201
|
Yue F, Bi P, Wang C, Li J, Liu X, Kuang S. Conditional Loss of Pten in Myogenic Progenitors Leads to Postnatal Skeletal Muscle Hypertrophy but Age-Dependent Exhaustion of Satellite Cells. Cell Rep 2017; 17:2340-2353. [PMID: 27880908 DOI: 10.1016/j.celrep.2016.11.002] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 09/19/2016] [Accepted: 10/25/2016] [Indexed: 02/07/2023] Open
Abstract
Skeletal muscle stem cells (satellite cells [SCs]) are normally maintained in a quiescent (G0) state. Muscle injury not only activates SCs locally, but also alerts SCs in distant uninjured muscles via circulating factors. The resulting GAlert SCs are adapted to regenerative cues and regenerate injured muscles more efficiently, but whether they provide any long-term benefits to SCs is unknown. Here, we report that embryonic myogenic progenitors lacking the phosphatase and tensin homolog (Pten) exhibit enhanced proliferation and differentiation, resulting in muscle hypertrophy but fewer SCs in adult muscles. Interestingly, Pten null SCs are predominantly in the GAlert state, even in the absence of an injury. The GAlert SCs are deficient in self-renewal and subjected to accelerated depletion during regeneration and aging and fail to repair muscle injury in old mice. Our findings demonstrate a key requirement of Pten in G0 entry of SCs and provide functional evidence that prolonged GAlert leads to stem cell depletion and regenerative failure.
Collapse
Affiliation(s)
- Feng Yue
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Pengpeng Bi
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Chao Wang
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Jie Li
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Xiaoqi Liu
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA; Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Shihuan Kuang
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA.
| |
Collapse
|
202
|
Djeghloul D, Kuranda K, Kuzniak I, Barbieri D, Naguibneva I, Choisy C, Bories JC, Dosquet C, Pla M, Vanneaux V, Socié G, Porteu F, Garrick D, Goodhardt M. Age-Associated Decrease of the Histone Methyltransferase SUV39H1 in HSC Perturbs Heterochromatin and B Lymphoid Differentiation. Stem Cell Reports 2017; 6:970-984. [PMID: 27304919 PMCID: PMC4911502 DOI: 10.1016/j.stemcr.2016.05.007] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 05/13/2016] [Accepted: 05/16/2016] [Indexed: 01/11/2023] Open
Abstract
The capacity of hematopoietic stem cells (HSC) to generate B lymphocytes declines with age, contributing to impaired immune function in the elderly. Here we show that the histone methyltransferase SUV39H1 plays an important role in human B lymphoid differentiation and that expression of SUV39H1 decreases with age in both human and mouse HSC, leading to a global reduction in H3K9 trimethylation and perturbed heterochromatin function. Further, we demonstrate that SUV39H1 is a target of microRNA miR-125b, a known regulator of HSC function, and that expression of miR-125b increases with age in human HSC. Overexpression of miR-125b and inhibition of SUV39H1 in young HSC induced loss of B cell potential. Conversely, both inhibition of miR-125 and enforced expression of SUV39H1 improved the capacity of HSC from elderly individuals to generate B cells. Our findings highlight the importance of heterochromatin regulation in HSC aging and B lymphopoiesis.
Collapse
Affiliation(s)
- Dounia Djeghloul
- INSERM UMRS-1126, Institut Universitaire d'Hématologie, Université Paris Diderot, Paris, France
| | - Klaudia Kuranda
- INSERM UMRS-1126, Institut Universitaire d'Hématologie, Université Paris Diderot, Paris, France
| | - Isabelle Kuzniak
- INSERM UMRS-1126, Institut Universitaire d'Hématologie, Université Paris Diderot, Paris, France
| | - Daniela Barbieri
- INSERM UMRS-1170, Gustave Roussy Cancer Campus, Université Paris Sud - Université Paris-Saclay, Villejuif, France
| | - Irina Naguibneva
- INSERM UMRS-967, Institut de Radiobiologie Cellulaire et Moléculaire, Commissariat à l'Energie Atomique, Fontenay-aux-Roses, France
| | - Caroline Choisy
- INSERM UMRS-1126, Institut Universitaire d'Hématologie, Université Paris Diderot, Paris, France
| | - Jean-Christophe Bories
- INSERM UMRS-1126, Institut Universitaire d'Hématologie, Université Paris Diderot, Paris, France
| | - Christine Dosquet
- INSERM UMRS-1131, Institut Universitaire d'Hématologie, Université Paris Diderot, Paris, France
| | - Marika Pla
- INSERM UMRS-1131, Institut Universitaire d'Hématologie, Université Paris Diderot, Paris, France
| | - Valérie Vanneaux
- AP-HP Unité de Thérapie Cellulaire, Centre d'Investigation Clinique en Biothérapie Cellulaire and INSERM UMRS-1160, Université Paris Diderot, Paris, France
| | - Gérard Socié
- AP-HP Hematology Transplantation and INSERM UMRS-1160, Université Paris Diderot, Paris, France
| | - Françoise Porteu
- INSERM UMRS-1170, Gustave Roussy Cancer Campus, Université Paris Sud - Université Paris-Saclay, Villejuif, France
| | - David Garrick
- INSERM UMRS-1126, Institut Universitaire d'Hématologie, Université Paris Diderot, Paris, France
| | - Michele Goodhardt
- INSERM UMRS-1126, Institut Universitaire d'Hématologie, Université Paris Diderot, Paris, France.
| |
Collapse
|
203
|
Dong Q, Gao H, Shi Y, Zhang F, Gu X, Wu A, Wang D, Chen Y, Bandyopadhyay A, Yeh IT, Daniel BJ, Chen Y, Zou Y, Rebel VL, Walter CA, Lu J, Huang C, Sun LZ. Aging is associated with an expansion of CD49f hi mammary stem cells that show a decline in function and increased transformation potential. Aging (Albany NY) 2017; 8:2754-2776. [PMID: 27852980 PMCID: PMC5191868 DOI: 10.18632/aging.101082] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 10/26/2016] [Indexed: 12/18/2022]
Abstract
Breast cancer incidence increases during aging, yet the mechanism of age-associated mammary tumorigenesis is unclear. Mammary stem cells are believed to play an important role in breast tumorigenesis, but how their function changes with age is unknown. We compared mammary epithelial cells isolated from young and old mammary glands of different cohorts of C57BL6/J and BALB/c mice, and our findings revealed that old mammary glands were characterized by increased basal cell pool comprised of mostly CD49fhi cells, altered luminal-to-basal cell ratio, and irregular ductal morphology. More interestingly, basal stem cells in old mice were increased in frequency, but showed a functional decline of differentiation and increased neoplastic transformation potential. Gene signature enrichment analysis revealed a significant enrichment of a luminal cell gene expression signature in the basal stem cell-enriched population from old mice, suggesting some luminal cells were expressing basal markers. Immunofluorescence staining confirmed the presence of luminal cells with high CD49f expression in hyperplastic lesions implicating these cells as undergoing luminal to basal phenotypic changes during aging. Whole transcriptome analysis showed elevated immune and inflammatory responses in old basal stem cells and stromal cells, which may be the underlying cause for increased CD49fhi basal-like cells in aged glands.
Collapse
Affiliation(s)
- Qiaoxiang Dong
- Department of Cellular & Structural Biology, University of Texas Health Science Center, San Antonio, TX 78299, USA.,School of Laboratory Medicine and Life Science, Wenzhou Medical University, University Town, Wenzhou 325035, China
| | - Hui Gao
- Department of Cellular & Structural Biology, University of Texas Health Science Center, San Antonio, TX 78299, USA.,School of Laboratory Medicine and Life Science, Wenzhou Medical University, University Town, Wenzhou 325035, China
| | - Yuanshuo Shi
- Department of Cellular & Structural Biology, University of Texas Health Science Center, San Antonio, TX 78299, USA.,Institute of Environmental Safety and Human Health, Wenzhou Medical University, University Town, Wenzhou 325035, China
| | - Fuchuang Zhang
- Department of Cellular & Structural Biology, University of Texas Health Science Center, San Antonio, TX 78299, USA.,Institute of Environmental Safety and Human Health, Wenzhou Medical University, University Town, Wenzhou 325035, China
| | - Xiang Gu
- Department of Cellular & Structural Biology, University of Texas Health Science Center, San Antonio, TX 78299, USA
| | - Anqi Wu
- Institute of Environmental Safety and Human Health, Wenzhou Medical University, University Town, Wenzhou 325035, China
| | - Danhan Wang
- Institute of Environmental Safety and Human Health, Wenzhou Medical University, University Town, Wenzhou 325035, China
| | - Yuanhong Chen
- Institute of Environmental Safety and Human Health, Wenzhou Medical University, University Town, Wenzhou 325035, China
| | - Abhik Bandyopadhyay
- Department of Cellular & Structural Biology, University of Texas Health Science Center, San Antonio, TX 78299, USA
| | - I-Tien Yeh
- Department of Pathology, University of Texas Health Science Center, San Antonio, TX 78299, USA
| | - Benjamin J Daniel
- Flow Cytometry Facility, University of Texas Health Science Center, San Antonio, TX 78299, USA
| | - Yidong Chen
- Department of Epidemiology and Biostatistics, University of Texas Health Science Center, San Antonio, TX 78299, USA.,Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX 78299, USA
| | - Yi Zou
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX 78299, USA
| | - Vivienne L Rebel
- Department of Cellular & Structural Biology, University of Texas Health Science Center, San Antonio, TX 78299, USA.,Cancer Therapy and Research Center, University of Texas Health Science Center, San Antonio, TX 78299, USA.,Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, TX 78299, USA
| | - Christi A Walter
- Department of Cellular & Structural Biology, University of Texas Health Science Center, San Antonio, TX 78299, USA
| | - Jianxin Lu
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, University Town, Wenzhou 325035, China
| | - Changjiang Huang
- Institute of Environmental Safety and Human Health, Wenzhou Medical University, University Town, Wenzhou 325035, China
| | - Lu-Zhe Sun
- Department of Cellular & Structural Biology, University of Texas Health Science Center, San Antonio, TX 78299, USA.,Cancer Therapy and Research Center, University of Texas Health Science Center, San Antonio, TX 78299, USA
| |
Collapse
|
204
|
Abstract
Several articles describe highly accurate age estimation methods based on human DNA-methylation data. It is not yet known whether similar epigenetic aging clocks can be developed based on blood methylation data from canids. Using Reduced Representation Bisulfite Sequencing, we assessed blood DNA-methylation data from 46 domesticated dogs (Canis familiaris) and 62 wild gray wolves (C. lupus). By regressing chronological dog age on the resulting CpGs, we defined highly accurate multivariate age estimators for dogs (based on 41 CpGs), wolves (67 CpGs), and both combined (115 CpGs). Age related DNA methylation changes in canids implicate similar gene ontology categories as those observed in humans suggesting an evolutionarily conserved mechanism underlying age-related DNA methylation in mammals.
Collapse
|
205
|
Impact of DNA methylation programming on normal and pre-leukemic hematopoiesis. Semin Cancer Biol 2017; 51:89-100. [PMID: 28964938 DOI: 10.1016/j.semcancer.2017.09.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 09/22/2017] [Accepted: 09/25/2017] [Indexed: 12/30/2022]
Abstract
Epigenome regulation is a critical mechanism that governs cell identity, lineage specification and developmental cell fates. With the advent of low-input and single-cell technologies as well as sophisticated cell labeling techniques, our understanding of transcriptional and epigenetic regulation of hematopoiesis is currently undergoing dramatic changes. Increasingly, evidence suggests that the epigenome conformation acts as a critical decision-making mechanism that instructs self-renewal, differentiation and developmental fates of hematopoietic progenitor cells. When dysregulated, this leads to the evolution of disease states such as leukemia. Indeed, aberrations in DNA methylation, histone modifications and genome architecture are characteristic features of many hematopoietic neoplasms in which epigenetic enzymes are frequently mutated. Sequencing studies and characterization of the epigenetic landscape in lymphomas, leukemias and in aged healthy individuals with clonal hematopoiesis have been indispensible to identify epigenetic regulators that play a role in transformation or pre-disposition to hematopoietic malignancies. In this review, we outline the current view of the hematopoietic system and the epigenetic mechanisms regulating hematopoiesis under homeostatic conditions, with a particular focus on the role of DNA methylation in this process. We will also summarize the current knowledge on the mechanisms underlying dysregulated DNA methylation in hematologic malignancies and how this contributes to our understanding of the physiological functions of epigenetic regulators in hematopoiesis.
Collapse
|
206
|
Wahlestedt M, Bryder D. The slippery slope of hematopoietic stem cell aging. Exp Hematol 2017; 56:1-6. [PMID: 28943295 DOI: 10.1016/j.exphem.2017.09.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 09/12/2017] [Accepted: 09/15/2017] [Indexed: 10/18/2022]
Abstract
The late stages of life, in most species including humans, are associated with a decline in the overall maintenance and health of the organism. This applies also to the hematopoietic system, where aging is not only associated with an increased predisposition for hematological malignancies, but also identified as a strong comorbidity factor for other diseases. Research during the last two decades has proposed that alterations at the level of hematopoietic stem cells (HSCs) might be a root cause for the hematological changes observed with age. However, the recent realization that not all HSCs are alike with regard to fundamental stem cell properties such as self-renewal and lineage potential has several implications for HSC aging, including the synchrony and the stability of the aging HSC state. To approach HSC aging from a clonal perspective, we recently took advantage of technical developments in cellular barcoding and combined this with the derivation of induced pluripotent stem cells (iPSCs). This allowed us to selectively approach HSCs functionally affected by age. The finding that such iPSCs were capable of fully regenerating multilineage hematopoiesis upon morula/blastocyst complementation provides compelling evidence that many aspects of HSC aging can be reversed, which indicates that a central mechanism underlying HSC aging is a failure to uphold the epigenomes associated with younger age. Here we discuss these findings in the context of the underlying causes that might influence HSC aging and the requirements and prospects for restoration of the aging HSC epigenome.
Collapse
Affiliation(s)
- Martin Wahlestedt
- Medical Faculty, Institution for Laboratory Medicine, Division of Molecular Hematology, Lund University, Lund, Sweden
| | - David Bryder
- Medical Faculty, Institution for Laboratory Medicine, Division of Molecular Hematology, Lund University, Lund, Sweden; StemTherapy, Lund University, Lund, Sweden.
| |
Collapse
|
207
|
Abstract
In mammals, caloric restriction consistently results in extended lifespan. Epigenetic information encoded by DNA methylation is tightly regulated, but shows a striking drift associated with age that includes both gains and losses of DNA methylation at various sites. Here, we report that epigenetic drift is conserved across species and the rate of drift correlates with lifespan when comparing mice, rhesus monkeys, and humans. Twenty-two to 30-year-old rhesus monkeys exposed to 30% caloric restriction since 7–14 years of age showed attenuation of age-related methylation drift compared to ad libitum-fed controls such that their blood methylation age appeared 7 years younger than their chronologic age. Even more pronounced effects were seen in 2.7–3.2-year-old mice exposed to 40% caloric restriction starting at 0.3 years of age. The effects of caloric restriction on DNA methylation were detectable across different tissues and correlated with gene expression. We propose that epigenetic drift is a determinant of lifespan in mammals. Caloric restriction has been shown to increase lifespan in mammals. Here, the authors provide evidence that age-related methylation drift correlates with lifespan and that caloric restriction in mice and rhesus monkeys results in attenuation of age-related methylation drift.
Collapse
|
208
|
Arthur-Farraj PJ, Morgan CC, Adamowicz M, Gomez-Sanchez JA, Fazal SV, Beucher A, Razzaghi B, Mirsky R, Jessen KR, Aitman TJ. Changes in the Coding and Non-coding Transcriptome and DNA Methylome that Define the Schwann Cell Repair Phenotype after Nerve Injury. Cell Rep 2017; 20:2719-2734. [PMID: 28903050 PMCID: PMC5608958 DOI: 10.1016/j.celrep.2017.08.064] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Revised: 06/17/2017] [Accepted: 08/18/2017] [Indexed: 12/12/2022] Open
Abstract
Repair Schwann cells play a critical role in orchestrating nerve repair after injury, but the cellular and molecular processes that generate them are poorly understood. Here, we perform a combined whole-genome, coding and non-coding RNA and CpG methylation study following nerve injury. We show that genes involved in the epithelial-mesenchymal transition are enriched in repair cells, and we identify several long non-coding RNAs in Schwann cells. We demonstrate that the AP-1 transcription factor C-JUN regulates the expression of certain micro RNAs in repair Schwann cells, in particular miR-21 and miR-34. Surprisingly, unlike during development, changes in CpG methylation are limited in injury, restricted to specific locations, such as enhancer regions of Schwann cell-specific genes (e.g., Nedd4l), and close to local enrichment of AP-1 motifs. These genetic and epigenomic changes broaden our mechanistic understanding of the formation of repair Schwann cell during peripheral nervous system tissue repair.
Collapse
Affiliation(s)
- Peter J Arthur-Farraj
- Department of Clinical Neurosciences, Addenbrooke's Hospital, University of Cambridge, Cambridge CB2 0QQ, UK; Department of Medicine, Imperial College, London W12 0NN, UK; Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK.
| | - Claire C Morgan
- Department of Medicine, Imperial College, London W12 0NN, UK
| | - Martyna Adamowicz
- Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH16 2XU, UK
| | - Jose A Gomez-Sanchez
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Shaline V Fazal
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Anthony Beucher
- Department of Medicine, Imperial College, London W12 0NN, UK
| | - Bonnie Razzaghi
- Department of Medicine, Imperial College, London W12 0NN, UK
| | - Rhona Mirsky
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Kristjan R Jessen
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Timothy J Aitman
- Department of Medicine, Imperial College, London W12 0NN, UK; Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH16 2XU, UK.
| |
Collapse
|
209
|
NRF2 Activation Impairs Quiescence and Bone Marrow Reconstitution Capacity of Hematopoietic Stem Cells. Mol Cell Biol 2017; 37:MCB.00086-17. [PMID: 28674188 DOI: 10.1128/mcb.00086-17] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 06/27/2017] [Indexed: 12/12/2022] Open
Abstract
Tissue stem cells are maintained in quiescence under physiological conditions but proliferate and differentiate to replenish mature cells under stressed conditions. The KEAP1-NRF2 system plays an essential role in stress response and cytoprotection against redox disturbance. To clarify the role of the KEAP1-NRF2 system in tissue stem cells, we focused on hematopoiesis in this study and used Keap1-deficient mice to examine the effects of persistent activation of NRF2 on long-term hematopoietic stem cells (LT-HSCs). We found that persistent activation of NRF2 due to Keap1 deficiency did not change the number of LT-HSCs but reduced their quiescence in steady-state hematopoiesis. During hematopoietic regeneration after bone marrow (BM) transplantation, persistent activation of NRF2 reduced the BM reconstitution capacity of LT-HSCs, suggesting that NRF2 reduces the quiescence of LT-HSCs and promotes their differentiation, leading to eventual exhaustion. Transient activation of NRF2 by an electrophilic reagent also promotes the entry of LT-HSCs into the cell cycle. Taken together, our findings show that NRF2 drives the cell cycle entry and differentiation of LT-HSCs at the expense of their quiescence and maintenance, an effect that appears to be beneficial for prompt recovery from blood loss. We propose that the appropriate control of NRF2 activity by KEAP1 is essential for maintaining HSCs and guarantees their stress-induced regenerative response.
Collapse
|
210
|
Abstract
During aging, the mechanisms that normally maintain health and stress resistance strikingly decline, resulting in decrepitude, frailty, and ultimately death. Exactly when and how this decline occurs is unknown. Changes in transcriptional networks and chromatin state lie at the heart of age-dependent decline. These epigenomic changes are not only observed during aging but also profoundly affect cellular function and stress resistance, thereby contributing to the progression of aging. We propose that the dysregulation of transcriptional and chromatin networks is a crucial component of aging. Understanding age-dependent epigenomic changes will yield key insights into how aging begins and progresses and should lead to the development of new therapeutics that delay or even reverse aging and age-related diseases.
Collapse
Affiliation(s)
- Lauren N Booth
- Department of Genetics, Stanford University, 300 Pasteur Drive, Stanford, CA 94305, USA
| | - Anne Brunet
- Department of Genetics, Stanford University, 300 Pasteur Drive, Stanford, CA 94305, USA; Glenn Laboratories for the Biology of Aging, Stanford University, 300 Pasteur Drive, Stanford, CA 94305, USA.
| |
Collapse
|
211
|
Takizawa H, Fritsch K, Kovtonyuk LV, Saito Y, Yakkala C, Jacobs K, Ahuja AK, Lopes M, Hausmann A, Hardt WD, Gomariz Á, Nombela-Arrieta C, Manz MG. Pathogen-Induced TLR4-TRIF Innate Immune Signaling in Hematopoietic Stem Cells Promotes Proliferation but Reduces Competitive Fitness. Cell Stem Cell 2017; 21:225-240.e5. [DOI: 10.1016/j.stem.2017.06.013] [Citation(s) in RCA: 157] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Revised: 04/22/2017] [Accepted: 06/19/2017] [Indexed: 02/06/2023]
|
212
|
Gross AM, Jaeger PA, Kreisberg JF, Licon K, Jepsen KL, Khosroheidari M, Morsey BM, Swindells S, Shen H, Ng CT, Flagg K, Chen D, Zhang K, Fox HS, Ideker T. Methylome-wide Analysis of Chronic HIV Infection Reveals Five-Year Increase in Biological Age and Epigenetic Targeting of HLA. Mol Cell 2017; 62:157-168. [PMID: 27105112 DOI: 10.1016/j.molcel.2016.03.019] [Citation(s) in RCA: 215] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 12/29/2015] [Accepted: 03/16/2016] [Indexed: 12/31/2022]
Abstract
HIV-infected individuals are living longer on antiretroviral therapy, but many patients display signs that in some ways resemble premature aging. To investigate and quantify the impact of chronic HIV infection on aging, we report a global analysis of the whole-blood DNA methylomes of 137 HIV+ individuals under sustained therapy along with 44 matched HIV- individuals. First, we develop and validate epigenetic models of aging that are independent of blood cell composition. Using these models, we find that both chronic and recent HIV infection lead to an average aging advancement of 4.9 years, increasing expected mortality risk by 19%. In addition, sustained infection results in global deregulation of the methylome across >80,000 CpGs and specific hypomethylation of the region encoding the human leukocyte antigen locus (HLA). We find that decreased HLA methylation is predictive of lower CD4 / CD8 T cell ratio, linking molecular aging, epigenetic regulation, and disease progression.
Collapse
Affiliation(s)
- Andrew M Gross
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA; Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Philipp A Jaeger
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jason F Kreisberg
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Katherine Licon
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kristen L Jepsen
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mahdieh Khosroheidari
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Brenda M Morsey
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Susan Swindells
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Hui Shen
- Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Cherie T Ng
- aTyr Pharmaceuticals, San Diego, CA 92121, USA
| | - Ken Flagg
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Ophthalmology and Biomaterials and Tissue Engineering Center, Institute for Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Guangzhou Kang Rui Biological Pharmaceutical Technology Company Ltd., Guangzhou 510005, China
| | - Daniel Chen
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Ophthalmology and Biomaterials and Tissue Engineering Center, Institute for Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kang Zhang
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Ophthalmology and Biomaterials and Tissue Engineering Center, Institute for Engineering in Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Veterans Administration Healthcare System, San Diego, CA 92093, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Howard S Fox
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA.
| | - Trey Ideker
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA; Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA.
| |
Collapse
|
213
|
Miousse IR, Chang J, Shao L, Pathak R, Nzabarushimana É, Kutanzi KR, Landes RD, Tackett AJ, Hauer-Jensen M, Zhou D, Koturbash I. Inter-Strain Differences in LINE-1 DNA Methylation in the Mouse Hematopoietic System in Response to Exposure to Ionizing Radiation. Int J Mol Sci 2017; 18:ijms18071430. [PMID: 28677663 PMCID: PMC5535921 DOI: 10.3390/ijms18071430] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 06/28/2017] [Accepted: 06/30/2017] [Indexed: 12/15/2022] Open
Abstract
Long Interspersed Nuclear Element 1 (LINE-1) retrotransposons are the major repetitive elements in mammalian genomes. LINE-1s are well-accepted as driving forces of evolution and critical regulators of the expression of genetic information. Alterations in LINE-1 DNA methylation may lead to its aberrant activity and are reported in virtually all human cancers and in experimental carcinogenesis. In this study, we investigated the endogenous DNA methylation status of the 5′ untranslated region (UTR) of LINE-1 elements in the bone marrow hematopoietic stem cells (HSCs), hematopoietic progenitor cells (HPCs), and mononuclear cells (MNCs) in radioresistant C57BL/6J and radiosensitive CBA/J mice and in response to ionizing radiation (IR). We demonstrated that basal levels of DNA methylation within the 5′-UTRs of LINE-1 elements did not differ significantly between the two mouse strains and were negatively correlated with the evolutionary age of LINE-1 elements. Meanwhile, the expression of LINE-1 elements was higher in CBA/J mice. At two months after irradiation to 0.1 or 1 Gy of 137Cs (dose rate 1.21 Gy/min), significant decreases in LINE-1 DNA methylation in HSCs were observed in prone to radiation-induced carcinogenesis CBA/J, but not C57BL/6J mice. At the same time, no residual DNA damage, increased ROS, or changes in the cell cycle were detected in HSCs of CBA/J mice. These results suggest that epigenetic alterations may potentially serve as driving forces of radiation-induced carcinogenesis; however, future studies are needed to demonstrate the direct link between the LINE-1 DNA hypomethylation and radiation carcinogenesis.
Collapse
Affiliation(s)
- Isabelle R Miousse
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | - Jianhui Chang
- Department of Pharmaceutical Sciences, Division of Radiation Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | - Lijian Shao
- Department of Pharmaceutical Sciences, Division of Radiation Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | - Rupak Pathak
- Department of Pharmaceutical Sciences, Division of Radiation Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | - Étienne Nzabarushimana
- Department of Bioinformatics, School of Informatics and Computing, Indiana University, Bloomington, IN 47408, USA.
| | - Kristy R Kutanzi
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | - Reid D Landes
- Department of Biostatistics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | - Alan J Tackett
- Department of Biochemistry, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | - Martin Hauer-Jensen
- Department of Pharmaceutical Sciences, Division of Radiation Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | - Daohong Zhou
- Department of Pharmaceutical Sciences, Division of Radiation Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | - Igor Koturbash
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| |
Collapse
|
214
|
Abstract
Myelodysplastic syndromes/myeloproliferative neoplasms (MDS/MPN) are aggressive myeloid malignancies recognized as a distinct category owing to their unique combination of dysplastic and proliferative features. Although current classification schemes still emphasize morphology and exclusionary criteria, disease-defining somatic mutations and/or germline predisposition alleles are increasingly incorporated into diagnostic algorithms. The developing picture suggests that phenotypes are driven mostly by epigenetic mechanisms that reflect a complex interplay between genotype, physiological processes such as ageing and interactions between malignant haematopoietic cells and the stromal microenvironment of the bone marrow. Despite the rapid accumulation of genetic knowledge, therapies have remained nonspecific and largely inefficient. In this Review, we discuss the pathogenesis of MDS/MPN, focusing on the relationship between genotype and phenotype and the molecular underpinnings of epigenetic dysregulation. Starting with the limitations of current therapies, we also explore how the available mechanistic data may be harnessed to inform strategies to develop rational and more effective treatments, and which gaps in our knowledge need to be filled to translate biological understanding into clinical progress.
Collapse
Affiliation(s)
- Michael W N Deininger
- Division of Hematology and Hematologic Malignancies, Department of Internal Medicine, University of Utah
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - Jeffrey W Tyner
- Knight Cancer Institute, Oregon Health and Science University
- Department of Cell, Developmental and Cancer Biology, Oregon Health &Science University, Portland, Oregon 97239, USA
| | - Eric Solary
- INSERM U1170, Gustave Roussy, Faculté de médecine Paris-Sud, Université Paris-Saclay, F-94805 Villejuif, France
- Department of Hematology, Gustave Roussy, F-94805 Villejuif, France
| |
Collapse
|
215
|
Shiels PG, McGuinness D, Eriksson M, Kooman JP, Stenvinkel P. The role of epigenetics in renal ageing. Nat Rev Nephrol 2017. [PMID: 28626222 DOI: 10.1038/nrneph.2017.78] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
An ability to separate natural ageing processes from processes specific to morbidities is required to understand the heterogeneity of age-related organ dysfunction. Mechanistic insight into how epigenetic factors regulate ageing throughout the life course, linked to a decline in renal function with ageing, is already proving to be of value in the analyses of clinical and epidemiological cohorts. Noncoding RNAs provide epigenetic regulatory circuits within the kidney, which reciprocally interact with DNA methylation processes, histone modification and chromatin. These interactions have been demonstrated to reflect the biological age and function of renal allografts. Epigenetic factors control gene expression and activity in response to environmental perturbations. They also have roles in highly conserved signalling pathways that modulate ageing, including the mTOR and insulin/insulin-like growth factor signalling pathways, and regulation of sirtuin activity. Nutrition, the gut microbiota, inflammation and environmental factors, including psychosocial and lifestyle stresses, provide potential mechanistic links between the epigenetic landscape of ageing and renal dysfunction. Approaches to modify the renal epigenome via nutritional intervention, targeting the methylome or targeting chromatin seem eminently feasible, although caution is merited owing to the potential for intergenerational and transgenerational effects.
Collapse
Affiliation(s)
- Paul G Shiels
- Section of Epigenetics, Institute of Cancer Sciences, Wolfson Wohl Translational Research Centre, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, UK
| | - Dagmara McGuinness
- Section of Epigenetics, Institute of Cancer Sciences, Wolfson Wohl Translational Research Centre, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1QH, UK
| | - Maria Eriksson
- Department of Biosciences and Nutrition (BioNut), H2, Eriksson, Novum 141, 83 Huddinge, Sweden
| | - Jeroen P Kooman
- Department of Internal Medicine, Division of Nephrology, Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastrich, Netherlands
| | - Peter Stenvinkel
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology, Karolinska University Hospital, Huddinge, Karolinska Institutet, SE-14157 Stockholm, Sweden
| |
Collapse
|
216
|
Shih AH, Meydan C, Shank K, Garrett-Bakelman FE, Ward PS, Intlekofer AM, Nazir A, Stein EM, Knapp K, Glass J, Travins J, Straley K, Gliser C, Mason CE, Yen K, Thompson CB, Melnick A, Levine RL. Combination Targeted Therapy to Disrupt Aberrant Oncogenic Signaling and Reverse Epigenetic Dysfunction in IDH2- and TET2-Mutant Acute Myeloid Leukemia. Cancer Discov 2017; 7:494-505. [PMID: 28193779 PMCID: PMC5413413 DOI: 10.1158/2159-8290.cd-16-1049] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Revised: 02/02/2017] [Accepted: 02/09/2017] [Indexed: 11/16/2022]
Abstract
Genomic studies in acute myeloid leukemias (AML) have identified mutations that drive altered DNA methylation, including TET2 and IDH2 Here, we show that models of AML resulting from TET2 or IDH2 mutations combined with FLT3ITD mutations are sensitive to 5-azacytidine or to the IDH2 inhibitor AG-221, respectively. 5-azacytidine and AG-221 treatment induced an attenuation of aberrant DNA methylation and transcriptional output and resulted in a reduction in leukemic blasts consistent with antileukemic activity. These therapeutic benefits were associated with restoration of leukemic cell differentiation, and the normalization of hematopoiesis was derived from mutant cells. By contrast, combining AG-221 or 5-azacytidine with FLT3 inhibition resulted in a reduction in mutant allele burden, progressive recovery of normal hematopoiesis from non-mutant stem-progenitor cells, and reversal of dysregulated DNA methylation and transcriptional output. Together, our studies suggest combined targeting of signaling and epigenetic pathways can increase therapeutic response in AML.Significance: AMLs with mutations in TET2 or IDH2 are sensitive to epigenetic therapy through inhibition of DNA methyltransferase activity by 5-azacytidine or inhibition of mutant IDH2 through AG-221. These inhibitors induce a differentiation response and can be used to inform mechanism-based combination therapy. Cancer Discov; 7(5); 494-505. ©2017 AACR.See related commentary by Thomas and Majeti, p. 459See related article by Yen et al., p. 478This article is highlighted in the In This Issue feature, p. 443.
Collapse
Affiliation(s)
- Alan H Shih
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Cem Meydan
- Department of Medicine/Hematology-Oncology and Department of Pharmacology, Weill Cornell Medical College, New York, New York
- Department of Physiology and Biophysics and the HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York
| | - Kaitlyn Shank
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Francine E Garrett-Bakelman
- Department of Medicine/Hematology-Oncology and Department of Pharmacology, Weill Cornell Medical College, New York, New York
| | - Patrick S Ward
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Andrew M Intlekofer
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Lymphoma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Abbas Nazir
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Eytan M Stein
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kristina Knapp
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jacob Glass
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine/Hematology-Oncology and Department of Pharmacology, Weill Cornell Medical College, New York, New York
| | | | - Kim Straley
- Agios Pharmaceuticals, Cambridge, Massachusetts
| | | | - Christopher E Mason
- Department of Physiology and Biophysics and the HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York
| | | | - Craig B Thompson
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ari Melnick
- Department of Medicine/Hematology-Oncology and Department of Pharmacology, Weill Cornell Medical College, New York, New York.
| | - Ross L Levine
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, New York
| |
Collapse
|
217
|
Biechonski S, Yassin M, Milyavsky M. DNA-damage response in hematopoietic stem cells: an evolutionary trade-off between blood regeneration and leukemia suppression. Carcinogenesis 2017; 38:367-377. [PMID: 28334174 DOI: 10.1093/carcin/bgx002] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 01/11/2017] [Indexed: 12/12/2022] Open
Abstract
Self-renewing and multipotent hematopoietic stem cells (HSCs) maintain lifelong hematopoiesis. Their enormous regenerative potential coupled with lifetime persistence in the body, in contrast with the Progenitors, demand tight control of HSCs genome stability. Indeed, failure to accurately repair DNA damage in HSCs is associated with bone marrow failure and accelerated leukemogenesis. Recent observations exposed remarkable differences in several DNA-damage response (DDR) aspects between HSCs and Progenitors, especially in their DNA-repair capacities and susceptibility to apoptosis. Human HSCs in comparison with Progenitors exhibit delayed DNA double-strand break rejoining, persistent DDR signaling activation, higher sensitivity to the cytotoxic effects of ionizing radiation and attenuated expression of DNA-repair genes. Importantly, the distinct DDR of HSCs was also documented in mouse models. Nevertheless, physiological significance and the molecular basis of the HSCs-specific DDR features are only partially understood. Taking radiation-induced DDR as a paradigm, this review will focus on the current advances in understanding the role of cell-intrinsic DDR regulators and the cellular microenvironment in balancing stemness with genome stability. Pre-leukemia HSCs and clonal hematopoiesis evolvement will be discussed as an evolutionary compromise between the need for lifelong blood regeneration and DDR. Uniquely for this review, we outline the differences in HSCs-related DDR as highlighted by various experimental systems and attempt to provide their critical analysis.
Collapse
Affiliation(s)
- Shahar Biechonski
- Department of Pathology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Muhammad Yassin
- Department of Pathology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Michael Milyavsky
- Department of Pathology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 69978, Israel
| |
Collapse
|
218
|
García-Prat L, Muñoz-Cánoves P. Aging, metabolism and stem cells: Spotlight on muscle stem cells. Mol Cell Endocrinol 2017; 445:109-117. [PMID: 27531569 DOI: 10.1016/j.mce.2016.08.021] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 08/11/2016] [Indexed: 12/15/2022]
Abstract
All tissues and organs undergo a progressive regenerative decline as they age. This decline has been mainly attributed to loss of stem cell number and/or function, and both stem cell-intrinsic changes and alterations in local niches and/or systemic environment over time are known to contribute to the stem cell aging phenotype. Advancing in the molecular understanding of the deterioration of stem cell cells with aging is key for targeting the specific causes of tissue regenerative dysfunction at advanced stages of life. Here, we revise exciting recent findings on why stem cells age and the consequences on tissue regeneration, with a special focus on regeneration of skeletal muscle. We also highlight newly identified common molecular pathways affecting diverse types of aging stem cells, such as altered proteostasis, metabolism, or senescence entry, and discuss the questions raised by these findings. Finally, we comment on emerging stem cell rejuvenation strategies, principally emanating from studies on muscle stem cells, which will surely burst tissue regeneration research for future benefit of the increasing human aging population.
Collapse
Affiliation(s)
- Laura García-Prat
- Tissue Regeneration Laboratory, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain; Cell Biology Group, Department of Experimental and Health Sciences, Pompeu Fabra; University (UPF) y CIBERNED, Barcelona, Spain
| | - Pura Muñoz-Cánoves
- Tissue Regeneration Laboratory, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain; Cell Biology Group, Department of Experimental and Health Sciences, Pompeu Fabra; University (UPF) y CIBERNED, Barcelona, Spain; ICREA, Barcelona, Spain.
| |
Collapse
|
219
|
Cole JJ, Robertson NA, Rather MI, Thomson JP, McBryan T, Sproul D, Wang T, Brock C, Clark W, Ideker T, Meehan RR, Miller RA, Brown-Borg HM, Adams PD. Diverse interventions that extend mouse lifespan suppress shared age-associated epigenetic changes at critical gene regulatory regions. Genome Biol 2017; 18:58. [PMID: 28351383 PMCID: PMC5370462 DOI: 10.1186/s13059-017-1185-3] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 03/01/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Age-associated epigenetic changes are implicated in aging. Notably, age-associated DNA methylation changes comprise a so-called aging "clock", a robust biomarker of aging. However, while genetic, dietary and drug interventions can extend lifespan, their impact on the epigenome is uncharacterised. To fill this knowledge gap, we defined age-associated DNA methylation changes at the whole-genome, single-nucleotide level in mouse liver and tested the impact of longevity-promoting interventions, specifically the Ames dwarf Prop1 df/df mutation, calorie restriction and rapamycin. RESULTS In wild-type mice fed an unsupplemented ad libitum diet, age-associated hypomethylation was enriched at super-enhancers in highly expressed genes critical for liver function. Genes harbouring hypomethylated enhancers were enriched for genes that change expression with age. Hypermethylation was enriched at CpG islands marked with bivalent activating and repressing histone modifications and resembled hypermethylation in liver cancer. Age-associated methylation changes are suppressed in Ames dwarf and calorie restricted mice and more selectively and less specifically in rapamycin treated mice. CONCLUSIONS Age-associated hypo- and hypermethylation events occur at distinct regulatory features of the genome. Distinct longevity-promoting interventions, specifically genetic, dietary and drug interventions, suppress some age-associated methylation changes, consistent with the idea that these interventions exert their beneficial effects, in part, by modulation of the epigenome. This study is a foundation to understand the epigenetic contribution to healthy aging and longevity and the molecular basis of the DNA methylation clock.
Collapse
Affiliation(s)
- John J Cole
- Beatson Institute for Cancer Research and University of Glasgow, Garscube Estate, G61 1BD, UK
| | - Neil A Robertson
- Beatson Institute for Cancer Research and University of Glasgow, Garscube Estate, G61 1BD, UK
| | - Mohammed Iqbal Rather
- Beatson Institute for Cancer Research and University of Glasgow, Garscube Estate, G61 1BD, UK
| | - John P Thomson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, UK
| | - Tony McBryan
- Beatson Institute for Cancer Research and University of Glasgow, Garscube Estate, G61 1BD, UK
| | - Duncan Sproul
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, UK
- Edinburgh Cancer Research Centre, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, UK
| | - Tina Wang
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Claire Brock
- Beatson Institute for Cancer Research and University of Glasgow, Garscube Estate, G61 1BD, UK
| | - William Clark
- Beatson Institute for Cancer Research and University of Glasgow, Garscube Estate, G61 1BD, UK
| | - Trey Ideker
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Richard R Meehan
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, UK
| | - Richard A Miller
- Department of Pathology and Glenn Center for the Biology of Aging, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Holly M Brown-Borg
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, 58203, USA.
| | - Peter D Adams
- Beatson Institute for Cancer Research and University of Glasgow, Garscube Estate, G61 1BD, UK.
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA.
| |
Collapse
|
220
|
The epigenetic landscape of age-related diseases: the geroscience perspective. Biogerontology 2017; 18:549-559. [PMID: 28352958 PMCID: PMC5514215 DOI: 10.1007/s10522-017-9695-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 03/14/2017] [Indexed: 12/11/2022]
Abstract
In this review, we summarize current knowledge regarding the epigenetics of age-related diseases, focusing on those studies that have described DNA methylation landscape in cardio-vascular diseases, musculoskeletal function and frailty. We stress the importance of adopting the conceptual framework of “geroscience”, which starts from the observation that advanced age is the major risk factor for several of these pathologies and aims at identifying the mechanistic links between aging and age-related diseases. DNA methylation undergoes a profound remodeling during aging, which includes global hypomethylation of the genome, hypermethylation at specific loci and an increase in inter-individual variation and in stochastic changes of DNA methylation values. These epigenetic modifications can be an important contributor to the development of age-related diseases, but our understanding on the complex relationship between the epigenetic signatures of aging and age-related disease is still poor. The most relevant results in this field come from the use of the so called “epigenetics clocks” in cohorts of subjects affected by age-related diseases. We report these studies in final section of this review.
Collapse
|
221
|
Hahn O, Grönke S, Stubbs TM, Ficz G, Hendrich O, Krueger F, Andrews S, Zhang Q, Wakelam MJ, Beyer A, Reik W, Partridge L. Dietary restriction protects from age-associated DNA methylation and induces epigenetic reprogramming of lipid metabolism. Genome Biol 2017; 18:56. [PMID: 28351387 PMCID: PMC5370449 DOI: 10.1186/s13059-017-1187-1] [Citation(s) in RCA: 148] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 03/02/2017] [Indexed: 12/11/2022] Open
Abstract
Background Dietary restriction (DR), a reduction in food intake without malnutrition, increases most aspects of health during aging and extends lifespan in diverse species, including rodents. However, the mechanisms by which DR interacts with the aging process to improve health in old age are poorly understood. DNA methylation could play an important role in mediating the effects of DR because it is sensitive to the effects of nutrition and can affect gene expression memory over time. Results Here, we profile genome-wide changes in DNA methylation, gene expression and lipidomics in response to DR and aging in female mouse liver. DR is generally strongly protective against age-related changes in DNA methylation. During aging with DR, DNA methylation becomes targeted to gene bodies and is associated with reduced gene expression, particularly of genes involved in lipid metabolism. The lipid profile of the livers of DR mice is correspondingly shifted towards lowered triglyceride content and shorter chain length of triglyceride-associated fatty acids, and these effects become more pronounced with age. Conclusions Our results indicate that DR remodels genome-wide patterns of DNA methylation so that age-related changes are profoundly delayed, while changes at loci involved in lipid metabolism affect gene expression and the resulting lipid profile. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1187-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Oliver Hahn
- Max Planck Institute for Biology of Ageing, 50931, Cologne, Germany.,Cellular Networks and Systems Biology, CECAD, University of Cologne, Joseph-Stelzmann-Str. 26, Cologne, 50931, Germany
| | - Sebastian Grönke
- Max Planck Institute for Biology of Ageing, 50931, Cologne, Germany
| | - Thomas M Stubbs
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Gabriella Ficz
- Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Oliver Hendrich
- Max Planck Institute for Biology of Ageing, 50931, Cologne, Germany
| | - Felix Krueger
- Bioinformatics Group, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Simon Andrews
- Bioinformatics Group, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Qifeng Zhang
- Inositide Lab, The Babraham Institute, Cambridge, CB22 3AT, UK
| | | | - Andreas Beyer
- Cellular Networks and Systems Biology, CECAD, University of Cologne, Joseph-Stelzmann-Str. 26, Cologne, 50931, Germany. .,Center for Molecular Medicine Cologne, University of Cologne, Cologne, 50931, Germany.
| | - Wolf Reik
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK. .,The Wellcome Trust Sanger Institute, Cambridge, CB10 1SA, UK.
| | - Linda Partridge
- Max Planck Institute for Biology of Ageing, 50931, Cologne, Germany. .,Department of Genetics, Evolution and Environment, Institute of Healthy Ageing, University College London, London, WC1E 6BT, UK.
| |
Collapse
|
222
|
Wang T, Tsui B, Kreisberg JF, Robertson NA, Gross AM, Yu MK, Carter H, Brown-Borg HM, Adams PD, Ideker T. Epigenetic aging signatures in mice livers are slowed by dwarfism, calorie restriction and rapamycin treatment. Genome Biol 2017; 18:57. [PMID: 28351423 PMCID: PMC5371228 DOI: 10.1186/s13059-017-1186-2] [Citation(s) in RCA: 193] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 03/01/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Global but predictable changes impact the DNA methylome as we age, acting as a type of molecular clock. This clock can be hastened by conditions that decrease lifespan, raising the question of whether it can also be slowed, for example, by conditions that increase lifespan. Mice are particularly appealing organisms for studies of mammalian aging; however, epigenetic clocks have thus far been formulated only in humans. RESULTS We first examined whether mice and humans experience similar patterns of change in the methylome with age. We found moderate conservation of CpG sites for which methylation is altered with age, with both species showing an increase in methylome disorder during aging. Based on this analysis, we formulated an epigenetic-aging model in mice using the liver methylomes of 107 mice from 0.2 to 26.0 months old. To examine whether epigenetic aging signatures are slowed by longevity-promoting interventions, we analyzed 28 additional methylomes from mice subjected to lifespan-extending conditions, including Prop1df/df dwarfism, calorie restriction or dietary rapamycin. We found that mice treated with these lifespan-extending interventions were significantly younger in epigenetic age than their untreated, wild-type age-matched controls. CONCLUSIONS This study shows that lifespan-extending conditions can slow molecular changes associated with an epigenetic clock in mice livers.
Collapse
Affiliation(s)
- Tina Wang
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Brian Tsui
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA.,Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jason F Kreisberg
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Neil A Robertson
- Beatson Institute for Cancer Research and University of Glasgow, Glasgow, UK
| | - Andrew M Gross
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA.,Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Michael Ku Yu
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA.,Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Hannah Carter
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA.,Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Holly M Brown-Borg
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND, 58202, USA
| | - Peter D Adams
- Beatson Institute for Cancer Research and University of Glasgow, Glasgow, UK.,Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Trey Ideker
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA.
| |
Collapse
|
223
|
Guidi N, Sacma M, Ständker L, Soller K, Marka G, Eiwen K, Weiss JM, Kirchhoff F, Weil T, Cancelas JA, Florian MC, Geiger H. Osteopontin attenuates aging-associated phenotypes of hematopoietic stem cells. EMBO J 2017; 36:840-853. [PMID: 28254837 PMCID: PMC5376966 DOI: 10.15252/embj.201694969] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 12/08/2016] [Accepted: 01/18/2017] [Indexed: 01/08/2023] Open
Abstract
Upon aging, hematopoietic stem cells (HSCs) undergo changes in function and structure, including skewing to myeloid lineages, lower reconstitution potential and loss of protein polarity. While stem cell intrinsic mechanisms are known to contribute to HSC aging, little is known on whether age-related changes in the bone marrow niche regulate HSC aging. Upon aging, the expression of osteopontin (OPN) in the murine bone marrow stroma is reduced. Exposure of young HSCs to an OPN knockout niche results in a decrease in engraftment, an increase in long-term HSC frequency and loss of stem cell polarity. Exposure of aged HSCs to thrombin-cleaved OPN attenuates aging of old HSCs, resulting in increased engraftment, decreased HSC frequency, increased stem cell polarity and a restored balance of lymphoid and myeloid cells in peripheral blood. Thus, our data suggest a critical role for reduced stroma-derived OPN for HSC aging and identify thrombin-cleaved OPN as a novel niche informed therapeutic approach for ameliorating HSC phenotypes associated with aging.
Collapse
Affiliation(s)
- Novella Guidi
- Institute of Molecular Medicine and Aging Research Center Ulm, University of Ulm, Ulm, Germany
| | - Mehmet Sacma
- Institute of Molecular Medicine and Aging Research Center Ulm, University of Ulm, Ulm, Germany
| | - Ludger Ständker
- Kompetenzzentrum Ulm Peptide Pharmaceuticals, University of Ulm, Ulm, Germany
| | - Karin Soller
- Institute of Molecular Medicine and Aging Research Center Ulm, University of Ulm, Ulm, Germany
| | - Gina Marka
- Institute of Molecular Medicine and Aging Research Center Ulm, University of Ulm, Ulm, Germany
| | - Karina Eiwen
- Institute of Molecular Medicine and Aging Research Center Ulm, University of Ulm, Ulm, Germany
| | - Johannes M Weiss
- Department of Dermatology and Allergic Diseases, Universitätsklinikum Ulm, Ulm, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Universitätsklinikum Ulm, Ulm, Germany
| | - Tanja Weil
- Institute of Organic Chemistry III, University of Ulm, Ulm, Germany
| | - Jose A Cancelas
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Maria Carolina Florian
- Institute of Molecular Medicine and Aging Research Center Ulm, University of Ulm, Ulm, Germany
| | - Hartmut Geiger
- Institute of Molecular Medicine and Aging Research Center Ulm, University of Ulm, Ulm, Germany .,Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| |
Collapse
|
224
|
Conserved effect of aging on DNA methylation and association with EZH2 polycomb protein in mice and humans. Mech Ageing Dev 2017; 162:27-37. [PMID: 28249716 DOI: 10.1016/j.mad.2017.02.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 01/11/2017] [Accepted: 02/16/2017] [Indexed: 11/22/2022]
Abstract
In humans, DNA methylation at specific CpG sites can be used to estimate the 'epigenetic clock', a biomarker of aging and health. The mechanisms that regulate the aging epigenome and level of conservation are not entirely clear. We performed affinity-based enrichment with methyl-CpG binding domain protein followed by high-throughput sequencing (MBD-seq) to assay DNA methylation in mouse samples. Consistent with previous reports, aging is associated with increase in methylation at CpG islands that likely overlap regulatory regions of genes that have been implicated in cancers (e.g., C1ql3, Srd5a2 and Ptk7). The differentially methylated regions in mice have high sequence conservation in humans and the pattern of methylation is also largely conserved between the two species. Based on human ENCODE data, these sites are targeted by polycomb proteins, including EZH2. Chromatin immunoprecipitation confirmed that these regions interact with EZH2 in mice as well, and there may be reduction in EZH2 occupancy with age at C1ql3. This adds to the growing evidence that EZH2 is part of the protein machinery that shapes the aging epigenome. The conservation in both sequence and methylation patterns of the age-dependent CpGs indicate that the epigenetic clock is a fundamental feature of aging in mammals.
Collapse
|
225
|
Ahmed ASI, Sheng MHC, Wasnik S, Baylink DJ, Lau KHW. Effect of aging on stem cells. World J Exp Med 2017; 7:1-10. [PMID: 28261550 PMCID: PMC5316899 DOI: 10.5493/wjem.v7.i1.1] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Revised: 11/19/2016] [Accepted: 12/09/2016] [Indexed: 02/06/2023] Open
Abstract
Pluripotent stem cells have the remarkable self-renewal ability and are capable of differentiating into multiple diverse cells. There is increasing evidence that the aging process can have adverse effects on stem cells. As stem cells age, their renewal ability deteriorates and their ability to differentiate into the various cell types is altered. Accordingly, it is suggested aging-induced deterioration of stem cell functions may play a key role in the pathophysiology of the various aging-associated disorders. Understanding the role of the aging process in deterioration of stem cell function is crucial, not only in understanding the pathophysiology of aging-associated disorders, but also in future development of novel effective stem cell-based therapies to treat aging-associated diseases. This review article first focuses on the basis of the various aging disease-related stem cell dysfunction. It then addresses the several concepts on the potential mechanism that causes aging-related stem cell dysfunction. It also briefly discusses the current potential therapies under development for aging-associated stem cell defects.
Collapse
|
226
|
The chronic myeloid leukemia stem cell: stemming the tide of persistence. Blood 2017; 129:1595-1606. [PMID: 28159740 DOI: 10.1182/blood-2016-09-696013] [Citation(s) in RCA: 200] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 11/04/2016] [Indexed: 12/14/2022] Open
Abstract
Chronic myeloid leukemia (CML) is caused by the acquisition of the tyrosine kinase BCR-ABL1 in a hemopoietic stem cell, transforming it into a leukemic stem cell (LSC) that self-renews, proliferates, and differentiates to give rise to a myeloproliferative disease. Although tyrosine kinase inhibitors (TKIs) that target the kinase activity of BCR-ABL1 have transformed CML from a once-fatal disease to a manageable one for the vast majority of patients, only ∼10% of those who present in chronic phase (CP) can discontinue TKI treatment and maintain a therapy-free remission. Strong evidence now shows that CML LSCs are resistant to the effects of TKIs and persist in all patients on long-term therapy, where they may promote acquired TKI resistance, drive relapse or disease progression, and inevitably represent a bottleneck to cure. Since their discovery in patients almost 2 decades ago, CML LSCs have become a well-recognized exemplar of the cancer stem cell and have been characterized extensively, with the aim of developing new curative therapeutic approaches based on LSC eradication. This review summarizes our current understanding of many of the pathways and mechanisms that promote the survival of the CP CML LSCs and how they can be a source of new gene coding mutations that impact in the clinic. We also review recent preclinical approaches that show promise to eradicate the LSC, and future challenges on the path to cure.
Collapse
|
227
|
Abstract
Until recently, there was broad consensus in the stem cell aging field that the phenotype of aged hematopoietic stem cells (HSCs) is fixed-dominated by cell-intrinsic regulatory mechanisms that cannot be altered by pharmacological or genetic means. The conventional thinking was that HSC aging could not be reverted by therapeutic intervention. This paradigm has started to shift dramatically, primarily because hallmarks of aged HSCs have been successfully reverted by distinct experimental approaches by multiple laboratories. We will discuss in this review these hallmarks of HSCs aging and the novel approaches that successfully ameliorated or even reverted aging-associated hallmarks of aged HSCs.
Collapse
Affiliation(s)
- Novella Guidi
- Institute for Molecular Medicine, Ulm University, Ulm, Germany.
| | - Hartmut Geiger
- Institute for Molecular Medicine, Ulm University, Ulm, Germany; Division of Experimental Hematology and Cancer Biology, Cincinnati Children׳s Hospital Medical Center, Cincinnati, OH, USA; Aging Research Center, Ulm University, Ulm, Germany.
| |
Collapse
|
228
|
Abstract
In this chapter we summarize the pros and cons of the notion that Runx3 is a major tumor suppressor gene (TSG). Inactivation of TSGs in normal cells provides a viability/growth advantage that contributes cell-autonomously to cancer. More than a decade ago it was suggested that RUNX3 is involved in gastric cancer development, a postulate extended later to other epithelial cancers portraying RUNX3 as a major TSG. However, evidence that Runx3 is not expressed in normal gastric and other epithelia has challenged the RUNX3-TSG paradigm. In contrast, RUNX3 is overexpressed in a significant fraction of tumor cells in various human epithelial cancers and its overexpression in pancreatic cancer cells promotes their migration, anchorage-independent growth and metastatic potential. Moreover, recent high-throughput quantitative genome-wide studies on thousands of human samples of various tumors and new investigations of the role of Runx3 in mouse cancer models have unequivocally demonstrated that RUNX3 is not a bona fide cell-autonomous TSG. Importantly, accumulating data demonstrated that RUNX3 functions in control of immunity and inflammation, thereby indirectly influencing epithelial tumor development.
Collapse
|
229
|
Jung H, Kim DO, Byun JE, Kim WS, Kim MJ, Song HY, Kim YK, Kang DK, Park YJ, Kim TD, Yoon SR, Lee HG, Choi EJ, Min SH, Choi I. Thioredoxin-interacting protein regulates haematopoietic stem cell ageing and rejuvenation by inhibiting p38 kinase activity. Nat Commun 2016; 7:13674. [PMID: 27929088 PMCID: PMC5155146 DOI: 10.1038/ncomms13674] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 10/25/2016] [Indexed: 01/11/2023] Open
Abstract
Ageing is a natural process in living organisms throughout their lifetime, and most elderly people suffer from ageing-associated diseases. One suggested way to tackle such diseases is to rejuvenate stem cells, which also undergo ageing. Here we report that the thioredoxin-interacting protein (TXNIP)-p38 mitogen-activated protein kinase (p38) axis regulates the ageing of haematopoietic stem cells (HSCs), by causing a higher frequency of long-term HSCs, lineage skewing, a decrease in engraftment, an increase in reactive oxygen species and loss of Cdc42 polarity. TXNIP inhibits p38 activity via direct interaction in HSCs. Furthermore, cell-penetrating peptide (CPP)-conjugated peptide derived from the TXNIP-p38 interaction motif inhibits p38 activity via this docking interaction. This peptide dramatically rejuvenates aged HSCs in vitro and in vivo. Our findings suggest that the TXNIP-p38 axis acts as a regulatory mechanism in HSC ageing and indicate the potent therapeutic potential of using CPP-conjugated peptide to rejuvenate aged HSCs.
The processes regulating the ageing of stem cells are not clearly defined. Here, the authors report that in haematopoietic stem cells (HSC) thioredoxin-interacting protein, known to regulate the cell cycle, binds to p38 mitogen-activated protein kinase and regulates HSC ageing and rejuvenation.
Collapse
Affiliation(s)
- Haiyoung Jung
- Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon 34141, Republic of Korea.,Department of Functional Genomics, University of Science and Technology, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Dong Oh Kim
- Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon 34141, Republic of Korea.,Department of Functional Genomics, University of Science and Technology, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Jae-Eun Byun
- Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon 34141, Republic of Korea.,Department of Biochemistry, School of Life Sciences, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Won Sam Kim
- Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon 34141, Republic of Korea.,Department of Functional Genomics, University of Science and Technology, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Mi Jeong Kim
- Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon 34141, Republic of Korea.,Department of Functional Genomics, University of Science and Technology, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Hae Young Song
- Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Young Kwan Kim
- Scripps Korea Antibody Institute, 1 Kangwondaehak-gil, Chuncheon 24341, Republic of Korea
| | - Du-Kyeong Kang
- Bioenergy and Biochemical Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Young-Jun Park
- Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon 34141, Republic of Korea.,Department of Functional Genomics, University of Science and Technology, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Tae-Don Kim
- Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon 34141, Republic of Korea.,Department of Functional Genomics, University of Science and Technology, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Suk Ran Yoon
- Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon 34141, Republic of Korea.,Department of Functional Genomics, University of Science and Technology, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Hee Gu Lee
- Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon 34141, Republic of Korea.,Department of Biomolecular Science, University of Science and Technology, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Eun-Ji Choi
- Department of Hematology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Sang-Hyun Min
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), 80 Chumbokro Dong-gu 41061, Daegu, Republic of Korea
| | - Inpyo Choi
- Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon 34141, Republic of Korea.,Department of Functional Genomics, University of Science and Technology, Yuseong-gu, Daejeon 34113, Republic of Korea
| |
Collapse
|
230
|
Li Y, Tollefsbol TO. Age-related epigenetic drift and phenotypic plasticity loss: implications in prevention of age-related human diseases. Epigenomics 2016; 8:1637-1651. [PMID: 27882781 PMCID: PMC5618938 DOI: 10.2217/epi-2016-0078] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Aging is considered as one of the most important developmental processes in organisms and is closely associated with global deteriorations of epigenetic markers such as aberrant methylomic patterns. This altered epigenomic state, referred to 'epigenetic drift', reflects deficient maintenance of epigenetic marks and contributes to impaired cellular and molecular functions in aged cells. Epigenetic drift-induced abnormal changes during aging are scantily repaired by epigenetic modulators. This inflexibility in the aged epigenome may lead to an age-related decline in phenotypic plasticity at the cellular and molecular levels due to epigenetic drift. This perspective aims to provide novel concepts for understanding epigenetic effects on the aging process and to provide insights into epigenetic prevention and therapeutic strategies for age-related human disease.
Collapse
Affiliation(s)
- Yuanyuan Li
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.,Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA.,Nutrition Obesity Research Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Trygve O Tollefsbol
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.,Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA.,Nutrition Obesity Research Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA.,Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA.,Comprehensive Center for Healthy Aging, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| |
Collapse
|
231
|
Beerman I. Accumulation of DNA damage in the aged hematopoietic stem cell compartment. Semin Hematol 2016; 54:12-18. [PMID: 28088982 DOI: 10.1053/j.seminhematol.2016.11.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 11/10/2016] [Indexed: 02/07/2023]
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.
Collapse
Affiliation(s)
- Isabel Beerman
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD.
| |
Collapse
|
232
|
Kovtonyuk LV, Fritsch K, Feng X, Manz MG, Takizawa H. Inflamm-Aging of Hematopoiesis, Hematopoietic Stem Cells, and the Bone Marrow Microenvironment. Front Immunol 2016; 7:502. [PMID: 27895645 PMCID: PMC5107568 DOI: 10.3389/fimmu.2016.00502] [Citation(s) in RCA: 234] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 10/27/2016] [Indexed: 12/19/2022] Open
Abstract
All hematopoietic and immune cells are continuously generated by hematopoietic stem cells (HSCs) and hematopoietic progenitor cells (HPCs) through highly organized process of stepwise lineage commitment. In the steady state, HSCs are mostly quiescent, while HPCs are actively proliferating and contributing to daily hematopoiesis. In response to hematopoietic challenges, e.g., life-threatening blood loss, infection, and inflammation, HSCs can be activated to proliferate and engage in blood formation. The HSC activation induced by hematopoietic demand is mediated by direct or indirect sensing mechanisms involving pattern recognition receptors or cytokine/chemokine receptors. In contrast to the hematopoietic challenges with obvious clinical symptoms, how the aging process, which involves low-grade chronic inflammation, impacts hematopoiesis remains undefined. Herein, we summarize recent findings pertaining to functional alternations of hematopoiesis, HSCs, and the bone marrow (BM) microenvironment during the processes of aging and inflammation and highlight some common cellular and molecular changes during the processes that influence hematopoiesis and its cells of origin, HSCs and HPCs, as well as the BM microenvironment. We also discuss how age-dependent alterations of the immune system lead to subclinical inflammatory states and how inflammatory signaling might be involved in hematopoietic aging. Our aim is to present evidence supporting the concept of “Inflamm-Aging,” or inflammation-associated aging of hematopoiesis.
Collapse
Affiliation(s)
- Larisa V Kovtonyuk
- Division of Hematology, University Hospital Zurich, University of Zurich , Zurich , Switzerland
| | - Kristin Fritsch
- Division of Hematology, University Hospital Zurich, University of Zurich , Zurich , Switzerland
| | - Xiaomin Feng
- International Research Center for Medical Sciences , Kumamoto , Japan
| | - Markus G Manz
- Division of Hematology, University Hospital Zurich, University of Zurich , Zurich , Switzerland
| | - Hitoshi Takizawa
- International Research Center for Medical Sciences , Kumamoto , Japan
| |
Collapse
|
233
|
Bernitz JM, Kim HS, MacArthur B, Sieburg H, Moore K. Hematopoietic Stem Cells Count and Remember Self-Renewal Divisions. Cell 2016; 167:1296-1309.e10. [PMID: 27839867 DOI: 10.1016/j.cell.2016.10.022] [Citation(s) in RCA: 192] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 07/08/2016] [Accepted: 10/12/2016] [Indexed: 01/22/2023]
Abstract
The ability of cells to count and remember their divisions could underlie many alterations that occur during development, aging, and disease. We tracked the cumulative divisional history of slow-cycling hematopoietic stem cells (HSCs) throughout adult life. This revealed a fraction of rarely dividing HSCs that contained all the long-term HSC (LT-HSC) activity within the aging HSC compartment. During adult life, this population asynchronously completes four traceable symmetric self-renewal divisions to expand its size before entering a state of dormancy. We show that the mechanism of expansion involves progressively lengthening periods between cell divisions, with long-term regenerative potential lost upon a fifth division. Our data also show that age-related phenotypic changes within the HSC compartment are divisional history dependent. These results suggest that HSCs accumulate discrete memory stages over their divisional history and provide evidence for the role of cellular memory in HSC aging.
Collapse
Affiliation(s)
- Jeffrey M Bernitz
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1496, New York, NY 10029, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1496, New York, NY 10029, USA; The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1496, New York, NY 10029, USA
| | - Huen Suk Kim
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1496, New York, NY 10029, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1496, New York, NY 10029, USA; The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1496, New York, NY 10029, USA
| | - Ben MacArthur
- Mathematical Sciences, University of Southampton, Southampton SO17 1BJ, UK; Centre for Human Development, Stem Cells and Regeneration, Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, UK; Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Hans Sieburg
- Vaccine Research Institute of San Diego, San Diego, CA 92121, USA
| | - Kateri Moore
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1496, New York, NY 10029, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1496, New York, NY 10029, USA.
| |
Collapse
|
234
|
Novack L, Yitshak-Sade M, Landau D, Kloog I, Sarov B, Karakis I. Association between ambient air pollution and proliferation of umbilical cord blood cells. ENVIRONMENTAL RESEARCH 2016; 151:783-788. [PMID: 27665250 DOI: 10.1016/j.envres.2016.09.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 09/13/2016] [Accepted: 09/14/2016] [Indexed: 06/06/2023]
Abstract
It has been established as a common knowledge that ambient air pollution (AAP) has an adverse effect on human health. The pathophysiological mechanism of this impact is likely to be related to the oxidative stress. In the current study we estimate the association between AAP and cell proliferation (CP) of umbilical cord blood cells, representing maternal organism most proximal to the fetal body. Blood samples were tested for proliferation in 292 enrolled Arab-Bedouin women at delivery (July 2012-March 2013). The estimates of AAP were defined by a hybrid satellite based model predicting both PM2.5 (particles<2.5µm in diameter) and PM10 (particles<10µm in diameter) as well as monitoring stations for gaseous air pollutants. Risk estimates of pollution exposure were adjusted to medical history, household risk factors and meteorological factors on the day of delivery or one week prior. Ambient ozone (O3) levels on 1, 2, 3and 4 days prior to delivery were associated with lower CP (Prevalence ratio (PR)=0.92, 0.92, 0.93, 0.93, respectively). Increase in inter-quartile range (IOR) of PM2.5 one day before delivery was associated with 9% increase in CP levels (PR=1.09). The positive direction in association was changed to negative association with CP for PM2.5 levels measured at more distant time periods (PR=0.90 and 0.93 for lags 5 and 6 days, respectively). Investigation of PM10 levels indicated a similar pattern (PR=1.05 for pollution values recorded one day before delivery and 0.93 and 0.95 for lags of 5 and 6 days, respectively). Carbon monoxide (CO) levels were associated with lower CP on the day of delivery and 1day prior (PR=0.92 and PR=0.94). To conclude, the levels of cell proliferation of umbilical cord blood cells appear to be associated with the AAP. More studies are needed to support our findings.
Collapse
Affiliation(s)
- L Novack
- Department of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
| | - M Yitshak-Sade
- Clinical Research Center, Soroka University Medical Center, Beer-Sheva, Israel
| | - D Landau
- Division of Neonatology, University Medical Center, Beer-Sheva, Israel
| | - I Kloog
- Department of Geography, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - B Sarov
- Department of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - I Karakis
- Environmental Epidemiology Department, Ministry of Health, Jerusalem, Israel; Ashkelon Academic College, Ashkelon, Israel
| |
Collapse
|
235
|
Durek P, Nordström K, Gasparoni G, Salhab A, Kressler C, de Almeida M, Bassler K, Ulas T, Schmidt F, Xiong J, Glažar P, Klironomos F, Sinha A, Kinkley S, Yang X, Arrigoni L, Amirabad A, Ardakani F, Feuerbach L, Gorka O, Ebert P, Müller F, Li N, Frischbutter S, Schlickeiser S, Cendon C, Fröhler S, Felder B, Gasparoni N, Imbusch C, Hutter B, Zipprich G, Tauchmann Y, Reinke S, Wassilew G, Hoffmann U, Richter A, Sieverling L, Chang HD, Syrbe U, Kalus U, Eils J, Brors B, Manke T, Ruland J, Lengauer T, Rajewsky N, Chen W, Dong J, Sawitzki B, Chung HR, Rosenstiel P, Schulz M, Schultze J, Radbruch A, Walter J, Hamann A, Polansky J. Epigenomic Profiling of Human CD4+ T Cells Supports a Linear Differentiation Model and Highlights Molecular Regulators of Memory Development. Immunity 2016; 45:1148-1161. [DOI: 10.1016/j.immuni.2016.10.022] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 06/22/2016] [Accepted: 07/22/2016] [Indexed: 12/21/2022]
|
236
|
Kramer A, Challen GA. The epigenetic basis of hematopoietic stem cell aging. Semin Hematol 2016; 54:19-24. [PMID: 28088983 DOI: 10.1053/j.seminhematol.2016.10.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 10/19/2016] [Accepted: 10/19/2016] [Indexed: 12/12/2022]
Abstract
Highly proliferative tissues such as the gut, skin, and bone marrow lose millions of cells each day to normal attrition and challenge from different biological adversities. To achieve a lifespan beyond the longevity of individual cell types, tissue-specific stem cells sustain these tissues throughout the life of a human. For example, the lifespan of erythrocytes is about 100 days and adults make about two million new erythrocytes every second. A small pool of hematopoietic stem cells (HSCs) in the bone marrow is responsible for the lifetime maintenance of these populations. However, there are changes that occur within the HSC pool during aging. Biologically, these changes manifest as blunted immune responses, decreased bone marrow cellularity, and increased risk of myeloid diseases. Understanding the molecular mechanisms underlying dysfunction of aging HSCs is an important focus of biomedical research. With advances in modern health care, the average age of the general population is ever increasing. If molecular or pharmacological interventions could be discovered that rejuvenate aging HSCs, it could reduce the burden of age related immune system compromise as well as open up new opportunities for treatment of hematological disorders with regenerative therapy.
Collapse
Affiliation(s)
- Ashley Kramer
- Section of Stem Cell Biology, Division of Oncology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO
| | - Grant A Challen
- Section of Stem Cell Biology, Division of Oncology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO; Developmental, Regenerative and Stem Cell Biology Program, Division of Biology and Biomedical Sciences, Washington University in St. Louis School of Medicine, St. Louis, MO.
| |
Collapse
|
237
|
Latchney SE, Calvi LM. The aging hematopoietic stem cell niche: Phenotypic and functional changes and mechanisms that contribute to hematopoietic aging. Semin Hematol 2016; 54:25-32. [PMID: 28088984 DOI: 10.1053/j.seminhematol.2016.10.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 10/13/2016] [Indexed: 11/11/2022]
Abstract
The hematopoietic system has the remarkable ability to provide a lifelong supply of mature cells that make up the entire blood and immune system. However, similar to other adult stem cell niches, the hematopoietic system is vulnerable to the detrimental effects of aging. This is a substantial health concern as the trend for population aging continues to increase. Identifying mechanisms that underlie hematopoietic aging is vital for understanding hematopoietic-related diseases. In this review, we first discuss the cellular hierarchy of the hematopoietic system and the components that make up the surrounding hematopoietic niche. We then provide an overview of the major phenotypes associated with hematopoietic aging and discuss recent research investigating cell-intrinsic and cell-extrinsic mechanisms of hematopoietic stem cell (HSCs) aging. We end by discussing the exciting new concept of possibly reversing the HSC aging process along with outstanding questions that remain to be answered.
Collapse
Affiliation(s)
- Sarah E Latchney
- Endocrine Metabolism Division, University of Rochester School of Medicine and Dentistry, Rochester NY
| | - Laura M Calvi
- Endocrine Metabolism Division, University of Rochester School of Medicine and Dentistry, Rochester NY; Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester NY.
| |
Collapse
|
238
|
Impact of combinatorial dysfunctions of Tet2 and Ezh2 on the epigenome in the pathogenesis of myelodysplastic syndrome. Leukemia 2016; 31:861-871. [DOI: 10.1038/leu.2016.268] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 08/31/2016] [Accepted: 09/06/2016] [Indexed: 12/11/2022]
|
239
|
Yang Z, Wong A, Kuh D, Paul DS, Rakyan VK, Leslie RD, Zheng SC, Widschwendter M, Beck S, Teschendorff AE. Correlation of an epigenetic mitotic clock with cancer risk. Genome Biol 2016; 17:205. [PMID: 27716309 PMCID: PMC5046977 DOI: 10.1186/s13059-016-1064-3] [Citation(s) in RCA: 178] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background Variation in cancer risk among somatic tissues has been attributed to variations in the underlying rate of stem cell division. For a given tissue type, variable cancer risk between individuals is thought to be influenced by extrinsic factors which modulate this rate of stem cell division. To date, no molecular mitotic clock has been developed to approximate the number of stem cell divisions in a tissue of an individual and which is correlated with cancer risk. Results Here, we integrate mathematical modeling with prior biological knowledge to construct a DNA methylation-based age-correlative model which approximates a mitotic clock in both normal and cancer tissue. By focusing on promoter CpG sites that localize to Polycomb group target genes that are unmethylated in 11 different fetal tissue types, we show that increases in DNA methylation at these sites defines a tick rate which correlates with the estimated rate of stem cell division in normal tissues. Using matched DNA methylation and RNA-seq data, we further show that it correlates with an expression-based mitotic index in cancer tissue. We demonstrate that this mitotic-like clock is universally accelerated in cancer, including pre-cancerous lesions, and that it is also accelerated in normal epithelial cells exposed to a major carcinogen. Conclusions Unlike other epigenetic and mutational clocks or the telomere clock, the epigenetic clock proposed here provides a concrete example of a mitotic-like clock which is universally accelerated in cancer and precancerous lesions. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1064-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Zhen Yang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, 320 Yue Yang Road, Shanghai, 200031, China
| | - Andrew Wong
- MRC Unit for Lifelong Health and Ageing at University College London, London, UK
| | - Diana Kuh
- MRC Unit for Lifelong Health and Ageing at University College London, London, UK
| | - Dirk S Paul
- Medical Genomics, UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK
| | - Vardhman K Rakyan
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK
| | - R David Leslie
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK
| | - Shijie C Zheng
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, 320 Yue Yang Road, Shanghai, 200031, China
| | - Martin Widschwendter
- Department of Women's Cancer, University College London, 74 Huntley Street, London, WC1E 6AU, UK
| | - Stephan Beck
- Medical Genomics, UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK
| | - Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, 320 Yue Yang Road, Shanghai, 200031, China. .,Department of Women's Cancer, University College London, 74 Huntley Street, London, WC1E 6AU, UK. .,Statistical Cancer Genomics, Paul O'Gorman Building, UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK.
| |
Collapse
|
240
|
Benetatos L, Vartholomatos G. On the potential role of DNMT1 in acute myeloid leukemia and myelodysplastic syndromes: not another mutated epigenetic driver. Ann Hematol 2016; 95:1571-82. [PMID: 26983918 DOI: 10.1007/s00277-016-2636-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 03/04/2016] [Indexed: 12/19/2022]
Abstract
DNA methylation is the most common epigenetic modification in the mammalian genome. DNA methylation is governed by the DNA methyltransferases mainly DNMT1, DNMT3A, and DNMT3B. DNMT1 methylates hemimethylated DNA ensuring accurate DNA methylation maintenance. DNMT1 is involved in the proper differentiation of hematopoietic stem cells (HSCs) through the interaction with effector molecules. DNMT1 is deregulated in acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS) as early as the leukemic stem cell stage. Through the interaction with fundamental transcription factors, non-coding RNAs, fusion oncogenes and by modulating core members of signaling pathways, it can affect leukemic cells biology. DNMT1 action might be also catalytic-independent highlighting a methylation-independent mode of action. In this review, we have gathered some current facts of DNMT1 role in AML and MDS and we also propose some perspectives for future studies.
Collapse
|
241
|
The dynamic changes of DNA methylation in primordial germ cell differentiation. Gene 2016; 591:305-12. [DOI: 10.1016/j.gene.2016.06.036] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 06/07/2016] [Accepted: 06/15/2016] [Indexed: 01/19/2023]
|
242
|
Madonna R, Novo G, Balistreri CR. Cellular and molecular basis of the imbalance between vascular damage and repair in ageing and age-related diseases: As biomarkers and targets for new treatments. Mech Ageing Dev 2016; 159:22-30. [DOI: 10.1016/j.mad.2016.03.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 03/07/2016] [Accepted: 03/12/2016] [Indexed: 12/24/2022]
|
243
|
Antenatal endogenous and exogenous glucocorticoids and their impact on immune ontogeny and long-term immunity. Semin Immunopathol 2016; 38:739-763. [DOI: 10.1007/s00281-016-0575-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 05/30/2016] [Indexed: 12/13/2022]
|
244
|
Buscarlet M, Tessier A, Provost S, Mollica L, Busque L. Human blood cell levels of 5-hydroxymethylcytosine (5hmC) decline with age, partly related to acquired mutations in TET2. Exp Hematol 2016; 44:1072-1084. [PMID: 27475703 DOI: 10.1016/j.exphem.2016.07.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 07/08/2016] [Accepted: 07/14/2016] [Indexed: 12/15/2022]
Abstract
Epigenetic alteration may play a role in age-associated dysfunction of stem cells and predispose to the development of hematological cancers. We analyzed global levels of hematopoietic 5-hydroxymethylcytosine (5hmC) and 5-methylcytosine (5mC) in a cross-sectional study comprising 198 unrelated individuals from four age categories (neonates, 25-30, 70-75, and >90 years old) by liquid chromatography-electrospray ionization-tandem mass spectrometry with multiple reaction monitoring. X-chromosome inactivation (XCI) ratios and telomere length (TL) were measured in all individuals by polymerase chain reaction. Sequencing of epigenetic regulator genes (including TET2, DNMT3A, ASXL1, IDH1, IDH2, and WT1) was performed in the two older subcohorts. We found that global 5hmC levels declined with age in human blood cells (27.5% reduction from birth to old age, p < 0.0005). The levels of 5mC underwent a more modest reduction (2.4% drop) between newborns and the elderly (p < 0.0005). Low 5hmC was associated with increased skewing of XCI (age-adjusted p = 0.0304) and reduced TL (age-adjusted p = 0.0354), both surrogate markers of clonal dominance. Of the 100 individuals over the age of 70, 16 had somatic mutations in TET2, 14 in DNMT3A, and none in IDH1, IDH2, or WT1. Individuals with TET2 mutations had significantly lower 5hmC (relative to unmutated individuals), whereas DNMT3A-mutated subjects did not. However, mutations in TET2 cannot account solely for the decline in 5hmC levels observed with aging because unmutated older individuals also had lower 5hmC levels compared with younger individuals. This suggests that the age-associated decline in 5hmC is multifactorial. Larger prospective studies are needed to determine whether 5hmC reduction is a biomarker of hematological cancer development.
Collapse
Affiliation(s)
| | - Alain Tessier
- Centre for Biological Applications of Mass Spectrometry, Department of Chemistry and Biochemistry, Concordia University, Montreal, Canada
| | - Sylvie Provost
- Beaulieu-Saucier Pharmacogenomics Centre, Montreal Heart Institute Research Centre, Montreal, Canada
| | - Luigina Mollica
- Research Centre, Montreal, Canada; Department of Hematology, Installation Hôpital Maisonneuve-Rosemont, Montreal, Canada; Université de Montréal, Montreal, Canada
| | - Lambert Busque
- Research Centre, Montreal, Canada; Department of Hematology, Installation Hôpital Maisonneuve-Rosemont, Montreal, Canada; Université de Montréal, Montreal, Canada.
| |
Collapse
|
245
|
Schultz MB, Sinclair DA. When stem cells grow old: phenotypes and mechanisms of stem cell aging. Development 2016; 143:3-14. [PMID: 26732838 DOI: 10.1242/dev.130633] [Citation(s) in RCA: 199] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
All multicellular organisms undergo a decline in tissue and organ function as they age. An attractive theory is that a loss in stem cell number and/or activity over time causes this decline. In accordance with this theory, aging phenotypes have been described for stem cells of multiple tissues, including those of the hematopoietic system, intestine, muscle, brain, skin and germline. Here, we discuss recent advances in our understanding of why adult stem cells age and how this aging impacts diseases and lifespan. With this increased understanding, it is feasible to design and test interventions that delay stem cell aging and improve both health and lifespan.
Collapse
Affiliation(s)
- Michael B Schultz
- Paul F. Glenn Center for the Biological Mechanisms of Aging, Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - David A Sinclair
- Paul F. Glenn Center for the Biological Mechanisms of Aging, Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
246
|
Chandel NS, Jasper H, Ho TT, Passegué E. Metabolic regulation of stem cell function in tissue homeostasis and organismal ageing. Nat Cell Biol 2016; 18:823-32. [PMID: 27428307 DOI: 10.1038/ncb3385] [Citation(s) in RCA: 208] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 06/08/2016] [Indexed: 12/11/2022]
Abstract
Many tissues and organ systems in metazoans have the intrinsic capacity to regenerate, which is driven and maintained largely by tissue-resident somatic stem cell populations. Ageing is accompanied by a deregulation of stem cell function and a decline in regenerative capacity, often resulting in degenerative diseases. The identification of strategies to maintain stem cell function and regulation is therefore a promising avenue to allay a wide range of age-related diseases. Studies in various organisms have revealed a central role for metabolic pathways in the regulation of stem cell function. Ageing is associated with extensive metabolic changes, and interventions that influence cellular metabolism have long been recognized as robust lifespan-extending measures. In this Review, we discuss recent advances in our understanding of the metabolic control of stem cell function, and how stem cell metabolism relates to homeostasis and ageing.
Collapse
Affiliation(s)
- Navdeep S Chandel
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611-2909, USA
| | - Heinrich Jasper
- The Buck Institute for Research on Aging, Novato, California 94945-1400, USA, and the Leibniz Institute on Aging-Fritz Lipmann Institute, Jena 07745, Germany
| | - Theodore T Ho
- Department of Medicine, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, California 94143-0667, USA
| | - Emmanuelle Passegué
- Department of Medicine, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, California 94143-0667, USA
| |
Collapse
|
247
|
Moehrle BM, Geiger H. Aging of hematopoietic stem cells: DNA damage and mutations? Exp Hematol 2016; 44:895-901. [PMID: 27402537 DOI: 10.1016/j.exphem.2016.06.253] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 06/27/2016] [Indexed: 12/15/2022]
Abstract
Aging in the hematopoietic system and the stem cell niche contributes to aging-associated phenotypes of hematopoietic stem cells (HSCs), including leukemia and aging-associated immune remodeling. Among others, the DNA damage theory of aging of HSCs is well established, based on the detection of a significantly larger amount of γH2AX foci and a higher tail moment in the comet assay, both initially thought to be associated with DNA damage in aged HSCs compared with young cells, and bone marrow failure in animals devoid of DNA repair factors. Novel data on the increase in and nature of DNA mutations in the hematopoietic system with age, the quality of the DNA damage response in aged HSCs, and the nature of γH2AX foci question a direct link between DNA damage and the DNA damage response and aging of HSCs, and rather favor changes in epigenetics, splicing-factors or three-dimensional architecture of the cell as major cell intrinsic factors of HSCs aging. Aging of HSCs is also driven by a strong contribution of aging of the niche. This review discusses the DNA damage theory of HSC aging in the light of these novel mechanisms of aging of HSCs.
Collapse
Affiliation(s)
| | - Hartmut Geiger
- Institute for Molecular Medicine, Ulm University, Ulm, Germany; Aging Research Center, Ulm University, Ulm, Germany; Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH.
| |
Collapse
|
248
|
Aging, Clonality, and Rejuvenation of Hematopoietic Stem Cells. Trends Mol Med 2016; 22:701-712. [PMID: 27380967 DOI: 10.1016/j.molmed.2016.06.003] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 06/02/2016] [Accepted: 06/07/2016] [Indexed: 01/12/2023]
Abstract
Aging is associated with reduced organ function and increased disease incidence. Hematopoietic stem cell (HSC) aging driven by both cell intrinsic and extrinsic factors is linked to impaired HSC self-renewal and regeneration, aging-associated immune remodeling, and increased leukemia incidence. Compromised DNA damage responses and the increased production of reactive oxygen species (ROS) have been previously causatively attributed to HSC aging. However, recent paradigm-shifting concepts, such as global epigenetic and cytoskeletal polarity shifts, cellular senescence, as well as the clonal selection of HSCs upon aging, provide new insights into HSC aging mechanisms. Rejuvenating agents that can reprogram the epigenetic status of aged HSCs or senolytic drugs that selectively deplete senescent cells provide promising translational avenues for attenuating hematopoietic aging and, potentially, alleviating aging-associated immune remodeling and myeloid malignancies.
Collapse
|
249
|
Abstract
Over the past decade, a growing number of studies have revealed that progressive changes to epigenetic information accompany aging in both dividing and nondividing cells. Functional studies in model organisms and humans indicate that epigenetic changes have a huge influence on the aging process. These epigenetic changes occur at various levels, including reduced bulk levels of the core histones, altered patterns of histone posttranslational modifications and DNA methylation, replacement of canonical histones with histone variants, and altered noncoding RNA expression, during both organismal aging and replicative senescence. The end result of epigenetic changes during aging is altered local accessibility to the genetic material, leading to aberrant gene expression, reactivation of transposable elements, and genomic instability. Strikingly, certain types of epigenetic information can function in a transgenerational manner to influence the life span of the offspring. Several important conclusions emerge from these studies: rather than being genetically predetermined, our life span is largely epigenetically determined; diet and other environmental influences can influence our life span by changing the epigenetic information; and inhibitors of epigenetic enzymes can influence life span of model organisms. These new findings provide better understanding of the mechanisms involved in aging. Given the reversible nature of epigenetic information, these studies highlight exciting avenues for therapeutic intervention in aging and age-associated diseases, including cancer.
Collapse
Affiliation(s)
- Sangita Pal
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
- Genes and Development Graduate Program, University of Texas Graduate School of the Biomedical Sciences at Houston, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jessica K. Tyler
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
- Corresponding author.
| |
Collapse
|
250
|
Rundberg Nilsson A, Soneji S, Adolfsson S, Bryder D, Pronk CJ. Human and Murine Hematopoietic Stem Cell Aging Is Associated with Functional Impairments and Intrinsic Megakaryocytic/Erythroid Bias. PLoS One 2016; 11:e0158369. [PMID: 27368054 PMCID: PMC4930192 DOI: 10.1371/journal.pone.0158369] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 06/14/2016] [Indexed: 02/02/2023] Open
Abstract
Aging within the human hematopoietic system associates with various deficiencies and disease states, including anemia, myeloid neoplasms and reduced adaptive immune responses. Similar phenotypes are observed in mice and have been linked to alterations arising at the hematopoietic stem cell (HSC) level. Such an association is, however, less established in human hematopoiesis and prompted us here to detail characteristics of the most primitive human hematopoietic compartments throughout ontogeny. In addition, we also attempted to interrogate similarities between aging human and murine hematopoiesis. Coupled to the transition from human cord blood (CB) to young and aged bone marrow (BM), we observed a gradual increase in frequency of candidate HSCs. This was accompanied by functional impairments, including decreased lymphoid output and reduced proliferative potential. Downstream of human HSCs, we observed decreasing levels of common lymphoid progenitors (CLPs), and increasing frequencies of megakaryocyte/erythrocyte progenitors (MEPs) with age, which could be linked to changes in lineage-affiliated gene expression patterns in aged human HSCs. These findings were paralleled in mice. Therefore, our data support the notion that age-related changes also in human hematopoiesis involve the HSC pool, with a prominent skewing towards the megakaryocytic/erythroid lineages, and suggests conserved mechanisms underlying aging of the blood cell system.
Collapse
Affiliation(s)
- Alexandra Rundberg Nilsson
- Medical Faculty, Division of Molecular Hematology, Institution for Laboratory Medicine, Lund University, Lund, Sweden
- Medical Faculty, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Shamit Soneji
- Medical Faculty, Division of Molecular Hematology, Institution for Laboratory Medicine, Lund University, Lund, Sweden
- Medical Faculty, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Sofia Adolfsson
- Medical Faculty, Division of Molecular Hematology, Institution for Laboratory Medicine, Lund University, Lund, Sweden
- Medical Faculty, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - David Bryder
- Medical Faculty, Division of Molecular Hematology, Institution for Laboratory Medicine, Lund University, Lund, Sweden
- Medical Faculty, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Cornelis Jan Pronk
- Medical Faculty, Division of Molecular Hematology, Institution for Laboratory Medicine, Lund University, Lund, Sweden
- Medical Faculty, Lund Stem Cell Center, Lund University, Lund, Sweden
- Department of Pediatric Oncology/Hematology, Skåne University Hospital, Lund, Sweden
- * E-mail:
| |
Collapse
|