101
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102
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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: 120] [Impact Index Per Article: 40.0] [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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103
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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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104
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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: 35] [Impact Index Per Article: 11.7] [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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105
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Abstract
Cancer cells acquire genotypic and phenotypic changes over the course of the disease. A minority of these changes enhance cell fitness, allowing a tumor to evolve and overcome environmental constraints and treatment. Cancer evolution is driven by diverse processes governed by different rules, such as discrete and irreversible genetic variants and continuous and reversible plastic reprogramming. In this perspective, we explore the role of cell plasticity in tumor evolution through specific examples. We discuss epigenetic and transcriptional reprogramming in "disease progression" of solid tumors, through the lens of the epithelial-to-mesenchymal transition, and "treatment resistance", in the context endocrine therapy in hormone-driven cancers. These examples offer a paradigm of the features and challenges of cell plastic evolution, and we investigate how recent technological advances can address these challenges. Cancer evolution is a multi-faceted process, whose understanding and harnessing will require an equally diverse prism of perspectives and approaches.
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Affiliation(s)
- Giovanni Ciriello
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Cancer Center Leman, Lausanne, Switzerland
| | - Luca Magnani
- Department of Surgery and Cancer, Imperial College London, London, UK
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106
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Bendikov-Bar I, Malitsky S, Itkin M, Rusal M, Sagi D. Metabolomic Changes Are Predictive of Aging in Laying Hens. J Gerontol A Biol Sci Med Sci 2021; 76:1757-1768. [PMID: 33978733 DOI: 10.1093/gerona/glab135] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Indexed: 11/14/2022] Open
Abstract
Aging in vertebrates is an extremely complex process that is still poorly understood. One confining factor to studying vertebrate aging is the lack of appropriate models. The laying hen is a good model to study vertebrate aging, as it can be maintained under standard housing conditions, its breeds are genetically well defined and it exhibits significant aging phenotypes at around 18 months of age. Furthermore, laying hens are maintained in a challenging realistic environment and possess a fully functional immune system. Here we used, for the first time, metabolomic profiling of laying hens' blood for identifying biomarkers of aging. Random forest classifier was used to quantify the quality of the markers and found that the markers can predict the correct age group of individuals with 90% accuracy. Animals under time-restricted feeding, a condition known to increase health span, appeared younger under the markers, indicating that the aging biomarkers can also predict the effectiveness of environmental treatments. Additionally, we found that noise, defined as the ratio between the standard deviation and the mean, is an exceptionally robust and universal biomarker of aging, as metabolomic noise increases significantly with age in laying hens, humans, and mice. Our study suggests the laying hen as a useful model to study aging in vertebrates and establishes metabolomic noise as a novel, universal biomarker of aging.
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Affiliation(s)
- Inna Bendikov-Bar
- Agricultural Research Organization, Volcani Center, Institute of Animal Science, Rishon LeZion, Israel
| | - Sergey Malitsky
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot,Israel
| | - Maxim Itkin
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot,Israel
| | - Mark Rusal
- Agricultural Research Organization, Volcani Center, Institute of Animal Science, Rishon LeZion, Israel
| | - Dror Sagi
- Agricultural Research Organization, Volcani Center, Institute of Animal Science, Rishon LeZion, Israel
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107
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Devenish LP, Mhlanga MM, Negishi Y. Immune Regulation in Time and Space: The Role of Local- and Long-Range Genomic Interactions in Regulating Immune Responses. Front Immunol 2021; 12:662565. [PMID: 34046034 PMCID: PMC8144502 DOI: 10.3389/fimmu.2021.662565] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/26/2021] [Indexed: 12/27/2022] Open
Abstract
Mammals face and overcome an onslaught of endogenous and exogenous challenges in order to survive. Typical immune cells and barrier cells, such as epithelia, must respond rapidly and effectively to encountered pathogens and aberrant cells to prevent invasion and eliminate pathogenic species before they become overgrown and cause harm. On the other hand, inappropriate initiation and failed termination of immune cell effector function in the absence of pathogens or aberrant tissue gives rise to a number of chronic, auto-immune, and neoplastic diseases. Therefore, the fine control of immune effector functions to provide for a rapid, robust response to challenge is essential. Importantly, immune cells are heterogeneous due to various factors relating to cytokine exposure and cell-cell interaction. For instance, tissue-resident macrophages and T cells are phenotypically, transcriptionally, and functionally distinct from their circulating counterparts. Indeed, even the same cell types in the same environment show distinct transcription patterns at the single cell level due to cellular noise, despite being robust in concert. Additionally, immune cells must remain quiescent in a naive state to avoid autoimmunity or chronic inflammatory states but must respond robustly upon activation regardless of their microenvironment or cellular noise. In recent years, accruing evidence from next-generation sequencing, chromatin capture techniques, and high-resolution imaging has shown that local- and long-range genome architecture plays an important role in coordinating rapid and robust transcriptional responses. Here, we discuss the local- and long-range genome architecture of immune cells and the resultant changes upon pathogen or antigen exposure. Furthermore, we argue that genome structures contribute functionally to rapid and robust responses under noisy and distinct cellular environments and propose a model to explain this phenomenon.
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Affiliation(s)
- Liam P Devenish
- Division of Chemical, Systems, and Synthetic Biology, Department of Integrative Biomedical Sciences, Institute of Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Musa M Mhlanga
- Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, Netherlands.,Epigenomics & Single Cell Biophysics Group, Department of Cell Biology, Radboud University, Nijmegen, Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Yutaka Negishi
- Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, Netherlands.,Epigenomics & Single Cell Biophysics Group, Department of Cell Biology, Radboud University, Nijmegen, Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
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108
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Zhang B, Long Q, Wu S, Xu Q, Song S, Han L, Qian M, Ren X, Liu H, Jiang J, Guo J, Zhang X, Chang X, Fu Q, Lam EWF, Campisi J, Kirkland JL, Sun Y. KDM4 Orchestrates Epigenomic Remodeling of Senescent Cells and Potentiates the Senescence-Associated Secretory Phenotype. NATURE AGING 2021; 1:454-472. [PMID: 34263179 PMCID: PMC8277122 DOI: 10.1038/s43587-021-00063-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 04/02/2021] [Indexed: 11/08/2022]
Abstract
Cellular senescence restrains the expansion of neoplastic cells through several layers of regulation. We report that the histone H3-specific demethylase KDM4 is expressed as human stromal cells undergo senescence. In clinical oncology, upregulated KDM4 and diminished H3K9/H3K36 methylation correlate with poorer survival of prostate cancer patients post-chemotherapy. Global chromatin accessibility mapping via ATAC-seq, and expression profiling through RNA-seq, reveal global changes of chromatin openness and spatiotemporal reprogramming of the transcriptomic landscape, which underlie the senescence-associated secretory phenotype (SASP). Selective targeting of KDM4 dampens the SASP of senescent stromal cells, promotes cancer cell apoptosis in the treatment-damaged tumor microenvironment (TME), and prolongs survival of experimental animals. Our study supports dynamic changes of H3K9/H3K36 methylation during senescence, identifies an unusually permissive chromatin state, and unmasks KDM4 as a key SASP modulator. KDM4 targeting presents a novel therapeutic avenue to manipulate cellular senescence and limit its contribution to age-related pathologies including cancer.
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Affiliation(s)
- Boyi Zhang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Qilai Long
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Shanshan Wu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Qixia Xu
- Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine & Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shuling Song
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Liu Han
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Min Qian
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiaohui Ren
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hanxin Liu
- Department of Pharmacology, Binzhou Medical University, Yantai, Shandong 264003, China
| | - Jing Jiang
- Department of Pharmacology, Binzhou Medical University, Yantai, Shandong 264003, China
| | - Jianming Guo
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Xiaoling Zhang
- Department of Orthopedic Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Xing Chang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
| | - Qiang Fu
- Department of Pharmacology, Binzhou Medical University, Yantai, Shandong 264003, China
| | - Eric W-F Lam
- Department of Surgery and Cancer, Imperial College London, London, W12 0NN, UK
| | - Judith Campisi
- Buck Institute for Research on Aging, Novato, CA 94945, USA
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - James L. Kirkland
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA
| | - Yu Sun
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- Institute of Health Sciences, Shanghai Jiao Tong University School of Medicine & Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- Department of Pharmacology, Binzhou Medical University, Yantai, Shandong 264003, China
- Department of Medicine and VAPSHCS, University of Washington, Seattle, WA 98195, USA
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109
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Pal D, Riester SM, Hasan B, Tufa SF, Dudakovic A, Keene DR, van Wijnen AJ, Schweitzer R. Ezh2 Is Essential for Patterning of Multiple Musculoskeletal Tissues but Dispensable for Tendon Differentiation. Stem Cells Dev 2021; 30:601-609. [PMID: 33757300 DOI: 10.1089/scd.2020.0209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
An efficient musculoskeletal system depends on the precise assembly and coordinated growth and function of muscles, skeleton, and tendons. However, the mechanisms that drive integrated musculoskeletal development and coordinated growth and differentiation of each of these tissues are still being uncovered. Epigenetic modifiers have emerged as critical regulators of cell fate differentiation, but so far almost nothing is known about their roles in tendon biology. Previous studies have shown that epigenetic modifications driven by Enhancer of zeste homolog 2 (EZH2), a major histone methyltransferase, have significant roles in vertebrate development including skeletal patterning and bone formation. We now find that targeting Ezh2 through the limb mesenchyme also has significant effects on tendon and muscle patterning, likely reflecting the essential roles of early mesenchymal cues mediated by Ezh2 for coordinated patterning and development of all tissues of the musculoskeletal system. Conversely, loss of Ezh2 in the tendon cells did not disrupt overall tendon structure or collagen organization suggesting that tendon differentiation and maturation are independent of Ezh2 signaling.
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Affiliation(s)
- Deepanwita Pal
- Research Division, Shriners Hospital for Children, Portland, Oregon, USA
| | - Scott M Riester
- Department of Orthopedic Surgery, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Bashar Hasan
- Department of Orthopedic Surgery, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Sara F Tufa
- Research Division, Shriners Hospital for Children, Portland, Oregon, USA
| | - Amel Dudakovic
- Department of Orthopedic Surgery, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Biochemistry & Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Douglas R Keene
- Research Division, Shriners Hospital for Children, Portland, Oregon, USA.,Department of Orthopedics, Oregon Health & Science University, Portland, USA
| | - Andre J van Wijnen
- Department of Orthopedic Surgery, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Biochemistry & Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Center for Regenerative Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Ronen Schweitzer
- Research Division, Shriners Hospital for Children, Portland, Oregon, USA.,Department of Orthopedics, Oregon Health & Science University, Portland, USA
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110
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Xie Z, Rahman I, Goniewicz ML, Li D. Perspectives on Epigenetics Alterations Associated with Smoking and Vaping. FUNCTION (OXFORD, ENGLAND) 2021; 2:zqab022. [PMID: 35330676 PMCID: PMC8788872 DOI: 10.1093/function/zqab022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/03/2021] [Accepted: 04/21/2021] [Indexed: 01/11/2023]
Abstract
Epigenetic alterations, including DNA methylation, microRNA, and long noncoding RNA, play important roles in the pathogenesis of numerous respiratory health conditions and diseases. Exposure to tobacco smoking has been found to be associated with epigenetic changes in the respiratory tract. Marketed as a less harmful alternative to combustible cigarettes, electronic cigarette (e-cigarette) has rapidly gained popularity in recent years, especially among youth and young adults. Accumulative evidence from both animal and human studies has shown that e-cigarette use (vaping) is also linked to similar respiratory health conditions as observed with cigarette smoking, including wheezing, asthma, and COPD. This review aims to provide an overview of current studies on associations of smoking and vaping with epigenetic alterations in respiratory cells and provide future research directions in epigenetic studies related to vaping.
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Affiliation(s)
- Zidian Xie
- Department of Clinical & Translational Research, University of Rochester Medical Center, Rochester, NY, USA
| | - Irfan Rahman
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Maciej L Goniewicz
- Department of Health Behavior, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, USA
| | - Dongmei Li
- Department of Clinical & Translational Research, University of Rochester Medical Center, Rochester, NY, USA,Address correspondence to D.L. (e-mail: )
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111
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Li WX, Dai SX, An SQ, Sun T, Liu J, Wang J, Liu LG, Xun Y, Yang H, Fan LX, Zhang XL, Liao WQ, You H, Tamagnone L, Liu F, Huang JF, Liu D. Transcriptome integration analysis and specific diagnosis model construction for Hodgkin's lymphoma, diffuse large B-cell lymphoma, and mantle cell lymphoma. Aging (Albany NY) 2021; 13:11833-11859. [PMID: 33885377 PMCID: PMC8109084 DOI: 10.18632/aging.202882] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 03/02/2021] [Indexed: 01/20/2023]
Abstract
Transcriptome differences between Hodgkin's lymphoma (HL), diffuse large B-cell lymphoma (DLBCL), and mantle cell lymphoma (MCL), which are all derived from B cell, remained unclear. This study aimed to construct lymphoma-specific diagnostic models by screening lymphoma marker genes. Transcriptome data of HL, DLBCL, and MCL were obtained from public databases. Lymphoma marker genes were screened by comparing cases and controls as well as the intergroup differences among lymphomas. A total of 9 HL marker genes, 7 DLBCL marker genes, and 4 MCL marker genes were screened in this study. Most HL marker genes were upregulated, whereas DLBCL and MCL marker genes were downregulated compared to controls. The optimal HL-specific diagnostic model contains one marker gene (MYH2) with an AUC of 0.901. The optimal DLBCL-specific diagnostic model contains 7 marker genes (LIPF, CCDC144B, PRO2964, PHF1, SFTPA2, NTS, and HP) with an AUC of 0.951. The optimal MCL-specific diagnostic model contains 3 marker genes (IGLV3-19, IGKV4-1, and PRB3) with an AUC of 0.843. The present study reveals the transcriptome data-based differences between HL, DLBCL, and MCL, when combined with other clinical markers, may help the clinical diagnosis and prognosis.
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Affiliation(s)
- Wen-Xing Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China.,Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Southern Medical University, Guangzhou, Guangdong, China
| | - Shao-Xing Dai
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - San-Qi An
- Biosafety Level-3 Laboratory, Life Sciences Institute & Guangxi Key Laboratory of AIDS Prevention and Treatment & Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Tingting Sun
- National School of Development, Peking University, Beijing 100871, China
| | - Justin Liu
- Department of Statistics, University of California, Riverside, CA 92521, USA
| | - Jun Wang
- Foshan Stomatology Hospital, School of Medicine, Foshan University, Foshan, Guangdong, China
| | | | - Yang Xun
- Foshan Stomatology Hospital, School of Medicine, Foshan University, Foshan, Guangdong, China
| | - Hua Yang
- Foshan Stomatology Hospital, School of Medicine, Foshan University, Foshan, Guangdong, China
| | - Li-Xia Fan
- Foshan Stomatology Hospital, School of Medicine, Foshan University, Foshan, Guangdong, China
| | - Xiao-Li Zhang
- Foshan Stomatology Hospital, School of Medicine, Foshan University, Foshan, Guangdong, China
| | - Wan-Qin Liao
- Foshan Stomatology Hospital, School of Medicine, Foshan University, Foshan, Guangdong, China
| | - Hua You
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Luca Tamagnone
- Istituto di Istologia ed Embriologia, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Fang Liu
- Foshan Stomatology Hospital, School of Medicine, Foshan University, Foshan, Guangdong, China
| | - Jing-Fei Huang
- Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Dahai Liu
- Foshan Stomatology Hospital, School of Medicine, Foshan University, Foshan, Guangdong, China
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112
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Levine LS, Hiam-Galvez KJ, Marquez DM, Tenvooren I, Madden MZ, Contreras DC, Dahunsi DO, Irish JM, Oluwole OO, Rathmell JC, Spitzer MH. Single-cell analysis by mass cytometry reveals metabolic states of early-activated CD8 + T cells during the primary immune response. Immunity 2021; 54:829-844.e5. [PMID: 33705706 PMCID: PMC8046726 DOI: 10.1016/j.immuni.2021.02.018] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 12/08/2020] [Accepted: 02/17/2021] [Indexed: 02/08/2023]
Abstract
Memory T cells are thought to rely on oxidative phosphorylation and short-lived effector T cells on glycolysis. Here, we investigated how T cells arrive at these states during an immune response. To understand the metabolic state of rare, early-activated T cells, we adapted mass cytometry to quantify metabolic regulators at single-cell resolution in parallel with cell signaling, proliferation, and effector function. We interrogated CD8+ T cell activation in vitro and in response to Listeria monocytogenes infection in vivo. This approach revealed a distinct metabolic state in early-activated T cells characterized by maximal expression of glycolytic and oxidative metabolic proteins. Cells in this transient state were most abundant 5 days post-infection before rapidly decreasing metabolic protein expression. Analogous findings were observed in chimeric antigen receptor (CAR) T cells interrogated longitudinally in advanced lymphoma patients. Our study demonstrates the utility of single-cell metabolic analysis by mass cytometry to identify metabolic adaptations of immune cell populations in vivo and provides a resource for investigations of metabolic regulation of immune responses across a variety of applications.
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Affiliation(s)
- Lauren S Levine
- Departments of Otolaryngology-Head and Neck Cancer, University of California, San Francisco, San Francisco, CA 94143, USA; G.W. Hooper Research Foundation, Department of Immunology and Microbiology, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kamir J Hiam-Galvez
- Departments of Otolaryngology-Head and Neck Cancer, University of California, San Francisco, San Francisco, CA 94143, USA; G.W. Hooper Research Foundation, Department of Immunology and Microbiology, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129, USA
| | - Diana M Marquez
- Departments of Otolaryngology-Head and Neck Cancer, University of California, San Francisco, San Francisco, CA 94143, USA; G.W. Hooper Research Foundation, Department of Immunology and Microbiology, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129, USA
| | - Iliana Tenvooren
- Departments of Otolaryngology-Head and Neck Cancer, University of California, San Francisco, San Francisco, CA 94143, USA; G.W. Hooper Research Foundation, Department of Immunology and Microbiology, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129, USA
| | - Matthew Z Madden
- Vanderbilt Center for Immunobiology, Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Diana C Contreras
- Vanderbilt Center for Immunobiology, Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Debolanle O Dahunsi
- Vanderbilt Center for Immunobiology, Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jonathan M Irish
- Vanderbilt Center for Immunobiology, Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Olalekan O Oluwole
- Department of Medicine, Division of Hematology/Oncology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jeffrey C Rathmell
- Vanderbilt Center for Immunobiology, Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Matthew H Spitzer
- Departments of Otolaryngology-Head and Neck Cancer, University of California, San Francisco, San Francisco, CA 94143, USA; G.W. Hooper Research Foundation, Department of Immunology and Microbiology, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129, USA.
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113
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Schijns V, Majhen D, van der Ley P, Thakur A, Summerfield A, Berisio R, Nativi C, Fernández-Tejada A, Alvarez-Dominguez C, Gizurarson S, Zamyatina A, Molinaro A, Rosano C, Jakopin Ž, Gursel I, McClean S. Rational Vaccine Design in Times of Emerging Diseases: The Critical Choices of Immunological Correlates of Protection, Vaccine Antigen and Immunomodulation. Pharmaceutics 2021; 13:501. [PMID: 33917629 PMCID: PMC8067490 DOI: 10.3390/pharmaceutics13040501] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 03/05/2021] [Accepted: 03/08/2021] [Indexed: 01/21/2023] Open
Abstract
Vaccines are the most effective medical intervention due to their continual success in preventing infections and improving mortality worldwide. Early vaccines were developed empirically however, rational design of vaccines can allow us to optimise their efficacy, by tailoring the immune response. Establishing the immune correlates of protection greatly informs the rational design of vaccines. This facilitates the selection of the best vaccine antigens and the most appropriate vaccine adjuvant to generate optimal memory immune T cell and B cell responses. This review outlines the range of vaccine types that are currently authorised and those under development. We outline the optimal immunological correlates of protection that can be targeted. Finally we review approaches to rational antigen selection and rational vaccine adjuvant design. Harnessing current knowledge on protective immune responses in combination with critical vaccine components is imperative to the prevention of future life-threatening diseases.
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Affiliation(s)
- Virgil Schijns
- Intravacc, Institute for Translational Vaccinology (Intravacc), Utrecht Science Park, 3721 MA Bilthoven, The Netherlands;
- Epitopoietic Research Corporation (ERC), 5374 RE Schaijk, The Netherlands
| | - Dragomira Majhen
- Laboratory for Cell Biology and Signalling, Division of Molecular Biology, Ruđer Bošković Instiute, HR-10000 Zagreb, Croatia;
| | - Peter van der Ley
- Intravacc, Institute for Translational Vaccinology (Intravacc), Utrecht Science Park, 3721 MA Bilthoven, The Netherlands;
| | - Aneesh Thakur
- Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark;
| | - Artur Summerfield
- Institute of Virology and Immunology, 3147 Mittelhausern, Switzerland;
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland
| | - Rita Berisio
- Institute of Biostructures and Bioimaging, National Research Council, I-80134 Naples, Italy;
| | - Cristina Nativi
- Department of Chemistry “Ugo Schiff”, University of Florence, 50019 Sesto Fiorentino, Italy;
| | - Alberto Fernández-Tejada
- Chemical Immunology Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Biscay Science and Technology Park, 48160 Derio-Bilbao, Spain;
- Ikerbasque, Basque Foundation for Science, 48009 Bilbao, Spain
| | - Carmen Alvarez-Dominguez
- Facultativo en plantilla (Research Faculty), Instituto de Investigación Marqués de Valdecilla (IDIVAL), 39011 Santander, Spain;
| | - Sveinbjörn Gizurarson
- Faculty of Pharmaceutical Sciences, University of Iceland, 107 Reykjavik, Iceland;
- Department of Pharmacy, College of Medicine, University of Malawi, Blantyre 3, Malawi
| | - Alla Zamyatina
- Department of Chemistry, University of Natural Resources and Life Sciences, 1190 Vienna, Austria;
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario Monte Santangelo, I-80126 Napoli, Italy;
- Department of Chemistry, School of Science, Osaka University, 1-1 Osaka University Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Camillo Rosano
- Proteomics and Mass Spectrometry Unit, IRCCS Policlinico San Martino, 16132 Genova-1, Italy;
| | - Žiga Jakopin
- Faculty of Pharmacy, University of Ljubljana, 1000 Ljubiljana, Slovenia;
| | - Ihsan Gursel
- Molecular Biology and Genetics Department, Science Faculty, Bilkent University, Bilkent, 06800 Ankara, Turkey;
| | - Siobhán McClean
- School of Biomolecular and Biomedical Sciences, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
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114
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Abstract
Single-cell sequencing-based methods for profiling gene transcript levels have revealed substantial heterogeneity in expression levels among morphologically indistinguishable cells. This variability has important functional implications for tissue biology and disease states such as cancer. Mapping of epigenomic information such as chromatin accessibility, nucleosome positioning, histone tail modifications and enhancer-promoter interactions in both bulk-cell and single-cell samples has shown that these characteristics of chromatin state contribute to expression or repression of associated genes. Advances in single-cell epigenomic profiling methods are enabling high-resolution mapping of chromatin states in individual cells. Recent studies using these techniques provide evidence that variations in different aspects of chromatin organization collectively define gene expression heterogeneity among otherwise highly similar cells.
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Affiliation(s)
- Benjamin Carter
- Laboratory of Epigenome Biology, Systems Biology Center, NHLBI, NIH, Bethesda, MD, USA.
| | - Keji Zhao
- Laboratory of Epigenome Biology, Systems Biology Center, NHLBI, NIH, Bethesda, MD, USA.
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115
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Pignolo RJ, Law SF, Chandra A. Bone Aging, Cellular Senescence, and Osteoporosis. JBMR Plus 2021; 5:e10488. [PMID: 33869998 PMCID: PMC8046105 DOI: 10.1002/jbm4.10488] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 02/17/2021] [Indexed: 12/15/2022] Open
Abstract
Changes in aging bone that lead to osteoporosis are mediated at multiple levels, including hormonal alterations, skeletal unloading, and accumulation of senescent cells. This pathological interplay is superimposed upon medical conditions, potentially bone-wasting medications, modifiable and unmodifiable personal risk factors, and genetic predisposition that accelerate bone loss with aging. In this study, the focus is on bone hemostasis and its dysregulation with aging. The major physiological changes with aging in bone and the role of cellular senescence in contributing to age-related osteoporosis are summarized. The aspects of bone aging are reviewed including remodeling deficits, uncoupling phenomena, inducers of cellular senescence related to bone aging, roles of the senescence-associated secretory phenotype, radiation-induced bone loss as a model for bone aging, and the accumulation of senescent cells in the bone microenvironment as a predominant mechanism for age-related osteoporosis. The study also addresses the rationale and potential for therapeutic interventions based on the clearance of senescent cells or suppression of the senescence-associated secretory phenotype. © 2021 The Authors. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research.
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Affiliation(s)
- Robert J Pignolo
- Department of MedicineMayo ClinicRochesterMNUSA
- Department of Physiology and Biomedical EngineeringMayo ClinicRochesterMNUSA
| | - Susan F Law
- Department of MedicineMayo ClinicRochesterMNUSA
| | - Abhishek Chandra
- Department of MedicineMayo ClinicRochesterMNUSA
- Department of Physiology and Biomedical EngineeringMayo ClinicRochesterMNUSA
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116
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Schultze JL, Aschenbrenner AC. COVID-19 and the human innate immune system. Cell 2021; 184:1671-1692. [PMID: 33743212 PMCID: PMC7885626 DOI: 10.1016/j.cell.2021.02.029] [Citation(s) in RCA: 434] [Impact Index Per Article: 144.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/19/2021] [Accepted: 02/10/2021] [Indexed: 01/08/2023]
Abstract
The introduction of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into the human population represents a tremendous medical and economic crisis. Innate immunity-as the first line of defense of our immune system-plays a central role in combating this novel virus. Here, we provide a conceptual framework for the interaction of the human innate immune system with SARS-CoV-2 to link the clinical observations with experimental findings that have been made during the first year of the pandemic. We review evidence that variability in innate immune system components among humans is a main contributor to the heterogeneous disease courses observed for coronavirus disease 2019 (COVID-19), the disease spectrum induced by SARS-CoV-2. A better understanding of the pathophysiological mechanisms observed for cells and soluble mediators involved in innate immunity is a prerequisite for the development of diagnostic markers and therapeutic strategies targeting COVID-19. However, this will also require additional studies addressing causality of events, which so far are lagging behind.
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Affiliation(s)
- Joachim L Schultze
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany; PRECISE Platform for Single Cell Genomics and Epigenomics at the DZNE and the University of Bonn, Bonn, Germany; Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany.
| | - Anna C Aschenbrenner
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany; PRECISE Platform for Single Cell Genomics and Epigenomics at the DZNE and the University of Bonn, Bonn, Germany; Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany; Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
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117
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Zhou X, Han X, Lyu SC, Bunning B, Kost L, Chang I, Cao S, Sampath V, Nadeau KC. Targeted DNA methylation profiling reveals epigenetic signatures in peanut allergy. JCI Insight 2021; 6:143058. [PMID: 33571165 PMCID: PMC8026193 DOI: 10.1172/jci.insight.143058] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 02/10/2021] [Indexed: 12/14/2022] Open
Abstract
DNA methylation (DNAm) has been shown to play a role in mediating food allergy; however, the mechanism by which it does so is poorly understood. In this study, we used targeted next-generation bisulfite sequencing to evaluate DNAm levels in 125 targeted highly informative genomic regions containing 602 CpG sites on 70 immune-related genes to understand whether DNAm can differentiate peanut allergy (PA) versus nonallergy (NA). We found PA-associated DNAm signatures associated with 12 genes (7 potentially novel to food allergy, 3 associated with Th1/Th2, and 2 associated with innate immunity), as well as DNAm signature combinations with superior diagnostic potential compared with serum peanut–specific IgE for PA versus NA. Furthermore, we found that, following peanut protein stimulation, peripheral blood mononuclear cell (PBMCs) from PA participants showed increased production of cognate cytokines compared with NA participants. The varying responses between PA and NA participants may be associated with the interaction between the modification of DNAm and the interference of environment. Using Euclidean distance analysis, we found that the distances of methylation profile comprising 12 DNAm signatures between PA and NA pairs in monozygotic (MZ) twins were smaller than those in randomly paired genetically unrelated individuals, suggesting that PA-related DNAm signatures may be associated with genetic factors.
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118
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Fu ZW, Li JH, Feng YR, Yuan X, Lu YT. The metabolite methylglyoxal-mediated gene expression is associated with histone methylglyoxalation. Nucleic Acids Res 2021; 49:1886-1899. [PMID: 33476385 PMCID: PMC7913762 DOI: 10.1093/nar/gkab014] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/09/2020] [Accepted: 01/06/2021] [Indexed: 12/11/2022] Open
Abstract
Methylglyoxal (MG) is a byproduct of glycolysis that functions in diverse mammalian developmental processes and diseases and in plant responses to various stresses, including salt stress. However, it is unknown whether MG-regulated gene expression is associated with an epigenetic modification. Here we report that MG methylglyoxalates H3 including H3K4 and increases chromatin accessibility, consistent with the result that H3 methylglyoxalation positively correlates with gene expression. Salt stress also increases H3 methylglyoxalation at salt stress responsive genes correlated to their higher expression. Following exposure to salt stress, salt stress responsive genes were expressed at higher levels in the Arabidopsis glyI2 mutant than in wild-type plants, but at lower levels in 35S::GLYI2 35S::GLYII4 plants, consistent with the higher and lower MG accumulation and H3 methylglyoxalation of target genes in glyI2 and 35S::GLYI2 35S::GLYII4, respectively. Further, ABI3 and MYC2, regulators of salt stress responsive genes, affect the distribution of H3 methylglyoxalation at salt stress responsive genes. Thus, MG functions as a histone-modifying group associated with gene expression that links glucose metabolism and epigenetic regulation.
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Affiliation(s)
- Zheng-Wei Fu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jian-Hui Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yu-Rui Feng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xiao Yuan
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Ying-Tang Lu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
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119
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Chikuma S, Yamanaka S, Nakagawa S, Ueda MT, Hayabuchi H, Tokifuji Y, Kanayama M, Okamura T, Arase H, Yoshimura A. TRIM28 Expression on Dendritic Cells Prevents Excessive T Cell Priming by Silencing Endogenous Retrovirus. THE JOURNAL OF IMMUNOLOGY 2021; 206:1528-1539. [PMID: 33619215 DOI: 10.4049/jimmunol.2001003] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/12/2021] [Indexed: 11/19/2022]
Abstract
Acquired immune reaction is initiated by dendritic cells (DCs), which present Ags to a few naive Ag-specific T cells. Deregulation of gene expression in DCs may alter the outcome of the immune response toward immunodeficiency and/or autoimmune diseases. Expression of TRIM28, a nuclear protein that mediates gene silencing through heterochromatin, decreased in DCs from old mice, suggesting alteration of gene regulation. Mice specifically lacking TRIM28 in DCs show increased DC population in the spleen and enhanced T cell priming toward inflammatory effector T cells, leading to acceleration and exacerbation in experimental autoimmune encephalomyelitis. TRIM28-deficient DCs were found to ectopically transcribe endogenous retrovirus (ERV) elements. Combined genome-wide analysis revealed a strong colocalization among the decreased repressive histone mark H3K9me3-transcribed ERV elements and the derepressed host genes that were related to inflammation in TRIM28-deficient DCs. This suggests that TRIM28 occupancy of ERV elements critically represses expression of proximal inflammatory genes on the genome. We propose that gene silencing through repressive histone modification by TRIM28 plays a role in maintaining the integrity of precise gene regulation in DCs, which prevents aberrant T cell priming to inflammatory effector T cells.
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Affiliation(s)
- Shunsuke Chikuma
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo 160-8582, Japan;
| | - Soichiro Yamanaka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa 259-1193, Japan
| | - Mahoko Takahashi Ueda
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa 259-1193, Japan.,Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Hodaka Hayabuchi
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Yukiko Tokifuji
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Masashi Kanayama
- Department of Biodefense Research, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Tadashi Okamura
- Department of Laboratory Animal Medicine, Research Institute, National Center for Global Health and Medicine, Tokyo 162-8655, Japan.,Department of Infectious Diseases, Research Institute, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
| | - Hisashi Arase
- Department of Immunochemistry, Research Institute for Microbial Disease, Osaka University, Osaka 565-0871, Japan; and.,Laboratory of Immunochemistry, World Premier International Research Center Initiative, Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan
| | - Akihiko Yoshimura
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo 160-8582, Japan
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120
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Mancarella D, Plass C. Epigenetic signatures in cancer: proper controls, current challenges and the potential for clinical translation. Genome Med 2021; 13:23. [PMID: 33568205 PMCID: PMC7874645 DOI: 10.1186/s13073-021-00837-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 01/21/2021] [Indexed: 12/26/2022] Open
Abstract
Epigenetic alterations are associated with normal biological processes such as aging or differentiation. Changes in global epigenetic signatures, together with genetic alterations, are driving events in several diseases including cancer. Comparative studies of cancer and healthy tissues found alterations in patterns of DNA methylation, histone posttranslational modifications, and changes in chromatin accessibility. Driven by sophisticated, next-generation sequencing-based technologies, recent studies discovered cancer epigenomes to be dominated by epigenetic patterns already present in the cell-of-origin, which transformed into a neoplastic cell. Tumor-specific epigenetic changes therefore need to be redefined and factors influencing epigenetic patterns need to be studied to unmask truly disease-specific alterations. The underlying mechanisms inducing cancer-associated epigenetic alterations are poorly understood. Studies of mutated epigenetic modifiers, enzymes that write, read, or edit epigenetic patterns, or mutated chromatin components, for example oncohistones, help to provide functional insights on how cancer epigenomes arise. In this review, we highlight the importance and define challenges of proper control tissues and cell populations to exploit cancer epigenomes. We summarize recent advances describing mechanisms leading to epigenetic changes in tumorigenesis and briefly discuss advances in investigating their translational potential.
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Affiliation(s)
- Daniela Mancarella
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany. .,Faculty of Biosciences, Ruprecht-Karls-University of Heidelberg, 69120, Heidelberg, Germany.
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,German Consortium for Translational Cancer Research (DKTK), 69120, Heidelberg, Germany
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121
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Principles of the Molecular and Cellular Mechanisms of Aging. J Invest Dermatol 2021; 141:951-960. [PMID: 33518357 DOI: 10.1016/j.jid.2020.11.018] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/23/2020] [Accepted: 11/02/2020] [Indexed: 12/13/2022]
Abstract
Aging can be defined as a state of progressive functional decline accompanied by an increase in mortality. Time-dependent accumulation of cellular damage, namely lesions and mutations in the DNA and misfolded proteins, impair organellar and cellular function. Ensuing cell fate alterations lead to the accumulation of dysfunctional cells and hamper homeostatic processes, thus limiting regenerative potential; trigger low-grade inflammation; and alter intercellular and intertissue communication. The accumulation of molecular damage together with modifications in the epigenetic landscape, dysregulation of gene expression, and altered endocrine communication, drive the aging process and establish age as the main risk factor for age-associated diseases and multimorbidity.
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122
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Bitman-Lotan E, Orian A. Nuclear organization and regulation of the differentiated state. Cell Mol Life Sci 2021; 78:3141-3158. [PMID: 33507327 PMCID: PMC8038961 DOI: 10.1007/s00018-020-03731-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 12/01/2020] [Accepted: 12/04/2020] [Indexed: 12/22/2022]
Abstract
Regulation of the differentiated identity requires active and continued supervision. Inability to maintain the differentiated state is a hallmark of aging and aging-related disease. To maintain cellular identity, a network of nuclear regulators is devoted to silencing previous and non-relevant gene programs. This network involves transcription factors, epigenetic regulators, and the localization of silent genes to heterochromatin. Together, identity supervisors mold and maintain the unique nuclear environment of the differentiated cell. This review describes recent discoveries regarding mechanisms and regulators that supervise the differentiated identity and protect from de-differentiation, tumorigenesis, and attenuate forced somatic cell reprograming. The review focuses on mechanisms involved in H3K9me3-decorated heterochromatin and the importance of nuclear lamins in cell identity. We outline how the biophysical properties of these factors are involved in self-compartmentalization of heterochromatin and cell identity. Finally, we discuss the relevance of these regulators to aging and age-related disease.
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Affiliation(s)
- Eliya Bitman-Lotan
- Rappaport Research Institute and Faculty of Medicine, The Rappaport Faculty of Medicine Technion-IIT, Technion Integrative Cancer Center (TICC), Technion-Israel Institute of Technology, Bat-Galim, 3109610, Haifa, Israel
| | - Amir Orian
- Rappaport Research Institute and Faculty of Medicine, The Rappaport Faculty of Medicine Technion-IIT, Technion Integrative Cancer Center (TICC), Technion-Israel Institute of Technology, Bat-Galim, 3109610, Haifa, Israel.
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123
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Abstract
Human lifespan is now longer than ever and, as a result, modern society is getting older. Despite that, the detailed mechanisms behind the ageing process and its impact on various tissues and organs remain obscure. In general, changes in DNA, RNA and protein structure throughout life impair their function. Haematopoietic ageing refers to the age-related changes affecting a haematopoietic system. Aged blood cells display different functional aberrations depending on their cell type, which might lead to the development of haematologic disorders, including leukaemias, anaemia or declining immunity. In contrast to traditional bulk assays, which are not suitable to dissect cell-to-cell variation, single-cell-level analysis provides unprecedented insight into the dynamics of age-associated changes in blood. In this Review, we summarise recent studies that dissect haematopoietic ageing at the single-cell level. We discuss what cellular changes occur during haematopoietic ageing at the genomic, transcriptomic, epigenomic and metabolomic level, and provide an overview of the benefits of investigating those changes with single-cell precision. We conclude by considering the potential clinical applications of single-cell techniques in geriatric haematology, focusing on the impact on haematopoietic stem cell transplantation in the elderly and infection studies, including recent COVID-19 research.
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Affiliation(s)
- Paulina M Strzelecka
- Department of Hematology, Oncology, and Tumor Immunology, Charité - Universitätsmedizin Berlin, 13353 Berlin, Germany
- German Consortium for Translational Cancer Research (DKTK), 69120 Heidelberg, Germany
| | - Frederik Damm
- Department of Hematology, Oncology, and Tumor Immunology, Charité - Universitätsmedizin Berlin, 13353 Berlin, Germany
- German Consortium for Translational Cancer Research (DKTK), 69120 Heidelberg, Germany
- Berlin Institute of Health, 10178 Berlin, Germany
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124
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Yan Z, Maecker HT, Brodin P, Nygaard UC, Lyu SC, Davis MM, Nadeau KC, Andorf S. Aging and CMV discordance are associated with increased immune diversity between monozygotic twins. IMMUNITY & AGEING 2021; 18:5. [PMID: 33461563 PMCID: PMC7812659 DOI: 10.1186/s12979-021-00216-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 01/08/2021] [Indexed: 12/18/2022]
Abstract
Background Broadly, much of variance in immune system phenotype has been linked to the influence of non-heritable factors rather than genetics. In particular, two non-heritable factors: aging and human cytolomegavirus (CMV) infection, have been known to account for significant inter-individual immune variance. However, many specific relationships between them and immune composition remain unclear, especially between individuals over narrower age ranges. Further exploration of these relationships may be useful for informing personalized intervention development. Results To address this need, we evaluated 41 different cell type frequencies by mass cytometry and identified their relationships with aging and CMV seropositivity. Analyses were done using 60 healthy individuals, including 23 monozygotic twin pairs, categorized into young (12–31 years) and middle-aged (42–59 years). Aging and CMV discordance were associated with increased immune diversity between monozygotic twins overall, and particularly strongly in various T cell populations. Notably, we identified 17 and 11 cell subset frequencies as relatively influenced and uninfluenced by non-heritable factors, respectively, with results that largely matched those from studies on older-aged cohorts. Next, CD4+ T cell frequency was shown to diverge with age in twins, but with lower slope than in demographically similar non-twins, suggesting that much inter-individual variance in this cell type can be attributed to interactions between genetic and environmental factors. Several cell frequencies previously associated with memory inflation, such as CD27- CD8+ T cells and CD161+ CD4+ T cells, were positively correlated with CMV seropositivity, supporting findings that CMV infection may incur rapid aging of the immune system. Conclusions Our study confirms previous findings that aging, even within a relatively small age range and by mid-adulthood, and CMV seropositivity, both contribute significantly to inter-individual immune diversity. Notably, we identify several key immune cell subsets that vary considerably with aging, as well as others associated with memory inflation which correlate with CMV seropositivity. Supplementary Information The online version contains supplementary material available at 10.1186/s12979-021-00216-1.
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Affiliation(s)
- Zheng Yan
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA, USA
| | - Holden T Maecker
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Petter Brodin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Unni C Nygaard
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA, USA.,Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Shu Chen Lyu
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA, USA
| | - Mark M Davis
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Kari C Nadeau
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA, USA
| | - Sandra Andorf
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA. .,Divisions of Biomedical Informatics and Allergy & Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
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125
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Boyce JH, Reisman BJ, Bachmann BO, Porco JA. Synthesis and Multiplexed Activity Profiling of Synthetic Acylphloroglucinol Scaffolds. Angew Chem Int Ed Engl 2021; 60:1263-1272. [PMID: 32965753 PMCID: PMC7855714 DOI: 10.1002/anie.202010338] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Indexed: 12/20/2022]
Abstract
Reported here are novel formic-acid-mediated rearrangements of dearomatized acylphloroglucinols to access a structurally diverse group of synthetic acylphloroglucinol scaffolds (SASs). Density-functional theory (DFT) optimized orbital and stereochemical analyses shed light on the mechanism of these rearrangements. Products were evaluated by multiplexed activity profiling (MAP), an unbiased platform which assays multiple biological readouts simultaneously at single-cell resolution for markers of cell signaling, and can aid in distinguishing genuine activity from assay interference. MAP identified a number of SASs that suppressed pS6 (Ser235/236), a marker for activation of the mTOR and ERK signaling pathways. These results illustrate how biomimetic synthesis and multiplexed activity profiling can reveal the pharmacological potential of novel chemotypes by diversity-oriented synthesis.
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Affiliation(s)
- Jonathan H Boyce
- Department of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, 590 Commonwealth Avenue, Boston, MA, 02215, USA
- Current Address: Department of Pharmaceutical Chemistry, University of California, San Francisco, 555 Mission Bay Blvd S., San Francisco, CA, 94158, USA
| | - Benjamin J Reisman
- Vanderbilt University, Chemistry Department, 7330 Stevenson Center, Nashville, TN, 37235, USA
| | - Brian O Bachmann
- Vanderbilt University, Chemistry Department, 7330 Stevenson Center, Nashville, TN, 37235, USA
| | - John A Porco
- Department of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, 590 Commonwealth Avenue, Boston, MA, 02215, USA
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126
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Zhu W, Jiang X, Sun H, Li Y, Shi W, Zheng M, Liu D, Ma A, Feng X. Global Lysine Acetylation and 2-Hydroxyisobutyrylation Profiling Reveals the Metabolism Conversion Mechanism in Giardia lamblia. Mol Cell Proteomics 2021; 20:100043. [PMID: 33376196 PMCID: PMC8724866 DOI: 10.1074/mcp.ra120.002353] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 12/01/2020] [Accepted: 12/29/2020] [Indexed: 12/13/2022] Open
Abstract
Giardia lamblia (G. lamblia) is the cause of giardiasis, a common infection that affects the general population of the world. Despite the constant possibility of damage because of their own metabolism, G. lamblia has survived and evolved to adapt to various environments. However, research on energy-metabolism conversion in G. lamblia is limited. This study aimed to reveal the dynamic metabolism conversion mechanism in G. lamblia under sugar starvation by detecting global lysine acetylation (Kac) and 2-hydroxyisobutyrylation (Khib) sites combined with quantitative proteome analyses. A total of 2999 acetylation sites on 956 proteins and 8877 2-hydroxyisobutyryl sites on 1546 proteins were quantified under sugar starvation. Integrated Kac and Khib data revealed that modified proteins were associated with arginine biosynthesis, glycolysis/gluconeogenesis, and alanine, aspartate, and glutamate metabolisms. These findings suggest that Kac and Khib were ubiquitous and provide deep insight into the metabolism conversion mechanism in G. lamblia under sugar starvation. Overall, these results can help delineate the biology of G. lamblia infections and reveal the evolutionary rule from prokaryote to eukaryote.
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Affiliation(s)
- Wenhe Zhu
- Academy of Basic Medicine, Jilin Medical University, Jilin, China
| | - Xiaoming Jiang
- Academy of Basic Medicine, Jilin Medical University, Jilin, China
| | - Hongyu Sun
- Academy of Basic Medicine, Jilin Medical University, Jilin, China
| | - Yawei Li
- Academy of Basic Medicine, Jilin Medical University, Jilin, China
| | - Wenyan Shi
- Academy of Basic Medicine, Jilin Medical University, Jilin, China
| | - Meiyu Zheng
- Academy of Basic Medicine, Jilin Medical University, Jilin, China
| | - Di Liu
- Academy of Basic Medicine, Jilin Medical University, Jilin, China
| | - Aixin Ma
- Academy of Basic Medicine, Jilin Medical University, Jilin, China
| | - Xianmin Feng
- Academy of Basic Medicine, Jilin Medical University, Jilin, China.
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127
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Abstract
PURPOSE OF REVIEW Our understanding of the effects of aging on human hematopoiesis has advanced significantly in recent years, yet the full ramifications of these findings are not fully understood. This review summarizes these findings and discusses their implication as they relate to malignant hematopoiesis. RECENT FINDINGS With human aging there is an impaired immune response, loss of hematopoietic stem cell (HSC) function, increase in clonal hematopoiesis, and higher frequency of myeloid malignancies. Although murine models have implicated abnormalities in DNA damage repair, autophagy, metabolism, and epigenetics, studies in primary human specimens are more limited. The development of age-related clonal hematopoiesis and the risk associated with this is one of the major findings in the field of recent years. This is accompanied by changes in bone marrow stem and progenitor composition, changes in the epigenetic program of stem cells and an inflammatory milieu in the bone marrow. The precise consequences of these changes for the development of age-related malignancies are still unclear. SUMMARY Advances in the field have begun to reveal the mechanisms driving human HSC loss of function with age. It will be critical to delineate between normal and malignant aging in order to better prevent age-associated myeloid malignancies.
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Affiliation(s)
- Emmalee R. Adelman
- Dept of Human Genetics, Miller School of Medicine, University of Miami
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami
| | - Maria E. Figueroa
- Dept of Human Genetics, Miller School of Medicine, University of Miami
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami
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128
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Shchukina I, Bagaitkar J, Shpynov O, Loginicheva E, Porter S, Mogilenko DA, Wolin E, Collins P, Demidov G, Artomov M, Zaitsev K, Sidorov S, Camell C, Bambouskova M, Arthur L, Swain A, Panteleeva A, Dievskii A, Kurbatsky E, Tsurinov P, Chernyatchik R, Dixit VD, Jovanovic M, Stewart SA, Daly MJ, Dmitriev S, Oltz EM, Artyomov MN. Enhanced epigenetic profiling of classical human monocytes reveals a specific signature of healthy aging in the DNA methylome. NATURE AGING 2021; 1:124-141. [PMID: 34796338 PMCID: PMC8597198 DOI: 10.1038/s43587-020-00002-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 10/06/2020] [Indexed: 12/20/2022]
Abstract
The impact of healthy aging on molecular programming of immune cells is poorly understood. Here, we report comprehensive characterization of healthy aging in human classical monocytes, with a focus on epigenomic, transcriptomic, and proteomic alterations, as well as the corresponding proteomic and metabolomic data for plasma, using healthy cohorts of 20 young and 20 older males (~27 and ~64 years old on average). For each individual, we performed eRRBS-based DNA methylation profiling, which allowed us to identify a set of age-associated differentially methylated regions (DMRs) - a novel, cell-type specific signature of aging in DNA methylome. Hypermethylation events were associated with H3K27me3 in the CpG islands near promoters of lowly-expressed genes, while hypomethylated DMRs were enriched in H3K4me1 marked regions and associated with age-related increase of expression of the corresponding genes, providing a link between DNA methylation and age-associated transcriptional changes in primary human cells.
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Affiliation(s)
- Irina Shchukina
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
- These authors contributed equally: Irina Shchukina, Juhi Bagaitkar, Oleg Shpynov
| | - Juhi Bagaitkar
- Department of Oral Immunology and Infectious Diseases, University of Louisville, Louisville, KY, USA
- These authors contributed equally: Irina Shchukina, Juhi Bagaitkar, Oleg Shpynov
| | - Oleg Shpynov
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
- JetBrains Research, St. Petersburg, Russia
- These authors contributed equally: Irina Shchukina, Juhi Bagaitkar, Oleg Shpynov
| | - Ekaterina Loginicheva
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Sofia Porter
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Denis A. Mogilenko
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Erica Wolin
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Patrick Collins
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | - German Demidov
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
- Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Mykyta Artomov
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Konstantin Zaitsev
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
- Present address: Computer Technologies Department, ITMO University, St. Petersburg, Russia
| | - Sviatoslav Sidorov
- Yale Center for Research on Aging, Yale School of Medicine, New Haven, CT, USA
| | - Christina Camell
- Yale Center for Research on Aging, Yale School of Medicine, New Haven, CT, USA
| | - Monika Bambouskova
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Laura Arthur
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Amanda Swain
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Alexandra Panteleeva
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | | | | | - Petr Tsurinov
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
- JetBrains Research, St. Petersburg, Russia
| | - Roman Chernyatchik
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
- JetBrains Research, St. Petersburg, Russia
| | - Vishwa Deep Dixit
- Yale Center for Research on Aging, Yale School of Medicine, New Haven, CT, USA
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Sheila A. Stewart
- Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Mark J. Daly
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
- Institute for Molecular Medicine, Helsinki, Finland
| | | | - Eugene M. Oltz
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Maxim N. Artyomov
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, USA
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129
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Elyahu Y, Monsonego A. Thymus involution sets the clock of the aging T-cell landscape: Implications for declined immunity and tissue repair. Ageing Res Rev 2021; 65:101231. [PMID: 33248315 DOI: 10.1016/j.arr.2020.101231] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 11/15/2020] [Accepted: 11/20/2020] [Indexed: 12/11/2022]
Abstract
Aging is generally characterized as a gradual increase in tissue damage, which is associated with senescence and chronic systemic inflammation and is evident in a variety of age-related diseases. The extent to which such tissue damage is a result of a gradual decline in immune regulation, which consequently compromises the capacity of the body to repair damages, has not been fully explored. Whereas CD4 T lymphocytes play a critical role in the orchestration of immunity, thymus involution initiates gradual changes in the CD4 T-cell landscape, which may significantly compromise tissue repair. In this review, we describe the lifespan accumulation of specific dysregulated CD4 T-cell subsets and their coevolution with systemic inflammation in the process of declined immunity and tissue repair capacity with age. Then, we discuss the process of thymus involution-which appears to be most pronounced around puberty-as a possible driver of the aging T-cell landscape. Finally, we identify individualized T cell-based early diagnostic biomarkers and therapeutic strategies for age-related diseases.
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Affiliation(s)
- Yehezqel Elyahu
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel; Zlotowski Neuroscience Center and Regenerative Medicine and Stem Cell Research Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel; National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Alon Monsonego
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel; Zlotowski Neuroscience Center and Regenerative Medicine and Stem Cell Research Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel; National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
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130
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Hallmarks of Health. Cell 2020; 184:33-63. [PMID: 33340459 DOI: 10.1016/j.cell.2020.11.034] [Citation(s) in RCA: 227] [Impact Index Per Article: 56.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 09/09/2020] [Accepted: 11/19/2020] [Indexed: 12/16/2022]
Abstract
Health is usually defined as the absence of pathology. Here, we endeavor to define health as a compendium of organizational and dynamic features that maintain physiology. The biological causes or hallmarks of health include features of spatial compartmentalization (integrity of barriers and containment of local perturbations), maintenance of homeostasis over time (recycling and turnover, integration of circuitries, and rhythmic oscillations), and an array of adequate responses to stress (homeostatic resilience, hormetic regulation, and repair and regeneration). Disruption of any of these interlocked features is broadly pathogenic, causing an acute or progressive derailment of the system coupled to the loss of numerous stigmata of health.
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131
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Channappanavar R, Perlman S. Age-related susceptibility to coronavirus infections: role of impaired and dysregulated host immunity. J Clin Invest 2020; 130:6204-6213. [PMID: 33085654 DOI: 10.1172/jci144115] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Human coronaviruses (hCoVs) cause severe respiratory illness in the elderly. Age-related impairments in innate immunity and suboptimal virus-specific T cell and antibody responses are believed to cause severe disease upon respiratory virus infections. This phenomenon has recently received increased attention, as elderly patients are at substantially elevated risk for severe COVID-19 disease and experience increased rates of mortality following SARS-CoV-2 infection compared with younger populations. However, the basis for age-related fatal pneumonia following pathogenic hCoVs is not well understood. In this Review, we provide an overview of our current understanding of hCoV-induced fatal pneumonia in the elderly. We describe host immune response to hCoV infections derived from studies of young and aged animal models and discuss the potential role of age-associated increases in sterile inflammation (inflammaging) and virus-induced dysregulated inflammation in causing age-related severe disease. We also highlight the existing gaps in our knowledge about virus replication and host immune responses to hCoV infection in young and aged individuals.
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Affiliation(s)
- Rudragouda Channappanavar
- Department of Acute and Tertiary Care and.,Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Stanley Perlman
- Department of Microbiology and Immunology and.,Stead Family Department of Pediatrics, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
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132
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Alkotob SS, Cannedy C, Harter K, Movassagh H, Paudel B, Prunicki M, Sampath V, Schikowski T, Smith E, Zhao Q, Traidl‐Hoffmann C, Nadeau KC. Advances and novel developments in environmental influences on the development of atopic diseases. Allergy 2020; 75:3077-3086. [PMID: 33037680 DOI: 10.1111/all.14624] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 10/05/2020] [Accepted: 10/05/2020] [Indexed: 12/12/2022]
Abstract
Although genetic factors play a role in the etiology of atopic disease, the rapid increases in the prevalence of these diseases over the last few decades suggest that environmental, rather than genetic factors are the driving force behind the increasing prevalence. In modern societies, there is increased time spent indoors, use of antibiotics, and consumption of processed foods and decreased contact with farm animals and pets, which limit exposure to environmental allergens, infectious parasitic worms, and microbes. The lack of exposure to these factors is thought to prevent proper education and training of the immune system. Increased industrialization and urbanization have brought about increases in organic and inorganic pollutants. In addition, Caesarian birth, birth order, increased use of soaps and detergents, tobacco smoke exposure and psychosomatic factors are other factors that have been associated with increased rate of allergic diseases. Here, we review current knowledge on the environmental factors that have been shown to affect the development of allergic diseases and the recent developments in the field.
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Affiliation(s)
- Shifaa Suhayl Alkotob
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University and Division of Pulmonary and Critical Care Medicine Department of Medicine Stanford University Stanford CA USA
| | - Cade Cannedy
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University and Division of Pulmonary and Critical Care Medicine Department of Medicine Stanford University Stanford CA USA
| | - Katharina Harter
- Chair and Institute of Environmental Medicine UNIKA‐TTechnical University of Munich and Helmholtz Zentrum München Augsburg Germany
| | - Hesam Movassagh
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University and Division of Pulmonary and Critical Care Medicine Department of Medicine Stanford University Stanford CA USA
| | - Bibek Paudel
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University and Division of Pulmonary and Critical Care Medicine Department of Medicine Stanford University Stanford CA USA
| | - Mary Prunicki
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University and Division of Pulmonary and Critical Care Medicine Department of Medicine Stanford University Stanford CA USA
| | - Vanitha Sampath
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University and Division of Pulmonary and Critical Care Medicine Department of Medicine Stanford University Stanford CA USA
| | - Tamara Schikowski
- IUF‐Leibniz Institute for Environmental Medicine Duesseldorf Germany
| | - Eric Smith
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University and Division of Pulmonary and Critical Care Medicine Department of Medicine Stanford University Stanford CA USA
| | - Qi Zhao
- IUF‐Leibniz Institute for Environmental Medicine Duesseldorf Germany
| | - Claudia Traidl‐Hoffmann
- Chair and Institute of Environmental Medicine UNIKA‐TTechnical University of Munich and Helmholtz Zentrum München Augsburg Germany
- CK‐CARE Christine Kühne Center for Allergy Research and Education Davos Switzerland
| | - Kari C. Nadeau
- Sean N. Parker Center for Allergy and Asthma Research at Stanford University and Division of Pulmonary and Critical Care Medicine Department of Medicine Stanford University Stanford CA USA
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133
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Zhang B, Gladyshev VN. How can aging be reversed? Exploring rejuvenation from a damage-based perspective. ADVANCED GENETICS (HOBOKEN, N.J.) 2020; 1:e10025. [PMID: 36619246 PMCID: PMC9744548 DOI: 10.1002/ggn2.10025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 03/13/2020] [Accepted: 03/17/2020] [Indexed: 01/11/2023]
Abstract
Advanced age is associated with accumulation of damage and other deleterious changes and a consequential systemic decline of function. This decline affects all organs and systems in an organism, leading to their inadaptability to the environment, and therefore is thought to be inevitable for humans and most animal species. However, in vitro and in vivo application of reprogramming strategies, which convert somatic cells to induced pluripotent stem cells, has demonstrated that the aged cells can be rejuvenated. Moreover, the data and theoretical considerations suggest that reversing the biological age of somatic cells (from old to young) and de-differentiating somatic cells into stem cells represent two distinct processes that take place during rejuvenation, and thus they may be differently targeted. We advance a stemness-function model to explain these data and discuss a possibility of rejuvenation from the perspective of damage accumulation. In turn, this suggests approaches to achieve rejuvenation of cells in vitro and in vivo.
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Affiliation(s)
- Bohan Zhang
- Division of Genetics, Department of Medicine, Brigham and Women's HospitalHarvard Medical SchoolBostonMassachusettsUSA
| | - Vadim N. Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's HospitalHarvard Medical SchoolBostonMassachusettsUSA
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134
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Uyar B, Palmer D, Kowald A, Murua Escobar H, Barrantes I, Möller S, Akalin A, Fuellen G. Single-cell analyses of aging, inflammation and senescence. Ageing Res Rev 2020; 64:101156. [PMID: 32949770 PMCID: PMC7493798 DOI: 10.1016/j.arr.2020.101156] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/23/2020] [Accepted: 08/25/2020] [Indexed: 02/09/2023]
Abstract
Single-cell gene expression (transcriptomics) data are becoming robust and abundant, and are increasingly used to track organisms along their life-course. This allows investigation into how aging affects cellular transcriptomes, and how changes in transcriptomes may underlie aging, including chronic inflammation (inflammaging), immunosenescence and cellular senescence. We compiled and tabulated aging-related single-cell datasets published to date, collected and discussed relevant findings, and inspected some of these datasets ourselves. We specifically note insights that cannot (or not easily) be based on bulk data. For example, in some datasets, the fraction of cells expressing p16 (CDKN2A), one of the most prominent markers of cellular senescence, was reported to increase, in addition to its upregulated mean expression over all cells. Moreover, we found evidence for inflammatory processes in most datasets, some of these driven by specific cells of the immune system. Further, single-cell data are specifically useful to investigate whether transcriptional heterogeneity (also called noise or variability) increases with age, and many (but not all) studies in our review report an increase in such heterogeneity. Finally, we demonstrate some stability of marker gene expression patterns across closely similar studies and suggest that single-cell experiments may hold the key to provide detailed insights whenever interventions (countering aging, inflammation, senescence, disease, etc.) are affecting cells depending on cell type.
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Affiliation(s)
- Bora Uyar
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Daniel Palmer
- Rostock University Medical Center, Institute for Biostatistics and Informatics in Medicine and Aging Research, Rostock, Germany
| | - Axel Kowald
- Rostock University Medical Center, Institute for Biostatistics and Informatics in Medicine and Aging Research, Rostock, Germany
| | - Hugo Murua Escobar
- Rostock University Medical Center, Department of Hematology, Oncology and Palliative Medicine, Department of Medicine III, Rostock, Germany
| | - Israel Barrantes
- Rostock University Medical Center, Institute for Biostatistics and Informatics in Medicine and Aging Research, Rostock, Germany
| | - Steffen Möller
- Rostock University Medical Center, Institute for Biostatistics and Informatics in Medicine and Aging Research, Rostock, Germany
| | - Altuna Akalin
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Georg Fuellen
- Rostock University Medical Center, Institute for Biostatistics and Informatics in Medicine and Aging Research, Rostock, Germany.
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135
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Zhao Y, Zhan JK, Liu Y. A Perspective on Roles Played by Immunosenescence in the Pathobiology of Alzheimer's Disease. Aging Dis 2020; 11:1594-1607. [PMID: 33269109 PMCID: PMC7673850 DOI: 10.14336/ad.2020.0205] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 02/05/2020] [Indexed: 12/26/2022] Open
Abstract
Alzheimer's disease (AD) is a chronic progressive neurodegenerative disorder. Aging is the most significant risk factor for late-onset AD. The age-associated changes in the immune system are termed immunosenescence. A close connection between immunosenescence and AD is increasingly recognized. This article provides an overview of immunosenescence and evidence for its role in the pathogenesis of AD and possible mechanisms as well as the outlook for drug development.
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Affiliation(s)
| | | | - Youshuo Liu
- Department of Geriatrics, Institute of Aging and Geriatrics, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
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136
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Boyce JH, Reisman BJ, Bachmann BO, Porco JA. Synthesis and Multiplexed Activity Profiling of Synthetic Acylphloroglucinol Scaffolds. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202010338] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jonathan H. Boyce
- Department of Chemistry and Center for Molecular Discovery (BU-CMD) Boston University 590 Commonwealth Avenue Boston MA 02215 USA
- Current Address: Department of Pharmaceutical Chemistry University of California, San Francisco 555 Mission Bay Blvd S. San Francisco CA 94158 USA
| | - Benjamin J. Reisman
- Vanderbilt University Chemistry Department 7330 Stevenson Center Nashville TN 37235 USA
| | - Brian O. Bachmann
- Vanderbilt University Chemistry Department 7330 Stevenson Center Nashville TN 37235 USA
| | - John A. Porco
- Department of Chemistry and Center for Molecular Discovery (BU-CMD) Boston University 590 Commonwealth Avenue Boston MA 02215 USA
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137
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Kurosawa S, Iwama A. Aging and leukemic evolution of hematopoietic stem cells under various stress conditions. Inflamm Regen 2020; 40:29. [PMID: 33292805 PMCID: PMC7643313 DOI: 10.1186/s41232-020-00138-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 08/13/2020] [Indexed: 12/18/2022] Open
Abstract
Hematopoietic stem cells (HSCs) have self-renewal capacity and differentiation potential into all lineages of blood cells throughout the lifetime of an organism. The function of HSCs gradually changes during aging. To date, various stress factors influencing HSC aging have been identified. The increased production of reactive oxygen species and DNA damage responses are causatively attributed to HSC aging. The increased apolarity is a prominent feature of aged HSCs, whereas it is less obvious in young HSCs. The bone marrow (BM) microenvironment niche is a crucial factor for HSC aging. Mesenchymal stem cells show skewed differentiation during aging, which leads to decreased bone formation and increased adipogenesis. The accumulation of adipocytes confers negative effects on hematopoiesis. Loss of sympathetic nerve fibers or adrenoreceptor β3 signaling induces premature HSC and niche aging. Epigenetic regulators such as polycomb group proteins and the sirtuin family of proteins act to prevent premature aging. Targeting these factors, several rejuvenation strategies for aged HSCs have been employed in mice. However, we still do not know whether these strategies can be extrapolated to human HSCs. Aging is frequently accompanied by the development of clonal hematopoiesis, which is called age-related clonal hematopoiesis (ARCH) or clonal hematopoiesis of indeterminate potential (CHIP). Most ARCH/CHIP mutations occur in genes encoding epigenetic regulators including DNMT3A, TET2, and ASXL1, which suggests the relevance of epigenetic drift during the aging process. ARCH/CHIP is a strong risk factor for subsequent hematologic cancer. Notably, it also has an impact on the development of non-malignant disorders such as coronary heart disease. Further studies are warranted to decipher the complete picture of molecular crosstalk that regulates HSC aging.
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Affiliation(s)
- Shuhei Kurosawa
- Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Atsushi Iwama
- Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan.
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Capturing and Understanding the Dynamics and Heterogeneity of Gene Expression in the Living Cell. Int J Mol Sci 2020; 21:ijms21218278. [PMID: 33167354 PMCID: PMC7663833 DOI: 10.3390/ijms21218278] [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: 09/23/2020] [Revised: 10/29/2020] [Accepted: 11/03/2020] [Indexed: 11/21/2022] Open
Abstract
The regulation of gene expression is a fundamental process enabling cells to respond to internal and external stimuli or to execute developmental programs. Changes in gene expression are highly dynamic and depend on many intrinsic and extrinsic factors. In this review, we highlight the dynamic nature of transient gene expression changes to better understand cell physiology and development in general. We will start by comparing recent in vivo procedures to capture gene expression in real time. Intrinsic factors modulating gene expression dynamics will then be discussed, focusing on chromatin modifications. Furthermore, we will dissect how cell physiology or age impacts on dynamic gene regulation and especially discuss molecular insights into acquired transcriptional memory. Finally, this review will give an update on the mechanisms of heterogeneous gene expression among genetically identical individual cells. We will mainly focus on state-of-the-art developments in the yeast model but also cover higher eukaryotic systems.
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139
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Yi SJ, Kim K. New Insights into the Role of Histone Changes in Aging. Int J Mol Sci 2020; 21:ijms21218241. [PMID: 33153221 PMCID: PMC7662996 DOI: 10.3390/ijms21218241] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/02/2020] [Accepted: 11/02/2020] [Indexed: 12/15/2022] Open
Abstract
Aging is the progressive decline or loss of function at the cellular, tissue, and organismal levels that ultimately leads to death. A number of external and internal factors, including diet, exercise, metabolic dysfunction, genome instability, and epigenetic imbalance, affect the lifespan of an organism. These aging factors regulate transcriptome changes related to the aging process through chromatin remodeling. Many epigenetic regulators, such as histone modification, histone variants, and ATP-dependent chromatin remodeling factors, play roles in chromatin reorganization. The key to understanding the role of gene regulatory networks in aging lies in characterizing the epigenetic regulators responsible for reorganizing and potentiating particular chromatin structures. This review covers epigenetic studies on aging, discusses the impact of epigenetic modifications on gene expression, and provides future directions in this area.
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140
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Fernández‐Zapata C, Leman JKH, Priller J, Böttcher C. The use and limitations of single-cell mass cytometry for studying human microglia function. Brain Pathol 2020; 30:1178-1191. [PMID: 33058349 PMCID: PMC8018011 DOI: 10.1111/bpa.12909] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 08/23/2020] [Accepted: 10/12/2020] [Indexed: 12/12/2022] Open
Abstract
Microglia, the resident innate immune cells of the central nervous system (CNS), play an important role in brain development and homoeostasis, as well as in neuroinflammatory, neurodegenerative and psychiatric diseases. Studies in animal models have been used to determine the origin and development of microglia, and how these cells alter their transcriptional and phenotypic signatures during CNS pathology. However, little is known about their human counterparts. Recent studies in human brain samples have harnessed the power of multiplexed single-cell technologies such as single-cell RNA sequencing (scRNA-seq) and mass cytometry (cytometry by time-of-flight [CyTOF]) to provide a comprehensive molecular view of human microglia in healthy and diseased brains. CyTOF is a powerful tool to study high-dimensional protein expression of human microglia (huMG) at the single-cell level. This technology widens the possibilities of high-throughput quantification (of over 60 targeted molecules) at a single-cell resolution. CyTOF can be combined with scRNA-seq for comprehensive analysis, as it allows single-cell analysis of post-translational modifications of proteins, which provides insights into cell signalling dynamics in targeted cells. In addition, imaging mass cytometry (IMC) has recently become commercially available, and will be useful for analysing multiple cell types in human brain sections. IMC leverages mass spectrometry to acquire spatial data of cell-cell interactions on tissue sections, using (theoretically) over 40 markers at the same time. In this review, we summarise recent studies of huMG using CyTOF and IMC analyses. The uses and limitations as well as future directions of these technologies are discussed.
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Affiliation(s)
- Camila Fernández‐Zapata
- Department of Neuropsychiatry and Laboratory of Molecular PsychiatryCharité – Universitätsmedizin BerlinBerlinGermany
| | - Julia K. H. Leman
- Department of Neuropsychiatry and Laboratory of Molecular PsychiatryCharité – Universitätsmedizin BerlinBerlinGermany
| | - Josef Priller
- Department of Neuropsychiatry and Laboratory of Molecular PsychiatryCharité – Universitätsmedizin BerlinBerlinGermany
- German Center for Neurodegenerative Diseases (DZNE)BerlinGermany
- UK Dementia Research Institute (DRI)University of EdinburghEdinburghUK
| | - Chotima Böttcher
- Department of Neuropsychiatry and Laboratory of Molecular PsychiatryCharité – Universitätsmedizin BerlinBerlinGermany
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141
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Luo G, Gao Q, Zhang S, Yan B. Probing infectious disease by single-cell RNA sequencing: Progresses and perspectives. Comput Struct Biotechnol J 2020; 18:2962-2971. [PMID: 33106757 PMCID: PMC7577221 DOI: 10.1016/j.csbj.2020.10.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 02/07/2023] Open
Abstract
The increasing application of single-cell RNA sequencing (scRNA-seq) technology in life science and biomedical research has significantly increased our understanding of the cellular heterogeneities in immunology, oncology and developmental biology. This review will summarize the development of various scRNA-seq technologies; primarily discussing the application of scRNA-seq on infectious diseases, and exploring the current development, challenges, and potential applications of scRNA-seq technology in the future.
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Key Words
- 3C, Chromosome Conformation Capture
- ACE2, Angiotensin-Converting Enzyme 2
- ARDS, acute respiratory distress syndrome
- ATAC-seq, Assay for Transposase-Accessible Chromatin using sequencing
- BCR, B cell receptor
- CEL-seq, Cell Expression by Linear amplification and Sequencing
- CLU, clusterin
- COVID-19, corona virus disease 2019
- CRISPR, Clustered Regularly Interspaced Short Palindromic Repeats
- CytoSeq, gene expression cytometry
- DENV, dengue virus
- FACS, fluorescence-activated cell sorting
- GNLY, granulysin
- GO analysis, Gene Ontology analysis
- HIV, Human Immunodeficiency Virus
- IAV, Influenza A virus
- IGHV/HD/HJ/HC, Immune globulin heavy V/D/J/C/ region
- IGLV/LJ/LC, Immune globulin light V/J/C/ region
- ILC, Innate Lymphoid Cell
- Infectious diseases
- LIGER, Linked Inference of Genomics Experimental Relationships
- MAGIC, Markov Affinity-based Graph Imputation of Cells
- MARS-seq, Massively parallel single-cell RNA sequencing
- MATCHER, Manifold Alignment To CHaracterize Experimental Relationships
- MCMV, mouse cytomegalovirus
- MERFISH, Multiplexed, Error Robust Fluorescent In Situ Hybridization
- MLV, Moloney Murine Leukemia Virus
- MOFA, Multi-Omics Factor Analysis
- MOI, multiplicity of infection
- PBMCs, peripheral blood mononuclear cells
- PLAC8, placenta-associated 8
- SARS-CoV-2, severe acute respiratory syndrome coronavirus 2
- SAVER, Single-cell Analysis Via Expression Recovery
- SPLit-seq, split pool ligation-based tranome sequencing
- STARTRAC, Single T-cell Analysis by RNA sequencing and TCR TRACking
- STRT-seq, Single-cell Tagged Reverse Transcription sequencing
- Single-cell RNA sequencing
- TCR, T cell receptor
- TSLP, thymic stromal lymphopoietin
- UMAP, Uniform Manifold Approximation and Projection
- UMI, Unique Molecular Identifier
- mcSCRB-seq, molecular crowding single-cell RNA barcoding and sequencing
- pDCs, plasmacytoid dendritic cells
- scRNA-seq, single cell RNA sequencing technology
- sci-RNA-seq, single-cell combinatorial indexing RNA sequencing
- seqFISH, sequential Fluorescent In Situ Hybridization
- smart-seq, switching mechanism at 5′ end of the RNA transcript sequencing
- t-SNE, t-Distributed stochastic neighbor embedding
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Affiliation(s)
- Geyang Luo
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Shanghai Public Health Clinical Center and Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Medical College and School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Qian Gao
- Shanghai Public Health Clinical Center and Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Medical College and School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Shuye Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Bo Yan
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
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142
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Zheng Y, Liu X, Le W, Xie L, Li H, Wen W, Wang S, Ma S, Huang Z, Ye J, Shi W, Ye Y, Liu Z, Song M, Zhang W, Han JDJ, Belmonte JCI, Xiao C, Qu J, Wang H, Liu GH, Su W. A human circulating immune cell landscape in aging and COVID-19. Protein Cell 2020; 11:740-770. [PMID: 32780218 PMCID: PMC7417788 DOI: 10.1007/s13238-020-00762-2] [Citation(s) in RCA: 169] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 07/01/2020] [Indexed: 12/21/2022] Open
Abstract
Age-associated changes in immune cells have been linked to an increased risk for infection. However, a global and detailed characterization of the changes that human circulating immune cells undergo with age is lacking. Here, we combined scRNA-seq, mass cytometry and scATAC-seq to compare immune cell types in peripheral blood collected from young and old subjects and patients with COVID-19. We found that the immune cell landscape was reprogrammed with age and was characterized by T cell polarization from naive and memory cells to effector, cytotoxic, exhausted and regulatory cells, along with increased late natural killer cells, age-associated B cells, inflammatory monocytes and age-associated dendritic cells. In addition, the expression of genes, which were implicated in coronavirus susceptibility, was upregulated in a cell subtype-specific manner with age. Notably, COVID-19 promoted age-induced immune cell polarization and gene expression related to inflammation and cellular senescence. Therefore, these findings suggest that a dysregulated immune system and increased gene expression associated with SARS-CoV-2 susceptibility may at least partially account for COVID-19 vulnerability in the elderly.
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Affiliation(s)
- Yingfeng Zheng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Xiuxing Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Wenqing Le
- Department of Critical Care, Wuhan Hankou Hospital, Wuhan, 430012, China
| | - Lihui Xie
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - He Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Wen Wen
- National Center for Liver Cancer, Second Military Medical University, Shanghai, 200433, China
| | - Si Wang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, CAS, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing, 100053, China
| | - Shuai Ma
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, CAS, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhaohao Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Jinguo Ye
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Wen Shi
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Yanxia Ye
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zunpeng Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Moshi Song
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, CAS, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Weiqi Zhang
- Institute for Stem Cell and Regeneration, CAS, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- China National Center for Bioinformation, Beijing, 100101, China
| | - Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, 100871, China
| | | | - Chuanle Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China
| | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regeneration, CAS, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Hongyang Wang
- National Center for Liver Cancer, Second Military Medical University, Shanghai, 200433, China.
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regeneration, CAS, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing, 100053, China.
| | - Wenru Su
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, 510060, China.
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143
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Zhang T, Warden AR, Li Y, Ding X. Progress and applications of mass cytometry in sketching immune landscapes. Clin Transl Med 2020; 10:e206. [PMID: 33135337 PMCID: PMC7556381 DOI: 10.1002/ctm2.206] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/28/2020] [Accepted: 09/28/2020] [Indexed: 12/16/2022] Open
Abstract
Recently emerged mass cytometry (cytometry by time-of-flight [CyTOF]) technology permits the identification and quantification of inherently diverse cellular systems, and the simultaneous measurement of functional attributes at the single-cell resolution. By virtue of its multiplex ability with limited need for compensation, CyTOF has led a critical role in immunological research fields. Here, we present an overview of CyTOF, including the introduction of CyTOF principle and advantages that make it a standalone tool in deciphering immune mysteries. We then discuss the functional assays, introduce the bioinformatics to interpret the data yield via CyTOF, and depict the emerging clinical and research applications of CyTOF technology in sketching immune landscape in a wide variety of diseases.
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Affiliation(s)
- Ting Zhang
- State Key laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghaiChina
| | - Antony R. Warden
- State Key laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghaiChina
| | - Yiyang Li
- State Key laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghaiChina
| | - Xianting Ding
- State Key laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical EngineeringShanghai Jiao Tong UniversityShanghaiChina
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144
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Mitsumori R, Sakaguchi K, Shigemizu D, Mori T, Akiyama S, Ozaki K, Niida S, Shimoda N. Lower DNA methylation levels in CpG island shores of CR1, CLU, and PICALM in the blood of Japanese Alzheimer's disease patients. PLoS One 2020; 15:e0239196. [PMID: 32991610 PMCID: PMC7523949 DOI: 10.1371/journal.pone.0239196] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 09/01/2020] [Indexed: 11/18/2022] Open
Abstract
The aim of the present study was to (1) investigate the relationship between late-onset Alzheimer’s disease (AD) and DNA methylation levels in six of the top seven AD-associated genes identified through a meta-analysis of recent genome wide association studies, APOE, BIN1, PICALM, CR1, CLU, and ABCA7, in blood, and (2) examine its applicability to the diagnosis of AD. We examined methylation differences at CpG island shores in the six genes using Sanger sequencing, and one of two groups of 48 AD patients and 48 elderly controls was used for a test or replication analysis. We found that methylation levels in three out of the six genes, CR1, CLU, and PICALM, were significantly lower in AD subjects. The combination of CLU methylation levels and the APOE genotype classified AD patients with AUC = 0.84 and 0.80 in the test and replication analyses, respectively. Our study implicates methylation differences at the CpG island shores of AD-associated genes in the onset of AD and suggests their diagnostic value.
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Affiliation(s)
- Risa Mitsumori
- Medical Genome Center, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan
| | - Kazuya Sakaguchi
- Department of Regenerative Medicine, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan
| | - Daichi Shigemizu
- Medical Genome Center, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan
| | - Taiki Mori
- Medical Genome Center, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan
| | - Shintaro Akiyama
- Medical Genome Center, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan
| | - Kouichi Ozaki
- Medical Genome Center, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan
| | - Shumpei Niida
- Medical Genome Center, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan
| | - Nobuyoshi Shimoda
- Department of Regenerative Medicine, National Center for Geriatrics and Gerontology, Obu, Aichi, Japan
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Abstract
Although the development of effective vaccines has saved countless lives from infectious diseases, the basic workings of the human immune system are complex and have required the development of animal models, such as inbred mice, to define mechanisms of immunity. More recently, new strategies and technologies have been developed to directly explore the human immune system with unprecedented precision. We discuss how these approaches are advancing our mechanistic understanding of human immunology and are facilitating the development of vaccines and therapeutics for infection, autoimmune diseases, and cancer.
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Affiliation(s)
- Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA.
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
- Stanford ChEM-H: Chemistry, Engineering and Medicine for Human Health, Stanford University, Stanford, CA 94305, USA
- Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mark M Davis
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
- Stanford University School of Medicine, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
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146
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Progress towards improving homing and engraftment of hematopoietic stem cells for clinical transplantation. Curr Opin Hematol 2020; 26:266-272. [PMID: 31045644 DOI: 10.1097/moh.0000000000000510] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PURPOSE OF REVIEW Hematopoietic cell transplantation (HCT) is a life-saving treatment for a variety of hematological and nonhematological disorders. Successful clinical outcomes after transplantation rely on adequate hematopoietic stem cell (HSC) numbers, and the homing and subsequent short-term and long-term engraftment of these cells in the bone marrow. Enhancing the homing capability of HSCs has the potential for high impact on improving HCT and patient survival. RECENT FINDINGS There are a number of ways to enhance HSC engraftment. Neutralizing negative epigenetic regulation by histone deacetylase 5 (HDAC5) increases surface CXCR4 expression and promotes human HSC homing and engraftment in immune-deficient NSG (NOD.Cg-Prkdc IL2rgt/Sz) mice. Short-term treatment of cells with glucocorticoids, pharmacological stabilization of hypoxia-inducible factor (HIF)-1α, increasing membrane lipid raft aggregation, and inhibition of dipeptidyl peptidase 4 (DPP4) facilitates HSC homing and engraftment. Added to these procedures, modulating the mitochondria permeability transition pore (MPTP) to mitigate ambient air-induced extra physiological oxygen stress/shock (EPHOSS) by hypoxic harvest and processing, or using cyclosporine A during air collection increases functional HSC numbers and improves HSC engraftment. SUMMARY A better understanding of the regulation of human HSC homing mediated by various signaling pathways will facilitate development of more efficient means to enhance HCT efficacy.
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147
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Epigenome-metabolome-microbiome axis in health and IBD. Curr Opin Microbiol 2020; 56:97-108. [PMID: 32920333 DOI: 10.1016/j.mib.2020.08.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/14/2020] [Accepted: 08/18/2020] [Indexed: 12/13/2022]
Abstract
Environmental triggers in the context of genetic susceptibility drive phenotypes of complex immune disorders such as Inflammatory bowel disease (IBD). One such trigger of IBD is perturbations in enteric commensal bacteria, fungi or viruses that shape both immune and neuronal state. The epigenome acts as an interface between microbiota and context-specific gene expression and is thus emerging as a third key contributor to IBD. Here we review evidence that the host epigenome plays a significant role in orchestrating the bidirectional crosstalk between mammals and their commensal microorganisms. We discuss disruption of chromatin regulatory regions and epigenetic enzyme mutants as a causative factor in IBD patients and mouse models of intestinal inflammation and consider the possible translation of this knowledge. Furthermore, we present emerging insights into the intricate connection between the microbiome and epigenetic enzyme activity via host or bacterial metabolites and how these interactions fine-tune the microorganism-host relationship.
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148
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Abstract
Adult stem cells undergo both replicative and chronological aging in their niches, with catastrophic declines in regenerative potential with age. Due to repeated environmental insults during aging, the chromatin landscape of stem cells erodes, with changes in both DNA and histone modifications, accumulation of damage, and altered transcriptional response. A body of work has shown that altered chromatin is a driver of cell fate changes and a regulator of self-renewal in stem cells and therefore a prime target for juvenescence therapeutics. This review focuses on chromatin changes in stem cell aging and provides a composite view of both common and unique epigenetic themes apparent from the studies of multiple stem cell types.
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Affiliation(s)
- Changyou Shi
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Lin Wang
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Payel Sen
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
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149
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Salmonella enterica serovar Typhi exposure elicits ex vivo cell-type-specific epigenetic changes in human gut cells. Sci Rep 2020; 10:13581. [PMID: 32788681 PMCID: PMC7423951 DOI: 10.1038/s41598-020-70492-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 06/22/2020] [Indexed: 01/25/2023] Open
Abstract
Salmonella enterica serovar Typhi (S. Typhi) causes substantial morbidity and mortality worldwide, particularly among young children. Humans develop an array of mucosal immune responses following S. Typhi infection. Whereas the cellular mechanisms involved in S. Typhi infection have been intensively studied, very little is known about the early chromatin modifications occurring in the human gut microenvironment that influence downstream immune responses. To address this gap in knowledge, cells isolated from human terminal ileum exposed ex vivo to the wild-type S. Typhi strain were stained with a 33-metal-labeled antibody panel for mass cytometry analyses of the early chromatin modifications modulated by S. Typhi. We measured the cellular levels of 6 classes of histone modifications, and 1 histone variant in 11 major cell subsets (i.e., B, CD3 + T, CD4 + T, CD8 + T, NK, TCR-γδ, Mucosal associated invariant (MAIT), and NKT cells as well as monocytes, macrophages, and epithelial cells). We found that arginine methylation might regulate the early-differentiation of effector-memory CD4+ T-cells following exposure to S. Typhi. We also found S. Typhi-induced post-translational modifications in histone methylation and acetylation associated with epithelial cells, NKT, MAIT, TCR-γδ, Monocytes, and CD8 + T-cells that are related to both gene activation and silencing.
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Arunachalam PS, Wimmers F, Mok CKP, Perera RAPM, Scott M, Hagan T, Sigal N, Feng Y, Bristow L, Tak-Yin Tsang O, Wagh D, Coller J, Pellegrini KL, Kazmin D, Alaaeddine G, Leung WS, Chan JMC, Chik TSH, Choi CYC, Huerta C, Paine McCullough M, Lv H, Anderson E, Edupuganti S, Upadhyay AA, Bosinger SE, Maecker HT, Khatri P, Rouphael N, Peiris M, Pulendran B. Systems biological assessment of immunity to mild versus severe COVID-19 infection in humans. Science 2020; 369:1210-1220. [PMID: 32788292 DOI: 10.1126/science.abc6261] [Citation(s) in RCA: 803] [Impact Index Per Article: 200.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/10/2020] [Accepted: 08/04/2020] [Indexed: 02/06/2023]
Abstract
Coronavirus disease 2019 (COVID-19) represents a global crisis, yet major knowledge gaps remain about human immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We analyzed immune responses in 76 COVID-19 patients and 69 healthy individuals from Hong Kong and Atlanta, Georgia, United States. In the peripheral blood mononuclear cells (PBMCs) of COVID-19 patients, we observed reduced expression of human leukocyte antigen class DR (HLA-DR) and proinflammatory cytokines by myeloid cells as well as impaired mammalian target of rapamycin (mTOR) signaling and interferon-α (IFN-α) production by plasmacytoid dendritic cells. By contrast, we detected enhanced plasma levels of inflammatory mediators-including EN-RAGE, TNFSF14, and oncostatin M-which correlated with disease severity and increased bacterial products in plasma. Single-cell transcriptomics revealed a lack of type I IFNs, reduced HLA-DR in the myeloid cells of patients with severe COVID-19, and transient expression of IFN-stimulated genes. This was consistent with bulk PBMC transcriptomics and transient, low IFN-α levels in plasma during infection. These results reveal mechanisms and potential therapeutic targets for COVID-19.
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Affiliation(s)
- Prabhu S Arunachalam
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Florian Wimmers
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Chris Ka Pun Mok
- HKU-Pasteur Research Pole, School of Public Health, HKU Li Ka Shing Faculty of Medicine, The University of Hong Kong (HKU), Hong Kong
| | - Ranawaka A P M Perera
- Centre of Influenza Research, School of Public Health, HKU Li Ka Shing Faculty of Medicine, HKU, Hong Kong
| | - Madeleine Scott
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA.,Center for Biomedical Informatics, Department of Medicine, 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
| | - Natalia Sigal
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yupeng Feng
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Laurel Bristow
- Hope Clinic of the Emory Vaccine Center, Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Decatur, GA 30030, USA
| | - Owen Tak-Yin Tsang
- Infectious Diseases Centre, Princess Margaret Hospital, Hospital Authority of Hong Kong, Hong Kong
| | - Dhananjay Wagh
- Stanford Functional Genomics Facility, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - John Coller
- Stanford Functional Genomics Facility, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kathryn L Pellegrini
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Dmitri Kazmin
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ghina Alaaeddine
- Hope Clinic of the Emory Vaccine Center, Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Decatur, GA 30030, USA
| | - Wai Shing Leung
- Infectious Diseases Centre, Princess Margaret Hospital, Hospital Authority of Hong Kong, Hong Kong
| | - Jacky Man Chun Chan
- Infectious Diseases Centre, Princess Margaret Hospital, Hospital Authority of Hong Kong, Hong Kong
| | - Thomas Shiu Hong Chik
- Infectious Diseases Centre, Princess Margaret Hospital, Hospital Authority of Hong Kong, Hong Kong
| | - Chris Yau Chung Choi
- Infectious Diseases Centre, Princess Margaret Hospital, Hospital Authority of Hong Kong, Hong Kong
| | - Christopher Huerta
- Hope Clinic of the Emory Vaccine Center, Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Decatur, GA 30030, USA
| | - Michele Paine McCullough
- Hope Clinic of the Emory Vaccine Center, Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Decatur, GA 30030, USA
| | - Huibin Lv
- HKU-Pasteur Research Pole, School of Public Health, HKU Li Ka Shing Faculty of Medicine, The University of Hong Kong (HKU), Hong Kong
| | - Evan Anderson
- Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Srilatha Edupuganti
- Hope Clinic of the Emory Vaccine Center, Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Decatur, GA 30030, USA
| | - Amit A Upadhyay
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Steve E Bosinger
- Emory Vaccine Center, Yerkes National Primate Research Center, Atlanta, GA 30329, USA.,Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30329, USA
| | - Holden Terry Maecker
- Institute for Immunity, Transplantation and Infection, 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.,Center for Biomedical Informatics, Department of Medicine, Stanford University School of Medicine, 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
| | - Malik Peiris
- HKU-Pasteur Research Pole, School of Public Health, HKU Li Ka Shing Faculty of Medicine, The University of Hong Kong (HKU), Hong Kong.,Centre of Influenza Research, School of Public Health, HKU Li Ka Shing Faculty of Medicine, HKU, Hong Kong
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA. .,Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
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