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Pahl MC, Sharma P, Thomas RM, Thompson Z, Mount Z, Pippin JA, Morawski PA, Sun P, Su C, Campbell D, Grant SFA, Wells AD. Dynamic chromatin architecture identifies new autoimmune-associated enhancers for IL2 and novel genes regulating CD4+ T cell activation. eLife 2024; 13:RP96852. [PMID: 39302339 DOI: 10.7554/elife.96852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2024] Open
Abstract
Genome-wide association studies (GWAS) have identified hundreds of genetic signals associated with autoimmune disease. The majority of these signals are located in non-coding regions and likely impact cis-regulatory elements (cRE). Because cRE function is dynamic across cell types and states, profiling the epigenetic status of cRE across physiological processes is necessary to characterize the molecular mechanisms by which autoimmune variants contribute to disease risk. We localized risk variants from 15 autoimmune GWAS to cRE active during TCR-CD28 co-stimulation of naïve human CD4+ T cells. To characterize how dynamic changes in gene expression correlate with cRE activity, we measured transcript levels, chromatin accessibility, and promoter-cRE contacts across three phases of naive CD4+ T cell activation using RNA-seq, ATAC-seq, and HiC. We identified ~1200 protein-coding genes physically connected to accessible disease-associated variants at 423 GWAS signals, at least one-third of which are dynamically regulated by activation. From these maps, we functionally validated a novel stretch of evolutionarily conserved intergenic enhancers whose activity is required for activation-induced IL2 gene expression in human and mouse, and is influenced by autoimmune-associated genetic variation. The set of genes implicated by this approach are enriched for genes controlling CD4+ T cell function and genes involved in human inborn errors of immunity, and we pharmacologically validated eight implicated genes as novel regulators of T cell activation. These studies directly show how autoimmune variants and the genes they regulate influence processes involved in CD4+ T cell proliferation and activation.
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Affiliation(s)
- Matthew C Pahl
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, United States
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, United States
| | - Prabhat Sharma
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, United States
- Department of Pathology, The Children's Hospital of Philadelphia, Philadelphia, United States
| | - Rajan M Thomas
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, United States
- Department of Pathology, The Children's Hospital of Philadelphia, Philadelphia, United States
| | - Zachary Thompson
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, United States
- Department of Pathology, The Children's Hospital of Philadelphia, Philadelphia, United States
| | - Zachary Mount
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, United States
- Department of Pathology, The Children's Hospital of Philadelphia, Philadelphia, United States
| | - James A Pippin
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, United States
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, United States
| | - Peter A Morawski
- Benaroya Research Institute at Virginia Mason, Seattle, United States
| | - Peng Sun
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, United States
- Department of Pathology, The Children's Hospital of Philadelphia, Philadelphia, United States
| | - Chun Su
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, United States
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, United States
| | - Daniel Campbell
- Benaroya Research Institute at Virginia Mason, Seattle, United States
- Department of Immunology, University of Washington School of Medicine, Seattle, United States
| | - Struan F A Grant
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, United States
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, United States
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
- Division of Endocrinology and Diabetes, The Children's Hospital of Philadelphia, Philadelphia, United States
| | - Andrew D Wells
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, United States
- Department of Pathology, The Children's Hospital of Philadelphia, Philadelphia, United States
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
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2
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Gong Q, Sharma M, Kuan EL, Glass MC, Chander A, Singh M, Graybuck LT, Thomson ZJ, LaFrance CM, Zaim SR, Peng T, Okada LY, Genge PC, Henderson KE, Dornisch EM, Layton ED, Wittig PJ, Heubeck AT, Mukuka NM, Reading J, Roll CR, Hernandez V, Parthasarathy V, Stuckey TJ, Musgrove B, Swanson E, Lord C, Weiss MDA, Phalen CG, Mettey RR, Lee KJ, Johanneson JB, Kawelo EK, Garber J, Krishnan U, Smithmyer M, Wherry EJ, Vella L, Henrickson SE, Kopp MS, Savage AK, Becker LA, Meijer P, Coffey EM, Goronzy JJ, Speake C, Bumol TF, Goldrath AW, Torgerson TR, Li XJ, Skene PJ, Buckner JH, Gustafson CE. Longitudinal Multi-omic Immune Profiling Reveals Age-Related Immune Cell Dynamics in Healthy Adults. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.10.612119. [PMID: 39314416 PMCID: PMC11419011 DOI: 10.1101/2024.09.10.612119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
The generation and maintenance of protective immunity is a dynamic interplay between host and environment that is impacted by age. Understanding fundamental changes in the healthy immune system that occur over a lifespan is critical in developing interventions for age-related susceptibility to infections and diseases. Here, we use multi-omic profiling (scRNA-seq, proteomics, flow cytometry) to examined human peripheral immunity in over 300 healthy adults, with 96 young and older adults followed over two years with yearly vaccination. The resulting resource includes scRNA-seq datasets of >16 million PBMCs, interrogating 71 immune cell subsets from our new Immune Health Atlas. This study allows unique insights into the composition and transcriptional state of immune cells at homeostasis, with vaccine perturbation, and across age. We find that T cells specifically accumulate age-related transcriptional changes more than other immune cells, independent from inflammation and chronic perturbation. Moreover, impaired memory B cell responses to vaccination are linked to a Th2-like state shift in older adults' memory CD4 T cells, revealing possible mechanisms of immune dysregulation during healthy human aging. This extensive resource is provided with a suite of exploration tools at https://apps.allenimmunology.org/aifi/insights/dynamics-imm-health-age/ to enhance data accessibility and further the understanding of immune health across age.
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Xu Y, Wang Z, Li S, Su J, Gao L, Ou J, Lin Z, Luo OJ, Xiao C, Chen G. An in-depth understanding of the role and mechanisms of T cells in immune organ aging and age-related diseases. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-024-2695-x. [PMID: 39231902 DOI: 10.1007/s11427-024-2695-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 07/28/2024] [Indexed: 09/06/2024]
Abstract
T cells play a critical and irreplaceable role in maintaining overall health. However, their functions undergo alterations as individuals age. It is of utmost importance to comprehend the specific characteristics of T-cell aging, as this knowledge is crucial for gaining deeper insights into the pathogenesis of aging-related diseases and developing effective therapeutic strategies. In this review, we have thoroughly examined the existing studies on the characteristics of immune organ aging. Furthermore, we elucidated the changes and potential mechanisms that occur in T cells during the aging process. Additionally, we have discussed the latest research advancements pertaining to T-cell aging-related diseases. These findings provide a fresh perspective for the study of T cells in the context of aging.
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Affiliation(s)
- Yudai Xu
- Department of Microbiology and Immunology, School of Medicine; Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou, 510632, China
- Key Laboratory of Viral Pathogenesis & Infection Prevention and Control (Jinan University), Ministry of Education, Guangzhou, 510632, China
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, School of Medicine, Jinan University, Guangzhou, 510632, China
| | - Zijian Wang
- Department of Microbiology and Immunology, School of Medicine; Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou, 510632, China
- Key Laboratory of Viral Pathogenesis & Infection Prevention and Control (Jinan University), Ministry of Education, Guangzhou, 510632, China
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, School of Medicine, Jinan University, Guangzhou, 510632, China
| | - Shumin Li
- Department of Microbiology and Immunology, School of Medicine; Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou, 510632, China
- Key Laboratory of Viral Pathogenesis & Infection Prevention and Control (Jinan University), Ministry of Education, Guangzhou, 510632, China
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, School of Medicine, Jinan University, Guangzhou, 510632, China
| | - Jun Su
- First Affiliated Hospital, Jinan University, Guangzhou, 510630, China
| | - Lijuan Gao
- Department of Microbiology and Immunology, School of Medicine; Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou, 510632, China
- Key Laboratory of Viral Pathogenesis & Infection Prevention and Control (Jinan University), Ministry of Education, Guangzhou, 510632, China
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, School of Medicine, Jinan University, Guangzhou, 510632, China
| | - Junwen Ou
- Anti Aging Medical Center, Clifford Hospital, Guangzhou, 511495, China
| | - Zhanyi Lin
- Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China
| | - Oscar Junhong Luo
- Department of Systems Biomedical Sciences, School of Medicine, Jinan University, Guangzhou, 510632, China
| | - Chanchan Xiao
- Department of Microbiology and Immunology, School of Medicine; Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou, 510632, China.
- Key Laboratory of Viral Pathogenesis & Infection Prevention and Control (Jinan University), Ministry of Education, Guangzhou, 510632, China.
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, School of Medicine, Jinan University, Guangzhou, 510632, China.
- The Sixth Affiliated Hospital of Jinan University (Dongguan Eastern Central Hospital), Jinan University, Dongguan, 523000, China.
- Zhuhai Institute of Jinan University, Jinan University, Zhuhai, 519070, China.
| | - Guobing Chen
- Department of Microbiology and Immunology, School of Medicine; Institute of Geriatric Immunology, School of Medicine, Jinan University, Guangzhou, 510632, China.
- Key Laboratory of Viral Pathogenesis & Infection Prevention and Control (Jinan University), Ministry of Education, Guangzhou, 510632, China.
- Guangdong-Hong Kong-Macau Great Bay Area Geroscience Joint Laboratory, School of Medicine, Jinan University, Guangzhou, 510632, China.
- The Sixth Affiliated Hospital of Jinan University (Dongguan Eastern Central Hospital), Jinan University, Dongguan, 523000, China.
- Zhuhai Institute of Jinan University, Jinan University, Zhuhai, 519070, China.
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4
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Patrick R, Naval-Sanchez M, Deshpande N, Huang Y, Zhang J, Chen X, Yang Y, Tiwari K, Esmaeili M, Tran M, Mohamed AR, Wang B, Xia D, Ma J, Bayliss J, Wong K, Hun ML, Sun X, Cao B, Cottle DL, Catterall T, Barzilai-Tutsch H, Troskie RL, Chen Z, Wise AF, Saini S, Soe YM, Kumari S, Sweet MJ, Thomas HE, Smyth IM, Fletcher AL, Knoblich K, Watt MJ, Alhomrani M, Alsanie W, Quinn KM, Merson TD, Chidgey AP, Ricardo SD, Yu D, Jardé T, Cheetham SW, Marcelle C, Nilsson SK, Nguyen Q, White MD, Nefzger CM. The activity of early-life gene regulatory elements is hijacked in aging through pervasive AP-1-linked chromatin opening. Cell Metab 2024; 36:1858-1881.e23. [PMID: 38959897 DOI: 10.1016/j.cmet.2024.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 03/28/2024] [Accepted: 06/06/2024] [Indexed: 07/05/2024]
Abstract
A mechanistic connection between aging and development is largely unexplored. Through profiling age-related chromatin and transcriptional changes across 22 murine cell types, analyzed alongside previous mouse and human organismal maturation datasets, we uncovered a transcription factor binding site (TFBS) signature common to both processes. Early-life candidate cis-regulatory elements (cCREs), progressively losing accessibility during maturation and aging, are enriched for cell-type identity TFBSs. Conversely, cCREs gaining accessibility throughout life have a lower abundance of cell identity TFBSs but elevated activator protein 1 (AP-1) levels. We implicate TF redistribution toward these AP-1 TFBS-rich cCREs, in synergy with mild downregulation of cell identity TFs, as driving early-life cCRE accessibility loss and altering developmental and metabolic gene expression. Such remodeling can be triggered by elevating AP-1 or depleting repressive H3K27me3. We propose that AP-1-linked chromatin opening drives organismal maturation by disrupting cell identity TFBS-rich cCREs, thereby reprogramming transcriptome and cell function, a mechanism hijacked in aging through ongoing chromatin opening.
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Affiliation(s)
- Ralph Patrick
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Marina Naval-Sanchez
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Nikita Deshpande
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Yifei Huang
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Jingyu Zhang
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Xiaoli Chen
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Ying Yang
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Kanupriya Tiwari
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Mohammadhossein Esmaeili
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Minh Tran
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Amin R Mohamed
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Binxu Wang
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Di Xia
- Genome Innovation Hub, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Jun Ma
- Genome Innovation Hub, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Jacqueline Bayliss
- Department of Anatomy and Physiology, Faculty of Medicine Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Kahlia Wong
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Michael L Hun
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Xuan Sun
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organization, Melbourne, VIC, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Benjamin Cao
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organization, Melbourne, VIC, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Denny L Cottle
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Tara Catterall
- St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Hila Barzilai-Tutsch
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia; Institut NeuroMyoGène, University Claude Bernard Lyon 1, 69008 Lyon, France
| | - Robin-Lee Troskie
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Zhian Chen
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Andrea F Wise
- Department of Pharmacology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Sheetal Saini
- Department of Pharmacology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Ye Mon Soe
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Snehlata Kumari
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Matthew J Sweet
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Helen E Thomas
- St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Ian M Smyth
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Anne L Fletcher
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Konstantin Knoblich
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Matthew J Watt
- Department of Anatomy and Physiology, Faculty of Medicine Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Majid Alhomrani
- Department of Clinical Laboratories Sciences, Faculty of Applied Medical Sciences, Taif University, Taif, Saudi Arabia; Research Centre for Health Sciences, Taif University, Taif, Saudi Arabia
| | - Walaa Alsanie
- Department of Clinical Laboratories Sciences, Faculty of Applied Medical Sciences, Taif University, Taif, Saudi Arabia; Research Centre for Health Sciences, Taif University, Taif, Saudi Arabia
| | - Kylie M Quinn
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC 3083, Australia
| | - Tobias D Merson
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia; National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ann P Chidgey
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Sharon D Ricardo
- Department of Pharmacology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Di Yu
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia; Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Thierry Jardé
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Cancer Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Department of Surgery, Cabrini Monash University, Malvern, VIC 3144, Australia
| | - Seth W Cheetham
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Christophe Marcelle
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia; Institut NeuroMyoGène, University Claude Bernard Lyon 1, 69008 Lyon, France
| | - Susan K Nilsson
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organization, Melbourne, VIC, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Quan Nguyen
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; School of Biomedical Sciences, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Melanie D White
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; School of Biomedical Sciences, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Christian M Nefzger
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia; Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia.
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5
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Hahn EE, Stiller J, Alexander MR, Grealy A, Taylor JM, Jackson N, Frere CH, Holleley CE. Century-old chromatin architecture revealed in formalin-fixed vertebrates. Nat Commun 2024; 15:6378. [PMID: 39075073 PMCID: PMC11286846 DOI: 10.1038/s41467-024-50668-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 07/18/2024] [Indexed: 07/31/2024] Open
Abstract
Gene expression is regulated by changes in chromatin architecture intrinsic to cellular differentiation and as an active response to environmental stimuli. Chromatin dynamics are a major driver of phenotypic diversity, regulation of development, and manifestation of disease. Remarkably, we know little about the evolutionary dynamics of chromatin reorganisation through time, data essential to characterise the impact of environmental stress during the ongoing biodiversity extinction crisis (20th-21st century). Linking the disparate fields of chromatin biology and museum science through their common use of the preservative formaldehyde (a constituent of formalin), we have generated historical chromatin profiles in museum specimens up to 117 years old. Historical chromatin profiles are reproducible, tissue-specific, sex-specific, and environmental condition-dependent in vertebrate specimens. Additionally, we show that over-fixation modulates differential chromatin accessibility to enable semi-quantitative estimates of relative gene expression in vertebrates and a yeast model. Our approach transforms formalin-fixed biological collections into an accurate, comprehensive, and global record of environmental impact on gene expression and phenotype.
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Affiliation(s)
- Erin E Hahn
- National Research Collections Australia, Commonwealth Scientific Industrial Research Organisation, Canberra, ACT 2601, Australia
| | - Jiri Stiller
- Agriculture and Food, Commonwealth Scientific Industrial Research Organisation, St Lucia, Queensland, 4067, Australia
| | - Marina R Alexander
- National Research Collections Australia, Commonwealth Scientific Industrial Research Organisation, Canberra, ACT 2601, Australia
| | - Alicia Grealy
- National Research Collections Australia, Commonwealth Scientific Industrial Research Organisation, Canberra, ACT 2601, Australia
| | - Jennifer M Taylor
- Agriculture and Food, Commonwealth Scientific Industrial Research Organisation, St Lucia, Queensland, 4067, Australia
| | - Nicola Jackson
- School of the Environment, University of Queensland, St Lucia, Queensland, 4067, Australia
| | - Celine H Frere
- School of the Environment, University of Queensland, St Lucia, Queensland, 4067, Australia
| | - Clare E Holleley
- National Research Collections Australia, Commonwealth Scientific Industrial Research Organisation, Canberra, ACT 2601, Australia.
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6
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Zheng Z, Li J, Liu T, Fan Y, Zhai QC, Xiong M, Wang QR, Sun X, Zheng QW, Che S, Jiang B, Zheng Q, Wang C, Liu L, Ping J, Wang S, Gao DD, Ye J, Yang K, Zuo Y, Ma S, Yang YG, Qu J, Zhang F, Jia P, Liu GH, Zhang W. DNA methylation clocks for estimating biological age in Chinese cohorts. Protein Cell 2024; 15:575-593. [PMID: 38482631 PMCID: PMC11259550 DOI: 10.1093/procel/pwae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 01/10/2024] [Indexed: 07/21/2024] Open
Abstract
Epigenetic clocks are accurate predictors of human chronological age based on the analysis of DNA methylation (DNAm) at specific CpG sites. However, a systematic comparison between DNA methylation data and other omics datasets has not yet been performed. Moreover, available DNAm age predictors are based on datasets with limited ethnic representation. To address these knowledge gaps, we generated and analyzed DNA methylation datasets from two independent Chinese cohorts, revealing age-related DNAm changes. Additionally, a DNA methylation aging clock (iCAS-DNAmAge) and a group of DNAm-based multi-modal clocks for Chinese individuals were developed, with most of them demonstrating strong predictive capabilities for chronological age. The clocks were further employed to predict factors influencing aging rates. The DNAm aging clock, derived from multi-modal aging features (compositeAge-DNAmAge), exhibited a close association with multi-omics changes, lifestyles, and disease status, underscoring its robust potential for precise biological age assessment. Our findings offer novel insights into the regulatory mechanism of age-related DNAm changes and extend the application of the DNAm clock for measuring biological age and aging pace, providing the basis for evaluating aging intervention strategies.
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Affiliation(s)
- Zikai Zheng
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiaming Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tianzi Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yanling Fan
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Qiao-Cheng Zhai
- Division of Orthopaedics, Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou 324000, China
- The Joint Innovation Center for Engineering in Medicine, Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou 324000, China
| | - Muzhao Xiong
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiao-Ran Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyan Sun
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qi-Wen Zheng
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Shanshan Che
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Beier Jiang
- The Joint Innovation Center for Engineering in Medicine, Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou 324000, China
| | - Quan Zheng
- The Joint Innovation Center for Engineering in Medicine, Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou 324000, China
| | - Cui Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lixiao Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiale Ping
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Si Wang
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
- Aging Biomarker Consortium, Beijing 100101, China
| | - Dan-Dan Gao
- The Joint Innovation Center for Engineering in Medicine, Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou 324000, China
| | - Jinlin Ye
- The Joint Innovation Center for Engineering in Medicine, Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou 324000, China
| | - Kuan Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuesheng Zuo
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuai Ma
- Aging Biomarker Consortium, Beijing 100101, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Yun-Gui Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Qu
- University of Chinese Academy of Sciences, Beijing 100049, China
- Aging Biomarker Consortium, Beijing 100101, China
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Feng Zhang
- Division of Orthopaedics, Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou 324000, China
| | - Peilin Jia
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Guang-Hui Liu
- University of Chinese Academy of Sciences, Beijing 100049, China
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
- Aging Biomarker Consortium, Beijing 100101, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Weiqi Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Aging Biomarker Consortium, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
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7
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Chen ACY, Jaiswal S, Martinez D, Yerinde C, Ji K, Miranda V, Fung ME, Weiss SA, Zschummel M, Taguchi K, Garris CS, Mempel TR, Hacohen N, Sen DR. The aged tumor microenvironment limits T cell control of cancer. Nat Immunol 2024; 25:1033-1045. [PMID: 38745085 DOI: 10.1038/s41590-024-01828-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 03/27/2024] [Indexed: 05/16/2024]
Abstract
The etiology and effect of age-related immune dysfunction in cancer is not completely understood. Here we show that limited priming of CD8+ T cells in the aged tumor microenvironment (TME) outweighs cell-intrinsic defects in limiting tumor control. Increased tumor growth in aging is associated with reduced CD8+ T cell infiltration and function. Transfer of T cells from young mice does not restore tumor control in aged mice owing to rapid induction of T cell dysfunction. Cell-extrinsic signals in the aged TME drive a tumor-infiltrating age-associated dysfunctional (TTAD) cell state that is functionally, transcriptionally and epigenetically distinct from canonical T cell exhaustion. Altered natural killer cell-dendritic cell-CD8+ T cell cross-talk in aged tumors impairs T cell priming by conventional type 1 dendritic cells and promotes TTAD cell formation. Aged mice are thereby unable to benefit from therapeutic tumor vaccination. Critically, myeloid-targeted therapy to reinvigorate conventional type 1 dendritic cells can improve tumor control and restore CD8+ T cell immunity in aging.
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Affiliation(s)
- Alex C Y Chen
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Sneha Jaiswal
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Carnegie Mellon University, Pittsburgh, PA, USA
| | - Daniela Martinez
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Cansu Yerinde
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Keely Ji
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Velita Miranda
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Megan E Fung
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Sarah A Weiss
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Maria Zschummel
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Kazuhiro Taguchi
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Christopher S Garris
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Thorsten R Mempel
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Nir Hacohen
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Debattama R Sen
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA.
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8
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Jin K, McCoy BM, Goldman EA, Usova V, Tkachev V, Chitsazan AD, Kakebeen A, Jeffery U, Creevy KE, Wills A, Snyder‐Mackler N, Promislow DEL. DNA methylation and chromatin accessibility predict age in the domestic dog. Aging Cell 2024; 23:e14079. [PMID: 38263575 PMCID: PMC11019125 DOI: 10.1111/acel.14079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 01/25/2024] Open
Abstract
Across mammals, the epigenome is highly predictive of chronological age. These "epigenetic clocks," most of which have been built using DNA methylation (DNAm) profiles, have gained traction as biomarkers of aging and organismal health. While the ability of DNAm to predict chronological age has been repeatedly demonstrated, the ability of other epigenetic features to predict age remains unclear. Here, we use two types of epigenetic information-DNAm, and chromatin accessibility as measured by ATAC-seq-to develop age predictors in peripheral blood mononuclear cells sampled from a population of domesticated dogs. We measured DNAm and ATAC-seq profiles for 71 dogs, building separate predictive clocks from each, as well as the combined dataset. We also use fluorescence-assisted cell sorting to quantify major lymphoid populations for each sample. We found that chromatin accessibility can accurately predict chronological age (R2 ATAC = 26%), though less accurately than the DNAm clock (R2 DNAm = 33%), and the clock built from the combined datasets was comparable to both (R2 combined = 29%). We also observed various populations of CD62L+ T cells significantly correlated with dog age. Finally, we found that all three clocks selected features that were in or near at least two protein-coding genes: BAIAP2 and SCARF2, both previously implicated in processes related to cognitive or neurological impairment. Taken together, these results highlight the potential of chromatin accessibility as a complementary epigenetic resource for modeling and investigating biologic age.
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Affiliation(s)
- Kelly Jin
- Department of Laboratory Medicine & PathologyUniversity of WashingtonSeattleWashingtonUSA
| | - Brianah M. McCoy
- Center for Evolution and MedicineArizona State UniversityTempeArizonaUSA
- School of Life SciencesArizona State UniversityTempeArizonaUSA
| | | | - Viktoria Usova
- Department of Laboratory Medicine & PathologyUniversity of WashingtonSeattleWashingtonUSA
| | - Victor Tkachev
- Division of Pediatric Hematology/OncologyBoston Children's HospitalBostonMassachusettsUSA
- Dana Farber Cancer InstituteBostonMassachusettsUSA
- Harvard Medical SchoolBostonMassachusettsUSA
| | - Alex D. Chitsazan
- Department of BiochemistryUniversity of WashingtonSeattleWashingtonUSA
| | - Anneke Kakebeen
- Department of BiochemistryUniversity of WashingtonSeattleWashingtonUSA
| | - Unity Jeffery
- College of Veterinary MedicineTexas A & M UniversityCollege StationTexasUSA
| | - Kate E. Creevy
- College of Veterinary MedicineTexas A & M UniversityCollege StationTexasUSA
| | - Andrea Wills
- Department of BiochemistryUniversity of WashingtonSeattleWashingtonUSA
| | - Noah Snyder‐Mackler
- Center for Evolution and MedicineArizona State UniversityTempeArizonaUSA
- School of Life SciencesArizona State UniversityTempeArizonaUSA
| | - Daniel E. L. Promislow
- Department of Laboratory Medicine & PathologyUniversity of WashingtonSeattleWashingtonUSA
- Department of BiologyUniversity of WashingtonSeattleWashingtonUSA
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9
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Morandini F, Rechsteiner C, Perez K, Praz V, Lopez Garcia G, Hinte LC, von Meyenn F, Ocampo A. ATAC-clock: An aging clock based on chromatin accessibility. GeroScience 2024; 46:1789-1806. [PMID: 37924441 PMCID: PMC10828344 DOI: 10.1007/s11357-023-00986-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 10/14/2023] [Indexed: 11/06/2023] Open
Abstract
The establishment of aging clocks highlighted the strong link between changes in DNA methylation and aging. Yet, it is not known if other epigenetic features could be used to predict age accurately. Furthermore, previous studies have observed a lack of effect of age-related changes in DNA methylation on gene expression, putting the interpretability of DNA methylation-based aging clocks into question. In this study, we explore the use of chromatin accessibility to construct aging clocks. We collected blood from 159 human donors and generated chromatin accessibility, transcriptomic, and cell composition data. We investigated how chromatin accessibility changes during aging and constructed a novel aging clock with a median absolute error of 5.27 years. The changes in chromatin accessibility used by the clock were strongly related to transcriptomic alterations, aiding clock interpretation. We additionally show that our chromatin accessibility clock performs significantly better than a transcriptomic clock trained on matched samples. In conclusion, we demonstrate that the clock relies on cell-intrinsic chromatin accessibility alterations rather than changes in cell composition. Further, we present a new approach to construct epigenetic aging clocks based on chromatin accessibility, which bear a direct link to age-related transcriptional alterations, but which allow for more accurate age predictions than transcriptomic clocks.
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Affiliation(s)
- Francesco Morandini
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Cheyenne Rechsteiner
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Kevin Perez
- EPITERNA SA, Route de la Corniche 5, Epalinges, Switzerland
| | - Viviane Praz
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Guillermo Lopez Garcia
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
- Departamento de Lenguajes y Ciencias de la Computación, Universidad de Málaga, Málaga, Spain
| | - Laura C Hinte
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | | | - Alejandro Ocampo
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland.
- EPITERNA SA, Route de la Corniche 5, Epalinges, Switzerland.
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10
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Durand A, Bonilla N, Level T, Ginestet Z, Lombès A, Guichard V, Germain M, Jacques S, Letourneur F, Do Cruzeiro M, Marchiol C, Renault G, Le Gall M, Charvet C, Le Bon A, Martin B, Auffray C, Lucas B. Type 1 interferons and Foxo1 down-regulation play a key role in age-related T-cell exhaustion in mice. Nat Commun 2024; 15:1718. [PMID: 38409097 PMCID: PMC10897180 DOI: 10.1038/s41467-024-45984-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/05/2024] [Indexed: 02/28/2024] Open
Abstract
Foxo family transcription factors are critically involved in multiple processes, such as metabolism, quiescence, cell survival and cell differentiation. Although continuous, high activity of Foxo transcription factors extends the life span of some species, the involvement of Foxo proteins in mammalian aging remains to be determined. Here, we show that Foxo1 is down-regulated with age in mouse T cells. This down-regulation of Foxo1 in T cells may contribute to the disruption of naive T-cell homeostasis with age, leading to an increase in the number of memory T cells. Foxo1 down-regulation is also associated with the up-regulation of co-inhibitory receptors by memory T cells and exhaustion in aged mice. Using adoptive transfer experiments, we show that the age-dependent down-regulation of Foxo1 in T cells is mediated by T-cell-extrinsic cues, including type 1 interferons. Taken together, our data suggest that type 1 interferon-induced Foxo1 down-regulation is likely to contribute significantly to T-cell dysfunction in aged mice.
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Affiliation(s)
- Aurélie Durand
- Université Paris-Cité, Institut Cochin, Centre National de la Recherche Scientifique (CNRS) UMR8104, Institut National de la Santé et de la Recherche Médicale (INSERM) U1016, 75014, Paris, France
| | - Nelly Bonilla
- Université Paris-Cité, Institut Cochin, Centre National de la Recherche Scientifique (CNRS) UMR8104, Institut National de la Santé et de la Recherche Médicale (INSERM) U1016, 75014, Paris, France
| | - Théo Level
- Université Paris-Cité, Institut Cochin, Centre National de la Recherche Scientifique (CNRS) UMR8104, Institut National de la Santé et de la Recherche Médicale (INSERM) U1016, 75014, Paris, France
| | - Zoé Ginestet
- Université Paris-Cité, Institut Cochin, Centre National de la Recherche Scientifique (CNRS) UMR8104, Institut National de la Santé et de la Recherche Médicale (INSERM) U1016, 75014, Paris, France
| | - Amélie Lombès
- Université Paris-Cité, Institut Cochin, Centre National de la Recherche Scientifique (CNRS) UMR8104, Institut National de la Santé et de la Recherche Médicale (INSERM) U1016, 75014, Paris, France
| | - Vincent Guichard
- Université Paris-Cité, Institut Cochin, Centre National de la Recherche Scientifique (CNRS) UMR8104, Institut National de la Santé et de la Recherche Médicale (INSERM) U1016, 75014, Paris, France
| | - Mathieu Germain
- Université Paris-Cité, Institut Cochin, Centre National de la Recherche Scientifique (CNRS) UMR8104, Institut National de la Santé et de la Recherche Médicale (INSERM) U1016, 75014, Paris, France
| | - Sébastien Jacques
- Université Paris-Cité, Institut Cochin, Centre National de la Recherche Scientifique (CNRS) UMR8104, Institut National de la Santé et de la Recherche Médicale (INSERM) U1016, 75014, Paris, France
| | - Franck Letourneur
- Université Paris-Cité, Institut Cochin, Centre National de la Recherche Scientifique (CNRS) UMR8104, Institut National de la Santé et de la Recherche Médicale (INSERM) U1016, 75014, Paris, France
| | - Marcio Do Cruzeiro
- Université Paris-Cité, Institut Cochin, Centre National de la Recherche Scientifique (CNRS) UMR8104, Institut National de la Santé et de la Recherche Médicale (INSERM) U1016, 75014, Paris, France
| | - Carmen Marchiol
- Université Paris-Cité, Institut Cochin, Centre National de la Recherche Scientifique (CNRS) UMR8104, Institut National de la Santé et de la Recherche Médicale (INSERM) U1016, 75014, Paris, France
| | - Gilles Renault
- Université Paris-Cité, Institut Cochin, Centre National de la Recherche Scientifique (CNRS) UMR8104, Institut National de la Santé et de la Recherche Médicale (INSERM) U1016, 75014, Paris, France
| | - Morgane Le Gall
- Université Paris-Cité, Institut Cochin, Centre National de la Recherche Scientifique (CNRS) UMR8104, Institut National de la Santé et de la Recherche Médicale (INSERM) U1016, 75014, Paris, France
| | - Céline Charvet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- CNRS UMR7104, Illkirch, France
- INSERM U1258, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Agnès Le Bon
- Université Paris-Cité, Institut Cochin, Centre National de la Recherche Scientifique (CNRS) UMR8104, Institut National de la Santé et de la Recherche Médicale (INSERM) U1016, 75014, Paris, France
| | - Bruno Martin
- Université Paris-Cité, Institut Cochin, Centre National de la Recherche Scientifique (CNRS) UMR8104, Institut National de la Santé et de la Recherche Médicale (INSERM) U1016, 75014, Paris, France
| | - Cédric Auffray
- Université Paris-Cité, Institut Cochin, Centre National de la Recherche Scientifique (CNRS) UMR8104, Institut National de la Santé et de la Recherche Médicale (INSERM) U1016, 75014, Paris, France
| | - Bruno Lucas
- Université Paris-Cité, Institut Cochin, Centre National de la Recherche Scientifique (CNRS) UMR8104, Institut National de la Santé et de la Recherche Médicale (INSERM) U1016, 75014, Paris, France.
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11
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Türk L, Filippov I, Arnold C, Zaugg J, Tserel L, Kisand K, Peterson P. Cytotoxic CD8 + Temra cells show loss of chromatin accessibility at genes associated with T cell activation. Front Immunol 2024; 15:1285798. [PMID: 38370415 PMCID: PMC10870784 DOI: 10.3389/fimmu.2024.1285798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 01/15/2024] [Indexed: 02/20/2024] Open
Abstract
As humans age, their memory T cell compartment expands due to the lifelong exposure to antigens. This expansion is characterized by terminally differentiated CD8+ T cells (Temra), which possess NK cell-like phenotype and are associated with chronic inflammatory conditions. Temra cells are predominantly driven by the sporadic reactivation of cytomegalovirus (CMV), yet their epigenomic patterns and cellular heterogeneity remain understudied. To address this gap, we correlated their gene expression profiles with chromatin openness and conducted single-cell transcriptome analysis, comparing them to other CD8+ subsets and CMV-responses. We confirmed that Temra cells exhibit high expression of genes associated with cytotoxicity and lower expression of costimulatory and chemokine genes. The data revealed that CMV-responsive CD8+ T cells (Tcmv) were predominantly derived from a mixed population of Temra and memory cells (Tcm/em) and shared their transcriptomic profiles. Using ATAC-seq analysis, we identified 1449 differentially accessible chromatin regions between CD8+ Temra and Tcm/em cells, of which only 127 sites gained chromatin accessibility in Temra cells. We further identified 51 gene loci, including costimulatory CD27, CD28, and ICOS genes, whose chromatin accessibility correlated with their gene expression. The differential chromatin regions Tcm/em cells were enriched in motifs that bind multiple transcriptional activators, such as Jun/Fos, NFkappaB, and STAT, whereas the open regions in Temra cells mainly contained binding sites of T-box transcription factors. Our single-cell analysis of CD8+CCR7loCD45RAhi sorted Temra population showed several subsets of Temra and NKT-like cells and CMC1+ Temra populations in older individuals that were shifted towards decreased cytotoxicity. Among CD8+CCR7loCD45RAhi sorted cells, we found a decreased proportion of IL7R+ Tcm/em-like and MAIT cells in individuals with high levels of CMV antibodies (CMVhi). These results shed new light on the molecular and cellular heterogeneity of CD8+ Temra cells and their relationship to aging and CMV infection.
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Affiliation(s)
- Lehte Türk
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Igor Filippov
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
- Qiagen Aarhus A/S, Aarhus, Denmark
| | - Christian Arnold
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Judith Zaugg
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Liina Tserel
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Kai Kisand
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Pärt Peterson
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
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12
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Paroli M, Caccavale R, Accapezzato D. Giant Cell Arteritis: Advances in Understanding Pathogenesis and Implications for Clinical Practice. Cells 2024; 13:267. [PMID: 38334659 PMCID: PMC10855045 DOI: 10.3390/cells13030267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 01/27/2024] [Accepted: 01/30/2024] [Indexed: 02/10/2024] Open
Abstract
Giant cell arteritis (GCA) is a noninfectious granulomatous vasculitis of unknown etiology affecting individuals older than 50 years. Two forms of GCA have been identified: a cranial form involving the medium-caliber temporal artery causing temporal arteritis (TA) and an extracranial form involving the large vessels, mainly the thoracic aorta and its branches. GCA generally affects individuals with a genetic predisposition, but several epigenetic (micro)environmental factors are often critical for the onset of this vasculitis. A key role in the pathogenesis of GCA is played by cells of both the innate and adaptive immune systems, which contribute to the formation of granulomas that may include giant cells, a hallmark of the disease, and arterial tertiary follicular organs. Cells of the vessel wall cells, including vascular smooth muscle cells (VSMCs) and endothelial cells, actively contribute to vascular remodeling responsible for vascular stenosis and ischemic complications. This review will discuss new insights into the molecular and cellular pathogenetic mechanisms of GCA, as well as the implications of these findings for the development of new diagnostic biomarkers and targeted drugs that could hopefully replace glucocorticoids (GCs), still the backbone of therapy for this vasculitis.
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Affiliation(s)
- Marino Paroli
- Department of Clinical, Internal, Anesthesiologic and Cardiovascular Sciences, Sapienza University of Rome, Polo Pontino, 04100 Latina, Italy; (R.C.); (D.A.)
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13
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O'Neill A, Mantri CK, Tan CW, Saron WAA, Nagaraj SK, Kala MP, Joy CM, Rathore APS, Tripathi S, Wang LF, St John AL. Mucosal SARS-CoV-2 vaccination of rodents elicits superior systemic T central memory function and cross-neutralising antibodies against variants of concern. EBioMedicine 2024; 99:104924. [PMID: 38113758 PMCID: PMC10772395 DOI: 10.1016/j.ebiom.2023.104924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 11/27/2023] [Accepted: 12/02/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND COVID-19 vaccines used in humans are highly effective in limiting disease and death caused by the SARS-CoV-2 virus, yet improved vaccines that provide greater protection at mucosal surfaces, which could reduce break-through infections and subsequent transmission, are still needed. METHODS Here we tested an intranasal (I.N.) vaccination with the receptor binding domain of Spike antigen of SARS-CoV-2 (S-RBD) in combination with the mucosal adjuvant mastoparan-7 compared with the sub-cutaneous (S.C.) route, adjuvanted by either M7 or the gold-standard adjuvant, alum, in mice, for immunological read-outs. The same formulation delivered I.N. or S.C. was tested in hamsters to assess efficacy. FINDINGS I.N. vaccination improved systemic T cell responses compared to an equivalent dose of antigen delivered S.C. and T cell phenotypes induced by I.N. vaccine administration included enhanced polyfunctionality (combined IFN-γ and TNF expression) and greater numbers of T central memory (TCM) cells. These phenotypes were T cell-intrinsic and could be recalled in the lungs and/or brachial LNs upon antigen challenge after adoptive T cell transfer to naïve recipients. Furthermore, mucosal vaccination induced antibody responses that were similarly effective in neutralising the binding of the parental strain of S-RBD to its ACE2 receptor, but showed greater cross-neutralising capacity against multiple variants of concern (VOC), compared to S.C. vaccination. I.N. vaccination provided significant protection from lung pathology compared to unvaccinated animals upon challenge with homologous and heterologous SARS-CoV-2 strains in a hamster model. INTERPRETATION These results highlight the role of nasal vaccine administration in imprinting an immune profile associated with long-term T cell retention and diversified neutralising antibody responses, which could be applied to improve vaccines for COVID-19 and other infectious diseases. FUNDING This study was funded by Duke-NUS Medical School, the Singapore Ministry of Education, the National Medical Research Council of Singapore and a DBT-BIRAC Grant.
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Affiliation(s)
- Aled O'Neill
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, 169857, Singapore
| | - Chinmay Kumar Mantri
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, 169857, Singapore
| | - Chee Wah Tan
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, 169857, Singapore; Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 117545, Singapore
| | - Wilfried A A Saron
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, 169857, Singapore
| | - Santhosh Kambaiah Nagaraj
- Centre for Infectious Disease Research, Microbiology and Cell Biology Department, Indian Institute of Science, Bengaluru, 560012, India
| | - Monica Palanichamy Kala
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, 169857, Singapore
| | - Christy Margarat Joy
- Centre for Infectious Disease Research, Microbiology and Cell Biology Department, Indian Institute of Science, Bengaluru, 560012, India
| | - Abhay P S Rathore
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, 169857, Singapore; Department of Pathology, Duke University Medical Centre, Durham, North Carolina, 27705, USA
| | - Shashank Tripathi
- Centre for Infectious Disease Research, Microbiology and Cell Biology Department, Indian Institute of Science, Bengaluru, 560012, India
| | - Lin-Fa Wang
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, 169857, Singapore; SingHealth Duke-NUS Global Health Institute, Singapore
| | - Ashley L St John
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, 169857, Singapore; Department of Pathology, Duke University Medical Centre, Durham, North Carolina, 27705, USA; SingHealth Duke-NUS Global Health Institute, Singapore; Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
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14
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Kasamatsu T. Implications of Senescent T Cells for Cancer Immunotherapy. Cancers (Basel) 2023; 15:5835. [PMID: 38136380 PMCID: PMC10742305 DOI: 10.3390/cancers15245835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
T-cell senescence is thought to result from the age-related loss of the ability to mount effective responses to pathogens and tumor cells. In addition to aging, T-cell senescence is caused by repeated antigenic stimulation and chronic inflammation. Moreover, we demonstrated that T-cell senescence was induced by treatment with DNA-damaging chemotherapeutic agents. The characteristics of therapy-induced senescent T (TIS-T) cells and general senescent T cells are largely similar. Senescent T cells demonstrate an increase in the senescence-associated beta-galactosidase-positive population, cell cycle arrest, secretion of senescence-associated secretory phenotypic factors, and metabolic reprogramming. Furthermore, senescent T cells downregulate the expression of the co-stimulatory molecules CD27 and CD28 and upregulate natural killer cell-related molecules. Moreover, TIS-T cells showed increased PD-1 expression. However, the loss of proliferative capacity and decreased expression of co-stimulatory molecules associated with T-cell senescence cause a decrease in T-cell immunocompetence. In this review, we discuss the characteristics of senescent T-cells, including therapy-induced senescent T cells.
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Affiliation(s)
- Tetsuhiro Kasamatsu
- Department of Laboratory Sciences, Gunma University Graduate School of Health Sciences, 3-39-22 Showa-machi, Maebashi 371-8514, Gunma, Japan
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15
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Tan J, Liang Y, Yang Z, He Q, Tong J, Deng Y, Guo W, Liang K, Tang J, Shi W, Yu B. Single-Cell Transcriptomics Reveals Crucial Cell Subsets and Functional Heterogeneity Associated With Carotid Atherosclerosis and Cerebrovascular Events. Arterioscler Thromb Vasc Biol 2023; 43:2312-2332. [PMID: 37881939 PMCID: PMC10659258 DOI: 10.1161/atvbaha.123.318974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 10/10/2023] [Indexed: 10/27/2023]
Abstract
BACKGROUND Carotid atherosclerosis is a chronic inflammatory disorder and is responsible for the vast majority of ischemic strokes. Inappropriate innate and adaptive immune responses synergize with malfunctional vascular wall cells to cause atherosclerotic lesions. Yet, functional characteristics of specific immune and endothelial cell subsets associated with atherosclerosis and cerebrovascular events are poorly understood. METHODS Here, using single-cell RNA sequencing, the unprecedentedly largest data set from 20 patients' carotid artery plaques and paired peripheral blood mononuclear cells was generated, with which an ultra-high-precision cellular landscape of the atherosclerotic microenvironment involving 372 070 cells was depicted. RESULTS Compared with peripheral blood mononuclear cells, 3 plaque-specific T-cell subsets exhibiting proatherogenic features of both activation and exhaustion were identified. Strikingly, usually antiatherogenic, CD4+FOXP3+ regulatory T cells from plaques of patients with symptomatic disease acquired proinflammatory properties by probably converting to T helper 17 and T helper 9 cells, while CD4+NR4A1+/C0 and CD8+SLC4A10+ T cells related to cerebrovascular events possessed atherogenic attributes including proinflammation, polarization, and exhaustion. In addition, monocyte-macrophage dynamics dominated innate immune response. Two plaque-specific monocyte subsets performed diametrically opposed functions, EREG+ monocytes promoted cerebrovascular events while C3+ monocytes are anti-inflammatory. Similarly, IGF1+ and HS3ST2+ macrophages with classical proinflammatory M1 macrophage features were annotated and contributed to cerebrovascular events. Moreover, SULF1+ (sulfatase-1) endothelial cells were also found to participate in cerebrovascular events through affecting plaque vulnerability. CONCLUSIONS This compendium of single-cell transcriptome data provides valuable insights into the cellular heterogeneity of the atherosclerotic microenvironment and the development of more precise cardiovascular immunotherapies.
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Affiliation(s)
- Jinyun Tan
- Vascular Surgery Division, General Surgery Department, Huashan Hospital Affiliated to Fudan University, Shanghai, China (J. Tan, Q.H., W.G., K.L., W.S., B.Y.)
- Shanghai Key Laboratory of Vascular Lesions Regulation and Remodeling, China (J. Tan, Y.L., Z.Y., J. Tong, J. Tang, W.S., B.Y.)
- Fudan Zhangjiang Institute, Fudan University, Shanghai, China (J. Tan, Y.L., Y.D.)
| | - Yongjun Liang
- Department of Vascular Surgery, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, China (Y.L., J. Tong, Y.D., J. Tang, B.Y.)
- Shanghai Key Laboratory of Vascular Lesions Regulation and Remodeling, China (J. Tan, Y.L., Z.Y., J. Tong, J. Tang, W.S., B.Y.)
- Fudan Zhangjiang Institute, Fudan University, Shanghai, China (J. Tan, Y.L., Y.D.)
| | - Zhou Yang
- Shanghai Key Laboratory of Vascular Lesions Regulation and Remodeling, China (J. Tan, Y.L., Z.Y., J. Tong, J. Tang, W.S., B.Y.)
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, China (Z.Y.)
| | - Qing He
- Vascular Surgery Division, General Surgery Department, Huashan Hospital Affiliated to Fudan University, Shanghai, China (J. Tan, Q.H., W.G., K.L., W.S., B.Y.)
| | - Jindong Tong
- Department of Vascular Surgery, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, China (Y.L., J. Tong, Y.D., J. Tang, B.Y.)
- Shanghai Key Laboratory of Vascular Lesions Regulation and Remodeling, China (J. Tan, Y.L., Z.Y., J. Tong, J. Tang, W.S., B.Y.)
| | - Ying Deng
- Department of Vascular Surgery, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, China (Y.L., J. Tong, Y.D., J. Tang, B.Y.)
- Fudan Zhangjiang Institute, Fudan University, Shanghai, China (J. Tan, Y.L., Y.D.)
| | - Wencheng Guo
- Vascular Surgery Division, General Surgery Department, Huashan Hospital Affiliated to Fudan University, Shanghai, China (J. Tan, Q.H., W.G., K.L., W.S., B.Y.)
| | - Kun Liang
- Vascular Surgery Division, General Surgery Department, Huashan Hospital Affiliated to Fudan University, Shanghai, China (J. Tan, Q.H., W.G., K.L., W.S., B.Y.)
| | - Jingdong Tang
- Department of Vascular Surgery, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, China (Y.L., J. Tong, Y.D., J. Tang, B.Y.)
- Shanghai Key Laboratory of Vascular Lesions Regulation and Remodeling, China (J. Tan, Y.L., Z.Y., J. Tong, J. Tang, W.S., B.Y.)
| | - Weihao Shi
- Vascular Surgery Division, General Surgery Department, Huashan Hospital Affiliated to Fudan University, Shanghai, China (J. Tan, Q.H., W.G., K.L., W.S., B.Y.)
- Shanghai Key Laboratory of Vascular Lesions Regulation and Remodeling, China (J. Tan, Y.L., Z.Y., J. Tong, J. Tang, W.S., B.Y.)
| | - Bo Yu
- Vascular Surgery Division, General Surgery Department, Huashan Hospital Affiliated to Fudan University, Shanghai, China (J. Tan, Q.H., W.G., K.L., W.S., B.Y.)
- Department of Vascular Surgery, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, China (Y.L., J. Tong, Y.D., J. Tang, B.Y.)
- Shanghai Key Laboratory of Vascular Lesions Regulation and Remodeling, China (J. Tan, Y.L., Z.Y., J. Tong, J. Tang, W.S., B.Y.)
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16
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Nehar-Belaid D, Sokolowski M, Ravichandran S, Banchereau J, Chaussabel D, Ucar D. Baseline immune states (BIS) associated with vaccine responsiveness and factors that shape the BIS. Semin Immunol 2023; 70:101842. [PMID: 37717525 DOI: 10.1016/j.smim.2023.101842] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/11/2023] [Indexed: 09/19/2023]
Abstract
Vaccines are among the greatest inventions in medicine, leading to the elimination or control of numerous diseases, including smallpox, polio, measles, rubella, and, most recently, COVID-19. Yet, the effectiveness of vaccines varies among individuals. In fact, while some recipients mount a robust response to vaccination that protects them from the disease, others fail to respond. Multiple clinical and epidemiological factors contribute to this heterogeneity in responsiveness. Systems immunology studies fueled by advances in single-cell biology have been instrumental in uncovering pre-vaccination immune cell types and genomic features (i.e., the baseline immune state, BIS) that have been associated with vaccine responsiveness. Here, we review clinical factors that shape the BIS, and the characteristics of the BIS associated with responsiveness to frequently studied vaccines (i.e., influenza, COVID-19, bacterial pneumonia, malaria). Finally, we discuss potential strategies to enhance vaccine responsiveness in high-risk groups, focusing specifically on older adults.
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Affiliation(s)
| | - Mark Sokolowski
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | | | | | - Damien Chaussabel
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA
| | - Duygu Ucar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA; Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT, USA.
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17
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Thomson Z, He Z, Swanson E, Henderson K, Phalen C, Zaim SR, Pebworth MP, Okada LY, Heubeck AT, Roll CR, Hernandez V, Weiss M, Genge PC, Reading J, Giles JR, Manne S, Dougherty J, Jasen CJ, Greenplate AR, Becker LA, Graybuck LT, Vasaikar SV, Szeto GL, Savage AK, Speake C, Buckner JH, Li XJ, Bumol TF, Wherry EJ, Torgerson TR, Vella LA, Henrickson SE, Skene PJ, Gustafson CE. Trimodal single-cell profiling reveals a novel pediatric CD8αα + T cell subset and broad age-related molecular reprogramming across the T cell compartment. Nat Immunol 2023; 24:1947-1959. [PMID: 37845489 PMCID: PMC10602854 DOI: 10.1038/s41590-023-01641-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 09/07/2023] [Indexed: 10/18/2023]
Abstract
Age-associated changes in the T cell compartment are well described. However, limitations of current single-modal or bimodal single-cell assays, including flow cytometry, RNA-seq (RNA sequencing) and CITE-seq (cellular indexing of transcriptomes and epitopes by sequencing), have restricted our ability to deconvolve more complex cellular and molecular changes. Here, we profile >300,000 single T cells from healthy children (aged 11-13 years) and older adults (aged 55-65 years) by using the trimodal assay TEA-seq (single-cell analysis of mRNA transcripts, surface protein epitopes and chromatin accessibility), which revealed that molecular programming of T cell subsets shifts toward a more activated basal state with age. Naive CD4+ T cells, considered relatively resistant to aging, exhibited pronounced transcriptional and epigenetic reprogramming. Moreover, we discovered a novel CD8αα+ T cell subset lost with age that is epigenetically poised for rapid effector responses and has distinct inhibitory, costimulatory and tissue-homing properties. Together, these data reveal new insights into age-associated changes in the T cell compartment that may contribute to differential immune responses.
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Affiliation(s)
| | - Ziyuan He
- Allen Institute for Immunology, Seattle, WA, USA
| | - Elliott Swanson
- Allen Institute for Immunology, Seattle, WA, USA
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Cole Phalen
- Allen Institute for Immunology, Seattle, WA, USA
| | | | | | | | | | - Charles R Roll
- Allen Institute for Immunology, Seattle, WA, USA
- Microbiology, Immunology and Cancer Biology (MICaB) Program, University of Minnesota, Minneapolis, Minneapolis, MN, USA
| | | | - Morgan Weiss
- Allen Institute for Immunology, Seattle, WA, USA
| | | | | | - Josephine R Giles
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Sasikanth Manne
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Jeanette Dougherty
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - C J Jasen
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Allison R Greenplate
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
- Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | | | - Suhas V Vasaikar
- Allen Institute for Immunology, Seattle, WA, USA
- Seagen, Bothell, WA, USA
| | - Gregory L Szeto
- Allen Institute for Immunology, Seattle, WA, USA
- Seagen, Bothell, WA, USA
| | | | - Cate Speake
- Center for Interventional Immunology, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - Jane H Buckner
- Center for Translational Immunology, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - Xiao-Jun Li
- Allen Institute for Immunology, Seattle, WA, USA
| | | | - E John Wherry
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | - Laura A Vella
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Pediatrics, Children's Hospital of Philadelphia and the University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sarah E Henrickson
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Pediatrics, Children's Hospital of Philadelphia and the University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
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18
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Quinn KM, Vicencio DM, La Gruta NL. The paradox of aging: Aging-related shifts in T cell function and metabolism. Semin Immunol 2023; 70:101834. [PMID: 37659169 DOI: 10.1016/j.smim.2023.101834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 08/17/2023] [Accepted: 08/17/2023] [Indexed: 09/04/2023]
Abstract
T cell survival, differentiation after stimulation, and function are intrinsically linked to distinct cellular metabolic states. The ability of T cells to readily transition between metabolic states enables flexibility to meet the changing energy demands defined by distinct effector states or T cell lineages. Immune aging is characterized, in part, by the loss of naïve T cells, accumulation of senescent T cells, severe dysfunction in memory phenotype T cells in particular, and elevated levels of inflammatory cytokines, or 'inflammaging'. Here, we review our current understanding of the phenotypic and functional changes that occur with aging in T cells, and how they relate to metabolic changes in the steady state and after T cell activation. We discuss the apparent contradictions in the aging T cell phenotype - where enhanced differentiation states and metabolic profiles in the steady state can correspond to a diminished capacity to adapt metabolically and functionally after T cell activation. Finally, we discuss key recent studies that indicate the enormous potential for aged T cell metabolism to induce systemic inflammaging and organism-wide multimorbidity, resulting in premature death.
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Affiliation(s)
- Kylie M Quinn
- School of Health and Biomedical Sciences, Royal Melbourne Institute of Technology University, Bundoora, Victoria, Australia; Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Daniela M Vicencio
- Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia; Division of Biomedical Sciences, Warwick Medical School, The University of Warwick, Coventry, UK
| | - Nicole L La Gruta
- Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
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19
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Angarola BL, Sharma S, Katiyar N, Gu Kang H, Nehar-Belaid D, Park S, Gott R, Eryilmaz GN, LaBarge MA, Palucka K, Chuang JH, Korstanje R, Ucar D, Anczukow O. Comprehensive single cell aging atlas of mammary tissues reveals shared epigenomic and transcriptomic signatures of aging and cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.20.563147. [PMID: 37961129 PMCID: PMC10634680 DOI: 10.1101/2023.10.20.563147] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Aging is the greatest risk factor for breast cancer; however, how age-related cellular and molecular events impact cancer initiation is unknown. We investigate how aging rewires transcriptomic and epigenomic programs of mouse mammary glands at single cell resolution, yielding a comprehensive resource for aging and cancer biology. Aged epithelial cells exhibit epigenetic and transcriptional changes in metabolic, pro-inflammatory, or cancer-associated genes. Aged stromal cells downregulate fibroblast marker genes and upregulate markers of senescence and cancer-associated fibroblasts. Among immune cells, distinct T cell subsets (Gzmk+, memory CD4+, γδ) and M2-like macrophages expand with age. Spatial transcriptomics reveal co-localization of aged immune and epithelial cells in situ. Lastly, transcriptional signatures of aging mammary cells are found in human breast tumors, suggesting mechanistic links between aging and cancer. Together, these data uncover that epithelial, immune, and stromal cells shift in proportions and cell identity, potentially impacting cell plasticity, aged microenvironment, and neoplasia risk.
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Affiliation(s)
| | | | - Neerja Katiyar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Hyeon Gu Kang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - SungHee Park
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Giray N Eryilmaz
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Mark A LaBarge
- Beckman Research Institute at City of Hope, Duarte, CA, USA
| | - Karolina Palucka
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Jeffrey H Chuang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Duygu Ucar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA
- Institute for Systems Genomics, UConn Health, Farmington, CT, USA
| | - Olga Anczukow
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA
- Institute for Systems Genomics, UConn Health, Farmington, CT, USA
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20
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Sturmlechner I, Jain A, Mu Y, Weyand CM, Goronzy JJ. T cell fate decisions during memory cell generation with aging. Semin Immunol 2023; 69:101800. [PMID: 37494738 PMCID: PMC10528238 DOI: 10.1016/j.smim.2023.101800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
The defense against infectious diseases, either through natural immunity or after vaccinations, relies on the generation and maintenance of protective T cell memory. Naïve T cells are at the center of memory T cell generation during primary responses. Upon activation, they undergo a complex, highly regulated differentiation process towards different functional states. Naïve T cells maintained into older age have undergone epigenetic adaptations that influence their fate decisions during differentiation. We review age-sensitive, molecular pathways and gene regulatory networks that bias naïve T cell differentiation towards effector cell generation at the expense of memory and Tfh cells. As a result, T cell differentiation in older adults is associated with release of bioactive waste products into the microenvironment, higher stress sensitivity as well as skewing towards pro-inflammatory signatures and shorter life spans. These maladaptations not only contribute to poor vaccine responses in older adults but also fuel a more inflammatory state.
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Affiliation(s)
- Ines Sturmlechner
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Abhinav Jain
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Yunmei Mu
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Cornelia M Weyand
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA; Department of Medicine, Division of Rheumatology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Jörg J Goronzy
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA; Department of Medicine, Division of Rheumatology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA; Robert and Arlene Kogod Center on Aging, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA.
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21
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Hu C, Wu H, Zhu Q, Cao N, Wang H. Cholesterol metabolism in T-cell aging: Accomplices or victims. FASEB J 2023; 37:e23136. [PMID: 37584624 DOI: 10.1096/fj.202300515r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 07/12/2023] [Accepted: 07/31/2023] [Indexed: 08/17/2023]
Abstract
Aging has a significant impact on the function and metabolism of T cells. Cholesterol, the most important sterol in mammals, is known as the "gold of the body" because it maintains membrane fluidity, rigidity, and signal transduction while also serving as a precursor of oxysterols, bile acids, and steroid hormones. Cholesterol homeostasis is primarily controlled by uptake, biosynthesis, efflux, and regulatory mechanisms. Previous studies have suggested that there are reciprocal interactions between cholesterol metabolism and T lymphocytes. Here, we will summarize the most recent advances in the effects of cholesterol and its derivatives on T-cell aging. We will furthermore discuss interventions that might be used to help older individuals with immune deficiencies or diminishing immune competence.
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Affiliation(s)
- Cexun Hu
- Department of Clinical Genetics, Yueyang Maternal and Child Health-Care Hospital, Yueyang, P.R. China
- Department of Immunology, Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, P.R. China
| | - Hongliang Wu
- Department of Clinical Genetics, Yueyang Maternal and Child Health-Care Hospital, Yueyang, P.R. China
| | - Qun Zhu
- Department of Clinical Genetics, Yueyang Maternal and Child Health-Care Hospital, Yueyang, P.R. China
| | - Na Cao
- Department of Hematology, Yueyang People's Hospital, Yueyang, P. R. China
- Yueyang Hospital Affiliated to Hunan Normal University, Yueyang, P.R. China
| | - Hui Wang
- Department of Immunology, Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu University, Zhenjiang, P.R. China
- Department of Immunology, School of Medicine, Jiangsu University, Zhenjiang, P.R. China
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22
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Escrig-Larena JI, Delgado-Pulido S, Mittelbrunn M. Mitochondria during T cell aging. Semin Immunol 2023; 69:101808. [PMID: 37473558 DOI: 10.1016/j.smim.2023.101808] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/30/2023] [Accepted: 07/10/2023] [Indexed: 07/22/2023]
Abstract
Mitochondrial dysfunction is a hallmark of aging that contributes to inflammaging. It is characterized by alterations of the mitochondrial DNA, reduced respiratory capacity, decreased mitochondrial membrane potential and increased reactive oxygen species production. These primary alterations disrupt other interconnected and important mitochondrial-related processes such as metabolism, mitochondrial dynamics and biogenesis, mitophagy, calcium homeostasis or apoptosis. In this review, we gather the current knowledge about the different mitochondrial processes which are altered during aging, with special focus on their contribution to age-associated T cell dysfunction and inflammaging.
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Affiliation(s)
- Jose Ignacio Escrig-Larena
- Consejo Superior de Investigaciones Científicas (CSIC), Centro de Biología Molcular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Sandra Delgado-Pulido
- Departamento de Biología Molecular, Facultad de Ciencias (UAM), Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - María Mittelbrunn
- Consejo Superior de Investigaciones Científicas (CSIC), Centro de Biología Molcular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid (UAM), Madrid, Spain.
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23
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Jain A, Sturmlechner I, Weyand CM, Goronzy JJ. Heterogeneity of memory T cells in aging. Front Immunol 2023; 14:1250916. [PMID: 37662959 PMCID: PMC10471982 DOI: 10.3389/fimmu.2023.1250916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/07/2023] [Indexed: 09/05/2023] Open
Abstract
Immune memory is a requisite and remarkable property of the immune system and is the biological foundation of the success of vaccinations in reducing morbidity from infectious diseases. Some vaccines and infections induce long-lasting protection, but immunity to other vaccines and particularly in older adults rarely persists over long time periods. Failed induction of an immune response and accelerated waning of immune memory both contribute to the immuno-compromised state of the older population. Here we review how T cell memory is influenced by age. T cell memory is maintained by a dynamic population of T cells that are heterogeneous in their kinetic parameters under homeostatic condition and their function. Durability of T cell memory can be influenced not only by the loss of a clonal progeny, but also by broader changes in the composition of functional states and transition of T cells to a dysfunctional state. Genome-wide single cell studies on total T cells have started to provide insights on the influence of age on cell heterogeneity over time. The most striking findings were a trend to progressive effector differentiation and the activation of pro-inflammatory pathways, including the emergence of CD4+ and CD8+ cytotoxic subsets. Genome-wide data on antigen-specific memory T cells are currently limited but can be expected to provide insights on how changes in T cell subset heterogeneity and transcriptome relate to durability of immune protection.
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Affiliation(s)
- Abhinav Jain
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN, United States
| | - Ines Sturmlechner
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN, United States
| | - Cornelia M. Weyand
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN, United States
- Department of Medicine, Division of Rheumatology, Mayo Clinic College of Medicine and Science, Rochester, MN, United States
| | - Jörg J. Goronzy
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN, United States
- Department of Medicine, Division of Rheumatology, Mayo Clinic College of Medicine and Science, Rochester, MN, United States
- Robert and Arlene Kogod Center on Aging, Mayo Clinic College of Medicine and Science, Rochester, MN, United States
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24
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Luo Q, Dwaraka VB, Chen Q, Tong H, Zhu T, Seale K, Raffaele JM, Zheng SC, Mendez TL, Chen Y, Carreras N, Begum S, Mendez K, Voisin S, Eynon N, Lasky-Su JA, Smith R, Teschendorff AE. A meta-analysis of immune-cell fractions at high resolution reveals novel associations with common phenotypes and health outcomes. Genome Med 2023; 15:59. [PMID: 37525279 PMCID: PMC10388560 DOI: 10.1186/s13073-023-01211-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 07/10/2023] [Indexed: 08/02/2023] Open
Abstract
BACKGROUND Changes in cell-type composition of tissues are associated with a wide range of diseases and environmental risk factors and may be causally implicated in disease development and progression. However, these shifts in cell-type fractions are often of a low magnitude, or involve similar cell subtypes, making their reliable identification challenging. DNA methylation profiling in a tissue like blood is a promising approach to discover shifts in cell-type abundance, yet studies have only been performed at a relatively low cellular resolution and in isolation, limiting their power to detect shifts in tissue composition. METHODS Here we derive a DNA methylation reference matrix for 12 immune-cell types in human blood and extensively validate it with flow-cytometric count data and in whole-genome bisulfite sequencing data of sorted cells. Using this reference matrix, we perform a directional Stouffer and fixed effects meta-analysis comprising 23,053 blood samples from 22 different cohorts, to comprehensively map associations between the 12 immune-cell fractions and common phenotypes. In a separate cohort of 4386 blood samples, we assess associations between immune-cell fractions and health outcomes. RESULTS Our meta-analysis reveals many associations of cell-type fractions with age, sex, smoking and obesity, many of which we validate with single-cell RNA sequencing. We discover that naïve and regulatory T-cell subsets are higher in women compared to men, while the reverse is true for monocyte, natural killer, basophil, and eosinophil fractions. Decreased natural killer counts associated with smoking, obesity, and stress levels, while an increased count correlates with exercise and sleep. Analysis of health outcomes revealed that increased naïve CD4 + T-cell and N-cell fractions associated with a reduced risk of all-cause mortality independently of all major epidemiological risk factors and baseline co-morbidity. A machine learning predictor built only with immune-cell fractions achieved a C-index value for all-cause mortality of 0.69 (95%CI 0.67-0.72), which increased to 0.83 (0.80-0.86) upon inclusion of epidemiological risk factors and baseline co-morbidity. CONCLUSIONS This work contributes an extensively validated high-resolution DNAm reference matrix for blood, which is made freely available, and uses it to generate a comprehensive map of associations between immune-cell fractions and common phenotypes, including health outcomes.
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Affiliation(s)
- Qi Luo
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Varun B Dwaraka
- TruDiagnostics, 881 Corporate Dr., Lexington, KY, 40503, USA
| | - Qingwen Chen
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Huige Tong
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Tianyu Zhu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Kirsten Seale
- Institute for Health and Sport (iHeS), Victoria University, Footscray, VIC, 3011, Australia
| | - Joseph M Raffaele
- PhysioAge LLC, 30 Central Park South / Suite 8A, New York, NY, 10019, USA
| | - Shijie C Zheng
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA
| | - Tavis L Mendez
- TruDiagnostics, 881 Corporate Dr., Lexington, KY, 40503, USA
| | - Yulu Chen
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | | | - Sofina Begum
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Kevin Mendez
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Sarah Voisin
- Institute for Health and Sport (iHeS), Victoria University, Footscray, VIC, 3011, Australia
| | - Nir Eynon
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Jessica A Lasky-Su
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
| | - Ryan Smith
- TruDiagnostics, 881 Corporate Dr., Lexington, KY, 40503, USA.
| | - Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China.
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25
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Buggert M, Price DA, Mackay LK, Betts MR. Human circulating and tissue-resident memory CD8 + T cells. Nat Immunol 2023:10.1038/s41590-023-01538-6. [PMID: 37349380 DOI: 10.1038/s41590-023-01538-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/04/2023] [Indexed: 06/24/2023]
Abstract
Our current knowledge of human memory CD8+ T cells is derived largely from studies of the intravascular space. However, emerging data are starting to challenge some of the dogmas based on this work, suggesting that a conceptual revision may be necessary. In this review, we provide a brief history of the field and summarize the biology of circulating and tissue-resident memory CD8+ T cells, which are ultimately responsible for effective immune surveillance. We also incorporate recent findings into a biologically integrated model of human memory CD8+ T cell differentiation. Finally, we address how future innovative human studies could improve our understanding of anatomically localized CD8+ T cells to inform the development of more effective immunotherapies and vaccines, the need for which has been emphasized by the global struggle to contain severe acute respiratory syndrome coronavirus 2.
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Affiliation(s)
- Marcus Buggert
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden.
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
- Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, UK
| | - Laura K Mackay
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Michael R Betts
- Institute for Immunology and Center for AIDS Research, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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26
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Liu Z, Liang Q, Ren Y, Guo C, Ge X, Wang L, Cheng Q, Luo P, Zhang Y, Han X. Immunosenescence: molecular mechanisms and diseases. Signal Transduct Target Ther 2023; 8:200. [PMID: 37179335 PMCID: PMC10182360 DOI: 10.1038/s41392-023-01451-2] [Citation(s) in RCA: 85] [Impact Index Per Article: 85.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 03/24/2023] [Accepted: 04/23/2023] [Indexed: 05/15/2023] Open
Abstract
Infection susceptibility, poor vaccination efficacy, age-related disease onset, and neoplasms are linked to innate and adaptive immune dysfunction that accompanies aging (known as immunosenescence). During aging, organisms tend to develop a characteristic inflammatory state that expresses high levels of pro-inflammatory markers, termed inflammaging. This chronic inflammation is a typical phenomenon linked to immunosenescence and it is considered the major risk factor for age-related diseases. Thymic involution, naïve/memory cell ratio imbalance, dysregulated metabolism, and epigenetic alterations are striking features of immunosenescence. Disturbed T-cell pools and chronic antigen stimulation mediate premature senescence of immune cells, and senescent immune cells develop a proinflammatory senescence-associated secretory phenotype that exacerbates inflammaging. Although the underlying molecular mechanisms remain to be addressed, it is well documented that senescent T cells and inflammaging might be major driving forces in immunosenescence. Potential counteractive measures will be discussed, including intervention of cellular senescence and metabolic-epigenetic axes to mitigate immunosenescence. In recent years, immunosenescence has attracted increasing attention for its role in tumor development. As a result of the limited participation of elderly patients, the impact of immunosenescence on cancer immunotherapy is unclear. Despite some surprising results from clinical trials and drugs, it is necessary to investigate the role of immunosenescence in cancer and other age-related diseases.
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Affiliation(s)
- Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
- Interventional Institute of Zhengzhou University, 450052, Zhengzhou, Henan, China
- Interventional Treatment and Clinical Research Center of Henan Province, 450052, Zhengzhou, Henan, China
| | - Qimeng Liang
- Nephrology Hospital, the First Affiliated Hospital of Zhengzhou University, Zhengzhou University, 4500052, Henan, China
| | - Yuqing Ren
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Chunguang Guo
- Department of Endovascular Surgery, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Xiaoyong Ge
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Libo Wang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yi Zhang
- Biotherapy Center and Cancer Center, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China.
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China.
- Interventional Institute of Zhengzhou University, 450052, Zhengzhou, Henan, China.
- Interventional Treatment and Clinical Research Center of Henan Province, 450052, Zhengzhou, Henan, China.
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27
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Richard D, Capellini TD, Diekman BO. Epigenetics as a mediator of genetic risk in osteoarthritis: role during development, homeostasis, aging, and disease progression. Am J Physiol Cell Physiol 2023; 324:C1078-C1088. [PMID: 36971423 PMCID: PMC10191130 DOI: 10.1152/ajpcell.00574.2022] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/16/2023] [Accepted: 03/16/2023] [Indexed: 03/29/2023]
Abstract
The identification of genomic loci that are associated with osteoarthritis (OA) has provided a starting point for understanding how genetic variation activates catabolic processes in the joint. However, genetic variants can only alter gene expression and cellular function when the epigenetic environment is permissive to these effects. In this review, we provide examples of how epigenetic shifts at distinct life stages can alter the risk for OA, which we posit is critical for the proper interpretation of genome-wide association studies (GWAS). During development, intensive work on the growth and differentiation factor 5 (GDF5) locus has revealed the importance of tissue-specific enhancer activity in controlling both joint development and the subsequent risk for OA. During homeostasis in adults, underlying genetic risk factors may help establish beneficial or catabolic "set points" that dictate tissue function, with a strong cumulative effect on OA risk. During aging, methylation changes and the reorganization of chromatin can "unmask" the effects of genetic variants. The destructive function of variants that alter aging would only mediate effects after reproductive competence and thus avoid any evolutionary selection pressure, as consistent with larger frameworks of biological aging and its relationship to disease. A similar "unmasking" may occur during OA progression, which is supported by the finding of distinct expression quantitative trait loci (eQTLs) in chondrocytes depending on the degree of tissue degradation. Finally, we propose that massively parallel reporter assays (MPRAs) will be a valuable tool to test the function of putative OA GWAS variants in chondrocytes from different life stages.
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Affiliation(s)
- Daniel Richard
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States
| | - Terence D Capellini
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States
| | - Brian O Diekman
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, and North Carolina State University, Raleigh, North Carolina, United States
- Thurston Arthritis Research Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States
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28
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Soto-Heredero G, Gómez de Las Heras MM, Escrig-Larena JI, Mittelbrunn M. Extremely Differentiated T Cell Subsets Contribute to Tissue Deterioration During Aging. Annu Rev Immunol 2023; 41:181-205. [PMID: 37126417 DOI: 10.1146/annurev-immunol-101721-064501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
There is a dramatic remodeling of the T cell compartment during aging. The most notorious changes are the reduction of the naive T cell pool and the accumulation of memory-like T cells. Memory-like T cells in older people acquire a phenotype of terminally differentiated cells, lose the expression of costimulatory molecules, and acquire properties of senescent cells. In this review, we focus on the different subsets of age-associated T cells that accumulate during aging. These subsets include extremely cytotoxic T cells with natural killer properties, exhausted T cells with altered cytokine production, and regulatory T cells that gain proinflammatory features. Importantly, all of these subsets lose their lymph node homing capacity and migrate preferentially to nonlymphoid tissues, where they contribute to tissue deterioration and inflammaging.
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Affiliation(s)
- Gonzalo Soto-Heredero
- Homeostasis de Tejidos y Órganos, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC) and Universidad Autónoma de Madrid, Madrid, Spain
- Departamento de Biología Molecular, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain;
- Instituto de Investigación Sanitaria del Hospital 12 de Octubre, Madrid, Spain
| | - Manuel M Gómez de Las Heras
- Homeostasis de Tejidos y Órganos, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC) and Universidad Autónoma de Madrid, Madrid, Spain
- Departamento de Biología Molecular, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain;
- Instituto de Investigación Sanitaria del Hospital 12 de Octubre, Madrid, Spain
| | - J Ignacio Escrig-Larena
- Homeostasis de Tejidos y Órganos, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC) and Universidad Autónoma de Madrid, Madrid, Spain
- Departamento de Biología Molecular, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain;
| | - María Mittelbrunn
- Homeostasis de Tejidos y Órganos, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC) and Universidad Autónoma de Madrid, Madrid, Spain
- Instituto de Investigación Sanitaria del Hospital 12 de Octubre, Madrid, Spain
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29
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Guo L, Li X, Gould T, Wang ZY, Cao W. T cell aging and Alzheimer's disease. Front Immunol 2023; 14:1154699. [PMID: 37081887 PMCID: PMC10110977 DOI: 10.3389/fimmu.2023.1154699] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/15/2023] [Indexed: 04/07/2023] Open
Abstract
The brain has long been considered an immune-privileged organ due to the presence of the blood-brain barrier (BBB). However, recent discoveries have revealed the underestimated role of T cells in the brain through the meningeal lymphatic system. Age is the primary risk factor for Alzheimer's disease (AD), resulting in marked age-dependent changes in T cells. Manipulating peripheral T cell immune response has been shown to impact AD, but the relationship between T cell aging and AD remains poorly understood. Given the limited success of targeting amyloid beta (Aβ) and the growing evidence of T cells' involvement in non-lymphoid organ aging, a deeper understanding of the relationship between T cells and AD in the context of aging is crucial for advancing therapeutic progress. In this review, we comprehensively examine existing studies on T cells and AD and offer an integrated perspective on their interconnections in the context of aging. This understanding can inform the development of new interventions to prevent or treat AD.
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Affiliation(s)
- Lin Guo
- Key Laboratory of Major Chronic Diseases of Nervous System of Liaoning Province, Health Sciences Institute of China Medical University, Shenyang, China
| | - Xiaoting Li
- Key Laboratory of Major Chronic Diseases of Nervous System of Liaoning Province, Health Sciences Institute of China Medical University, Shenyang, China
- Department of Rehabilitation, Shengjing Hospital of China Medical University, Shenyang, China
| | | | - Zhan-You Wang
- Key Laboratory of Major Chronic Diseases of Nervous System of Liaoning Province, Health Sciences Institute of China Medical University, Shenyang, China
| | - Wenqiang Cao
- Key Laboratory of Major Chronic Diseases of Nervous System of Liaoning Province, Health Sciences Institute of China Medical University, Shenyang, China
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30
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Rose JR, Akdogan-Ozdilek B, Rahmberg AR, Powell MD, Hicks SL, Scharer CD, Boss JM. Distinct transcriptomic and epigenomic modalities underpin human memory T cell subsets and their activation potential. Commun Biol 2023; 6:363. [PMID: 37012418 PMCID: PMC10070634 DOI: 10.1038/s42003-023-04747-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 03/22/2023] [Indexed: 04/05/2023] Open
Abstract
Human memory T cells (MTC) are poised to rapidly respond to antigen re-exposure. Here, we derived the transcriptional and epigenetic programs of resting and ex vivo activated, circulating CD4+ and CD8+ MTC subsets. A progressive gradient of gene expression from naïve to TCM to TEM is observed, which is accompanied by corresponding changes in chromatin accessibility. Transcriptional changes suggest adaptations of metabolism that are reflected in altered metabolic capacity. Other differences involve regulatory modalities comprised of discrete accessible chromatin patterns, transcription factor binding motif enrichment, and evidence of epigenetic priming. Basic-helix-loop-helix factor motifs for AHR and HIF1A distinguish subsets and predict transcription networks to sense environmental changes. Following stimulation, primed accessible chromatin correlate with an augmentation of MTC gene expression as well as effector transcription factor gene expression. These results identify coordinated epigenetic remodeling, metabolic, and transcriptional changes that enable MTC subsets to ultimately respond to antigen re-encounters more efficiently.
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Affiliation(s)
- James R Rose
- Department of Microbiology and Immunology, and the Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Bagdeser Akdogan-Ozdilek
- Department of Microbiology and Immunology, and the Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Andrew R Rahmberg
- Barrier Immunity Section, Laboratory of Viral Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Michael D Powell
- Department of Microbiology and Immunology, and the Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Sakeenah L Hicks
- Department of Microbiology and Immunology, and the Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Christopher D Scharer
- Department of Microbiology and Immunology, and the Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Jeremy M Boss
- Department of Microbiology and Immunology, and the Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, 30322, USA.
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31
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Ford BR, Poholek AC. Regulation and Immunotherapeutic Targeting of the Epigenome in Exhausted CD8 T Cell Responses. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:869-879. [PMID: 36947818 PMCID: PMC10037537 DOI: 10.4049/jimmunol.2200681] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 01/04/2023] [Indexed: 03/24/2023]
Abstract
Exhaustion is a state of CD8 T cell differentiation that occurs in settings of chronic Ag such as tumors, chronic viral infection, and autoimmunity. Cellular differentiation is driven by a series of environmental signals that promote epigenetic landscapes that set transcriptomes needed for function. For CD8 T cells, the epigenome that underlies exhaustion is distinct from effector and memory cell differentiation, suggesting that signals early on set in motion a process where the epigenome is modified to promote a trajectory toward a dysfunctional state. Although we know many signals that promote exhaustion, putting this in the context of the epigenetic changes that occur during differentiation has been less clear. In this review, we aim to summarize the epigenetic changes associated with exhaustion in the context of signals that promote it, highlighting immunotherapeutic studies that support these observations or areas for future therapeutic opportunities.
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Affiliation(s)
- B Rhodes Ford
- Division of Pediatric Rheumatology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA; and Department of Immunology, University of Pittsburgh, Pittsburgh, PA
| | - Amanda C Poholek
- Division of Pediatric Rheumatology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA; and Department of Immunology, University of Pittsburgh, Pittsburgh, PA
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32
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Karakaslar EO, Katiyar N, Hasham M, Youn A, Sharma S, Chung C, Marches R, Korstanje R, Banchereau J, Ucar D. Transcriptional activation of Jun and Fos members of the AP-1 complex is a conserved signature of immune aging that contributes to inflammaging. Aging Cell 2023; 22:e13792. [PMID: 36840360 PMCID: PMC10086525 DOI: 10.1111/acel.13792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 12/20/2022] [Accepted: 01/25/2023] [Indexed: 02/26/2023] Open
Abstract
Diverse mouse strains have different health and life spans, mimicking the diversity among humans. To capture conserved aging signatures, we studied long-lived C57BL/6J and short-lived NZO/HILtJ mouse strains by profiling transcriptomes and epigenomes of immune cells from peripheral blood and the spleen from young and old mice. Transcriptional activation of the AP-1 transcription factor complex, particularly Fos, Junb, and Jun genes, was the most significant and conserved aging signature across tissues and strains. ATAC-seq data analyses showed that the chromatin around these genes was more accessible with age and there were significantly more binding sites for these TFs with age across all studied tissues, targeting pro-inflammatory molecules including Il6. Age-related increases in binding sites of JUN and FOS factors were also conserved in human peripheral blood ATAC-seq data. Single-cell RNA-seq data from the mouse aging cell atlas Tabula Muris Senis showed that the expression of these genes increased with age in B, T, NK cells, and macrophages, with macrophages from old mice expressing these molecules more abundantly than other cells. Functional data showed that upon myeloid cell activation via poly(I:C), the levels of JUN protein and its binding activity increased more significantly in spleen cells from old compared to young mice. In addition, upon activation, old cells produced more IL6 compared to young cells. In sum, we showed that the aging-related transcriptional activation of Jun and Fos family members in AP-1 complex is conserved across immune tissues and long- and short-living mouse strains, possibly contributing to increased inflammation with age.
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Affiliation(s)
- Emin Onur Karakaslar
- The Jackson Laboratory for Genomic MedicineFarmingtonConnecticutUSA
- Leiden University Medical Center (LUMC)LeidenThe Netherlands
| | - Neerja Katiyar
- The Jackson Laboratory for Genomic MedicineFarmingtonConnecticutUSA
| | - Muneer Hasham
- The Jackson Laboratory for Mammalian GeneticsBar HarborMaineUSA
| | | | | | - Cheng‐han Chung
- The Jackson Laboratory for Genomic MedicineFarmingtonConnecticutUSA
| | - Radu Marches
- The Jackson Laboratory for Genomic MedicineFarmingtonConnecticutUSA
| | - Ron Korstanje
- The Jackson Laboratory for Mammalian GeneticsBar HarborMaineUSA
| | - Jacques Banchereau
- The Jackson Laboratory for Genomic MedicineFarmingtonConnecticutUSA
- ImmunaiNew YorkNew YorkUSA
| | - Duygu Ucar
- The Jackson Laboratory for Genomic MedicineFarmingtonConnecticutUSA
- Department of Genetics and Genome SciencesUniversity of Connecticut Health CenterFarmingtonConnecticutUSA
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33
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Cao W, Sturmlechner I, Zhang H, Jin J, Hu B, Jadhav RR, Fang F, Weyand CM, Goronzy JJ. TRIB2 safeguards naive T cell homeostasis during aging. Cell Rep 2023; 42:112195. [PMID: 36884349 PMCID: PMC10118747 DOI: 10.1016/j.celrep.2023.112195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 12/24/2022] [Accepted: 02/15/2023] [Indexed: 03/08/2023] Open
Abstract
Naive CD4+ T cells are more resistant to age-related loss than naive CD8+ T cells, suggesting mechanisms that preferentially protect naive CD4+ T cells during aging. Here, we show that TRIB2 is more abundant in naive CD4+ than CD8+ T cells and counteracts quiescence exit by suppressing AKT activation. TRIB2 deficiency increases AKT activity and accelerates proliferation and differentiation in response to interleukin-7 (IL-7) in humans and during lymphopenia in mice. TRIB2 transcription is controlled by the lineage-determining transcription factors ThPOK and RUNX3. Ablation of Zbtb7b (encoding ThPOK) and Cbfb (obligatory RUNT cofactor) attenuates the difference in lymphopenia-induced proliferation between naive CD4+ and CD8+ cells. In older adults, ThPOK and TRIB2 expression wanes in naive CD4+ T cells, causing loss of naivety. These findings assign TRIB2 a key role in regulating T cell homeostasis and provide a model to explain the lesser resilience of CD8+ T cells to undergo changes with age.
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Affiliation(s)
- Wenqiang Cao
- Key Laboratory of Major Chronic Diseases of Nervous System of Liaoning Province, Health Sciences Institute of China Medical University, Shenyang 110122, China; Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, CA 94305, USA; Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA.
| | - Ines Sturmlechner
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Huimin Zhang
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, CA 94305, USA; Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Jun Jin
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, CA 94305, USA; Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Bin Hu
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, CA 94305, USA
| | - Rohit R Jadhav
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, CA 94305, USA; Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Fengqin Fang
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, CA 94305, USA; Department of Laboratory Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200336, China
| | - Cornelia M Weyand
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, CA 94305, USA; Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA; Department of Medicine, Division of Rheumatology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA
| | - Jörg J Goronzy
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, CA 94305, USA; Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA; Department of Medicine, Division of Rheumatology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA; Robert and Arlene Kogod Center on Aging, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, USA.
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Han S, Georgiev P, Ringel AE, Sharpe AH, Haigis MC. Age-associated remodeling of T cell immunity and metabolism. Cell Metab 2023; 35:36-55. [PMID: 36473467 PMCID: PMC10799654 DOI: 10.1016/j.cmet.2022.11.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 10/14/2022] [Accepted: 11/09/2022] [Indexed: 12/12/2022]
Abstract
Aging results in remodeling of T cell immunity and is associated with poor clinical outcomes in age-related diseases such as cancer. Among the hallmarks of aging, changes in host and cellular metabolism critically affect the development, maintenance, and function of T cells. Although metabolic perturbations impact anti-tumor T cell responses, the link between age-associated metabolic dysfunction and anti-tumor immunity remains unclear. In this review, we summarize recent advances in our understanding of aged T cell metabolism, with a focus on the bioenergetic and immunologic features of T cell subsets unique to the aging process. We also survey insights into mechanisms of metabolic T cell dysfunction in aging and discuss the impacts of aging on the efficacy of cancer immunotherapy. As the average life expectancy continues to increase, understanding the interplay between age-related metabolic reprogramming and maladaptive T cell immunity will be instrumental for the development of therapeutic strategies for older patients.
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Affiliation(s)
- SeongJun Han
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Peter Georgiev
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Alison E Ringel
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Arlene H Sharpe
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA.
| | - Marcia C Haigis
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
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35
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Zhang H, Jadhav RR, Cao W, Goronzy IN, Zhao TV, Jin J, Ohtsuki S, Hu Z, Morales J, Greenleaf WJ, Weyand CM, Goronzy JJ. Aging-associated HELIOS deficiency in naive CD4 + T cells alters chromatin remodeling and promotes effector cell responses. Nat Immunol 2023; 24:96-109. [PMID: 36510022 PMCID: PMC10118794 DOI: 10.1038/s41590-022-01369-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 10/24/2022] [Indexed: 12/14/2022]
Abstract
Immune aging combines cellular defects in adaptive immunity with the activation of pathways causing a low-inflammatory state. Here we examined the influence of age on the kinetic changes in the epigenomic and transcriptional landscape induced by T cell receptor (TCR) stimulation in naive CD4+ T cells. Despite attenuated TCR signaling in older adults, TCR activation accelerated remodeling of the epigenome and induced transcription factor networks favoring effector cell differentiation. We identified increased phosphorylation of STAT5, at least in part due to aberrant IL-2 receptor and lower HELIOS expression, as upstream regulators. Human HELIOS-deficient, naive CD4+ T cells, when transferred into human-synovium-mouse chimeras, infiltrated tissues more efficiently. Inhibition of IL-2 or STAT5 activity in T cell responses of older adults restored the epigenetic response pattern to the one seen in young adults. In summary, reduced HELIOS expression in non-regulatory naive CD4+ T cells in older adults directs T cell fate decisions toward inflammatory effector cells that infiltrate tissue.
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Affiliation(s)
- Huimin Zhang
- Department of Immunology, Mayo Clinic, Rochester, MN, USA
- Department of Medicine, Stanford University, Stanford, CA, USA
| | - Rohit R Jadhav
- Department of Immunology, Mayo Clinic, Rochester, MN, USA
- Department of Medicine, Stanford University, Stanford, CA, USA
| | - Wenqiang Cao
- Department of Immunology, Mayo Clinic, Rochester, MN, USA
- Department of Medicine, Stanford University, Stanford, CA, USA
- Health Sciences Institute, China Medical University, Shenyang, China
| | - Isabel N Goronzy
- Biochemistry and Molecular Biophysics, California Institute of Technology, Pasadena, CA, USA
| | - Tuantuan V Zhao
- Department of Medicine, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Rheumatology, Mayo Clinic, Rochester, MN, USA
| | - Jun Jin
- Department of Immunology, Mayo Clinic, Rochester, MN, USA
- Department of Medicine, Stanford University, Stanford, CA, USA
| | - Shozo Ohtsuki
- Department of Medicine, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Rheumatology, Mayo Clinic, Rochester, MN, USA
| | - Zhaolan Hu
- Department of Medicine, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Rheumatology, Mayo Clinic, Rochester, MN, USA
| | - Jose Morales
- Department of Medicine, Division of Rheumatology, Mayo Clinic, Rochester, MN, USA
| | | | - Cornelia M Weyand
- Department of Immunology, Mayo Clinic, Rochester, MN, USA
- Department of Medicine, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Rheumatology, Mayo Clinic, Rochester, MN, USA
| | - Jörg J Goronzy
- Department of Immunology, Mayo Clinic, Rochester, MN, USA.
- Department of Medicine, Stanford University, Stanford, CA, USA.
- Department of Medicine, Division of Rheumatology, Mayo Clinic, Rochester, MN, USA.
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Abstract
Age is the key risk factor for diseases and disabilities of the elderly. Efforts to tackle age-related diseases and increase healthspan have suggested targeting the ageing process itself to 'rejuvenate' physiological functioning. However, achieving this aim requires measures of biological age and rates of ageing at the molecular level. Spurred by recent advances in high-throughput omics technologies, a new generation of tools to measure biological ageing now enables the quantitative characterization of ageing at molecular resolution. Epigenomic, transcriptomic, proteomic and metabolomic data can be harnessed with machine learning to build 'ageing clocks' with demonstrated capacity to identify new biomarkers of biological ageing.
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Affiliation(s)
- Jarod Rutledge
- Department of Genetics, Stanford University, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Paul F. Glenn Center for the Biology of Ageing, Stanford University School of Medicine, Stanford, CA, USA
| | - Hamilton Oh
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Paul F. Glenn Center for the Biology of Ageing, Stanford University School of Medicine, Stanford, CA, USA
- Graduate Program in Stem Cell and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Tony Wyss-Coray
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA.
- Paul F. Glenn Center for the Biology of Ageing, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.
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37
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Stamatis P, Turesson C, Michailidou D, Mohammad AJ. Pathogenesis of giant cell arteritis with focus on cellular populations. Front Med (Lausanne) 2022; 9:1058600. [PMID: 36465919 PMCID: PMC9714577 DOI: 10.3389/fmed.2022.1058600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 10/31/2022] [Indexed: 08/27/2023] Open
Abstract
Giant cell arteritis (GCA), the most common non-infectious vasculitis, mainly affects elderly individuals. The disease usually affects the aorta and its main supra-aortic branches causing both general symptoms of inflammation and specific ischemic symptoms because of the limited blood flow due to arterial structural changes in the inflamed arteries. The pathogenesis of the GCA is complex and includes a dysregulated immune response that affects both the innate and the adaptive immunity. During the last two decades several studies have investigated interactions among antigen-presenting cells and lymphocytes, which contribute to the formation of the inflammatory infiltrate in the affected arteries. Toll-like receptor signaling and interactions through the VEGF-Notch-Jagged1 pathway are emerging as crucial events of the aberrant inflammatory response, facilitating among others the migration of inflammatory cells to the inflamed arteries and their interactions with the local stromal milieu. The increased use of checkpoint inhibitors in cancer immunotherapy and their immune-related adverse events has fed interest in the role of checkpoint dysfunction in GCA, and recent studies suggest a dysregulated check point system which is unable to suppress the inflammation in the previously immune-privileged arteries, leading to vasculitis. The role of B-cells is currently reevaluated because of new reports of considerable numbers of plasma cells in inflamed arteries as well as the formation of artery tertiary lymphoid organs. There is emerging evidence on previously less studied cell populations, such as the neutrophils, CD8+ T-cells, T regulatory cells and tissue residing memory cells as well as for stromal cells which were previously considered as innocent bystanders. The aim of this review is to summarize the evidence in the literature regarding the cell populations involved in the pathogenesis of GCA and especially in the context of an aged, immune system.
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Affiliation(s)
- Pavlos Stamatis
- Rheumatology, Department of Clinical Sciences, Lund University, Lund, Sweden
- Rheumatology, Sunderby Hospital, Luleå, Sweden
| | - Carl Turesson
- Rheumatology, Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
| | - Despina Michailidou
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA, United States
| | - Aladdin J. Mohammad
- Rheumatology, Department of Clinical Sciences, Lund University, Lund, Sweden
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
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Shen Z, Patel MV, Rodriguez-Garcia M, Wira CR. Aging beyond menopause selectively decreases CD8+ T cell numbers but enhances cytotoxic activity in the human endometrium. Immun Ageing 2022; 19:55. [PMID: 36371240 PMCID: PMC9652910 DOI: 10.1186/s12979-022-00312-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 10/23/2022] [Indexed: 11/15/2022]
Abstract
BACKGROUND Regulation of endometrial (EM) CD8+ T cells, which provide protection through cell-mediated cytotoxicity, is essential for successful reproduction, and protection against sexually transmitted infections and potential tumors. We have previously demonstrated that EM CD8+ T cell cytotoxicity is suppressed directly and indirectly by sex hormones and enhanced after menopause. What remains unclear is whether CD8+ T cell protection and the contribution of tissue-resident (CD103+) and non-resident (CD103-) T cell populations in the EM change as women age following menopause. RESULTS Using hysterectomy EM tissues, we found that EM CD8+ T cell numbers declined significantly in the years following menopause. Despite an overall decline in CD8+ T cells, cytotoxic activity per cell for both CD103- and CD103 + CD8+ T cells increased with age. Investigation of the underlying mechanisms responsible for cytotoxicity indicated that the percentage of total granzyme A and granzyme B positive CD8+ T cells, but not perforin, increased significantly after menopause and remained high and constant as women aged. Additionally, baseline TNFα production by EM CD8+ T cells increased significantly in the years following menopause, and estradiol suppressed TNFα secretion. Moreover, in response to PMA activation, TNFα and IFNγ were significantly up-regulated, and CD103-CD8+ T cells up-regulation of TNFα, IFNγ and IL-6 increased as women aged. CONCLUSIONS Understanding the underlying factors involved in regulating cell-mediated protection of the EM by CD8+ T cells will contribute to the foundation of information essential for developing therapeutic tools to protect women against gynecological cancers and infections as they age.
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Affiliation(s)
- Zheng Shen
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, One Medical Center Drive, Lebanon, NH, 03756, USA
| | - Mickey V Patel
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, One Medical Center Drive, Lebanon, NH, 03756, USA
| | | | - Charles R Wira
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, One Medical Center Drive, Lebanon, NH, 03756, USA.
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Huo X, Guo T, Wang K, Yao B, Li D, Li H, Chen W, Wang L, Wu Z. Methylation-based reclassification and risk stratification of skull-base chordomas. Front Oncol 2022; 12:960005. [PMID: 36439461 PMCID: PMC9691996 DOI: 10.3389/fonc.2022.960005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 10/11/2022] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND Skull-base chordomas are rare malignant bone cancers originating from the remnant of the notochord. Survival is variable, and clinical or molecular factors cannot reliably predict their outcomes. This study therefore identified epigenetic subtypes that defined new chordoma epigenetic profiles and their corresponding characteristics. METHODS Methylation profiles of 46 chordoma-resected neoplasms between 2008 and 2014, along with clinical information, were collected. K-means consensus clustering and principal component analysis were used to identify and validate the clusters. Single-sample gene set enrichment analysis, methylCIBERSORT algorithm, and copy number analysis were used to identify the characteristics of the clusters. RESULTS Unsupervised clustering analysis confirmed two clusters with a progression-free survival difference. Gene set enrichment analysis indicated that the early and late estrogen response pathways and the hypoxia pathway were activated whereas the inflammatory and interferon gamma responses were suppressed. Forty-six potential therapeutic targets corresponding to differentially methylated sites were identified from chordoma patients. Subgroups with a worse outcome were characterized by low immune cell infiltration, higher tumor purity, and higher stemness indices. Moreover, copy number amplifications mostly occurred in cluster 1 tumors and the high-risk group. Additionally, the presence of a CCNE1 deletion was exclusively found in the group of chordoma patients with better outcome, whereas RB1 and CDKN2A/2B deletions were mainly found in the group of chordoma patients with worse outcome. CONCLUSIONS Chordoma prognostic epigenetic subtypes were identified, and their corresponding characteristics were found to be variable.
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Affiliation(s)
- Xulei Huo
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing, China
| | - Tengxian Guo
- Department of Neurosurgery, Beijing Fengtai Hospital, Beijing, China
| | - Ke Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing, China
| | - Bohan Yao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing, China
| | - Da Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing, China
| | - Huan Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing, China
| | - Wei Chen
- Beijing Advanced Innovation Centre for Biomedical Engineering, Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Liang Wang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Zhen Wu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing, China
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40
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Bonavida V, Frame M, Nguyen KH, Rajurkar S, Venketaraman V. Mycobacterium tuberculosis: Implications of Ageing on Infection and Maintaining Protection in the Elderly. Vaccines (Basel) 2022; 10:1892. [PMID: 36366400 PMCID: PMC9693366 DOI: 10.3390/vaccines10111892] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/05/2022] [Accepted: 11/06/2022] [Indexed: 09/10/2024] Open
Abstract
Several reports have suggested that ageing negatively affects the human body resulting in the alteration of various parameters important for sufficient immune health. Although, the breakdown of innate and adaptive immunity has been hypothesized to increase an individual's susceptibility to infections including Mycobacteria tuberculosis (M. tb), little research has been done to bridge this gap and understand the pathophysiology underlying how ageing increases the pathogenesis of M. tb infection. Our objective was to study research from a plethora of resources to better understand the pathogenesis of ageing and its link to the human immune system. To achieve this goal, this article explores how ageing decreases the collective T-cell immune response, reduces glutathione (GSH) production, over activates the mammalian target of rapamycin (mTORC1) pathway, inhibits autophagy and mitophagy, and alters various protective genes/transcription factors. Specifically highlighting how each of these pathways cripple an individual's immune system and increases their susceptibility from M. tb infection. Furthermore, research summarized in this article gives rise to an additional mechanism of susceptibility to M. tb infection which includes a potential defect in antigen presenting by dendritic cells rather than the T-cells response. Inflammaging has also been shown to play a role in the ageing of the immune system and can also potentially be a driving factor for increased susceptibility to M. tb infection in the elderly. In addition, this article features possible preventative strategies that could decrease infections like M. tb in this population. These strategies would need to be further explored and range from immunomodulators, like Everolimus to antioxidant supplementation through GSH intake. We have also proposed the need to research these therapies in conjunction with the administration of the BCG vaccine, especially in endemic populations, to better understand the risk contracting M. tb infection as well as ways to prevent infection in the first place.
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Affiliation(s)
- Victor Bonavida
- Department of Basic Medical Sciences, College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Mitchell Frame
- Department of Basic Medical Sciences, College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Kevin H. Nguyen
- Department of Basic Medical Sciences, College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Shlok Rajurkar
- Division of Biological Sciences, University California Berkeley, Berkeley, CA 94720, USA
| | - Vishwanath Venketaraman
- Department of Basic Medical Sciences, College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA
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41
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Lambert S, Cao W, Zhang H, Colville A, Liu JY, Weyand CM, Goronzy JJ, Gustafson CE. The influence of three-dimensional structure on naïve T cell homeostasis and aging. FRONTIERS IN AGING 2022; 3:1045648. [PMID: 36419548 PMCID: PMC9676450 DOI: 10.3389/fragi.2022.1045648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/24/2022] [Indexed: 11/09/2022]
Abstract
A breakdown in cellular homeostasis is thought to drive naïve T cell aging, however the link between naïve T cell homeostasis and aging in humans is poorly understood. To better address this, we developed a lymphoid organoid system that maintains resting naïve T cells for more than 2 weeks, in conjunction with high CD45RA expression. Deep phenotypic characterization of naïve T cells across age identified reduced CD45RA density as a hallmark of aging. A conversion from CD45RAhigh naive cells to a CD45RAlow phenotype was reproduced within our organoid system by structural breakdown, but not by stromal cell aging or reduced lymphocyte density, and mediated by alternative CD45 splicing. Together, these data suggest that external influences within the lymph node microenvironment may cause phenotypic conversion of naïve T cells in older adults.
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Affiliation(s)
- Simon Lambert
- Department of Medicine, Veterans Administration Healthcare System, Palo Alto, CA, United States
| | - Wenqiang Cao
- Department of Medicine, Veterans Administration Healthcare System, Palo Alto, CA, United States,Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States,Health Sciences Institute, Key Laboratory of Major Chronic Diseases of Nervous System of Liaoning Province, China Medical University, Shenyang, China
| | - Huimin Zhang
- Department of Medicine, Veterans Administration Healthcare System, Palo Alto, CA, United States,Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Alex Colville
- Paul F. Glenn Center for Biology of Aging and Department of Neurology and Neurological Science, Stanford University School of Medicine, Stanford, CA, United States
| | - Jie-Yu Liu
- Paul F. Glenn Center for Biology of Aging and Department of Neurology and Neurological Science, Stanford University School of Medicine, Stanford, CA, United States
| | - Cornelia M. Weyand
- Department of Medicine, Veterans Administration Healthcare System, Palo Alto, CA, United States,Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Jorg J. Goronzy
- Department of Medicine, Veterans Administration Healthcare System, Palo Alto, CA, United States,Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Claire E. Gustafson
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States,Allen Institute for Immunology, Seattle, WA, United States,*Correspondence: Claire E. Gustafson,
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Rückert T, Lareau CA, Mashreghi MF, Ludwig LS, Romagnani C. Clonal expansion and epigenetic inheritance of long-lasting NK cell memory. Nat Immunol 2022; 23:1551-1563. [PMID: 36289449 PMCID: PMC9663309 DOI: 10.1038/s41590-022-01327-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/09/2022] [Indexed: 11/08/2022]
Abstract
Clonal expansion of cells with somatically diversified receptors and their long-term maintenance as memory cells is a hallmark of adaptive immunity. Here, we studied pathogen-specific adaptation within the innate immune system, tracking natural killer (NK) cell memory to human cytomegalovirus (HCMV) infection. Leveraging single-cell multiomic maps of ex vivo NK cells and somatic mitochondrial DNA mutations as endogenous barcodes, we reveal substantial clonal expansion of adaptive NK cells in HCMV+ individuals. NK cell clonotypes were characterized by a convergent inflammatory memory signature enriched for AP1 motifs superimposed on a private set of clone-specific accessible chromatin regions. NK cell clones were stably maintained in specific epigenetic states over time, revealing that clonal inheritance of chromatin accessibility shapes the epigenetic memory repertoire. Together, we identify clonal expansion and persistence within the human innate immune system, suggesting that these mechanisms have evolved independent of antigen-receptor diversification.
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Affiliation(s)
- Timo Rückert
- Innate Immunity, Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), ein Leibniz Institut, Berlin, Germany.
| | - Caleb A Lareau
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Mir-Farzin Mashreghi
- Therapeutic Gene Regulation, Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), ein Leibniz Institut, Berlin, Germany
| | - Leif S Ludwig
- Berlin Institute of Health at Charité Universitätsmedizin Berlin, Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Chiara Romagnani
- Innate Immunity, Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), ein Leibniz Institut, Berlin, Germany.
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Medizinische Klinik für Gastroenterologie, Infektiologie und Rheumatologie, Berlin, Germany.
- Leibniz-Science Campus Chronic Inflammation, Berlin, Germany.
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Anikeeva N, Steblyanko M, Kuri-Cervantes L, Buggert M, Betts MR, Sykulev Y. The immune synapses reveal aberrant functions of CD8 T cells during chronic HIV infection. Nat Commun 2022; 13:6436. [PMID: 36307445 PMCID: PMC9616955 DOI: 10.1038/s41467-022-34157-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 10/14/2022] [Indexed: 02/05/2023] Open
Abstract
Chronic HIV infection causes persistent low-grade inflammation that induces premature aging of the immune system including senescence of memory and effector CD8 T cells. To uncover the reasons of gradually diminished potency of CD8 T cells from people living with HIV, here we expose the T cells to planar lipid bilayers containing ligands for T-cell receptor and a T-cell integrins and analyze the cellular morphology, dynamics of synaptic interface formation and patterns of the cellular degranulation. We find a large fraction of phenotypically naive T cells from chronically infected people are capable to form mature synapse with focused degranulation, a signature of a differentiated T cells. Further, differentiation of aberrant naive T cells may lead to the development of anomalous effector T cells undermining their capacity to control HIV and other pathogens that could be contained otherwise.
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Affiliation(s)
- Nadia Anikeeva
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Maria Steblyanko
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Leticia Kuri-Cervantes
- Department of Microbiology and Institute of Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marcus Buggert
- Department of Microbiology and Institute of Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Michael R Betts
- Department of Microbiology and Institute of Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yuri Sykulev
- Departments of Immunology and Medical Oncology, Thomas Jefferson University, Philadelphia, PA, USA.
- Sydney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA.
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44
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Singh B, Kumar Rai A. Loss of immune regulation in aged T-cells: A metabolic review to show lack of ability to control responses within the self. Hum Immunol 2022; 83:808-817. [DOI: 10.1016/j.humimm.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 09/19/2022] [Accepted: 10/04/2022] [Indexed: 11/04/2022]
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45
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Heterogeneity and transcriptome changes of human CD8 + T cells across nine decades of life. Nat Commun 2022; 13:5128. [PMID: 36050300 PMCID: PMC9436929 DOI: 10.1038/s41467-022-32869-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 08/22/2022] [Indexed: 12/03/2022] Open
Abstract
The decline of CD8+ T cell functions contributes to deteriorating health with aging, but the mechanisms that underlie this phenomenon are not well understood. We use single-cell RNA sequencing with both cross-sectional and longitudinal samples to assess how human CD8+ T cell heterogeneity and transcriptomes change over nine decades of life. Eleven subpopulations of CD8+ T cells and their dynamic changes with age are identified. Age-related changes in gene expression result from changes in the percentage of cells expressing a given transcript, quantitative changes in the transcript level, or a combination of these two. We develop a machine learning model capable of predicting the age of individual cells based on their transcriptomic features, which are closely associated with their differentiation and mutation burden. Finally, we validate this model in two separate contexts of CD8+ T cell aging: HIV infection and CAR T cell expansion in vivo. The characterisation of T cells during aging is important to predict functional outcomes in vaccination or infection. Here the authors use flow cytometry and scRNA sequencing to transcriptionally age CD8 T cells and then use a machine learning model to interpret cell age from transcriptional profiles.
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Bozukova M, Nikopoulou C, Kleinenkuhnen N, Grbavac D, Goetsch K, Tessarz P. Aging is associated with increased chromatin accessibility and reduced polymerase pausing in liver. Mol Syst Biol 2022; 18:e11002. [PMID: 36082605 PMCID: PMC9459415 DOI: 10.15252/msb.202211002] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 08/09/2022] [Accepted: 08/15/2022] [Indexed: 11/29/2022] Open
Abstract
Regulation of gene expression is linked to the organization of the genome. With age, chromatin alterations occur on all levels of genome organization, accompanied by changes in the gene expression profile. However, little is known about the changes in the level of transcriptional regulation. Here, we used a multi-omics approach and integrated ATAC-, RNA- and NET-seq to identify age-related changes in the chromatin landscape of murine liver and to investigate how these are linked to transcriptional regulation. We provide the first systematic inventory of the connection between aging, chromatin accessibility, and transcriptional regulation in a whole tissue. Aging in murine liver is characterized by an increase in chromatin accessibility at promoter regions, but not in an increase in transcriptional output. Instead, aging is accompanied by a decrease in promoter-proximal pausing of RNA polymerase II (Pol II), while initiation of transcription is not decreased as assessed by RNA polymerase mapping using CUT&RUN. Based on the data reported, we propose that these age-related changes in transcriptional regulation are due to a reduced stability of the pausing complex.
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Affiliation(s)
- Mihaela Bozukova
- Max Planck Research Group ‘Chromatin and Ageing’Max Planck Institute for Biology of AgeingCologneGermany
| | - Chrysa Nikopoulou
- Max Planck Research Group ‘Chromatin and Ageing’Max Planck Institute for Biology of AgeingCologneGermany
| | - Niklas Kleinenkuhnen
- Max Planck Research Group ‘Chromatin and Ageing’Max Planck Institute for Biology of AgeingCologneGermany
- Faculty of Medicine, Institute of Medical Statistics and Computational BiologyUniversity of CologneCologneGermany
| | - Dora Grbavac
- Max Planck Research Group ‘Chromatin and Ageing’Max Planck Institute for Biology of AgeingCologneGermany
- Present address:
Center for Integrative GenomicsUniversity of LausanneLausanneSwitzerland
| | - Katrin Goetsch
- Max Planck Research Group ‘Chromatin and Ageing’Max Planck Institute for Biology of AgeingCologneGermany
| | - Peter Tessarz
- Max Planck Research Group ‘Chromatin and Ageing’Max Planck Institute for Biology of AgeingCologneGermany
- Cellular Stress Responses in Aging‐Associated Diseases (CECAD)University of CologneCologneGermany
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Fang F, Cao W, Mu Y, Okuyama H, Li L, Qiu J, Weyand CM, Goronzy JJ. IL-4 prevents adenosine-mediated immunoregulation by inhibiting CD39 expression. JCI Insight 2022; 7:e157509. [PMID: 35730568 PMCID: PMC9309057 DOI: 10.1172/jci.insight.157509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 05/13/2022] [Indexed: 11/17/2022] Open
Abstract
The ectonucleotidase CD39 functions as a checkpoint in purinergic signaling on effector T cells. By depleting eATP and initiating the generation of adenosine, it impairs memory cell development and contributes to T cell exhaustion, thereby causing defective tumor immunity and deficient T cell responses in older adults who have increased CD39 expression. Tuning enzymatic activity of CD39 and targeting the transcriptional regulation of ENTPD1 can be used to modulate purinergic signaling. Here, we describe that STAT6 phosphorylation downstream of IL-4 signaling represses CD39 expression on activated T cells by inducing a transcription factor network including GATA3, GFI1, and YY1. GATA3 suppresses ENTPD1 transcription through prevention of RUNX3 recruitment to the ENTPD1 promoter. Conversely, pharmacological STAT6 inhibition decreases T cell effector functions via increased CD39 expression, resulting in the defective signaling of P2X receptors by ATP and stimulation of A2A receptors by adenosine. Our studies suggest that inhibiting the STAT6 pathway to increase CD39 expression has the potential to treat autoimmune disease while stimulation of the pathway could improve T cell immunity.
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Affiliation(s)
- Fengqin Fang
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, California, USA
- Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, California, USA
- Department of Laboratory Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenqiang Cao
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, California, USA
- Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, California, USA
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota, USA
- Health Sciences Institute, China Medical University, Shenyang, China
| | - Yunmei Mu
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota, USA
| | - Hirohisa Okuyama
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota, USA
| | - Lingjie Li
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Reproductive Medicine, Shanghai, China
| | - Jingtao Qiu
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, California, USA
| | - Cornelia M. Weyand
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, California, USA
- Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, California, USA
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota, USA
- Department of Medicine/Rheumatology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota, USA
| | - Jörg J. Goronzy
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, California, USA
- Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, California, USA
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota, USA
- Department of Medicine/Rheumatology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota, USA
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48
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Hirai T, Yoshioka Y. Considerations of CD8+ T Cells for Optimized Vaccine Strategies Against Respiratory Viruses. Front Immunol 2022; 13:918611. [PMID: 35774782 PMCID: PMC9237416 DOI: 10.3389/fimmu.2022.918611] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/20/2022] [Indexed: 11/13/2022] Open
Abstract
The primary goal of vaccines that protect against respiratory viruses appears to be the induction of neutralizing antibodies for a long period. Although this goal need not be changed, recent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have drawn strong attention to another arm of acquired immunity, CD8+ T cells, which are also called killer T cells. Recent evidence accumulated during the coronavirus disease 2019 (COVID-19) pandemic has revealed that even variants of SARS-CoV-2 that escaped from neutralizing-antibodies that were induced by either infection or vaccination could not escape from CD8+ T cell-mediated immunity. In addition, although traditional vaccine platforms, such as inactivated virus and subunit vaccines, are less efficient in inducing CD8+ T cells, newly introduced platforms for SARS-CoV-2, namely, mRNA and adenoviral vector vaccines, can induce strong CD8+ T cell-mediated immunity in addition to inducing neutralizing antibodies. However, CD8+ T cells function locally and need to be at the site of infection to control it. To fully utilize the protective performance of CD8+ T cells, it would be insufficient to induce only memory cells circulating in blood, using injectable vaccines; mucosal immunization could be required to set up CD8+ T cells for the optimal protection. CD8+ T cells might also contribute to the pathology of the infection, change their function with age and respond differently to booster vaccines in comparison with antibodies. Herein, we overview cutting-edge ideas on CD8+ T cell-mediated immunity that can enable the rational design of vaccines for respiratory viruses.
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Affiliation(s)
- Toshiro Hirai
- Vaccine Creation Group, BIKEN Innovative Vaccine Research Alliance Laboratories, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Vaccine Creation Group, BIKEN Innovative Vaccine Research Alliance Laboratories, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- Laboratory of Nano-design for Innovative Drug Development, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Japan
- *Correspondence: Toshiro Hirai,
| | - Yasuo Yoshioka
- Vaccine Creation Group, BIKEN Innovative Vaccine Research Alliance Laboratories, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Vaccine Creation Group, BIKEN Innovative Vaccine Research Alliance Laboratories, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- Laboratory of Nano-design for Innovative Drug Development, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Japan
- The Research Foundation for Microbial Diseases of Osaka University, Suita, Japan
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Maity AK, Hu X, Zhu T, Teschendorff AE. Inference of age-associated transcription factor regulatory activity changes in single cells. NATURE AGING 2022; 2:548-561. [PMID: 37118452 DOI: 10.1038/s43587-022-00233-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 05/03/2022] [Indexed: 04/30/2023]
Abstract
Transcription factors (TFs) control cell identity and function. How their activity is altered during healthy aging is critical for an improved understanding of aging and disease risk, yet relatively little is known about such changes at cell-type resolution. Here we present and validate a TF activity estimation method for single cells from the hematopoietic system that is based on TF regulons, and apply it to a mouse single-cell RNA-sequencing atlas, to infer age-associated differentiation activity changes in the immune cells of different organs. This revealed an age-associated signature of macrophage dedifferentiation, which is shared across tissue types, and aggravated in tumor-associated macrophages. By extending the analysis to all major cell types, we reveal cell-type and tissue-type-independent age-associated alterations to regulatory factors controlling antigen processing, inflammation, collagen processing and circadian rhythm, that are implicated in age-related diseases. Finally, our study highlights the limitations of using TF expression to infer age-associated changes, underscoring the need to use regulatory activity inference methods.
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Affiliation(s)
- Alok K Maity
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xue Hu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Tianyu Zhu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
- UCL Cancer Institute, Paul O'Gorman Building, University College London, London, UK.
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Li Y, Jin J, Wang Y. SIRT6 Widely Regulates Aging, Immunity, and Cancer. Front Oncol 2022; 12:861334. [PMID: 35463332 PMCID: PMC9019339 DOI: 10.3389/fonc.2022.861334] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/14/2022] [Indexed: 12/14/2022] Open
Abstract
SIRT6 is a member of the Sir2-like family in mammals. Recent structural and biochemical studies have characterized SIRT6 as having deacetylation, defatty-acylation, and mono-ADP-ribosylation activities, which determine its important regulatory roles during physiological and pathological processes. This review focuses mainly on the regulatory functions of SIRT6 in aging, cancer, and, especially, immunity. Particular attention is paid to studies illustrating the critical role of SIRT6 in the regulation of immune cells from the viewpoints of immunesenescence, immunometabolism, and tumor immunology. Owing to its role in regulating the function of the immune system, SIRT6 can be considered to be a potential therapeutic target for the treatment of diseases.
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Affiliation(s)
- Yunjia Li
- The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Heifei, China
| | - Jing Jin
- Institute of Immunology and the Chinese Academy of Sciences (CAS) Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medicine and Medical Center, University of Science and Technology of China, Hefei, China
| | - Yi Wang
- The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Heifei, China.,Institute of Immunology and the Chinese Academy of Sciences (CAS) Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medicine and Medical Center, University of Science and Technology of China, Hefei, China
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