1
|
Low E, Smith LA, Miwa S, Fielder E, Przyborski S, von Zglinicki T. Senescent Dermal Fibroblasts Decrease Stemness in Basal Keratinocytes in a Bioengineered Model of Human Full-Thickness Skin. J Invest Dermatol 2024:S0022-202X(24)01916-X. [PMID: 39047968 DOI: 10.1016/j.jid.2024.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 07/01/2024] [Accepted: 07/03/2024] [Indexed: 07/27/2024]
Affiliation(s)
- Evon Low
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lucy A Smith
- Department of Biosciences, Durham University, Durham, United Kingdom
| | - Satomi Miwa
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Edward Fielder
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Stefan Przyborski
- Department of Biosciences, Durham University, Durham, United Kingdom; Reprocell Europe Limited, Thomson Pavilion, Glasgow, United Kingdom.
| | - Thomas von Zglinicki
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom.
| |
Collapse
|
2
|
Howes AM, Dea NC, Ghosh D, Krishna K, Wang Y, Li Y, Morrison B, Toussaint KC, Dawson MR. Fibroblast senescence-associated extracellular matrix promotes heterogeneous lung niche. APL Bioeng 2024; 8:026119. [PMID: 38855444 PMCID: PMC11161856 DOI: 10.1063/5.0204393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 05/24/2024] [Indexed: 06/11/2024] Open
Abstract
Senescent cell accumulation in the pulmonary niche is associated with heightened susceptibility to age-related disease, tissue alterations, and ultimately a decline in lung function. Our current knowledge of senescent cell-extracellular matrix (ECM) dynamics is limited, and our understanding of how senescent cells influence spatial ECM architecture changes over time is incomplete. Herein is the design of an in vitro model of senescence-associated extracellular matrix (SA-ECM) remodeling using a senescent lung fibroblast-derived matrix that captures the spatiotemporal dynamics of an evolving senescent ECM architecture. Multiphoton second-harmonic generation microscopy was utilized to examine the spatial and temporal dynamics of fibroblast SA-ECM remodeling, which revealed a biphasic process that established a disordered and heterogeneous architecture. Additionally, we observed that inhibition of transforming growth factor-β signaling during SA-ECM remodeling led to improved local collagen fiber organization. Finally, we examined patient samples diagnosed with pulmonary fibrosis to further tie our results of the in vitro model to clinical outcomes. Moreover, we observed that the senescence marker p16 is correlated with local collagen fiber disorder. By elucidating the temporal dynamics of SA-ECM remodeling, we provide further insight on the role of senescent cells and their contributions to pathological ECM remodeling.
Collapse
Affiliation(s)
| | - Nova C. Dea
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 029012, USA
| | - Deepraj Ghosh
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 029012, USA
| | - Krishangi Krishna
- School of Engineering, Brown University, Providence, Rhode Island 02912, USA
| | - Yihong Wang
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island 02912, USA
| | - Yanxi Li
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 029012, USA
| | - Braxton Morrison
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 029012, USA
| | - Kimani C. Toussaint
- School of Engineering, Brown University, Providence, Rhode Island 02912, USA
| | - Michelle R. Dawson
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 029012, USA
| |
Collapse
|
3
|
Matveeva D, Kashirina D, Ezdakova M, Larina I, Buravkova L, Ratushnyy A. Senescence-Associated Alterations in Matrisome of Mesenchymal Stem Cells. Int J Mol Sci 2024; 25:5332. [PMID: 38791371 PMCID: PMC11120844 DOI: 10.3390/ijms25105332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/26/2024] [Accepted: 04/30/2024] [Indexed: 05/26/2024] Open
Abstract
The process of aging is intimately linked to alterations at the tissue and cellular levels. Currently, the role of senescent cells in the tissue microenvironment is still being investigated. Despite common characteristics, different cell populations undergo distinctive morphofunctional changes during senescence. Mesenchymal stem cells (MSCs) play a pivotal role in maintaining tissue homeostasis. A multitude of studies have examined alterations in the cytokine profile that determine their regulatory function. The extracellular matrix (ECM) of MSCs is a less studied aspect of their biology. It has been shown to modulate the activity of neighboring cells. Therefore, investigating age-related changes in the MSC matrisome is crucial for understanding the mechanisms of tissue niche ageing. This study conducted a broad proteomic analysis of the matrisome of separated fractions of senescent MSCs, including the ECM, conditioned medium (CM), and cell lysate. This is the first time such an analysis has been conducted. It has been established that there is a shift in production towards regulatory molecules and a significant downregulation of the main structural and adhesion proteins of the ECM, particularly collagens, fibulins, and fibrilins. Additionally, a decrease in the levels of cathepsins, galectins, S100 proteins, and other proteins with cytoprotective, anti-inflammatory, and antifibrotic properties has been observed. However, the level of inflammatory proteins and regulators of profibrotic pathways increases. Additionally, there is an upregulation of proteins that can directly cause prosenescent effects on microenvironmental cells (SERPINE1, THBS1, and GDF15). These changes confirm that senescent MSCs can have a negative impact on other cells in the tissue niche, not only through cytokine signals but also through the remodeled ECM.
Collapse
Affiliation(s)
| | | | | | | | | | - Andrey Ratushnyy
- Institute of Biomedical Problems, Russian Academy of Sciences, Khoroshevskoye Shosse, 76a, 123007 Moscow, Russia; (D.M.); (D.K.); (M.E.); (I.L.); (L.B.)
| |
Collapse
|
4
|
Brown JC, McMichael BD, Vandadi V, Mukherjee A, Salzler HR, Matera AG. Lysine-36 of Drosophila histone H3.3 supports adult longevity. G3 (BETHESDA, MD.) 2024; 14:jkae030. [PMID: 38366796 PMCID: PMC10989886 DOI: 10.1093/g3journal/jkae030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 01/16/2023] [Accepted: 02/04/2024] [Indexed: 02/18/2024]
Abstract
Aging is a multifactorial process that disturbs homeostasis, increases disease susceptibility, and ultimately results in death. Although the definitive set of molecular mechanisms responsible for aging remain to be discovered, epigenetic change over time is proving to be a promising piece of the puzzle. Several post-translational histone modifications have been linked to the maintenance of longevity. Here, we focus on lysine-36 of the replication-independent histone protein, H3.3 (H3.3K36). To interrogate the role of this residue in Drosophila developmental gene regulation, we generated a lysine-to-arginine mutant that blocks the activity of its cognate-modifying enzymes. We found that an H3.3BK36R mutation causes a significant reduction in adult lifespan, accompanied by dysregulation of the genomic and transcriptomic architecture. Transgenic co-expression of wild-type H3.3B completely rescues the longevity defect. Because H3.3 is known to accumulate in nondividing tissues, we carried out transcriptome profiling of young vs aged adult fly heads. The data show that loss of H3.3K36 results in age-dependent misexpression of NF-κB and other innate immune target genes, as well as defects in silencing of heterochromatin. We propose H3.3K36 maintains the postmitotic epigenomic landscape, supporting longevity by regulating both pericentric and telomeric retrotransposons and by suppressing aberrant immune signaling.
Collapse
Affiliation(s)
- John C Brown
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Benjamin D McMichael
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Vasudha Vandadi
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Aadit Mukherjee
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Harmony R Salzler
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA
| | - A Gregory Matera
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
- RNA Discovery Center, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| |
Collapse
|
5
|
Nyström A. The intertwined aging, the extracellular matrix, and fibrosis. Am J Physiol Cell Physiol 2024; 326:C645-C646. [PMID: 38223933 DOI: 10.1152/ajpcell.00018.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 01/11/2024] [Accepted: 01/11/2024] [Indexed: 01/16/2024]
Affiliation(s)
- Alexander Nyström
- Department of Dermatology, Medical Faculty, Medical Center - University of Freiburg, Freiburg, Germany
| |
Collapse
|
6
|
Brown JC, McMichael BD, Vandadi V, Mukherjee A, Salzler HR, Matera AG. Lysine-36 of Drosophila histone H3.3 supports adult longevity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.28.559962. [PMID: 38196611 PMCID: PMC10775331 DOI: 10.1101/2023.09.28.559962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Aging is a multifactorial process that disturbs homeostasis, increases disease susceptibility, and ultimately results in death. Although the definitive set of molecular mechanisms responsible for aging remain to be discovered, epigenetic change over time is proving to be a promising piece of the puzzle. Several posttranslational histone modifications (PTMs) have been linked to the maintenance of longevity. Here, we focus on lysine-36 of the replication-independent histone protein, H3.3 (H3.3K36). To interrogate the role of this residue in Drosophila developmental gene regulation, we generated a lysine to arginine mutant that blocks the activity of its cognate modifying enzymes. We found that an H3.3BK36R mutation causes a significant reduction in adult lifespan, accompanied by dysregulation of the genomic and transcriptomic architecture. Transgenic co-expression of wild-type H3.3B completely rescues the longevity defect. Because H3.3 is known to accumulate in non-dividing tissues, we carried out transcriptome profiling of young vs aged adult fly heads. The data show that loss of H3.3K36 results in age-dependent misexpression of NF-κB and other innate immune target genes, as well as defects in silencing of heterochromatin. We propose H3.3K36 maintains the postmitotic epigenomic landscape, supporting longevity by regulating both pericentric and telomeric retrotransposons and by suppressing aberrant immune signaling.
Collapse
Affiliation(s)
- John C. Brown
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Benjamin D. McMichael
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Vasudha Vandadi
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Aadit Mukherjee
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Harmony R. Salzler
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - A. Gregory Matera
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- RNA Discovery Center, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| |
Collapse
|
7
|
Qu Y, Ji Z. A tissue ubiquitous gene set for cellular senescence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.21.568150. [PMID: 38045252 PMCID: PMC10690237 DOI: 10.1101/2023.11.21.568150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
An accurate gene set for cellular senescence is crucial for identifying and studying senescent cells in single-cell RNA-seq datasets. We integrated nine existing senescence gene sets and identified a core senescence gene set comprising four genes: CDKN1A, CDKN2A, IL6, and CDKN2B. We found that these genes are ubiquitously associated with cellular senescence across human and mouse tissues. Using this gene set, we identified cell types enriched with senescent cells and cell-cell communication targets and pathways associated with cellular senescence in human and mouse single-cell datasets.
Collapse
Affiliation(s)
- Yilong Qu
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - Zhicheng Ji
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| |
Collapse
|
8
|
Nyström A, Schaefer L. An American Journal of Physiology-Cell Physiology for the present and the future. Am J Physiol Cell Physiol 2023; 325:C1155-C1157. [PMID: 37746699 DOI: 10.1152/ajpcell.00455.2023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 09/20/2023] [Accepted: 09/20/2023] [Indexed: 09/26/2023]
Affiliation(s)
- Alexander Nyström
- Department of Dermatology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Liliana Schaefer
- Institute of Pharmacology and Toxicology, Goethe University, Frankfurt, Germany
| |
Collapse
|