1
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Ma F, Cao Y, Du H, Braikia FZ, Zong L, Ollikainen N, Bayer M, Qiu X, Park B, Roy R, Nandi S, Sarantopoulou D, Ziman A, Bianchi AH, Beerman I, Zhao K, Grosschedl R, Sen R. Three-dimensional chromatin reorganization regulates B cell development during ageing. Nat Cell Biol 2024; 26:991-1002. [PMID: 38866970 PMCID: PMC11178499 DOI: 10.1038/s41556-024-01424-9] [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: 11/01/2022] [Accepted: 04/16/2024] [Indexed: 06/14/2024]
Abstract
The contribution of three-dimensional genome organization to physiological ageing is not well known. Here we show that large-scale chromatin reorganization distinguishes young and old bone marrow progenitor (pro-) B cells. These changes result in increased interactions at the compartment level and reduced interactions within topologically associated domains (TADs). The gene encoding Ebf1, a key B cell regulator, switches from compartment A to B with age. Genetically reducing Ebf1 recapitulates some features of old pro-B cells. TADs that are most reduced with age contain genes important for B cell development, including the immunoglobulin heavy chain (Igh) locus. Weaker intra-TAD interactions at Igh correlate with altered variable (V), diversity (D) and joining (J) gene recombination. Our observations implicate three-dimensional chromatin reorganization as a major driver of pro-B cell phenotypes that impair B lymphopoiesis with age.
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Affiliation(s)
- Fei Ma
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | - Yaqiang Cao
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung and Blood Institute, Bethesda, MD, USA
| | - Hansen Du
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | - Fatima Zohra Braikia
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | - Le Zong
- Epigenetics and Stem Cell Init, Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - Noah Ollikainen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | - Marc Bayer
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Xiang Qiu
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | - Bongsoo Park
- Epigenetics and Stem Cell Init, Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - Roshni Roy
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | - Satabdi Nandi
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | - Dimitra Sarantopoulou
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | | | - Aisha Haley Bianchi
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | - Isabel Beerman
- Epigenetics and Stem Cell Init, Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - Keji Zhao
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung and Blood Institute, Bethesda, MD, USA
| | - Rudolf Grosschedl
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Ranjan Sen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA.
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2
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Veres T, Kerestély M, Kovács BM, Keresztes D, Schulc K, Seitz E, Vassy Z, Veres DV, Csermely P. Cellular forgetting, desensitisation, stress and ageing in signalling networks. When do cells refuse to learn more? Cell Mol Life Sci 2024; 81:97. [PMID: 38372750 PMCID: PMC10876757 DOI: 10.1007/s00018-024-05112-7] [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: 10/09/2023] [Revised: 11/09/2023] [Accepted: 01/02/2024] [Indexed: 02/20/2024]
Abstract
Recent findings show that single, non-neuronal cells are also able to learn signalling responses developing cellular memory. In cellular learning nodes of signalling networks strengthen their interactions e.g. by the conformational memory of intrinsically disordered proteins, protein translocation, miRNAs, lncRNAs, chromatin memory and signalling cascades. This can be described by a generalized, unicellular Hebbian learning process, where those signalling connections, which participate in learning, become stronger. Here we review those scenarios, where cellular signalling is not only repeated in a few times (when learning occurs), but becomes too frequent, too large, or too complex and overloads the cell. This leads to desensitisation of signalling networks by decoupling signalling components, receptor internalization, and consequent downregulation. These molecular processes are examples of anti-Hebbian learning and 'forgetting' of signalling networks. Stress can be perceived as signalling overload inducing the desensitisation of signalling pathways. Ageing occurs by the summative effects of cumulative stress downregulating signalling. We propose that cellular learning desensitisation, stress and ageing may be placed along the same axis of more and more intensive (prolonged or repeated) signalling. We discuss how cells might discriminate between repeated and unexpected signals, and highlight the Hebbian and anti-Hebbian mechanisms behind the fold-change detection in the NF-κB signalling pathway. We list drug design methods using Hebbian learning (such as chemically-induced proximity) and clinical treatment modalities inducing (cancer, drug allergies) desensitisation or avoiding drug-induced desensitisation. A better discrimination between cellular learning, desensitisation and stress may open novel directions in drug design, e.g. helping to overcome drug resistance.
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Affiliation(s)
- Tamás Veres
- Department of Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Márk Kerestély
- Department of Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Borbála M Kovács
- Department of Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Dávid Keresztes
- Department of Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Klára Schulc
- Department of Molecular Biology, Semmelweis University, Budapest, Hungary
- Division of Oncology, Department of Internal Medicine and Oncology, Semmelweis University, Budapest, Hungary
| | - Erik Seitz
- Department of Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Zsolt Vassy
- Department of Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Dániel V Veres
- Department of Molecular Biology, Semmelweis University, Budapest, Hungary
- Turbine Ltd, Budapest, Hungary
| | - Peter Csermely
- Department of Molecular Biology, Semmelweis University, Budapest, Hungary.
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3
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Ananthamohan K, Stelzer JE, Sadayappan S. Hypertrophic cardiomyopathy in MYBPC3 carriers in aging. THE JOURNAL OF CARDIOVASCULAR AGING 2024; 4:9. [PMID: 38406555 PMCID: PMC10883298 DOI: 10.20517/jca.2023.29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Hypertrophic cardiomyopathy (HCM) is characterized by abnormal thickening of the myocardium, leading to arrhythmias, heart failure, and elevated risk of sudden cardiac death, particularly among the young. This inherited disease is predominantly caused by mutations in sarcomeric genes, among which those in the cardiac myosin binding protein-C3 (MYBPC3) gene are major contributors. HCM associated with MYBPC3 mutations usually presents in the elderly and ranges from asymptomatic to symptomatic forms, affecting numerous cardiac functions and presenting significant health risks with a spectrum of clinical manifestations. Regulation of MYBPC3 expression involves various transcriptional and translational mechanisms, yet the destiny of mutant MYBPC3 mRNA and protein in late-onset HCM remains unclear. Pathogenesis related to MYBPC3 mutations includes nonsense-mediated decay, alternative splicing, and ubiquitin-proteasome system events, leading to allelic imbalance and haploinsufficiency. Aging further exacerbates the severity of HCM in carriers of MYBPC3 mutations. Advancements in high-throughput omics techniques have identified crucial molecular events and regulatory disruptions in cardiomyocytes expressing MYBPC3 variants. This review assesses the pathogenic mechanisms that promote late-onset HCM through the lens of transcriptional, post-transcriptional, and post-translational modulation of MYBPC3, underscoring its significance in HCM across carriers. The review also evaluates the influence of aging on these processes and MYBPC3 levels during HCM pathogenesis in the elderly. While pinpointing targets for novel medical interventions to conserve cardiac function remains challenging, the emergence of personalized omics offers promising avenues for future HCM treatments, particularly for late-onset cases.
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Affiliation(s)
- Kalyani Ananthamohan
- Department of Internal Medicine, Division of Cardiovascular Health and Disease, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Julian E. Stelzer
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH 45267, USA
| | - Sakthivel Sadayappan
- Department of Internal Medicine, Division of Cardiovascular Health and Disease, University of Cincinnati, Cincinnati, OH 45267, USA
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4
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Gao Z, Wang M, Smith A, Boyes J. YY1 Binding to Regulatory Elements That Lack Enhancer Activity Promotes Locus Folding and Gene Activation. J Mol Biol 2023; 435:168315. [PMID: 37858706 DOI: 10.1016/j.jmb.2023.168315] [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: 08/14/2023] [Revised: 09/25/2023] [Accepted: 10/12/2023] [Indexed: 10/21/2023]
Abstract
Enhancers activate their cognate promoters over huge distances but how enhancer/promoter interactions become established is not completely understood. There is strong evidence that cohesin-mediated loop extrusion is involved but this does not appear to be a universal mechanism. Here, we identify an element within the mouse immunoglobulin lambda (Igλ) light chain locus, HSCλ1, that has characteristics of active regulatory elements but lacks intrinsic enhancer or promoter activity. Remarkably, knock-out of the YY1 binding site from HSCλ1 reduces Igλ transcription significantly and disrupts enhancer/promoter interactions, even though these elements are >10 kb from HSCλ1. Genome-wide analyses of mouse embryonic stem cells identified 2671 similar YY1-bound, putative genome organizing elements that lie within CTCF/cohesin loop boundaries but that lack intrinsic enhancer activity. We suggest that such elements play a fundamental role in locus folding and in facilitating enhancer/promoter interactions.
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Affiliation(s)
- Zeqian Gao
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Miao Wang
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Alastair Smith
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Joan Boyes
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
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5
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Wang X, Gu WC, Li J, Ma BG. EVRC: reconstruction of chromosome 3D structure models using error-vector resultant algorithm with clustering coefficient. BIOINFORMATICS (OXFORD, ENGLAND) 2023; 39:btad638. [PMID: 37847746 DOI: 10.1093/bioinformatics/btad638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 09/28/2023] [Accepted: 10/16/2023] [Indexed: 10/19/2023]
Abstract
MOTIVATION Reconstruction of 3D structure models is of great importance for the study of chromosome function. Software tools for this task are highly needed. RESULTS We present a novel reconstruction algorithm, called EVRC, which utilizes co-clustering coefficients and error-vector resultant for chromosome 3D structure reconstruction. As an update of our previous EVR algorithm, EVRC now can deal with both single and multiple chromosomes in structure modeling. To evaluate the effectiveness and accuracy of the EVRC algorithm, we applied it to simulation datasets and real Hi-C datasets. The results show that the reconstructed structures have high similarity to the original/real structures, indicating the effectiveness and robustness of the EVRC algorithm. Furthermore, we applied the algorithm to the 3D conformation reconstruction of the wild-type and mutant Arabidopsis thaliana chromosomes and demonstrated the differences in structural characteristics between different chromosomes. We also accurately showed the conformational change in the centromere region of the mutant compared with the wild-type of Arabidopsis chromosome 1. Our EVRC algorithm is a valuable software tool for the field of chromatin structure reconstruction, and holds great promise for advancing our understanding on the chromosome functions. AVAILABILITY AND IMPLEMENTATION The software is available at https://github.com/mbglab/EVRC.
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Affiliation(s)
- Xiao Wang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Wei-Cheng Gu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Jie Li
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Bin-Guang Ma
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
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6
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Yeo RW, Zhou OY, Zhong BL, Sun ED, Navarro Negredo P, Nair S, Sharmin M, Ruetz TJ, Wilson M, Kundaje A, Dunn AR, Brunet A. Chromatin accessibility dynamics of neurogenic niche cells reveal defects in neural stem cell adhesion and migration during aging. NATURE AGING 2023; 3:866-893. [PMID: 37443352 PMCID: PMC10353944 DOI: 10.1038/s43587-023-00449-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 06/02/2023] [Indexed: 07/15/2023]
Abstract
The regenerative potential of brain stem cell niches deteriorates during aging. Yet the mechanisms underlying this decline are largely unknown. Here we characterize genome-wide chromatin accessibility of neurogenic niche cells in vivo during aging. Interestingly, chromatin accessibility at adhesion and migration genes decreases with age in quiescent neural stem cells (NSCs) but increases with age in activated (proliferative) NSCs. Quiescent and activated NSCs exhibit opposing adhesion behaviors during aging: quiescent NSCs become less adhesive, whereas activated NSCs become more adhesive. Old activated NSCs also show decreased migration in vitro and diminished mobilization out of the niche for neurogenesis in vivo. Using tension sensors, we find that aging increases force-producing adhesions in activated NSCs. Inhibiting the cytoskeletal-regulating kinase ROCK reduces these adhesions, restores migration in old activated NSCs in vitro, and boosts neurogenesis in vivo. These results have implications for restoring the migratory potential of NSCs and for improving neurogenesis in the aged brain.
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Affiliation(s)
- Robin W Yeo
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Olivia Y Zhou
- Department of Genetics, Stanford University, Stanford, CA, USA
- Stanford Biophysics Program, Stanford University, Stanford, CA, USA
- Stanford Medical Scientist Training Program, Stanford University, Stanford, CA, USA
| | - Brian L Zhong
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
| | - Eric D Sun
- Department of Genetics, Stanford University, Stanford, CA, USA
- Biomedical Informatics Graduate Program, Stanford University, Stanford, CA, USA
| | | | - Surag Nair
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Mahfuza Sharmin
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Tyson J Ruetz
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Mikaela Wilson
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Alexander R Dunn
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
| | - Anne Brunet
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Glenn Laboratories for the Biology of Aging, Stanford University, Stanford, CA, USA.
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA.
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7
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Monzó C, Gkioni L, Beyer A, Valenzano DR, Grönke S, Partridge L. Dietary restriction mitigates the age-associated decline in mouse B cell receptor repertoire diversity. Cell Rep 2023; 42:112722. [PMID: 37384530 PMCID: PMC10391628 DOI: 10.1016/j.celrep.2023.112722] [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: 01/16/2023] [Revised: 05/07/2023] [Accepted: 06/13/2023] [Indexed: 07/01/2023] Open
Abstract
Aging impairs the capacity to respond to novel antigens, reducing immune protection against pathogens and vaccine efficacy. Dietary restriction (DR) extends life- and health span in diverse animals. However, little is known about the capacity of DR to combat the decline in immune function. Here, we study the changes in B cell receptor (BCR) repertoire during aging in DR and control mice. By sequencing the variable region of the BCR heavy chain in the spleen, we show that DR preserves diversity and attenuates the increase in clonal expansions throughout aging. Remarkably, mice starting DR in mid-life have repertoire diversity and clonal expansion rates indistinguishable from chronic DR mice. In contrast, in the intestine, these traits are unaffected by either age or DR. Reduced within-individual B cell repertoire diversity and increased clonal expansions are correlated with higher morbidity, suggesting a potential contribution of B cell repertoire dynamics to health during aging.
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Affiliation(s)
- Carolina Monzó
- Department Biological Mechanisms of Ageing, Max Planck Institute for Biology of Ageing, 50931 Cologne, North Rhine Westphalia, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Age-Associated Diseases (CECAD), Faculty of Medicine and Faculty of Mathematics and Natural Sciences, University of Cologne, 50931 Cologne, Germany
| | - Lisonia Gkioni
- Department Biological Mechanisms of Ageing, Max Planck Institute for Biology of Ageing, 50931 Cologne, North Rhine Westphalia, Germany
| | - Andreas Beyer
- Cologne Excellence Cluster on Cellular Stress Responses in Age-Associated Diseases (CECAD), Faculty of Medicine and Faculty of Mathematics and Natural Sciences, University of Cologne, 50931 Cologne, Germany
| | - Dario Riccardo Valenzano
- Microbiome-Host Interactions in Ageing Group, Max Planck Institute for Biology of Ageing, 50931 Cologne, North Rhine Westphalia, Germany; Evolutionary Biology/Microbiome-Host Interactions in Aging Group: Fritz Lipmann Institute - Leibniz Institute on Aging, 07745 Jena, Thuringia, Germany.
| | - Sebastian Grönke
- Department Biological Mechanisms of Ageing, Max Planck Institute for Biology of Ageing, 50931 Cologne, North Rhine Westphalia, Germany.
| | - Linda Partridge
- Department Biological Mechanisms of Ageing, Max Planck Institute for Biology of Ageing, 50931 Cologne, North Rhine Westphalia, Germany; Genetics, Evolution & Environment Group, Institute of Healthy Ageing, University College London, London WC1E 6BT, UK.
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8
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Bredthauer C, Fischer A, Ahari AJ, Cao X, Weber J, Rad L, Rad R, Wachutka L, Gagneur J. Transmicron: accurate prediction of insertion probabilities improves detection of cancer driver genes from transposon mutagenesis screens. Nucleic Acids Res 2023; 51:e21. [PMID: 36617985 PMCID: PMC9976929 DOI: 10.1093/nar/gkac1215] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/06/2022] [Accepted: 12/17/2022] [Indexed: 01/10/2023] Open
Abstract
Transposon screens are powerful in vivo assays used to identify loci driving carcinogenesis. These loci are identified as Common Insertion Sites (CISs), i.e. regions with more transposon insertions than expected by chance. However, the identification of CISs is affected by biases in the insertion behaviour of transposon systems. Here, we introduce Transmicron, a novel method that differs from previous methods by (i) modelling neutral insertion rates based on chromatin accessibility, transcriptional activity and sequence context and (ii) estimating oncogenic selection for each genomic region using Poisson regression to model insertion counts while controlling for neutral insertion rates. To assess the benefits of our approach, we generated a dataset applying two different transposon systems under comparable conditions. Benchmarking for enrichment of known cancer genes showed improved performance of Transmicron against state-of-the-art methods. Modelling neutral insertion rates allowed for better control of false positives and stronger agreement of the results between transposon systems. Moreover, using Poisson regression to consider intra-sample and inter-sample information proved beneficial in small and moderately-sized datasets. Transmicron is open-source and freely available. Overall, this study contributes to the understanding of transposon biology and introduces a novel approach to use this knowledge for discovering cancer driver genes.
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Affiliation(s)
- Carl Bredthauer
- TUM School of Computation, Information and Technology, Technical University of Munich, 81675 Munich, Germany.,Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany.,Computational Health Center, Helmholtz Zentrum Munich, Neuherberg, Germany
| | - Anja Fischer
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Ata Jadid Ahari
- TUM School of Computation, Information and Technology, Technical University of Munich, 81675 Munich, Germany
| | - Xueqi Cao
- TUM School of Computation, Information and Technology, Technical University of Munich, 81675 Munich, Germany.,Graduate School of Quantitative Biosciences (QBM), Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Julia Weber
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Lena Rad
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany.,Institute for Experimental Cancer Therapy, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany.,German Cancer Consortium (DKTK), 69120 Heidelberg, Germany.,Department of Medicine II, Klinikum rechts der Isar, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Leonhard Wachutka
- TUM School of Computation, Information and Technology, Technical University of Munich, 81675 Munich, Germany
| | - Julien Gagneur
- TUM School of Computation, Information and Technology, Technical University of Munich, 81675 Munich, Germany.,Computational Health Center, Helmholtz Zentrum Munich, Neuherberg, Germany.,Institute of Human Genetics, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany
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9
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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: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [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 Ageing, Cologne, Germany
| | - Chrysa Nikopoulou
- Max Planck Research Group 'Chromatin and Ageing', Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Niklas Kleinenkuhnen
- Max Planck Research Group 'Chromatin and Ageing', Max Planck Institute for Biology of Ageing, Cologne, Germany.,Faculty of Medicine, Institute of Medical Statistics and Computational Biology, University of Cologne, Cologne, Germany
| | - Dora Grbavac
- Max Planck Research Group 'Chromatin and Ageing', Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Katrin Goetsch
- Max Planck Research Group 'Chromatin and Ageing', Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Peter Tessarz
- Max Planck Research Group 'Chromatin and Ageing', Max Planck Institute for Biology of Ageing, Cologne, Germany.,Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
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10
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Wang Y, Zhao J, Chen S, Li D, Yang J, Zhao X, Qin M, Guo M, Chen C, He Z, Zhou Y, Xu L. Let-7 as a Promising Target in Aging and Aging-Related Diseases: A Promise or a Pledge. Biomolecules 2022; 12:biom12081070. [PMID: 36008964 PMCID: PMC9406090 DOI: 10.3390/biom12081070] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 12/10/2022] Open
Abstract
The abnormal regulation and expression of microRNA (miRNA) are closely related to the aging process and the occurrence and development of aging-related diseases. Lethal-7 (let-7) was discovered in Caenorhabditis elegans (C. elegans) and plays an important role in development by regulating cell fate regulators. Accumulating evidence has shown that let-7 is elevated in aging tissues and participates in multiple pathways that regulate the aging process, including affecting tissue stem cell function, body metabolism, and various aging-related diseases (ARDs). Moreover, recent studies have found that let-7 plays an important role in the senescence of B cells, suggesting that let-7 may also participate in the aging process by regulating immune function. Therefore, these studies show the diversity and complexity of let-7 expression and regulatory functions during aging. In this review, we provide a detailed overview of let-7 expression regulation as well as its role in different tissue aging and aging-related diseases, which may provide new ideas for enriching the complex expression regulation mechanism and pathobiological function of let-7 in aging and related diseases and ultimately provide help for the development of new therapeutic strategies.
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Affiliation(s)
- Ya Wang
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China; (Y.W.); (J.Z.); (S.C.); (D.L.); (J.Y.); (X.Z.); (M.Q.); (M.G.); (C.C.)
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Juanjuan Zhao
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China; (Y.W.); (J.Z.); (S.C.); (D.L.); (J.Y.); (X.Z.); (M.Q.); (M.G.); (C.C.)
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Shipeng Chen
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China; (Y.W.); (J.Z.); (S.C.); (D.L.); (J.Y.); (X.Z.); (M.Q.); (M.G.); (C.C.)
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Dongmei Li
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China; (Y.W.); (J.Z.); (S.C.); (D.L.); (J.Y.); (X.Z.); (M.Q.); (M.G.); (C.C.)
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Jing Yang
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China; (Y.W.); (J.Z.); (S.C.); (D.L.); (J.Y.); (X.Z.); (M.Q.); (M.G.); (C.C.)
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Xu Zhao
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China; (Y.W.); (J.Z.); (S.C.); (D.L.); (J.Y.); (X.Z.); (M.Q.); (M.G.); (C.C.)
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Ming Qin
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China; (Y.W.); (J.Z.); (S.C.); (D.L.); (J.Y.); (X.Z.); (M.Q.); (M.G.); (C.C.)
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Mengmeng Guo
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China; (Y.W.); (J.Z.); (S.C.); (D.L.); (J.Y.); (X.Z.); (M.Q.); (M.G.); (C.C.)
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Chao Chen
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China; (Y.W.); (J.Z.); (S.C.); (D.L.); (J.Y.); (X.Z.); (M.Q.); (M.G.); (C.C.)
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Zhixu He
- The Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine of Zunyi Medical University, Zunyi 563000, China;
| | - Ya Zhou
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China; (Y.W.); (J.Z.); (S.C.); (D.L.); (J.Y.); (X.Z.); (M.Q.); (M.G.); (C.C.)
- Department of Medical Physics, Zunyi Medical University, Zunyi 563000, China
- Correspondence: (Y.Z.); (L.X.)
| | - Lin Xu
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China; (Y.W.); (J.Z.); (S.C.); (D.L.); (J.Y.); (X.Z.); (M.Q.); (M.G.); (C.C.)
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
- Correspondence: (Y.Z.); (L.X.)
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11
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Wu Z, Wang L, Fan L, Tang H, Zuo X, Gu D, Lu X, Li Y, Wu J, Qin S, Xia Y, Zhu H, Wang L, Xu W, Li J, Jin H. Exploring the significance of PAK1 through chromosome conformation signatures in ibrutinib-resistant chronic lymphocytic leukaemia. Mol Oncol 2022; 16:2920-2935. [PMID: 35811334 PMCID: PMC9394240 DOI: 10.1002/1878-0261.13281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 06/06/2022] [Accepted: 07/07/2022] [Indexed: 11/17/2022] Open
Abstract
Ibrutinib exerts promising anticancer effects in chronic lymphocytic leukaemia (CLL). However, acquired resistance occurs during treatment, necessitating the exploration of underlying mechanisms. Although three‐dimensional genome organization has been identified as a major player in the development and progression of cancer, including drug resistance, little is known regarding its role in CLL. Therefore, we investigated the molecular mechanisms underlying ibrutinib resistance through multi‐omics analysis, including high‐throughput chromosome conformation capture (Hi‐C) technology. We demonstrated that the therapeutic response to ibrutinib is associated with the expression of p21‐activated kinase 1 (PAK1). PAK1, which was up‐regulated in CLL and associated with patients' survival, was involved in cell proliferation, glycolysis and oxidative phosphorylation. Furthermore, the PAK1 inhibitor IPA‐3 exerted an anti‐tumour effect and its combination with ibrutinib exhibited a synergistic effect in ibrutinib‐sensitive and ‐resistant cells. These findings suggest the oncogenic role of PAK1 in CLL progression and drug resistance, highlighting PAK1 as a potential diagnostic marker and therapeutic target in CLL including ibrutinib‐resistant CLL.
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Affiliation(s)
- Zijuan Wu
- Department of Hematology, Pukou CLL Center, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, China.,Key Laboratory of Hematology of Nanjing Medical University, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, China
| | - Luqiao Wang
- Department of Hematology, Pukou CLL Center, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, China.,Key Laboratory of Hematology of Nanjing Medical University, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, China
| | - Lei Fan
- Department of Hematology, Pukou CLL Center, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, China.,Key Laboratory of Hematology of Nanjing Medical University, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, China
| | - Hanning Tang
- Department of Hematology, Pukou CLL Center, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, China.,Key Laboratory of Hematology of Nanjing Medical University, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, China
| | - Xiaoling Zuo
- Department of Hematology, Pukou CLL Center, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, China.,Key Laboratory of Hematology of Nanjing Medical University, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, China
| | - Danling Gu
- Department of Hematology, Pukou CLL Center, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, China.,Key Laboratory of Hematology of Nanjing Medical University, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, China
| | - Xueying Lu
- Department of Hematology, Pukou CLL Center, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, China.,Key Laboratory of Hematology of Nanjing Medical University, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, China
| | - Yue Li
- Department of Hematology, Pukou CLL Center, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, China.,Key Laboratory of Hematology of Nanjing Medical University, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, China
| | - Jiazhu Wu
- Department of Hematology, Pukou CLL Center, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, China.,Key Laboratory of Hematology of Nanjing Medical University, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, China
| | - Shuchao Qin
- Department of Hematology, Pukou CLL Center, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, China.,Key Laboratory of Hematology of Nanjing Medical University, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, China
| | - Yi Xia
- Department of Hematology, Pukou CLL Center, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, China.,Key Laboratory of Hematology of Nanjing Medical University, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, China
| | - Huayuan Zhu
- Department of Hematology, Pukou CLL Center, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, China.,Key Laboratory of Hematology of Nanjing Medical University, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, China
| | - Li Wang
- Department of Hematology, Pukou CLL Center, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, China.,Key Laboratory of Hematology of Nanjing Medical University, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, China
| | - Wei Xu
- Department of Hematology, Pukou CLL Center, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, China.,Key Laboratory of Hematology of Nanjing Medical University, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, China
| | - Jianyong Li
- Department of Hematology, Pukou CLL Center, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, China.,Key Laboratory of Hematology of Nanjing Medical University, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, China.,National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Hui Jin
- Department of Hematology, Pukou CLL Center, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, China.,Key Laboratory of Hematology of Nanjing Medical University, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Personalized Cancer Medicine, Nanjing Medical University, China.,National Clinical Research Center for Hematologic Diseases, The First Affiliated Hospital of Soochow University, Suzhou, China
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12
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Interconnections between Inflammageing and Immunosenescence during Ageing. Cells 2022; 11:cells11030359. [PMID: 35159168 PMCID: PMC8834134 DOI: 10.3390/cells11030359] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 01/13/2022] [Accepted: 01/15/2022] [Indexed: 02/04/2023] Open
Abstract
Acute inflammation is a physiological response to injury or infection, with a cascade of steps that ultimately lead to the recruitment of immune cells to clear invading pathogens and heal wounds. However, chronic inflammation arising from the continued presence of the initial trigger, or the dysfunction of signalling and/or effector pathways, is harmful to health. While successful ageing in older adults, including centenarians, is associated with low levels of inflammation, elevated inflammation increases the risk of poor health and death. Hence inflammation has been described as one of seven pillars of ageing. Age-associated sterile, chronic, and low-grade inflammation is commonly termed inflammageing-it is not simply a consequence of increasing chronological age, but is also a marker of biological ageing, multimorbidity, and mortality risk. While inflammageing was initially thought to be caused by "continuous antigenic load and stress", reports from the last two decades describe a much more complex phenomenon also involving cellular senescence and the ageing of the immune system. In this review, we explore some of the main sources and consequences of inflammageing in the context of immunosenescence and highlight potential interventions. In particular, we assess the contribution of cellular senescence to age-associated inflammation, identify patterns of pro- and anti-inflammatory markers characteristic of inflammageing, describe alterations in the ageing immune system that lead to elevated inflammation, and finally assess the ways that diet, exercise, and pharmacological interventions can reduce inflammageing and thus, improve later life health.
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13
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Lee JL, Linterman MA. Mechanisms underpinning poor antibody responses to vaccines in ageing. Immunol Lett 2022; 241:1-14. [PMID: 34767859 PMCID: PMC8765414 DOI: 10.1016/j.imlet.2021.11.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/29/2021] [Accepted: 11/08/2021] [Indexed: 12/13/2022]
Abstract
Vaccines are a highly effective intervention for conferring protection against infections and reducing the associated morbidity and mortality in vaccinated individuals. However, ageing is often associated with a functional decline in the immune system that results in poor antibody production in older individuals after vaccination. A key contributing factor of this age-related decline in vaccine efficacy is the reduced size and function of the germinal centre (GC) response. GCs are specialised microstructures where B cells undergo affinity maturation and diversification of their antibody genes, before differentiating into long-lived antibody-secreting plasma cells and memory B cells. The GC response requires the coordinated interaction of many different cell types, including B cells, T follicular helper (Tfh) cells, T follicular regulatory (Tfr) cells and stromal cell subsets like follicular dendritic cells (FDCs). This review discusses how ageing affects different components of the GC reaction that contribute to its limited output and ultimately impaired antibody responses in older individuals after vaccination. An understanding of the mechanisms underpinning the age-related decline in the GC response is crucial in informing strategies to improve vaccine efficacy and extend the healthy lifespan amongst older people.
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Affiliation(s)
- Jia Le Lee
- Immunology Program, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK.
| | - Michelle A Linterman
- Immunology Program, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK.
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14
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Laverre A, Tannier E, Necsulea A. Long-range promoter-enhancer contacts are conserved during evolution and contribute to gene expression robustness. Genome Res 2021; 32:280-296. [PMID: 34930799 PMCID: PMC8805723 DOI: 10.1101/gr.275901.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 12/16/2021] [Indexed: 11/25/2022]
Abstract
Gene expression is regulated through complex molecular interactions, involving cis-acting elements that can be situated far away from their target genes. Data on long-range contacts between promoters and regulatory elements are rapidly accumulating. However, it remains unclear how these regulatory relationships evolve and how they contribute to the establishment of robust gene expression profiles. Here, we address these questions by comparing genome-wide maps of promoter-centered chromatin contacts in mouse and human. We show that there is significant evolutionary conservation of cis-regulatory landscapes, indicating that selective pressures act to preserve not only regulatory element sequences but also their chromatin contacts with target genes. The extent of evolutionary conservation is remarkable for long-range promoter–enhancer contacts, illustrating how the structure of regulatory landscapes constrains large-scale genome evolution. We show that the evolution of cis-regulatory landscapes, measured in terms of distal element sequences, synteny, or contacts with target genes, is significantly associated with gene expression evolution.
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Affiliation(s)
- Alexandre Laverre
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive
| | - Eric Tannier
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive, Centre de recherche Inria de Lyon
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15
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Immune Memory in Aging: a Wide Perspective Covering Microbiota, Brain, Metabolism, and Epigenetics. Clin Rev Allergy Immunol 2021; 63:499-529. [PMID: 34910283 PMCID: PMC8671603 DOI: 10.1007/s12016-021-08905-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2021] [Indexed: 11/06/2022]
Abstract
Non-specific innate and antigen-specific adaptive immunological memories are vital evolutionary adaptations that confer long-lasting protection against a wide range of pathogens. Adaptive memory is established by memory T and B lymphocytes following the recognition of an antigen. On the other hand, innate immune memory, also called trained immunity, is imprinted in innate cells such as macrophages and natural killer cells through epigenetic and metabolic reprogramming. However, these mechanisms of memory generation and maintenance are compromised as organisms age. Almost all immune cell types, both mature cells and their progenitors, go through age-related changes concerning numbers and functions. The aging immune system renders the elderly highly susceptible to infections and incapable of mounting a proper immune response upon vaccinations. Besides the increased infectious burden, older individuals also have heightened risks of metabolic and neurodegenerative diseases, which have an immunological component. This review discusses how immune function, particularly the establishment and maintenance of innate and adaptive immunological memory, regulates and is regulated by epigenetics, metabolic processes, gut microbiota, and the central nervous system throughout life, with a focus on old age. We explain in-depth how epigenetics and cellular metabolism impact immune cell function and contribute or resist the aging process. Microbiota is intimately linked with the immune system of the human host, and therefore, plays an important role in immunological memory during both homeostasis and aging. The brain, which is not an immune-isolated organ despite former opinion, interacts with the peripheral immune cells, and the aging of both systems influences the health of each other. With all these in mind, we aimed to present a comprehensive view of the aging immune system and its consequences, especially in terms of immunological memory. The review also details the mechanisms of promising anti-aging interventions and highlights a few, namely, caloric restriction, physical exercise, metformin, and resveratrol, that impact multiple facets of the aging process, including the regulation of innate and adaptive immune memory. We propose that understanding aging as a complex phenomenon, with the immune system at the center role interacting with all the other tissues and systems, would allow for more effective anti-aging strategies.
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16
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Rakshit T, Melters DP, Dimitriadis EK, Dalal Y. Mechanical properties of nucleoprotein complexes determined by nanoindentation spectroscopy. Nucleus 2021; 11:264-282. [PMID: 32954931 PMCID: PMC7529419 DOI: 10.1080/19491034.2020.1816053] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The interplay between transcription factors, chromatin remodelers, 3-D organization, and mechanical properties of the chromatin fiber controls genome function in eukaryotes. Besides the canonical histones which fold the bulk of the chromatin into nucleosomes, histone variants create distinctive chromatin domains that are thought to regulate transcription, replication, DNA damage repair, and faithful chromosome segregation. Whether histone variants translate distinctive biochemical or biophysical properties to their associated chromatin structures, and whether these properties impact chromatin dynamics as the genome undergoes a multitude of transactions, is an important question in biology. Here, we describe single-molecule nanoindentation tools that we developed specifically to determine the mechanical properties of histone variant nucleosomes and their complexes. These methods join an array of cutting-edge new methods that further our quantitative understanding of the response of chromatin to intrinsic and extrinsic forces which act upon it during biological transactions in the nucleus.
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Affiliation(s)
- Tatini Rakshit
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH , Bethesda, MD, USA.,Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences , Salt Lake, India
| | - Daniël P Melters
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH , Bethesda, MD, USA
| | - Emilios K Dimitriadis
- Trans-NIH Shared Resource on Biomedical Engineering and Physical Science, National Cancer Institute, NIH , Bethesda, MD, USA
| | - Yamini Dalal
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH , Bethesda, MD, USA
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17
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Capturing and Understanding the Dynamics and Heterogeneity of Gene Expression in the Living Cell. Int J Mol Sci 2020; 21:ijms21218278. [PMID: 33167354 PMCID: PMC7663833 DOI: 10.3390/ijms21218278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/29/2020] [Accepted: 11/03/2020] [Indexed: 11/21/2022] Open
Abstract
The regulation of gene expression is a fundamental process enabling cells to respond to internal and external stimuli or to execute developmental programs. Changes in gene expression are highly dynamic and depend on many intrinsic and extrinsic factors. In this review, we highlight the dynamic nature of transient gene expression changes to better understand cell physiology and development in general. We will start by comparing recent in vivo procedures to capture gene expression in real time. Intrinsic factors modulating gene expression dynamics will then be discussed, focusing on chromatin modifications. Furthermore, we will dissect how cell physiology or age impacts on dynamic gene regulation and especially discuss molecular insights into acquired transcriptional memory. Finally, this review will give an update on the mechanisms of heterogeneous gene expression among genetically identical individual cells. We will mainly focus on state-of-the-art developments in the yeast model but also cover higher eukaryotic systems.
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18
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Yi SJ, Kim K. New Insights into the Role of Histone Changes in Aging. Int J Mol Sci 2020; 21:ijms21218241. [PMID: 33153221 PMCID: PMC7662996 DOI: 10.3390/ijms21218241] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/02/2020] [Accepted: 11/02/2020] [Indexed: 12/15/2022] Open
Abstract
Aging is the progressive decline or loss of function at the cellular, tissue, and organismal levels that ultimately leads to death. A number of external and internal factors, including diet, exercise, metabolic dysfunction, genome instability, and epigenetic imbalance, affect the lifespan of an organism. These aging factors regulate transcriptome changes related to the aging process through chromatin remodeling. Many epigenetic regulators, such as histone modification, histone variants, and ATP-dependent chromatin remodeling factors, play roles in chromatin reorganization. The key to understanding the role of gene regulatory networks in aging lies in characterizing the epigenetic regulators responsible for reorganizing and potentiating particular chromatin structures. This review covers epigenetic studies on aging, discusses the impact of epigenetic modifications on gene expression, and provides future directions in this area.
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19
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Miyazaki K, Watanabe H, Yoshikawa G, Chen K, Hidaka R, Aitani Y, Osawa K, Takeda R, Ochi Y, Tani-Ichi S, Uehata T, Takeuchi O, Ikuta K, Ogawa S, Kondoh G, Lin YC, Ogata H, Miyazaki M. The transcription factor E2A activates multiple enhancers that drive Rag expression in developing T and B cells. Sci Immunol 2020; 5:5/51/eabb1455. [PMID: 32887843 DOI: 10.1126/sciimmunol.abb1455] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 07/21/2020] [Indexed: 01/09/2023]
Abstract
Cell type-specific gene expression is driven by the interplay between lineage-specific transcription factors and cis-regulatory elements to which they bind. Adaptive immunity relies on RAG-mediated assembly of T cell receptor (TCR) and immunoglobulin (Ig) genes. Although Rag1 and Rag2 expression is largely restricted to adaptive lymphoid lineage cells, it remains unclear how Rag gene expression is regulated in a cell lineage-specific manner. Here, we identified three distinct cis-regulatory elements, a T cell lineage-specific enhancer (R-TEn) and the two B cell-specific elements, R1B and R2B By generating mice lacking either R-TEn or R1B and R2B, we demonstrate that these distinct sets of regulatory elements drive the expression of Rag genes in developing T and B cells. What these elements have in common is their ability to bind the transcription factor E2A. By generating a mouse strain that carries a mutation within the E2A binding site of R-TEn, we demonstrate that recruitment of E2A to this site is essential for orchestrating changes in chromatin conformation that drive expression of Rag genes in T cells. By mapping cis-regulatory elements and generating multiple mouse strains lacking distinct enhancer elements, we demonstrate expression of Rag genes in developing T and B cells to be driven by distinct sets of E2A-dependent cis-regulatory modules.
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Affiliation(s)
- Kazuko Miyazaki
- Laboratory of Immunology, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Hitomi Watanabe
- Laboratory of Integrative Biological Sciences, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Genki Yoshikawa
- Institute for Chemical Research, Kyoto University, Uji 611-0011, Japan
| | - Kenian Chen
- Baylor Institute for Immunology Research, Baylor Scott & White Research Institute, Dallas, TX, USA
| | - Reiko Hidaka
- Laboratory of Immunology, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Yuki Aitani
- Laboratory of Immunology, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Kai Osawa
- Laboratory of Immunology, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Rie Takeda
- Laboratory of Integrative Biological Sciences, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Yotaro Ochi
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Shizue Tani-Ichi
- Laboratory of Immune Regulation, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Takuya Uehata
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Osamu Takeuchi
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Koichi Ikuta
- Laboratory of Immune Regulation, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan.,Institute for the Advanced Study of Human Biology (WPI ASHBi), Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan.,Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | - Gen Kondoh
- Laboratory of Integrative Biological Sciences, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Yin C Lin
- Baylor Institute for Immunology Research, Baylor Scott & White Research Institute, Dallas, TX, USA
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Uji 611-0011, Japan
| | - Masaki Miyazaki
- Laboratory of Immunology, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan.
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20
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Identification of novel genes associated with longevity in Drosophila melanogaster - a computational approach. Aging (Albany NY) 2019; 11:11244-11267. [PMID: 31794428 PMCID: PMC6932890 DOI: 10.18632/aging.102527] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/18/2019] [Indexed: 12/13/2022]
Abstract
Despite a growing number of studies on longevity in Drosophila, genetic factors influencing lifespan are still poorly understood. In this paper we propose a conceptually new approach for the identification of novel longevity-associated genes and potential target genes for SNPs in non-coding regions by utilizing the knowledge of co-location of various loci, governed by the three-dimensional architecture of the Drosophila genome. Firstly, we created networks between genes/genomic regions harboring SNPs deemed to be significant in two longevity GWAS summary statistics datasets using intra- and inter-chromosomal interaction frequencies (Hi-C data) as a measure of co-location. These networks were further extended to include regions strongly interacting with previously selected regions. Using various network measures, literature search and additional bioinformatics resources, we investigated the plausibility of genes found to have genuine association with longevity. Several of the newly identified genes were common between the two GWAS datasets and these possessed human orthologs. We also found that the proportion of non-coding SNPs in borders between topologically associated domains is significantly higher than expected by chance. Assuming co-location, we investigated potential target genes for non-coding SNPs. This approach therefore offers a stepping stone to identification of novel genes and SNP targets linked to human longevity.
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21
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Shapiro MR, Atkinson MA, Brusko TM. Pleiotropic roles of the insulin-like growth factor axis in type 1 diabetes. Curr Opin Endocrinol Diabetes Obes 2019; 26:188-194. [PMID: 31145130 PMCID: PMC7135378 DOI: 10.1097/med.0000000000000484] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
PURPOSE OF REVIEW We review studies demonstrating lowered levels of insulin-like growth factors (IGFs) in patients with recent-onset type 1 diabetes (T1D) and discuss their potential roles in the disorder's pathogenesis. RECENT FINDINGS IGFs have long been recognized as a class of hormones that promote growth, development, and cellular metabolism throughout the human body. More recently, studies have noted an association between reduced pancreatic weight/volume and T1D. Thus, we believe it is important to understand pancreatic regulation of IGF expression and bioavailability, as well as the impact of IGFs on pancreatic growth and islet health. Additional studies of IGFs have been extended to their influence on the inflammatory/regulatory balance of monocytes, B cells, and T cells; features which have been previously established to show dysregulation in settings of T1D. SUMMARY These data suggest that IGFs may prevent known impairments in the pancreas and immune system in T1D and underscore the need to extend these studies, some of which were performed in health or other autoimmune diseases, toward T1D specifically. Collectively, the work emphasized here support the potential therapeutic use of IGFs in T1D prevention efforts as pancreatic growth factors and/or immunoregulatory agents.
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Affiliation(s)
- Melanie R. Shapiro
- Department of Pathology, Immunology, and Laboratory Medicine, The University of Florida Diabetes Institute, Gainesville, Florida, USA
| | - Mark A. Atkinson
- Department of Pathology, Immunology, and Laboratory Medicine, The University of Florida Diabetes Institute, Gainesville, Florida, USA
- Department of Pediatrics, The University of Florida Diabetes Institute, Gainesville, Florida, USA
| | - Todd M. Brusko
- Department of Pathology, Immunology, and Laboratory Medicine, The University of Florida Diabetes Institute, Gainesville, Florida, USA
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Transcriptome analysis identifies a robust gene expression program in the mouse intestinal epithelium on aging. Sci Rep 2019; 9:10410. [PMID: 31320724 PMCID: PMC6639340 DOI: 10.1038/s41598-019-46966-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 07/03/2019] [Indexed: 12/14/2022] Open
Abstract
The intestinal epithelium undergoes constant regeneration driven by intestinal stem cells. How old age affects the transcriptome in this highly dynamic tissue is an important, but poorly explored question. Using transcriptomics on sorted intestinal stem cells and adult enterocytes, we identified candidate genes, which change expression on aging. Further validation of these on intestinal epithelium of multiple middle-aged versus old-aged mice highlighted the consistent up-regulation of the expression of the gene encoding chemokine receptor Ccr2, a mediator of inflammation and several disease processes. We observed also increased expression of Strc, coding for stereocilin, and dramatically decreased expression of Rps4l, coding for a ribosome subunit. Ccr2 and Rps4l are located close to the telomeric regions of chromosome 9 and 6, respectively. As only few genes were differentially expressed and we did not observe significant protein level changes of identified ageing markers, our analysis highlights the overall robustness of murine intestinal epithelium gene expression to old age.
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Nikopoulou C, Parekh S, Tessarz P. Ageing and sources of transcriptional heterogeneity. Biol Chem 2019; 400:867-878. [DOI: 10.1515/hsz-2018-0449] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 03/27/2019] [Indexed: 12/14/2022]
Abstract
Abstract
Cellular heterogeneity is an important contributor to biological function and is employed by cells, tissues and organisms to adapt, compensate, respond, defend and/or regulate specific processes. Research over the last decades has revealed that transcriptional noise is a major driver for cell-to-cell variability. In this review we will discuss sources of transcriptional variability, in particular bursting of gene expression and how it could contribute to cellular states and fate decisions. We will highlight recent developments in single cell sequencing technologies that make it possible to address cellular heterogeneity in unprecedented detail. Finally, we will review recent literature, in which these new technologies are harnessed to address pressing questions in the field of ageing research, such as transcriptional noise and cellular heterogeneity in the course of ageing.
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Affiliation(s)
- Chrysa Nikopoulou
- Max Planck Research Group ‘Chromatin and Ageing’ , Max Planck Institute for Biology of Ageing , Joseph-Stelzmann-Str. 9b , D-50931 Cologne , Germany
| | - Swati Parekh
- Max Planck Research Group ‘Chromatin and Ageing’ , Max Planck Institute for Biology of Ageing , Joseph-Stelzmann-Str. 9b , D-50931 Cologne , Germany
| | - Peter Tessarz
- Max Planck Research Group ‘Chromatin and Ageing’ , Max Planck Institute for Biology of Ageing , Joseph-Stelzmann-Str. 9b , D-50931 Cologne , Germany
- Cluster of Excellence in Cellular Stress Responses in Aging-Associated Diseases (CECAD) , University of Cologne , Joseph-Stelzmann-Str. 26 , D-50931 Cologne , Germany
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