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Allegra A, Caserta S, Mirabile G, Gangemi S. Aging and Age-Related Epigenetic Drift in the Pathogenesis of Leukemia and Lymphomas: New Therapeutic Targets. Cells 2023; 12:2392. [PMID: 37830606 PMCID: PMC10572300 DOI: 10.3390/cells12192392] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/24/2023] [Accepted: 09/28/2023] [Indexed: 10/14/2023] Open
Abstract
One of the traits of cancer cells is abnormal DNA methylation patterns. The idea that age-related epigenetic changes may partially explain the increased risk of cancer in the elderly is based on the observation that aging is also accompanied by comparable changes in epigenetic patterns. Lineage bias and decreased stem cell function are signs of hematopoietic stem cell compartment aging. Additionally, aging in the hematopoietic system and the stem cell niche have a role in hematopoietic stem cell phenotypes linked with age, such as leukemia and lymphoma. Understanding these changes will open up promising pathways for therapies against age-related disorders because epigenetic mechanisms are reversible. Additionally, the development of high-throughput epigenome mapping technologies will make it possible to identify the "epigenomic identity card" of every hematological disease as well as every patient, opening up the possibility of finding novel molecular biomarkers that can be used for diagnosis, prediction, and prognosis.
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Affiliation(s)
- Alessandro Allegra
- Division of Hematology, Department of Human Pathology in Adulthood and Childhood “Gaetano Barresi”, University of Messina, Via Consolare Valeria, 98125 Messina, Italy; (S.C.); (G.M.)
| | - Santino Caserta
- Division of Hematology, Department of Human Pathology in Adulthood and Childhood “Gaetano Barresi”, University of Messina, Via Consolare Valeria, 98125 Messina, Italy; (S.C.); (G.M.)
| | - Giuseppe Mirabile
- Division of Hematology, Department of Human Pathology in Adulthood and Childhood “Gaetano Barresi”, University of Messina, Via Consolare Valeria, 98125 Messina, Italy; (S.C.); (G.M.)
| | - Sebastiano Gangemi
- Allergy and Clinical Immunology Unit, Department of Clinical and Experimental Medicine, University of Messina, Via Consolare Valeria, 98125 Messina, Italy;
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2
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Xu Y, Zhang Z, Zhao Y, Zhao C, Shi M, Dong X, Zhang J, Tan L, Zhang L, Zhao Y. TRAPPC1 is essential for the maintenance and differentiation of common myeloid progenitors in mice. EMBO Rep 2023; 24:e55503. [PMID: 36440617 PMCID: PMC9900341 DOI: 10.15252/embr.202255503] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 11/14/2022] [Accepted: 11/17/2022] [Indexed: 11/29/2022] Open
Abstract
Myeloid cell development in bone marrow is essential for the maintenance of peripheral immune homeostasis. However, the role of intracellular protein trafficking pathways during myeloid cell differentiation is currently unknown. By mining bioinformatics data, we identify trafficking protein particle complex subunit 1 (TRAPPC1) as continuously upregulated during myeloid cell development. Using inducible ER-TRAPPC1 knockout mice and bone marrow chimeric mouse models, we demonstrate that TRAPPC1 deficiency causes severe monocyte and neutrophil defects, accompanied by a selective decrease in common myeloid progenitors (CMPs) and subsequent cell subsets in bone marrow. TRAPPC1-deleted CMPs differentiate poorly into monocytes and neutrophils in vivo and in vitro, in addition to exhibiting enhanced endoplasmic reticulum stress and apoptosis via a Ca2+ -mitochondria-dependent pathway. Cell cycle arrest and senescence of TRAPPC1-deleted CMPs are mediated by the activation of pancreatic endoplasmic reticulum kinase and the upregulation of cyclin-dependent kinase inhibitor p21. This study reveals the essential role of TRAPPC1 in the maintenance and differentiation of CMPs and highlights the significance of protein processing and trafficking processes in myeloid cell development.
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Affiliation(s)
- Yanan Xu
- State Key Laboratory of Membrane BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
| | - Zhaoqi Zhang
- State Key Laboratory of Membrane BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Cunji Medical SchoolUniversity of Chinese Academy of SciencesBeijingChina
| | - Yang Zhao
- State Key Laboratory of Membrane BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
| | - Chenxu Zhao
- State Key Laboratory of Membrane BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Cunji Medical SchoolUniversity of Chinese Academy of SciencesBeijingChina
| | - Mingpu Shi
- State Key Laboratory of Membrane BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Cunji Medical SchoolUniversity of Chinese Academy of SciencesBeijingChina
| | - Xue Dong
- State Key Laboratory of Membrane BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Cunji Medical SchoolUniversity of Chinese Academy of SciencesBeijingChina
| | - Jiayu Zhang
- State Key Laboratory of Membrane BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Cunji Medical SchoolUniversity of Chinese Academy of SciencesBeijingChina
| | - Liang Tan
- Kidney Transplantation DepartmentSecond Xiangya Hospital of Central South UniversityChangshaChina
| | - Lianfeng Zhang
- Key Laboratory of Human Diseases Comparative Medicine, Ministry of Health, Institute of Laboratory Animal ScienceChinese Academy of Medical Sciences, Peking Union Medical CollegeBeijingChina
| | - Yong Zhao
- State Key Laboratory of Membrane BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Cunji Medical SchoolUniversity of Chinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
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3
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Ziarniak K, Yang T, Boycott C, Beetch M, Sassek M, Grzeda E, Ma Y, Sliwowska JH, Stefanska B. DNA hypermethylation of Kiss1r promoter and reduction of hepatic Kiss1r in female rats with type 2 diabetes. Epigenetics 2022; 17:2332-2346. [PMID: 36094166 PMCID: PMC9665141 DOI: 10.1080/15592294.2022.2119120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Kisspeptin, produced from the brain and peripheral tissues, may constitute an important link in metabolic regulation in response to external cues, such as diet. The kisspeptin system is well described in the brain. However, its function and regulation in the peripheral tissues, especially in relation to metabolic disease and sex differences, remain to be elucidated. As Kiss1 and Kiss1r, encoding for kisspeptin and kisspeptin receptors, respectively, are altered by overnutrition/fasting and regulated by DNA methylation during puberty and cancer, epigenetic mechanisms in metabolic disorders are highly probable. In the present study, we experimentally induced type 2 diabetes mellitus (DM2) in female Wistar rats using high-fat diet/streptozocin. We analysed expression and DNA methylation of Kiss1 and Kiss1r in the peripheral tissues, using quantitative-reverse-transcription PCR (qRT-PCR) and pyrosequencing. We discovered differential expression of Kiss1 and Kiss1r in peripheral organs in DM2 females, as compared with healthy controls, and the profile differed from patterns reported earlier in males. DM2 in females was linked to the increased Kiss1 mRNA in the liver and increased Kiss1r mRNA in the liver and adipose tissue. However, Kiss1r promoter was hypermethylated in the liver, suggesting gene silencing. Indeed, the increase in DNA methylation of Kiss1r promoter was accompanied by a reduction in Kiss1r protein, implying epigenetic or translational gene repression. Our results deliver novel evidence for tissue-specific differences in Kiss1 and Kiss1r expression in peripheral organs in DM2 females and suggest DNA methylation as a player in regulation of the hepatic kisspeptin system in DM2.
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Affiliation(s)
- Kamil Ziarniak
- Laboratory of Neurobiology, Department of Zoology, Faculty of Veterinary Medicine and Animal Sciences, Poznan University of Life Sciences, Poznan, Poland.,Molecular and Cell Biology Unit, Poznan University of Medical Sciences, Poznan, Poland
| | - Tony Yang
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, the University of British Columbia, Vancouver, BC, Canada
| | - Cayla Boycott
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, the University of British Columbia, Vancouver, BC, Canada
| | - Megan Beetch
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, the University of British Columbia, Vancouver, BC, Canada
| | - Maciej Sassek
- Department of Animal Physiology, Biochemistry and Biostructure, Poznan University of Life Sciences, Poznan, Poland
| | - Emilia Grzeda
- Laboratory of Neurobiology, Department of Zoology, Faculty of Veterinary Medicine and Animal Sciences, Poznan University of Life Sciences, Poznan, Poland
| | - Yuexi Ma
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, the University of British Columbia, Vancouver, BC, Canada
| | - Joanna H Sliwowska
- Laboratory of Neurobiology, Department of Zoology, Faculty of Veterinary Medicine and Animal Sciences, Poznan University of Life Sciences, Poznan, Poland
| | - Barbara Stefanska
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, the University of British Columbia, Vancouver, BC, Canada
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4
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Chondronasiou D, Gill D, Mosteiro L, Urdinguio RG, Berenguer‐Llergo A, Aguilera M, Durand S, Aprahamian F, Nirmalathasan N, Abad M, Martin‐Herranz DE, Stephan‐Otto Attolini C, Prats N, Kroemer G, Fraga MF, Reik W, Serrano M. Multi-omic rejuvenation of naturally aged tissues by a single cycle of transient reprogramming. Aging Cell 2022; 21:e13578. [PMID: 35235716 PMCID: PMC8920440 DOI: 10.1111/acel.13578] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 12/01/2022] Open
Abstract
The expression of the pluripotency factors OCT4, SOX2, KLF4, and MYC (OSKM) can convert somatic differentiated cells into pluripotent stem cells in a process known as reprogramming. Notably, partial and reversible reprogramming does not change cell identity but can reverse markers of aging in cells, improve the capacity of aged mice to repair tissue injuries, and extend longevity in progeroid mice. However, little is known about the mechanisms involved. Here, we have studied changes in the DNA methylome, transcriptome, and metabolome in naturally aged mice subject to a single period of transient OSKM expression. We found that this is sufficient to reverse DNA methylation changes that occur upon aging in the pancreas, liver, spleen, and blood. Similarly, we observed reversion of transcriptional changes, especially regarding biological processes known to change during aging. Finally, some serum metabolites and biomarkers altered with aging were also restored to young levels upon transient reprogramming. These observations indicate that a single period of OSKM expression can drive epigenetic, transcriptomic, and metabolomic changes toward a younger configuration in multiple tissues and in the serum.
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Affiliation(s)
- Dafni Chondronasiou
- Institute for Research in Biomedicine (IRB Barcelona)Barcelona Institute of Science and Technology (BIST)BarcelonaSpain
| | - Diljeet Gill
- Epigenetics ProgrammeBabraham InstituteCambridgeUK
| | | | - Rocio G. Urdinguio
- Cancer Epigenetics and Nanomedicine LaboratoryNanomaterials and Nanotechnology Research Center (CINN CSIC)OviedoSpain
- Health Research Institute of Asturias (ISPA)OviedoSpain
- Institute of Oncology of Asturias (IUOPA)University of OviedoOviedoSpain
- Department of Organisms and Systems Biology (BOS)University of OviedoOviedoSpain
- CIBER of Rare Diseases (CIBERER)OviedoSpain
| | - Antonio Berenguer‐Llergo
- Institute for Research in Biomedicine (IRB Barcelona)Barcelona Institute of Science and Technology (BIST)BarcelonaSpain
| | - Mònica Aguilera
- Institute for Research in Biomedicine (IRB Barcelona)Barcelona Institute of Science and Technology (BIST)BarcelonaSpain
| | - Sylvere Durand
- Metabolomics and Cell Biology PlatformsInstitut Gustave RoussyVillejuifFrance
- Centre de Recherche des CordeliersEquipe Labellisée par la Ligue Contre le CancerUniversité de ParisSorbonne UniversitéParisFrance
- Inserm U1138Institut Universitaire de FranceParisFrance
| | - Fanny Aprahamian
- Metabolomics and Cell Biology PlatformsInstitut Gustave RoussyVillejuifFrance
- Centre de Recherche des CordeliersEquipe Labellisée par la Ligue Contre le CancerUniversité de ParisSorbonne UniversitéParisFrance
- Inserm U1138Institut Universitaire de FranceParisFrance
| | - Nitharsshini Nirmalathasan
- Metabolomics and Cell Biology PlatformsInstitut Gustave RoussyVillejuifFrance
- Centre de Recherche des CordeliersEquipe Labellisée par la Ligue Contre le CancerUniversité de ParisSorbonne UniversitéParisFrance
- Inserm U1138Institut Universitaire de FranceParisFrance
| | - Maria Abad
- Vall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
| | | | - Camille Stephan‐Otto Attolini
- Institute for Research in Biomedicine (IRB Barcelona)Barcelona Institute of Science and Technology (BIST)BarcelonaSpain
| | - Neus Prats
- Institute for Research in Biomedicine (IRB Barcelona)Barcelona Institute of Science and Technology (BIST)BarcelonaSpain
| | - Guido Kroemer
- Metabolomics and Cell Biology PlatformsInstitut Gustave RoussyVillejuifFrance
- Centre de Recherche des CordeliersEquipe Labellisée par la Ligue Contre le CancerUniversité de ParisSorbonne UniversitéParisFrance
- Inserm U1138Institut Universitaire de FranceParisFrance
- Pôle de BiologieHôpital Européen Georges PompidouAP‐HPParisFrance
- Suzhou Institute for Systems MedicineChinese Academy of Medical SciencesSuzhouChina
- Department of Women's and Children's HealthKarolinska InstituteKarolinska University HospitalStockholmSweden
| | - Mario F. Fraga
- Cancer Epigenetics and Nanomedicine LaboratoryNanomaterials and Nanotechnology Research Center (CINN CSIC)OviedoSpain
- Health Research Institute of Asturias (ISPA)OviedoSpain
- Institute of Oncology of Asturias (IUOPA)University of OviedoOviedoSpain
- Department of Organisms and Systems Biology (BOS)University of OviedoOviedoSpain
- CIBER of Rare Diseases (CIBERER)OviedoSpain
| | - Wolf Reik
- Epigenetics ProgrammeBabraham InstituteCambridgeUK
- Centre for Trophoblast ResearchUniversity of CambridgeCambridgeUK
- Wellcome Trust Sanger InstituteCambridgeUK
- Altos Labs Cambridge InstituteCambridgeUK
| | - Manuel Serrano
- Institute for Research in Biomedicine (IRB Barcelona)Barcelona Institute of Science and Technology (BIST)BarcelonaSpain
- Catalan Institution for Research and Advanced Studies (ICREA)BarcelonaSpain
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5
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Immune Memory in Aging: a Wide Perspective Covering Microbiota, Brain, Metabolism, and Epigenetics. Clin Rev Allergy Immunol 2021; 63:499-529. [PMID: 34910283 PMCID: PMC8671603 DOI: 10.1007/s12016-021-08905-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2021] [Indexed: 11/06/2022]
Abstract
Non-specific innate and antigen-specific adaptive immunological memories are vital evolutionary adaptations that confer long-lasting protection against a wide range of pathogens. Adaptive memory is established by memory T and B lymphocytes following the recognition of an antigen. On the other hand, innate immune memory, also called trained immunity, is imprinted in innate cells such as macrophages and natural killer cells through epigenetic and metabolic reprogramming. However, these mechanisms of memory generation and maintenance are compromised as organisms age. Almost all immune cell types, both mature cells and their progenitors, go through age-related changes concerning numbers and functions. The aging immune system renders the elderly highly susceptible to infections and incapable of mounting a proper immune response upon vaccinations. Besides the increased infectious burden, older individuals also have heightened risks of metabolic and neurodegenerative diseases, which have an immunological component. This review discusses how immune function, particularly the establishment and maintenance of innate and adaptive immunological memory, regulates and is regulated by epigenetics, metabolic processes, gut microbiota, and the central nervous system throughout life, with a focus on old age. We explain in-depth how epigenetics and cellular metabolism impact immune cell function and contribute or resist the aging process. Microbiota is intimately linked with the immune system of the human host, and therefore, plays an important role in immunological memory during both homeostasis and aging. The brain, which is not an immune-isolated organ despite former opinion, interacts with the peripheral immune cells, and the aging of both systems influences the health of each other. With all these in mind, we aimed to present a comprehensive view of the aging immune system and its consequences, especially in terms of immunological memory. The review also details the mechanisms of promising anti-aging interventions and highlights a few, namely, caloric restriction, physical exercise, metformin, and resveratrol, that impact multiple facets of the aging process, including the regulation of innate and adaptive immune memory. We propose that understanding aging as a complex phenomenon, with the immune system at the center role interacting with all the other tissues and systems, would allow for more effective anti-aging strategies.
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6
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Randhawa V, Kumar M. An integrated network analysis approach to identify potential key genes, transcription factors, and microRNAs regulating human hematopoietic stem cell aging. Mol Omics 2021; 17:967-984. [PMID: 34605522 DOI: 10.1039/d1mo00199j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hematopoietic stem cells (HSCs) undergo functional deterioration with increasing age that causes loss of their self-renewal and regenerative potential. Despite various efforts, significant success in identifying molecular regulators of HSC aging has not been achieved, one prime reason being the non-availability of appropriate human HSC samples. To demonstrate the scope of integrating and re-analyzing the HSC transcriptomics data available, we used existing tools and databases to structure a sequential data analysis pipeline to predict potential candidate genes, transcription factors, and microRNAs simultaneously. This sequential approach comprises (i) collecting matched young and aged mice HSC sample datasets, (ii) identifying differentially expressed genes, (iii) identifying human homologs of differentially expressed genes, (iv) inferring gene co-expression network modules, and (v) inferring the microRNA-transcription factor-gene regulatory network. Systems-level analyses of HSC interaction networks provided various insights based on which several candidates were predicted. For example, 16 HSC aging-related candidate genes were predicted (e.g., CD38, BRCA1, AGTR1, GSTM1, etc.) from GCN analysis. Following this, the shortest path distance-based analyses of the regulatory network predicted several novel candidate miRNAs and TFs. Among these, miR-124-3p was a common regulator in candidate gene modules, while TFs MYC and SP1 were identified to regulate various candidate genes. Based on the regulatory interactions among candidate genes, TFs, and miRNAs, a potential regulation model of biological processes in each of the candidate modules was predicted, which provided systems-level insights into the molecular complexity of each module to regulate HSC aging.
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Affiliation(s)
- Vinay Randhawa
- Virology Unit and Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific & Industrial Research, Chandigarh-160036, India.
| | - Manoj Kumar
- Virology Unit and Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific & Industrial Research, Chandigarh-160036, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
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7
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Borgoni S, Kudryashova KS, Burka K, de Magalhães JP. Targeting immune dysfunction in aging. Ageing Res Rev 2021; 70:101410. [PMID: 34280555 DOI: 10.1016/j.arr.2021.101410] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/28/2021] [Accepted: 07/14/2021] [Indexed: 12/23/2022]
Abstract
Human aging is a multifactorial phenomenon that affects numerous organ systems and cellular processes, with the immune system being one of the most dysregulated. Immunosenescence, the gradual deterioration of the immune system, and inflammaging, a chronic inflammatory state that persists in the elderly, are among the plethora of immune changes that occur during aging. Almost all populations of immune cells change with age in terms of numbers and/or activity. These alterations are in general highly detrimental, resulting in an increased susceptibility to infections, reduced healing abilities, and altered homeostasis that promote the emergence of age-associated diseases such as cancer, diabetes, and other diseases associated with inflammation. Thanks to recent developments, several strategies have been proposed to target central immunological processes or specific immune subpopulations affected by aging. These therapeutic approaches could soon be applied in the clinic to slow down or even reverse specific age-induced immune changes in order to rejuvenate the immune system and prevent or reduce the impact of various diseases. Due to its systemic nature and interconnection with all the other systems in the body, the immune system is an attractive target for aging intervention because relatively targeted modifications to a small set of cells have the potential to improve the health of multiple organ systems. Therefore, anti-aging immune targeting therapies could represent a potent approach for improving healthspan. Here, we review aging changes in the major components of the immune system, we summarize the current immune-targeting therapeutic approaches in the context of aging and discuss the future directions in the field of immune rejuvenation.
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8
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Keenan CR. Heterochromatin and Polycomb as regulators of haematopoiesis. Biochem Soc Trans 2021; 49:805-814. [PMID: 33929498 PMCID: PMC8106494 DOI: 10.1042/bst20200737] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 12/23/2022]
Abstract
Haematopoiesis is the process by which multipotent haematopoietic stem cells are transformed into each and every type of terminally differentiated blood cell. Epigenetic silencing is critical for this process by regulating the transcription of cell-cycle genes critical for self-renewal and differentiation, as well as restricting alternative fate genes to allow lineage commitment and appropriate differentiation. There are two distinct forms of transcriptionally repressed chromatin: H3K9me3-marked heterochromatin and H3K27me3/H2AK119ub1-marked Polycomb (often referred to as facultative heterochromatin). This review will discuss the role of these distinct epigenetic silencing mechanisms in regulating normal haematopoiesis, how these contribute to age-related haematopoietic dysfunction, and the rationale for therapeutic targeting of these pathways in the treatment of haematological malignancies.
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Affiliation(s)
- Christine R. Keenan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
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9
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A comprehensive transcriptome signature of murine hematopoietic stem cell aging. Blood 2021; 138:439-451. [PMID: 33876187 DOI: 10.1182/blood.2020009729] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 04/02/2021] [Indexed: 01/11/2023] Open
Abstract
We surveyed 16 published and unpublished data sets to determine whether a consistent pattern of transcriptional deregulation in aging murine hematopoietic stem cells (HSC) exists. Despite substantial heterogeneity between individual studies, we uncovered a core and robust HSC aging signature. We detected increased transcriptional activation in aged HSCs, further confirmed by chromatin accessibility analysis. Unexpectedly, using two independent computational approaches, we established that deregulated aging genes consist largely of membrane-associated transcripts, including many cell surface molecules previously not associated with HSC biology. We show that Selp, the most consistent deregulated gene, is not merely a marker for aged HSCs but is associated with HSC functional decline. Additionally, single-cell transcriptomics analysis revealed increased heterogeneity of the aged HSC pool. We identify the presence of transcriptionally "young-like" HSCs in aged bone marrow. We share our results as an online resource and demonstrate its utility by confirming that exposure to sympathomimetics, and deletion of Dnmt3a/b, molecularly resembles HSC rejuvenation or aging, respectively.
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10
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Grigoryan A, Pospiech J, Krämer S, Lipka D, Liehr T, Geiger H, Kimura H, Mulaw MA, Florian MC. Attrition of X Chromosome Inactivation in Aged Hematopoietic Stem Cells. Stem Cell Reports 2021; 16:708-716. [PMID: 33798450 PMCID: PMC8072063 DOI: 10.1016/j.stemcr.2021.03.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 01/03/2023] Open
Abstract
During X chromosome inactivation (XCI), the inactive X chromosome (Xi) is recruited to the nuclear lamina at the nuclear periphery. Beside X chromosome reactivation resulting in a highly penetrant aging-like hematopoietic malignancy, little is known about XCI in aged hematopoietic stem cells (HSCs). Here, we demonstrate that LaminA/C defines a distinct repressive nuclear compartment for XCI in young HSCs, and its reduction in aged HSCs correlates with an impairment in the overall control of XCI. Integrated omics analyses reveal higher variation in gene expression, global hypomethylation, and significantly increased chromatin accessibility on the X chromosome (Chr X) in aged HSCs. In summary, our data support the role of LaminA/C in the establishment of a special repressive compartment for XCI in HSCs, which is impaired upon aging.
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Affiliation(s)
- Ani Grigoryan
- Institute of Molecular Medicine and Stem Cell Aging, University of Ulm, Albert-Einstein-Allee 11c, 89081 Ulm, Germany
| | - Johannes Pospiech
- Institute of Molecular Medicine and Stem Cell Aging, University of Ulm, Albert-Einstein-Allee 11c, 89081 Ulm, Germany
| | - Stephen Krämer
- Section Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) & National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany; Bioinformatics and Omics Data Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany; Faculty of Biosciences, University of Heidelberg, Heidelberg, Germany; Biomedical Informatics, Data Mining and Data Analytics, Faculty of Applied Computer Science and Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Daniel Lipka
- Section Translational Cancer Epigenomics, Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) & National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Am Klinikum 1, 07747 Jena, Germany
| | - Hartmut Geiger
- Institute of Molecular Medicine and Stem Cell Aging, University of Ulm, Albert-Einstein-Allee 11c, 89081 Ulm, Germany
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Medhanie A Mulaw
- Institute of Molecular Medicine and Stem Cell Aging, University of Ulm, Albert-Einstein-Allee 11c, 89081 Ulm, Germany; Department of Internal Medicine I, University Hospital Ulm, Ulm, Germany.
| | - Maria Carolina Florian
- Institute of Molecular Medicine and Stem Cell Aging, University of Ulm, Albert-Einstein-Allee 11c, 89081 Ulm, Germany; Stem Cell Aging Group, Regenerative Medicine Program, Bellvitge Institute for Biomedical Research (IDIBELL) and Program for advancing the Clinical Translation of Regenerative Medicine of Catalonia, P-CMR[C], Av. Gran Via 199-203, 08908, L'Hospitalet de Llobregat, Barcelona, Spain; Center for Networked Biomedical Research on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain.
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11
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Zhang L, Mack R, Breslin P, Zhang J. Molecular and cellular mechanisms of aging in hematopoietic stem cells and their niches. J Hematol Oncol 2020; 13:157. [PMID: 33228751 PMCID: PMC7686726 DOI: 10.1186/s13045-020-00994-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 11/09/2020] [Indexed: 02/08/2023] Open
Abstract
Aging drives the genetic and epigenetic changes that result in a decline in hematopoietic stem cell (HSC) functioning. Such changes lead to aging-related hematopoietic/immune impairments and hematopoietic disorders. Understanding how such changes are initiated and how they progress will help in the development of medications that could improve the quality life for the elderly and to treat and possibly prevent aging-related hematopoietic diseases. Here, we review the most recent advances in research into HSC aging and discuss the role of HSC-intrinsic events, as well as those that relate to the aging bone marrow niche microenvironment in the overall processes of HSC aging. In addition, we discuss the potential mechanisms by which HSC aging is regulated.
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Affiliation(s)
- Lei Zhang
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, IL, 60153, USA
| | - Ryan Mack
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, IL, 60153, USA
| | - Peter Breslin
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, IL, 60153, USA.,Departments of Molecular/Cellular Physiology and Department of Biology, Loyola University Medical Center and Loyola University Chicago, Chicago, IL, 60660, USA
| | - Jiwang Zhang
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, IL, 60153, USA. .,Department of Pathology, Loyola University Medical Center, Maywood, IL, 60153, USA.
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12
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Raj K, Horvath S. Current perspectives on the cellular and molecular features of epigenetic ageing. Exp Biol Med (Maywood) 2020; 245:1532-1542. [PMID: 32276545 DOI: 10.1177/1535370220918329] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
IMPACT STATEMENT The field of epigenetic ageing is relatively new, and the speed of its expansion presents a challenge in keeping abreast with new discoveries and their implications. Several reviews have already addressed the great number of pathologies, health conditions, life-style, and external stressors that are associated with changes to the rate of epigenetic ageing. While these associations highlight and affirm the ability of epigenetic clock to capture biologically meaningful changes associated with age, they do not inform us about the underlying mechanisms. In this very early period since the development of the clock, there have been rather limited experimental research that are aimed at uncovering the mechanism. Hence, the perspective that we proffer is derived from available but nevertheless limited lines of evidence that together provide a seemingly coherent narrative that can be tested. This, we believe would be helpful towards uncovering the workings of the epigenetic clock.
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Affiliation(s)
- Kenneth Raj
- Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, Didcot, Oxfordshire OX11 0RQ, UK
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, CA 90095, USA and Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, CA 90095, USA
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13
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Mejia-Ramirez E, Florian MC. Understanding intrinsic hematopoietic stem cell aging. Haematologica 2019; 105:22-37. [PMID: 31806687 PMCID: PMC6939535 DOI: 10.3324/haematol.2018.211342] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 11/14/2019] [Indexed: 01/03/2023] Open
Abstract
Hematopoietic stem cells (HSC) sustain blood production over the entire life-span of an organism. It is of extreme importance that these cells maintain self-renewal and differentiation potential over time in order to preserve homeostasis of the hematopoietic system. Many of the intrinsic aspects of HSC are affected by the aging process resulting in a deterioration in their potential, independently of their microenvironment. Here we review recent findings characterizing most of the intrinsic aspects of aged HSC, ranging from phenotypic to molecular alterations. Historically, DNA damage was thought to be the main cause of HSC aging. However, over recent years, many new findings have defined an increasing number of biological processes that intrinsically change with age in HSC. Epigenetics and chromatin architecture, together with autophagy, proteostasis and metabolic changes, and how they are interconnected, are acquiring growing importance for understanding the intrinsic aging of stem cells. Given the increase in populations of older subjects worldwide, and considering that aging is the primary risk factor for most diseases, understanding HSC aging becomes particularly relevant also in the context of hematologic disorders, such as myelodysplastic syndromes and acute myeloid leukemia. Research on intrinsic mechanisms responsible for HSC aging is providing, and will continue to provide, new potential molecular targets to possibly ameliorate or delay aging of the hematopoietic system and consequently improve the outcome of hematologic disorders in the elderly. The niche-dependent contributions to hematopoietic aging are discussed in another review in this same issue of the Journal.
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Affiliation(s)
- Eva Mejia-Ramirez
- Center for Regenerative Medicine in Barcelona (CMRB), Bellvitge Institute for Biomedical Research (IDIBELL), Barcelona, Spain.,Center for Networked Biomedical Research on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, 28029, Spain
| | - Maria Carolina Florian
- Center for Regenerative Medicine in Barcelona (CMRB), Bellvitge Institute for Biomedical Research (IDIBELL), Barcelona, Spain .,Institute of Molecular Medicine and Stem Cell Aging, Ulm University, Ulm, Germany EM-R and MCF contributed equally to this work
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14
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Keenan CR, Allan RS. Epigenomic drivers of immune dysfunction in aging. Aging Cell 2019; 18:e12878. [PMID: 30488545 PMCID: PMC6351880 DOI: 10.1111/acel.12878] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 09/26/2018] [Accepted: 10/18/2018] [Indexed: 12/17/2022] Open
Abstract
Aging inevitably leads to reduced immune function, leaving the elderly more susceptible to infections, less able to respond to pathogen challenges, and less responsive to preventative vaccinations. No cell type is exempt from the ravages of age, and extensive studies have found age-related alterations in the frequencies and functions of both stem and progenitor cells, as well as effector cells of both the innate and adaptive immune systems. The intrinsic functional reduction in immune competence is also associated with low-grade chronic inflammation, termed "inflamm-aging," which further perpetuates immune dysfunction. While many of these age-related cellular changes are well characterized, understanding the molecular changes that underpin the functional decline has proven more difficult. Changes in chromatin are increasingly appreciated as a causative mechanism of cellular and organismal aging across species. These changes include increased genomic instability through loss of heterochromatin and increased DNA damage, telomere attrition, and epigenetic alterations. In this review, we discuss the connections between chromatin, immunocompetence, and the loss of function associated with mammalian immune aging. Through understanding the molecular events which underpin the phenotypic changes observed in the aged immune system, it is hoped that the aged immune system can be restored to provide youthful immunity once more.
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Affiliation(s)
- Christine R. Keenan
- The Walter and Eliza Hall Institute of Medical Research Parkville Victoria Australia
- Department of Medical Biology The University of Melbourne Parkville Victoria Australia
| | - Rhys S. Allan
- The Walter and Eliza Hall Institute of Medical Research Parkville Victoria Australia
- Department of Medical Biology The University of Melbourne Parkville Victoria Australia
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15
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Cakouros D, Gronthos S. Epigenetic Regulation of Bone Marrow Stem Cell Aging: Revealing Epigenetic Signatures associated with Hematopoietic and Mesenchymal Stem Cell Aging. Aging Dis 2019; 10:174-189. [PMID: 30705777 PMCID: PMC6345334 DOI: 10.14336/ad.2017.1213] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 12/13/2017] [Indexed: 12/18/2022] Open
Abstract
In this review we explore the importance of epigenetics as a contributing factor for aging adult stem cells. We summarize the latest findings of epigenetic factors deregulated as adult stem cells age and the consequence on stem cell self-renewal and differentiation, with a focus on adult stem cells in the bone marrow. With the latest whole genome bisulphite sequencing and chromatin immunoprecipitations we are able to decipher an emerging pattern common for adult stem cells in the bone marrow niche and how this might correlate to epigenetic enzymes deregulated during aging. We begin by briefly discussing the initial observations in yeast, drosophila and Caenorhabditis elegans (C. elegans) that led to the breakthrough research that identified the role of epigenetic changes associated with lifespan and aging. We then focus on adult stem cells, specifically in the bone marrow, which lends strong support for the deregulation of DNA methyltransferases, histone deacetylases, acetylates, methyltransferases and demethylases in aging stem cells, and how their corresponding epigenetic modifications influence gene expression and the aging phenotype. Given the reversible nature of epigenetic modifications we envisage “epi” targeted therapy as a means to reprogram aged stem cells into their younger counterparts.
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Affiliation(s)
- Dimitrios Cakouros
- 1Mesenchymal Stem Cell Laboratory, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia.,2South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Stan Gronthos
- 1Mesenchymal Stem Cell Laboratory, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia.,2South Australian Health and Medical Research Institute, Adelaide, SA, Australia
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16
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Epigenetic alterations in longevity regulators, reduced life span, and exacerbated aging-related pathology in old father offspring mice. Proc Natl Acad Sci U S A 2018; 115:E2348-E2357. [PMID: 29467291 PMCID: PMC5877957 DOI: 10.1073/pnas.1707337115] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Advanced age is not only a major risk factor for a range of disorders within an aging individual but may also enhance susceptibility for disease in the next generation. In humans, advanced paternal age has been associated with increased risk for a number of diseases. Experiments in rodent models have provided initial evidence that paternal age can influence behavioral traits in offspring animals, but the overall scope and extent of paternal age effects on health and disease across the life span remain underexplored. Here, we report that old father offspring mice showed a reduced life span and an exacerbated development of aging traits compared with young father offspring mice. Genome-wide epigenetic analyses of sperm from aging males and old father offspring tissue identified differentially methylated promoters, enriched for genes involved in the regulation of evolutionarily conserved longevity pathways. Gene expression analyses, biochemical experiments, and functional studies revealed evidence for an overactive mTORC1 signaling pathway in old father offspring mice. Pharmacological mTOR inhibition during the course of normal aging ameliorated many of the aging traits that were exacerbated in old father offspring mice. These findings raise the possibility that inherited alterations in longevity pathways contribute to intergenerational effects of aging in old father offspring mice.
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17
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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.
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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.
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18
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Petkovich DA, Podolskiy DI, Lobanov AV, Lee SG, Miller RA, Gladyshev VN. Using DNA Methylation Profiling to Evaluate Biological Age and Longevity Interventions. Cell Metab 2017; 25:954-960.e6. [PMID: 28380383 PMCID: PMC5578459 DOI: 10.1016/j.cmet.2017.03.016] [Citation(s) in RCA: 223] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 01/09/2017] [Accepted: 03/21/2017] [Indexed: 12/31/2022]
Abstract
The DNA methylation levels of certain CpG sites are thought to reflect the pace of human aging. Here, we developed a robust predictor of mouse biological age based on 90 CpG sites derived from partial blood DNA methylation profiles. The resulting clock correctly determines the age of mouse cohorts, detects the longevity effects of calorie restriction and gene knockouts, and reports rejuvenation of fibroblast-derived iPSCs. The data show that mammalian DNA methylomes are characterized by CpG sites that may represent the organism's biological age. They are scattered across the genome, they are distinct in human and mouse, and their methylation gradually changes with age. The clock derived from these sites represents a biomarker of aging and can be used to determine the biological age of organisms and evaluate interventions that alter the rate of aging.
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Affiliation(s)
- Daniel A Petkovich
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Dmitriy I Podolskiy
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Alexei V Lobanov
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Sang-Goo Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Richard A Miller
- Department of Pathology and Geriatrics Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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19
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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.
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20
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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.
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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.
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21
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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.
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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.
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22
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Class II major histocompatibility complex mutant mice to study the germ-line bias of T-cell antigen receptors. Proc Natl Acad Sci U S A 2016; 113:E5608-17. [PMID: 27588903 DOI: 10.1073/pnas.1609717113] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The interaction of αβ T-cell antigen receptors (TCRs) with peptides bound to MHC molecules lies at the center of adaptive immunity. Whether TCRs have evolved to react with MHC or, instead, processes in the thymus involving coreceptors and other molecules select MHC-specific TCRs de novo from a random repertoire is a longstanding immunological question. Here, using nuclease-targeted mutagenesis, we address this question in vivo by generating three independent lines of knockin mice with single-amino acid mutations of conserved class II MHC amino acids that often are involved in interactions with the germ-line-encoded portions of TCRs. Although the TCR repertoire generated in these mutants is similar in size and diversity to that in WT mice, the evolutionary bias of TCRs for MHC is suggested by a shift and preferential use of some TCR subfamilies over others in mice expressing the mutant class II MHCs. Furthermore, T cells educated on these mutant MHC molecules are alloreactive to each other and to WT cells, and vice versa, suggesting strong functional differences among these repertoires. Taken together, these results highlight both the flexibility of thymic selection and the evolutionary bias of TCRs for MHC.
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23
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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]
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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.
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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.
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25
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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.
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26
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Kuzmina NS, Lapteva NS, Rubanovich AV. Hypermethylation of gene promoters in peripheral blood leukocytes in humans long term after radiation exposure. ENVIRONMENTAL RESEARCH 2016; 146:10-17. [PMID: 26708527 DOI: 10.1016/j.envres.2015.12.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 12/07/2015] [Accepted: 12/08/2015] [Indexed: 06/05/2023]
Abstract
Some human genes known to undergo age-related promoter hypermethylation. These epigenetic modifications are similar to those occurring in the course of certain diseases, e.g. some types of cancer, which in turn may also associate with age. Given external genotoxic factors may additionally contribute to hypermethylation, this study was designed to analyzes, using methylation-sensitive polymerase chain reaction (PCR), the CpG island hypermethylation in RASSF1A, CDKN2A (including p16/INK4A and p14/ARF) and GSTP1 promoters in peripheral blood leukocytes of individuals exposed to ionizing radiation long time ago. One hundred and twenty-four irradiated subjects (24-77 years old at sampling: 83 Chernobyl Nuclear Power Plant clean-up workers, 21 nuclear workers, 20 residents of territories with radioactive contamination) and 208 unirradiated volunteers (19-77 years old at sampling) were enrolled. In addition, 74 non-exposed offspring (2-51 years old at sampling) born to irradiated parents were examined. The frequency of individuals displaying promoter methylation of at least one gene in exposed group was significantly higher as compared to the control group (OR=5.44, 95% CI=2.62-11.76, p=3.9×10(-7)). No significant difference was found between the frequency of subjects with the revealed promoter methylation in the group of offspring born to irradiated parents and in the control group. The increase in the number of methylated loci of RASSF1A and p14/ARF was associated with age (β=0.242; p=1.7×10(-5)). In contrast, hypermethylation of p16/INK4A and GSTP1 genes correlated with the fact of radiation exposure only (β=0.290; p=1.7×10(-7)). The latter finding demonstrates that methylation changes in blood leukocytes of healthy subjects exposed to radiation resemble those reported in human malignancies. Additional studies are required to identify the dose-response of epigenetic markers specifically associating with radiation-induced premature aging and/or with the development of age-associated cancer and non-cancer diseases.
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Affiliation(s)
- Nina S Kuzmina
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.
| | - Nellya Sh Lapteva
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
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27
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Current and Emerging Technologies for the Analysis of the Genome-Wide and Locus-Specific DNA Methylation Patterns. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 945:343-430. [DOI: 10.1007/978-3-319-43624-1_15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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28
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Wahlestedt M, Pronk CJ, Bryder D. Concise review: hematopoietic stem cell aging and the prospects for rejuvenation. Stem Cells Transl Med 2014; 4:186-94. [PMID: 25548388 DOI: 10.5966/sctm.2014-0132] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Because of the continuous increases in lifetime expectancy, the incidence of age-related diseases will, unless counteracted, represent an increasing problem at both the individual and socioeconomic levels. Studies on the processes of blood cell formation have revealed several shortcomings as a consequence of chronological age. They include a reduced ability to mount adaptive immune responses and a blood cell composition skewed toward myeloid cells, with the latter coinciding with a dramatically increased incidence of myelogenous diseases, including cancer. Conversely, the dominant forms of acute leukemia affecting children associate with the lymphoid lineages. A growing body of evidence has suggested that aging of various organs and cellular systems, including the hematopoietic system, associates with a functional demise of tissue-resident stem cell populations. Mechanistically, DNA damage and/or altered transcriptional landscapes appear to be major drivers of the hematopoietic stem cell aging state, with recent data proposing that stem cell aging phenotypes are characterized by at least some degree of reversibility. These findings suggest the possibility of rejuvenating, or at least dampening, stem cell aging phenotypes in the elderly for therapeutic benefit.
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Affiliation(s)
- Martin Wahlestedt
- Immunology Section, Institution for Experimental Medical Science, Lund University, Lund, Sweden; Department of Pediatric Oncology/Hematology, Skåne University Hospital, Lund, Sweden
| | - Cornelis Jan Pronk
- Immunology Section, Institution for Experimental Medical Science, Lund University, Lund, Sweden; Department of Pediatric Oncology/Hematology, Skåne University Hospital, Lund, Sweden
| | - David Bryder
- Immunology Section, Institution for Experimental Medical Science, Lund University, Lund, Sweden; Department of Pediatric Oncology/Hematology, Skåne University Hospital, Lund, Sweden
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Fernández AF, Bayón GF, Urdinguio RG, Toraño EG, García MG, Carella A, Petrus-Reurer S, Ferrero C, Martinez-Camblor P, Cubillo I, García-Castro J, Delgado-Calle J, Pérez-Campo FM, Riancho JA, Bueno C, Menéndez P, Mentink A, Mareschi K, Claire F, Fagnani C, Medda E, Toccaceli V, Brescianini S, Moran S, Esteller M, Stolzing A, de Boer J, Nisticò L, Stazi MA, Fraga MF. H3K4me1 marks DNA regions hypomethylated during aging in human stem and differentiated cells. Genome Res 2014; 25:27-40. [PMID: 25271306 PMCID: PMC4317171 DOI: 10.1101/gr.169011.113] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In differentiated cells, aging is associated with hypermethylation of DNA regions enriched in repressive histone post-translational modifications. However, the chromatin marks associated with changes in DNA methylation in adult stem cells during lifetime are still largely unknown. Here, DNA methylation profiling of mesenchymal stem cells (MSCs) obtained from individuals aged 2 to 92 yr identified 18,735 hypermethylated and 45,407 hypomethylated CpG sites associated with aging. As in differentiated cells, hypermethylated sequences were enriched in chromatin repressive marks. Most importantly, hypomethylated CpG sites were strongly enriched in the active chromatin mark H3K4me1 in stem and differentiated cells, suggesting this is a cell type–independent chromatin signature of DNA hypomethylation during aging. Analysis of scedasticity showed that interindividual variability of DNA methylation increased during aging in MSCs and differentiated cells, providing a new avenue for the identification of DNA methylation changes over time. DNA methylation profiling of genetically identical individuals showed that both the tendency of DNA methylation changes and scedasticity depended on nongenetic as well as genetic factors. Our results indicate that the dynamics of DNA methylation during aging depend on a complex mixture of factors that include the DNA sequence, cell type, and chromatin context involved and that, depending on the locus, the changes can be modulated by genetic and/or external factors.
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Affiliation(s)
- Agustín F Fernández
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Gustavo F Bayón
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Rocío G Urdinguio
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Estela G Toraño
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, 33006 Oviedo, Spain
| | - María G García
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Antonella Carella
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Sandra Petrus-Reurer
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Cecilia Ferrero
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Pablo Martinez-Camblor
- Oficina de Investigación Biosanitaria (OIB-FICYT) de Asturias, 33005 Oviedo, Spain and Universidad Autónoma de Chile, Chile
| | - Isabel Cubillo
- Unidad de Biotecnología Celular, Área de Genética Humana, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Javier García-Castro
- Unidad de Biotecnología Celular, Área de Genética Humana, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Jesús Delgado-Calle
- Department of Internal Medicine, Hospital U.M. Valdecilla, University of Cantabria, IDIVAL, 39011 Santander, Spain
| | - Flor M Pérez-Campo
- Department of Internal Medicine, Hospital U.M. Valdecilla, University of Cantabria, IDIVAL, 39011 Santander, Spain
| | - José A Riancho
- Department of Internal Medicine, Hospital U.M. Valdecilla, University of Cantabria, IDIVAL, 39011 Santander, Spain
| | - Clara Bueno
- Josep Carreras Leukemia Research Institute, School of Medicine, University of Barcelona, 08036 Barcelona, Spain
| | - Pablo Menéndez
- Josep Carreras Leukemia Research Institute, School of Medicine, University of Barcelona, 08036 Barcelona, Spain; Institut Català de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Anouk Mentink
- MIRA Institute of Biomedical Technology and Technical Medicine, University of Twente, 7500 AE Enschede, The Netherlands
| | - Katia Mareschi
- Pediatric Onco-Hematology, Stem Cell Transplantation and Cellular Therapy Division, City of Science and Health of Turin, Regina Margherita Children's Hospital, 10126 Turin, Italy; Department of Public Health and Pediatrics, University of Turin, 10126 Turin, Italy
| | - Fabian Claire
- Translational Centre for Regenerative Medicine, University of Leipzig, 04103 Leipzig, Germany
| | - Corrado Fagnani
- Genetic Epidemiology Unit, National Centre of Epidemiology, Surveillance and Health Promotion; Istituto Superiore di Sanità; Viale Regina Elena 299, 00161, Rome, Italy
| | - Emanuela Medda
- Genetic Epidemiology Unit, National Centre of Epidemiology, Surveillance and Health Promotion; Istituto Superiore di Sanità; Viale Regina Elena 299, 00161, Rome, Italy
| | - Virgilia Toccaceli
- Genetic Epidemiology Unit, National Centre of Epidemiology, Surveillance and Health Promotion; Istituto Superiore di Sanità; Viale Regina Elena 299, 00161, Rome, Italy
| | - Sonia Brescianini
- Genetic Epidemiology Unit, National Centre of Epidemiology, Surveillance and Health Promotion; Istituto Superiore di Sanità; Viale Regina Elena 299, 00161, Rome, Italy
| | - Sebastián Moran
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Catalonia, Spain
| | - Manel Esteller
- Institut Català de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain; Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 Barcelona, Catalonia, Spain; Department of Physiological Sciences II, School of Medicine, University of Barcelona, 08036 Barcelona, Catalonia, Spain
| | - Alexandra Stolzing
- Translational Centre for Regenerative Medicine, University of Leipzig, 04103 Leipzig, Germany; Loughborough University, Wolfson School of Mechanical and Manufacturing Engineering, LE11 3TU Loughborough, United Kingdom
| | - Jan de Boer
- MIRA Institute of Biomedical Technology and Technical Medicine, University of Twente, 7500 AE Enschede, The Netherlands; cBITE laboratory, Merln Institute of Technology-inspired Regenerative Medicine, Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Lorenza Nisticò
- Genetic Epidemiology Unit, National Centre of Epidemiology, Surveillance and Health Promotion; Istituto Superiore di Sanità; Viale Regina Elena 299, 00161, Rome, Italy
| | - Maria A Stazi
- Genetic Epidemiology Unit, National Centre of Epidemiology, Surveillance and Health Promotion; Istituto Superiore di Sanità; Viale Regina Elena 299, 00161, Rome, Italy
| | - Mario F Fraga
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, 33006 Oviedo, Spain; Department of Immunology and Oncology, National Center for Biotechnology, CNB-CSIC, Cantoblanco, 28049 Madrid, Spain
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Beerman I, Rossi DJ. Epigenetic regulation of hematopoietic stem cell aging. Exp Cell Res 2014; 329:192-9. [PMID: 25261778 DOI: 10.1016/j.yexcr.2014.09.013] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2014] [Accepted: 09/11/2014] [Indexed: 12/27/2022]
Abstract
Aging is invariably associated with alterations of the hematopoietic stem cell (HSC) compartment, including loss of functional capacity, altered clonal composition, and changes in lineage contribution. Although accumulation of DNA damage occurs during HSC aging, it is unlikely such consistent aging phenotypes could be solely attributed to changes in DNA integrity. Another mechanism by which heritable traits could contribute to the changes in the functional potential of aged HSCs is through alterations in the epigenetic landscape of adult stem cells. Indeed, recent studies on hematopoietic stem cells have suggested that altered epigenetic profiles are associated with HSC aging and play a key role in modulating the functional potential of HSCs at different stages during ontogeny. Even small changes of the epigenetic landscape can lead to robustly altered expression patterns, either directly by loss of regulatory control or through indirect, additive effects, ultimately leading to transcriptional changes of the stem cells. Potential drivers of such changes in the epigenetic landscape of aged HSCs include proliferative history, DNA damage, and deregulation of key epigenetic enzymes and complexes. This review will focus largely on the two most characterized epigenetic marks - DNA methylation and histone modifications - but will also discuss the potential role of non-coding RNAs in regulating HSC function during aging.
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Affiliation(s)
- Isabel Beerman
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children׳s Hospital, MA 02116, USA.
| | - Derrick J Rossi
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children׳s Hospital, MA 02116, USA
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