Integrated multi-omics approach revealed cellular senescence landscape
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE210285 | GEO | 2022/08/15
REPOSITORIES: GEO
Similar Datasets
Project description:Integrated multi-omics approach revealed cellular senescence landscape
| PRJNA865031 | ENA
Project description:Aging is a major unmodifiable risk factor for cardiovascular disease (CVD). Replicative endothelial senescence (RES), characterized by permanent cell-cycle arrest and a senescence-associated secretory phenotype (SASP), is a hallmark of vascular aging and contributes to endothelial dysfunction. However, RES molecular mechanisms, particularly the role of extracellular vesicles (EVs), remain poorly understood. To elucidate these mechanisms, an integrated multi-omics approach (proteomics, transcriptomics, and miRNA profiling) was used to characterize senescent endothelial cells (ECs) and their secreted EVs compared with early-passage counterparts. Senescent ECs and EVs displayed canonical senescence signatures, exhibiting enrichment of cell cycle, DNA damage response, p53 and NF-κB signaling, and SASP components, which are strongly linked to CVD. Senescent EVs also showed a marked suppression of RNA metabolism, chromatin organization, and repair machinery, while carrying pro-inflammatory, adipogenic, and angiogenic mediators, reinforcing their role as vectors of secondary cellular senescence. Multi-omics integration revealed a coordinated regulatory network involving transcription factors (e.g., REST) and miRNAs. Angiogenic regulators miR-22-3p and miR-126-5p also emerged as RES mediators in both ECs and EVs, with miR-22-3p exhibiting compartment-specific regulation. Downregulation of key miRNAs (miR-335-3p, miR-590-3p, miR-29, and miR-17 families) promoted the derepression of downstream targets, driving endothelial phenotypic drift and dysfunction, primarily characterized by impaired PI3K–Akt signaling, maladaptive angiogenesis, and extracellular matrix remodeling. Our study provides a comprehensive map of RES-driven molecular alterations, identifying potential candidate biomarkers and therapeutic targets for age-related CVD. These findings also emphasize the role of EVs in propagating senescence and CVD risk, opening perspectives for EV-based interventions to counteract vascular aging.
2025-12-01 | GSE311039 | GEO
Project description:Aging is a major unmodifiable risk factor for cardiovascular disease (CVD). Replicative endothelial senescence (RES), characterized by permanent cell-cycle arrest and a senescence-associated secretory phenotype (SASP), is a hallmark of vascular aging and contributes to endothelial dysfunction. However, RES molecular mechanisms, particularly the role of extracellular vesicles (EVs), remain poorly understood. To elucidate these mechanisms, an integrated multi-omics approach (proteomics, transcriptomics, and miRNA profiling) was used to characterize senescent endothelial cells (ECs) and their secreted EVs compared with early-passage counterparts. Senescent ECs and EVs displayed canonical senescence signatures, exhibiting enrichment of cell cycle, DNA damage response, p53 and NF-κB signaling, and SASP components, which are strongly linked to CVD. Senescent EVs also showed a marked suppression of RNA metabolism, chromatin organization, and repair machinery, while carrying pro-inflammatory, adipogenic, and angiogenic mediators, reinforcing their role as vectors of secondary cellular senescence. Multi-omics integration revealed a coordinated regulatory network involving transcription factors (e.g., REST) and miRNAs. Angiogenic regulators miR-22-3p and miR-126-5p also emerged as RES mediators in both ECs and EVs, with miR-22-3p exhibiting compartment-specific regulation. Downregulation of key miRNAs (miR-335-3p, miR-590-3p, miR-29, and miR-17 families) promoted the derepression of downstream targets, driving endothelial phenotypic drift and dysfunction, primarily characterized by impaired PI3K–Akt signaling, maladaptive angiogenesis, and extracellular matrix remodeling. Our study provides a comprehensive map of RES-driven molecular alterations, identifying potential candidate biomarkers and therapeutic targets for age-related CVD. These findings also emphasize the role of EVs in propagating senescence and CVD risk, opening perspectives for EV-based interventions to counteract vascular aging.
2025-12-01 | GSE311038 | GEO
Project description:A major aging hallmark is the accumulation of cellular senescence burden. Over time senescent cells contribute to tissue deterioration through chronic inflammation and fibrosis driven by the Senescence-Associated Secretory Phenotype (SASP). The human ovary is one of the first organs to age, and prominent age-related fibroinflammation within the ovarian microenvironment is consistent with the presence of senescent cells. However, bona fide senescent cells have not been validated in the human ovary. Therefore, we established a doxorubicin-induced model of cellular senescence to define a signature of ovarian senescent cells. Explants of human postmenopausal ovarian cortex and medulla were treated with doxorubicin for 24 hours followed by culture for up to 10 days in doxorubicin-free medium. Tissue viability was confirmed by histology, lack of apoptosis, and continued glucose consumption by explants. Single nuclei sequencing and proteomics revealed an unbiased signature of ovarian senescence. We identified distinct senescence profiles for the cortex and medulla, driven predominantly by epithelial and stromal cells. Proteomics uncovered subregional differences in addition to 120 proteins common to the cortex and medulla SASP. Integration of transcriptomic and proteomic analyses revealed 26 shared markers, defining a robust senotype of doxorubicin-induced senescence unique to the postmenopausal ovary. A subset of these proteins - Lumican, SOD2, MYH9 , and Periostin - were mapped onto native tissue to reveal compartment-specific localization. This senotype will help determine the role of cellular senescence in ovarian aging and inform the development of biomarkers to identify and therapeutic applications to slow or reverse ovarian aging, senescence, and cancer.
| MSV000095932 | MassIVE
Project description:Cellular senescence is characterized by a permanent growth arrest and is associated with tissue aging and cancer. Senescent cells secrete a number of different cytokines referred to as the senescence-associated secretory phenotype (SASP), which impacts the surrounding tissue and immune response. Here, we found that senescent cells exhibit higher rates of protein synthesis compared to proliferating cells and identified eIF5A as a crucial regulator of this process. Polyamine metabolism and hypusination of eIF5A play a pivotal role in sustaining elevated levels of protein synthesis in senescent cells. Mechanistically, we identified a p53-dependent program in senescent cells that maintains hypusination levels of eIF5A. Finally, we demonstrate that functional eIF5A is required for synthesizing mitochondrial ribosomal proteins and monitoring the immune clearance of premalignant senescent cells in vivo. Our findings establish an important role of protein synthesis during cellular senescence and suggest a link between eIF5A, polyamine metabolism and senescence immune surveillance.
2024-08-14 | MTBLS10690 | MetaboLights
Project description:Cellular senescence is the most intuitive manifestation of individual senescence, and m6A is one of the most common modifications in mRNA, playing an important role in regulating gene expression, splicing, RNA stability, and mRNA degradation. Previous research has suggested that m6A levels play an important role in the occurrence and development of aging and aging-related diseases. However, there are few reports on the role of m6A in cellular senescence. Here, we conducted combined MeRIP-seq and RNA-Seq analyses on non-senescent and senescent MEFs and WI-38 cells. The results revealed substantial disparities in the distribution of m6A sites across the transcriptome between senescent and non-senescent cells.
2025-04-18 | GSE264231 | GEO
Project description:RNA-seq was performed on LFS MDAH041 cells that were young (PD10-12), aging (PD17-19) and replicatively senescent (PD28-30), as well as spontaneously immortal cells and cells that were induced into senescence or quiescence, in order to profile the pathways common in all 4 types of sensecence and the pathways affected as a cell approaches senescence. RNA was sequenced in biological triplicates of each sample using the Illumina HiSeq2000
2015-02-01 | E-GEOD-60340 | biostudies-arrayexpress
Project description:Mammalian aging is characterized by the progressive loss of tissue integrity and function manifesting in ill health and increased risk for developing multiple chronic conditions. Accumulation of senescent cells in aging tissues partly contributes to this decline as targeted depletion of senescent cells in vivo ameliorates many age-related phenotypes. However, the fundamental molecular mechanisms responsible for the decline of cellular health and fitness during senescence and aging are largely unknown. In this study, we investigated whether chromatin-mediated loss of transcriptional fidelity, known to contribute to fitness and survival in yeast and worms, also occurs during human cellular senescence and mouse aging. Our findings reveal that aberrant transcription initiation inside genes is widespread in senescence and aging. It co-occurs with changes in the chromatin landscape and formation of non-canonical transcription start sites. Interventions that alter spurious transcripts have dramatic consequences on cellular health primarily affecting intracellular signal transduction pathways. We propose that spurious transcription is a conserved hallmark of aging that promotes a noisy transcriptome and a degradation of coherent transcriptional networks.
2023-01-02 | GSE158392 | GEO
Project description:Mammalian aging is characterized by the progressive loss of tissue integrity and function manifesting in ill health and increased risk for developing multiple chronic conditions. Accumulation of senescent cells in aging tissues partly contributes to this decline as targeted depletion of senescent cells in vivo ameliorates many age-related phenotypes. However, the fundamental molecular mechanisms responsible for the decline of cellular health and fitness during senescence and aging are largely unknown. In this study, we investigated whether chromatin-mediated loss of transcriptional fidelity, known to contribute to fitness and survival in yeast and worms, also occurs during human cellular senescence and mouse aging. Our findings reveal that aberrant transcription initiation inside genes is widespread in senescence and aging. It co-occurs with changes in the chromatin landscape and formation of non-canonical transcription start sites. Interventions that alter spurious transcripts have dramatic consequences on cellular health primarily affecting intracellular signal transduction pathways. We propose that spurious transcription is a conserved hallmark of aging that promotes a noisy transcriptome and a degradation of coherent transcriptional networks.
2023-01-02 | GSE158391 | GEO
Project description:Mammalian aging is characterized by the progressive loss of tissue integrity and function manifesting in ill health and increased risk for developing multiple chronic conditions. Accumulation of senescent cells in aging tissues partly contributes to this decline as targeted depletion of senescent cells in vivo ameliorates many age-related phenotypes. However, the fundamental molecular mechanisms responsible for the decline of cellular health and fitness during senescence and aging are largely unknown. In this study, we investigated whether chromatin-mediated loss of transcriptional fidelity, known to contribute to fitness and survival in yeast and worms, also occurs during human cellular senescence and mouse aging. Our findings reveal that aberrant transcription initiation inside genes is widespread in senescence and aging. It co-occurs with changes in the chromatin landscape and formation of non-canonical transcription start sites. Interventions that alter spurious transcripts have dramatic consequences on cellular health primarily affecting intracellular signal transduction pathways. We propose that spurious transcription is a conserved hallmark of aging that promotes a noisy transcriptome and a degradation of coherent transcriptional networks.
2023-01-02 | GSE157489 | GEO