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Gao Q, Ji Z, Wang L, Owzar K, Li QJ, Chan C, Xie J. SifiNet: a robust and accurate method to identify feature gene sets and annotate cells. Nucleic Acids Res 2024; 52:e46. [PMID: 38647069 PMCID: PMC11109959 DOI: 10.1093/nar/gkae307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 03/25/2024] [Accepted: 04/14/2024] [Indexed: 04/25/2024] Open
Abstract
SifiNet is a robust and accurate computational pipeline for identifying distinct gene sets, extracting and annotating cellular subpopulations, and elucidating intrinsic relationships among these subpopulations. Uniquely, SifiNet bypasses the cell clustering stage, commonly integrated into other cellular annotation pipelines, thereby circumventing potential inaccuracies in clustering that may compromise subsequent analyses. Consequently, SifiNet has demonstrated superior performance in multiple experimental datasets compared with other state-of-the-art methods. SifiNet can analyze both single-cell RNA and ATAC sequencing data, thereby rendering comprehensive multi-omic cellular profiles. It is conveniently available as an open-source R package.
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Affiliation(s)
- Qi Gao
- Department of Biostatistics and Bioinformatics, Duke University, USA
| | - Zhicheng Ji
- Department of Biostatistics and Bioinformatics, Duke University, USA
| | - Liuyang Wang
- Department of Molecular Genetics and Microbiology, Duke University, USA
| | - Kouros Owzar
- Department of Biostatistics and Bioinformatics, Duke University, USA
| | - Qi-Jing Li
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore
| | - Cliburn Chan
- Department of Biostatistics and Bioinformatics, Duke University, USA
| | - Jichun Xie
- Department of Biostatistics and Bioinformatics, Duke University, USA
- Department of Mathematics, Duke University, USA
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Abu-Romman A, Scholand KK, Govindarajan G, Yu Z, Pal-Ghosh S, Stepp MA, de Paiva CS. Age-Related Differences in the Mouse Corneal Epithelial Transcriptome and Their Impact on Corneal Wound Healing. Invest Ophthalmol Vis Sci 2024; 65:21. [PMID: 38739085 PMCID: PMC11098051 DOI: 10.1167/iovs.65.5.21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 04/24/2024] [Indexed: 05/14/2024] Open
Abstract
Purpose Aging is a risk factor for dry eye. We sought to identify changes in the aged mouse corneal epithelial transcriptome and determine how age affects corneal sensitivity, re-epithelialization, and barrier reformation after corneal debridement. Methods Corneal epithelium of female C57BL/6J (B6) mice of different ages (2, 12, 18, and 24 months) was collected, RNA extracted, and bulk RNA sequencing performed. Cornea sensitivity was measured with an esthesiometer in 2- to 3-month-old, 12- to 13-month-old, 18- to 19-month-old, and 22- to 25-month-old female and male mice. The 2-month-old and 18-month-old female and male mice underwent unilateral corneal debridement using a blunt blade. Wound size and fluorescein staining were visualized and photographed at different time points, and a re-epithelialization rate curve was calculated. Results There were 157 differentially expressed genes in aged mice compared with young mice. Several pathways downregulated with age control cell migration, proteoglycan synthesis, and collagen trimerization, assembly, biosynthesis, and degradation. Male mice had decreased corneal sensitivity compared with female mice at 12 and 24 months of age. Aged mice, irrespective of sex, had delayed corneal re-epithelialization in the first 48 hours and worse corneal fluorescein staining intensity at day 14 than young mice. Conclusions Aged corneal epithelium has an altered transcriptome. Aged mice regardless of sex heal more slowly and displayed more signs of corneal epithelial defects after wounding than young mice. These results indicate that aging significantly alters the corneal epithelium and its ability to coordinate healing.
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Affiliation(s)
- Anmar Abu-Romman
- Ocular Surface Center, Cullen Eye Institute, Department of Ophthalmology, Baylor College of Medicine, Houston, Texas, United States
| | - Kaitlin K. Scholand
- Ocular Surface Center, Cullen Eye Institute, Department of Ophthalmology, Baylor College of Medicine, Houston, Texas, United States
- Department of Biosciences, Rice University, Houston, Texas, United States
| | - Gowthaman Govindarajan
- Ocular Surface Center, Cullen Eye Institute, Department of Ophthalmology, Baylor College of Medicine, Houston, Texas, United States
| | - Zhiyuan Yu
- Ocular Surface Center, Cullen Eye Institute, Department of Ophthalmology, Baylor College of Medicine, Houston, Texas, United States
| | - Sonali Pal-Ghosh
- Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, Washington, DC, United States
| | - Mary A. Stepp
- Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, Washington, DC, United States
- Department of Ophthalmology, The George Washington University School of Medicine and Health Sciences, Washington, DC, United States
| | - Cintia S. de Paiva
- Ocular Surface Center, Cullen Eye Institute, Department of Ophthalmology, Baylor College of Medicine, Houston, Texas, United States
- Department of Biosciences, Rice University, Houston, Texas, United States
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Gao Q, Ji Z, Wang L, Owzar K, Li QJ, Chan C, Xie J. SifiNet: A robust and accurate method to identify feature gene sets and annotate cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.24.541352. [PMID: 37577619 PMCID: PMC10418061 DOI: 10.1101/2023.05.24.541352] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
SifiNet is a robust and accurate computational pipeline for identifying distinct gene sets, extracting and annotating cellular subpopulations, and elucidating intrinsic relationships among these subpopulations. Uniquely, SifiNet bypasses the cell clustering stage, commonly integrated into other cellular annotation pipelines, thereby circumventing potential inaccuracies in clustering that may compromise subsequent analyses. Consequently, SifiNet has demonstrated superior performance in multiple experimental datasets compared with other state-of-the-art methods. SifiNet can analyze both single-cell RNA and ATAC sequencing data, thereby rendering comprehensive multiomic cellular profiles. It is conveniently available as an open-source R package.
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Outskouni Z, Christodoulou C, Goutas A, Kyriazis ID, Paraskevopoulou A, Laliotis GP, Matsakidou A, Gogas A, Trachana V. Cryptomphalus aspersa Egg Extract Protects against Human Stem Cell Stress-Induced Premature Senescence. Int J Mol Sci 2024; 25:3715. [PMID: 38612526 PMCID: PMC11011511 DOI: 10.3390/ijms25073715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 03/23/2024] [Accepted: 03/25/2024] [Indexed: 04/14/2024] Open
Abstract
Cellular senescence is a tightly regulated pathophysiologic process and is caused by replicative exhaustion or external stressors. Since naturally derived bioactive compounds with anti-ageing properties have recently captured scientific interest, we analysed the anti-ageing and antioxidant efficacy of Cryptomphalus aspersa egg extract (CAEE). Its effects on stemness, wound-healing properties, antioxidant defense mechanisms, and DNA damage repair ability of Human Wharton's jelly mesenchymal stem cells (WJ-MSCs) were analysed. Our results revealed that CAEE fortifies WJ-MSCs stemness, which possibly ameliorates their wound-healing ability. Additionally, we show that CAEE possesses a strong antioxidant capacity as demonstrated by the elevation of the levels of the basic antioxidant molecule, GSH, and the induction of the NRF2, a major antioxidant regulator. In addition, CAEE alleviated cells' oxidative stress and therefore prevented stress-induced premature senescence (SIPS). Furthermore, we demonstrated that the prevention of SIPS could be mediated via the extract's ability to induce autophagy, as indicated by the elevation of the protein levels of all basic autophagic molecules and the increase in formation of autophagolysosomes in CAEE-treated WJ-MSCs. Moreover, CAEE-treated cells exhibited decreased Caveolin-1 levels. We propose that Cryptomphalus aspersa egg extract comprises bioactive compounds that can demonstrate strong antioxidant/anti-ageing effects by regulating the Caveolin-1-autophagy-senescence molecular axis.
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Affiliation(s)
- Zozo Outskouni
- Department of Biology, Faculty of Medicine, University of Thessaly, 41500 Larisa, Greece; (Z.O.); (C.C.); (A.G.); (I.D.K.)
| | - Christina Christodoulou
- Department of Biology, Faculty of Medicine, University of Thessaly, 41500 Larisa, Greece; (Z.O.); (C.C.); (A.G.); (I.D.K.)
| | - Andreas Goutas
- Department of Biology, Faculty of Medicine, University of Thessaly, 41500 Larisa, Greece; (Z.O.); (C.C.); (A.G.); (I.D.K.)
- Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Ioannis D. Kyriazis
- Department of Biology, Faculty of Medicine, University of Thessaly, 41500 Larisa, Greece; (Z.O.); (C.C.); (A.G.); (I.D.K.)
| | - Adamantini Paraskevopoulou
- Laboratory of Food Chemistry & Technology, School of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (A.P.); (A.M.)
| | - George P. Laliotis
- Laboratory of Animal Breeding and Husbandry, Department of Animal Science, Agricultural University of Athens, 75 Iera Odos, 11855 Athens, Greece;
| | - Anthia Matsakidou
- Laboratory of Food Chemistry & Technology, School of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (A.P.); (A.M.)
| | | | - Varvara Trachana
- Department of Biology, Faculty of Medicine, University of Thessaly, 41500 Larisa, Greece; (Z.O.); (C.C.); (A.G.); (I.D.K.)
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Dvir-Ginzberg M, Maatuf YH, Mobasheri A. Do we understand sex-related differences governing dimorphic disease mechanisms in preclinical animal models of osteoarthritis? Osteoarthritis Cartilage 2024:S1063-4584(24)01127-0. [PMID: 38531464 DOI: 10.1016/j.joca.2024.03.113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/20/2024] [Accepted: 03/20/2024] [Indexed: 03/28/2024]
Abstract
Research conducted using murine preclinical models of osteoarthritis (OA) over the last three decades has brought forth many exciting developments showcasing mechanisms and pathways that drive disease pathogenesis. These models have identified therapeutic targets that can be modulated via innovative biologicals and pharmaceuticals. However, many of these approaches have failed to translate to humans and reach the clinic. This commentary aims to highlight some of the key hurdles in the translation of novel findings using preclinical OA models with a focus on sex-related differences and variations in chondrosenescence in these animal models. Notably, besides chondrosenescence, other signaling mechanisms have been shown to be affected by sexual dimorphism (i.e. TGFβ signaling, EGFR/integrin α1β1 and Trpv4). Preclinical models of OA mainly utilize male mice due to their capacity to manifest fast progressing OA structural phenotype compared to female mice. This experimental trend has overlooked and ignored the sex-related effects of numerous mechanisms affecting joint structure, that influence OA structural progression. Future work should focus on analyzing both sexes and understanding sex-related differences, which will enable us to gain a better understanding of the progression of OA based on sex-related mechanistic discrepancies, and potentially improve translatability.
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Affiliation(s)
- Mona Dvir-Ginzberg
- Laboratory of Cartilage Biology, Institute of BioMedical and Oral Research, Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Yonathan H Maatuf
- Laboratory of Cartilage Biology, Institute of BioMedical and Oral Research, Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ali Mobasheri
- Research Unit of Health Sciences and Technology, Faculty of Medicine, University of Oulu, Oulu, Finland; Department of Regenerative Medicine, State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania; Department of Joint Surgery, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China; World Health Organization Collaborating Center for Public Health Aspects of Musculoskeletal Health and Aging, Université de Liège, Liège, Belgium
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Huang Y, Lei L, Zhu J, Zheng J, Li Z, Wang H, Wang J, Zheng Z. Pain behavior and phenotype in a modified anterior lumbar disc puncture mouse model. JOR Spine 2024; 7:e1284. [PMID: 38249720 PMCID: PMC10797215 DOI: 10.1002/jsp2.1284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 09/03/2023] [Accepted: 09/06/2023] [Indexed: 01/23/2024] Open
Abstract
Background An experimental study was performed to improve the anterior approach model of intervertebral disc degeneration (IVDD). Objective The aims of this study were to investigate the anterior approach model of IVDD for the cause of death, phenotypes, and underlying mechanisms of low back pain in mice. Method In this study, we conducted an anterior puncture procedure on a cohort of 300 C57BL/6J mice that were 8 weeks old. Our investigation focused on exploring the causes of death in the study population (n = 300) and assessing the time-course changes in various parameters, including radiographical, histological, immunofluorescence, and immunohistochemistry analyses (n = 10). Additionally, we conducted behavioral assessments on a subset of the animals (n = 30). Results Transverse vertebral artery rupture is a major factor in surgical death. Radiographical analyses showed that the hydration of the nucleus pulposus began to decrease at 2 weeks after puncture and obviously disappeared over 4 weeks. 3D-CT showed that disc height was significantly decreased at 4 weeks. Osteophyte at the anterior vertebral rims was observed at 2 weeks after the puncture. As the time course increased, histological analyses showed progressive disruption of the destruction of the extracellular matrix and increased secretion of inflammatory cytokines and apoptosis. Behavioral signs of low back pain were increased between the puncture and sham groups at 4 weeks. Conclusion The improvement of anterior intervertebral disc approach model in mice will be useful to investigate underlying mechanisms and potential therapeutic strategies for behavior and phenotypes. Furthermore, the application of vibrational pre-treatment can be used to increase the sensitivity of axial back pain in the model, thereby providing researchers with a reliable method for measuring this critical phenotype.
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Affiliation(s)
- Yuming Huang
- Department of Spine SurgeryThe First Affiliated Hospital of Sun Yat‐sen UniversityGuangzhouChina
- Sun Yan Sen UniversityPain Research CenterGuangzhouChina
- Guangdong Province Key Laboratory of Orthopaedics and TraumatologyGuangzhouChina
| | - Linchuan Lei
- Department of Spine SurgeryThe First Affiliated Hospital of Sun Yat‐sen UniversityGuangzhouChina
- Sun Yan Sen UniversityPain Research CenterGuangzhouChina
- Laboratory of General Surgery, The First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Jian Zhu
- Department of Spine SurgeryThe First Affiliated Hospital of Sun Yat‐sen UniversityGuangzhouChina
- Sun Yan Sen UniversityPain Research CenterGuangzhouChina
- Guangdong Province Key Laboratory of Orthopaedics and TraumatologyGuangzhouChina
| | - Jinjian Zheng
- Department of Spine SurgeryThe First Affiliated Hospital of Sun Yat‐sen UniversityGuangzhouChina
- Sun Yan Sen UniversityPain Research CenterGuangzhouChina
- Guangdong Province Key Laboratory of Orthopaedics and TraumatologyGuangzhouChina
| | - Zemin Li
- Department of Spine SurgeryThe First Affiliated Hospital of Sun Yat‐sen UniversityGuangzhouChina
- Sun Yan Sen UniversityPain Research CenterGuangzhouChina
- Guangdong Province Key Laboratory of Orthopaedics and TraumatologyGuangzhouChina
| | - Hua Wang
- Department of Spine SurgeryThe First Affiliated Hospital of Sun Yat‐sen UniversityGuangzhouChina
- Sun Yan Sen UniversityPain Research CenterGuangzhouChina
- Guangdong Province Key Laboratory of Orthopaedics and TraumatologyGuangzhouChina
| | - Jianru Wang
- Department of Spine SurgeryThe First Affiliated Hospital of Sun Yat‐sen UniversityGuangzhouChina
- Sun Yan Sen UniversityPain Research CenterGuangzhouChina
| | - Zhaomin Zheng
- Department of Spine SurgeryThe First Affiliated Hospital of Sun Yat‐sen UniversityGuangzhouChina
- Sun Yan Sen UniversityPain Research CenterGuangzhouChina
- Guangdong Province Key Laboratory of Orthopaedics and TraumatologyGuangzhouChina
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Budamagunta V, Kumar A, Rani A, Manohar Sindhu S, Yang Y, Zhou D, Foster TC. Senolytic treatment alleviates doxorubicin-induced chemobrain. Aging Cell 2024; 23:e14037. [PMID: 38225896 PMCID: PMC10861213 DOI: 10.1111/acel.14037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/21/2023] [Accepted: 10/23/2023] [Indexed: 01/17/2024] Open
Abstract
Doxorubicin (Dox), a widely used treatment for cancer, can result in chemotherapy-induced cognitive impairments (chemobrain). Chemobrain is associated with inflammation and oxidative stress similar to aging. As such, Dox treatment has also been used as a model of aging. However, it is unclear if Dox induces brain changes similar to that observed during aging since Dox does not readily enter the brain. Rather, the mechanism for chemobrain likely involves the induction of peripheral cellular senescence and the release of senescence-associated secretory phenotype (SASP) factors and these SASP factors can enter the brain to disrupt cognition. We examined the effect of Dox on peripheral and brain markers of aging and cognition. In addition, we employed the senolytic, ABT-263, which also has limited access to the brain. The results indicate that plasma SASP factors enter the brain, activating microglia, increasing oxidative stress, and altering gene transcription. In turn, the synaptic function required for memory was reduced in response to altered redox signaling. ABT-263 prevented or limited most of the Dox-induced effects. The results emphasize a link between cognitive decline and the release of SASP factors from peripheral senescent cells and indicate some differences as well as similarities between advanced age and Dox treatment.
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Affiliation(s)
- Vivekananda Budamagunta
- Department of Neuroscience, McKnight Brain InstituteUniversity of FloridaGainesvilleFloridaUSA
- Genetics and Genomics Graduate Program, Genetics InstituteUniversity of FloridaGainesvilleFloridaUSA
- Department of Pharmacodynamics, College of PharmacyUniversity of FloridaGainesvilleFloridaUSA
| | - Ashok Kumar
- Department of Neuroscience, McKnight Brain InstituteUniversity of FloridaGainesvilleFloridaUSA
| | - Asha Rani
- Department of Neuroscience, McKnight Brain InstituteUniversity of FloridaGainesvilleFloridaUSA
| | - Sahana Manohar Sindhu
- Genetics and Genomics Graduate Program, Genetics InstituteUniversity of FloridaGainesvilleFloridaUSA
| | - Yang Yang
- Department of Pharmacodynamics, College of PharmacyUniversity of FloridaGainesvilleFloridaUSA
| | - Daohong Zhou
- Department of Pharmacodynamics, College of PharmacyUniversity of FloridaGainesvilleFloridaUSA
- Department of Biochemistry and Structural BiologyUniversity of Texas Health Science Center at San AntonioSan AntonioTexasUSA
| | - Thomas C. Foster
- Department of Neuroscience, McKnight Brain InstituteUniversity of FloridaGainesvilleFloridaUSA
- Genetics and Genomics Graduate Program, Genetics InstituteUniversity of FloridaGainesvilleFloridaUSA
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Demby T, Gross PS, Mandelblatt J, Huang JK, Rebeck GW. The chemotherapeutic agent doxorubicin induces brain senescence, with modulation by APOE genotype. Exp Neurol 2024; 371:114609. [PMID: 37944881 DOI: 10.1016/j.expneurol.2023.114609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/18/2023] [Accepted: 11/06/2023] [Indexed: 11/12/2023]
Abstract
Many cancer patients experience serious cognitive problems related to their treatment, which can greatly affect their quality of life. The molecular mechanisms of this cancer chemotherapy-induced cognitive impairment (CICI) are unknown, thus slowing the development of preventative approaches. We hypothesized that cancer chemotherapies could induce cellular senescence in the brain, creating a pro-inflammatory environment and damaging normal brain communication. We tested this hypothesis using the common chemotherapeutic agent doxorubicin in two independent mouse models. In the first model, we used mice that express tdTomato under the pdkn2a (p16) promoter; p16 is a regulator of cellular senescence, and its upregulation is denoted by the presence of fluorescently tagged cells. Two weeks after exposure to three doses of 5 mg/kg doxorubicin, the number of tdTomato positive cells were increased nearly three-fold in both the cerebral cortex and the hippocampus. tdTomato staining co-localized with neurons, microglia, oligodendrocyte precursor cells, and endothelial cells, but not astrocytes. In the second model, we used APOE knock-in mice, since the APOE4 allele is a risk factor for CICI in humans and mouse models. We isolated RNA from the cerebral cortex of APOE3 and APOE4 mice from one to 21 days after a single dose of 10 mg/kg doxorubicin. Using NanoString analysis of over 700 genes related to neuroinflammation and RT-qPCR analysis of cerebral cortex transcripts, we found two-fold induction of four senescence-related genes at three weeks in the APOE4 mice compared to the APOE3 control mice: p21(cdkn1a), p16, Gadd45a, and Egr1. We conclude that doxorubicin promotes cellular senescence pathways in the brain, supporting the hypothesis that drugs to eliminate senescent cells could be useful in preventing CICI.
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Affiliation(s)
- Tamar Demby
- National Institute of Diabetes and Digestive and Kidney Disease, Bethesda, MD, United States of America
| | - Phillip S Gross
- Interdisciplinary Program in Neuroscience, Georgetown University, Washington, DC, United States of America
| | - Jeanne Mandelblatt
- Department of Oncology, Georgetown Lombardi Comprehensive Cancer Center and Georgetown Lombardi Institute for Cancer and Aging Research, Georgetown University, Washington, DC, United States of America
| | - Jeffrey K Huang
- Department of Biology, Georgetown University, Washington, DC, United States of America
| | - G William Rebeck
- Department of Neuroscience, Georgetown University, Washington, DC, United States of America.
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Zhang Y, Wang X, Li W, Yang Y, Wu Z, Lyu Y, Yue C. Intestinal microbiota: a new perspective on delaying aging? Front Microbiol 2023; 14:1268142. [PMID: 38098677 PMCID: PMC10720643 DOI: 10.3389/fmicb.2023.1268142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 11/17/2023] [Indexed: 12/17/2023] Open
Abstract
The global aging situation is severe, and the medical pressures associated with aging issues should not be underestimated. The need and feasibility of studying aging and intervening in aging have been confirmed. Aging is a complex natural physiological progression, which involves the irreversible deterioration of body cells, tissues, and organs with age, leading to enhanced risk of disease and ultimately death. The intestinal microbiota has a significant role in sustaining host dynamic balance, and the study of bidirectional communication networks such as the brain-gut axis provides important directions for human disease research. Moreover, the intestinal microbiota is intimately linked to aging. This review describes the intestinal microbiota changes in human aging and analyzes the causal controversy between gut microbiota changes and aging, which are believed to be mutually causal, mutually reinforcing, and inextricably linked. Finally, from an anti-aging perspective, this study summarizes how to achieve delayed aging by targeting the intestinal microbiota. Accordingly, the study aims to provide guidance for further research on the intestinal microbiota and aging.
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Affiliation(s)
- Yuemeng Zhang
- Yan’an Key Laboratory of Microbial Drug Innovation and Transformation, School of Basic Medicine, Yan’an University, Yan’an, Shaanxi, China
| | - Xiaomei Wang
- Yan’an University of Physical Education, Yan’an University, Yan’an, Shaanxi, China
| | - Wujuan Li
- Yan’an Key Laboratory of Microbial Drug Innovation and Transformation, School of Basic Medicine, Yan’an University, Yan’an, Shaanxi, China
| | - Yi Yang
- Yan’an Key Laboratory of Microbial Drug Innovation and Transformation, School of Basic Medicine, Yan’an University, Yan’an, Shaanxi, China
| | - Zhuoxuan Wu
- Yan’an Key Laboratory of Microbial Drug Innovation and Transformation, School of Basic Medicine, Yan’an University, Yan’an, Shaanxi, China
| | - Yuhong Lyu
- Yan’an Key Laboratory of Microbial Drug Innovation and Transformation, School of Basic Medicine, Yan’an University, Yan’an, Shaanxi, China
| | - Changwu Yue
- Yan’an Key Laboratory of Microbial Drug Innovation and Transformation, School of Basic Medicine, Yan’an University, Yan’an, Shaanxi, China
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Jo MJ, Lee JK, Kim JE, Ko GJ. Molecular Mechanisms Associated with Aging Kidneys and Future Perspectives. Int J Mol Sci 2023; 24:16912. [PMID: 38069234 PMCID: PMC10707287 DOI: 10.3390/ijms242316912] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
The rapid growth of the elderly population is making the need for extensive and advanced information about age-related organ dysfunction a crucial research area. The kidney is one of the organs most affected by aging. Aged kidneys undergo functional decline, characterized by a reduction in kidney size, decreased glomerular filtration rate, alterations in renal blood flow, and increased inflammation and fibrosis. This review offers a foundation for understanding the functional and molecular mechanisms of aging kidneys and for selecting identifying appropriate targets for future treatments of age-related kidney issues.
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Affiliation(s)
- Min-Jee Jo
- Department of Internal Medicine, Korea University College of Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea; (M.-J.J.); (J.-K.L.); (J.-E.K.)
- Institute of Convergence New Drug Development, Korea University College of Medicine, Seoul 08308, Republic of Korea
| | - Joo-Kyung Lee
- Department of Internal Medicine, Korea University College of Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea; (M.-J.J.); (J.-K.L.); (J.-E.K.)
| | - Ji-Eun Kim
- Department of Internal Medicine, Korea University College of Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea; (M.-J.J.); (J.-K.L.); (J.-E.K.)
| | - Gang-Jee Ko
- Department of Internal Medicine, Korea University College of Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea; (M.-J.J.); (J.-K.L.); (J.-E.K.)
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Clayton ZS, Rossman MJ, Mahoney SA, Venkatasubramanian R, Maurer GS, Hutton DA, VanDongen NS, Greenberg NT, Longtine AG, Ludwig KR, Brunt VE, LaRocca TJ, Campisi J, Melov S, Seals DR. Cellular Senescence Contributes to Large Elastic Artery Stiffening and Endothelial Dysfunction With Aging: Amelioration With Senolytic Treatment. Hypertension 2023; 80:2072-2087. [PMID: 37593877 PMCID: PMC10530538 DOI: 10.1161/hypertensionaha.123.21392] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 08/02/2023] [Indexed: 08/19/2023]
Abstract
BACKGROUND Here, we assessed the role of cellular senescence and the senescence associated secretory phenotype (SASP) in age-related aortic stiffening and endothelial dysfunction. METHODS We studied young (6-8 mo) and old (27-29 mo) p16-3MR mice, which allows for genetic-based clearance of senescent cells with ganciclovir (GCV). We also treated old C57BL/6N mice with the senolytic ABT-263. RESULTS In old mice, GCV reduced aortic stiffness assessed by aortic pulse wave velocity (PWV; 477±10 vs. 382±7 cm/s, P<0.05) to young levels (old-GCV vs. young-vehicle, P=0.35); ABT-263 also reduced aortic PWV in old mice (446±9 to 356±11 cm/s, P<0.05). Aortic adventitial collagen was reduced by GCV (P<0.05) and ABT-263 (P=0.12) in old mice. To show an effect of the circulating SASP, we demonstrated that plasma exposure from Old-vehicle p16-3MR mice, but not from Old-GCV mice, induced aortic stiffening assessed ex vivo (elastic modulus; P<0.05). Plasma proteomics implicated glycolysis in circulating SASP-mediated aortic stiffening. In old p16-3MR mice, GCV increased endothelial function assessed via peak carotid artery endothelium-dependent dilation (EDD; Old-GCV, 94±1% vs. Old-vehicle, 84±2%, P<0.05) to young levels (Old-GCV vs. young-vehicle, P=0.98), and EDD was higher in old C57BL/6N mice treated with ABT-263 vs. vehicle (96±1% vs. 82±3%, P<0.05). Improvements in endothelial function were mediated by increased nitric oxide (NO) bioavailability (P<0.05) and reduced oxidative stress (P<0.05). Circulating SASP factors related to NO signaling were associated with greater NO-mediated EDD following senescent cell clearance. CONCLUSIONS Cellular senescence and the SASP contribute to vascular aging and senolytics hold promise for improving age-related vascular function.
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Affiliation(s)
- Zachary S. Clayton
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO
| | - Matthew J. Rossman
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO
| | - Sophia A. Mahoney
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO
| | | | - Grace S. Maurer
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO
| | - David A. Hutton
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO
| | | | - Nathan T. Greenberg
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO
| | - Abigail G. Longtine
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO
| | - Katelyn R. Ludwig
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO
| | - Vienna E. Brunt
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO
| | - Thomas J. LaRocca
- Department of Health & Exercise Science, Colorado State University, Fort Collins, CO
- Center for Healthy Aging, Colorado State University, Fort Collins, CO
| | - Judith Campisi
- The Buck Institute for Research on Aging, Novato, CA
- Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Simon Melov
- The Buck Institute for Research on Aging, Novato, CA
| | - Douglas R. Seals
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO
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12
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Sasamoto N, Stewart PA, Wang T, Thompson ZJ, Yoder SJ, Hecht JL, Cleveland JL, Conejo‐Garcia J, Fridley BL, Terry KL, Tworoger SS. Associations between prediagnostic aspirin use and ovarian tumor gene expression. Cancer Med 2023; 12:18405-18417. [PMID: 37525619 PMCID: PMC10523980 DOI: 10.1002/cam4.6386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 04/25/2023] [Accepted: 07/19/2023] [Indexed: 08/02/2023] Open
Abstract
BACKGROUND Aspirin use has been associated with reduced ovarian cancer risk, yet the underlying biological mechanisms are not fully understood. To gain mechanistic insights, we assessed the association between prediagnosis low and regular-dose aspirin use and gene expression profiles in ovarian tumors. METHODS RNA sequencing was performed on high-grade serous, poorly differentiated, and high-grade endometrioid ovarian cancer tumors from the Nurses' Health Study (NHS), NHSII, and New England Case-Control Study (n = 92 cases for low, 153 cases for regular-dose aspirin). Linear regression identified differentially expressed genes associated with aspirin use, adjusted for birth decade and cohort. False discovery rates (FDR) were used to account for multiple testing and gene set enrichment analysis was used to identify biological pathways. RESULTS No individual genes were significantly differentially expressed in ovarian tumors in low or regular-dose aspirin users accounting for multiple comparisons. However, current versus never use of low-dose aspirin was associated with upregulation of immune pathways (e.g., allograft rejection, FDR = 5.8 × 10-10 ; interferon-gamma response, FDR = 2.0 × 10-4 ) and downregulation of estrogen response pathways (e.g., estrogen response late, FDR = 4.9 × 10-8 ). Ovarian tumors from current regular aspirin users versus never users were also associated with upregulation in interferon pathways (FDR <1.5 × 10-4 ) and downregulation of multiple extracellular matrix (ECM) architecture pathways (e.g., ECM organization, 4.7 × 10-8 ). CONCLUSION Our results suggest low and regular-dose aspirin may impair ovarian tumorigenesis in part via enhancing adaptive immune response and decreasing metastatic potential supporting the likely differential effects on ovarian carcinogenesis and progression by dose of aspirin.
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Affiliation(s)
- Naoko Sasamoto
- Department of Obstetrics and GynecologyBrigham and Women's Hospital and Harvard Medical SchoolBostonMassachusettsUSA
| | - Paul A. Stewart
- Department of Biostatistics and BioinformaticsH. Lee Moffitt Cancer Center and Research InstituteTampaFloridaUSA
| | - Tianyi Wang
- Department of Cancer EpidemiologyH. Lee Moffitt Cancer Center and Research InstituteTampaFloridaUSA
| | - Zachary J. Thompson
- Department of Biostatistics and BioinformaticsH. Lee Moffitt Cancer Center and Research InstituteTampaFloridaUSA
| | - Sean J. Yoder
- Molecular Genomics Core FacilityH. Lee Moffitt Cancer Center and Research InstituteTampaFloridaUSA
| | - Jonathan L. Hecht
- Department of PathologyBeth Israel Deaconess Medical Center and Harvard Medical SchoolBostonMassachusettsUSA
| | - John L. Cleveland
- Department of Tumor BiologyH. Lee Moffitt Cancer Center and Research InstituteTampaFloridaUSA
| | - Jose Conejo‐Garcia
- Department of ImmunologyH. Lee Moffitt Cancer Center and Research InstituteTampaFloridaUSA
| | - Brooke L. Fridley
- Department of Biostatistics and BioinformaticsH. Lee Moffitt Cancer Center and Research InstituteTampaFloridaUSA
| | - Kathryn L. Terry
- Department of Obstetrics and GynecologyBrigham and Women's Hospital and Harvard Medical SchoolBostonMassachusettsUSA
- Department of EpidemiologyHarvard T.H. Chan School of Public HealthBostonMassachusettsUSA
| | - Shelley S. Tworoger
- Department of Cancer EpidemiologyH. Lee Moffitt Cancer Center and Research InstituteTampaFloridaUSA
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13
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Wu J, Jiang Y, Sun J, Sun X. Identification and Validation of an Aging-Associated circRNA-miRNA-mRNA Network in Neovascular Age-Related Macular Degeneration. Gerontology 2023; 69:1218-1231. [PMID: 37604141 PMCID: PMC10614246 DOI: 10.1159/000531287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 05/22/2023] [Indexed: 08/23/2023] Open
Abstract
INTRODUCTION Neovascular age-related macular degeneration (NVAMD) is a leading cause of severe vision impairment in the elderly. Aging is one of the most pivotal underlying molecular mechanisms of NVAMD. METHODS In this study, we identified the potential aging-related genes involved in NVAMD. Considering that noncoding RNAs are vital regulators of NVAMD progression, we further explored and constructed an aging-originated circRNA-miRNA-mRNA network of NVAMD. Differential expression of 23 aging-associated genes was identified based on sequencing data and the Human Aging Genomic Resources tool at a threshold of p < 0.05, and log2|fold change| > 1. RESULTS We screened 12 microRNAs (miRNAs) using public datasets and miRNet database. A total of 13 circRNAs were subsequently mined using the starBase tool. Merging these 13 circRNAs, 12 miRNAs, and 15 genes together, we obtained 281 pairs of circRNA-miRNA and 30 pairs of miRNA-mRNA. CONCLUSION We created an aging-related circRNA-miRNA-mRNA network, which could be a promising target for future AMD treatments.
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Affiliation(s)
- Jiali Wu
- School of Medicine, Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China,
- National Clinical Research Center for Ophthalmic Diseases, Shanghai, China,
| | - Yuxin Jiang
- School of Medicine, Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China
- National Clinical Research Center for Ophthalmic Diseases, Shanghai, China
| | - Junran Sun
- School of Medicine, Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China
- National Clinical Research Center for Ophthalmic Diseases, Shanghai, China
- Shanghai Key Laboratory of Fundus Diseases, Shanghai, China
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Xiaodong Sun
- School of Medicine, Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China
- National Clinical Research Center for Ophthalmic Diseases, Shanghai, China
- Shanghai Key Laboratory of Fundus Diseases, Shanghai, China
- Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
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14
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Doolittle ML, Saul D, Kaur J, Rowsey JL, Vos SJ, Pavelko KD, Farr JN, Monroe DG, Khosla S. Multiparametric senescent cell phenotyping reveals targets of senolytic therapy in the aged murine skeleton. Nat Commun 2023; 14:4587. [PMID: 37524694 PMCID: PMC10390564 DOI: 10.1038/s41467-023-40393-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 07/26/2023] [Indexed: 08/02/2023] Open
Abstract
Senescence drives organismal aging, yet the deep characterization of senescent cells in vivo remains incomplete. Here, we apply mass cytometry by time-of-flight using carefully validated antibodies to analyze senescent cells at single-cell resolution. We use multiple criteria to identify senescent mesenchymal cells that are growth-arrested and resistant to apoptosis. These p16 + Ki67-BCL-2+ cells are highly enriched for senescence-associated secretory phenotype and DNA damage markers, are strongly associated with age, and their percentages are increased in late osteoblasts/osteocytes and CD24high osteolineage cells. Moreover, both late osteoblasts/osteocytes and CD24high osteolineage cells are robustly cleared by genetic and pharmacologic senolytic therapies in aged mice. Following isolation, CD24+ skeletal cells exhibit growth arrest, senescence-associated β-galactosidase positivity, and impaired osteogenesis in vitro. These studies thus provide an approach using multiplexed protein profiling to define senescent mesenchymal cells in vivo and identify specific skeletal cell populations cleared by senolytics.
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Affiliation(s)
- Madison L Doolittle
- Division of Endocrinology, Diabetes and Metabolism, Mayo Clinic, Rochester, MN, 55905, USA
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, 55905, USA
| | - Dominik Saul
- Division of Endocrinology, Diabetes and Metabolism, Mayo Clinic, Rochester, MN, 55905, USA
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, 55905, USA
- Department for Trauma and Reconstructive Surgery, BG Clinic, University of Tübingen, Tübingen, Germany
| | - Japneet Kaur
- Division of Endocrinology, Diabetes and Metabolism, Mayo Clinic, Rochester, MN, 55905, USA
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jennifer L Rowsey
- Division of Endocrinology, Diabetes and Metabolism, Mayo Clinic, Rochester, MN, 55905, USA
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, 55905, USA
| | - Stephanie J Vos
- Division of Endocrinology, Diabetes and Metabolism, Mayo Clinic, Rochester, MN, 55905, USA
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, 55905, USA
| | - Kevin D Pavelko
- Department of Immunology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Joshua N Farr
- Division of Endocrinology, Diabetes and Metabolism, Mayo Clinic, Rochester, MN, 55905, USA
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, 55905, USA
| | - David G Monroe
- Division of Endocrinology, Diabetes and Metabolism, Mayo Clinic, Rochester, MN, 55905, USA
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, 55905, USA
| | - Sundeep Khosla
- Division of Endocrinology, Diabetes and Metabolism, Mayo Clinic, Rochester, MN, 55905, USA.
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, 55905, USA.
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15
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Yang JH, Petty CA, Dixon-McDougall T, Lopez MV, Tyshkovskiy A, Maybury-Lewis S, Tian X, Ibrahim N, Chen Z, Griffin PT, Arnold M, Li J, Martinez OA, Behn A, Rogers-Hammond R, Angeli S, Gladyshev VN, Sinclair DA. Chemically induced reprogramming to reverse cellular aging. Aging (Albany NY) 2023; 15:5966-5989. [PMID: 37437248 PMCID: PMC10373966 DOI: 10.18632/aging.204896] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 07/04/2023] [Indexed: 07/14/2023]
Abstract
A hallmark of eukaryotic aging is a loss of epigenetic information, a process that can be reversed. We have previously shown that the ectopic induction of the Yamanaka factors OCT4, SOX2, and KLF4 (OSK) in mammals can restore youthful DNA methylation patterns, transcript profiles, and tissue function, without erasing cellular identity, a process that requires active DNA demethylation. To screen for molecules that reverse cellular aging and rejuvenate human cells without altering the genome, we developed high-throughput cell-based assays that distinguish young from old and senescent cells, including transcription-based aging clocks and a real-time nucleocytoplasmic compartmentalization (NCC) assay. We identify six chemical cocktails, which, in less than a week and without compromising cellular identity, restore a youthful genome-wide transcript profile and reverse transcriptomic age. Thus, rejuvenation by age reversal can be achieved, not only by genetic, but also chemical means.
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Affiliation(s)
- Jae-Hyun Yang
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Christopher A. Petty
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Thomas Dixon-McDougall
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Maria Vina Lopez
- Molecular and Biomedical Sciences, University of Maine, Orono, ME 04467, USA
| | - Alexander Tyshkovskiy
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119234, Russia
| | - Sun Maybury-Lewis
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Xiao Tian
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Nabilah Ibrahim
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Zhili Chen
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Patrick T. Griffin
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Matthew Arnold
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Jien Li
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Oswaldo A. Martinez
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA 02115, USA
- Department of Biology and Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Alexander Behn
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Ryan Rogers-Hammond
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA 02115, USA
| | - Suzanne Angeli
- Molecular and Biomedical Sciences, University of Maine, Orono, ME 04467, USA
| | - Vadim N. Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - David A. Sinclair
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA 02115, USA
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16
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Berkowicz P, Totoń-Żurańska J, Kwiatkowski G, Jasztal A, Csípő T, Kus K, Tyrankiewicz U, Orzyłowska A, Wołkow P, Tóth A, Chlopicki S. Accelerated ageing and coronary microvascular dysfunction in chronic heart failure in Tgαq*44 mice. GeroScience 2023; 45:1619-1648. [PMID: 36692592 PMCID: PMC10400753 DOI: 10.1007/s11357-022-00716-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 12/12/2022] [Indexed: 01/25/2023] Open
Abstract
Age represents a major risk factor in heart failure (HF). However, the mechanisms linking ageing and HF are not clear. We aimed to identify the functional, morphological and transcriptomic changes that could be attributed to cardiac ageing in a model of slowly progressing HF in Tgαq*44 mice in reference to the cardiac ageing process in FVB mice. In FVB mice, ageing resulted in the impairment of diastolic cardiac function and in basal coronary flow (CF), perivascular and interstitial fibrosis without changes in the cardiac activity of angiotensin-converting enzyme (ACE) or aldosterone plasma concentration. In Tgαq*44 mice, HF progression was featured by the impairment of systolic and diastolic cardiac function and in basal CF that was associated with a distinct rearrangement of the capillary architecture, pronounced perivascular and interstitial fibrosis, progressive activation of cardiac ACE and systemic angiotensin-aldosterone-dependent pathways. Interestingly, cardiac ageing genes and processes were represented in Tgαq*44 mice not only in late but also in early phases of HF, as evidenced by cardiac transcriptome analysis. Thirty-four genes and 8 biological processes, identified as being ageing related, occurred early and persisted along HF progression in Tgαq*44 mice and were mostly associated with extracellular matrix remodelling and fibrosis compatible with perivascular fibrosis resulting in coronary microvascular dysfunction (CMD) in Tgαq*44 mice. In conclusion, accelerated and persistent cardiac ageing contributes to the pathophysiology of chronic HF in Tgαq*44 mice. In particular, prominent perivascular fibrosis of microcirculation resulting in CMD represents an accelerated cardiac ageing phenotype that requires targeted treatment in chronic HF.
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Affiliation(s)
- Piotr Berkowicz
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Krakow, Poland
| | - Justyna Totoń-Żurańska
- Centre for Medical Genomics OMICRON, Jagiellonian University Medical College, Krakow, Poland
| | - Grzegorz Kwiatkowski
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Krakow, Poland
| | - Agnieszka Jasztal
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Krakow, Poland
| | - Tamás Csípő
- Division of Clinical Physiology, Department of Cardiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Department of Public Health, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - Kamil Kus
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Krakow, Poland
| | - Urszula Tyrankiewicz
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Krakow, Poland
| | - Anna Orzyłowska
- Department of Neurosurgery and Paediatric Neurosurgery, Medical University of Lublin, Lublin, Poland
| | - Paweł Wołkow
- Centre for Medical Genomics OMICRON, Jagiellonian University Medical College, Krakow, Poland
| | - Attila Tóth
- Division of Clinical Physiology, Department of Cardiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Stefan Chlopicki
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Krakow, Poland.
- Faculty of Medicine, Chair of Pharmacology, Jagiellonian University Medical College, Krakow, Poland.
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17
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Goutas A, Outskouni Z, Papathanasiou I, Georgakopoulou A, Karpetas GE, Gonos ES, Trachana V. The establishment of mitotic errors-driven senescence depends on autophagy. Redox Biol 2023; 62:102701. [PMID: 37094517 PMCID: PMC10149375 DOI: 10.1016/j.redox.2023.102701] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 04/05/2023] [Accepted: 04/12/2023] [Indexed: 04/26/2023] Open
Abstract
We and others have reported that senescence onset is accompanied by genomic instability that is evident by several defects, such as aneuploidy or erroneous mitosis features. Here, we report that these defects also appear in young cells upon oxidative insult. We provide evidence that these errors could be the consequence of oxidative stress (OS)- either exogenous or senescence-associated - overriding the spindle assembly checkpoint (SAC). Young cells treated with Η2Ο2 as well as older cells fail to maintain mitotic arrest in the presence of spindle poisons and a significant higher percentage of them have supernumerary centrosomes and centrosome related anomalous characteristics. We also report that aging is escorted by expression modifications of SAC components, and especially of Bub1b/BubR1. Bub1b/BubR1 has been previously reported to decrease naturally upon aging. Here, we show that there is an initial increase in Bub1b/BubR1 levels, feasibly as part of the cells' response against OS-driven genomic instability, that is followed by its autophagy dependent degradation. This provides an explanation that was missing regarding the molecular entity responsible for the downregulation of Bub1b/BubR1 upon aging, especially since it is well established, by us and others, that the proteasome function decays as cells age. These results, not only serve the previously reported notion of a shift from proteasome to autophagy-dependent degradation upon aging, but also provide a mechanistic insight for mitotic errors-driven senescence. We believe that our conclusions deepen our understanding regarding the homeostatic function of autophagy that serves the establishment of senescence as a barrier against cellular transformation.
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Affiliation(s)
- Andreas Goutas
- Department of Biology, Faculty of Medicine, School of Health Sciences, University of Thessaly, Biopolis, Larissa, 41500, Greece.
| | - Zozo Outskouni
- Department of Biology, Faculty of Medicine, School of Health Sciences, University of Thessaly, Biopolis, Larissa, 41500, Greece.
| | - Ioanna Papathanasiou
- Department of Biology, Faculty of Medicine, School of Health Sciences, University of Thessaly, Biopolis, Larissa, 41500, Greece.
| | - Aphrodite Georgakopoulou
- Hematology Department, Hematopoietic Cell Transplant (HCT) Unit, Gene and Cell Therapy Center, George Papanikolaou Hospital, Thessaloniki, 57010, Greece.
| | - Georgios E Karpetas
- Department of Medical Informatics, Faculty of Medicine, School of Health Sciences, University of Thessaly, Biopolis, Larissa, 41500, Greece.
| | - Efstathios S Gonos
- Hellenic Pasteur Institute, Athens, 11521, Greece; Institute of Biology, Medical Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, 11635, Greece.
| | - Varvara Trachana
- Department of Biology, Faculty of Medicine, School of Health Sciences, University of Thessaly, Biopolis, Larissa, 41500, Greece.
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18
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Harries LW. Dysregulated RNA processing and metabolism: a new hallmark of ageing and provocation for cellular senescence. FEBS J 2023; 290:1221-1234. [PMID: 35460337 DOI: 10.1111/febs.16462] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/28/2022] [Accepted: 04/21/2022] [Indexed: 12/23/2022]
Abstract
The human genome is capable of producing hundreds of thousands of different proteins and non-coding RNAs from <20 000 genes, in a co-ordinated and regulated fashion. This is achieved by a collection of phenomena known as mRNA processing and metabolism, and encompasses events in the life cycle of an RNA from synthesis to degradation. These factors are critical determinants of cellular adaptability and plasticity, which allows the cell to adjust its transcriptomic output in response to its internal and external environment. Evidence is building that dysfunctional RNA processing and metabolism may be a key contributor to the development of cellular senescence. Senescent cells by definition have exited cell cycle, but have gained functional features such as the secretion of the senescence-associated secretory phenotype (SASP), a known driver of chronic disease and perhaps even ageing itself. In this review, I will outline the impact of dysregulated mRNA processing and metabolism on senescence and ageing at the level of genes, cells and systems, and describe the mechanisms by which progressive deterioration in these processes may impact senescence and organismal ageing. Finally, I will present the evidence implicating this important process as a new hallmark of ageing, which could be harnessed in the future to develop new senotherapeutic interventions for chronic disease.
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19
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Doolittle ML, Saul D, Kaur J, Rowsey JL, Vos SJ, Pavelko KD, Farr JN, Monroe DG, Khosla S. Multiparametric senescent cell phenotyping reveals CD24 osteolineage cells as targets of senolytic therapy in the aged murine skeleton. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.12.523760. [PMID: 36711531 PMCID: PMC9882155 DOI: 10.1101/2023.01.12.523760] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Senescence drives organismal aging, yet the deep characterization of senescent cells in vivo remains incomplete. Here, we applied mass cytometry by time-of-flight (CyTOF) using carefully validated antibodies to analyze senescent cells at single-cell resolution. We used multiple criteria to identify senescent mesenchymal cells that were growth arrested and resistant to apoptosis (p16+/Ki67-/BCL-2+; "p16KB" cells). These cells were highly enriched for senescence-associated secretory phenotype (SASP) and DNA damage markers and were strongly associated with age. p16KB cell percentages were also increased in CD24+ osteolineage cells, which exhibited an inflammatory SASP in aged mice and were robustly cleared by both genetic and pharmacologic senolytic therapies. Following isolation, CD24+ skeletal cells exhibited growth arrest, SA-βgal positivity, and impaired osteogenesis in vitro . These studies thus provide a new approach using multiplexed protein profiling by CyTOF to define senescent mesenchymal cells in vivo and identify a highly inflammatory, senescent CD24+ osteolineage population cleared by senolytics.
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Affiliation(s)
- Madison L. Doolittle
- Division of Endocrinology, Diabetes and Metabolism, Mayo Clinic, Rochester, MN, 55905, USA
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA
| | - Dominik Saul
- Division of Endocrinology, Diabetes and Metabolism, Mayo Clinic, Rochester, MN, 55905, USA
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA
- Department for Trauma and Reconstructive Surgery, BG Clinic, University of Tübingen, Germany
| | - Japneet Kaur
- Division of Endocrinology, Diabetes and Metabolism, Mayo Clinic, Rochester, MN, 55905, USA
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA
| | - Jennifer L. Rowsey
- Division of Endocrinology, Diabetes and Metabolism, Mayo Clinic, Rochester, MN, 55905, USA
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA
| | - Stephanie J. Vos
- Division of Endocrinology, Diabetes and Metabolism, Mayo Clinic, Rochester, MN, 55905, USA
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA
| | - Kevin D. Pavelko
- Department of Immunology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Joshua N. Farr
- Division of Endocrinology, Diabetes and Metabolism, Mayo Clinic, Rochester, MN, 55905, USA
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA
| | - David G. Monroe
- Division of Endocrinology, Diabetes and Metabolism, Mayo Clinic, Rochester, MN, 55905, USA
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA
| | - Sundeep Khosla
- Division of Endocrinology, Diabetes and Metabolism, Mayo Clinic, Rochester, MN, 55905, USA
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA
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20
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Malek G, Campisi J, Kitazawa K, Webster C, Lakkaraju A, Skowronska-Krawczyk D. Does senescence play a role in age-related macular degeneration? Exp Eye Res 2022; 225:109254. [PMID: 36150544 PMCID: PMC10032649 DOI: 10.1016/j.exer.2022.109254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 09/07/2022] [Accepted: 09/14/2022] [Indexed: 12/29/2022]
Abstract
Advanced age is the most established risk factor for developing age-related macular degeneration (AMD), one of the leading causes of visual impairment in the elderly, in Western and developed countries. Similarly, after middle age, there is an exponential increase in pathologic molecular and cellular events that can induce senescence, traditionally defined as an irreversible loss of the cells' ability to divide and most recently reported to also occur in select post-mitotic and terminally differentiated cells, such as neurons. Together these facts raise the question as to whether or not cellular senescence, may play a role in the development of AMD. A number of studies have reported the effect of ocular-relevant inducers of senescence using primarily in vitro models of poorly polarized, actively dividing retinal pigment epithelial (RPE) cell lines. However, in interpretating the data, the fidelity of these culture models to the RPE in vivo, must be considered. Fewer studies have explored the presence and/or impact of senescent cells in in vivo models that present with phenotypic features of AMD, leaving this an open field for further investigation. The goal of this review is to discuss current thoughts on the potential role of senescence in AMD development and progression, with consideration of the model systems used and their relevance to human disease.
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Affiliation(s)
- Goldis Malek
- Duke Eye Center, Department of Ophthalmology, Duke University School of Medicine, Durham, NC, USA; Department of Pathology, Duke University School of Medicine, Durham, NC, USA.
| | - Judith Campisi
- Buck Institute for Research on Aging, Novato, CA, USA; Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Koji Kitazawa
- Buck Institute for Research on Aging, Novato, CA, USA; Department of Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Corey Webster
- Buck Institute for Research on Aging, Novato, CA, USA
| | - Aparna Lakkaraju
- Departments of Ophthalmology and Anatomy, School of Medicine, University of California, San Francisco, CA, USA
| | - Dorota Skowronska-Krawczyk
- Department of Physiology and Biophysics, Department of Ophthalmology, Center for Translational Vision Research, School of Medicine, University of California, Irvine, CA, USA
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21
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Hu X, Guo L, Liu G, Dai Z, Wang L, Zhang J, Wang J. Novel cellular senescence-related risk model identified as the prognostic biomarkers for lung squamous cell carcinoma. Front Oncol 2022; 12:997702. [DOI: 10.3389/fonc.2022.997702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/20/2022] [Indexed: 11/18/2022] Open
Abstract
BackgroundLung cancer is one of the top causes of cancer-related death worldwide. Cellular senescence is a characteristic of cell cycle arrest that plays a role in carcinogenesis and immune microenvironment modulation. Despite this, the clinical and immune cell infiltration features of senescence in lung squamous cell carcinoma (LUSC) are unknown.MethodsThe Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) were used to get RNA-seq data and clinical information for LUSC. The least absolute shrinkage and selection operator (LASSO)-Cox regression, receiver operating characteristic (ROC), and Kaplan-Meier analysis were used to evaluate a risk model for predicting overall survival based on six differentially expressed genes. The tumor microenvironment (TME) and immunotherapy response were also studied.ResultsTo discriminate LUSC into high- and low-risk subgroups, a risk model comprised of six cellular senescence-related genes (CDKN1A, CEBPB, MDH1, SIX1, SNAI1, and SOX5) was developed. The model could stratify patients into high-risk and low-risk groups, according to ROC and Kaplan-Meier analysis. In the TCGA-LUSC and GSE73403 cohorts, the high-risk group had a worse prognosis (P<0.05), and was associated with immune cell inactivation and being insensitive to immunotherapy in IMvigor210.ConclusionsWe discovered a new LUSC classification based on six cellular senescence-related genes, which will aid in identifying patients who will benefit from anti-PD-1 treatment. Targeting senescence-related genes appears to be another option for improving clinical therapy for LUSC.
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22
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Yang J, Song J, Kim SJ, You G, Lee JB, Mok H. Chronic infrared-A irradiation-induced photoaging of human dermal fibroblasts from different donors at physiological temperature. PHOTODERMATOLOGY, PHOTOIMMUNOLOGY & PHOTOMEDICINE 2022; 38:571-581. [PMID: 35437847 DOI: 10.1111/phpp.12793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 04/05/2022] [Accepted: 04/15/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND In this study, we examined cellular responses to acute and chronic IRA irradiation at mild and natural levels of exposure in two types of human fibroblasts, each isolated from a different donor, at physiological temperature (34°C). METHOD Two types of human dermal fibroblasts (derived from a 20- and 50-year-old women, respectively) were exposed to different repeat numbers of IRA exposure (3, 6, 10, and 14 times; 42 mW/cm2 ) at a frequency of 3-4 times per week (4 h per irradiation). Cellular responses to acute and chronic IRA irradiation were examined by reactive oxygen species (ROS) level, apoptotic signals, cellular morphology, and collagen level. RESULTS We demonstrated that chronic IRA irradiation-induced severe cellular damage, including prolonged cell proliferation, increased intracellular ROS levels, activated cellular apoptosis, and elongated cell morphology, whereas acute IRA irradiation had negligible effects at 34°C. In addition, it was evident that the degree of cellular damage due to IRA irradiation differed according to the type of fibroblasts. CONCLUSIONS Considering the severe cellular damage induced by chronic IRA irradiation without heat, continuous exposure of skin to IRA irradiation during daily life may be harmful enough to induce photoaging.
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Affiliation(s)
- Jiwon Yang
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, Korea
| | - Jihyeon Song
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, Korea
| | | | - Gayeon You
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, Korea
| | | | - Hyejung Mok
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, Korea
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23
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Huang W, Hickson LJ, Eirin A, Kirkland JL, Lerman LO. Cellular senescence: the good, the bad and the unknown. Nat Rev Nephrol 2022; 18:611-627. [PMID: 35922662 PMCID: PMC9362342 DOI: 10.1038/s41581-022-00601-z] [Citation(s) in RCA: 212] [Impact Index Per Article: 106.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2022] [Indexed: 01/10/2023]
Abstract
Cellular senescence is a ubiquitous process with roles in tissue remodelling, including wound repair and embryogenesis. However, prolonged senescence can be maladaptive, leading to cancer development and age-related diseases. Cellular senescence involves cell-cycle arrest and the release of inflammatory cytokines with autocrine, paracrine and endocrine activities. Senescent cells also exhibit morphological alterations, including flattened cell bodies, vacuolization and granularity in the cytoplasm and abnormal organelles. Several biomarkers of cellular senescence have been identified, including SA-βgal, p16 and p21; however, few markers have high sensitivity and specificity. In addition to driving ageing, senescence of immune and parenchymal cells contributes to the development of a variety of diseases and metabolic disorders. In the kidney, senescence might have beneficial roles during development and recovery from injury, but can also contribute to the progression of acute kidney injury and chronic kidney disease. Therapies that target senescence, including senolytic and senomorphic drugs, stem cell therapies and other interventions, have been shown to extend lifespan and reduce tissue injury in various animal models. Early clinical trials confirm that senotherapeutic approaches could be beneficial in human disease. However, larger clinical trials are needed to translate these approaches to patient care.
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Affiliation(s)
- Weijun Huang
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
- Key Laboratory of Chinese Internal Medicine of Ministry of Education and Beijing, Dongzhimen Hospital Affiliated to Beijing University of Chinese Medicine, Beijing, China
| | - LaTonya J Hickson
- Division of Nephrology and Hypertension, Mayo Clinic, Jacksonville, FL, USA
| | - Alfonso Eirin
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - James L Kirkland
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA
| | - Lilach O Lerman
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA.
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24
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Zhang B, Ma X, Huang B, Jiang Q, Loor JJ, Lv X, Zhang W, Li M, Wen J, Yin Y, Wang J, Yang W, Xu C. Transcriptomics of circulating neutrophils in dairy cows with subclinical hypocalcemia. Front Vet Sci 2022; 9:959831. [PMID: 36176696 PMCID: PMC9514324 DOI: 10.3389/fvets.2022.959831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
Hypocalcemia is closely associated with inflammatory diseases in dairy cows. Recent research has underscored the key role of calcium in the adaptations of the innate immune system during this period. The main objective in the present study was to compare the transcriptome profiles and analyze differences in the expression of neutrophil (PMNL) immune function-related genes and calcium binding-related genes in hypocalcemic cows. At 2 days postpartum, a concentration >2.10 mmol Ca2+/L was used to classify cows as controls (CON), and a concentration <2.00 mmol Ca2+/L used to classify cows as low-calcium (LCAL) (n = 8 in each group). A routine medical examination was conducted by the attending veterinarian to ensure there were no other complications and that the blood β-hydroxybutyrate was <1.2 mmol/L. Blood was collected from the tail vein (20 mL) to isolate PMNL, and 5 cows in each group were used for RNA sequencing and statistical analysis of gene expression differences. Transcriptome RNA-seq sequencing analysis was via omicsstudio using the R package edgeR. GO and KEGG enrichment analysis were used for bioinformatics. The remaining 3 cows in each group were used for validation of RNA sequencing data via quantitative PCR, which confirmed the observed responses. Compared with CON, 158 genes in LCAL were significantly up-regulated and 296 genes were down-regulated. The downregulation of Interleukin-12 (CXCL12), Tubulin beta chain (TUBB1), L1 cell adhesion molecule (L1CAM), and Myeloperoxidase (MPO) indicated a decrease in immune function of PMNL in LCAL cows. The decreased expression of calcium-binding pathway-related genes in PMNL of LCAL cows indicated a decrease in immune function of PMNL likely related to calcium ions. For example, cartilage acid protein 1 (CRTAC1) and calcium/calmodulin-dependent kinase 4 (CAMK4) were significantly reduced in LCAL cows. The upregulation of Cyclin dependent kinase inhibitor 1A (CDKN1A), Perforin 1 (PRF1), and Homeodomain interacting protein kinase 3 (HIPK3) indicated that LCAL led to greater cell apoptosis and senescence. Overall, the analyses indicated that the reduction in PMNL immune function during hypocalcemia is associated with downregulation of intracellular Ca2+ related genes and upregulation of genes controlling apoptosis and senescence. Together, these alterations contribute to an immunosuppressive state during the transition period.
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Affiliation(s)
- Bingbing Zhang
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Xinru Ma
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Baoyin Huang
- Animal Husbandry and Veterinary Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihaer, China
| | - Qianming Jiang
- Mammalian NutriPhysioGenomics, Division of Nutritional Sciences, Department of Animal Sciences, University of Illinois, Urbana, IL, United States
| | - Juan J. Loor
- Mammalian NutriPhysioGenomics, Division of Nutritional Sciences, Department of Animal Sciences, University of Illinois, Urbana, IL, United States
| | - Xinquan Lv
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Wei Zhang
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Ming Li
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Jianan Wen
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Yufeng Yin
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Jingjing Wang
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Wei Yang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Chuang Xu
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
- College of Veterinary Medicine, China Agricultural University, Beijing, China
- *Correspondence: Chuang Xu
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P16INK4A—More Than a Senescence Marker. Life (Basel) 2022; 12:life12091332. [PMID: 36143369 PMCID: PMC9501954 DOI: 10.3390/life12091332] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Aging is a biological feature that is characterized by gradual degeneration of function in cells, tissues, organs, or an intact organism due to the accumulation of environmental factors and stresses with time. Several factors have been attributed to aging such as oxidative stress and augmented production or exposure to reactive oxygen species, inflammatory cytokines production, telomere shortening, DNA damage, and, importantly, the deposit of senescent cells. These are irreversibly mitotically inactive, yet metabolically active cells. The reason underlying their senescence lies within the extrinsic and the intrinsic arms. The extrinsic arm is mainly characterized by the expression and the secretory profile known as the senescence-associated secretory phenotype (SASP). The intrinsic arm results from the impact of several genes meant to regulate the cell cycle, such as tumor suppressor genes. P16INK4A is a tumor suppressor and cell cycle regulator that has been linked to aging and senescence. Extensive research has revealed that p16 expression is significantly increased in senescent cells, as well as during natural aging or age-related pathologies. Based on this fact, p16 is considered as a specific biomarker for detecting senescent cells and aging. Other studies have found that p16 is not only a senescence marker, but also a protein with many functions outside of senescence and aging. In this paper, we discuss and shed light on several studies that show the different functions of p16 and provide insights in its role in several biological processes besides senescence and aging.
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26
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Yang J, Zhang MY, Du YM, Ji XL, Qu YQ. Identification and Validation of CDKN1A and HDAC1 as Senescence-Related Hub Genes in Chronic Obstructive Pulmonary Disease. Int J Chron Obstruct Pulmon Dis 2022; 17:1811-1825. [PMID: 35975032 PMCID: PMC9375999 DOI: 10.2147/copd.s374684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 07/31/2022] [Indexed: 01/06/2023] Open
Abstract
Purpose Cellular senescence participates in the occurrence and development of chronic obstructive pulmonary disease (COPD). This study aimed to identify senescence-related hub genes and explore effective diagnostic markers and therapeutic targets for COPD. Methods The microarray data from the GSE38974 dataset was downloaded from the Gene Expression Omnibus (GEO) database. The overlapping genes between genes from the GSE38974 dataset and CellAge database were considered differentially expressed senescence-related genes (DESRGs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed using R software. Protein-protein interaction (PPI), miRNA-mRNA network, and competitive endogenous RNA (ceRNA) network were constructed and visualized by Cytoscape software. GSE100281 and GSE103174 datasets were employed to validate the expression and diagnostic value of hub genes. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was used to measure the mRNA levels of hub genes in peripheral blood mononuclear cells (PBMCs) from COPD and control samples. Results A total of 23 DESRGs were identified between COPD samples and healthy controls. Enrichment analysis revealed that DESRGs were mainly related to apoptosis and senescence. Moreover, four hub genes and two key clusters were acquired by Cytohubba and MCODE plugin, respectively. CDKN1A and HDAC1 were verified as final hub genes based on GSE100281 and GSE103174 datasets validation. The mRNA expression level of CDKN1A was negatively related to forced expiratory volume in 1 second/forced vital capacity (FEV1/FVC), and HDAC1 expression had the opposite correlation. Finally, an HDAC1-based ceRNA network, including 6 miRNAs and 11 lncRNAs, was constructed. Conclusion We identified two senescence-related hub genes, CDKN1A and HDAC1, which may be effective biomarkers for COPD diagnosis and treatment. An HDAC1-related ceRNA network was constructed to clarify the role of senescence in COPD pathogenesis.
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Affiliation(s)
- Jie Yang
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Shandong Key Laboratory of Infectious Respiratory Diseases, Jinan, People's Republic of China.,Department of Gerontology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, People's Republic of China
| | - Meng-Yu Zhang
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Shandong Key Laboratory of Infectious Respiratory Diseases, Jinan, People's Republic of China
| | - Yi-Ming Du
- Department of Gerontology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, People's Republic of China
| | - Xiu-Li Ji
- Department of Pulmonary Disease, Jinan Traditional Chinese Medicine Hospital, Jinan, People's Republic of China
| | - Yi-Qing Qu
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Shandong Key Laboratory of Infectious Respiratory Diseases, Jinan, People's Republic of China
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Abstract
Senescence is a cell fate that contributes to multiple aging-related pathologies. Despite profound age-associated changes in skeletal muscle (SkM), whether its constituent cells are prone to senesce has not been methodically examined. Herein, using single cell and bulk RNA-sequencing and complementary imaging methods on SkM of young and old mice, we demonstrate that a subpopulation of old fibroadipogenic progenitors highly expresses p16 Ink4a together with multiple senescence-related genes and, concomitantly, exhibits DNA damage and chromatin reorganization. Through analysis of isolated myofibers, we also detail a senescence phenotype within a subset of old cells, governed instead by p2 Cip1 . Administration of a senotherapeutic intervention to old mice countered age-related molecular and morphological changes and improved SkM strength. Finally, we found that the senescence phenotype is conserved in SkM from older humans. Collectively, our data provide compelling evidence for cellular senescence as a hallmark and potentially tractable mediator of SkM aging.
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28
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Durik M, Keyes WM. Senescence diversity in muscle aging. NATURE AGING 2022; 2:570-572. [PMID: 37117776 DOI: 10.1038/s43587-022-00255-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Affiliation(s)
- Matej Durik
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- CNRS, UMR 7104, Illkirch, France
- Inserm, UMR-S 1258, Illkirch, France
- Université de Strasbourg, IGBMC UMR 7104, UMR-S 1258, Illkirch, France
| | - William M Keyes
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.
- CNRS, UMR 7104, Illkirch, France.
- Inserm, UMR-S 1258, Illkirch, France.
- Université de Strasbourg, IGBMC UMR 7104, UMR-S 1258, Illkirch, France.
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29
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Zha Y, Zhuang W, Yang Y, Zhou Y, Li H, Liang J. Senescence in Vascular Smooth Muscle Cells and Atherosclerosis. Front Cardiovasc Med 2022; 9:910580. [PMID: 35722104 PMCID: PMC9198250 DOI: 10.3389/fcvm.2022.910580] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/04/2022] [Indexed: 12/12/2022] Open
Abstract
Vascular smooth muscle cells (VSMCs) are the primary cell type involved in the atherosclerosis process; senescent VSMCs are observed in both aged vessels and atherosclerotic plaques. Factors associated with the atherosclerotic process, including oxidative stress, inflammation, and calcium-regulating factors, are closely linked to senescence in VSMCs. A number of experimental studies using traditional cellular aging markers have suggested that anti-aging biochemical agents could be used to treat atherosclerosis. However, doubt has recently been cast on such potential due to the increasingly apparent complexity of VSMCs status and an incomplete understanding of the role that these cells play in the atherosclerosis process, as well as a lack of specific or spectrum-limited cellular aging markers. The utility of anti-aging drugs in atherosclerosis treatment should be reevaluated. Promotion of a healthy lifestyle, exploring in depth the characteristics of each cell type associated with atherosclerosis, including VSMCs, and development of targeted drug delivery systems will ensure efficacy whilst evaluation of the safety and tolerability of drug use should be key aims of future anti-atherosclerosis research. This review summarizes the characteristics of VSMC senescence during the atherosclerosis process, the factors regulating this process, as well as an overview of progress toward the development and application of anti-aging drugs.
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Affiliation(s)
- Yiwen Zha
- Medical College, Yangzhou University, Yangzhou, China
| | - Wenwen Zhuang
- Medical College, Yangzhou University, Yangzhou, China
| | - Yongqi Yang
- Medical College, Yangzhou University, Yangzhou, China
| | - Yue Zhou
- Medical College, Yangzhou University, Yangzhou, China
| | - Hongliang Li
- Medical College, Yangzhou University, Yangzhou, China
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- *Correspondence: Hongliang Li,
| | - Jingyan Liang
- Medical College, Yangzhou University, Yangzhou, China
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou University, Yangzhou, China
- Jingyan Liang,
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Tan H, Xu J, Liu Y. Ageing, cellular senescence and chronic kidney disease: experimental evidence. Curr Opin Nephrol Hypertens 2022; 31:235-243. [PMID: 35142744 PMCID: PMC9035037 DOI: 10.1097/mnh.0000000000000782] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
PURPOSE OF REVIEW Chronic kidney disease (CKD) is often viewed as an accelerated and premature ageing of the kidney, as they share common pathological features characterized by cellular senescence. In this review, we summarize the experimental evidence linking cellular senescence to the pathobiology of kidney ageing and CKD, and discuss the strategies for targeting senescent cells in developing therapeutics for ageing-related kidney disorders. RECENT FINDINGS Kidney ageing and CKD are featured with increased cellular senescence, an irreversible state of cell cycle arrest and the cessation of cell division. Senescent cells secrete a diverse array of proinflammatory and profibrotic factors known as senescence-associated secretory phenotype (SASP). Secondary senescence can be induced by primary senescent cells via a mechanism involving direct contact or the SASP. Various senolytic therapies aiming to selectively remove senescent cells in vivo have been developed. Senostatic approaches to suppress senescence or inhibit SASP, as well as nutrient signalling regulators are also validated in animal models of ageing. SUMMARY These recent studies provide experimental evidence supporting the notion that accumulation of senescent cells and their associated SASP is a main driver leading to structural and functional organ degeneration in CKD and other ageing-related disorder.
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Affiliation(s)
- Huishi Tan
- State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jie Xu
- State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Youhua Liu
- State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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31
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Chandra A, Lagnado AB, Farr JN, Doolittle M, Tchkonia T, Kirkland JL, LeBrasseur NK, Robbins PD, Niedernhofer LJ, Ikeno Y, Passos JF, Monroe DG, Pignolo RJ, Khosla S. Targeted clearance of p21- but not p16-positive senescent cells prevents radiation-induced osteoporosis and increased marrow adiposity. Aging Cell 2022; 21:e13602. [PMID: 35363946 PMCID: PMC9124310 DOI: 10.1111/acel.13602] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 03/09/2022] [Accepted: 03/20/2022] [Indexed: 12/14/2022] Open
Abstract
Cellular senescence, which is a major cause of tissue dysfunction with aging and multiple other conditions, is known to be triggered by p16Ink4a or p21Cip1 , but the relative contributions of each pathway toward inducing senescence are unclear. Here, we directly addressed this issue by first developing and validating a p21-ATTAC mouse with the p21Cip1 promoter driving a "suicide" transgene encoding an inducible caspase-8 which, upon induction, selectively kills p21Cip1 -expressing senescent cells. Next, we used the p21-ATTAC mouse and the established p16-INK-ATTAC mouse to directly compare the contributions of p21Cip1 versus p16Ink4a in driving cellular senescence in a condition where a tissue phenotype (bone loss and increased marrow adiposity) is clearly driven by cellular senescence-specifically, radiation-induced osteoporosis. Using RNA in situ hybridization, we confirmed the reduction in radiation-induced p21Cip1 - or p16Ink4a -driven transcripts following senescent cell clearance in both models. However, only clearance of p21Cip1 +, but not p16Ink4a +, senescent cells prevented both radiation-induced osteoporosis and increased marrow adiposity. Reduction in senescent cells with dysfunctional telomeres following clearance of p21Cip1 +, but not p16Ink4a +, senescent cells also reduced several of the radiation-induced pro-inflammatory senescence-associated secretory phenotype factors. Thus, by directly comparing senescent cell clearance using two parallel genetic models, we demonstrate that radiation-induced osteoporosis is driven predominantly by p21Cip1 - rather than p16Ink4a -mediated cellular senescence. Further, this approach can be used to dissect the contributions of these pathways in other senescence-associated conditions, including aging across tissues.
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Affiliation(s)
- Abhishek Chandra
- Department of Physiology and Biomedical EngineeringMayo ClinicRochesterMinnesotaUSA
- Robert and Arlene Kogod Center on AgingMayo ClinicRochesterMinnesotaUSA
| | - Anthony B. Lagnado
- Department of Physiology and Biomedical EngineeringMayo ClinicRochesterMinnesotaUSA
- Robert and Arlene Kogod Center on AgingMayo ClinicRochesterMinnesotaUSA
| | - Joshua N. Farr
- Department of Physiology and Biomedical EngineeringMayo ClinicRochesterMinnesotaUSA
- Robert and Arlene Kogod Center on AgingMayo ClinicRochesterMinnesotaUSA
- Division of EndocrinologyMayo ClinicRochesterMinnesotaUSA
| | - Madison Doolittle
- Robert and Arlene Kogod Center on AgingMayo ClinicRochesterMinnesotaUSA
- Division of EndocrinologyMayo ClinicRochesterMinnesotaUSA
| | - Tamara Tchkonia
- Department of Physiology and Biomedical EngineeringMayo ClinicRochesterMinnesotaUSA
- Robert and Arlene Kogod Center on AgingMayo ClinicRochesterMinnesotaUSA
| | - James L. Kirkland
- Department of Physiology and Biomedical EngineeringMayo ClinicRochesterMinnesotaUSA
- Robert and Arlene Kogod Center on AgingMayo ClinicRochesterMinnesotaUSA
| | - Nathan K. LeBrasseur
- Robert and Arlene Kogod Center on AgingMayo ClinicRochesterMinnesotaUSA
- Department of Physical Medicine and RehabilitationMayo ClinicRochesterMinnesotaUSA
| | - Paul D. Robbins
- Institute on the Biology of Aging and MetabolismDepartment of Biochemistry, Molecular Biology and BiophysicsUniversity of MinnesotaMinneapolisMinnesotaUSA
| | - Laura J. Niedernhofer
- Institute on the Biology of Aging and MetabolismDepartment of Biochemistry, Molecular Biology and BiophysicsUniversity of MinnesotaMinneapolisMinnesotaUSA
| | - Yuji Ikeno
- Department of Pathology and Laboratory MedicineUniversity of Texas Health Science CenterSan AntonioTexasUSA
| | - João F. Passos
- Department of Physiology and Biomedical EngineeringMayo ClinicRochesterMinnesotaUSA
- Robert and Arlene Kogod Center on AgingMayo ClinicRochesterMinnesotaUSA
| | - David G. Monroe
- Robert and Arlene Kogod Center on AgingMayo ClinicRochesterMinnesotaUSA
- Division of EndocrinologyMayo ClinicRochesterMinnesotaUSA
| | - Robert J. Pignolo
- Department of Physiology and Biomedical EngineeringMayo ClinicRochesterMinnesotaUSA
- Robert and Arlene Kogod Center on AgingMayo ClinicRochesterMinnesotaUSA
- Division of EndocrinologyMayo ClinicRochesterMinnesotaUSA
| | - Sundeep Khosla
- Department of Physiology and Biomedical EngineeringMayo ClinicRochesterMinnesotaUSA
- Robert and Arlene Kogod Center on AgingMayo ClinicRochesterMinnesotaUSA
- Division of EndocrinologyMayo ClinicRochesterMinnesotaUSA
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Sakellakis M, Flores L, Ramachandran S. Patterns of indolence in prostate cancer (Review). Exp Ther Med 2022; 23:351. [PMID: 35493432 PMCID: PMC9019743 DOI: 10.3892/etm.2022.11278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/11/2022] [Indexed: 11/20/2022] Open
Abstract
Although prostate cancer is a major cause of cancer-related mortality worldwide, most patients will have a relatively indolent clinical course. Contrary to most other types of cancer, even the diagnosis of locally advanced or metastatic disease is not always lethal. The present review aimed to summarize what is known regarding the underlying mechanisms related to the indolent course of subsets of prostate cancer, at various stages. The data suggested that no specific gene alteration by itself was responsible for carcinogenesis or disease aggressiveness. However, pathway analysis identified genetic aberrations in multiple critical pathways that tend to accumulate over the course of the disease. The progression from indolence into aggressive disease is associated with a complex interplay in which genetic and epigenetic factors are involved. The effect of the immune tumor microenvironment is also very important. Emerging evidence has suggested that the upregulation of pathways related to cellular aging and senescence can identify patients with indolent disease. In addition, a number of tumors enter a long-lasting quiescent state. Further research will determine whether halting tumor evolution is a feasible option, and whether the life of patients can be markedly prolonged by inducing tumor senescence or long-term dormancy.
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Affiliation(s)
- Minas Sakellakis
- Fourth Oncology Department and Comprehensive Clinical Trials Center, Metropolitan Hospital, 18547 Athens, Greece
| | - Laura Flores
- Department of Stem Cell Transplantation and Cellular Therapy, MD Anderson Cancer Center, University of Texas, Houston, TX 77025, USA
| | - Sumankalai Ramachandran
- Department of Genitourinary Oncology, MD Anderson Cancer Center, University of Texas, Houston, TX 77025, USA
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Dynamic Spatiotemporal Expression Pattern of the Senescence-Associated Factor p16Ink4a in Development and Aging. Cells 2022; 11:cells11030541. [PMID: 35159350 PMCID: PMC8833900 DOI: 10.3390/cells11030541] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 01/27/2022] [Accepted: 02/02/2022] [Indexed: 02/01/2023] Open
Abstract
A plethora of factors have been attributed to underly aging, including oxidative stress, telomere shortening and cellular senescence. Several studies have shown a significant role of the cyclin-dependent kinase inhibitor p16ink4a in senescence and aging. However, its expression in development has been less well documented. Therefore, to further clarify a potential role of p16 in development and aging, we conducted a developmental expression study of p16, as well as of p19ARF and p21, and investigated their expression on the RNA level in brain, heart, liver, and kidney of mice at embryonic, postnatal, adult, and old ages. P16 expression was further assessed on the protein level by immunohistochemistry. Expression of p16 was highly dynamic in all organs in embryonic and postnatal stages and increased dramatically in old mice. Expression of p19 and p21 was less variable and increased to a moderate extent at old age. In addition, we observed a predominant expression of p16 mRNA and protein in liver endothelial cells versus non-endothelial cells of old mice, which suggests a functional role specifically in liver endothelium of old subjects. Thus, p16 dynamic spatiotemporal expression might implicate p16 in developmental and physiological processes in addition to its well-known function in the build-up of senescence.
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