand breaks (DSBs) catalyzed by the I-Pol endonuclease at specific genomic loci. The genomic DNA breaks, introduced without inducing insertion or deletion mutations (indels) in a mouse model, were targeted to 19 non-coding regions and one region in ribosomal DNA (rDNA), the latter shown to not have a significant effect on the function or transcription of rDNA [1]. With that experimental model in place, the authors present experimental evidence supporting a model that epigenetic changes drive aging via this inducible DNA break mechanism. After demonstrating the phenotypic alterations of this accelerated aging, they attempt to reverse selective phenotypes by resetting the altered epigenetic landscape. Establishing a causal relationship between epigenetic changes and aging, and how this connection might be manipulated to overturn cellular features of aging, is provocative and merits further study.
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Ayyar S, Beerman I. Detection of DNA Damage in Hematopoietic Stem Cells. Methods Mol Biol 2023; 2567:11-28. [PMID: 36255692 DOI: 10.1007/978-1-0716-2679-5_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Single-cell gel electrophoresis (SCGE or Comet assay) and the Fast Halo assay, also known as the Halo assay, are powerful tools to generate DNA damage measurements with single-cell resolution. Though these techniques are prone to have variability, they can be robust tools for quantifying DNA damage when planned and executed carefully. Here, we present both assays and highlight each technique's advantages and challenges in measuring DNA damage in cells with limiting cell number, such as hematopoietic stem cells (HSCs). The Comet assay is highly sensitive at the cost of increased variability. The Halo assay attenuates some of the effects of variability present in the Comet assay but does not eliminate them entirely and is less sensitive. Overall, the Comet and Halo assays are powerful means of directly measuring DNA damage. We recommend the below methods for detecting damage in hematopoietic stem cells, but the methods can easily be adjusted for measuring damage in any type of single cells in suspension.
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Affiliation(s)
- Saipriya Ayyar
- Epigenetics and Stem Cell Unit, Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - Isabel Beerman
- Epigenetics and Stem Cell Unit, Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA.
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7
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Yanai H, Dunn C, Park B, Coletta C, McDevitt RA, McNeely T, Leone M, Wersto RP, Perdue KA, Beerman I. Male rat leukocyte population dynamics predict a window for intervention in aging. eLife 2022; 11:76808. [PMID: 35507394 PMCID: PMC9150891 DOI: 10.7554/elife.76808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 05/03/2022] [Indexed: 12/03/2022] Open
Abstract
Many age-associated changes in the human hematopoietic system have been reproduced in murine models; however, such changes have not been as robustly explored in rats despite the fact these larger rodents are more physiologically similar to humans. We examined peripheral blood of male F344 rats ranging from 3 to 27 months of age and found significant age-associated changes with distinct leukocyte population shifts. We report CD25+ CD4+ population frequency is a strong predictor of healthy aging, generate a model using blood parameters, and find rats with blood profiles that diverge from chronologic age indicate debility; thus, assessments of blood composition may be useful for non-lethal disease profiling or as a surrogate measure for efficacy of aging interventions. Importantly, blood parameters and DNA methylation alterations, defined distinct juncture points during aging, supporting a non-linear aging process. Our results suggest these inflection points are important considerations for aging interventions. Overall, we present rat blood aging metrics that can serve as a resource to evaluate health and the effects of interventions in a model system physiologically more reflective of humans. Our blood contains many types of white blood cells, which play important roles in defending the body against infections and other threats to our health. The number of these cells changes with age, and this in turn contributes to many other alterations that happen in the body as we get older. For example, the immune system generally gets weaker at fighting infections and preventing other cells from developing into cancer. On top of that, the white blood cells themselves can become cancerous, resulting in several types of blood cancer that are more likely to happen in older people. Many previous studies have examined how the number of white blood cells changes with age in humans and mice. However, our understanding of this process in rats is still poor, despite the fact that the way the human body works has more in common with the rat body than the mouse body. Here, Yanai, Dunn et al. have studied samples of blood from rats between three to 27 months old. The experiments found that it is possible to accurately predict the age of healthy rats by measuring the frequency of populations of white blood cells, especially a certain type known as CD25+ CD4+ cells. If the animals had any form of illness, their predicted age deviated from their actual age. Furthermore, while some changes in the blood were gradual and continuous, others displayed distinct shifts when the rats reached specific ages. In the future, these findings may be used as a tool to help researchers diagnose illnesses in rats before the animals develop symptoms, or to more easily establish if a treatment is having a positive effect on the rats’ health. The work of Yanai, Dunn et al. also provides new insights into aging that could potentially aid the design of new screening methods to predict cancer and intervene using a model system that is more similar to humans.
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Affiliation(s)
- Hagai Yanai
- Flow Cytometry Core, National Institute on Aging, Baltimore, United States
| | - Christopher Dunn
- Flow Cytometry Core, National Institute on Aging, Baltimore, United States
| | - Bongsoo Park
- Epigenetics and Stem Cell Unit, National Institute on Aging, Baltimore, United States
| | - Christopher Coletta
- Computational Biology and Genomics Core, National Institute on Aging, Baltimore, United States
| | - Ross A McDevitt
- Comparative Medicine Section, National Institute on Aging, Baltimore, United States
| | - Taylor McNeely
- Epigenetics and Stem Cell Unit, National Institute on Aging, Baltimore, United States
| | - Michael Leone
- Epigenetics and Stem Cell Unit, National Institute on Aging, Baltimore, United States
| | - Robert P Wersto
- Flow Cytometry Core, National Institute on Aging, Baltimore, United States
| | - Kathy A Perdue
- Comparative Medicine Section, National Institute on Aging, Baltimore, United States
| | - Isabel Beerman
- Epigenetics and Stem Cell Unit, National Institute on Aging, Baltimore, United States
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8
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Tsitsipatis D, Martindale JL, Ubaida‐Mohien C, Lyashkov A, Yanai H, Kashyap A, Shin CH, Herman AB, Ji E, Yang J, Munk R, Dunn C, Lukyanenko Y, Yang X, Chia CW, Karikkineth AC, Zukley L, D’Agostino J, Kaileh M, Cui C, Beerman I, Ferrucci L, Gorospe M. Proteomes of primary skin fibroblasts from healthy individuals reveal altered cell responses across the life span. Aging Cell 2022; 21:e13609. [PMID: 35429111 PMCID: PMC9124301 DOI: 10.1111/acel.13609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 03/24/2022] [Indexed: 02/04/2023] Open
Abstract
Changes in the proteome of different human tissues with advancing age are poorly characterized. Here, we studied the proteins present in primary skin fibroblasts collected from 82 healthy individuals across a wide age spectrum (22-89 years old) who participated in the GESTALT (Genetic and Epigenetic Signatures of Translational Aging Laboratory Testing) study of the National Institute on Aging, NIH. Proteins were extracted from lysed fibroblasts and subjected to liquid chromatography-mass spectrometry analysis, and the expression levels of 9341 proteins were analyzed using linear regression models. We identified key pathways associated with skin fibroblast aging, including autophagy, scavenging of reactive oxygen species (ROS), ribosome biogenesis, DNA replication, and DNA repair. Changes in these prominent pathways were corroborated using molecular and cell culture approaches. Our study establishes a framework of the global proteome governing skin fibroblast aging and points to possible biomarkers and therapeutic targets.
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Affiliation(s)
- Dimitrios Tsitsipatis
- Laboratory of Genetics and GenomicsNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Jennifer L. Martindale
- Laboratory of Genetics and GenomicsNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Ceereena Ubaida‐Mohien
- Translational Gerontology BranchNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Alexey Lyashkov
- Translational Gerontology BranchNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Hagai Yanai
- Translational Gerontology BranchNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Amogh Kashyap
- Translational Gerontology BranchNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Chang Hoon Shin
- Laboratory of Genetics and GenomicsNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Allison B. Herman
- Laboratory of Genetics and GenomicsNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Eunbyul Ji
- Laboratory of Genetics and GenomicsNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Jen‐Hao Yang
- Laboratory of Genetics and GenomicsNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Rachel Munk
- Laboratory of Genetics and GenomicsNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Christopher Dunn
- Laboratory of Molecular Biology and ImmunologyNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Yevgeniya Lukyanenko
- Translational Gerontology BranchNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Xiaoling Yang
- Laboratory of Genetics and GenomicsNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Chee W. Chia
- Clinical Research CoreNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Ajoy C. Karikkineth
- Clinical Research CoreNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Linda Zukley
- Clinical Research CoreNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Jarod D’Agostino
- Clinical Research CoreNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Mary Kaileh
- Laboratory of Molecular Biology and ImmunologyNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Chang‐Yi Cui
- Laboratory of Genetics and GenomicsNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Isabel Beerman
- Translational Gerontology BranchNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Luigi Ferrucci
- Translational Gerontology BranchNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
| | - Myriam Gorospe
- Laboratory of Genetics and GenomicsNational Institute on AgingNational Institutes of Health Intramural Research ProgramBaltimoreMarylandUSA
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Abstract
Increased age is blamed for a wide range of bone physiological changes, and although the underlying mechanisms affecting the decreased capacity for fracture healing are not fully understood, they are clearly linked to changes at the cellular level. Recent evidence suggests potential roles of senescent cells in response to most tissue injuries, including bone fractures. In this issue of the JCI, Liu, Zhang, and co-authors showed that a senolytic drug cocktail cleared senescent cells from the callus and improved bone fracture repair in aged mice. Understanding how senescent cells emerge at fracture sites and how their timely removal improves fracture healing should provide insights for effective therapeutic approaches in old age.
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10
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Hare JM, Beerman I. Potential of Stem Cell-Based Therapy to Restore Function in Aging Systems: Are We There Yet? J Gerontol A Biol Sci Med Sci 2022; 77:1292-1294. [PMID: 34984451 PMCID: PMC9255684 DOI: 10.1093/gerona/glac003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Indexed: 01/07/2023] Open
Abstract
While there is extensive interest in geroscience approaches to health and disease, few basic science discoveries have made their way into clinical trials. Herein, we comment on cell-based therapies, in which supplementing robust stem cell capacity to aged systems theoretically could lead to sustained improvement. This exciting approach has undergone translational development, and we highlight studies targeting a single system and others aimed at treating overall aging frailty by restoring the aged stem cell niches that underly diminished endogenous regenerative capacity.
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Affiliation(s)
- Joshua M Hare
- The Interdisciplinary Stem Cell Institute, Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Isabel Beerman
- Address correspondence to: Isabel Beerman, PhD, Epigenetics and Stem Cell Unit, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, BRC, 251 Bayview Blvd, Suite 100/10C220, Baltimore, MD 21224, USA. E-mail:
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11
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Beerman I. Effects of Caloric Restriction on the Epigenetic Landscape of Hematopoietic Stem Cells. Innov Aging 2021. [PMCID: PMC8754975 DOI: 10.1093/geroni/igab046.1973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
During aging, alterations of hematopoietic stem cells are associated with functional decline of the blood system. Caloric restriction (CR) interventions have been reported to improve adult stem cells in other tissue types during aging so we sought to evaluate the effects of CR on the aged HSC compartment. We find significant epigenetic alterations in HSCs isolated from aged mice after life-long CR compared to ad libitum fed aged mice. We further evaluated the epigenetic landscapes and functional potential of aged HSCs shortly after allowing life-long CR mice access to ad libitum food. We uncover epigenetic modification associated with functional alterations of the HSCs, defining potential mechanisms by which restrictions in food consumption affect the aging hematopoietic compartment.
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12
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Gutierrez-Rodrigues F, Beerman I, Groarke EM, Patel BA, Spitofsky N, Dillon LW, Raffo DQ, Hourigan CS, Kajigaya S, Ferrucci L, Young NS. Utility of plasma cell-free DNA for de novo detection and quantification of clonal hematopoiesis. Haematologica 2021; 107:1815-1826. [PMID: 34587721 PMCID: PMC9335099 DOI: 10.3324/haematol.2021.279230] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Indexed: 12/03/2022] Open
Abstract
Although cell-free DNA (cfDNA) tests have emerged as a potential non-invasive alternative to bone marrow biopsies for monitoring clonal hematopoiesis in hematologic diseases, whether commercial cfDNA assays can be implemented for the detection and quantification of de novo clonal hematopoiesis in place of blood cells is uncertain. In this study, peripheral plasma cfDNA samples available from patients with aplastic anemia (n=25) or myelodysplastic syndromes (n=27) and a healthy cohort (n=107) were screened for somatic variants in genes related to hematologic malignancies using a Clinical Laboratory Improvement Amendments-certified panel. Results were further compared to DNA sequencing of matched blood cells. In reported results, 85% of healthy subjects, 36% of patients with aplastic anemia and 74% of patients with myelodysplastic syndromes were found to have somatic cfDNA variants, most frequently in DNMT3A, TET2, ASXL1 and SF3B1. However, concordance between cfDNA and blood cell findings was poor for the detection of clonal hematopoiesis when the allele frequency of the variants was <10%, which was mostly observed in the healthy and aplastic anemia cohorts but not in patients with myelodysplastic syndromes. After filtering data for potential artifacts due to low variant allele frequency and sequencing depth, the frequency of clonal hematopoiesis in cfDNA from healthy individuals and patients with aplastic anemia decreased to 52% and 20%, respectively. cfDNA and matched blood cells were not interchangeable for tracking changes in allele burdens as their agreement by Bland-Altman analysis was poor. A commercial cfDNA assay had good performance for de novo detection of clonal hematopoiesis in myelodysplastic syndromes, but showed no advantage over blood cells in diseases with low allele burdens or in healthy individuals.
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Affiliation(s)
| | - Isabel Beerman
- Translational Gerontology Branch, National Institute on Aging, NIH, BRC, Baltimore, Maryland
| | - Emma M Groarke
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland 20892-1202
| | - Bhavisha A Patel
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland 20892-1202
| | - Nina Spitofsky
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland 20892-1202
| | - Laura W Dillon
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland 20892-1202
| | - Diego Quinones Raffo
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland 20892-1202
| | - Christopher S Hourigan
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland 20892-1202
| | - Sachiko Kajigaya
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland 20892-1202
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, NIH, BRC, Baltimore, Maryland
| | - Neal S Young
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland 20892-1202
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13
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Beerman I, Zong L, Tanaka-Yano M, Yanai H, Tekan-Turhan F. Interventions to Drive Improved Functional Potential of Aged or Dysfunctional Hematopoietic Stem Cells. Innov Aging 2020. [PMCID: PMC7742551 DOI: 10.1093/geroni/igaa057.2665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Stem cell dysfunction is a hallmark of aging, associated with the decline of physical and cognitive abilities of humans and other mammals. Therefore, it has become an active area of research within the aging and stem cell fields, and various techniques have been employed to mitigate the decline of stem cell function both in vitro and in vivo. We have examined changes in the hematopoietic system after interventions and show modest, but positive effects on the aged system as well as the aged stem cells
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Affiliation(s)
| | - Le Zong
- NIA / NIH, Baltimore, Maryland, United States
| | | | - Hagai Yanai
- NIA / NIH, Baltimore, Maryland, United States
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14
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Lodde V, Floris M, Beerman I, Munk R, Guha R, Steri M, Orrù V, Abdelmohsen K, Crompton PD, Gorospe M, Idda ML, Cucca F. Evolutionarily Selected Overexpression of the Cytokine BAFF Enhances Mucosal Immune Response Against P. falciparum. Front Immunol 2020; 11:575103. [PMID: 33123155 PMCID: PMC7573158 DOI: 10.3389/fimmu.2020.575103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/24/2020] [Indexed: 12/29/2022] Open
Abstract
We have previously shown that a variant of the TNFSF13B gene that we called BAFF-var increases the production of the cytokine BAFF, upregulating humoral immunity and increasing the risk for certain autoimmune diseases. In addition, genetic population signatures revealed that BAFF-var was evolutionarily advantageous, most likely by increasing resistance to malaria infection, which is a prime candidate for selective pressure. To evaluate whether the increased soluble BAFF (sBAFF) production confers protection, we experimentally assessed the role of BAFF-var in response to malaria antigens. Lysates of erythrocytes infected with Plasmodium falciparum (iRBCs) or left uninfected (uRBCs, control) were used to treat peripheral blood mononuclear cells (PBMCs) with distinct BAFF genotypes. The PBMCs purified from BAFF-var donors and treated with iRBCs showed different levels of specific cells, immunoglobulins, and cytokines as compared with BAFF-WT. In particular, a relevant differential effect on mucosal immunity B subpopulations have been observed. These findings point to specific immune cells and molecules through which the evolutionary selected BAFF-var may have improved fitness during P. falciparum infection.
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Affiliation(s)
- Valeria Lodde
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Italy
| | - Matteo Floris
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Italy
| | - Isabel Beerman
- Epigenetics and Stem Cell Unit, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States
| | - Rachel Munk
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, United States
| | - Rajan Guha
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, United States
| | - Maristella Steri
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Italy
| | - Valeria Orrù
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Italy
| | - Kotb Abdelmohsen
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, United States
| | - Peter D. Crompton
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, United States
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, United States
| | - Maria Laura Idda
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Italy
| | - Francesco Cucca
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Italy
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15
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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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16
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Spehar K, Pan A, Beerman I. Restoring aged stem cell functionality: Current progress and future directions. Stem Cells 2020; 38:1060-1077. [PMID: 32473067 PMCID: PMC7483369 DOI: 10.1002/stem.3234] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/07/2020] [Accepted: 05/11/2020] [Indexed: 12/15/2022]
Abstract
Stem cell dysfunction is a hallmark of aging, associated with the decline of physical and cognitive abilities of humans and other mammals [Cell 2013;153:1194]. Therefore, it has become an active area of research within the aging and stem cell fields, and various techniques have been employed to mitigate the decline of stem cell function both in vitro and in vivo. While some techniques developed in model organisms are not directly translatable to humans, others show promise in becoming clinically relevant to delay or even mitigate negative phenotypes associated with aging. This review focuses on diet, treatment, and small molecule interventions that provide evidence of functional improvement in at least one type of aged adult stem cell.
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Affiliation(s)
- Kevin Spehar
- Epigenetics and Stem Cell Aging Unit, Translational Gerontology Branch, National Institute on Aging, NIH, BRC, Baltimore, Maryland
| | - Andrew Pan
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia
| | - Isabel Beerman
- Epigenetics and Stem Cell Aging Unit, Translational Gerontology Branch, National Institute on Aging, NIH, BRC, Baltimore, Maryland
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17
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Hare JM, Beerman I. Regenerative Medicine and the Biology of Aging. J Gerontol A Biol Sci Med Sci 2019; 74:1339-1340. [PMID: 31125054 DOI: 10.1093/gerona/glz132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Joshua M Hare
- Interdisciplinary Stem Cell Institute, Department of Medicine, University of Miami, Miller School of Medicine, Florida
| | - Isabel Beerman
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, Maryland
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18
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Scaramozza A, Park D, Kollu S, Beerman I, Sun X, Rossi DJ, Lin CP, Scadden DT, Crist C, Brack AS. Lineage Tracing Reveals a Subset of Reserve Muscle Stem Cells Capable of Clonal Expansion under Stress. Cell Stem Cell 2019; 24:944-957.e5. [PMID: 31006621 DOI: 10.1016/j.stem.2019.03.020] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 02/09/2019] [Accepted: 03/22/2019] [Indexed: 01/10/2023]
Abstract
Stem cell heterogeneity is recognized as functionally relevant for tissue homeostasis and repair. The identity, context dependence, and regulation of skeletal muscle satellite cell (SC) subsets remains poorly understood. We identify a minor subset of Pax7+ SCs that is indelibly marked by an inducible Mx1-Cre transgene in vivo, is enriched for Pax3 expression, and has reduced ROS (reactive oxygen species) levels. Mx1+ SCs possess potent stem cell activity upon transplantation but minimally contribute to endogenous muscle repair, due to their relative low abundance. In contrast, a dramatic clonal expansion of Mx1+ SCs allows extensive contribution to muscle repair and niche repopulation upon selective pressure of radiation stress, consistent with reserve stem cell (RSC) properties. Loss of Pax3 in RSCs increased ROS content and diminished survival and stress tolerance. These observations demonstrate that the Pax7+ SC pool contains a discrete population of radiotolerant RSCs that undergo clonal expansion under severe stress.
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Affiliation(s)
- Annarita Scaramozza
- The Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Department of Orthopedic Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Dongsu Park
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Swapna Kollu
- Center of Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Isabel Beerman
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Xuefeng Sun
- The Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Department of Orthopedic Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Derrick J Rossi
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Charles P Lin
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Advanced Microscopy Program, Wellman Center for Photomedicine and Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - David T Scadden
- Center of Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Colin Crist
- Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, Montréal, QC H3T 1E2, Canada; Department of Human Genetics, McGill University, Montréal, QC H3A 0C7, Canada
| | - Andrew S Brack
- The Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Department of Orthopedic Surgery, University of California, San Francisco, San Francisco, CA 94143, USA.
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19
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Zhang Y, Charlton J, Karnik R, Beerman I, Smith ZD, Gu H, Boyle P, Mi X, Clement K, Pop R, Gnirke A, Rossi DJ, Meissner A. Targets and genomic constraints of ectopic Dnmt3b expression. eLife 2018; 7:e40757. [PMID: 30468428 PMCID: PMC6251628 DOI: 10.7554/elife.40757] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/09/2018] [Indexed: 12/19/2022] Open
Abstract
DNA methylation plays an essential role in mammalian genomes and expression of the responsible enzymes is tightly controlled. Deregulation of the de novo DNA methyltransferase DNMT3B is frequently observed across cancer types, yet little is known about its ectopic genomic targets. Here, we used an inducible transgenic mouse model to delineate rules for abnormal DNMT3B targeting, as well as the constraints of its activity across different cell types. Our results explain the preferential susceptibility of certain CpG islands to aberrant methylation and point to transcriptional state and the associated chromatin landscape as the strongest predictors. Although DNA methylation and H3K27me3 are usually non-overlapping at CpG islands, H3K27me3 can transiently co-occur with DNMT3B-induced DNA methylation. Our genome-wide data combined with ultra-deep locus-specific bisulfite sequencing suggest a distributive activity of ectopically expressed Dnmt3b that leads to discordant CpG island hypermethylation and provides new insights for interpreting the cancer methylome.
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Affiliation(s)
- Yingying Zhang
- Department of Stem Cell and Regenerative BiologyHarvard UniversityMassachusettsUnited States
| | - Jocelyn Charlton
- Department of Stem Cell and Regenerative BiologyHarvard UniversityMassachusettsUnited States
- Department of Genome RegulationMax Planck Institute for Molecular GeneticsBerlinGermany
| | - Rahul Karnik
- Department of Stem Cell and Regenerative BiologyHarvard UniversityMassachusettsUnited States
| | - Isabel Beerman
- Department of Stem Cell and Regenerative BiologyHarvard UniversityMassachusettsUnited States
- Department of PediatricsHarvard Medical SchoolMassachusettsUnited States
- Program in Cellular and Molecular Medicine, Division of Hematology/OncologyBoston Children's HospitalMassachusettsUnited States
| | - Zachary D Smith
- Department of Stem Cell and Regenerative BiologyHarvard UniversityMassachusettsUnited States
| | - Hongcang Gu
- Broad Institute of MIT and HarvardMassachusettsUnited States
| | - Patrick Boyle
- Broad Institute of MIT and HarvardMassachusettsUnited States
| | - Xiaoli Mi
- Department of Stem Cell and Regenerative BiologyHarvard UniversityMassachusettsUnited States
| | - Kendell Clement
- Department of Stem Cell and Regenerative BiologyHarvard UniversityMassachusettsUnited States
| | - Ramona Pop
- Department of Stem Cell and Regenerative BiologyHarvard UniversityMassachusettsUnited States
| | - Andreas Gnirke
- Broad Institute of MIT and HarvardMassachusettsUnited States
| | - Derrick J Rossi
- Department of Stem Cell and Regenerative BiologyHarvard UniversityMassachusettsUnited States
- Department of PediatricsHarvard Medical SchoolMassachusettsUnited States
- Program in Cellular and Molecular Medicine, Division of Hematology/OncologyBoston Children's HospitalMassachusettsUnited States
| | - Alexander Meissner
- Department of Stem Cell and Regenerative BiologyHarvard UniversityMassachusettsUnited States
- Department of Genome RegulationMax Planck Institute for Molecular GeneticsBerlinGermany
- Broad Institute of MIT and HarvardMassachusettsUnited States
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20
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21
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Beerman I. Stress: Is a little bit beneficial? Exp Hematol 2018. [DOI: 10.1016/j.exphem.2018.06.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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22
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Beerman I, Ziller M, Unterman A, Feinberg A, Meissner A, Rossi D. Age-associated clonal dominance of myeloid-biased HSC is underwritten by unique transcriptional and epigenetic alterations. Exp Hematol 2017. [DOI: 10.1016/j.exphem.2017.06.317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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23
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Beerman I, Luis TC, Singbrant S, Lo Celso C, Méndez-Ferrer S. The evolving view of the hematopoietic stem cell niche. Exp Hematol 2017; 50:22-26. [PMID: 28189651 DOI: 10.1016/j.exphem.2017.01.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 01/22/2017] [Indexed: 01/01/2023]
Abstract
Hematopoietic stem cells (HSCs) reside in specialized microenvironments known as niches. The niche is essential to support HSC function and to maintain a correct balance between self-renewal and differentiation. Recent advances in defining different mesenchymal and endothelial bone marrow cell populations, as well as hematopoietic stem and progenitor cells, greatly enhanced our understanding of these niches and of the molecular mechanisms by which they regulate HSC function. In addition to the role in maintaining HSC homeostasis, the niche has also been implicated in the pathogenesis of blood disorders including hematological malignancies. Characterizing the extrinsic regulators and the cellular context in which the niches interact with HSCs will be crucial to define new strategies to enhance blood regeneration. Furthermore, a better understanding of the role of the niche in leukemia development will open new possibilities for the treatment of these disorders by using therapies aiming to target the leukemic niche specifically. To update on recent findings on this topic, the International Society for Experimental Hematology (ISEH) organized a webinar, presented by Prof. Sean J. Morrison and Dr. Simón Méndez-Ferrer and moderated by Dr. Cristina Lo Celso, entitled "The evolving view of the hematopoietic stem cell niche," which we summarize here.
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Affiliation(s)
- Isabel Beerman
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA.
| | - Tiago C Luis
- Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Sofie Singbrant
- Department of Molecular Medicine, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Cristina Lo Celso
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, UK
| | - Simon Méndez-Ferrer
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain; Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute and Department of Haematology, University of Cambridge, and National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
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24
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Abstract
Aging is associated with loss of functional potential of multiple tissue systems, and there has been significant interest in understanding how tissue-specific cells contribute to this decline. DNA damage accumulation has been widely associated with aging in differentiated cell types. However, tissue-specific stem cells were once thought to be a geno-protected population, as damage accrued in a stem cell population has the potential to be inherited by differentiated progeny, as well as propagated within the stem cell compartment through self-renewal divisions. This review will discuss the evidence for DNA damage accumulation in the aged HSC compartment, potential drivers, and finally the consequences of the acquired damage.
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Affiliation(s)
- Isabel Beerman
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD.
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25
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Inoue S, Li WY, Tseng A, Beerman I, Elia AJ, Bendall SC, Lemonnier F, Kron KJ, Cescon DW, Hao Z, Lind EF, Takayama N, Planello AC, Shen SY, Shih AH, Larsen DM, Li Q, Snow BE, Wakeham A, Haight J, Gorrini C, Bassi C, Thu KL, Murakami K, Elford AR, Ueda T, Straley K, Yen KE, Melino G, Cimmino L, Aifantis I, Levine RL, De Carvalho DD, Lupien M, Rossi DJ, Nolan GP, Cairns RA, Mak TW. Mutant IDH1 Downregulates ATM and Alters DNA Repair and Sensitivity to DNA Damage Independent of TET2. Cancer Cell 2016; 30:337-348. [PMID: 27424808 PMCID: PMC5022794 DOI: 10.1016/j.ccell.2016.05.018] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 04/01/2016] [Accepted: 05/31/2016] [Indexed: 12/20/2022]
Abstract
Mutations in the isocitrate dehydrogenase-1 gene (IDH1) are common drivers of acute myeloid leukemia (AML) but their mechanism is not fully understood. It is thought that IDH1 mutants act by inhibiting TET2 to alter DNA methylation, but there are significant unexplained clinical differences between IDH1- and TET2-mutant diseases. We have discovered that mice expressing endogenous mutant IDH1 have reduced numbers of hematopoietic stem cells (HSCs), in contrast to Tet2 knockout (TET2-KO) mice. Mutant IDH1 downregulates the DNA damage (DD) sensor ATM by altering histone methylation, leading to impaired DNA repair, increased sensitivity to DD, and reduced HSC self-renewal, independent of TET2. ATM expression is also decreased in human IDH1-mutated AML. These findings may have implications for treatment of IDH-mutant leukemia.
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Affiliation(s)
- Satoshi Inoue
- The Campbell Family Institute for Breast Cancer Research, University Health Network, Toronto, ON M5G 2C1, Canada; The Princess Margaret Cancer Centre and Ontario Cancer Institute, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Wanda Y Li
- The Campbell Family Institute for Breast Cancer Research, University Health Network, Toronto, ON M5G 2C1, Canada; The Princess Margaret Cancer Centre and Ontario Cancer Institute, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Alan Tseng
- The Campbell Family Institute for Breast Cancer Research, University Health Network, Toronto, ON M5G 2C1, Canada; The Princess Margaret Cancer Centre and Ontario Cancer Institute, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Isabel Beerman
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 00133, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Andrew J Elia
- The Campbell Family Institute for Breast Cancer Research, University Health Network, Toronto, ON M5G 2C1, Canada; The Princess Margaret Cancer Centre and Ontario Cancer Institute, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Sean C Bendall
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - François Lemonnier
- The Campbell Family Institute for Breast Cancer Research, University Health Network, Toronto, ON M5G 2C1, Canada; The Princess Margaret Cancer Centre and Ontario Cancer Institute, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Ken J Kron
- The Princess Margaret Cancer Centre and Ontario Cancer Institute, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - David W Cescon
- The Campbell Family Institute for Breast Cancer Research, University Health Network, Toronto, ON M5G 2C1, Canada; The Princess Margaret Cancer Centre and Ontario Cancer Institute, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Zhenyue Hao
- The Campbell Family Institute for Breast Cancer Research, University Health Network, Toronto, ON M5G 2C1, Canada; The Princess Margaret Cancer Centre and Ontario Cancer Institute, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Evan F Lind
- The Campbell Family Institute for Breast Cancer Research, University Health Network, Toronto, ON M5G 2C1, Canada; The Princess Margaret Cancer Centre and Ontario Cancer Institute, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Naoya Takayama
- The Princess Margaret Cancer Centre and Ontario Cancer Institute, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Aline C Planello
- The Princess Margaret Cancer Centre and Ontario Cancer Institute, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Morphology, Piracicaba Dental School, UNICAMP, Piracicaba, SP 13414-903, Brazil
| | - Shu Yi Shen
- The Princess Margaret Cancer Centre and Ontario Cancer Institute, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Alan H Shih
- Human Oncology and Pathogenesis Program, Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Qinxi Li
- The Campbell Family Institute for Breast Cancer Research, University Health Network, Toronto, ON M5G 2C1, Canada; The Princess Margaret Cancer Centre and Ontario Cancer Institute, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Bryan E Snow
- The Campbell Family Institute for Breast Cancer Research, University Health Network, Toronto, ON M5G 2C1, Canada; The Princess Margaret Cancer Centre and Ontario Cancer Institute, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Andrew Wakeham
- The Campbell Family Institute for Breast Cancer Research, University Health Network, Toronto, ON M5G 2C1, Canada; The Princess Margaret Cancer Centre and Ontario Cancer Institute, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Jillian Haight
- The Campbell Family Institute for Breast Cancer Research, University Health Network, Toronto, ON M5G 2C1, Canada; The Princess Margaret Cancer Centre and Ontario Cancer Institute, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Chiara Gorrini
- The Campbell Family Institute for Breast Cancer Research, University Health Network, Toronto, ON M5G 2C1, Canada; The Princess Margaret Cancer Centre and Ontario Cancer Institute, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Christian Bassi
- The Campbell Family Institute for Breast Cancer Research, University Health Network, Toronto, ON M5G 2C1, Canada; The Princess Margaret Cancer Centre and Ontario Cancer Institute, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Kelsie L Thu
- The Campbell Family Institute for Breast Cancer Research, University Health Network, Toronto, ON M5G 2C1, Canada; The Princess Margaret Cancer Centre and Ontario Cancer Institute, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Kiichi Murakami
- The Campbell Family Institute for Breast Cancer Research, University Health Network, Toronto, ON M5G 2C1, Canada; The Princess Margaret Cancer Centre and Ontario Cancer Institute, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Alisha R Elford
- The Campbell Family Institute for Breast Cancer Research, University Health Network, Toronto, ON M5G 2C1, Canada; The Princess Margaret Cancer Centre and Ontario Cancer Institute, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Takeshi Ueda
- The Campbell Family Institute for Breast Cancer Research, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Disease Model Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima 734-8553, Japan
| | | | | | - Gerry Melino
- Medical Research Council, Toxicology Unit, Leicester LE1 9HN, UK; Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome 00133, Italy
| | - Luisa Cimmino
- Department of Pathology, Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Iannis Aifantis
- Department of Pathology, Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Ross L Levine
- Human Oncology and Pathogenesis Program, Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Daniel D De Carvalho
- The Princess Margaret Cancer Centre and Ontario Cancer Institute, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Mathieu Lupien
- The Princess Margaret Cancer Centre and Ontario Cancer Institute, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Derrick J Rossi
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 00133, USA
| | - Garry P Nolan
- The Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Rob A Cairns
- The Campbell Family Institute for Breast Cancer Research, University Health Network, Toronto, ON M5G 2C1, Canada; The Princess Margaret Cancer Centre and Ontario Cancer Institute, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Tak W Mak
- The Campbell Family Institute for Breast Cancer Research, University Health Network, Toronto, ON M5G 2C1, Canada; The Princess Margaret Cancer Centre and Ontario Cancer Institute, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada.
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26
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Abstract
The hematopoietic system undergoes many changes during aging, but the causes and molecular mechanisms behind these changes are not well understood. Wang et al. have recently implicated a circadian rhythm gene, Per2, as playing a role in the DNA damage response and in the expression of lymphoid genes in aged hematopoietic stem cells.
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Affiliation(s)
- Paula Gutierrez-Martinez
- Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Derrick J Rossi
- Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA; Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Isabel Beerman
- Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
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27
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Kokkaliaris KD, Lucas D, Beerman I, Kent DG, Perié L. Understanding hematopoiesis from a single-cell standpoint. Exp Hematol 2016; 44:447-50. [PMID: 26997547 DOI: 10.1016/j.exphem.2016.03.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 03/04/2016] [Indexed: 12/11/2022]
Abstract
The cellular diversity of the hematopoietic system has been extensively studied, and a plethora of cell surface markers have been used to discriminate and prospectively purify different blood cell types. However, even within phenotypically identical fractions of hematopoietic stem and progenitor cells or lineage-restricted progenitors, significant functional heterogeneity is observed when single cells are analyzed. To address these challenges, researchers are now using techniques to follow single cells and their progeny to improve our understanding of the underlying functional heterogeneity. On November 19, 2015, Dr. David Kent and Dr. Leïla Perié, two emerging young group leaders, presented their recent efforts to dissect the functional properties of individual cells with a webinar series organized by the International Society for Experimental Hematology. Here, we provide a summary of the presented methods for cell labeling and clonal tracking and discuss how these different techniques have been employed to study hematopoiesis.
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Affiliation(s)
- Konstantinos D Kokkaliaris
- Cell Systems Dynamics Research Group, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
| | - Daniel Lucas
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI
| | - Isabel Beerman
- Program of Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA
| | - David G Kent
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge University, Cambridge, UK
| | - Leïla Perié
- Institut Curie, PSL Research University, Paris, France
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28
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Thomas DD, Sommer AG, Balazs AB, Beerman I, Murphy GJ, Rossi D, Mostoslavsky G. Insulin-like growth factor 2 modulates murine hematopoietic stem cell maintenance through upregulation of p57. Exp Hematol 2016; 44:422-433.e1. [PMID: 26872540 DOI: 10.1016/j.exphem.2016.01.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 01/29/2016] [Accepted: 01/31/2016] [Indexed: 01/12/2023]
Abstract
Hematopoietic stem cells (HSC) rely on a highly regulated molecular network to balance self-renewal and lineage specification to sustain life-long hematopoiesis. Despite a plethora of studies aimed at identifying molecules governing HSC fate, our current knowledge of the genes responsible is limited. We have found insulin-like growth factor 2 (IGF2) to be expressed predominantly within long-term HSCs. This study examines IGF2 expression patterns and the effects of the gene in HSCs. Through the overexpression and knockdown of IGF2 within purified HSCs, we report that IGF2 expression increases HSC-derived multilineage colonies in vitro and enhances hematopoietic contribution in vivo on competitive bone marrow transplantation. The effects of IGF2 are mediated by direct upregulation of the CDKi p57, exclusively within long-term HSCs, via activation of the PI3K-Akt pathway. Increased expression of p57 resulted in a concomitant increase in HSCs in the G0/G1 stage of the cell cycle. Analysis of genomic DNA methylation revealed that HSCs exhibited a hypomethylated state within the promoter region of the CDKN1C (p57) gene, providing a potential mechanism for the exclusive effects of IGF2 within HSCs. Our studies indicate a novel role for IGF2 in regulating HSC cell cycle and illustrate potential novel therapeutic targets for hematologic diseases.
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Affiliation(s)
- Dolly D Thomas
- Section of Gastroenterology, Department of Medicine, Boston University School of Medicine, Boston, MA; Center for Regenerative Medicine (CReM), Boston University and Boston Medical Center, Boston, MA
| | - Andreia Gianotti Sommer
- Section of Gastroenterology, Department of Medicine, Boston University School of Medicine, Boston, MA; Center for Regenerative Medicine (CReM), Boston University and Boston Medical Center, Boston, MA
| | | | - Isabel Beerman
- Department of Stem Cell and Regenerative Biology, Harvard Medical School, Boston, MA
| | - George J Murphy
- Center for Regenerative Medicine (CReM), Boston University and Boston Medical Center, Boston, MA
| | - Derrick Rossi
- Department of Stem Cell and Regenerative Biology, Harvard Medical School, Boston, MA
| | - Gustavo Mostoslavsky
- Section of Gastroenterology, Department of Medicine, Boston University School of Medicine, Boston, MA; Center for Regenerative Medicine (CReM), Boston University and Boston Medical Center, Boston, MA.
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29
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Beerman I, Ziller M, Vandiver A, Gaudin R, Kirchhausen T, Feinberg A, Meissner A, Rossi D. AGE-associated clonal dominance of myeloid-biased HSC is underwritten by unique transcriptional and epigenetic alterations. Exp Hematol 2015. [DOI: 10.1016/j.exphem.2015.06.065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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30
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Abstract
Stem cell decline is an important cellular driver of aging-associated pathophysiology in multiple tissues. Epigenetic regulation is central to establishing and maintaining stem cell function, and emerging evidence indicates that epigenetic dysregulation contributes to the altered potential of stem cells during aging. Unlike terminally differentiated cells, the impact of epigenetic dysregulation in stem cells is propagated beyond self; alterations can be heritably transmitted to differentiated progeny, in addition to being perpetuated and amplified within the stem cell pool through self-renewal divisions. This Review focuses on recent studies examining epigenetic regulation of tissue-specific stem cells in homeostasis, aging, and aging-related disease.
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Affiliation(s)
- Isabel Beerman
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02116, USA
| | - Derrick J Rossi
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02116, USA.
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31
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Abstract
Aging is invariably associated with alterations of the hematopoietic stem cell (HSC) compartment, including loss of functional capacity, altered clonal composition, and changes in lineage contribution. Although accumulation of DNA damage occurs during HSC aging, it is unlikely such consistent aging phenotypes could be solely attributed to changes in DNA integrity. Another mechanism by which heritable traits could contribute to the changes in the functional potential of aged HSCs is through alterations in the epigenetic landscape of adult stem cells. Indeed, recent studies on hematopoietic stem cells have suggested that altered epigenetic profiles are associated with HSC aging and play a key role in modulating the functional potential of HSCs at different stages during ontogeny. Even small changes of the epigenetic landscape can lead to robustly altered expression patterns, either directly by loss of regulatory control or through indirect, additive effects, ultimately leading to transcriptional changes of the stem cells. Potential drivers of such changes in the epigenetic landscape of aged HSCs include proliferative history, DNA damage, and deregulation of key epigenetic enzymes and complexes. This review will focus largely on the two most characterized epigenetic marks - DNA methylation and histone modifications - but will also discuss the potential role of non-coding RNAs in regulating HSC function during aging.
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Affiliation(s)
- Isabel Beerman
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children׳s Hospital, MA 02116, USA.
| | - Derrick J Rossi
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children׳s Hospital, MA 02116, USA
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32
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Beerman I, Seita J, Inlay M, Weissman I, Rossi D. Hematopoietic stem cell quiescence attenuates DNA damage repair and response contributing to age-dependent DNA damage accumulation. Exp Hematol 2014. [DOI: 10.1016/j.exphem.2014.07.083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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33
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Beerman I, Seita J, Inlay MA, Weissman IL, Rossi DJ. Quiescent hematopoietic stem cells accumulate DNA damage during aging that is repaired upon entry into cell cycle. Cell Stem Cell 2014; 15:37-50. [PMID: 24813857 DOI: 10.1016/j.stem.2014.04.016] [Citation(s) in RCA: 318] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 03/18/2014] [Accepted: 04/17/2014] [Indexed: 12/12/2022]
Abstract
Hematopoietic stem cells (HSCs) maintain homeostasis and regenerate the blood system throughout life. It has been postulated that HSCs may be uniquely capable of preserving their genomic integrity in order to ensure lifelong function. To directly test this, we quantified DNA damage in HSCs and downstream progenitors from young and old mice, revealing that strand breaks significantly accrue in HSCs during aging. DNA damage accumulation in HSCs was associated with broad attenuation of DNA repair and response pathways that was dependent upon HSC quiescence. Accordingly, cycling fetal HSCs and adult HSCs driven into cycle upregulated these pathways leading to repair of strand breaks. Our results demonstrate that HSCs are not comprehensively geno-protected during aging. Rather, HSC quiescence and concomitant attenuation of DNA repair and response pathways underlies DNA damage accumulation in HSCs during aging. These results provide a potential mechanism through which premalignant mutations accrue in HSCs.
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Affiliation(s)
- Isabel Beerman
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.,Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children's Hospital, MA 02116, USA
| | - Jun Seita
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford CA 94305, USA
| | - Matthew A Inlay
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford CA 94305, USA.,Sue and Bill Gross Stem Cell Research Center, Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA 92697, USA
| | - Irving L Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford CA 94305, USA
| | - Derrick J Rossi
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.,Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children's Hospital, MA 02116, USA.,Harvard Stem Cell Institute, Cambridge, MA 02138, USA
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34
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Beerman I, Bock C, Garrison BS, Smith ZD, Gu H, Meissner A, Rossi DJ. Proliferation-dependent alterations of the DNA methylation landscape underlie hematopoietic stem cell aging. Cell Stem Cell 2013; 12:413-25. [PMID: 23415915 DOI: 10.1016/j.stem.2013.01.017] [Citation(s) in RCA: 329] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 12/17/2012] [Accepted: 01/25/2013] [Indexed: 12/15/2022]
Abstract
The functional potential of hematopoietic stem cells (HSCs) declines during aging, and in doing so, significantly contributes to hematopoietic pathophysiology in the elderly. To explore the relationship between age-associated HSC decline and the epigenome, we examined global DNA methylation of HSCs during ontogeny in combination with functional analysis. Although the DNA methylome is generally stable during aging, site-specific alterations of DNA methylation occur at genomic regions associated with hematopoietic lineage potential and selectively target genes expressed in downstream progenitor and effector cells. We found that age-associated HSC decline, replicative limits, and DNA methylation are largely dependent on the proliferative history of HSCs, yet appear to be telomere-length independent. Physiological aging and experimentally enforced proliferation of HSCs both led to DNA hypermethylation of genes regulated by Polycomb Repressive Complex 2. Our results provide evidence that epigenomic alterations of the DNA methylation landscape contribute to the functional decline of HSCs during aging.
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Affiliation(s)
- Isabel Beerman
- Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02116, USA
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35
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Bock C, Beerman I, Lien WH, Smith ZD, Gu H, Boyle P, Gnirke A, Fuchs E, Rossi DJ, Meissner A. DNA methylation dynamics during in vivo differentiation of blood and skin stem cells. Mol Cell 2012; 47:633-47. [PMID: 22841485 DOI: 10.1016/j.molcel.2012.06.019] [Citation(s) in RCA: 278] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Revised: 04/09/2012] [Accepted: 06/21/2012] [Indexed: 01/19/2023]
Abstract
DNA methylation is a mechanism of epigenetic regulation that is common to all vertebrates. Functional studies underscore its relevance for tissue homeostasis, but the global dynamics of DNA methylation during in vivo differentiation remain underexplored. Here we report high-resolution DNA methylation maps of adult stem cell differentiation in mouse, focusing on 19 purified cell populations of the blood and skin lineages. DNA methylation changes were locus specific and relatively modest in magnitude. They frequently overlapped with lineage-associated transcription factors and their binding sites, suggesting that DNA methylation may protect cells from aberrant transcription factor activation. DNA methylation and gene expression provided complementary information, and combining the two enabled us to infer the cellular differentiation hierarchy of the blood lineage directly from genome-scale data. In summary, these results demonstrate that in vivo differentiation of adult stem cells is associated with small but informative changes in the genomic distribution of DNA methylation.
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Affiliation(s)
- Christoph Bock
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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36
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Gharavi AG, Kiryluk K, Choi M, Li Y, Hou P, Xie J, Sanna-Cherchi S, Men CJ, Julian BA, Wyatt RJ, Novak J, He JC, Wang H, Lv J, Zhu L, Wang W, Wang Z, Yasuno K, Gunel M, Mane S, Umlauf S, Tikhonova I, Beerman I, Savoldi S, Magistroni R, Ghiggeri GM, Bodria M, Lugani F, Ravani P, Ponticelli C, Allegri L, Boscutti G, Frasca G, Amore A, Peruzzi L, Coppo R, Izzi C, Viola BF, Prati E, Salvadori M, Mignani R, Gesualdo L, Bertinetto F, Mesiano P, Amoroso A, Scolari F, Chen N, Zhang H, Lifton RP. Genome-wide association study identifies susceptibility loci for IgA nephropathy. Nat Genet 2011; 43:321-7. [PMID: 21399633 DOI: 10.1038/ng.787] [Citation(s) in RCA: 461] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Accepted: 02/15/2011] [Indexed: 12/15/2022]
Abstract
We carried out a genome-wide association study of IgA nephropathy, a major cause of kidney failure worldwide. We studied 1,194 cases and 902 controls of Chinese Han ancestry, with targeted follow up in Chinese and European cohorts comprising 1,950 cases and 1,920 controls. We identified three independent loci in the major histocompatibility complex, as well as a common deletion of CFHR1 and CFHR3 at chromosome 1q32 and a locus at chromosome 22q12 that each surpassed genome-wide significance (P values for association between 1.59 × 10⁻²⁶ and 4.84 × 10⁻⁹ and minor allele odds ratios of 0.63-0.80). These five loci explain 4-7% of the disease variance and up to a tenfold variation in interindividual risk. Many of the alleles that protect against IgA nephropathy impart increased risk for other autoimmune or infectious diseases, and IgA nephropathy risk allele frequencies closely parallel the variation in disease prevalence among Asian, European and African populations, suggesting complex selective pressures.
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Affiliation(s)
- Ali G Gharavi
- Department of Medicine, Columbia University College of Physicians and Surgeons, New York, New York, USA
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37
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Abstract
IgA nephropathy is the most common form of primary glomerulonephritis. Variations in clinical manifestations indicate that a diagnosis of IgA nephropathy encompasses multiple disease subsets that cannot be distinguished on the basis of renal pathology or clinical variables alone. Familial forms of the disease have been reported throughout the world, but are probably under-recognized because associated urinary abnormalities are often intermittent in affected family members. IgA nephropathy has complex determination, with different genes probably causing disease in different patient subgroups. Of the many pathogenic mechanisms reported, defects in IgA1 glycosylation that lead to formation of immune complexes have been consistently implicated. Here, we present the evidence for genetic contributions to the disease, review clinical patterns of familial disease, and summarize some of the most promising genetic studies conducted to date. Linkage-based approaches to the study of familial forms of the disease have identified significant or suggestive loci on chromosomes 6q22-23, 2q36, 4q26-31, 17q12-22 and 3p24-23, but no causal gene has yet been identified. Many interesting, but poorly replicated, genetic association studies have also been reported. We discuss recent developments in analytic tools that should enable genetic studies of sporadic forms of disease by the genome-wide association approach.
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Affiliation(s)
- Isabel Beerman
- Department of Genetics, Yale University, New Haven, CT, USA
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38
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Abstract
It is common to have missing genotypes in practical genetic studies, but the exact underlying missing data mechanism is generally unknown to the investigators. Although some statistical methods can handle missing data, they usually assume that genotypes are missing at random, that is, at a given marker, different genotypes and different alleles are missing with the same probability. These include those methods on haplotype frequency estimation and haplotype association analysis. However, it is likely that this simple assumption does not hold in practice, yet few studies to date have examined the magnitude of the effects when this simplifying assumption is violated. In this study, we demonstrate that the violation of this assumption may lead to serious bias in haplotype frequency estimates, and haplotype association analysis based on this assumption can induce both false-positive and false-negative evidence of association. To address this limitation in the current methods, we propose a general missing data model to characterize missing data patterns across a set of two or more markers simultaneously. We prove that haplotype frequencies and missing data probabilities are identifiable if and only if there is linkage disequilibrium between these markers under our general missing data model. Simulation studies on the analysis of haplotypes consisting of two single nucleotide polymorphisms illustrate that our proposed model can reduce the bias both for haplotype frequency estimates and association analysis due to incorrect assumption on the missing data mechanism. Finally, we illustrate the utilities of our method through its application to a real data set.
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Affiliation(s)
- Nianjun Liu
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, USA
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39
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Izzi C, Sanna-Cherchi S, Prati E, Belleri R, Remedio A, Tardanico R, Foramitti M, Guerini S, Viola BF, Movilli E, Beerman I, Lifton R, Leone L, Gharavi A, Scolari F. Familial aggregation of primary glomerulonephritis in an Italian population isolate: Valtrompia study. Kidney Int 2006; 69:1033-40. [PMID: 16528253 PMCID: PMC5849459 DOI: 10.1038/sj.ki.5000185] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Hereditary factors are suspected to contribute to the pathogenesis of sporadic primary glomerulonephritis, but their contribution is difficult to delineate in the general population. We studied the prevalence of primary glomerulonephritis in an isolated population from the extreme northern Valtrompia valley, Northern Italy. Investigation of medical records, community urinary screening program and molecular characterization of the population's ancestry were performed; genealogies of affected individuals were researched. Forty-three patients with primary glomerulonephritis were identified: 25 had biopsy-proven disease (11 immunoglobulin A (IgA) nephropathy; eight mesangial proliferative glomerulonephritis without IgA deposits; four focal segmental glomerular sclerosis; two membranous nephropathy), and 18 had clinical glomerulonephritis. All 43 patients originated from three mountain villages (Collio, San Colombano, and Bovegno). In contrast, we found only four cases of primary glomerulonephritis in two nearby villages (Pezzaze and Tavernole) that shared similar population histories and lifestyles, demonstrating heterogeneity of risk factors for glomerulonephritis (P=3 x 10(-5)). All 43 affected individuals could be traced back to common ancestors (XVI-XVII centuries), enabling the construction of three large pedigree including three parent-child affected pairs and five affected siblings pairs. Molecular data showed lower genetic diversity and increased inbreeding in the Valtrompia population compared to the control population. Molecular and genealogical evidence of limited set of founders and the absence of shared nephritogenic environmental factors suggest that our patients share a common genetic susceptibility to the development of primary glomerulonephritis. Further molecular study of our families will offer the possibility to shed light on the genetic background underlying these glomerular disorders.
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Affiliation(s)
- C Izzi
- Division of Nephrology, Brescia University, Italy
| | - S Sanna-Cherchi
- Division of Nephrology, Columbia University, New York, New York, USA
| | - E Prati
- Dialysis Unit, Ospedale di Desenzano, Brescia, Italy
| | - R Belleri
- Azienda Sanitaria Locale of Brescia, Italy
| | - A Remedio
- Azienda Sanitaria Locale of Brescia, Italy
| | - R Tardanico
- Pathology Department, Spedali Civili, Brescia, Italy
| | - M Foramitti
- Division of Nephrology, Brescia University, Italy
| | - S Guerini
- Division of Nephrology, Brescia University, Italy
| | - BF Viola
- Division of Nephrology, Brescia University, Italy
| | - E Movilli
- Division of Nephrology, Brescia University, Italy
| | - I Beerman
- Departments of Genetics, Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, USA
| | - R Lifton
- Departments of Genetics, Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, USA
| | - L Leone
- Azienda Sanitaria Locale of Brescia, Italy
| | - A Gharavi
- Division of Nephrology, Columbia University, New York, New York, USA
| | - F Scolari
- Division of Nephrology, Brescia University, Italy
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40
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Parsch J, Russell JA, Beerman I, Hartl DL, Stephan W. Deletion of a conserved regulatory element in the Drosophila Adh gene leads to increased alcohol dehydrogenase activity but also delays development. Genetics 2000; 156:219-27. [PMID: 10978287 PMCID: PMC1461225 DOI: 10.1093/genetics/156.1.219] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In vivo levels of enzymatic activity may be increased through either structural or regulatory changes. Here we use Drosophila melanogaster alcohol dehydrogenase (ADH) in an experimental test for selective differences between these two mechanisms. The well-known ADH-Slow (S)/Fast (F) amino acid replacement leads to a twofold increase in activity by increasing the catalytic efficiency of the enzyme. Disruption of a highly conserved, negative regulatory element in the Adh 3' UTR also leads to a twofold increase in activity, although this is achieved by increasing in vivo Adh mRNA and protein concentrations. These two changes appear to be under different types of selection, with positive selection favoring the amino acid replacement and purifying selection maintaining the 3' UTR sequence. Using transgenic experiments we show that deletion of the conserved 3' UTR element increases adult and larval Adh expression in both the ADH-F and ADH-S genetic backgrounds. However, the 3' UTR deletion also leads to a significant increase in developmental time in both backgrounds. ADH allozyme type has no detectable effect on development. These results demonstrate a negative fitness effect associated with Adh overexpression. This provides a mechanism whereby natural selection can discriminate between alternative pathways of increasing enzymatic activity.
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Affiliation(s)
- J Parsch
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
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Lohe AR, Timmons C, Beerman I, Lozovskaya ER, Hartl DL. Self-inflicted wounds, template-directed gap repair and a recombination hotspot. Effects of the mariner transposase. Genetics 2000; 154:647-56. [PMID: 10655218 PMCID: PMC1460940 DOI: 10.1093/genetics/154.2.647] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Aberrant repair products of mariner transposition occur at a frequency of approximately 1/500 per target element per generation. Among 100 such mutations in the nonautonomous element peach, most had aberrations in the 5' end of peach (40 alleles), in the 3' end of peach (11 alleles), or a deletion of peach with or without deletion of flanking genomic DNA (29 alleles). Most mariner mutations can be explained by exonuclease "nibble" and host-mediated repair of the double-stranded gap created by the transposase, in contrast to analogous mutations in the P element. In mariner, mutations in the 5' inverted repeat are smaller and more frequent than those in the 3' inverted repeat, but secondary mutations in target elements with a 5' lesion usually had 3' lesions resembling those normally found at the 5' end. We suggest that the mariner transposase distinguishes between the 5' and 3' ends of the element, and that the 5' end is relatively more protected after strand scission. We also find: (1) that homolog-dependent gap repair is a frequent accompaniment to mariner excision, estimated as 30% of all excision events; and (2) that mariner is a hotspot of recombination in Drosophila females, but only in the presence of functional transposase.
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Affiliation(s)
- A R Lohe
- Commonwealth Scientific and Industrial Research Organization, Division of Plant Industry, Canberra ACT 2601, Australia
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