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Bafor EE, Erwin-Cohen RA, Martin T, Baker C, Kimmel AE, Duverger O, Fenimore JM, Ramba M, Spindel T, Hess MM, Sanford M, Lazarevic V, Benayoun BA, Young HA, Valencia JC. Aberrant CD8 +T cells drive reproductive dysfunction in female mice with elevated IFN-γ levels. Front Immunol 2024; 15:1368572. [PMID: 38698852 PMCID: PMC11064017 DOI: 10.3389/fimmu.2024.1368572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 03/22/2024] [Indexed: 05/05/2024] Open
Abstract
Introduction Interferon-gamma (IFN-γ) is pivotal in orchestrating immune responses during healthy pregnancy. However, its dysregulation, often due to autoimmunity, infections, or chronic inflammatory conditions, is implicated in adverse reproductive outcomes such as pregnancy failure or infertility. Additionally, the underlying immunological mechanisms remain elusive. Methods Here, we explore the impact of systemic IFN-γ elevation on cytotoxic T cell responses in female reproduction utilizing a systemic lupus-prone mouse model with impaired IFN-γ degradation. Results Our findings reveal that heightened IFN-γ levels triggered the infiltration of CD8+T cells in the pituitary gland and female reproductive tract (FRT), resulting in prolactin deficiency and subsequent infertility. Furthermore, we demonstrate that chronic IFN-γ elevation increases effector memory CD8+T cells in the murine ovary and uterus. Discussion These insights broaden our understanding of the role of elevated IFN-γ in female reproductive dysfunction and suggest CD8+T cells as potential immunotherapeutic targets in female reproductive disorders associated with chronic systemic IFN-γ elevation.
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Affiliation(s)
- Enitome E. Bafor
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, United States
| | - Rebecca A. Erwin-Cohen
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, United States
| | - Toni Martin
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, United States
| | - Clayton Baker
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, United States
- Molecular and Computational Biology Department, University of Southern California, Dornsife College of Letters, Arts and Sciences, Los Angeles, CA, United States
| | - Adrienne E. Kimmel
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, United States
| | - Olivier Duverger
- Craniofacial Anomalies and Regeneration Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, United States
| | - John M. Fenimore
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, United States
| | - Meredith Ramba
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, United States
| | - Thea Spindel
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, United States
| | - Megan M. Hess
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, United States
| | - Michael Sanford
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, United States
| | - Vanja Lazarevic
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
| | - Bérénice A. Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, United States
- Molecular and Computational Biology Department, University of Southern California, Dornsife College of Letters, Arts and Sciences, Los Angeles, CA, United States
| | - Howard A. Young
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, United States
| | - Julio C. Valencia
- Cancer Innovation Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, United States
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2
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McGill CJ, Christensen A, Qian W, Thorwald MA, Lugo JG, Namvari S, White OS, Finch CE, Benayoun BA, Pike CJ. Protection against APOE4 -associated aging phenotypes with the longevity-promoting intervention 17α-estradiol in male mice. bioRxiv 2024:2024.03.12.584678. [PMID: 38559059 PMCID: PMC10980056 DOI: 10.1101/2024.03.12.584678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The apolipoprotein ε4 allele ( APOE4 ) is associated with decreased longevity, increased vulnerability to age-related declines, and disorders across multiple systems. Interventions that promote healthspan and lifespan represent a promising strategy to attenuate the development of APOE4 -associated aging phenotypes. Here we studied the ability of the longevity-promoting intervention 17α-estradiol (17αE2) to protect against age-related impairments in APOE4 versus the predominant APOE3 genotype using early middle-aged mice with knock-in of human APOE alleles. Beginning at age 10 months, male APOE3 or APOE4 mice were treated for 20 weeks with 17αE2 or vehicle then compared for indices of aging phenotypes body-wide. Across peripheral and neural measures, APOE4 was associated with poorer outcomes. Notably, 17αE2 treatment improved outcomes in a genotype-dependent manner favoring APOE4 mice. These data demonstrate a positive APOE4 bias in 17αE2-mediated healthspan actions, suggesting that longevity-promoting interventions may be useful in mitigating deleterious age-related risks associated with APOE4 genotype.
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Baker C, Benayoun BA. Menopause Is More Than Just Loss of Fertility. Public Policy Aging Rep 2023; 33:113-119. [PMID: 38155935 PMCID: PMC10751372 DOI: 10.1093/ppar/prad023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Indexed: 12/30/2023]
Affiliation(s)
- Clayton Baker
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, USA
- Molecular and Computational Biology Department, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, California, USA
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, USA
- Molecular and Computational Biology Department, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, California, USA
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McGill CJ, Ewald CY, Benayoun BA. Sex-dimorphic expression of extracellular matrix genes in mouse bone marrow neutrophils. PLoS One 2023; 18:e0294859. [PMID: 38032907 PMCID: PMC10688658 DOI: 10.1371/journal.pone.0294859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/08/2023] [Indexed: 12/02/2023] Open
Abstract
The mammalian innate immune system is sex-dimorphic. Neutrophils are the most abundant leukocyte in humans and represent innate immunity's first line of defense. We previously found that primary mouse bone marrow neutrophils show widespread sex-dimorphism throughout life, including at the transcriptional level. Extracellular matrix [ECM]-related terms were observed among the top sex-dimorphic genes. Since the ECM is emerging as an important regulator of innate immune responses, we sought to further investigate the transcriptomic profile of primary mouse bone marrow neutrophils at both the bulk and single-cell level to understand how biological sex may influence ECM component expression in neutrophils throughout life. Here, using curated gene lists of ECM components and unbiased weighted gene co-expression network analysis [WGCNA], we find that multiple ECM-related gene sets show widespread female-bias in expression in primary mouse neutrophils. Since many immune-related diseases (e.g., rheumatoid arthritis) are more prevalent in females, our work may provide insights into the pathogenesis of sex-dimorphic inflammatory diseases.
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Affiliation(s)
- Cassandra J. McGill
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, United States of America
| | - Collin Y. Ewald
- Laboratory of Extracellular Matrix Regeneration, Department of Health Sciences and Technology, Institute of Translational Medicine, Swiss Federal Institute of Technology (ETH Zürich), Schwerzenbach, Switzerland
| | - Bérénice A. Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, United States of America
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, California, United States of America
- Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, Los Angeles, California, United States of America
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, California, United States of America
- USC Stem Cell Initiative, Los Angeles, California, United States of America
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5
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Bravo JI, Mizrahi CR, Kim S, Zhang L, Suh Y, Benayoun BA. An eQTL-based Approach Reveals Candidate Regulators of LINE-1 RNA Levels in Lymphoblastoid Cells. bioRxiv 2023:2023.08.15.553416. [PMID: 37645920 PMCID: PMC10461994 DOI: 10.1101/2023.08.15.553416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Long interspersed element 1 (L1) are a family of autonomous, actively mobile transposons that occupy ~17% of the human genome. A number of pleiotropic effects induced by L1 (promoting genome instability, inflammation, or cellular senescence) have been observed, and L1's contributions to aging and aging diseases is an area of active research. However, because of the cell type-specific nature of transposon control, the catalogue of L1 regulators remains incomplete. Here, we employ an eQTL approach leveraging transcriptomic and genomic data from the GEUVADIS and 1000Genomes projects to computationally identify new candidate regulators of L1 RNA levels in lymphoblastoid cell lines. To cement the role of candidate genes in L1 regulation, we experimentally modulate the levels of top candidates in vitro, including IL16, STARD5, HSDB17B12, and RNF5, and assess changes in TE family expression by Gene Set Enrichment Analysis (GSEA). Remarkably, we observe subtle but widespread upregulation of TE family expression following IL16 and STARD5 overexpression. Moreover, a short-term 24-hour exposure to recombinant human IL16 was sufficient to transiently induce subtle, but widespread, upregulation of L1 subfamilies. Finally, we find that many L1 expression-associated genetic variants are co-associated with aging traits across genome-wide association study databases. Our results expand the catalogue of genes implicated in L1 RNA control and further suggest that L1-derived RNA contributes to aging processes. Given the ever-increasing availability of paired genomic and transcriptomic data, we anticipate this new approach to be a starting point for more comprehensive computational scans for transposon transcriptional regulators.
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Affiliation(s)
- Juan I. Bravo
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Graduate program in the Biology of Aging, University of Southern California, Los Angeles, CA 90089, USA
| | - Chanelle R. Mizrahi
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- USC Gerontology Enriching MSTEM to Enhance Diversity in Aging Program, University of Southern California, Los Angeles, CA 90089, USA
| | - Seungsoo Kim
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Lucia Zhang
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Quantitative and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089, USA
| | - Yousin Suh
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Bérénice A. Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089, USA
- Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, Los Angeles, CA 90089, USA
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089, USA
- USC Stem Cell Initiative, Los Angeles, CA 90089, USA
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Teefy BB, Lemus AJJ, Adler A, Xu A, Bhala R, Hsu K, Benayoun BA. Widespread sex dimorphism across single-cell transcriptomes of adult African turquoise killifish tissues. Cell Rep 2023; 42:113237. [PMID: 37837621 PMCID: PMC10842523 DOI: 10.1016/j.celrep.2023.113237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/18/2023] [Accepted: 09/25/2023] [Indexed: 10/16/2023] Open
Abstract
The African turquoise killifish (Nothobranchius furzeri), the shortest-lived vertebrate that can be bred in captivity, is an emerging model organism for aging research. Here, we describe a multitissue, single-cell gene expression atlas of female and male blood, kidney, liver, and spleen. We annotate 22 cell types, define marker genes, and infer differentiation trajectories. We find pervasive sex-dimorphic gene expression across cell types. Sex-dimorphic genes tend to be linked to lipid metabolism, consistent with clear differences in lipid storage in female vs. male turquoise killifish livers. We use machine learning to predict sex using single-cell gene expression and identify potential markers for molecular sex identity. As a proof of principle, we show that our atlas can be used to deconvolute existing bulk RNA sequencing (RNA-seq) data to obtain accurate estimates of cell type proportions. This atlas can be a resource to the community that could be leveraged to develop cell-type-specific expression in transgenic animals.
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Affiliation(s)
- Bryan B Teefy
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Aaron J J Lemus
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA; Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts, and Sciences, Los Angeles, CA 90089, USA
| | - Ari Adler
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Alan Xu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA; Quantitative & Computational Biology Department, USC Dornsife College of Letters, Arts, and Sciences, Los Angeles, CA 90089, USA
| | - Rajyk Bhala
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Katelyn Hsu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA; Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts, and Sciences, Los Angeles, CA 90089, USA
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA; Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts, and Sciences, Los Angeles, CA 90089, USA; Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, Los Angeles, CA 90089, USA; Epigenetics and Gene Regulation, USC Norris Comprehensive Cancer Center, Los Angeles, CA 90089, USA; USC Stem Cell Initiative, Los Angeles, CA 90089, USA.
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7
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Xu A, Teefy BB, Lu RJ, Nozownik S, Tyers AM, Valenzano DR, Benayoun BA. Transcriptomes of aging brain, heart, muscle, and spleen from female and male African turquoise killifish. Sci Data 2023; 10:695. [PMID: 37828039 PMCID: PMC10570339 DOI: 10.1038/s41597-023-02609-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 09/28/2023] [Indexed: 10/14/2023] Open
Abstract
The African turquoise killifish is an emerging vertebrate model organism with great potential for aging research due to its naturally short lifespan. Thus far, turquoise killifish aging 'omic' studies have examined a single organ, single sex and/or evaluated samples from non-reference strains. Here, we describe a resource dataset of ribosomal RNA-depleted RNA-seq libraries generated from the brain, heart, muscle, and spleen from both sexes, as well as young and old animals, in the reference GRZ turquoise killifish strain. We provide basic quality control steps and demonstrate the utility of our dataset by performing differential gene expression and gene ontology analyses by age and sex. Importantly, we show that age has a greater impact than sex on transcriptional landscapes across probed tissues. Finally, we confirm transcription of transposable elements (TEs), which are highly abundant and increase in expression with age in brain tissue. This dataset will be a useful resource for exploring gene and TE expression as a function of both age and sex in a powerful naturally short-lived vertebrate model.
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Affiliation(s)
- Alan Xu
- Quantitative & Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA, 90089, USA
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Bryan B Teefy
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Ryan J Lu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
- Graduate Program in the Biology of Aging, University of Southern California, Los Angeles, CA, USA
| | - Séverine Nozownik
- Unit of Forensic Genetics, University Center of Legal Medicine, Lausanne, Switzerland
| | - Alexandra M Tyers
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann Strasse 9b, 50931, Cologne, Germany
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Vairão, Portugal
| | - Dario R Valenzano
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann Strasse 9b, 50931, Cologne, Germany
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA.
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA, 90089, USA.
- Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, Los Angeles, CA, 90089, USA.
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA, 90089, USA.
- USC Stem Cell Initiative, Los Angeles, CA, 90089, USA.
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Singh PP, Benayoun BA. Considerations for reproducible omics in aging research. Nat Aging 2023; 3:921-930. [PMID: 37386258 PMCID: PMC10527412 DOI: 10.1038/s43587-023-00448-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 06/01/2023] [Indexed: 07/01/2023]
Abstract
Technical advancements over the past two decades have enabled the measurement of the panoply of molecules of cells and tissues including transcriptomes, epigenomes, metabolomes and proteomes at unprecedented resolution. Unbiased profiling of these molecular landscapes in the context of aging can reveal important details about mechanisms underlying age-related functional decline and age-related diseases. However, the high-throughput nature of these experiments creates unique analytical and design demands for robustness and reproducibility. In addition, 'omic' experiments are generally onerous, making it crucial to effectively design them to eliminate as many spurious sources of variation as possible as well as account for any biological or technical parameter that may influence such measures. In this Perspective, we provide general guidelines on best practices in the design and analysis of omic experiments in aging research from experimental design to data analysis and considerations for long-term reproducibility and validation of such studies.
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Affiliation(s)
- Param Priya Singh
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA.
- Bakar Aging Research Institute, University of California, San Francisco, San Francisco, CA, USA.
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA.
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA, USA.
- Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, Los Angeles, CA, USA.
- Epigenetics and Gene Regulation, USC Norris Comprehensive Cancer Center, Los Angeles, CA, USA.
- USC Stem Cell Initiative, Los Angeles, CA, USA.
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Lear BP, Thompson EAN, Rodriguez K, Arndt ZP, Khullar S, Klosa PC, Lu RJ, Morrow CS, Risgaard R, Peterson ER, Teefy BB, Bhattacharyya A, Sousa AMM, Wang D, Benayoun BA, Moore DL. Age-maintained human neurons demonstrate a developmental loss of intrinsic neurite growth ability. bioRxiv 2023:2023.05.23.541995. [PMID: 37292613 PMCID: PMC10245848 DOI: 10.1101/2023.05.23.541995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Injury to adult mammalian central nervous system (CNS) axons results in limited regeneration. Rodent studies have revealed a developmental switch in CNS axon regenerative ability, yet whether this is conserved in humans is unknown. Using human fibroblasts from 8 gestational-weeks to 72 years-old, we performed direct reprogramming to transdifferentiate fibroblasts into induced neurons (Fib-iNs), avoiding pluripotency which restores cells to an embryonic state. We found that early gestational Fib-iNs grew longer neurites than all other ages, mirroring the developmental switch in regenerative ability in rodents. RNA-sequencing and screening revealed ARID1A as a developmentally-regulated modifier of neurite growth in human neurons. These data suggest that age-specific epigenetic changes may drive the intrinsic loss of neurite growth ability in human CNS neurons during development. One-Sentence Summary: Directly-reprogrammed human neurons demonstrate a developmental decrease in neurite growth ability.
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Teefy BB, Lemus AJ, Adler A, Xu A, Bhala R, Hsu K, Benayoun BA. Widespread sex-dimorphism across single-cell transcriptomes of adult African turquoise killifish tissues. bioRxiv 2023:2023.05.05.539616. [PMID: 37214847 PMCID: PMC10197525 DOI: 10.1101/2023.05.05.539616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The African turquoise killifish (Nothobranchius furzeri), the shortest-lived vertebrate that can be bred in captivity, is an emerging model organism to study vertebrate aging. Here we describe the first multi-tissue, single-cell gene expression atlas of female and male turquoise killifish tissues comprising immune and metabolic cells from the blood, kidney, liver, and spleen. We were able to annotate 22 distinct cell types, define associated marker genes, and infer differentiation trajectories. Using this dataset, we found pervasive sex-dimorphic gene expression across cell types, especially in the liver. Sex-dimorphic genes tended to be involved in processes related to lipid metabolism, and indeed, we observed clear differences in lipid storage in female vs. male turquoise killifish livers. Importantly, we use machine-learning to predict sex using single-cell gene expression in our atlas and identify potential transcriptional markers for molecular sex identity in this species. As proof-of-principle, we show that our atlas can be used to deconvolute existing liver bulk RNA-seq data in this species to obtain accurate estimates of cell type proportions across biological conditions. We believe that this single-cell atlas can be a resource to the community that could notably be leveraged to identify cell type-specific genes for cell type-specific expression in transgenic animals.
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Affiliation(s)
- Bryan B. Teefy
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Aaron J.J. Lemus
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089, USA
| | - Ari Adler
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Alan Xu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Quantitative & Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089, USA
| | - Rajyk Bhala
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Katelyn Hsu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089, USA
| | - Bérénice A. Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089, USA
- Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, Los Angeles, CA 90089, USA
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089, USA
- USC Stem Cell Initiative, Los Angeles, CA 90089, USA
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McGill CJ, Ewald CY, Benayoun BA. Sex-dimorphic expression of extracellular matrix genes in mouse bone marrow neutrophils. bioRxiv 2023:2023.02.25.530027. [PMID: 36909511 PMCID: PMC10002647 DOI: 10.1101/2023.02.25.530027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
The mammalian innate immune system is sex-dimorphic. Neutrophils are the most abundant leukocyte in humans and represent innate immunity's first line of defense. We previously found that primary mouse bone marrow neutrophils show widespread sex-dimorphism throughout life, including at the transcriptional level. Extracellular matrix [ECM]-related terms were observed among the top sex-dimorphic genes. Since the ECM is emerging as an important regulator of innate immune responses, we sought to further investigate the transcriptomic profile of primary mouse bone marrow neutrophils at both the bulk and single-cell level to understand how biological sex may influence ECM component expression in neutrophils throughout life. Here, using curated gene lists of ECM components and unbiased weighted gene co-expression network analysis [WGCNA], we find that multiple ECM-related gene sets show widespread female-bias in expression in primary mouse neutrophils. Since many immune-related diseases (e.g., rheumatoid arthritis) are more prevalent in females, our work may provide insights into the pathogenesis of sex-dimorphic inflammatory diseases.
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Affiliation(s)
- Cassandra J McGill
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Collin Y Ewald
- Laboratory of Extracellular Matrix Regeneration, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH Zürich), Schwerzenbach, Switzerland
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089, USA
- Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, Los Angeles, CA 90089, USA
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089, USA
- USC Stem Cell Initiative, Los Angeles, CA 90089, USA
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Abstract
A recent report by Yang et al. in Cell demonstrates that faithful DNA double-strand breaks and repair cycles phenocopy many aspects of aging in mice. Whether this progeroid phenotype is caused by a loss of epigenetic information remains to be conclusively determined.
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Affiliation(s)
- Bryan B Teefy
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA; Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089, USA; Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, Los Angeles, CA 90089, USA; USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089, USA; USC Stem Cell Initiative, Los Angeles, CA 90089, USA.
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13
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Teefy B, Malone M, Benayoun BA. Differential Expression Analysis of Nothobranchius furzeri Transposable Elements from RNA-seq Data. Cold Spring Harb Protoc 2023; 2023:35-47. [PMID: 36223994 PMCID: PMC9812909 DOI: 10.1101/pdb.prot107748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Transposable elements (TEs) comprise large fractions of eukaryotic genomes, but their repetitive nature and high copy number makes bioinformatic analyses more complex. Here, we report three robust pipelines to analyze TE expression from RNA-seq data in a non-model organism, the African turquoise killifish Nothobranchius furzeri Our protocol can be run with either a genomic or transcriptomic reference depending on available computational resources, with options both for limited memory usage and for more computationally intensive analyses. Our protocol leverages both standard software for classical RNA-seq analysis pipelines as well as software specialized for TEs. This protocol uses input RNA-seq data from Illumina reads and can use data in either single-end or paired-end layout. Here, we show how to start from input RNA-seq data from aging killifish tissues using a publicly available data set from which we take single and paired reads, trim adapters, align and count trimmed reads, and perform differential expression analyses for TEs.
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Affiliation(s)
- Bryan Teefy
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California 90089, USA
| | - Matthew Malone
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California 90089, USA
- Master's program in Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California 90089, USA
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, California 90089, USA
- Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, Los Angeles, California 90089, USA
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, California 90089, USA
- USC Stem Cell Initiative, Los Angeles, California 90089, USA
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14
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Mehalko K, Kim M, Paye S, Koh K, Lu RJ, Benayoun BA. Lack of accelerated ovarian aging in a follicle-stimulating hormone receptor haploinsufficiency model. Transl Med Aging 2023; 7:1-8. [PMID: 36714222 PMCID: PMC9878709 DOI: 10.1016/j.tma.2023.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Follicle-stimulation hormone (FSH) and FSH receptor (FSHR) signaling is essential for lifelong ovarian and endocrine functions in females. Previous studies have reported that Fshr haploinsufficiency in female mice led to accelerated ovarian aging, including anticipated progressive fertility decline, irregular estrus cycles, increased follicular atresia and premature ovarian failure at 7 to 9 months of age. Interestingly, these phenotypes resemble key characteristics of human menopause and thus Fshr haploinsufficiency was proposed as a promising research mouse model of menopause. However, the Fshr haploinsufficiency model had not been fully explored, especially at the molecular level. In this study, we characterized the ovarian and endocrine functions of a Fshr heterozygous knockout allele that was generated on the C57BL/6 genetic background as part of the Knockout Mouse Project (KOMP). Based on our analyses of these mice using a breeding assay, ovarian tissue histology and serum hormone quantifications (i.e. FSH, AMH, INHA) analyses, the KOMP Fshr heterozygous knockout female mice do not show the anticipated phenotypes of ovarian aging in terms of fertility and endocrine function. We further confirmed that the expression of Fshr is unaltered in the ovaries of the KOMP Fshr heterozygous knockout animals compared to wild-type. Together, our data suggests that the KOMP Fshr heterozygous knockout strain does not recapitulate the previously reported ovarian aging phenotypes associated to another model of Fshr haploinsufficiency.
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Affiliation(s)
- Kristen Mehalko
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Minhoo Kim
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Sanjana Paye
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Kelly Koh
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Ryan J. Lu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Bérénice A. Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA.,Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089, USA.,Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, Los Angeles, CA 90089, USA.,USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089, USA.,USC Stem Cell Initiative, Los Angeles, CA 90089, USA.,Corresponding Author’s Information: Bérénice A. Benayoun, +1 (213) 821-5997,
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15
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Teefy BB, Adler A, Xu A, Hsu K, Singh PP, Benayoun BA. Dynamic regulation of gonadal transposon control across the lifespan of the naturally short-lived African turquoise killifish. Genome Res 2023; 33:141-153. [PMID: 36577520 PMCID: PMC9977155 DOI: 10.1101/gr.277301.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 12/23/2022] [Indexed: 12/30/2022]
Abstract
Although germline cells are considered to be functionally "immortal," both the germline and supporting somatic cells in the gonad within an organism experience aging. With increased age at parenthood, the age-related decline in reproductive success has become an important biological issue for an aging population. However, molecular mechanisms underlying reproductive aging across sexes in vertebrates remain poorly understood. To decipher molecular drivers of vertebrate gonadal aging across sexes, we perform longitudinal characterization of the gonadal transcriptome throughout the lifespan in the naturally short-lived African turquoise killifish (Nothobranchius furzeri). By combining mRNA-seq and small RNA-seq from 26 individuals, we characterize the aging gonads of young-adult, middle-aged, and old female and male fish. We analyze changes in transcriptional patterns of genes, transposable elements (TEs), and piRNAs. We find that testes seem to undergo only marginal changes during aging. In contrast, in middle-aged ovaries, the time point associated with peak female fertility in this strain, PIWI pathway components are transiently down-regulated, TE transcription is elevated, and piRNA levels generally decrease, suggesting that egg quality may already be declining at middle-age. Furthermore, we show that piRNA ping-pong biogenesis declines steadily with age in ovaries, whereas it is maintained in aging testes. To our knowledge, this data set represents the most comprehensive transcriptomic data set for vertebrate gonadal aging. This resource also highlights important pathways that are regulated during reproductive aging in either ovaries or testes, which could ultimately be leveraged to help restore aspects of youthful reproductive function.
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Affiliation(s)
- Bryan B Teefy
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California 90089, USA
| | - Ari Adler
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California 90089, USA
| | - Alan Xu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California 90089, USA.,Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, California 90089, USA
| | - Katelyn Hsu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California 90089, USA.,Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, California 90089, USA
| | - Param Priya Singh
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California 90089, USA.,Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, California 90089, USA.,Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, Los Angeles, California 90089, USA.,USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, California 90089, USA.,USC Stem Cell Initiative, Los Angeles, California 90089, USA
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16
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McGill CJ, Christensen A, Qian W, Benayoun BA, Pike CJ. The longevity‐promoting intervention 17α‐Estradiol protects against aging phenotypes in
APOE4
mice. Alzheimers Dement 2022. [DOI: 10.1002/alz.064816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | | | - Wenjie Qian
- University of Southern California Los Angeles CA USA
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17
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Taylor S, Isobe S, Cao A, Contrepois K, Benayoun BA, Jiang L, Wang L, Melemenidis S, Ozen MO, Otsuki S, Shinohara T, Sweatt AJ, Kaplan J, Moonen JR, Marciano DP, Gu M, Miyagawa K, Hayes B, Sierra RG, Kupitz CJ, Del Rosario PA, Hsi A, Thompson AAR, Ariza ME, Demirci U, Zamanian RT, Haddad F, Nicolls MR, Snyder MP, Rabinovitch M. Endogenous Retroviral Elements Generate Pathologic Neutrophils in Pulmonary Arterial Hypertension. Am J Respir Crit Care Med 2022; 206:1019-1034. [PMID: 35696338 PMCID: PMC9801997 DOI: 10.1164/rccm.202102-0446oc] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Rationale: The role of neutrophils and their extracellular vesicles (EVs) in the pathogenesis of pulmonary arterial hypertension is unclear. Objectives: To relate functional abnormalities in pulmonary arterial hypertension neutrophils and their EVs to mechanisms uncovered by proteomic and transcriptomic profiling. Methods: Production of elastase, release of extracellular traps, adhesion, and migration were assessed in neutrophils from patients with pulmonary arterial hypertension and control subjects. Proteomic analyses were applied to explain functional perturbations, and transcriptomic data were used to find underlying mechanisms. CD66b-specific neutrophil EVs were isolated from plasma of patients with pulmonary arterial hypertension, and we determined whether they produce pulmonary hypertension in mice. Measurements and Main Results: Neutrophils from patients with pulmonary arterial hypertension produce and release increased neutrophil elastase, associated with enhanced extracellular traps. They exhibit reduced migration and increased adhesion attributed to elevated β1-integrin and vinculin identified by proteomic analysis and previously linked to an antiviral response. This was substantiated by a transcriptomic IFN signature that we related to an increase in human endogenous retrovirus K envelope protein. Transfection of human endogenous retrovirus K envelope in a neutrophil cell line (HL-60) increases neutrophil elastase and IFN genes, whereas vinculin is increased by human endogenous retrovirus K deoxyuridine triphosphate diphosphatase that is elevated in patient plasma. Neutrophil EVs from patient plasma contain increased neutrophil elastase and human endogenous retrovirus K envelope and induce pulmonary hypertension in mice, mitigated by elafin, an elastase inhibitor. Conclusions: Elevated human endogenous retroviral elements and elastase link a neutrophil innate immune response to pulmonary arterial hypertension.
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Affiliation(s)
- Shalina Taylor
- Vera Moulton Wall Center for Pulmonary Vascular Diseases,,Stanford Cardiovascular Institute,,Department of Pediatrics – Cardiology
| | - Sarasa Isobe
- Vera Moulton Wall Center for Pulmonary Vascular Diseases,,Stanford Cardiovascular Institute,,Department of Pediatrics – Cardiology
| | - Aiqin Cao
- Vera Moulton Wall Center for Pulmonary Vascular Diseases,,Stanford Cardiovascular Institute,,Department of Pediatrics – Cardiology
| | | | - Bérénice A. Benayoun
- Leonard Davis School of Gerontology and,Department of Molecular and Computational Biology, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, California
| | - Lihua Jiang
- Stanford Cardiovascular Institute,,Department of Genetics
| | - Lingli Wang
- Vera Moulton Wall Center for Pulmonary Vascular Diseases,,Stanford Cardiovascular Institute,,Department of Pediatrics – Cardiology
| | | | - Mehmet O. Ozen
- Department of Radiology Canary Center for Cancer Early Detection
| | - Shoichiro Otsuki
- Vera Moulton Wall Center for Pulmonary Vascular Diseases,,Stanford Cardiovascular Institute,,Department of Pediatrics – Cardiology
| | - Tsutomu Shinohara
- Vera Moulton Wall Center for Pulmonary Vascular Diseases,,Stanford Cardiovascular Institute,,Department of Pediatrics – Cardiology
| | - Andrew J. Sweatt
- Vera Moulton Wall Center for Pulmonary Vascular Diseases,,Department of Medicine – Pulmonary and Critical Care Medicine, and
| | - Jordan Kaplan
- Vera Moulton Wall Center for Pulmonary Vascular Diseases,,Stanford Cardiovascular Institute,,Department of Pediatrics – Cardiology
| | - Jan-Renier Moonen
- Vera Moulton Wall Center for Pulmonary Vascular Diseases,,Stanford Cardiovascular Institute,,Department of Pediatrics – Cardiology
| | | | - Mingxia Gu
- Vera Moulton Wall Center for Pulmonary Vascular Diseases,,Stanford Cardiovascular Institute,,Department of Pediatrics – Cardiology
| | - Kazuya Miyagawa
- Vera Moulton Wall Center for Pulmonary Vascular Diseases,,Stanford Cardiovascular Institute,,Department of Pediatrics – Cardiology
| | - Brandon Hayes
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California
| | - Raymond G. Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California
| | - Christopher J. Kupitz
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California
| | - Patricia A. Del Rosario
- Vera Moulton Wall Center for Pulmonary Vascular Diseases,,Department of Medicine – Pulmonary and Critical Care Medicine, and
| | - Andrew Hsi
- Vera Moulton Wall Center for Pulmonary Vascular Diseases
| | - A. A. Roger Thompson
- Vera Moulton Wall Center for Pulmonary Vascular Diseases,,Stanford Cardiovascular Institute,,Department of Pediatrics – Cardiology,,Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, United Kingdom; and
| | - Maria E. Ariza
- Department of Cancer Biology and Genetics and,Institute for Behavioral Medicine Research, The Ohio State University Wexner Medical Center, Columbus, Ohio
| | | | - Roham T. Zamanian
- Vera Moulton Wall Center for Pulmonary Vascular Diseases,,Department of Medicine – Pulmonary and Critical Care Medicine, and
| | - Francois Haddad
- Stanford Cardiovascular Institute,,Department of Medicine – Cardiovascular Medicine, Stanford University, Stanford, California
| | - Mark R. Nicolls
- Vera Moulton Wall Center for Pulmonary Vascular Diseases,,Stanford Cardiovascular Institute,,Department of Medicine – Pulmonary and Critical Care Medicine, and
| | | | - Marlene Rabinovitch
- Vera Moulton Wall Center for Pulmonary Vascular Diseases,,Stanford Cardiovascular Institute,,Department of Pediatrics – Cardiology
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18
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Barman PK, Shin JE, Lewis SA, Kang S, Wu D, Wang Y, Yang X, Nagarkatti PS, Nagarkatti M, Messaoudi I, Benayoun BA, Goodridge HS. Production of MHCII-expressing classical monocytes increases during aging in mice and humans. Aging Cell 2022; 21:e13701. [PMID: 36040389 PMCID: PMC9577948 DOI: 10.1111/acel.13701] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/05/2022] [Indexed: 01/25/2023] Open
Abstract
Aging is associated with increased monocyte production and altered monocyte function. Classical monocytes are heterogenous and a shift in their subset composition may underlie some of their apparent functional changes during aging. We have previously shown that mouse granulocyte-monocyte progenitors (GMPs) produce "neutrophil-like" monocytes (NeuMo), whereas monocyte-dendritic cell progenitors (MDPs) produce monocyte-derived dendritic cell (moDC)-producing monocytes (DCMo). Here, we demonstrate that classical monocytes from the bone marrow of old male and female mice have higher expression of DCMo signature genes (H2-Aa, H2-Ab1, H2-Eb1, Cd74), and that more classical monocytes express MHCII and CD74 protein. Moreover, we show that bone marrow MDPs and classical monocytes from old mice yield more moDC. We also demonstrate higher expression of Aw112010 in old monocytes and that Aw112010 lncRNA activity regulates MHCII induction in macrophages, which suggests that elevated Aw112010 levels may underlie increased MHCII expression during monocyte aging. Finally, we show that classical monocyte expression of MHCII is also elevated during healthy aging in humans. Thus, aging-associated changes in monocyte production may underlie altered monocyte function and have implications for aging-associated disorders.
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Affiliation(s)
- Pijus K. Barman
- Board of Governors Regenerative Medicine InstituteCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA,Research Division of Immunology in the Department of Biomedical SciencesCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA
| | - Juliana E. Shin
- Board of Governors Regenerative Medicine InstituteCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA,Research Division of Immunology in the Department of Biomedical SciencesCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA
| | - Sloan A. Lewis
- Department of Molecular Biology and BiochemistryUniversity of CaliforniaIrvineCaliforniaUSA,Institute for ImmunologyUniversity of CaliforniaIrvineCaliforniaUSA
| | - Seokjo Kang
- Board of Governors Regenerative Medicine InstituteCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA,Research Division of Immunology in the Department of Biomedical SciencesCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA
| | - Di Wu
- Applied Genomics, Computation and Translational Core, Cedars‐Sinai CancerCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA
| | - Yizhou Wang
- Applied Genomics, Computation and Translational Core, Cedars‐Sinai CancerCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA
| | - Xiaoming Yang
- Department of Pathology, Microbiology and Immunology, School of MedicineUniversity of South CarolinaColumbiaSouth CarolinaUSA
| | - Prakash S. Nagarkatti
- Department of Pathology, Microbiology and Immunology, School of MedicineUniversity of South CarolinaColumbiaSouth CarolinaUSA
| | - Mitzi Nagarkatti
- Department of Pathology, Microbiology and Immunology, School of MedicineUniversity of South CarolinaColumbiaSouth CarolinaUSA
| | - Ilhem Messaoudi
- Department of Molecular Biology and BiochemistryUniversity of CaliforniaIrvineCaliforniaUSA,Institute for ImmunologyUniversity of CaliforniaIrvineCaliforniaUSA,Department of Microbiology, Immunology and Molecular Genetics in the College of MedicineUniversity of KentuckyLexingtonKentuckyUSA
| | - Bérénice A. Benayoun
- Leonard Davis School of GerontologyUniversity of Southern CaliforniaLos AngelesCaliforniaUSA,Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and SciencesUniversity of Southern CaliforniaLos AngelesCaliforniaUSA,Biochemistry and Molecular Medicine Department, USC Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Helen S. Goodridge
- Board of Governors Regenerative Medicine InstituteCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA,Research Division of Immunology in the Department of Biomedical SciencesCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA
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19
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Morrow CS, Arndt ZP, Klosa PC, Peng B, Zewdie EY, Benayoun BA, Moore DL. Adult fibroblasts use aggresomes only in distinct cell-states. Sci Rep 2022; 12:15001. [PMID: 36056070 PMCID: PMC9440096 DOI: 10.1038/s41598-022-19055-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 08/23/2022] [Indexed: 11/17/2022] Open
Abstract
The aggresome is a protein turnover system in which proteins are trafficked along microtubules to the centrosome for degradation. Despite extensive focus on aggresomes in immortalized cell lines, it remains unclear if the aggresome is conserved in all primary cells and all cell-states. Here we examined the aggresome in primary adult mouse dermal fibroblasts shifted into four distinct cell-states. We found that in response to proteasome inhibition, quiescent and immortalized fibroblasts formed aggresomes, whereas proliferating and senescent fibroblasts did not. Using this model, we generated a resource to provide a characterization of the proteostasis networks in which the aggresome is used and transcriptomic features associated with the presence or absence of aggresome formation. Using this resource, we validate a previously reported role for p38 MAPK signaling in aggresome formation and identify TAK1 as a novel driver of aggresome formation upstream of p38 MAPKs. Together, our data demonstrate that the aggresome is a non-universal protein degradation system which can be used cell-state specifically and provide a resource for studying aggresome formation and function.
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Affiliation(s)
| | - Zachary P Arndt
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, USA
| | - Payton C Klosa
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, USA
| | - Bo Peng
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, USA
| | - Eden Y Zewdie
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, USA
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Darcie L Moore
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, USA.
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20
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Chen Y, Kim M, Paye S, Benayoun BA. Sex as a Biological Variable in Nutrition Research: From Human Studies to Animal Models. Annu Rev Nutr 2022; 42:227-250. [PMID: 35417195 PMCID: PMC9398923 DOI: 10.1146/annurev-nutr-062220-105852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Biological sex is a fundamental source of phenotypic variability across species. Males and females have different nutritional needs and exhibit differences in nutrient digestion and utilization, leading to different health outcomes throughout life. With personalized nutrition gaining popularity in scientific research and clinical practice, it is important to understand the fundamentals of sex differences in nutrition research. Here, we review key studies that investigate sex dimorphism in nutrition research: sex differences in nutrient intake and metabolism, sex-dimorphic response in nutrient-restricted conditions, and sex differences in diet and gut microbiome interactions. Within each area above, factors from sex chromosomes, sex hormones, and sex-specific loci are highlighted.
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Affiliation(s)
- Yilin Chen
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, USA;
| | - Minhoo Kim
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, USA;
| | - Sanjana Paye
- Department of Molecular and Computational Biology, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, California, USA
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, USA;
- Department of Molecular and Computational Biology, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, California, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
- Epigenetics and Gene Regulation Program, USC Norris Comprehensive Cancer Center, Los Angeles, California, USA
- USC Stem Cell Initiative, University of Southern California, Los Angeles, California, USA
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21
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Teefy BB, Adler A, Bhala R, Benayoun BA. Gentle Isolation of Nuclei from the Brain Tissue of Adult African Turquoise Killifish, a Naturally Short-Lived Model for Aging Research. J Vis Exp 2022:10.3791/64165. [PMID: 36036603 PMCID: PMC9828740 DOI: 10.3791/64165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Studying brain aging at single-cell resolution in vertebrate systems remains challenging due to cost, time, and technical constraints. Here, we demonstrate a protocol to generate single-nucleus RNA sequencing (snRNA-seq) libraries from the brains of the naturally short-lived vertebrate African turquoise killifish Nothobranchius furzeri. The African turquoise killifish has a lifespan of 4-6 months and can be housed in a cost-effective manner, thus reducing cost and time barriers to study vertebrate brain aging. However, tailored protocols are needed to isolate nuclei of sufficient quality for downstream single-cell experiments from the brain of young and aged fish. Here, we demonstrate an empirically optimized protocol for the isolation of high-quality nuclei from the brain of adult African turquoise killifish, a critical step in the generation of high-quality single nuclei omic libraries. Furthermore, we show that the steps to reduce contaminating background RNA are important to clearly distinguish cell types. In summary, this protocol demonstrates the feasibility of studying brain aging in non-traditional vertebrate model organisms.
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Affiliation(s)
- Bryan B. Teefy
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Ari Adler
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Rajyk Bhala
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Bérénice A. Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA.,Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA, USA.,Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, Los Angeles, CA, USA.,USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA, USA.,USC Stem Cell Initiative, Los Angeles, CA, USA
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22
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Benayoun BA, Lu RJ, Kim M, McGill CJ. Sex‐dimorphism in aging: are we missing half of the picture? FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.0i135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Ryan J. Lu
- University of Southern CaliforniaLos AngelesCA
| | - Minhoo Kim
- University of Southern CaliforniaLos AngelesCA
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23
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Lu R, Wang E, Kim M, Sampatkumar NK, Benayoun BA. Aging alters murine peritoneal macrophages in a sex-dimorphic fashion. The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.164.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Aging is accompanied by general immune dysfunction, which is hypothesized to underlie the pathogenesis of many age-related diseases. In addition, there is accumulating evidence that aging is highly sex-dimorphic. However, the interactions of age and sex on the genomic and functional landscape of immune cells remain largely unexplored. To address this question, we have interrogated cells of the peritoneal cavity, an easily accessible immune niche, during aging in both sexes of C57BL/6 mice using single cell RNA-seq and flow cytometry. Interestingly, we found that macrophages were the most affected by age and sex among peritoneal immune cells, and that their frequency significantly dropped with aging. Macrophages are important for the initiating and resolving of inflammation, and dysfunction can contribute to inflammaging. Thus, we decided to further investigate the potentially sex-dimorphic impact of aging on the genomic landscape and function of peritoneal macrophages. We generated bulk RNA-seq data from purified peritoneal macrophages and identified genes modulated with aging as a function of sex. Complementing this ‘omic’ dataset, we performed an array of functional assays using purified peritoneal macrophages. We observed sex-dependent functional alterations, such as female-specific decrease in phagocytic ability. From our RNA-seq analysis, we identified potential regulators of phagocytosis that are significantly downregulated with age only in females. We are currently validating whether the potential regulators may indeed drive the observed female-specific decrease in phagocytic capabilities. Ultimately, this project will help delineate sex dimorphic mechanisms modulating immune aging.
This work was supported by a Diana Jacobs Kalman/AFAR Scholarships for Research in the Biology of Aging and NIA T32 AG052374 (to R.J.L.), GCRLE-2020 post-doctoral fellowship from the Global Consortium for Reproductive Longevity and Equality at the Buck Institute, made possible by the Bia-Echo Foundation, (to M.K.), and NIA R00 AG049934, Pew Biomedical Scholar award #00034120, an innovator grant from the Rose Hills foundation, and the Kathleen Gilmore Biology of Aging research award (to B.A.B). This work was also partially supported by NCI Cancer Center Support Grant P30 CA014089 through the use of shared resources.
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Affiliation(s)
- Ryan Lu
- 1University of Southern California
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24
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Abstract
While investigating sex-differences in T-cell aging, Mkhikian et al., identified a role for excessive IL-7 signaling and N-glycan branching in age-related mouse and human female T-cell dysfunction. These findings point to the increasingly-recognized importance of the impact of biological sex on immune aging and delineate new targetable pathways in age-related immune dysfunction.
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Affiliation(s)
- Cassandra J McGill
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
- Graduate Program in the Biology of Aging, University of Southern California, Los Angeles, CA, USA
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA.
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA, USA.
- Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, Los Angeles, CA, USA.
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA, USA.
- USC Stem Cell Initiative, Los Angeles, CA, USA.
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Abstract
Studies involving neutrophils are steadily increasing, thus creating a need for more optimized and thorough protocols for studying neutrophil function. Here, we present our protocol for extracting mouse bone marrow neutrophils, estimating the purity of isolated neutrophils, and assessing their ability to induce NETosis upon an external cue. We test two isolation protocols that can be used to attain neutrophils to assess NETosis induction. This approach allows for the parallel assessment of NETosis induction in cohorts larger than 10 samples. For complete details on the use and execution of this protocol, please refer to Lu et al., 2021.
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Affiliation(s)
- Cassandra J. McGill
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Graduate Program in the Biology of Aging, University of Southern California, Los Angeles, CA 90089, USA
| | - Ryan J. Lu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Graduate Program in the Biology of Aging, University of Southern California, Los Angeles, CA 90089, USA
| | - Bérénice A. Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089, USA
- Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, Los Angeles, CA 90089, USA
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089, USA
- USC Stem Cell Initiative, Los Angeles, CA 90089, USA
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26
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Qian W, Christensen A, Lu R, Finch CE, Benayoun BA, Pike CJ. 17alpha‐estradiol improves systemic and neural outcomes in middle‐aged APOE4 mice. Alzheimers Dement 2021. [DOI: 10.1002/alz.054279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Wenjie Qian
- University of Southern California Los Angeles CA USA
| | | | - Ryan Lu
- University of Southern California Los Angeles CA USA
| | - Caleb E Finch
- USC Leonard Davis School of Gerontology Los Angeles CA USA
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27
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Guerrero GA, Derisbourg MJ, Mayr FA, Wester LE, Giorda M, Dinort JE, Hartman MD, Schilling K, Alonso-De Gennaro MJ, Lu RJ, Benayoun BA, Denzel MS. NHR-8 and P-glycoproteins uncouple xenobiotic resistance from longevity in chemosensory C. elegans mutants. eLife 2021; 10:53174. [PMID: 34448454 PMCID: PMC8460253 DOI: 10.7554/elife.53174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 08/25/2021] [Indexed: 12/18/2022] Open
Abstract
Longevity is often associated with stress resistance, but whether they are causally linked is incompletely understood. Here we investigate chemosensory-defective Caenorhabditis elegans mutants that are long-lived and stress resistant. We find that mutants in the intraflagellar transport protein gene osm-3 were significantly protected from tunicamycin-induced ER stress. While osm-3 lifespan extension is dependent on the key longevity factor DAF-16/FOXO, tunicamycin resistance was not. osm-3 mutants are protected from bacterial pathogens, which is pmk-1 p38 MAP kinase dependent, while TM resistance was pmk-1 independent. Expression of P-glycoprotein (PGP) xenobiotic detoxification genes was elevated in osm-3 mutants and their knockdown or inhibition with verapamil suppressed tunicamycin resistance. The nuclear hormone receptor nhr-8 was necessary to regulate a subset of PGPs. We thus identify a cell-nonautonomous regulation of xenobiotic detoxification and show that separate pathways are engaged to mediate longevity, pathogen resistance, and xenobiotic detoxification in osm-3 mutants.
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Affiliation(s)
| | | | - Felix Amc Mayr
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Laura E Wester
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Marco Giorda
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - J Eike Dinort
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | | | - Klara Schilling
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | | | - Ryan J Lu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, Los Angeles, United States
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, Los Angeles, United States
| | - Martin S Denzel
- Max Planck Institute for Biology of Ageing, Cologne, Germany.,CECAD - Cluster of Excellence University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
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28
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Lu RJ, Taylor S, Contrepois K, Kim M, Bravo JI, Ellenberger M, Sampathkumar NK, Benayoun BA. Multi-omic profiling of primary mouse neutrophils predicts a pattern of sex and age-related functional regulation. Nat Aging 2021; 1:715-733. [PMID: 34514433 PMCID: PMC8425468 DOI: 10.1038/s43587-021-00086-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 06/10/2021] [Indexed: 12/18/2022]
Abstract
Neutrophils are the most abundant human white blood cell and constitute a first line of defense in the innate immune response. Neutrophils are short-lived cells, and thus the impact of organismal aging on neutrophil biology, especially as a function of biological sex, remains poorly understood. Here, we describe a multi-omic resource of mouse primary bone marrow neutrophils from young and old female and male mice, at the transcriptomic, metabolomic and lipidomic levels. We identify widespread regulation of neutrophil 'omics' landscapes with organismal aging and biological sex. In addition, we leverage our resource to predict functional differences, including changes in neutrophil responses to activation signals. To date, this dataset represents the largest multi-omics resource for neutrophils across sex and ages. This resource identifies neutrophil characteristics which could be targeted to improve immune responses as a function of sex and/or age.
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Affiliation(s)
- Ryan J. Lu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Graduate program in the Biology of Aging, University of Southern California, Los Angeles, CA 90089, USA
| | - Shalina Taylor
- Departments of Pediatrics and of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kévin Contrepois
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Minhoo Kim
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Juan I. Bravo
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Graduate program in the Biology of Aging, University of Southern California, Los Angeles, CA 90089, USA
| | | | - Nirmal K. Sampathkumar
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Present Address: UK-Dementia Research Institute, Institute of Psychiatry, Psychology and Neuroscience, Basic and Clinical Neuroscience Institute, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, UK
| | - Bérénice A. Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089, USA
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089
- USC Stem Cell Initiative, Los Angeles, CA 90089, USA
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29
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Abstract
Researchers need in vitro models that mirror the biology of organisms. Primary fibroblasts play essential roles in wound healing and are present in many tissues. They are widely used in studies of cell cycle control, reprogramming, and aging. Though extraction protocols exist, alternatives that maximize use of available resources are useful. Here, we present our protocol for extracting primary fibroblasts from adult mouse ear pinnae, an often-discarded source of primary cells, which consistently yield large, pure numbers of primary fibroblasts. Primary fibroblasts are isolated from adult mouse ear pinnae, an often-unused tissue Fibroblasts can be isolated from mice of varying sex, age, and genotype Fibroblast cultures are highly pure, with >90% THY1.2 or PDGFRα staining
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Affiliation(s)
- Juan I. Bravo
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Graduate Program in the Biology of Aging, University of Southern California, Los Angeles, CA 90089, USA
- Corresponding author
| | - Minhoo Kim
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Bérénice A. Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Neuroscience Graduate Program, University of Southern California, Los Angeles, CA 90089, USA
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089, USA
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089, USA
- USC Stem Cell Initiative, Los Angeles, CA 90089, USA
- Corresponding author
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30
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Lu RJ, Wang EK, Benayoun BA. Functional genomics of inflamm-aging and immunosenescence. Brief Funct Genomics 2021; 21:43-55. [PMID: 33690792 DOI: 10.1093/bfgp/elab009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 01/26/2021] [Accepted: 01/29/2021] [Indexed: 02/07/2023] Open
Abstract
The aging population is at a higher risk for age-related diseases and infections. This observation could be due to immunosenescence: the decline in immune efficacy of both the innate and the adaptive immune systems. Age-related immune decline also links to the concept of 'inflamm-aging,' whereby aging is accompanied by sterile chronic inflammation. Along with a decline in immune function, aging is accompanied by a widespread of 'omics' remodeling. Transcriptional landscape changes linked to key pathways of immune function have been identified across studies, such as macrophages having decreased expression of genes associated to phagocytosis, a major function of macrophages. Therefore, a key mechanism underlying innate immune cell dysfunction during aging may stem from dysregulation of youthful genomic networks. In this review, we discuss both molecular and cellular phenotypes of innate immune cells that contribute to age-related inflammation.
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Affiliation(s)
- Ryan J Lu
- Leonard Davis School of Gerontology at the University of Southern California
| | - Emily K Wang
- Leonard Davis School of Gerontology at the University of Southern California
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology at the University of Southern California
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31
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Fritsch C, Gout JF, Haroon S, Towheed A, Chung C, LaGosh J, McGann E, Zhang X, Song Y, Simpson S, Danthi PS, Benayoun BA, Wallace D, Thomas K, Lynch M, Vermulst M. Genome-wide surveillance of transcription errors in response to genotoxic stress. Proc Natl Acad Sci U S A 2021; 118:e2004077118. [PMID: 33443141 PMCID: PMC7817157 DOI: 10.1073/pnas.2004077118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mutagenic compounds are a potent source of human disease. By inducing genetic instability, they can accelerate the evolution of human cancers or lead to the development of genetically inherited diseases. Here, we show that in addition to genetic mutations, mutagens are also a powerful source of transcription errors. These errors arise in dividing and nondividing cells alike, affect every class of transcripts inside cells, and, in certain cases, greatly exceed the number of mutations that arise in the genome. In addition, we reveal the kinetics of transcription errors in response to mutagen exposure and find that DNA repair is required to mitigate transcriptional mutagenesis after exposure. Together, these observations have far-reaching consequences for our understanding of mutagenesis in human aging and disease, and suggest that the impact of DNA damage on human physiology has been greatly underestimated.
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Affiliation(s)
- C Fritsch
- Department of Cellular and Molecular Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - J-F Gout
- School of Life Sciences, Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762
| | - S Haroon
- Department of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - A Towheed
- Touro College of Osteopathic Medicine, Middletown, NY 10940
| | - C Chung
- School of Gerontology, University of Southern California, Los Angeles, CA 90089
| | - J LaGosh
- School of Gerontology, University of Southern California, Los Angeles, CA 90089
| | - E McGann
- School of Gerontology, University of Southern California, Los Angeles, CA 90089
| | - X Zhang
- Bioinforx, Inc., Madison, WI 53719
| | - Y Song
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, University of Pennsylvania, Philadelphia, PA 19104
| | - S Simpson
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824
| | - P S Danthi
- School of Gerontology, University of Southern California, Los Angeles, CA 90089
| | - B A Benayoun
- School of Gerontology, University of Southern California, Los Angeles, CA 90089
| | - D Wallace
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, University of Pennsylvania, Philadelphia, PA 19104
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - K Thomas
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824
| | - M Lynch
- School of Life Sciences, Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85287;
| | - M Vermulst
- School of Gerontology, University of Southern California, Los Angeles, CA 90089;
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104
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32
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Kim M, Benayoun BA. A multiomic atlas for the exploration of healthy aging in human monocytes. Nat Aging 2021; 1:19-21. [PMID: 37117994 DOI: 10.1038/s43587-020-00007-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Affiliation(s)
- Minhoo Kim
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA.
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA, USA.
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA, USA.
- USC Stem Cell Initiative, Los Angeles, CA, USA.
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33
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Kim M, Benayoun BA. The microbiome: an emerging key player in aging and longevity. Transl Med Aging 2020; 4:103-116. [PMID: 32832742 PMCID: PMC7437988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023] Open
Abstract
Revolutionary advancements of high-throughput sequencing and metagenomic tools have provided new insights to microbiome function, including a bidirectional relationship between the microbiome and host aging. The intestinal tract is the largest surface in the human body that directly interacts with foreign antigens - it is covered with extremely complex and diverse community of microorganisms, known as the gut microbiome. In a healthy gut, microbial communities maintain a homeostatic metabolism and reside within the host in a state of immune tolerance. Abnormal shifts in the gut microbiome, however, have been implicated in the pathogenesis of age-related chronic diseases, including obesity, cardiovascular diseases and neurodegenerative diseases. The gut microbiome is emerging as a key factor in the aging process. In this review, we describe studies of humans and model organisms that suggest a direct causal role of the gut microbiome on host aging. Additionally, we also discuss sex-dimorphism in the gut microbiome and its possible roles in age-related sex-dimorphic phenotypes. We also provide an overview of widely used microbiome analysis methods and tools which could be used to explore the impact of microbiome remodeling on aging.
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Affiliation(s)
- Minhoo Kim
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Bérénice A. Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089, USA
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089, USA
- USC Stem Cell Initiative, Los Angeles, CA 90089, USA
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34
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Abstract
Our understanding of the molecular regulation of aging and age-related diseases is still in its infancy, requiring in-depth characterization of the molecular landscape shaping these complex phenotypes. Emerging classes of molecules with promise as aging modulators include transposable elements, circRNAs and the mitochondrial transcriptome. Analytical complexity means that these molecules are often overlooked, even though they exhibit strong associations with aging and, in some cases, may directly contribute to its progress. Here, we review the links between these novel factors and age-related phenotypes, and we suggest tools that can be easily incorporated into existing pipelines to better understand the aging process.
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Affiliation(s)
- Juan I Bravo
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Graduate Program in the Biology of Aging, University of Southern California, Los Angeles, CA 90089, USA
| | - Séverine Nozownik
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Magistère européen de Génétique, Université Paris Diderot-Paris 7, Paris 75014, France
| | - Prakroothi S Danthi
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Neuroscience Graduate Program, University of Southern California, Los Angeles, CA 90089, USA
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089, USA
- USC Stem Cell Initiative, Los Angeles, CA 90089, USA
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35
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Lu R, Brown SB, Sampathkumar NK, Shen C, Chae J, Benayoun BA. Extensive sex-dimorphism in age-related transcriptional remodeling in mouse peritoneal macrophages. The Journal of Immunology 2020. [DOI: 10.4049/jimmunol.204.supp.226.22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Chronic low-level inflammation is one of the hallmarks of aging. In addition, age-related diseases share common inflammatory mechanisms, a phenomenon named “inflamm-aging”. To date, the effect of age and sex on the genomic landscape of macrophages is largely unexplored, especially regarding sex-dimorphic trajectories in aging macrophages. Based on accumulating evidence indicating aging is highly sex-dimorphic, we hypothesize that aging will affect the phenotype of immune cells, such as macrophages, in a sex-dimorphic manner. To test our hypothesis, we used female and male C57BL/6N mice aged 4 and 20 months to investigate resident peritoneal macrophages. We generated RNA-seq data from purified peritoneal macrophages and identified genes modulated with aging as a function of sex. Complementing this ‘omic’ dataset, we performed an array of functional assays for these cells in several cohorts of aging mice, including immunophenotyping, metabolic profiling, lysosomal acidification tracking, phagocytic efficiency, etc. We observed sex-dependent functional decline, such as a male-specific decrease in macrophage ability to acidify lysosomes upon exposure to Zymosan. Interestingly, aspects of age-related functional changes may be mediated by age-related changes in circulating sex hormones. We are currently analyzing our single cell RNA-seq datasets from peritoneal lavages of naïve aging female and male mice, and generating complementary datasets that are profiling chromatin-level changes to identify putative drivers of age-related transcriptional and functional remodeling in macrophages. Ultimately, this project will help delineate sex dimorphic mechanisms modulating “inflamm-aging”.
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Affiliation(s)
- Ryan Lu
- 1Leonard Davis School of Gerontology, University of Southern California
| | - Shelby B Brown
- 1Leonard Davis School of Gerontology, University of Southern California
| | | | - Courtney Shen
- 1Leonard Davis School of Gerontology, University of Southern California
| | - Jisoo Chae
- 1Leonard Davis School of Gerontology, University of Southern California
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36
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Benayoun BA, Lu R, Sampathkumar NK. Sex-dimorphic trajectories in aging macrophage populations. The Journal of Immunology 2020. [DOI: 10.4049/jimmunol.204.supp.152.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
The existence of human supercentenarians reveals a surprising predictor for exceptional longevity: being female. Not only are 33 out of 34 living supercentenarians women, women are also more resistant to most diseases responsible for age-related morbidity in the US. However, because most molecular aging studies generally opt to use only one sex, sex-driven differences in aging remain poorly understood. A key compartment that can actively respond to sex-specific inputs throughout life is the immune system. Indeed, the majority of age-related diseases share common inflammatory mechanisms, a phenomenon described as “inflamm-aging”. Macrophages play an important role in the inflammatory response throughout life, and are considered major mediators of this phenomenon. Thus, to unbiasedly dissect sex differences in immune aging, we generated ‘omics’ data from 4 and 20 months old female and male mice. Intriguingly, we found that transcriptional aging in primary macrophage populations varies strongly between sexes, with up to 20-fold more aging changes in female vs. male cells. Pathways specifically downregulated in females with aging included lysosome, inflammation and phagolysosome. We confirmed experimentally that metabolic preferences of macrophages are indeed directly modulated in this context (e.g. glycolytic preference for male-derived cells). Our results support the notion that there are functional differences in aging trajectories in the immune system of female vs. male mice. Our research could provide new insights into the molecular underpinnings of sex-dimorphism in aging and disease.
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Affiliation(s)
| | - Ryan Lu
- 1Leonard Davis School of Gerontology, University of Southern California
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37
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Benayoun BA, Veitia RA. Special issue on "Molecular genetics of aging and longevity": a critical time in the field of geroscience. Hum Genet 2020; 139:275-276. [PMID: 32052140 DOI: 10.1007/s00439-020-02125-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA.
- Molecular and Computational Biology Department, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA, 90089, USA.
- USC Stem Cell Initiative, Los Angeles, CA, 90089, USA.
| | - Reiner A Veitia
- Institut Jacques Monod, CNRS UMR7592, Université de Paris, Paris, France.
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38
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Sampathkumar NK, Bravo JI, Chen Y, Danthi PS, Donahue EK, Lai RW, Lu R, Randall LT, Vinson N, Benayoun BA. Widespread sex dimorphism in aging and age-related diseases. Hum Genet 2020; 139:333-356. [PMID: 31677133 PMCID: PMC7031050 DOI: 10.1007/s00439-019-02082-w] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 10/26/2019] [Indexed: 02/07/2023]
Abstract
Although aging is a conserved phenomenon across evolutionary distant species, aspects of the aging process have been found to differ between males and females of the same species. Indeed, observations across mammalian studies have revealed the existence of longevity and health disparities between sexes, including in humans (i.e. with a female or male advantage). However, the underlying mechanisms for these sex differences in health and lifespan remain poorly understood, and it is unclear which aspects of this dimorphism stem from hormonal differences (i.e. predominance of estrogens vs. androgens) or from karyotypic differences (i.e. XX vs. XY sex chromosome complement). In this review, we discuss the state of the knowledge in terms of sex dimorphism in various aspects of aging and in human age-related diseases. Where the interplay between sex differences and age-related differences has not been explored fully, we present the state of the field to highlight important future research directions. We also discuss various dietary, drug or genetic interventions that were shown to improve longevity in a sex-dimorphic fashion. Finally, emerging tools and models that can be leveraged to decipher the mechanisms underlying sex differences in aging are also briefly discussed.
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Affiliation(s)
- Nirmal K Sampathkumar
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
- Maurice Wohl Clinical Neuroscience Institute, King's College London, London, UK
| | - Juan I Bravo
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
- Graduate Program in the Biology of Aging, University of Southern California, Los Angeles, CA, 90089, USA
| | - Yilin Chen
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
- Masters Program in Nutrition, Healthspan, and Longevity, University of Southern California, Los Angeles, CA, 90089, USA
| | - Prakroothi S Danthi
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Erin K Donahue
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
- Neuroscience Graduate Program, University of Southern California, Los Angeles, CA, 90089, USA
| | - Rochelle W Lai
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Ryan Lu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
- Graduate Program in the Biology of Aging, University of Southern California, Los Angeles, CA, 90089, USA
| | - Lewis T Randall
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
- Graduate Program in the Biology of Aging, University of Southern California, Los Angeles, CA, 90089, USA
| | - Nika Vinson
- Department of Urology, Pelvic Medicine and Reconstructive Surgery, UCLA David Geffen School of Medicine, Los Angeles, CA, 90024, USA
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA.
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA, 90089, USA.
- USC Stem Cell Initiative, Los Angeles, CA, 90089, USA.
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39
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Abstract
In multi-cellular organisms, the control of gene expression is key not only for development, but also for adult cellular homeostasis, and deregulation of gene expression correlates with aging. A key layer in the study of gene regulation mechanisms lies at the level of chromatin: cellular chromatin states (i.e. the 'epigenome') can tune transcriptional profiles, and, in line with the prevalence of transcriptional alterations with aging, accumulating evidence suggests that the chromatin landscape is altered with aging across cell types and species. However, although alterations in the chromatin make-up of cells are considered to be a hallmark of aging, little is known of the genomic loci that are specifically affected by age-related chromatin state remodeling and of their biological significance. Here, we report the analysis of genome-wide profiles of core histone H3 occupancy in aging male mouse tissues (i.e. heart, liver, cerebellum and olfactory bulb) and primary cultures of neural stem cells. We find that, although no drastic changes in H3 levels are observed, local changes in H3 occupancy occur with aging across tissues and cells with both regions of increased or decreased occupancy. These changes are compatible with a general increase in chromatin accessibility at pro-inflammatory genes and may thus mechanistically underlie known shift in gene expression programs during aging.
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Affiliation(s)
- Yilin Chen
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA.,Master of Science in Nutrition, Healthspan, and Longevity, University of Southern California, Los Angeles, CA 90089, USA
| | - Juan I Bravo
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA.,Graduate program in the Biology of Aging, University of Southern California, Los Angeles, CA 90089, USA
| | - Jyung Mean Son
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Changhan Lee
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA.,USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089, USA.,Biomedical Sciences, Graduate School, Ajou University, Suwon 16499, Republic of Korea
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA.,USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089, USA.,USC Stem Cell Initiative, Los Angeles, CA 90089, USA
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Abstract
The majority of age-related diseases share common inflammatory mechanisms, a phenomenon which has been described as "inflamm-aging," and genetic variants in immune and inflammatory genes are significantly associated with exceptional human longevity and/or age-related diseases. Consistently, aging is associated with increased macrophage infiltration into tissues. Macrophages are a key component of the innate immune system and the inflammatory response, which accomplish key tasks such as phagocytosis, antigen presentation, and cytokine production. Phagocytosis is the process by which specialized cells that can clear harmful foreign particles, pathogens, and dead or dying cells. Upon phagocytosis, foreign particles are internalized in vesicles, forming phagosomes. Phagosomes go on to fuse with lysosomes, and the ingested particles are neutralized by lysosomal enzymes. Macrophages have two main origins: tissue-resident macrophages differentiate from specific embryonic progenitors, whereas monocyte-derived macrophages differentiate from bone-marrow progenitors. Because of their key role in inflammation and damage repair, macrophages are a key cell type in age-related inflammatory diseases. Here, we describe an efficient method to quantify the phagocytotic ability of two types of primary macrophages in aging mice: bone marrow-derived macrophages (BMDMs) and tissue-resident peritoneal macrophages.
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Affiliation(s)
- Ryan Lu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA.,Graduate Program in the Biology of Aging, University of Southern California, Los Angeles, CA, USA
| | - Nirmal K Sampathkumar
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA. .,USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA, USA. .,USC Stem Cell Initiative, Los Angeles, CA, USA.
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Benayoun BA, Lu RA, Sampathkumar NK. SEX-DIMORPHISM IN THE GENOMIC REGULATION OF AGING. Innov Aging 2019. [PMCID: PMC6846027 DOI: 10.1093/geroni/igz038.2825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
The current cohort of human supercentenarians reveals a surprising predictor for achieving such an exceptional longevity: being female. Indeed, out of 34 living supercentenarians, 33 are women. We obtained samples from 4 and 20 months old female and male mice. Our data indicates that cytokine levels are differentially regulated with age in males vs. females, with pro-inflammatory cytokines specifically upregulated in the serum of old males, but not females. Because of the central role of macrophages in inflammation and their infiltration in tissues with age, we have generated RNA-seq from purified macrophages of aging animals. Female macrophages displayed ~7-20-fold more transcriptional remodeling with aging than males. Pathways specifically downregulated in females with aging included lysosome, inflammation and phagolysosome. Consistently, our data shows that aged female, but not male macrophages, display decreased phagocytic efficiency. Our results support the notion that there are differences in aging trajectories in female vs. male mice.
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Affiliation(s)
- Bérénice A Benayoun
- University of Southern California, Leonard Davis School of Gerontology, Los Angeles, California, United States
| | - Ryan A Lu
- University of Southern California, Los Angeles, California, United States
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43
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Affiliation(s)
- Bérénice A Benayoun
- University of Southern California, Leonard Davis School of Gerontology, Los Angeles, California, United States
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44
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Navar E, Benayoun BA, Sampathkumar N, Chae J. INVESTIGATING THE ROLE OF AHR IN MEDIATING SEX DIFFERENCES OF AGING MACROPHAGES. Innov Aging 2019. [PMCID: PMC6846351 DOI: 10.1093/geroni/igz038.3080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
“Inflamm-aging” describes a state of chronic low-grade inflammation which occurs with age in the absence of infection. This process is related to many chronic age-related diseases. Aryl hydrocarbon receptor (Ahr), is a transcription factor that is thought to decrease inflammation, and decrease of Ahr with aging only in females was previously observed in a macrophage RNA-seq with aging. Based on this, I hypothesized that 1) Ahr expression will decrease with age in female cells; and 2) phagocytic activity and Ahr expression in macrophages will increase when exposed to estrogens (E2). To test these hypotheses, Ahr signaling was quantified by RT-qPCR in aging male and female mice BMDMs, and in macrophages that were treated with E2. I also performed a phagocytosis assay on macrophages treated with E2. I found a significant downregulation of Ahr in old female BMDMs. Ahrr (Ahr Repressor) was significantly downregulated in both old female and males with aging. Arnt (Ahr Nuclear Translocator) did not significantly change with aging. The qPCR performed on the E2 treated cells showed no significant trend for Ahr regulation. Finally, the phagocytosis assay revealed an overall increase in phagocytosis activity in cells treated with estrogen. Our hypotheses were supported by data showing a decrease in Ahr expression with age and increase in phagocytosis activity in estrogen treated cells. The RT-qPCR results for the E2 treated cells did not support our hypothesis, but could stem from a relatively short exposure time for estrogen.
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Affiliation(s)
- Evelyn Navar
- University of California at Davis, Davis, California, United States
| | - Bérénice A Benayoun
- University of Southern California, Leonard Davis School of Gerontology, Los Angeles, California, United States
| | - Nirmal Sampathkumar
- University of Southern California, Leonard Davis School of Gerontology, Los Angeles, California, United States
| | - Jisoo Chae
- University of Southern California, Leonard Davis School of Gerontology, Los Angeles, California, United States
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45
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Affiliation(s)
- Bérénice A. Benayoun
- Leonard Davis School of GerontologyUniversity of Southern California Los Angeles CA 90089 USA
- USC Norris Comprehensive Cancer CenterEpigenetics and Gene Regulation Program Los Angeles CA 90089 USA
- USC Stem Cell Initiative Los Angeles CA 90089 USA
| | - Changhan Lee
- Leonard Davis School of GerontologyUniversity of Southern California Los Angeles CA 90089 USA
- USC Norris Comprehensive Cancer CenterEpigenetics and Gene Regulation Program Los Angeles CA 90089 USA
- Biomedical Sciences, Graduate SchoolAjou University Suwon 16499 Republic of Korea
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Abstract
Mitochondria are increasingly being recognized as information hubs that sense cellular changes and transmit messages to other cellular components, such as the nucleus, the endoplasmic reticulum (ER), the Golgi apparatus, and lysosomes. Nonetheless, the interaction between mitochondria and the nucleus is of special interest because they both host part of the cellular genome. Thus, the communication between genome-bearing organelles would likely include gene expression regulation. Multiple nuclear-encoded proteins have been known to regulate mitochondrial gene expression. On the contrary, no mitochondrial-encoded factors are known to actively regulate nuclear gene expression. MOTS-c (mitochondrial open reading frame of the 12S ribosomal RNA type-c) is a recently identified peptide encoded within the mitochondrial 12S ribosomal RNA gene that has metabolic functions. Notably, MOTS-c can translocate to the nucleus upon metabolic stress (e.g., glucose restriction and oxidative stress) and directly regulate adaptive nuclear gene expression to promote cellular homeostasis. It is hypothesized that cellular fitness requires the coevolved mitonuclear genomes to coordinate adaptive responses using gene-encoded factors that cross-regulate the opposite genome. This suggests that cellular gene expression requires the bipartite split genomes to operate as a unified system, rather than the nucleus being the sole master regulator.
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Affiliation(s)
- Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation Program, Los Angeles, CA, 90089, USA
- USC Stem Cell Initiative, Los Angeles, CA, 90089, USA
| | - Changhan Lee
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation Program, Los Angeles, CA, 90089, USA
- Biomedical Sciences, Graduate School, Ajou University, Suwon, 16499, Republic of Korea
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47
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Abstract
In multi-cellular organisms, the control of gene expression is key not only for development, but also for adult cellular homeostasis, and gene expression has been observed to be deregulated with aging. In this review, we discuss the current knowledge on the transcriptional alterations that have been described to occur with age in metazoans. First, we discuss age-related transcriptional changes in protein-coding genes, the expected functional impact of such changes, and how known pro-longevity interventions impact these changes. Second, we discuss the changes and impact of emerging aspects of transcription in aging, including age-related changes in splicing, lncRNAs and circRNAs. Third, we discuss the changes and potential impact of transcription of transposable elements with aging. Fourth, we highlight small ncRNAs and their potential impact on the regulation of aging phenotypes. Understanding the aging transcriptome will be key to identify important regulatory targets, and ultimately slow-down or reverse aging and extend healthy lifespan in humans.
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Affiliation(s)
- Rochelle W Lai
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Ryan Lu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Prakroothi S Danthi
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Juan I Bravo
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089; Graduate program in the Biology of Aging, University of Southern California, Los Angeles, CA 90089, USA
| | - Alexandre Goumba
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | | | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089; USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089; USC Stem Cell Initiative, Los Angeles, CA 90089, USA
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Benayoun BA, Pollina EA, Singh PP, Mahmoudi S, Harel I, Casey KM, Dulken BW, Kundaje A, Brunet A. Remodeling of epigenome and transcriptome landscapes with aging in mice reveals widespread induction of inflammatory responses. Genome Res 2019; 29:697-709. [PMID: 30858345 PMCID: PMC6442391 DOI: 10.1101/gr.240093.118] [Citation(s) in RCA: 167] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 01/25/2019] [Indexed: 12/20/2022]
Abstract
Aging is accompanied by the functional decline of tissues. However, a systematic study of epigenomic and transcriptomic changes across tissues during aging is missing. Here, we generated chromatin maps and transcriptomes from four tissues and one cell type from young, middle-aged, and old mice—yielding 143 high-quality data sets. We focused on chromatin marks linked to gene expression regulation and cell identity: histone H3 trimethylation at lysine 4 (H3K4me3), a mark enriched at promoters, and histone H3 acetylation at lysine 27 (H3K27ac), a mark enriched at active enhancers. Epigenomic and transcriptomic landscapes could easily distinguish between ages, and machine-learning analysis showed that specific epigenomic states could predict transcriptional changes during aging. Analysis of data sets from all tissues identified recurrent age-related chromatin and transcriptional changes in key processes, including the up-regulation of immune system response pathways such as the interferon response. The up-regulation of the interferon response pathway with age was accompanied by increased transcription and chromatin remodeling at specific endogenous retroviral sequences. Pathways misregulated during mouse aging across tissues, notably innate immune pathways, were also misregulated with aging in other vertebrate species—African turquoise killifish, rat, and humans—indicating common signatures of age across species. To date, our data set represents the largest multitissue epigenomic and transcriptomic data set for vertebrate aging. This resource identifies chromatin and transcriptional states that are characteristic of young tissues, which could be leveraged to restore aspects of youthful functionality to old tissues.
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Affiliation(s)
- Bérénice A Benayoun
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Elizabeth A Pollina
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Param Priya Singh
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Salah Mahmoudi
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Itamar Harel
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Kerriann M Casey
- Department of Comparative Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Ben W Dulken
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA.,Department of Computer Science, Stanford University, Stanford, California 94305, USA
| | - Anne Brunet
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA.,Paul F. Glenn Laboratories for the Biology of Aging, Stanford University, Stanford, California 94305, USA
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Kim KH, Son JM, Benayoun BA, Lee C. The Mitochondrial-Encoded Peptide MOTS-c Translocates to the Nucleus to Regulate Nuclear Gene Expression in Response to Metabolic Stress. Cell Metab 2018; 28:516-524.e7. [PMID: 29983246 PMCID: PMC6185997 DOI: 10.1016/j.cmet.2018.06.008] [Citation(s) in RCA: 166] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 04/07/2018] [Accepted: 06/13/2018] [Indexed: 01/09/2023]
Abstract
Cellular homeostasis is coordinated through communication between mitochondria and the nucleus, organelles that each possess their own genomes. Whereas the mitochondrial genome is regulated by factors encoded in the nucleus, the nuclear genome is currently not known to be actively controlled by factors encoded in the mitochondrial DNA. Here, we show that MOTS-c, a peptide encoded in the mitochondrial genome, translocates to the nucleus and regulates nuclear gene expression following metabolic stress in a 5'-adenosine monophosphate-activated protein kinase (AMPK)-dependent manner. In the nucleus, MOTS-c regulated a broad range of genes in response to glucose restriction, including those with antioxidant response elements (ARE), and interacted with ARE-regulating stress-responsive transcription factors, such as nuclear factor erythroid 2-related factor 2 (NFE2L2/NRF2). Our findings indicate that the mitochondrial and nuclear genomes co-evolved to independently encode for factors to cross-regulate each other, suggesting that mitonuclear communication is genetically integrated.
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Affiliation(s)
- Kyung Hwa Kim
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Jyung Mean Son
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA; USC Norris Comprehensive Cancer Center, Los Angeles, CA 90089, USA; USC Stem Cell Initiative, Los Angeles, CA 90089, USA
| | - Changhan Lee
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA; USC Norris Comprehensive Cancer Center, Los Angeles, CA 90089, USA; Biomedical Sciences, Graduate School, Ajou University, Suwon 16499, Republic of Korea.
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50
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Contrepois K, Coudereau C, Benayoun BA, Schuler N, Roux PF, Bischof O, Courbeyrette R, Carvalho C, Thuret JY, Ma Z, Derbois C, Nevers MC, Volland H, Redon CE, Bonner WM, Deleuze JF, Wiel C, Bernard D, Snyder MP, Rübe CE, Olaso R, Fenaille F, Mann C. Histone variant H2A.J accumulates in senescent cells and promotes inflammatory gene expression. Nat Commun 2017; 8:14995. [PMID: 28489069 PMCID: PMC5436145 DOI: 10.1038/ncomms14995] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 02/20/2017] [Indexed: 01/02/2023] Open
Abstract
The senescence of mammalian cells is characterized by a proliferative arrest in response to stress and the expression of an inflammatory phenotype. Here we show that histone H2A.J, a poorly studied H2A variant found only in mammals, accumulates in human fibroblasts in senescence with persistent DNA damage. H2A.J also accumulates in mice with aging in a tissue-specific manner and in human skin. Knock-down of H2A.J inhibits the expression of inflammatory genes that contribute to the senescent-associated secretory phenotype (SASP), and over expression of H2A.J increases the expression of some of these genes in proliferating cells. H2A.J accumulation may thus promote the signalling of senescent cells to the immune system, and it may contribute to chronic inflammation and the development of aging-associated diseases.
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Affiliation(s)
- Kévin Contrepois
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
- Department of Genetics, Stanford University, Stanford, California 94305-5120, USA
| | - Clément Coudereau
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Bérénice A. Benayoun
- Department of Genetics, Stanford University, Stanford, California 94305-5120, USA
- Paul F. Glenn Laboratories for the Biology of Aging, Stanford University, Stanford, California 94305-5120, USA
| | - Nadine Schuler
- Department of Radiation Oncology, Saarland University, 66421 Homburg (Saar), Germany
| | - Pierre-François Roux
- Institut Pasteur/INSERM U933, Laboratory of Nuclear Organization and Oncogenesis, Department of Cell Biology and Infection, 75015 Paris, France
| | - Oliver Bischof
- Institut Pasteur/INSERM U933, Laboratory of Nuclear Organization and Oncogenesis, Department of Cell Biology and Infection, 75015 Paris, France
| | - Régis Courbeyrette
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Cyril Carvalho
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Jean-Yves Thuret
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Zhihai Ma
- Department of Genetics, Stanford University, Stanford, California 94305-5120, USA
| | | | - Marie-Claire Nevers
- CEA, Service de Pharmacologie et Immunoanalyse (SPI), INRA, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - Hervé Volland
- CEA, Service de Pharmacologie et Immunoanalyse (SPI), INRA, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - Christophe E. Redon
- Laboratory of Molecular Pharmacology, C.C.R., N.C.I., N.I.H., Bethesda, Maryland 20892, USA
| | - William M. Bonner
- Laboratory of Molecular Pharmacology, C.C.R., N.C.I., N.I.H., Bethesda, Maryland 20892, USA
| | | | - Clotilde Wiel
- Inserm U1052, Centre de Recherche en Cancérologie de Lyon, CNRS UMR5286, Centre Léon Bérard, Université de Lyon 69008, Lyon, France
| | - David Bernard
- Inserm U1052, Centre de Recherche en Cancérologie de Lyon, CNRS UMR5286, Centre Léon Bérard, Université de Lyon 69008, Lyon, France
| | - Michael P. Snyder
- Department of Genetics, Stanford University, Stanford, California 94305-5120, USA
| | - Claudia E. Rübe
- Department of Radiation Oncology, Saarland University, 66421 Homburg (Saar), Germany
| | | | - François Fenaille
- CEA, IBITECS, Service de Pharmacologie et d'Immunoanalyse, UMR 0496, Laboratoire d'Etude du Métabolisme des Médicaments, MetaboHUB-Paris, Université Paris Saclay, F-91191 Gif-sur-Yvette cedex, France
| | - Carl Mann
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
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