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Kokorudz C, Radford BN, Dean W, Hemberger M. Advanced Maternal Age Differentially Affects Embryonic Tissues with the Most Severe Impact on the Developing Brain. Cells 2022; 12:cells12010076. [PMID: 36611870 PMCID: PMC9818809 DOI: 10.3390/cells12010076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/15/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022] Open
Abstract
Advanced maternal age (AMA) poses the single greatest risk to a successful pregnancy. Apart from the impact of AMA on oocyte fitness, aged female mice often display defects in normal placentation. Placental defects in turn are tightly correlated with brain and cardiovascular abnormalities. It therefore follows that placenta, brain and heart development may be particularly susceptible to the impact of AMA. In the current study, we compared global transcriptomes of placentas, brains, hearts, and facial prominences from mid-gestation mouse conceptuses developed in young control (7-13 wks) and aging (43-50 wks) females. We find that AMA increases transcriptional heterogeneity in all tissues, but particularly in fetal brain. Importantly, even overtly normally developed embryos from older females display dramatic expression changes in neurodevelopmental genes. These transcriptomic alterations in the brain are likely induced by defects in placental development. Using trophoblast stem cells (TSCs) as a model, we show that exposure to aging uterine stromal cell-conditioned medium interferes with normal TSC proliferation and causes precocious differentiation, recapitulating many of the defects observed in placentas from aged females. These data highlight the increased risk of AMA on reproductive outcome, with neurodevelopment being the most sensitive to such early perturbations and with potential for lifelong impact.
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Affiliation(s)
- Caroline Kokorudz
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
- Alberta Children’s Hospital Research Institute, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
| | - Bethany N. Radford
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
- Alberta Children’s Hospital Research Institute, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
| | - Wendy Dean
- Alberta Children’s Hospital Research Institute, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
- Department of Cell Biology and Anatomy, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
- Correspondence: (W.D.); (M.H.)
| | - Myriam Hemberger
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
- Alberta Children’s Hospital Research Institute, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
- Correspondence: (W.D.); (M.H.)
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52
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Hurvitz N, Elkhateeb N, Sigawi T, Rinsky-Halivni L, Ilan Y. Improving the effectiveness of anti-aging modalities by using the constrained disorder principle-based management algorithms. FRONTIERS IN AGING 2022; 3:1044038. [PMID: 36589143 PMCID: PMC9795077 DOI: 10.3389/fragi.2022.1044038] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/22/2022] [Indexed: 12/15/2022]
Abstract
Aging is a complex biological process with multifactorial nature underlined by genetic, environmental, and social factors. In the present paper, we review several mechanisms of aging and the pre-clinically and clinically studied anti-aging therapies. Variability characterizes biological processes from the genome to cellular organelles, biochemical processes, and whole organs' function. Aging is associated with alterations in the degrees of variability and complexity of systems. The constrained disorder principle defines living organisms based on their inherent disorder within arbitrary boundaries and defines aging as having a lower variability or moving outside the boundaries of variability. We focus on associations between variability and hallmarks of aging and discuss the roles of disorder and variability of systems in the pathogenesis of aging. The paper presents the concept of implementing the constrained disease principle-based second-generation artificial intelligence systems for improving anti-aging modalities. The platform uses constrained noise to enhance systems' efficiency and slow the aging process. Described is the potential use of second-generation artificial intelligence systems in patients with chronic disease and its implications for the aged population.
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Affiliation(s)
- Noa Hurvitz
- Faculty of Medicine, Hebrew University and Department of Medicine, Hadassah Medical Center, Jerusalem, Israel
| | - Narmine Elkhateeb
- Faculty of Medicine, Hebrew University and Department of Medicine, Hadassah Medical Center, Jerusalem, Israel
| | - Tal Sigawi
- Faculty of Medicine, Hebrew University and Department of Medicine, Hadassah Medical Center, Jerusalem, Israel
| | - Lilah Rinsky-Halivni
- Braun School of Public Health, Hebrew University of Jerusalem, Jerusalem, Israel,Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Yaron Ilan
- Faculty of Medicine, Hebrew University and Department of Medicine, Hadassah Medical Center, Jerusalem, Israel,*Correspondence: Yaron Ilan,
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53
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Ganesan A, Dermadi D, Kalesinskas L, Donato M, Sowers R, Utz PJ, Khatri P. Inferring direction of associations between histone modifications using a neural processes-based framework. iScience 2022; 26:105756. [PMID: 36619977 PMCID: PMC9813700 DOI: 10.1016/j.isci.2022.105756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/19/2022] [Accepted: 12/06/2022] [Indexed: 12/12/2022] Open
Abstract
Current technologies do not allow predicting interactions between histone post-translational modifications (HPTMs) at a system-level. We describe a computational framework, imputation-followed-by-inference, to predict directed association between two HPTMs using EpiTOF, a mass cytometry-based platform that allows profiling multiple HPTMs at a single-cell resolution. Using EpiTOF profiles of >55,000,000 peripheral mononuclear blood cells from 158 healthy human subjects, we show that neural processes (NP) have significantly higher accuracy than linear regression and k-nearest neighbors models to impute the abundance of an HPTM. Next, we infer the direction of association to show we recapitulate known HPTM associations and identify several previously unidentified ones in healthy individuals. Using this framework in an influenza vaccine cohort, we identify changes in associations between 6 pairs of HPTMs 30 days following vaccination, of which several have been shown to be involved in innate memory. These results demonstrate the utility of our framework in identifying directed interactions between HPTMs.
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Affiliation(s)
- Ananthakrishnan Ganesan
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA,Institute for Computational and Mathematical Engineering, School of Engineering, Stanford University, Stanford, CA 94305, USA,Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Denis Dermadi
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA,Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Laurynas Kalesinskas
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA,Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Michele Donato
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA,Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Rosalie Sowers
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA,Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Paul J. Utz
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA,Division of Immunology and Rheumatology, Department of Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA 94305, USA,Center for Biomedical Informatics Research, Department of Medicine, School of Medicine, Stanford University, Stanford, CA 94305, USA,Corresponding author
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54
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Aylon Y, Furth N, Mallel G, Friedlander G, Nataraj NB, Dong M, Hassin O, Zoabi R, Cohen B, Drendel V, Salame TM, Mukherjee S, Harpaz N, Johnson R, Aulitzky WE, Yarden Y, Shema E, Oren M. Breast cancer plasticity is restricted by a LATS1-NCOR1 repressive axis. Nat Commun 2022; 13:7199. [PMID: 36443319 PMCID: PMC9705295 DOI: 10.1038/s41467-022-34863-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 11/10/2022] [Indexed: 11/29/2022] Open
Abstract
Breast cancer, the most frequent cancer in women, is generally classified into several distinct histological and molecular subtypes. However, single-cell technologies have revealed remarkable cellular and functional heterogeneity across subtypes and even within individual breast tumors. Much of this heterogeneity is attributable to dynamic alterations in the epigenetic landscape of the cancer cells, which promote phenotypic plasticity. Such plasticity, including transition from luminal to basal-like cell identity, can promote disease aggressiveness. We now report that the tumor suppressor LATS1, whose expression is often downregulated in human breast cancer, helps maintain luminal breast cancer cell identity by reducing the chromatin accessibility of genes that are characteristic of a "basal-like" state, preventing their spurious activation. This is achieved via interaction of LATS1 with the NCOR1 nuclear corepressor and recruitment of HDAC1, driving histone H3K27 deacetylation near NCOR1-repressed "basal-like" genes. Consequently, decreased expression of LATS1 elevates the expression of such genes and facilitates slippage towards a more basal-like phenotypic identity. We propose that by enforcing rigorous silencing of repressed genes, the LATS1-NCOR1 axis maintains luminal cell identity and restricts breast cancer progression.
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Affiliation(s)
- Yael Aylon
- grid.13992.300000 0004 0604 7563Department of Molecular Cell Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Noa Furth
- grid.13992.300000 0004 0604 7563Department of Immunology and Regenerative Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Giuseppe Mallel
- grid.13992.300000 0004 0604 7563Department of Molecular Cell Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Gilgi Friedlander
- grid.13992.300000 0004 0604 7563Department of Life Sciences Core Facilities, The Nancy & Stephen Grand Israel National Center for Personalized Medicine (G-INCPM), The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Nishanth Belugali Nataraj
- grid.13992.300000 0004 0604 7563Department of Immunology and Regenerative Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Meng Dong
- grid.502798.10000 0004 0561 903XDr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology and University of Tuebingen, Stuttgart, Germany
| | - Ori Hassin
- grid.13992.300000 0004 0604 7563Department of Molecular Cell Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Rawan Zoabi
- grid.13992.300000 0004 0604 7563Department of Molecular Cell Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Benjamin Cohen
- grid.13992.300000 0004 0604 7563Department of Immunology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Vanessa Drendel
- grid.416008.b0000 0004 0603 4965Department of Pathology, Robert Bosch Hospital, Stuttgart, Germany
| | - Tomer Meir Salame
- grid.13992.300000 0004 0604 7563Flow Cytometry Unit, Department of Life Sciences Core Facilities, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Saptaparna Mukherjee
- grid.13992.300000 0004 0604 7563Department of Molecular Cell Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Nofar Harpaz
- grid.13992.300000 0004 0604 7563Department of Immunology and Regenerative Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Randy Johnson
- grid.240145.60000 0001 2291 4776Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Walter E. Aulitzky
- grid.416008.b0000 0004 0603 4965Department of Hematology, Oncology and Palliative Medicine, Robert Bosch Hospital, Stuttgart, Germany
| | - Yosef Yarden
- grid.13992.300000 0004 0604 7563Department of Immunology and Regenerative Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Efrat Shema
- grid.13992.300000 0004 0604 7563Department of Immunology and Regenerative Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Moshe Oren
- grid.13992.300000 0004 0604 7563Department of Molecular Cell Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
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55
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Epigenetic regulation of aging: implications for interventions of aging and diseases. Signal Transduct Target Ther 2022; 7:374. [PMID: 36336680 PMCID: PMC9637765 DOI: 10.1038/s41392-022-01211-8] [Citation(s) in RCA: 126] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/14/2022] [Accepted: 09/28/2022] [Indexed: 11/09/2022] Open
Abstract
Aging is accompanied by the decline of organismal functions and a series of prominent hallmarks, including genetic and epigenetic alterations. These aging-associated epigenetic changes include DNA methylation, histone modification, chromatin remodeling, non-coding RNA (ncRNA) regulation, and RNA modification, all of which participate in the regulation of the aging process, and hence contribute to aging-related diseases. Therefore, understanding the epigenetic mechanisms in aging will provide new avenues to develop strategies to delay aging. Indeed, aging interventions based on manipulating epigenetic mechanisms have led to the alleviation of aging or the extension of the lifespan in animal models. Small molecule-based therapies and reprogramming strategies that enable epigenetic rejuvenation have been developed for ameliorating or reversing aging-related conditions. In addition, adopting health-promoting activities, such as caloric restriction, exercise, and calibrating circadian rhythm, has been demonstrated to delay aging. Furthermore, various clinical trials for aging intervention are ongoing, providing more evidence of the safety and efficacy of these therapies. Here, we review recent work on the epigenetic regulation of aging and outline the advances in intervention strategies for aging and age-associated diseases. A better understanding of the critical roles of epigenetics in the aging process will lead to more clinical advances in the prevention of human aging and therapy of aging-related diseases.
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56
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Metzner K, Darawsha O, Wang M, Gaur N, Cheng Y, Rödiger A, Frahm C, Witte OW, Perocchi F, Axer H, Grosskreutz J, Brill MS. Age-dependent increase of cytoskeletal components in sensory axons in human skin. Front Cell Dev Biol 2022; 10:965382. [PMID: 36393849 PMCID: PMC9664158 DOI: 10.3389/fcell.2022.965382] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 10/12/2022] [Indexed: 01/24/2023] Open
Abstract
Aging is a complex process characterized by several molecular and cellular imbalances. The composition and stability of the neuronal cytoskeleton is essential for the maintenance of homeostasis, especially in long neurites. Using human skin biopsies containing sensory axons from a cohort of healthy individuals, we investigate alterations in cytoskeletal content and sensory axon caliber during aging via quantitative immunostainings. Cytoskeletal components show an increase with aging in both sexes, while elevation in axon diameter is only evident in males. Transcriptomic data from aging males illustrate various patterns in gene expression during aging. Together, the data suggest gender-specific changes during aging in peripheral sensory axons, possibly influencing cytoskeletal functionality and axonal caliber. These changes may cumulatively increase susceptibility of aged individuals to neurodegenerative diseases.
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Affiliation(s)
- Klara Metzner
- Department of Neurology, Jena University Hospital, Jena, Germany,Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany
| | - Omar Darawsha
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany
| | - Mengzhe Wang
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany
| | - Nayana Gaur
- Department of Neurology, Jena University Hospital, Jena, Germany,Laboratory Animal Centre, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Yiming Cheng
- Helmholtz Diabetes Center (HDC), Helmholtz Center Munich, Institute for Diabetes and Obesity, Munich, Germany
| | | | - Christiane Frahm
- Department of Neurology, Jena University Hospital, Jena, Germany
| | - Otto W. Witte
- Department of Neurology, Jena University Hospital, Jena, Germany
| | - Fabiana Perocchi
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany,Helmholtz Diabetes Center (HDC), Helmholtz Center Munich, Institute for Diabetes and Obesity, Munich, Germany,Munich Cluster of Systems Neurology (SyNergy), Munich, Germany
| | - Hubertus Axer
- Department of Neurology, Jena University Hospital, Jena, Germany
| | - Julian Grosskreutz
- Precision Neurology of the University of Lübeck, Lübeck, Germany,PMI Cluster, University of Lübeck, Lübeck, Germany
| | - Monika S. Brill
- Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany,Munich Cluster of Systems Neurology (SyNergy), Munich, Germany,*Correspondence: Monika S. Brill,
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57
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Development of Single-Cell Transcriptomics and Its Application in COVID-19. Viruses 2022; 14:v14102271. [PMID: 36298825 PMCID: PMC9611071 DOI: 10.3390/v14102271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 09/30/2022] [Accepted: 10/11/2022] [Indexed: 11/07/2022] Open
Abstract
Over the last three years, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-related health crisis has claimed over six million lives and caused USD 12 trillion losses to the global economy. SARS-CoV-2 continuously mutates and evolves with a high basic reproduction number (R0), resulting in a variety of clinical manifestations ranging from asymptomatic infection to acute respiratory distress syndrome (ARDS) and even death. To gain a better understanding of coronavirus disease 2019 (COVID-19), it is critical to investigate the components that cause various clinical manifestations. Single-cell sequencing has substantial advantages in terms of identifying differentially expressed genes among individual cells, which can provide a better understanding of the various physiological and pathological processes. This article reviewed the use of single-cell transcriptomics in COVID-19 research, examined the immune response disparities generated by SARS-CoV-2, and offered insights regarding how to improve COVID-19 diagnosis and treatment plans.
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58
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Song Q, Hou Y, Zhang Y, Liu J, Wang Y, Fu J, Zhang C, Cao M, Cui Y, Zhang X, Wang X, Zhang J, Liu C, Zhang Y, Wang P. Integrated multi-omics approach revealed cellular senescence landscape. Nucleic Acids Res 2022; 50:10947-10963. [PMID: 36243980 PMCID: PMC9638896 DOI: 10.1093/nar/gkac885] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/27/2022] [Accepted: 10/01/2022] [Indexed: 11/14/2022] Open
Abstract
Cellular senescence is a complex multifactorial biological phenomenon that plays essential roles in aging, and aging-related diseases. During this process, the senescent cells undergo gene expression altering and chromatin structure remodeling. However, studies on the epigenetic landscape of senescence using integrated multi-omics approaches are limited. In this research, we performed ATAC-seq, RNA-seq and ChIP-seq on different senescent types to reveal the landscape of senescence and identify the prime regulatory elements. We also obtained 34 key genes and deduced that NAT1, PBX1 and RRM2, which interacted with each other, could be the potential markers of aging and aging-related diseases. In summary, our work provides the landscape to study accessibility dynamics and transcriptional regulations in cellular senescence. The application of this technique in different types of senescence allows us to identify the regulatory elements responsible for the substantial regulation of transcription, providing the insights into molecular mechanisms of senescence.
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Affiliation(s)
- Qiao Song
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Yuli Hou
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Yiyin Zhang
- Shanghai Jiayin Biotechnology, Shanghai 200092, PR China
| | - Jing Liu
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Yaqi Wang
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Jingxuan Fu
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Chi Zhang
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Min Cao
- Department of Clinical Laboratory, Beijing Huairou Hospital, Beijing 101400, PR China
| | - Yuting Cui
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Xiaomin Zhang
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Xiaoling Wang
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Jingjing Zhang
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Congcong Liu
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Yingzhen Zhang
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
| | - Peichang Wang
- Department of Clinical laboratory, Xuanwu Hospital, National Clinical Research Center for Geriatric Diseases, Capital Medical University, Beijing 100053, PR China
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59
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Tissue-specific impacts of aging and genetics on gene expression patterns in humans. Nat Commun 2022; 13:5803. [PMID: 36192477 PMCID: PMC9530233 DOI: 10.1038/s41467-022-33509-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 09/21/2022] [Indexed: 11/09/2022] Open
Abstract
Age is the primary risk factor for many common human diseases. Here, we quantify the relative contributions of genetics and aging to gene expression patterns across 27 tissues from 948 humans. We show that the predictive power of expression quantitative trait loci is impacted by age in many tissues. Jointly modelling the contributions of age and genetics to transcript level variation we find expression heritability (h2) is consistent among tissues while the contribution of aging varies by >20-fold with [Formula: see text] in 5 tissues. We find that while the force of purifying selection is stronger on genes expressed early versus late in life (Medawar's hypothesis), several highly proliferative tissues exhibit the opposite pattern. These non-Medawarian tissues exhibit high rates of cancer and age-of-expression-associated somatic mutations. In contrast, genes under genetic control are under relaxed constraint. Together, we demonstrate the distinct roles of aging and genetics on expression phenotypes.
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60
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Barman PK, Shin JE, Lewis SA, Kang S, Wu D, Wang Y, Yang X, Nagarkatti PS, Nagarkatti M, Messaoudi I, Benayoun BA, Goodridge HS. Production of MHCII-expressing classical monocytes increases during aging in mice and humans. Aging Cell 2022; 21:e13701. [PMID: 36040389 PMCID: PMC9577948 DOI: 10.1111/acel.13701] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/05/2022] [Indexed: 01/25/2023] Open
Abstract
Aging is associated with increased monocyte production and altered monocyte function. Classical monocytes are heterogenous and a shift in their subset composition may underlie some of their apparent functional changes during aging. We have previously shown that mouse granulocyte-monocyte progenitors (GMPs) produce "neutrophil-like" monocytes (NeuMo), whereas monocyte-dendritic cell progenitors (MDPs) produce monocyte-derived dendritic cell (moDC)-producing monocytes (DCMo). Here, we demonstrate that classical monocytes from the bone marrow of old male and female mice have higher expression of DCMo signature genes (H2-Aa, H2-Ab1, H2-Eb1, Cd74), and that more classical monocytes express MHCII and CD74 protein. Moreover, we show that bone marrow MDPs and classical monocytes from old mice yield more moDC. We also demonstrate higher expression of Aw112010 in old monocytes and that Aw112010 lncRNA activity regulates MHCII induction in macrophages, which suggests that elevated Aw112010 levels may underlie increased MHCII expression during monocyte aging. Finally, we show that classical monocyte expression of MHCII is also elevated during healthy aging in humans. Thus, aging-associated changes in monocyte production may underlie altered monocyte function and have implications for aging-associated disorders.
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Affiliation(s)
- Pijus K. Barman
- Board of Governors Regenerative Medicine InstituteCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA,Research Division of Immunology in the Department of Biomedical SciencesCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA
| | - Juliana E. Shin
- Board of Governors Regenerative Medicine InstituteCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA,Research Division of Immunology in the Department of Biomedical SciencesCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA
| | - Sloan A. Lewis
- Department of Molecular Biology and BiochemistryUniversity of CaliforniaIrvineCaliforniaUSA,Institute for ImmunologyUniversity of CaliforniaIrvineCaliforniaUSA
| | - Seokjo Kang
- Board of Governors Regenerative Medicine InstituteCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA,Research Division of Immunology in the Department of Biomedical SciencesCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA
| | - Di Wu
- Applied Genomics, Computation and Translational Core, Cedars‐Sinai CancerCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA
| | - Yizhou Wang
- Applied Genomics, Computation and Translational Core, Cedars‐Sinai CancerCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA
| | - Xiaoming Yang
- Department of Pathology, Microbiology and Immunology, School of MedicineUniversity of South CarolinaColumbiaSouth CarolinaUSA
| | - Prakash S. Nagarkatti
- Department of Pathology, Microbiology and Immunology, School of MedicineUniversity of South CarolinaColumbiaSouth CarolinaUSA
| | - Mitzi Nagarkatti
- Department of Pathology, Microbiology and Immunology, School of MedicineUniversity of South CarolinaColumbiaSouth CarolinaUSA
| | - Ilhem Messaoudi
- Department of Molecular Biology and BiochemistryUniversity of CaliforniaIrvineCaliforniaUSA,Institute for ImmunologyUniversity of CaliforniaIrvineCaliforniaUSA,Department of Microbiology, Immunology and Molecular Genetics in the College of MedicineUniversity of KentuckyLexingtonKentuckyUSA
| | - Bérénice A. Benayoun
- Leonard Davis School of GerontologyUniversity of Southern CaliforniaLos AngelesCaliforniaUSA,Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and SciencesUniversity of Southern CaliforniaLos AngelesCaliforniaUSA,Biochemistry and Molecular Medicine Department, USC Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Helen S. Goodridge
- Board of Governors Regenerative Medicine InstituteCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA,Research Division of Immunology in the Department of Biomedical SciencesCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA
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61
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Pérez RF, Tejedor JR, Fernández AF, Fraga MF. Aging and cancer epigenetics: Where do the paths fork? Aging Cell 2022; 21:e13709. [PMID: 36103298 PMCID: PMC9577950 DOI: 10.1111/acel.13709] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 08/29/2022] [Indexed: 01/25/2023] Open
Abstract
Aging and cancer are clearly associated processes, at both the epidemiological and molecular level. Epigenetic mechanisms are good candidates to explain the molecular links between the two phenomena, but recent reports have also revealed considerable differences, particularly regarding the loss of DNA methylation in the two processes. The large-scale generation and availability of genome-wide epigenetic data now permits systematic studies to be undertaken which may help clarify the similarities and differences between aging and cancer epigenetic alterations. In addition, the development of epigenetic clocks provides a new dimension in which to investigate diseases at the molecular level. Here, we examine current and future questions about the roles of DNA methylation mechanisms as causal factors in the processes of aging and cancer so that we may better understand if and how aging-associated epigenetic alterations lead to tumorigenesis. It seems certain that comprehending the molecular mechanisms underlying epigenetic clocks, especially with regard to somatic stem cell aging, combined with applying single-cell epigenetic-age profiling technologies to aging and cancer cohorts, and the integration of existing and upcoming epigenetic evidence within the genetic damage models of aging will prove to be crucial to improving understanding of these two interrelated phenomena.
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Affiliation(s)
- Raúl Fernández Pérez
- Cancer Epigenetics and Nanomedicine LaboratoryNanomaterials and Nanotechnology Research Center (CINN‐CSIC)El EntregoSpain,Health Research Institute of Asturias (ISPA‐FINBA)Institute of Oncology of Asturias (IUOPA) and Department of Organisms and Systems Biology (BOS)University of OviedoOviedoSpain,Rare Diseases CIBER (CIBERER)Carlos III Health Institute (ISCIII)MadridSpain
| | - Juan Ramón Tejedor
- Cancer Epigenetics and Nanomedicine LaboratoryNanomaterials and Nanotechnology Research Center (CINN‐CSIC)El EntregoSpain,Health Research Institute of Asturias (ISPA‐FINBA)Institute of Oncology of Asturias (IUOPA) and Department of Organisms and Systems Biology (BOS)University of OviedoOviedoSpain,Rare Diseases CIBER (CIBERER)Carlos III Health Institute (ISCIII)MadridSpain
| | - Agustín Fernández Fernández
- Cancer Epigenetics and Nanomedicine LaboratoryNanomaterials and Nanotechnology Research Center (CINN‐CSIC)El EntregoSpain,Health Research Institute of Asturias (ISPA‐FINBA)Institute of Oncology of Asturias (IUOPA) and Department of Organisms and Systems Biology (BOS)University of OviedoOviedoSpain,Rare Diseases CIBER (CIBERER)Carlos III Health Institute (ISCIII)MadridSpain
| | - Mario Fernández Fraga
- Cancer Epigenetics and Nanomedicine LaboratoryNanomaterials and Nanotechnology Research Center (CINN‐CSIC)El EntregoSpain,Health Research Institute of Asturias (ISPA‐FINBA)Institute of Oncology of Asturias (IUOPA) and Department of Organisms and Systems Biology (BOS)University of OviedoOviedoSpain,Rare Diseases CIBER (CIBERER)Carlos III Health Institute (ISCIII)MadridSpain
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Abstract
The immune system is highly complex and distributed throughout an organism, with hundreds to thousands of cell states existing in parallel with diverse molecular pathways interacting in a highly dynamic and coordinated fashion. Although the characterization of individual genes and molecules is of the utmost importance for understanding immune-system function, high-throughput, high-resolution omics technologies combined with sophisticated computational modeling and machine-learning approaches are creating opportunities to complement standard immunological methods with new insights into immune-system dynamics. Like systems immunology itself, immunology researchers must take advantage of these technologies and form their own diverse networks, connecting with researchers from other disciplines. This Review is an introduction and 'how-to guide' for immunologists with no particular experience in the field of omics but with the intention to learn about and apply these systems-level approaches, and for immunologists who want to make the most of interdisciplinary networks.
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63
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A stem cell aging framework, from mechanisms to interventions. Cell Rep 2022; 41:111451. [DOI: 10.1016/j.celrep.2022.111451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 09/04/2022] [Accepted: 09/14/2022] [Indexed: 11/19/2022] Open
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Zieneldien T, Kim J, Sawmiller D, Cao C. The Immune System as a Therapeutic Target for Alzheimer’s Disease. Life (Basel) 2022; 12:life12091440. [PMID: 36143476 PMCID: PMC9506058 DOI: 10.3390/life12091440] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/11/2022] [Accepted: 09/14/2022] [Indexed: 11/25/2022] Open
Abstract
Alzheimer’s disease (AD) is a heterogeneous neurodegenerative disorder and is the most common cause of dementia. Furthermore, aging is considered the most critical risk factor for AD. However, despite the vast amount of research and resources allocated to the understanding and development of AD treatments, setbacks have been more prominent than successes. Recent studies have shown that there is an intricate connection between the immune and central nervous systems, which can be imbalanced and thereby mediate neuroinflammation and AD. Thus, this review examines this connection and how it can be altered with AD. Recent developments in active and passive immunotherapy for AD are also discussed as well as suggestions for improving these therapies moving forward.
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Affiliation(s)
- Tarek Zieneldien
- Department of Pharmaceutical Science, Taneja College of Pharmacy, University of South Florida, Tampa, FL 33612, USA
| | - Janice Kim
- Department of Pharmaceutical Science, Taneja College of Pharmacy, University of South Florida, Tampa, FL 33612, USA
| | - Darrell Sawmiller
- MegaNano BioTech, Inc., 3802 Spectrum Blvd. Suite 122, Tampa, FL 33612, USA
| | - Chuanhai Cao
- Department of Pharmaceutical Science, Taneja College of Pharmacy, University of South Florida, Tampa, FL 33612, USA
- USF-Health Byrd Alzheimer’s Institute, University of South Florida, Tampa, FL 33613, USA
- Correspondence:
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65
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The landscape of aging. SCIENCE CHINA LIFE SCIENCES 2022; 65:2354-2454. [PMID: 36066811 PMCID: PMC9446657 DOI: 10.1007/s11427-022-2161-3] [Citation(s) in RCA: 101] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 07/05/2022] [Indexed: 02/07/2023]
Abstract
Aging is characterized by a progressive deterioration of physiological integrity, leading to impaired functional ability and ultimately increased susceptibility to death. It is a major risk factor for chronic human diseases, including cardiovascular disease, diabetes, neurological degeneration, and cancer. Therefore, the growing emphasis on “healthy aging” raises a series of important questions in life and social sciences. In recent years, there has been unprecedented progress in aging research, particularly the discovery that the rate of aging is at least partly controlled by evolutionarily conserved genetic pathways and biological processes. In an attempt to bring full-fledged understanding to both the aging process and age-associated diseases, we review the descriptive, conceptual, and interventive aspects of the landscape of aging composed of a number of layers at the cellular, tissue, organ, organ system, and organismal levels.
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66
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Fujino T, Asada S, Goyama S, Kitamura T. Mechanisms involved in hematopoietic stem cell aging. Cell Mol Life Sci 2022; 79:473. [PMID: 35941268 PMCID: PMC11072869 DOI: 10.1007/s00018-022-04356-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/27/2022] [Accepted: 05/05/2022] [Indexed: 11/03/2022]
Abstract
Hematopoietic stem cells (HSCs) undergo progressive functional decline over time due to both internal and external stressors, leading to aging of the hematopoietic system. A comprehensive understanding of the molecular mechanisms underlying HSC aging will be valuable in developing novel therapies for HSC rejuvenation and to prevent the onset of several age-associated diseases and hematological malignancies. This review considers the general causes of HSC aging that range from cell-intrinsic factors to cell-extrinsic factors. In particular, epigenetics and inflammation have been implicated in the linkage of HSC aging, clonality, and oncogenesis. The challenges in clarifying mechanisms of HSC aging have accelerated the development of therapeutic interventions to rejuvenate HSCs, the major goal of aging research; these details are also discussed in this review.
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Affiliation(s)
- Takeshi Fujino
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan
| | - Shuhei Asada
- The Institute of Laboratory Animals, Tokyo Women's Medical University, Tokyo, 1628666, Japan
| | - Susumu Goyama
- Division of Molecular Oncology Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, 1088639, Japan
| | - Toshio Kitamura
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan.
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Uthamacumaran A, Zenil H. A Review of Mathematical and Computational Methods in Cancer Dynamics. Front Oncol 2022; 12:850731. [PMID: 35957879 PMCID: PMC9359441 DOI: 10.3389/fonc.2022.850731] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 05/25/2022] [Indexed: 12/16/2022] Open
Abstract
Cancers are complex adaptive diseases regulated by the nonlinear feedback systems between genetic instabilities, environmental signals, cellular protein flows, and gene regulatory networks. Understanding the cybernetics of cancer requires the integration of information dynamics across multidimensional spatiotemporal scales, including genetic, transcriptional, metabolic, proteomic, epigenetic, and multi-cellular networks. However, the time-series analysis of these complex networks remains vastly absent in cancer research. With longitudinal screening and time-series analysis of cellular dynamics, universally observed causal patterns pertaining to dynamical systems, may self-organize in the signaling or gene expression state-space of cancer triggering processes. A class of these patterns, strange attractors, may be mathematical biomarkers of cancer progression. The emergence of intracellular chaos and chaotic cell population dynamics remains a new paradigm in systems medicine. As such, chaotic and complex dynamics are discussed as mathematical hallmarks of cancer cell fate dynamics herein. Given the assumption that time-resolved single-cell datasets are made available, a survey of interdisciplinary tools and algorithms from complexity theory, are hereby reviewed to investigate critical phenomena and chaotic dynamics in cancer ecosystems. To conclude, the perspective cultivates an intuition for computational systems oncology in terms of nonlinear dynamics, information theory, inverse problems, and complexity. We highlight the limitations we see in the area of statistical machine learning but the opportunity at combining it with the symbolic computational power offered by the mathematical tools explored.
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Affiliation(s)
| | - Hector Zenil
- Machine Learning Group, Department of Chemical Engineering and Biotechnology, The University of Cambridge, Cambridge, United Kingdom
- The Alan Turing Institute, British Library, London, United Kingdom
- Oxford Immune Algorithmics, Reading, United Kingdom
- Algorithmic Dynamics Lab, Karolinska Institute, Stockholm, Sweden
- Algorithmic Nature Group, LABORES, Paris, France
- *Correspondence: Hector Zenil,
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68
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Cai Z, Long T, Zhao Y, Lin R, Wang Y. Epigenetic Regulation in Knee Osteoarthritis. Front Genet 2022; 13:942982. [PMID: 35873487 PMCID: PMC9304589 DOI: 10.3389/fgene.2022.942982] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/20/2022] [Indexed: 12/02/2022] Open
Abstract
Osteoarthritis (OA) is a complicated disease with both hereditary and environmental causes. Despite an increase in reports of possible OA risk loci, it has become clear that genetics is not the sole cause of osteoarthritis. Epigenetics, which can be triggered by environmental influences and result in transcriptional alterations, may have a role in OA pathogenesis. The majority of recent research on the epigenetics of OA has been focused on DNA methylation, histone modification, and non-coding RNAs. However, this study will explore epigenetic regulation in OA at the present stage. How genetics, environmental variables, and epigenetics interact will be researched, shedding light for future studies. Their possible interaction and control processes open up new avenues for the development of innovative osteoarthritis treatment and diagnostic techniques.
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Affiliation(s)
| | - Teng Long
- *Correspondence: Teng Long, ; You Wang,
| | | | | | - You Wang
- *Correspondence: Teng Long, ; You Wang,
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69
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Pan L, Ku WL, Tang Q, Cao Y, Zhao K. scPCOR-seq enables co-profiling of chromatin occupancy and RNAs in single cells. Commun Biol 2022; 5:678. [PMID: 35804086 PMCID: PMC9270334 DOI: 10.1038/s42003-022-03584-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 06/14/2022] [Indexed: 11/30/2022] Open
Abstract
Cell-to-cell variation in gene expression is a widespread phenomenon, which may play important roles in cellular differentiation, function, and disease development1–9. Chromatin is implicated in contributing to the cellular heterogeneity in gene expression10–16. Fully understanding the mechanisms of cellular heterogeneity requires simultaneous measurement of RNA and occupancy of histone modifications and transcription factors on chromatin due to their critical roles in transcriptional regulation17,18. We generally term the occupancy of histone modifications and transcription factors as Chromatin occupancy. Here, we report a technique, termed scPCOR-seq (single-cell Profiling of Chromatin Occupancy and RNAs Sequencing), for simultaneously profiling genome-wide chromatin protein binding or histone modification marks and RNA expression in the same cell. We demonstrated that scPCOR-seq can profile either H3K4me3 or RNAPII and RNAs in a mixture of human H1, GM12878 and 293 T cells at a single-cell resolution and either H3K4me3, RNAPII, or RNA profile can correctly separate the cells. Application of scPCOR-seq to the in vitro differentiation of the erythrocyte precursor CD36 cells from human CD34 stem or progenitor cells revealed that H3K4me3 and RNA exhibit distinct properties in clustering cells during differentiation. Overall, our work provides a promising approach to understand the relationships among different omics layers. scPCOR-seq is a single-cell sequencing technique that enables simultaneous profiling of genome-wide chromatin protein binding or histone modification marks and RNA expression in the same cell.
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Affiliation(s)
- Lixia Pan
- Laboratory of Epigenome Biology, Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Wai Lim Ku
- Laboratory of Epigenome Biology, Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Qingsong Tang
- Laboratory of Epigenome Biology, Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yaqiang Cao
- Laboratory of Epigenome Biology, Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Keji Zhao
- Laboratory of Epigenome Biology, Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
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Brennan K, Zheng H, Fahrner JA, Shin JH, Gentles AJ, Schaefer B, Sunwoo JB, Bernstein JA, Gevaert O. NSD1 mutations deregulate transcription and DNA methylation of bivalent developmental genes in Sotos syndrome. Hum Mol Genet 2022; 31:2164-2184. [PMID: 35094088 PMCID: PMC9262396 DOI: 10.1093/hmg/ddac026] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/04/2022] [Accepted: 01/19/2022] [Indexed: 11/13/2022] Open
Abstract
Sotos syndrome (SS), the most common overgrowth with intellectual disability (OGID) disorder, is caused by inactivating germline mutations of NSD1, which encodes a histone H3 lysine 36 methyltransferase. To understand how NSD1 inactivation deregulates transcription and DNA methylation (DNAm), and to explore how these abnormalities affect human development, we profiled transcription and DNAm in SS patients and healthy control individuals. We identified a transcriptional signature that distinguishes individuals with SS from controls and was also deregulated in NSD1-mutated cancers. Most abnormally expressed genes displayed reduced expression in SS; these downregulated genes consisted mostly of bivalent genes and were enriched for regulators of development and neural synapse function. DNA hypomethylation was strongly enriched within promoters of transcriptionally deregulated genes: overexpressed genes displayed hypomethylation at their transcription start sites while underexpressed genes featured hypomethylation at polycomb binding sites within their promoter CpG island shores. SS patients featured accelerated molecular aging at the levels of both transcription and DNAm. Overall, these findings indicate that NSD1-deposited H3K36 methylation regulates transcription by directing promoter DNA methylation, partially by repressing polycomb repressive complex 2 (PRC2) activity. These findings could explain the phenotypic similarity of SS to OGID disorders that are caused by mutations in PRC2 complex-encoding genes.
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Affiliation(s)
- Kevin Brennan
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Hong Zheng
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Jill A Fahrner
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - June Ho Shin
- Department of Otolaryngology – Head and Neck Surgery, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Andrew J Gentles
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Bradley Schaefer
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - John B Sunwoo
- Department of Otolaryngology – Head and Neck Surgery, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Jonathan A Bernstein
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Olivier Gevaert
- Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
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Single-cell epigenetic analysis reveals principles of chromatin states in H3.3-K27M gliomas. Mol Cell 2022; 82:2696-2713.e9. [PMID: 35716669 DOI: 10.1016/j.molcel.2022.05.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 03/28/2022] [Accepted: 05/18/2022] [Indexed: 11/23/2022]
Abstract
Cancer cells are highly heterogeneous at the transcriptional level and epigenetic state. Methods to study epigenetic heterogeneity are limited in throughput and information obtained per cell. Here, we adapted cytometry by time-of-flight (CyTOF) to analyze a wide panel of histone modifications in primary tumor-derived lines of diffused intrinsic pontine glioma (DIPG). DIPG is a lethal glioma, driven by a histone H3 lysine 27 mutation (H3-K27M). We identified two epigenetically distinct subpopulations in DIPG, reflecting inherent heterogeneity in expression of the mutant histone. These two subpopulations are robust across tumor lines derived from different patients and show differential proliferation capacity and expression of stem cell and differentiation markers. Moreover, we demonstrate the use of these high-dimensional data to elucidate potential interactions between histone modifications and epigenetic alterations during the cell cycle. Our work establishes new concepts for the analysis of epigenetic heterogeneity in cancer that could be applied to diverse biological systems.
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72
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Ren SC, Mao N, Yi S, Ma X, Zou JQ, Tang X, Fan JM. Vascular Calcification in Chronic Kidney Disease: An Update and Perspective. Aging Dis 2022; 13:673-697. [PMID: 35656113 PMCID: PMC9116919 DOI: 10.14336/ad.2021.1024] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 10/24/2021] [Indexed: 12/13/2022] Open
Abstract
Chronic kidney disease is a devastating condition resulting from irreversible loss of nephron numbers and function and leading to end-stage renal disease and mineral disorders. Vascular calcification, an ectopic deposition of calcium-phosphate salts in blood vessel walls and heart valves, is an independent risk factor of cardiovascular morbidity and mortality in chronic kidney disease. Moreover, aging and related metabolic disorders are essential risk factors for chronic kidney disease and vascular calcification. Marked progress has been recently made in understanding and treating vascular calcification in chronic kidney disease. However, there is a paucity of systematic reviews summarizing this progress, and investigating unresolved issues is warranted. In this systematic review, we aimed to overview the underlying mechanisms of vascular calcification in chronic kidney diseases and discuss the impact of chronic kidney disease on the pathophysiology of vascular calcification. Additionally, we summarized potential clinical diagnostic biomarkers and therapeutic applications for vascular calcification with chronic kidney disease. This review may offer new insights into the pathogenesis, diagnosis, and therapeutic intervention of vascular calcification.
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Affiliation(s)
- Si-Chong Ren
- Chengdu Medical College, Chengdu, China.
- Department of Nephrology, First Affiliated Hospital of Chengdu Medical College, Chengdu, China.
- Center for Translational Medicine, Sichuan Academy of Traditional Chinese Medicine, Chengdu, China.
| | - Nan Mao
- Chengdu Medical College, Chengdu, China.
- Department of Nephrology, First Affiliated Hospital of Chengdu Medical College, Chengdu, China.
| | - Si Yi
- Chengdu Medical College, Chengdu, China.
- Clinical Research Center for Geriatrics of Sichuan Province, Chengdu, China.
| | - Xin Ma
- Chengdu Medical College, Chengdu, China.
- Department of Nephrology, First Affiliated Hospital of Chengdu Medical College, Chengdu, China.
| | - Jia-Qiong Zou
- Chengdu Medical College, Chengdu, China.
- Department of Nephrology, First Affiliated Hospital of Chengdu Medical College, Chengdu, China.
| | - Xiaoqiang Tang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Jun-Ming Fan
- Chengdu Medical College, Chengdu, China.
- Clinical Research Center for Geriatrics of Sichuan Province, Chengdu, China.
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Fiocchi C, Iliopoulos D. Inflammatory Bowel Disease Therapy: Beyond the Immunome. Front Immunol 2022; 13:864762. [PMID: 35615360 PMCID: PMC9124778 DOI: 10.3389/fimmu.2022.864762] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/11/2022] [Indexed: 12/19/2022] Open
Affiliation(s)
- Claudio Fiocchi
- Department of Inflammation & Immunity, Lerner Research Institute Cleveland, Cleveland, OH, United States
- Department of Gastroenterology, Hepatology & Nutrition, Digestive Disease and Surgery Institute, Cleveland Clinic, Cleveland, OH, United States
- *Correspondence: Claudio Fiocchi,
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Li W, Feng SS, Wu H, Deng J, Zhou WY, Jia MX, Shi Y, Ma L, Zeng XX, Zuberi Z, Fu D, Liu X, Chen Z. Comprehensive Analysis of CDK1-Associated ceRNA Network Revealing the Key Pathways LINC00460/LINC00525-Hsa-Mir-338-FAM111/ZWINT as Prognostic Biomarkers in Lung Adenocarcinoma Combined with Experiments. Cells 2022; 11:cells11071220. [PMID: 35406786 PMCID: PMC8997540 DOI: 10.3390/cells11071220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/20/2022] [Accepted: 03/29/2022] [Indexed: 12/10/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is the leading cause of cancer deaths worldwide, and effective biomarkers are still lacking for early detection and prognosis prediction. Here, based on gene expression profiles of LUAD patients from The Cancer Genome Atlas (TCGA), 806 long non-coding RNAs (lncRNAs), 122 microRNAs (miRNAs) and 1269 mRNAs associated with CDK1 were identified. The regulatory axis of LINC00460/LINC00525-hsa-mir-338-FAM111B/ZWINT was determined according to the correlation between gene expression and patient prognosis. The abnormal up-regulation of FAM111B/ZWINT in LUAD was related to hypomethylation. Furthermore, immune infiltration analysis suggested FAM111B/ZWINT could affect the development and prognosis of cancer by regulating the LUAD immune microenvironment. EMT feature analysis suggested that FAM111B/ZWINT promoted tumor spread through the EMT process. Functional analysis showed FAM111B/ZWINT was involved in cell cycle events such as DNA replication and chromosome separation. We analyzed the HERB and GSCALite databases to identify potential target medicines that may play a role in the treatment of LUAD. Finally, the expression of LINC00460/LINC00525-hsa-mir-338-FAM111B/ZWINT axis was verified in LUAD cells by RT-qPCR, and these results were consistent with bioinformatics analysis. Overall, we constructed a CDK1-related ceRNA network and revealed the LINC00460/LINC00525-hsa-mir-338-FAM111/ZWINT pathways as potential diagnostic biomarkers or therapeutic targets of LUAD.
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Affiliation(s)
- Wen Li
- College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou 412007, China; (W.L.); (S.-S.F.); (J.D.); (L.M.); (X.-X.Z.)
- National Engineering Research Center of Rice and Byproduct Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China; (H.W.); (M.-X.J.); (Y.S.)
| | - Shan-Shan Feng
- College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou 412007, China; (W.L.); (S.-S.F.); (J.D.); (L.M.); (X.-X.Z.)
| | - Hao Wu
- National Engineering Research Center of Rice and Byproduct Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China; (H.W.); (M.-X.J.); (Y.S.)
| | - Jing Deng
- College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou 412007, China; (W.L.); (S.-S.F.); (J.D.); (L.M.); (X.-X.Z.)
| | - Wang-Yan Zhou
- Department of Medical Record, Hengyang Medical School, The First Affiliated Hospital, University of South China, Hengyang 421001, China;
| | - Ming-Xi Jia
- National Engineering Research Center of Rice and Byproduct Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China; (H.W.); (M.-X.J.); (Y.S.)
| | - Yi Shi
- National Engineering Research Center of Rice and Byproduct Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China; (H.W.); (M.-X.J.); (Y.S.)
| | - Liang Ma
- College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou 412007, China; (W.L.); (S.-S.F.); (J.D.); (L.M.); (X.-X.Z.)
| | - Xiao-Xi Zeng
- College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou 412007, China; (W.L.); (S.-S.F.); (J.D.); (L.M.); (X.-X.Z.)
| | - Zavuga Zuberi
- Department of Science and Laboratory Technology, Dar es Salaam Institute of Technology, Dar es Salaam P.O. Box 2958, Tanzania;
| | - Da Fu
- Central Laboratory for Medical Research, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai 200072, China;
| | - Xiang Liu
- Department of Thoracic Surgery, Hengyang Medical School, The Second Affiliated Hospital, University of South China, Hengyang 421001, China
- Correspondence: (X.L.); (Z.C.); Tel.: +86-0734-889-9990 (X.L.); +86-158-6971-6968 (Z.C.)
| | - Zhu Chen
- College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou 412007, China; (W.L.); (S.-S.F.); (J.D.); (L.M.); (X.-X.Z.)
- Correspondence: (X.L.); (Z.C.); Tel.: +86-0734-889-9990 (X.L.); +86-158-6971-6968 (Z.C.)
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Furth N, Shema E. It’s all in the combination: decoding the epigenome for cancer research and diagnostics. Curr Opin Genet Dev 2022; 73:101899. [PMID: 35091256 PMCID: PMC9168437 DOI: 10.1016/j.gde.2022.101899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 12/20/2021] [Accepted: 12/28/2021] [Indexed: 12/14/2022]
Abstract
Genome regulation is governed by the dynamics of chromatin modifications. The extensive and diverse array of DNA and histone modifications allow multiple elements to act combinatorically and direct tissue-specific and cell-specific outcomes. Yet, our ability to elucidate these complex combinations and link them to normal genome regulation, as well as understand their deregulation in cancer, has been hindered by the lack of suitable technologies. Here, we describe recent findings indicating the importance of the combinatorial epigenome, and novel methodologies to measure and characterize these combinations. These complementary methods span multiple disciplines, providing a means to decode epigenetic combinations and link them to biological outcomes. Finally, we discuss the promise of harnessing the rich combinatorial epigenetic information to improve cancer diagnostics and monitoring.
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Affiliation(s)
- Noa Furth
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Efrat Shema
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel.
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76
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Fraschilla I, Amatullah H, Jeffrey KL. One genome, many cell states: epigenetic control of innate immunity. Curr Opin Immunol 2022; 75:102173. [PMID: 35405493 PMCID: PMC9081230 DOI: 10.1016/j.coi.2022.102173] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/23/2022] [Accepted: 02/23/2022] [Indexed: 12/15/2022]
Abstract
A hallmark of the innate immune system is its ability to rapidly initiate short-lived or sustained transcriptional programs in a cell-specific and pathogen-specific manner that is dependent on dynamic chromatin states. Much of the epigenetic landscape is set during cellular differentiation; however, pathogens and other environmental cues also induce changes in chromatin that can either promote tolerance or 'train' innate immune cells for amplified secondary responses. We review chromatin processes that enable innate immune cell differentiation and functional transcriptional responses in naive or experienced cells, in concert with signal transduction and cellular metabolic shifts. We discuss how immune chromatin mechanisms are maladapted in disease and novel therapeutic approaches for cellular reprogramming.
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Affiliation(s)
- Isabella Fraschilla
- Division of Gastroenterology and Center for the Study of Inflammatory Bowel Disease, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Program in Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Hajera Amatullah
- Division of Gastroenterology and Center for the Study of Inflammatory Bowel Disease, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Kate L Jeffrey
- Division of Gastroenterology and Center for the Study of Inflammatory Bowel Disease, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Program in Immunology, Harvard Medical School, Boston, MA 02115, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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77
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Li G, Ma L, He S, Luo R, Wang B, Zhang W, Song Y, Liao Z, Ke W, Xiang Q, Feng X, Wu X, Zhang Y, Wang K, Yang C. WTAP-mediated m 6A modification of lncRNA NORAD promotes intervertebral disc degeneration. Nat Commun 2022; 13:1469. [PMID: 35304463 PMCID: PMC8933458 DOI: 10.1038/s41467-022-28990-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 02/15/2022] [Indexed: 12/11/2022] Open
Abstract
N6-methyladenosine (m6A) is the most prevalent RNA modification at the posttranscriptional level and involved in various diseases and cellular processes. However, the underlying mechanism of m6A regulation in intervertebral disc degeneration (IVDD) remains elusive. Here, we show that methylation of the lncRNA NORAD significantly increases in senescent nucleus pulposus cells (NPCs) by m6A sequencing. Subsequent loss- and gain-of-function experiments reveal WTAP is increased in senescent NPCs due to an epigenetic increase in H3K4me3 of the promoter mediated by KDM5a, and significantly promotes NORAD m6A modification. Furthermore, YTHDF2-mediated decay of NORAD is enhanced in senescent NPCs, and then deficiency of NORAD results in less sequestraion of PUMILIO proteins, contributing to the augmented activity of PUM1/2, thus repressing the expression of target E2F3 mRNAs and promoting the cellular senescence. Here, we show interruption of NORAD m6A modification or the NORAD/PUMILIO/E2F3 axis could serve as a potential therapeutic target to inhibit the senescence of NPCs and development of IVDD. Intervertebral disc degeneration (IVDD) is the leading cause of low back pain and Nucleus pulposus cell senescence contributes a lot to its progression. Here, the authors reveal WTAP-mediated m6A modification of lncRNA NORAD promotes IVDD.
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Affiliation(s)
- Gaocai Li
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Liang Ma
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Shujie He
- Department of Cardiology, Union Hospital, and Key Laboratory of Biological Targeted Therapy of the Ministry of Education, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Rongjin Luo
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Bingjin Wang
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Weifeng Zhang
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Yu Song
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Zhiwei Liao
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Wencan Ke
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Qian Xiang
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Xiaobo Feng
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Xinghuo Wu
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Yukun Zhang
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China
| | - Kun Wang
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China.
| | - Cao Yang
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China.
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78
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How to Slow Down the Ticking Clock: Age-Associated Epigenetic Alterations and Related Interventions to Extend Life Span. Cells 2022; 11:cells11030468. [PMID: 35159278 PMCID: PMC8915189 DOI: 10.3390/cells11030468] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 01/26/2022] [Indexed: 02/04/2023] Open
Abstract
Epigenetic alterations pose one major hallmark of organismal aging. Here, we provide an overview on recent findings describing the epigenetic changes that arise during aging and in related maladies such as neurodegeneration and cancer. Specifically, we focus on alterations of histone modifications and DNA methylation and illustrate the link with metabolic pathways. Age-related epigenetic, transcriptional and metabolic deregulations are highly interconnected, which renders dissociating cause and effect complicated. However, growing amounts of evidence support the notion that aging is not only accompanied by epigenetic alterations, but also at least in part induced by those. DNA methylation clocks emerged as a tool to objectively determine biological aging and turned out as a valuable source in search of factors positively and negatively impacting human life span. Moreover, specific epigenetic signatures can be used as biomarkers for age-associated disorders or even as targets for therapeutic approaches, as will be covered in this review. Finally, we summarize recent potential intervention strategies that target epigenetic mechanisms to extend healthy life span and provide an outlook on future developments in the field of longevity research.
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79
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Hematopoiesis, Inflammation and Aging-The Biological Background and Clinical Impact of Anemia and Increased C-Reactive Protein Levels on Elderly Individuals. J Clin Med 2022; 11:jcm11030706. [PMID: 35160156 PMCID: PMC8836692 DOI: 10.3390/jcm11030706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 01/27/2023] Open
Abstract
Anemia and systemic signs of inflammation are common in elderly individuals and are associated with decreased survival. The common biological context for these two states is then the hallmarks of aging, i.e., genomic instability, telomere shortening, epigenetic alterations, loss of proteostasis, deregulated nutrient sensing, mitochondrial dysfunction, cellular senescence, stem cell exhaustion and altered intercellular communication. Such aging-associated alterations of hematopoietic stem cells are probably caused by complex mechanisms and depend on both the aging of hematopoietic (stem) cells and on the supporting stromal cells. The function of inflammatory or immunocompetent cells is also altered by aging. The intracellular signaling initiated by soluble proinflammatory mediators (e.g., IL1, IL6 and TNFα) is altered during aging and contributes to the development of both the inhibition of erythropoiesis with anemia as well as to the development of the acute-phase reaction as a systemic sign of inflammation with increased CRP levels. Both anemia and increased CRP levels are associated with decreased overall survival and increased cardiovascular mortality. The handling of elderly patients with inflammation and/or anemia should in our opinion be individualized; all of them should have a limited evaluation with regard to the cause of the abnormalities, but the extent of additional and especially invasive diagnostic evaluation should be based on an overall clinical evaluation and the possible therapeutic consequences.
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80
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Kusi M, Zand M, Lin LL, Chen M, Lopez A, Lin CL, Wang CM, Lucio ND, Kirma NB, Ruan J, Huang THM, Mitsuya K. 2-Hydroxyglutarate destabilizes chromatin regulatory landscape and lineage fidelity to promote cellular heterogeneity. Cell Rep 2022; 38:110220. [PMID: 35021081 PMCID: PMC8811753 DOI: 10.1016/j.celrep.2021.110220] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 09/23/2021] [Accepted: 12/15/2021] [Indexed: 02/07/2023] Open
Abstract
The epigenome delineates lineage-specific transcriptional programs and restricts cell plasticity to prevent non-physiological cell fate transitions. Although cell diversification fosters tumor evolution and therapy resistance, upstream mechanisms that regulate the stability and plasticity of the cancer epigenome remain elusive. Here we show that 2-hydroxyglutarate (2HG) not only suppresses DNA repair but also mediates the high-plasticity chromatin landscape. A combination of single-cell epigenomics and multi-omics approaches demonstrates that 2HG disarranges otherwise well-preserved stable nucleosome positioning and promotes cell-to-cell variability. 2HG induces loss of motif accessibility to the luminal-defining transcriptional factors FOXA1, FOXP1, and GATA3 and a shift from luminal to basal-like gene expression. Breast tumors with high 2HG exhibit enhanced heterogeneity with undifferentiated epigenomic signatures linked to adverse prognosis. Further, ascorbate-2-phosphate (A2P) eradicates heterogeneity and impairs growth of high 2HG-producing breast cancer cells. These findings suggest 2HG as a key determinant of cancer plasticity and provide a rational strategy to counteract tumor cell evolution. Kusi et al. show that the oncometabolite 2-hydroxyglutarate (2HG) initiates cell-level epigenome fluctuations in the chromatin regulatory landscape, accompanied by loss of lineage fidelity. Breast tumors with high 2HG accumulation exhibit enhanced cellular heterogeneity with undifferentiated stem-like epigenomic signatures. The findings suggest metabolic derangement as a molecular origin of breast cancer heterogeneity.
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Affiliation(s)
- Meena Kusi
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Maryam Zand
- Department of Computer Science, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Li-Ling Lin
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Meizhen Chen
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Anthony Lopez
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Chun-Lin Lin
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Chiou-Miin Wang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Nicholas D Lucio
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Nameer B Kirma
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Jianhua Ruan
- Department of Computer Science, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Tim H-M Huang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA.
| | - Kohzoh Mitsuya
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA.
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81
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Bermick J, Schaller M. Epigenetic regulation of pediatric and neonatal immune responses. Pediatr Res 2022; 91:297-327. [PMID: 34239066 DOI: 10.1038/s41390-021-01630-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/01/2021] [Accepted: 06/09/2021] [Indexed: 02/06/2023]
Abstract
Epigenetic regulation of transcription is a collective term that refers to mechanisms known to regulate gene transcription without changing the underlying DNA sequence. These mechanisms include DNA methylation and histone tail modifications which influence chromatin accessibility, and microRNAs that act through post-transcriptional gene silencing. Epigenetics is known to regulate a variety of biological processes, and the role of epigtenetics in immunity and immune-mediated diseases is becoming increasingly recognized. While DNA methylation is the most widely studied, each of these systems play an important role in the development and maintenance of appropriate immune responses. There is clear evidence that epigenetic mechanisms contribute to developmental stage-specific immune responses in a cell-specific manner. There is also mounting evidence that prenatal exposures alter epigenetic profiles and subsequent immune function in exposed offspring. Early life exposures that are associated with poor long-term health outcomes also appear to impact immune specific epigenetic patterning. Finally, each of these epigenetic mechanisms contribute to the pathogenesis of a wide variety of diseases that manifest during childhood. This review will discuss each of these areas in detail. IMPACT: Epigenetics, including DNA methylation, histone tail modifications, and microRNA expression, dictate immune cell phenotypes. Epigenetics influence immune development and subsequent immune health. Prenatal, perinatal, and postnatal exposures alter immune cell epigenetic profiles and subsequent immune function. Numerous pediatric-onset diseases have an epigenetic component. Several successful strategies for childhood diseases target epigenetic mechanisms.
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Affiliation(s)
- Jennifer Bermick
- Department of Pediatrics, Division of Neonatology, University of Iowa, Iowa City, IA, USA. .,Iowa Inflammation Program, University of Iowa, Iowa City, IA, USA.
| | - Matthew Schaller
- Department of Pulmonary, Critical Care & Sleep Medicine, University of Florida, Gainesville, FL, USA
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82
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Physiological Ovarian Aging Is Associated with Altered Expression of Post-Translational Modifications in Mice. Int J Mol Sci 2021; 23:ijms23010002. [PMID: 35008428 PMCID: PMC8744712 DOI: 10.3390/ijms23010002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 12/22/2022] Open
Abstract
Post-translational modifications (PTMs) have been confirmed to be involved in multiple female reproductive events, but their role in physiological ovarian aging is far from elucidated. In this study, mice aged 3, 12 or 17 months (3M, 12M, 17M) were selected as physiological ovarian aging models. The expression of female reproductive function-related genes, the global profiles of PTMs, and the level of histone modifications and related regulatory enzymes were examined during physiological ovarian aging in the mice by quantitative real-time PCR and western blot, respectively. The results showed that the global protein expression of Kbhb (lysineβ-hydroxybutyryllysine), Khib (lysine 2-hydroxyisobutyryllysine), Kglu (lysineglutaryllysine), Kmal (lysinemalonyllysine), Ksucc (lysinesuccinyllysine), Kcr (lysinecrotonyllysine), Kbu (lysinebutyryllysine), Kpr (lysinepropionyllysine), SUMO1 (SUMO1 modification), ub (ubiquitination), P-Typ (phosphorylation), and 3-nitro-Tyr (nitro-tyrosine) increased significantly as mice aged. Moreover, the modification level of Kme2 (lysinedi-methyllysine) and Kac (lysineacetyllysine) was the highest in the 3M mice and the lowest in 12M mice. In addition, only trimethylation of histone lysine was up-regulated progressively and significantly with increasing age (p < 0.001), H4 ubiquitination was obviously higher in the 12M and 17M mice than 3M (p < 0.001), whereas the modification of Kpr (lysinepropionylation) and O-GlcNA in 17M was significantly decreased compared with the level in 3M mice (p < 0.05, p < 0.01). Furthermore, the expression levels of the TIP60, P300, PRDM9, KMT5B, and KMT5C genes encoding PTM regulators were up-regulated in 17M compared to 3M female mice (p < 0.05). These findings indicate that altered related regulatory enzymes and PTMs are associated with physiological ovarian aging in mice, which is expected to provide useful insights for the delay of ovarian aging and the diagnosis and treatment of female infertility.
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83
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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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84
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Human immune diversity: from evolution to modernity. Nat Immunol 2021; 22:1479-1489. [PMID: 34795445 DOI: 10.1038/s41590-021-01058-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/17/2021] [Indexed: 02/08/2023]
Abstract
The extreme diversity of the human immune system, forged and maintained throughout evolutionary history, provides a potent defense against opportunistic pathogens. At the same time, this immune variation is the substrate upon which a plethora of immune-associated diseases develop. Genetic analysis suggests that thousands of individually weak loci together drive up to half of the observed immune variation. Intense selection maintains this genetic diversity, even selecting for the introgressed Neanderthal or Denisovan alleles that have reintroduced variation lost during the out-of-Africa migration. Variations in age, sex, diet, environmental exposure, and microbiome each potentially explain the residual variation, with proof-of-concept studies demonstrating both plausible mechanisms and correlative associations. The confounding interaction of many of these variables currently makes it difficult to assign definitive contributions. Here, we review the current state of play in the field, identify the key unknowns in the causality of immune variation, and identify the multidisciplinary pathways toward an improved understanding.
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85
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Kluever V, Fornasiero EF. Principles of brain aging: Status and challenges of modeling human molecular changes in mice. Ageing Res Rev 2021; 72:101465. [PMID: 34555542 DOI: 10.1016/j.arr.2021.101465] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 01/22/2023]
Abstract
Due to the extension of human life expectancy, the prevalence of cognitive impairment is rising in the older portion of society. Developing new strategies to delay or attenuate cognitive decline is vital. For this purpose, it is imperative to understand the cellular and molecular events at the basis of brain aging. While several organs are directly accessible to molecular analysis through biopsies, the brain constitutes a notable exception. Most of the molecular studies are performed on postmortem tissues, where cell death and tissue damage have already occurred. Hence, the study of the molecular aspects of cognitive decline largely relies on animal models and in particular on small mammals such as mice. What have we learned from these models? Do these animals recapitulate the changes observed in humans? What should we expect from future mouse studies? In this review we answer these questions by summarizing the state of the research that has addressed cognitive decline in mice from several perspectives, including genetic manipulation and omics strategies. We conclude that, while extremely valuable, mouse models have limitations that can be addressed by the optimal design of future studies and by ensuring that results are cross-validated in the human context.
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86
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Zhang H, Weyand CM, Goronzy JJ. Hallmarks of the aging T-cell system. FEBS J 2021; 288:7123-7142. [PMID: 33590946 PMCID: PMC8364928 DOI: 10.1111/febs.15770] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/24/2021] [Accepted: 02/15/2021] [Indexed: 12/21/2022]
Abstract
The adaptive immune system has the enormous challenge to protect the host through the generation and differentiation of pathogen-specific short-lived effector T cells while in parallel developing long-lived memory cells to control future encounters with the same pathogen. A complex regulatory network is needed to preserve a population of naïve cells over lifetime that exhibit sufficient diversity of antigen receptors to respond to new antigens, while also sustaining immune memory. In parallel, cells need to maintain their proliferative potential and the plasticity to differentiate into different functional lineages. Initial signs of waning immune competence emerge after 50 years of age, with increasing clinical relevance in the 7th-10th decade of life. Morbidity and mortality from infections increase, as drastically exemplified by the current COVID-19 pandemic. Many vaccines, such as for the influenza virus, are poorly effective to generate protective immunity in older individuals. Age-associated changes occur at the level of the T-cell population as well as the functionality of its cellular constituents. The system highly relies on the self-renewal of naïve and memory T cells, which is robust but eventually fails. Genetic and epigenetic modifications contribute to functional differences in responsiveness and differentiation potential. To some extent, these changes arise from defective maintenance; to some, they represent successful, but not universally beneficial adaptations to the aging host. Interventions that can compensate for the age-related defects and improve immune responses in older adults are increasingly within reach.
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Affiliation(s)
- Huimin Zhang
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA, USA
- Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, CA, USA
| | - Cornelia M. Weyand
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA, USA
- Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, CA, USA
| | - Jörg J. Goronzy
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA, USA
- Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, CA, USA
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87
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Visram A, Kourelis TV. Aging-associated immune system changes in multiple myeloma: The dark side of the moon. Cancer Treat Res Commun 2021; 29:100494. [PMID: 34837796 DOI: 10.1016/j.ctarc.2021.100494] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 11/18/2021] [Indexed: 02/08/2023]
Abstract
Multiple myeloma (MM) is a disease of the elderly. Changes that occur in the immune system with aging, also known as immunosenescence, have been associated with decreased tumor immunosurveillance and are thought to contribute to the development of MM and other cancers in the elderly. Once MM establishes itself in the bone marrow, immunosenescence related changes have been observed in the immune tumor microenvironment (iTME) and are driven by the malignant cells. The efficacy of novel immunotherapies used to treat MM has been blunted by detrimental iTME changes that occur at later disease stages and are, to some extent, driven by prior therapies. In this review, we discuss general changes that occur in the immune system with aging as well as our current knowledge of immunosenescence in MM. We discuss the differences and overlap between T cell senescence and exhaustion as well as potential methods to prevent or reverse immunosenescence. We focus predominantly on T cell immunosenescence which has been better evaluated in this disease and is more pertinent to novel MM immunotherapies. Our lack of understanding of the drivers of immunosenescence at each stage of the disease, from precursor stages to heavily pretreated MM, represents a major barrier to improving the efficacy of novel and existing therapies.
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Affiliation(s)
- Alissa Visram
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN United States; Department of Medicine, Division of Hematology, University of Ottawa, Ottawa Hospital Research Institute, Ontario, Canada
| | - Taxiarchis V Kourelis
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN United States.
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88
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Lozupone M, Mollica A, Berardino G, Sardone R, Panza F. Could epigenetics play a role in suicidal behavior in older age? Epigenomics 2021; 14:73-79. [PMID: 34784757 DOI: 10.2217/epi-2021-0390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Tweetable abstract There is growing evidence of a role of environmental exposures in the pathogenesis and epigenetics of suicidal behavior in older age.
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Affiliation(s)
- Madia Lozupone
- Neurodegenerative Disease Unit, Department of Basic Medical Sciences, Neuroscience & Sense Organs, University of Bari Aldo Moro, Bari, 70100, Italy
| | - Anita Mollica
- Psychiatric Unit, Department of Clinical & Experimental Medicine, University of Foggia, Foggia, 71122, Italy
| | - Giuseppe Berardino
- Psychiatric Unit, Department of Clinical & Experimental Medicine, University of Foggia, Foggia, 71122, Italy
| | - Rodolfo Sardone
- Salus In Apulia Study: Frailty Phenotypes Research Unit, National Institute of Gastroenterology 'Saverio de Bellis', Research Hospital, Castellana Grotte Bari, 70013, Italy
| | - Francesco Panza
- Salus In Apulia Study: Frailty Phenotypes Research Unit, National Institute of Gastroenterology 'Saverio de Bellis', Research Hospital, Castellana Grotte Bari, 70013, Italy
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89
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Tinnevelt GH, Wouters K, Postma GJ, Folcarelli R, Jansen JJ. High-throughput single cell data analysis - A tutorial. Anal Chim Acta 2021; 1185:338872. [PMID: 34711307 DOI: 10.1016/j.aca.2021.338872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 06/28/2021] [Accepted: 07/21/2021] [Indexed: 11/30/2022]
Abstract
White blood cells protect the body against disease but may also cause chronic inflammation, auto-immune diseases or leukemia. There are many different white blood cell types whose identity and function can be studied by measuring their protein expression. Therefore, high-throughput analytical instruments were developed to measure multiple proteins on millions of single cells. The information-rich biochemistry information may only be fully extracted using multivariate statistics. Here we show an overview of the most essential steps for multivariate data analysis of single cell data. We used white blood cells (immunology) as a case study, but a similar approach may be used in environment or biotech research. The first step is analyzing the study design and subsequently formulating a research question. The three main designs are immunophenotyping (finding different cell types), cell activation and rare cell discovery. When preparing the data it is essential to consider the design and focus on the cell type of interest by removing all unwanted events. After pre-processing, the ten-thousands to millions of single cells per sample need to be converted into a cellular distribution. For immunophenotyping a clustering method such as Self-Organizing Maps is useful and for cell activation a model that describes the covariance such as Principal Component Analysis is useful. In rare cell discovery it is useful to first model all common cells and remove them to find the rare cells. Finally discriminant analysis based on the cellular distribution may highlight which cell (sub)types are different between groups.
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Affiliation(s)
- Gerjen H Tinnevelt
- Radboud University, Institute for Molecules and Materials, Analytical Chemistry, P.O. Box 9010, 6500, GL, Nijmegen, the Netherlands.
| | - Kristiaan Wouters
- Department of Internal Medicine, Laboratory of Metabolism and Vascular Medicine, P.O. Box 616 (UNS50/14), 6200, MD, Maastricht, the Netherlands
| | - Geert J Postma
- Radboud University, Institute for Molecules and Materials, Analytical Chemistry, P.O. Box 9010, 6500, GL, Nijmegen, the Netherlands
| | - Rita Folcarelli
- Corbion, Arkelsedijk 46, 4206, AC, Gorinchem, the Netherlands
| | - Jeroen J Jansen
- Radboud University, Institute for Molecules and Materials, Analytical Chemistry, P.O. Box 9010, 6500, GL, Nijmegen, the Netherlands
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90
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Aging, Bone Marrow and Next-Generation Sequencing (NGS): Recent Advances and Future Perspectives. Int J Mol Sci 2021; 22:ijms222212225. [PMID: 34830107 PMCID: PMC8620539 DOI: 10.3390/ijms222212225] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/07/2021] [Accepted: 11/09/2021] [Indexed: 12/28/2022] Open
Abstract
The aging of bone marrow (BM) remains a very imperative and alluring subject, with an ever-increasing interest among fellow scientists. A considerable amount of progress has been made in this field with the established ‘hallmarks of aging’ and continued efforts to investigate the age-related changes observed within the BM. Inflammaging is considered as a low-grade state of inflammation associated with aging, and whilst the possible mechanisms by which aging occurs are now largely understood, the processes leading to the underlying changes within aged BM remain elusive. The ability to identify these changes and detect such alterations at the genetic level are key to broadening the knowledgebase of aging BM. Next-generation sequencing (NGS) is an important molecular-level application presenting the ability to not only determine genomic base changes but provide transcriptional profiling (RNA-seq), as well as a high-throughput analysis of DNA–protein interactions (ChIP-seq). Utilising NGS to explore the genetic alterations occurring over the aging process within alterative cell types facilitates the comprehension of the molecular and cellular changes influencing the dynamics of aging BM. Thus, this review prospects the current landscape of BM aging and explores how NGS technology is currently being applied within this ever-expanding field of research.
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91
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Evaluating the beneficial effects of dietary restrictions: A framework for precision nutrigeroscience. Cell Metab 2021; 33:2142-2173. [PMID: 34555343 PMCID: PMC8845500 DOI: 10.1016/j.cmet.2021.08.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 08/17/2021] [Accepted: 08/30/2021] [Indexed: 12/12/2022]
Abstract
Dietary restriction (DR) has long been viewed as the most robust nongenetic means to extend lifespan and healthspan. Many aging-associated mechanisms are nutrient responsive, but despite the ubiquitous functions of these pathways, the benefits of DR often vary among individuals and even among tissues within an individual, challenging the aging research field. Furthermore, it is often assumed that lifespan interventions like DR will also extend healthspan, which is thus often ignored in aging studies. In this review, we provide an overview of DR as an intervention and discuss the mechanisms by which it affects lifespan and various healthspan measures. We also review studies that demonstrate exceptions to the standing paradigm of DR being beneficial, thus raising new questions that future studies must address. We detail critical factors for the proposed field of precision nutrigeroscience, which would utilize individualized treatments and predict outcomes using biomarkers based on genotype, sex, tissue, and age.
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92
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H3K4 di-methylation governs smooth muscle lineage identity and promotes vascular homeostasis by restraining plasticity. Dev Cell 2021; 56:2765-2782.e10. [PMID: 34582749 PMCID: PMC8567421 DOI: 10.1016/j.devcel.2021.09.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 07/09/2021] [Accepted: 08/30/2021] [Indexed: 12/15/2022]
Abstract
Epigenetic mechanisms contribute to the regulation of cell differentiation and function. Vascular smooth muscle cells (SMCs) are specialized contractile cells that retain phenotypic plasticity even after differentiation. Here, by performing selective demethylation of histone H3 lysine 4 di-methylation (H3K4me2) at SMC-specific genes, we uncovered that H3K4me2 governs SMC lineage identity. Removal of H3K4me2 via selective editing in cultured vascular SMCs and in murine arterial vasculature led to loss of differentiation and reduced contractility due to impaired recruitment of the DNA methylcytosine dioxygenase TET2. H3K4me2 editing altered SMC adaptative capacities during vascular remodeling due to loss of miR-145 expression. Finally, H3K4me2 editing induced a profound alteration of SMC lineage identity by redistributing H3K4me2 toward genes associated with stemness and developmental programs, thus exacerbating plasticity. Our studies identify the H3K4me2-TET2-miR145 axis as a central epigenetic memory mechanism controlling cell identity and function, whose alteration could contribute to various pathophysiological processes.
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93
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Epigenetic networks driving T cell identity and plasticity during immunosenescence. Trends Genet 2021; 38:120-123. [PMID: 34561103 DOI: 10.1016/j.tig.2021.08.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/27/2021] [Accepted: 08/31/2021] [Indexed: 01/09/2023]
Abstract
The aging process is associated with the accumulation of epigenetic alterations in immune cells, although the origin of these changes is not clear. Understanding this epigenetic drift in the immune system can provide essential information about the progression of the aging process and the immune history of each individual.
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94
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Natarajan K, Eisfeldt J, Hammond M, Laffita-Mesa JM, Patra K, Khoshnood B, Öijerstedt L, Graff C. Single-cell multimodal analysis in a case with reduced penetrance of Progranulin-Frontotemporal Dementia. Acta Neuropathol Commun 2021; 9:132. [PMID: 34344473 PMCID: PMC8336016 DOI: 10.1186/s40478-021-01234-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/23/2021] [Indexed: 11/10/2022] Open
Abstract
We identified an autosomal dominant progranulin mutation carrier without symptoms of dementia in her lifetime (Reduced Penetrance Mutation Carrier, RedPenMC). This resistance to develop expected pathology presents a unique opportunity to interrogate neurodegenerative mechanisms. We performed multimodal single-nuclei analyses of post-mortem frontal cortex from RedPenMC, including transcriptomics and global levels of chromatin marks. RedPenMC had an increased ratio of GRN-expressing microglia, higher levels of activating histone mark H3k4me3 in microglia and lower levels of the repressive chromatin marks H3k9me1 and H3k9me3 in the frontal cortex than her affected mutation carrier son and evidence of higher protein levels of progranulin in both plasma and brain homogenates. Although the study is limited to one case, the results support that restoring brain progranulin levels may be sufficient to escape neurodegeneration and FTD. In addition to previously identified modifier genes, it is possible that epigenetic marks may contribute to the increased progranulin expression in cases of reduced penetrance. These findings may stimulate similar follow-up studies and new therapeutic approaches.
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95
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Desterke C, Bennaceur-Griscelli A, Turhan AG. EGR1 dysregulation defines an inflammatory and leukemic program in cell trajectory of human-aged hematopoietic stem cells (HSC). Stem Cell Res Ther 2021; 12:419. [PMID: 34294125 PMCID: PMC8296523 DOI: 10.1186/s13287-021-02498-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 07/08/2021] [Indexed: 12/24/2022] Open
Abstract
Background During aging, hematopoietic stem cells (HSC) lose progressively both their self-renewal and differentiation potential. The precise molecular mechanisms of this phenomenon are not well established. To uncover the molecular events underlying this event, we have performed a bioinformatics analysis of 650 single-cell transcriptomes. Methods Single-cell transcriptome analyses of expression heterogeneity, cell cycle, and cell trajectory in human cell compartment enriched in hematopoietic stem cell compartment were investigated in the bone marrow according to the age of the donors. Identification of aging-related nodules was identified by weighted correlation network analysis in this primitive compartment. Results The analysis of single-cell transcriptomes allowed to uncover a major upregulation of EGR1 in human-aged lineage−CD34+CD38− cells which present cell cycle dysregulation with reduction of G2/M phase according to less expression of CCND2 during S phase. EGR1 upregulation in aging hematopoietic stem cells was found to be independent of cell cycle phases and gender. EGR1 expression trajectory in aged HSC highlighted a signature enriched in hematopoietic and immune disorders with the best induction of AP-1 complex and quiescence regulators such as EGR1, BTG2, JUNB, and NR41A. Sonic Hedgehog-related TMEM107 transmembrane molecule followed also EGR1 cell trajectory. EGR1-dependent gene weighted network analysis in human HSC-associated IER2 target protein-specific regulators of PP2A activity, IL1B, TNFSF10 ligands, and CD69, SELP membrane molecules in old HSC module with immune and leukemogenic signature. In contrast, for young HSC which were found with different cell cycle phase progression, its specific module highlighted upregulation of HIF1A hypoxic factor, PDE4B immune marker, DRAK2 (STK17B) T cell apoptosis regulator, and MYADM myeloid-associated marker. Conclusion EGR1 was found to be connected to the aging of human HSC and highlighted a specific cell trajectory contributing to the dysregulation of an inflammatory and leukemia-related transcriptional program in aged human HSCs. EGR1 and its program were found to be connected to the aging of human HSC with dissociation of quiescence property and cell cycle phase progression in this primitive hematopoietic compartment. Supplementary Information The online version contains supplementary material available at 10.1186/s13287-021-02498-0.
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Affiliation(s)
| | - Annelise Bennaceur-Griscelli
- INSERM UA9, University Paris-Saclay, 94800, Villejuif, France.,ESTeam Paris Sud, INGESTEM National IPSC Infrastructure, University Paris-Saclay, 94800, Villejuif, France.,Division of Hematology, APHP-Paris Saclay University Hospitals, Le Kremlin Bicêtre 94275, 94800, Villejuif, France.,Faculty of Medicine, University Paris Saclay, 94275, Le Kremlin Bicêtre, France
| | - Ali G Turhan
- INSERM UA9, University Paris-Saclay, 94800, Villejuif, France. .,ESTeam Paris Sud, INGESTEM National IPSC Infrastructure, University Paris-Saclay, 94800, Villejuif, France. .,Division of Hematology, APHP-Paris Saclay University Hospitals, Le Kremlin Bicêtre 94275, 94800, Villejuif, France. .,Faculty of Medicine, University Paris Saclay, 94275, Le Kremlin Bicêtre, France.
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96
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Wimmers F, Donato M, Kuo A, Ashuach T, Gupta S, Li C, Dvorak M, Foecke MH, Chang SE, Hagan T, De Jong SE, Maecker HT, van der Most R, Cheung P, Cortese M, Bosinger SE, Davis M, Rouphael N, Subramaniam S, Yosef N, Utz PJ, Khatri P, Pulendran B. The single-cell epigenomic and transcriptional landscape of immunity to influenza vaccination. Cell 2021; 184:3915-3935.e21. [PMID: 34174187 PMCID: PMC8316438 DOI: 10.1016/j.cell.2021.05.039] [Citation(s) in RCA: 123] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/15/2021] [Accepted: 05/25/2021] [Indexed: 12/13/2022]
Abstract
Emerging evidence indicates a fundamental role for the epigenome in immunity. Here, we mapped the epigenomic and transcriptional landscape of immunity to influenza vaccination in humans at the single-cell level. Vaccination against seasonal influenza induced persistently diminished H3K27ac in monocytes and myeloid dendritic cells (mDCs), which was associated with impaired cytokine responses to Toll-like receptor stimulation. Single-cell ATAC-seq analysis revealed an epigenomically distinct subcluster of monocytes with reduced chromatin accessibility at AP-1-targeted loci after vaccination. Similar effects were observed in response to vaccination with the AS03-adjuvanted H5N1 pandemic influenza vaccine. However, this vaccine also stimulated persistently increased chromatin accessibility at interferon response factor (IRF) loci in monocytes and mDCs. This was associated with elevated expression of antiviral genes and heightened resistance to the unrelated Zika and Dengue viruses. These results demonstrate that vaccination stimulates persistent epigenomic remodeling of the innate immune system and reveal AS03's potential as an epigenetic adjuvant.
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Affiliation(s)
- Florian Wimmers
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michele Donato
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alex Kuo
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tal Ashuach
- Department of Electrical Engineering and Computer Sciences and Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Shakti Gupta
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive MC 0412, La Jolla, CA 92093, USA
| | - Chunfeng Li
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mai Dvorak
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mariko Hinton Foecke
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sarah E Chang
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Thomas Hagan
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sanne E De Jong
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Holden T Maecker
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Peggie Cheung
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mario Cortese
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Steven E Bosinger
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Mark Davis
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Nadine Rouphael
- Hope Clinic of the Emory Vaccine Center, Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Decatur, GA 30030, USA
| | - Shankar Subramaniam
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive MC 0412, La Jolla, CA 92093, USA
| | - Nir Yosef
- Department of Electrical Engineering and Computer Sciences and Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | - Paul J Utz
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Biomedical Informatics Research, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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97
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98
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Inflammation, epigenetics, and metabolism converge to cell senescence and ageing: the regulation and intervention. Signal Transduct Target Ther 2021; 6:245. [PMID: 34176928 PMCID: PMC8236488 DOI: 10.1038/s41392-021-00646-9] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 05/09/2021] [Accepted: 05/13/2021] [Indexed: 02/05/2023] Open
Abstract
Remarkable progress in ageing research has been achieved over the past decades. General perceptions and experimental evidence pinpoint that the decline of physical function often initiates by cell senescence and organ ageing. Epigenetic dynamics and immunometabolic reprogramming link to the alterations of cellular response to intrinsic and extrinsic stimuli, representing current hotspots as they not only (re-)shape the individual cell identity, but also involve in cell fate decision. This review focuses on the present findings and emerging concepts in epigenetic, inflammatory, and metabolic regulations and the consequences of the ageing process. Potential therapeutic interventions targeting cell senescence and regulatory mechanisms, using state-of-the-art techniques are also discussed.
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99
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Cortese M, Sherman AC, Rouphael NG, Pulendran B. Systems Biological Analysis of Immune Response to Influenza Vaccination. Cold Spring Harb Perspect Med 2021; 11:cshperspect.a038596. [PMID: 32152245 DOI: 10.1101/cshperspect.a038596] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The last decade has witnessed tremendous progress in immunology and vaccinology, owing to several scientific and technological breakthroughs. Systems vaccinology is a field that has emerged at the forefront of vaccine research and development and provides a unique way to probe immune responses to vaccination in humans. The goals of systems vaccinology are to use systems-based approaches to define signatures that can be used to predict vaccine immunogenicity and efficacy and to delineate the molecular mechanisms driving protective immunity. The application of systems biological approaches in influenza vaccination studies has enabled the discovery of early signatures that predict immunogenicity to vaccination and yielded novel mechanistic insights about vaccine-induced immunity. Here we review the contributions of systems vaccinology to influenza vaccine development and critically examine the potential of systems vaccinology toward enabling the development of a universal influenza vaccine that provides robust and durable immunity against diverse influenza viruses.
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Affiliation(s)
- Mario Cortese
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, California 94305, USA
| | - Amy C Sherman
- Hope Clinic of the Emory Vaccine Center, Decatur, Georgia 30030, USA
| | - Nadine G Rouphael
- Hope Clinic of the Emory Vaccine Center, Decatur, Georgia 30030, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, California 94305, USA.,Department of Pathology, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford University, Stanford, California 94305, USA.,Department of Pathology, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford University, Stanford, California 94305, USA
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100
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Cheung P, Schaffert S, Chang SE, Dvorak M, Donato M, Macaubas C, Foecke MH, Li TM, Zhang L, Coan JP, Schulert GS, Grom AA, Henderson LA, Nigrovic PA, Elias JE, Gozani O, Mellins ED, Khatri P, Utz PJ, Kuo AJ. Repression of CTSG, ELANE and PRTN3-mediated histone H3 proteolytic cleavage promotes monocyte-to-macrophage differentiation. Nat Immunol 2021; 22:711-722. [PMID: 34017121 PMCID: PMC8159908 DOI: 10.1038/s41590-021-00928-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 04/05/2021] [Indexed: 12/31/2022]
Abstract
Chromatin undergoes extensive reprogramming during immune cell differentiation. Here we report the repression of controlled histone H3 amino terminus proteolytic cleavage (H3ΔN) during monocyte-to-macrophage development. This abundant histone mark in human peripheral blood monocytes is catalyzed by neutrophil serine proteases (NSPs) cathepsin G, neutrophil elastase and proteinase 3. NSPs are repressed as monocytes mature into macrophages. Integrative epigenomic analysis reveals widespread H3ΔN distribution across the genome in a monocytic cell line and primary monocytes, which becomes largely undetectable in fully differentiated macrophages. H3ΔN is enriched at permissive chromatin and actively transcribed genes. Simultaneous NSP depletion in monocytic cells results in H3ΔN loss and further increase in chromatin accessibility, which likely primes the chromatin for gene expression reprogramming. Importantly, H3ΔN is reduced in monocytes from patients with systemic juvenile idiopathic arthritis, an autoinflammatory disease with prominent macrophage involvement. Overall, we uncover an epigenetic mechanism that primes the chromatin to facilitate macrophage development.
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Affiliation(s)
- Peggie Cheung
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Steven Schaffert
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Center for Biomedical Informatics Research, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Sarah E Chang
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Mai Dvorak
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Michele Donato
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Center for Biomedical Informatics Research, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Claudia Macaubas
- Program in Immunology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Mariko H Foecke
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Tie-Mei Li
- Department of Biology, Stanford University, Stanford, CA, USA
| | | | - John P Coan
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Grant S Schulert
- Division of Rheumatology, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Alexei A Grom
- Division of Rheumatology, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Lauren A Henderson
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Peter A Nigrovic
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Or Gozani
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Elizabeth D Mellins
- Program in Immunology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA.
- Center for Biomedical Informatics Research, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
| | - Paul J Utz
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA.
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
| | - Alex J Kuo
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA.
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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